data/scipeerai_bench/scipeerai_bench_clean.csv

paper_id,doi,title,authors,year,journal,source_db,category,is_fraud,fraud_confidence,fraud_types,retraction_date,retraction_reason,pubpeer_url,stat_audit_score,figure_forensics_score,methodology_score,citation_score,reproducibility_score,novelty_score,grim_score,sprite_score,granularity_score,pcurve_score,effect_size_score,retraction_score,cartel_score,llm_score,overall_risk_score,abstract_text,full_text_path,field_of_study,labeling_method,labeled_by,notes
SPB-0289,10.3390/nu14020348,The Role of Diet in Prognosis among Cancer Survivors: A Systematic Review and Meta-Analysis of Dietary Patterns and Diet Interventions.,"Castro-Espin Carlota, Agudo Antonio",2022,Nutrients,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cancer survival continues to improve in high-income countries, partly explained by advances in screening and treatment. Previous studies have mainly examined the relationship between individual dietary components and cancer prognosis in tumours with good therapeutic response (breast, colon and prostate cancers). The aim of this review is to assess qualitatively (and quantitatively where appropriate) the associations of dietary patterns and cancer prognosis from published prospective cohort studies, as well as the effect of diet interventions by means of randomised controlled trials (RCT). A systematic search was conducted in PubMed, and a total of 35 prospective cohort studies and 14 RCT published between 2011 and 2021 were selected. Better overall diet quality was associated with improved survival among breast and colorectal cancer survivors; adherence to the Mediterranean diet was associated to lower risk of mortality in colorectal and prostate cancer survivors. A meta-analysis using",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35057525
SPB-0290,10.1161/CIRCULATIONAHA.121.056355,Direct Oral Anticoagulants Versus Warfarin in Patients With Atrial Fibrillation: Patient-Level Network Meta-Analyses of Randomized Clinical Trials With Interaction Testing by Age and Sex.,"Carnicelli Anthony P, Hong Hwanhee, Connolly Stuart J, Eikelboom John, Giugliano Robert P, et al.",2022,Circulation,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Direct oral anticoagulants (DOACs) are preferred over warfarin for stroke prevention in atrial fibrillation. Meta-analyses using individual patient data offer substantial advantages over study-level data. We used individual patient data from the COMBINE AF (A Collaboration Between Multiple Institutions to Better Investigate Non-Vitamin K Antagonist Oral Anticoagulant Use in Atrial Fibrillation) database, which includes all patients randomized in the 4 pivotal trials of DOACs versus warfarin in atrial fibrillation (RE-LY [Randomized Evaluation of Long-Term Anticoagulation Therapy], ROCKET AF [Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared With Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation], ARISTOTLE [Apixaban for Reduction in Stroke and Other Thromboembolic Events in Atrial Fibrillation], and ENGAGE AF-TIMI 48 [Effective Anticoagulation With Factor Xa Next Generation in Atrial Fibrillation-Thrombolysis in Myocardial Infarction",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:34985309
SPB-0291,10.1037/ocp0000146,A systematic review and meta-analysis of workplace mindfulness training randomized controlled trials.,"Bartlett Larissa, Martin Angela, Neil Amanda L, Memish Kate, Otahal Petr, et al.",2019,Journal of occupational health psychology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This meta-analytic review responds to promises in the research literature and public domain about the benefits of workplace mindfulness training. It synthesizes randomized controlled trial evidence from workplace-delivered training for changes in mindfulness, stress, mental health, well-being, and work performance outcomes. Going beyond extant reviews, this article explores the influence of variability in workforce and intervention characteristics for reducing perceived stress. Meta-effect estimates (Hedge's g) were computed using data from 23 studies. Results indicate beneficial effects following training for mindfulness (g = 0.45, p < .001) and stress (g = 0.56, p < .001), anxiety (g = 0.62, p < .001) and psychological distress (g = 0.69, p < .001), and for well-being (g = 0.46, p = .002) and sleep (g = 0.26, p = .003). No conclusions could be drawn from pooled data for burnout due to ambivalence in results, for depression due to publication bias, or for work performance due to insuf",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30714811
SPB-0292,10.2519/jospt.2017.7096,The Effectiveness of Trigger Point Dry Needling for Musculoskeletal Conditions by Physical Therapists: A Systematic Review and Meta-analysis.,"Gattie Eric, Cleland Joshua A, Snodgrass Suzanne",2017,The Journal of orthopaedic and sports physical therapy,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Study Design Systematic review and meta-analysis. Background An increasing number of physical therapists in the United States and throughout the world are using dry needling to treat musculoskeletal pain. Objective To examine the short- and long-term effectiveness of dry needling delivered by a physical therapist for any musculoskeletal pain condition. Methods Electronic databases were searched. Eligible randomized controlled trials included those with human subjects who had musculoskeletal conditions that were treated with dry needling performed by a physical therapist, compared with a control or other intervention. The overall quality of the evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation. Results The initial search returned 218 articles. After screening, 13 were included. Physiotherapy Evidence Database quality scale scores ranged from 4 to 9 (out of a maximum score of 10), with a median score of 7. Eight meta-analyses were performed",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28158962
SPB-0293,10.1038/s41440-023-01467-9,Effects of aerobic exercise on blood pressure in patients with hypertension: a systematic review and dose-response meta-analysis of randomized trials.,"Jabbarzadeh Ganjeh Bahareh, Zeraattalab-Motlagh Sheida, Jayedi Ahmad, Daneshvar Mojtaba, Gohari Zahra, et al.",2024,Hypertension research : official journal of the Japanese Society of Hypertension,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"We aimed to evaluate the dose-dependent effects of aerobic exercise on systolic (SBP) and diastolic blood pressure (DBP) and haemodynamic factors in adults with hypertension. PubMed, Scopus, and Web of Science were searched to April 2022 for randomized trials of aerobic exercise in adults with hypertension. We conducted a random-effects meta-analysis to estimate mean differences (MDs) and 95%CIs for each 30 min/week increase in aerobic exercise. The certainty of evidence was rated using the GRADE approach. The analysis of 34 trials with 1787 participants indicated that each 30 min/week aerobic exercise reduced SBP by 1.78 mmHg (95%CI: -2.22 to -1.33; n = 34, GRADE=low), DBP by 1.23 mmHg (95%CI: -1.53 to -0.93; n = 34, GRADE=moderate), resting heart rate (MD = -1.08 bpm, 95%CI: -1.46 to -0.71; n = 23, GRADE=low), and mean arterial pressure (MD = -1.37 mmHg, 95%CI: -1.80 to -0.93; n = 9, GRADE = low). A nonlinear dose-dependent decrement was seen on SBP and DBP, with the greatest decreme",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37872373
SPB-0294,10.3389/fimmu.2023.1143548,Probiotics fortify intestinal barrier function: a systematic review and meta-analysis of randomized trials.,"Zheng Yanfei, Zhang Zengliang, Tang Ping, Wu Yuqi, Zhang Anqi, et al.",2023,Frontiers in immunology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Probiotics play a vital role in treating immune and inflammatory diseases by improving intestinal barrier function; however, a comprehensive evaluation is missing. The present study aimed to explore the impact of probiotics on the intestinal barrier and related immune function, inflammation, and microbiota composition. A systematic review and meta-analyses were conducted. Four major databases (PubMed, Science Citation Index Expanded, CENTRAL, and Embase) were thoroughly searched. Weighted mean differences were calculated for continuous outcomes with corresponding 95% confidence intervals (CIs), heterogeneity among studies was evaluated utilizing I2 statistic (Chi-Square test), and data were pooled using random effects meta-analyses. Meta-analysis of data from a total of 26 RCTs (n = 1891) indicated that probiotics significantly improved gut barrier function measured by levels of TER (MD, 5.27, 95% CI, 3.82 to 6.72, P < 0.00001), serum zonulin (SMD, -1.58, 95% CI, -2.49 to -0.66, P = 0.",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37168869
SPB-0295,10.1016/j.ijnurstu.2021.103976,Repositioning for pressure injury prevention in adults: An abridged Cochrane systematic review and meta-analysis.,"Gillespie Brigid M, Walker Rachel M, Latimer Sharon L, Thalib Lukman, Whitty Jennifer A, et al.",2021,International journal of nursing studies,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"A pressure injury is an area of localised damage to the skin and underlying tissues. Patient repositioning is an important prevention strategy, as those with limited mobility are at increased risk of developing pressure injury. To assess the clinical and cost-effectiveness of repositioning schedules on the prevention of pressure injury in adults. Systematic review and meta-analysis. The Cochrane Wounds Specialised Register; the Cochrane Central Register of Controlled Trials; MEDLINE (Ovid); Embase (Ovid) and Cumulative Index of Nursing and Allied Health Literature Plus (EBSCO) were searched in February 2019. No restrictions were applied to language or date of publication. Studies were eligible if they were randomised controlled trials including cluster trials, published or unpublished, and undertaken in any healthcare setting that assessed the clinical and/or cost effectiveness of repositioning schedules for prevention of pressure injury in adults. Methodological quality of the studies",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:34090235
SPB-0296,10.1177/03331024231159366,Evaluating the efficacy of CGRP mAbs and gepants for the preventive treatment of migraine: A systematic review and network meta-analysis of phase 3 randomised controlled trials.,"Haghdoost Faraidoon, Puledda Francesca, Garcia-Azorin David, Huessler Eva-Maria, Messina Roberta, et al.",2023,Cephalalgia : an international journal of headache,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Several novel treatments targeting the calcitonin gene-related peptide pathway have been developed for migraine. We evaluated the efficacy of these medications, including atogepant, rimegepant, erenumab, eptinezumab, fremanezumab, and galcanezumab, for the prevention of migraine via network meta-analysis. Databases, including MEDLINE via PubMed, EMBASE, and Cochrane central, were systematically reviewed, and all eligible phase 3 randomised controlled trials were included. Nineteen studies (n = 14,584 participants) were included. Studies included episodic (n = 11) and chronic (n = 4) migraine or both (n = 4). All interventions, except for eptinzumab 30 mg, significantly reduced mean monthly migraine days compared to placebo. All medications had a higher ≥50% responder rate than placebo and results were statistically significant in those with the subcutaneous or intravenous route of administrations, but not with the oral one. All medications significantly reduced mean monthly headache da",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:36855951
SPB-0297,10.1177/2047487317739978,Psychological interventions for coronary heart disease: Cochrane systematic review and meta-analysis.,"Richards Suzanne H, Anderson Lindsey, Jenkinson Caroline E, Whalley Ben, Rees Karen, et al.",2018,European journal of preventive cardiology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Background Although psychological interventions are recommended for the management of coronary heart disease (CHD), there remains considerable uncertainty regarding their effectiveness. Design Systematic review and meta-analysis of randomised controlled trials (RCTs) of psychological interventions for CHD. Methods The Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, CINAHL and PsycINFO were searched to April 2016. Retrieved papers, systematic reviews and trial registries were hand-searched. We included RCTs with at least 6 months of follow-up, comparing the direct effects of psychological interventions to usual care for patients following myocardial infarction or revascularisation or with a diagnosis of angina pectoris or CHD defined by angiography. Two authors screened titles for inclusion, extracted data and assessed risk of bias. Studies were pooled using random effects meta-analysis and meta-regression was used to explore study-level predictors. Results Thirty-five ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29212370
SPB-0298,10.1002/14651858.CD001751.pub3,Nonsteroidal anti-inflammatory drugs for dysmenorrhoea.,"Marjoribanks Jane, Ayeleke Reuben Olugbenga, Farquhar Cindy, Proctor Michelle",2015,The Cochrane database of systematic reviews,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Dysmenorrhoea is a common gynaecological problem consisting of painful cramps accompanying menstruation, which in the absence of any underlying abnormality is known as primary dysmenorrhoea. Research has shown that women with dysmenorrhoea have high levels of prostaglandins, hormones known to cause cramping abdominal pain. Nonsteroidal anti-inflammatory drugs (NSAIDs) are drugs that act by blocking prostaglandin production. They inhibit the action of cyclooxygenase (COX), an enzyme responsible for the formation of prostaglandins. The COX enzyme exists in two forms, COX-1 and COX-2. Traditional NSAIDs are considered 'non-selective' because they inhibit both COX-1 and COX-2 enzymes. More selective NSAIDs that solely target COX-2 enzymes (COX-2-specific inhibitors) were launched in 1999 with the aim of reducing side effects commonly reported in association with NSAIDs, such as indigestion, headaches and drowsiness. To determine the effectiveness and safety of NSAIDs in the treatment of pr",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26224322
SPB-0299,10.1080/16506073.2018.1560358,Psychological and pharmacological treatments for generalized anxiety disorder (GAD): a meta-analysis of randomized controlled trials.,"Carl Emily, Witcraft Sara M, Kauffman Brooke Y, Gillespie Eilis M, Becker Eni S, et al.",2020,Cognitive behaviour therapy,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The purpose of this meta-analysis was to provide updated pooled effect sizes of evidence-based psychotherapies and medications for generalized anxiety disorder (GAD) and to investigate potential moderators of outcomes. Seventy-nine randomized controlled trials (RCT) including 11,002 participants with a diagnosis of GAD were included in a meta-analysis that tested the efficacy of psychotherapies or medications for GAD. Psychotherapy showed a medium to large effect size (g = 0.76) and medication showed a small effect size (g = 0.38) on GAD outcomes. Psychotherapy also showed a medium effect on depression outcomes (g = 0.64) as did medications (g = 0.59). Younger age was associated with a larger effect size for psychotherapy (p < 0.05). There was evidence of publication bias in psychotherapy studies. This analysis found a medium to large effect for empirically supported psychotherapy interventions on GAD outcomes and a small effect for medications on GAD outcomes. Both groups showed a med",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30760112
SPB-0300,10.3390/nu8080483,Effect of Probiotics on Depression: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.,"Huang Ruixue, Wang Ke, Hu Jianan",2016,Nutrients,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"It has been reported that gut probiotics play a major role in the bidirectional communication between the gut and the brain. Probiotics may be essential to people with depression, which remains a global health challenge, as depression is a metabolic brain disorder. However, the efficacy of probiotics for depression is controversial. This study aimed to systematically review the existing evidence on the effect of probiotics-based interventions on depression. Randomized, controlled trials, identified through screening multiple databases and grey literature, were included in the meta-analysis. The meta-analysis was performed using Review Manager 5.3 software using a fixed-effects model. The meta-analysis showed that probiotics significantly decreased the depression scale score (MD (depressive disorder) = -0.30, 95% CI (-0.51--0.09), p = 0.005) in the subjects. Probiotics had an effect on both the healthy population (MD = -0.25, 95% CI (-0.47--0.03), p = 0.03) and patients with major depre",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:27509521
SPB-0301,10.1016/j.jocn.2021.08.009,Effects of cognitive motor dual-task training on stroke patients: A RCT-based meta-analysis.,"Zhou Qiang, Yang Hongchang, Zhou Quanfu, Pan Hongyao",2021,Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Based on a randomized controlled trial (RCT), this meta-analysis aimed to comprehensively analyze the effects of cognitive motor dual-task training (CMDT) on stroke patients. The electronic databases PubMed, Embase, and the Cochrane Library were searched for papers on the influence of CMDT on stroke patients. Weighted mean difference (WMD) and 95% confidence interval (95% CI) were used as effect sizes. Cochran's Q and I<sup>2</sup> tests were performed for heterogeneity. Thirteen articles involving 326 patients were included in the study. The meta-analysis showed that CMDT significantly improved the walking balance of patients with stroke (P = 0.01). In addition, CMDT significantly improved the gait ability of patients with stroke (P < 0.0001). Furthermore, CMDT had a significant effect on the improvement of upper limb ability in patients with stroke (P < 0.00001). CMDT could significantly improve balance ability, gait, and upper limb function in patients with chronic stroke, which is ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:34509248
SPB-0302,10.3390/nu14030679,Effect of Magnesium Supplementation on Inflammatory Parameters: A Meta-Analysis of Randomized Controlled Trials.,"Veronese Nicola, Pizzol Damiano, Smith Lee, Dominguez Ligia J, Barbagallo Mario",2022,Nutrients,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Magnesium (Mg) may have several beneficial effects on human health outcomes. One hypothesized mechanism eliciting such effects is the action of Mg on serum inflammatory parameters. However, studies on this topic to date have several important limitations. Therefore, the present systematic review and meta-analysis aimed to summarize the current state of the art of all randomized control trials (RCTs) investigating the effects of Mg supplementation versus placebo on serum parameters of inflammation. We searched several databases until 23 November 2021 for RCTs. Eligible studies were RCTs investigating the effect of oral Mg supplementation vs. placebo and having serum inflammatory markers as an outcome. Among 2484 papers initially screened, 17 randomized controlled trials (889 participants; mean age: 46 years; females: 62.5%) were included. Generally, a low risk of bias was present. In meta-analysis, Mg supplementation significantly decreased serum C reactive protein (CRP) and increased n",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35277037
SPB-0303,10.1161/HYPERTENSIONAHA.116.07664,Effects of Magnesium Supplementation on Blood Pressure: A Meta-Analysis of Randomized Double-Blind Placebo-Controlled Trials.,"Zhang Xi, Li Yufeng, Del Gobbo Liana C, Rosanoff Andrea, Wang Jiawei, et al.",2016,"Hypertension (Dallas, Tex. : 1979)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The antihypertensive effect of magnesium (Mg) supplementation remains controversial. We aimed to quantify the effect of oral Mg supplementation on blood pressure (BP) by synthesizing available evidence from randomized, double-blind, placebo-controlled trials. We searched trials of Mg supplementation on normotensive and hypertensive adults published up to February 1, 2016 from MEDLINE and EMBASE databases; 34 trials involving 2028 participants were eligible for this meta-analysis. Weighted mean differences of changes in BP and serum Mg were calculated by random-effects meta-analysis. Mg supplementation at a median dose of 368 mg/d for a median duration of 3 months significantly reduced systolic BP by 2.00 mm Hg (95% confidence interval, 0.43-3.58) and diastolic BP by 1.78 mm Hg (95% confidence interval, 0.73-2.82); these reductions were accompanied by 0.05 mmol/L (95% confidence interval, 0.03, 0.07) elevation of serum Mg compared with placebo. Using a restricted cubic spline curve, we ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:27402922
SPB-0304,10.1016/j.neurom.2023.06.002,Transcutaneous Electrical Stimulation for Neurogenic Bladder After Spinal Cord Injury: A Systematic Review and Meta-Analysis.,"Jiang Yangyang, Li Xiang, Guo Suhui, Wei Zhengshu, Xu Senming, et al.",2024,Neuromodulation : journal of the International Neuromodulation Society,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This review aims to assess the efficacy of transcutaneous electrical nerve stimulation (TENS) for neurogenic bladder after spinal cord injury (SCI). A systematic search was conducted of seven electronic data bases from inception to Dec 31, 2022, to identify randomized controlled trials that studied TENS for neurogenic bladder after SCI. The primary outcomes were maximum cystometric capacity (MCC) and residual urine volume (RUV). Secondary outcomes included maximum detrusor pressure, flow rate, and bladder diary. Random effects models were used in all analyses. Eleven trials involving 881 participants were included. Meta-analysis showed that TENS in addition to conventional treatment had larger MCC (mean difference [MD] 50.55 ml, 95% CI 27.81-73.29, p＜0.0001) and lower RUV (MD -22.96 ml, 95% CI -33.45 to -12.47, p＜0.0001) than did conventional treatment only. Compared with magnetic stimulation, no differences were observed with TENS for MCC (MD -14.49 ml, 95% CI -48.97 to 19.98, p = 0.4",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37642626
SPB-0305,10.1016/j.jad.2023.05.048,The efficacy and safety of transcutaneous auricular vagus nerve stimulation in the treatment of depressive disorder: A systematic review and meta-analysis of randomized controlled trials.,"Tan Chaoren, Qiao Meng, Ma Yue, Luo Yi, Fang Jiliang, et al.",2023,Journal of affective disorders,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Transcutaneous auricular vagus nerve stimulation (taVNS) is used for treating depression but the efficacy and safety have not been well assessed. This study was conducted to evaluate the efficacy and safety of taVNS in depression. The retrieval databases included English databases of PubMed, Web of Science, Embase, the Cochrane Library and PsycINFO, and Chinese databases of CNKI, Wanfang, VIP and Sino Med, and the retrieval period was from their inception to November 10, 2022. The clinical trial registers (ClinicalTrials.gov and Chinese Clinical Trial Registry) were also searched. Standardized mean difference and the risk ratio were used as the effect indicator and the effect size was represented by the 95 % confidence interval. Revised Cochrane risk-of-bias tool for randomized trials and the Grades of Recommendation, Assessment, Development and Evaluation system were used to assess the risk of bias and quality of evidence respectively. Totally, 12 studies of 838 participants were incl",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37230264
SPB-0306,10.1007/s00455-023-10626-6,Neuromuscular Electrical Stimulation for Post-Stroke Dysphagia Treatment: A Systemic Evaluation and Meta-Analysis of Randomized Controlled Trials.,"Wang Zhenni, Xiao Zihao, Shen Qin, Zhao Na, Zhang Weiming",2024,Dysphagia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Neuromuscular electrical stimulation (NMES) is a novel treatment method that stimulates patients' swallowing functions. This systemic review was designed to evaluate the impact of NMES on dysphagia in stroke patients. Databases including PubMed, Embase, Web of Science, and Cochrane Library were searched from the date of establishment to January 28th, 2022. Two investigators identified all included studies and compared the swallowing function after NMES treatment with traditional therapy (TT). The Cochrane risk bias assessment tool was utilized to analyze the quality of included studies. Research outcomes included Swallowing Quality of Life (SWAL-QoL), Penetration-Aspiration Scale (PAS), Functional Oral Intake Scale (FOIS), Dysphagia Outcomes and Severity Scale (DOSS), the Repeat Salivary Swallowing Test (RSST), and Water Swallowing Test (WST). We extracted the mean and standard deviation of specific outcomes at the baseline level and after the treatment in both NMES and TT groups for s",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37914887
SPB-0307,10.1016/j.nrl.2017.07.009,Effectiveness of omega-3 fatty acid supplementation in patients with Alzheimer disease: A systematic review and meta-analysis.,"Araya-Quintanilla F, Gutiérrez-Espinoza H, Sánchez-Montoya U, Muñoz-Yañez M J, Baeza-Vergara A, et al.",2020,Neurologia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Alzheimer disease (AD) is a neurodegenerative disease characterised by progressive dementia associated with global cognitive dysfunction. We conducted a systematic review and meta-analysis of clinical trials evaluating omega-3 supplementation in patients with AD. To determine if there is scientific evidence of the effectiveness of omega-3 supplementation in improving cognitive function in patients with AD. We included only randomised controlled trials (RCTs) from the following databases: Medline, Cochrane Central, Cinahl, and LILACS. An electronic search was also conducted using Google Scholar. Six articles met the eligibility criteria. The risk of bias was assessed following the Cochrane method. There is no consistent evidence to support the effectiveness of omega-3 supplementation in improving cognitive function in AD patients in the short and medium term.",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28986068
SPB-0308,10.3389/fimmu.2023.1024120,Efficacy and safety of dietary polyphenols in rheumatoid arthritis: A systematic review and meta-analysis of 47 randomized controlled trials.,"Long Zhiyong, Xiang Wang, He Qi, Xiao Wei, Wei Huagen, et al.",2023,Frontiers in immunology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To evaluate safety and efficacy of dietary polyphenols in the treatment of rheumatoid arthritis (RA). CNKI, Pubmed, Cochrane library, Embase were searched to collect randomized controlled trials (RCTs) of dietary polyphenols in the treatment of RA. The databases were searched from the time of their establishment to November 8nd, 2022. After 2 reviewers independently screened the literature, extracted data, and assessed the risk of bias of the included studies, Meta-analysis was performed using RevMan5.4 software. A total of 49 records (47 RCTs) were finally included, involving 3852 participants and 15 types of dietary polyphenols (Cinnamon extract, Cranberry extract, Crocus sativus L. extract, Curcumin, Garlic extract, Ginger extract, Hesperidin, Olive oil, Pomegranate extract, Puerarin, Quercetin, Resveratrol, Sesamin, Tea polyphenols, Total glucosides of paeony). Pomegranate extract, Resveratrol, Garlic extract, Puerarin, Hesperidin, Ginger extract, Cinnamon extract, Sesamin only inv",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37033930
SPB-0309,10.3390/nu14142831,Inositol Nutritional Supplementation for the Prevention of Gestational Diabetes Mellitus: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.,"Wei Jingshu, Yan Jie, Yang Huixia",2022,Nutrients,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This study was aimed at assessing the efficacy and safety of inositol nutritional supplementation during pregnancy for the prevention of GDM. PubMed, Embase, MEDLINE, and Cochrane library were systematically searched for randomized controlled trails (RCTs) in this field until May 2022. Primary outcomes were the incidence for GDM and plasma glucose levels by oral glucose tolerance test (OGTT). Pooled results were expressed as relative risk (RR) or mean difference (MD) with a 95% confidence interval (95% CI). Seven RCTs with 1321 participants were included in this study. Compared with the control group, 4 g myo-inositol (MI) supplementation per day significantly decreased the incidence of GDM (RR = 0.30, 95% CI (0.18, 0.49), p < 0.00001). It significantly decreased the plasma glucose levels of OGTT regarding fasting-glucose OGTT (MD = −4.20, 95% CI (−5.87, −2.54), p < 0.00001), 1-h OGTT (MD = −8.75, 95% CI (−12.42, −5.08), p < 0.00001), and 2-h OGTT (MD = −8.59, 95% CI (−11.81, −5.83), p",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35889788
SPB-0310,10.1016/j.bja.2022.12.001,Effect of perioperative benzodiazepine use on intraoperative awareness and postoperative delirium: a systematic review and meta-analysis of randomised controlled trials and observational studies.,"Wang Eugene, Belley-Côté Emilie P, Young Jack, He Henry, Saud Haris, et al.",2023,British journal of anaesthesia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Benzodiazepine use is associated with delirium, and guidelines recommend avoiding them in older and critically ill patients. Their perioperative use remains common because of perceived benefits. We searched CENTRAL, MEDLINE, CINAHL, PsycInfo, and Web of Science from inception to June 2021. Pairs of reviewers identified randomised controlled trials and prospective observational studies comparing perioperative use of benzodiazepines with other agents or placebo in patients undergoing surgery. Two reviewers independently abstracted data, which we combined using a random-effects model. Our primary outcomes were delirium, intraoperative awareness, and mortality. We included 34 randomised controlled trials (n=4354) and nine observational studies (n=3309). Observational studies were considered separately. Perioperative benzodiazepines did not increase the risk of delirium (n=1352; risk ratio [RR] 1.43; 95% confidence interval [CI]: 0.9-2.27; I<sup>2</sup>=72%; P=0.13; very low-quality evidenc",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:36621439
SPB-0311,10.1016/S2468-1253(17)30054-7,Restrictive versus liberal blood transfusion for gastrointestinal bleeding: a systematic review and meta-analysis of randomised controlled trials.,"Odutayo Ayodele, Desborough Michael J R, Trivella Marialena, Stanley Adrian J, Dorée Carolyn, et al.",2017,The lancet. Gastroenterology & hepatology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Acute upper gastrointestinal bleeding is a leading indication for red blood cell (RBC) transfusion worldwide, although optimal thresholds for transfusion are debated. We searched MEDLINE, Embase, CENTRAL, CINAHL, and the Transfusion Evidence Library from inception to Oct 20, 2016, for randomised controlled trials comparing restrictive and liberal RBC transfusion strategies for acute upper gastrointestinal bleeding. Main outcomes were mortality, rebleeding, ischaemic events, and mean RBC transfusion. We computed pooled estimates for each outcome by random effects meta-analysis, and individual participant data for a cluster randomised trial were re-analysed to facilitate meta-analysis. We compared treatment effects between patient subgroups, including patients with liver cirrhosis, patients with non-variceal upper gastrointestinal bleeding, and patients with ischaemic heart disease at baseline. We included four published and one unpublished randomised controlled trial, totalling 1965 par",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28397699
SPB-0312,10.1016/j.physio.2022.09.004,Prevention of low back and pelvic girdle pain during pregnancy: a systematic review and meta-analysis of randomised controlled trials with GRADE recommendations.,"Santos Flávia F, Lourenço Bianca M, Souza Mateus B, Maia Laísa B, Oliveira Vinicius C, et al.",2023,Physiotherapy,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Low back (LBP) and pelvic girdle pain (PGP) during pregnancy are related to high direct and indirect costs. It is important to clarify evidence regarding interventions to manage and prevent these conditions. Investigate the efficacy and acceptability of the interventions to prevent LBP and PGP during pregnancy. Searches were conducted up to January 6th, 2021 in the MEDLINE, PEDro, Cochrane Library, SPORTDiscus, CINAHL, AMED, Embase and PsycInfo databases STUDY ELIGIBILITY CRITERIA: (1) Pregnant women without LBP and/or PGP; (2) any prevention strategy on incidence of LBP and PGP and sick leave; (3) comparison to control; (4) quasi and randomised controlled trial. Two reviewers performed screening, data extraction and methodological quality assessments. Meta-analysis was performed and Relative Risks (RRs) and 95% confidence intervals (CIs) were reported. Six randomised controlled trials involving 2231 participants were included in the review. Evidence of moderate quality was found that ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:36288631
SPB-0313,10.1111/jocn.16397,Effect of virtual reality technology as intervention for people with kinesiophobia: A meta-analysis of randomised controlled trials.,"Wang Shanshan, Sun Jiao, Yin Xin, Li Hongyan",2023,Journal of clinical nursing,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To explore the effectiveness of Virtual Reality Technology in reducing kinesiophobia in people. Kinesiophobia is an important psychosocial factor affecting the pain experience and has a significant negative impact on rehabilitation. Virtual reality technology has been widely used in the treatment of phobias, mental disorders and anxiety disorders. However, the effect of virtual reality technology on people with kinesiophobia has been reported with inconsistent results. A meta-analysis of randomised controlled trials. This study systematically searched PubMed, Web of Science, PsycINFO, CINAHL, Embase, Cochrane Library, Medline, Scopus and four Chinese databases. The standardised mean difference (SMD) was calculated using random-effects models, and the Cochrane Collaboration's tool was used to assess the risk of bias in each study. The PRISMA 2020 checklist provided by the EQUATOR network was used. Eleven randomised controlled trials involving a total of 488 subjects were included. Meta-",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35692077
SPB-0314,10.1007/s40265-021-01661-4,Third-Generation Antiseizure Medications for Adjunctive Treatment of Focal-Onset Seizures in Adults: A Systematic Review and Network Meta-analysis.,"Lattanzi Simona, Trinka Eugen, Zaccara Gaetano, Striano Pasquale, Russo Emilio, et al.",2022,Drugs,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Brivaracetam (BRV), cenobamate (CNB), eslicarbazepine acetate (ESL), lacosamide (LCM) and perampanel (PER) are antiseizure medications (ASMs) approved for adjunctive treatment of focal-onset seizures. So far, no randomised controlled trial directly compared the efficacy and safety of these drugs. We estimated the comparative efficacy and safety of these ASMs for the treatment of focal-onset seizures in adults with epilepsy using a network meta-analysis (NMA). We systematically searched (June week 4, 2021) MEDLINE (accessed by PubMed), the Cochrane Central Register of Controlled Trials (CENTRAL), and the US National Institutes of Health Clinical Trials Registry ( http://www.clinicaltrials.gov ). There were no date limitations or language restrictions. Randomised, double-blinded, controlled, parallel-group, add-on studies that compared oral BRV, CNB, ESL, LCM, and PER versus any comparator over maintenance periods of at least 12 weeks and included adult patients with focal seizures uncon",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35061214
SPB-0315,10.1007/s40279-023-01826-z,"Injury Rates, Mechanisms, Risk Factors and Prevention Strategies in Youth Rugby Union: What's All the Ruck-Us About? A Systematic Review and Meta-analysis.","West Stephen W, Shill Isla J, Bailey Stuart, Syrydiuk Reid A, Hayden K Alix, et al.",2023,"Sports medicine (Auckland, N.Z.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Rugby Union is a collision team sport played globally. Despite this, significant concerns have been raised regarding the sport's safety, particularly in youth players. Given this, a review of injury rates, risk factors and prevention strategies is required across different youth age groups as well as in males and females. The objective of this systematic review (SR) and meta-analysis was to investigate injury and concussion rates, risk factors and primary prevention strategies in youth rugby. To be included, studies were required to report either rates, risk factors or prevention strategies in youth rugby and to have a randomised controlled trial, quasi-experimental, cohort, case control, or ecological study design. Exclusion criteria included non-peer-reviewed grey literature, conference abstracts, case studies, previous systematic reviews and studies not written in English. Nine databases were searched. The full search strategy and list of sources are available and pre-registered on ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37191819
SPB-0316,10.1002/smi.2857,Contemplative interventions and employee distress: A meta-analysis.,"Slemp Gavin R, Jach Hayley K, Chia Austin, Loton Daniel J, Kern Margaret L",2019,Stress and health : journal of the International Society for the Investigation of Stress,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Mindfulness, meditation, and other practices that form contemplative interventions are increasingly offered in workplaces to support employee mental health. Studies have reported benefits across various populations, yet researchers have expressed concerns that adoption of such interventions has outpaced scientific evidence. We reappraise the extant literature by meta-analytically testing the efficacy of contemplative interventions in reducing psychological distress in employees (meta-analysed set: k = 119; N = 6,044). Complementing other reviews, we also examine a range of moderators and the impact of biases that could artificially inflate effect sizes. Results suggested interventions were generally effective in reducing employee distress, yielding small to moderate effects that were sustained at last follow-up. Effects were moderated by the type of contemplative intervention offered and the type of control group utilized. We also found evidence of publication bias, which is likely inf",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30698328
SPB-0317,10.12659/MSM.909995,Efficacy and Safety of Acupuncture for Essential Hypertension: A Meta-Analysis.,"Chen Hao, Shen Fei-Er, Tan Xiao-Dong, Jiang Wen-Bo, Gu Yi-Huang",2018,Medical science monitor : international medical journal of experimental and clinical research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"BACKGROUND The aim of this study was to assess the efficacy and safety of acupuncture therapy for patients with hypertension. MATERIAL AND METHODS We searched PubMed, Embase, the Cochrane Library, the Chinese Biomedical Literature Database, the Chinese National Knowledge Infrastructure, and the Wan-fang Data Database from inception through 29 April 2017. Randomized controlled trials investigating acupuncture therapy for hypertension were included. Review Manager 5.3 software was used for the data analysis. RESULTS A total of 30 RCTs involving 2107 patients were included. The overall methodological quality of the included studies was low. Pooled results demonstrate that acupuncture plus anti-hypertensive drugs is better than anti-hypertensive drugs alone at reducing systolic and diastolic blood pressure (SBP and DBP). The same result was observed for pooled data from experiments that compared acupuncture plus medication to sham acupuncture plus medication at reducing SBP and DBP. Howeve",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29735972
SPB-0318,10.1016/S2213-2600(16)00057-6,Association between driving pressure and development of postoperative pulmonary complications in patients undergoing mechanical ventilation for general anaesthesia: a meta-analysis of individual patient data.,"Neto Ary Serpa, Hemmes Sabrine N T, Barbas Carmen S V, Beiderlinden Martin, Fernandez-Bustamante Ana, et al.",2016,The Lancet. Respiratory medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Protective mechanical ventilation strategies using low tidal volume or high levels of positive end-expiratory pressure (PEEP) improve outcomes for patients who have had surgery. The role of the driving pressure, which is the difference between the plateau pressure and the level of positive end-expiratory pressure is not known. We investigated the association of tidal volume, the level of PEEP, and driving pressure during intraoperative ventilation with the development of postoperative pulmonary complications. We did a meta-analysis of individual patient data from randomised controlled trials of protective ventilation during general anesthaesia for surgery published up to July 30, 2015. The main outcome was development of postoperative pulmonary complications (postoperative lung injury, pulmonary infection, or barotrauma). We included data from 17 randomised controlled trials, including 2250 patients. Multivariate analysis suggested that driving pressure was associated with the developm",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26947624
SPB-0319,10.1002/alr.21746,Placebo-controlled assessment of somnolence effect of cetirizine: a meta-analysis.,"Du Qiong, Zhou Yingchun",2016,International forum of allergy & rhinology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"It has been found that the most common adverse reaction which occurs more frequently on cetirizine than on placebo is somnolence. However, the somnolence rate varied widely among different studies. The objective of this study was to assess the somnolence effect of cetirizine 10 mg daily compared to placebo in patients aged 6 years and older using meta-analysis and explore the sources of heterogeneity among different studies. Databases were searched for randomized controlled trials (RCTs) of cetirizine published before 2015. Overall risk differences (RDs) were determined by meta-analyses of 13 trials using the DerSimonian and Laird (D&L) method based on fixed-effects and random-effect models, respectively. The Q statistic, H statistic, and I(2) were calculated for heterogeneity analysis. Subgroup analysis, Galbraith plot, sensitivity analysis, and meta-regression were also performed to explore the sources of heterogeneity. Various analyses showed that heterogeneity existed among the 13 ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26990040
SPB-0320,10.1016/j.jdent.2019.07.008,Network meta-analysis on the effect of desensitizing toothpastes on dentine hypersensitivity.,"Hu Meng-Long, Zheng Gang, Lin Hong, Yang Meng, Zhang You-Dong, et al.",2019,Journal of dentistry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This network meta-analysis compares different desensitizing toothpastes and placebo in terms of their effects on dentine hypersensitivity (DH) at 2, 4, and 8 weeks. A systematic electronic literature search of four databases, and a manual search, were performed to identify randomized controlled trials (RCTs) on different desensitizing toothpastes for the treatment of DH. Pair-wise and network meta-analyses were performed to analyze the desensitization effect at 2, 4, and 8 weeks. The risk of bias was assessed based on the Cochrane guidelines and funnel plots. Statistical heterogeneity, inconsistencies, and ranking probability were also evaluated. A total of 30 RCTs were included in the network meta-analysis, which included eight desensitizing toothpastes. There was no significant difference in the effect among calcium sodium phosphosilicate-containing (CSPS), potassium-containing (K) and strontium-containing (Sr) toothpastes. In addition, there was no significant difference between flu",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:31325467
SPB-0321,10.1017/S1041610218002168,A systematic review and meta-analysis on the effect of reminiscence therapy for people with dementia.,"Park Kyongok, Lee Seonhye, Yang JeongEun, Song Taekwon, Hong Gwi-Ryung Son",2019,International psychogeriatrics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The main objective of this study was to conduct a meta-analysis to identify the effects of reminiscence therapy in people with dementia (PWD). A systematic search of randomized controlled trials (RCTs) was conducted using bibliographic databases. A total of 157 original published studies were identified in the search, and 24 complete articles were included in the final review to check for the level of evidence. Two of the study authors independently assessed the quality of the included studies using the ""Risk of Bias"" (ROB) tool developed by the Cochrane Collaboration. Depression, quality of life, and behavioral and psychological symptoms of dementia (BPSD) were selected to measure the effect of reminiscence therapy. To determine the effects of reminiscence therapy on these variables, each individual study was analyzed using Comprehensive Meta-Analysis Software® (Biostat, Englewood, NJ, USA). The overall effect size was presented using standardized mean differences (SMDs) and 95% confi",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30712519
SPB-0322,10.1007/s10151-022-02629-6,Early vs. standard reversal ileostomy: a systematic review and meta-analysis.,"O'Sullivan N J, Temperley H C, Nugent T S, Low E Z, Kavanagh D O, et al.",2022,Techniques in coloproctology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Formation of a defunctioning loop ileostomy is common after mid and low rectal resection. Historically, they were reversed between 3 and 6 months after initial resection. Recently, earlier closure (< 14 days) has been suggested by some current randomised controlled trials. The aim of this study was to investigate the effect of early stoma closure on surgical and patient outcomes. A systematic review of the current randomised controlled trial literature comparing early and standard ileostomy closure after rectal surgery was performed. Specifically, we examined surgical outcomes including; morbidity, mortality and quality of life. Six studies met the predefined criteria and were included in our analysis. 275 patients underwent early stoma closure compared with 259 patients having standard closure. Overall morbidity was similar between both groups (25.5% vs. 21.6%) (OR, 1.47; 95% CI 0.75-2.87). However, there tended to be more reoperations (8.4 vs. 4.2%) (OR, 2.02, 95% CI 0.99-4.14) and s",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35596904
SPB-0323,10.1136/bmjopen-2018-022879,Efficacy and safety of the pulsed electromagnetic field in osteoarthritis: a meta-analysis.,"Wu Ziying, Ding Xiang, Lei Guanghua, Zeng Chao, Wei Jie, et al.",2018,BMJ open,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To investigate the efficacy and safety of the pulsed electromagnetic field (PEMF) therapy in treating osteoarthritis (OA). Meta-analysis. PubMed, Embase, the Cochrane Library and Web of Science were searched through 13 October 2017. Randomised controlled trials compared the efficacy of PEMF therapy with sham control in patients with OA. Pain, function, adverse effects and characteristics of participants were extracted. RevMan V.5.2 was used to perform statistical analyses. Twelve trials were included, among which ten trials involved knee OA, two involved cervical OA and one involved hand OA. The PEMF group showed more significant pain alleviation than the sham group in knee OA (standardised mean differences (SMD)=-0.54, 95% CI -1.04 to -0.04, p=0.03) and hand OA (SMD=-2.85, 95% CI -3.65 to -2.04, p<0.00001), but not in cervical OA. Similarly, comparing with the sham-control treatment, significant function improvement was observed in the PEMF group in both knee and hand OA patients (SMD",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30552258
SPB-0324,10.1007/s00345-023-04673-9,Systematic review and meta-analysis of the efficacy of exercise intervention in kidney transplant recipients.,"Zhang Dongxu, Yu Liqian, Xia Bowen, Zhang Xin, Liang Pu, et al.",2023,World journal of urology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"There is uncertainty about the beneficial effects of exercise intervention for kidney transplant recipients. The purpose of our meta-analysis is to estimate the efficacy of exercise intervention in kidney transplant recipients. A database search according to the PICOS framework was performed for all published randomized, double-blind, placebo-controlled trials (RCTs) about exercise intervention for kidney transplant recipients. The databases involved include PubMed, Embase, and Cochrane Library. A total of 16 RCTs (involving 827 patients) in compliance with inclusion criteria were included in our study. The results demonstrated that adequate exercise intervention improved statistically in creatinine clearance [mean difference (MD) =  - 0.29, 95% confidence interval (CI) - 0.46 to - 0.11, p = 0.001], serum urea (MD = - 21.57, 95% CI - 35.84 to - 7.29, p = 0.003), VO<sub>2</sub> peak (MD = 3.20, 95% CI 1.97-4.43, p < 0.00001), high-density lipoprotein-cholesterol (HDL-C) (MD = 0.21, 95% ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:37882807
SPB-0325,10.1016/j.ijnurstu.2017.04.005,Oxygen therapy for acute myocardial infarction: A systematic review and meta-analysis.,"Fu Shimin, Lv Xia, Fang Qin, Liu Zhiping",2017,International journal of nursing studies,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Potential benefits or risks of oxygen inhalation for patients with acute myocardial infarction are not fully understood. We performed this study to systematically assess the effectiveness and safety of oxygen therapy for patients with acute myocardial infarction. A systematic review and meta-analysis. We searched randomized controlled trials systematically in PubMed, EMBASE, Web of Science and Cochrane Library up to June 2016. Randomized controlled trials that estimated the effectiveness and safety of oxygen therapy for patients with acute myocardial infarction were identified by two independent reviewers. The primary outcomes were short-term mortality and recurrent rate of myocardial infarction, and the secondary outcomes were arrhythmia incidence and pain incidence. Relative risks (RRs) and 95% confidence intervals (CIs) were used to measure the pooled data. A total of five randomized controlled trials were in accordance with inclusion criteria and were included in this meta-analysis",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28595112
SPB-0326,10.3390/nu14020303,Critical Appraisal of Large Vitamin D Randomized Controlled Trials.,"Pilz Stefan, Trummer Christian, Theiler-Schwetz Verena, Grübler Martin R, Verheyen Nicolas D, et al.",2022,Nutrients,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"As a consequence of epidemiological studies showing significant associations of vitamin D deficiency with a variety of adverse extra-skeletal clinical outcomes including cardiovascular diseases, cancer, and mortality, large vitamin D randomized controlled trials (RCTs) have been designed and conducted over the last few years. The vast majority of these trials did not restrict their study populations to individuals with vitamin D deficiency, and some even allowed moderate vitamin D supplementation in the placebo groups. In these RCTs, there were no significant effects on the primary outcomes, including cancer, cardiovascular events, and mortality, but explorative outcome analyses and meta-analyses revealed indications for potential benefits such as reductions in cancer mortality or acute respiratory infections. Importantly, data from RCTs with relatively high doses of vitamin D supplementation did, by the vast majority, not show significant safety issues, except for trials in critically",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35057483
SPB-0327,10.1111/jhn.12963,Quality improvement strategies enhance primary care dietetics: A systematic review and meta-analysis.,"Kirkegaard Amy, Ball Lauren, Mitchell Lana, Brickley Bryce, Williams Lauren T",2022,Journal of human nutrition and dietetics : the official journal of the British Dietetic Association,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Quality improvement strategies have been widely applied in health care; however, little is known about their use in primary care dietetics. This review aims to describe and evaluate the effectiveness of quality improvement strategies that seek to improve patient outcomes by enhancing dietetic care compared to standard dietetic care. The study employed a systematic review and meta-analysis design following PRISMA guidelines and included studies up to March 2021. Studies were included if they used a randomised controlled trial (RCT) design to evaluate the effect of a quality improvement strategy applied to care delivered by a dietitian on patient outcomes. A meta-analysis was conducted where there were sufficient studies with homogeneous populations and outcome measures. Twelve RCTs (n = 1604) met the inclusion criteria for review and five studies (n = 511) were eligible for meta-analysis for glycated haemoglobin in patients with type 2 diabetes. The most frequently reported quality impr",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:34725871
SPB-0328,10.1097/MD.0000000000029767,Efficacy of ginseng supplements on disease-related fatigue: A systematic review and meta-analysis.,"Zhu Jianxun, Xu Xiaoru, Zhang Xin, Zhuo Yue, Chen Shaotao, et al.",2022,Medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Ginseng has been believed to provide energy, physical health, and well-being to patients for hundreds of years. Fatigue is a multidimensional symptom with unknown etiology and varying severity, and lots of patients suffer from fatigue. We search for research of ginseng treatment of disease-related fatigue in adult patients in Pubmed, Embase, Medline, and Cochrane library. Two independent reviewers assessed included studies and met to develop consensus on included studies. And we used Review Manager 5.3 software to evaluate the risk of bias. The present meta-analysis included 12 randomized controlled trial containing 1298 patients. In the fixed-effect meta-analysis of 12 randomized controlled trial, ginseng supplements had a statistically significant efficacy on disease-related fatigue reduction (standardized mean difference = 0.33, 95% confidence interval = 0.44-0.22). The use of ginseng supplements is benefit for patients to reduce disease-related fatigue.",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35776997
SPB-0329,10.1136/bmjopen-2018-027953,Cochrane systematic review and meta-analysis of botulinum toxin for the prevention of migraine.,"Herd Clare P, Tomlinson Claire L, Rick Caroline, Scotton William J, Edwards Julie, et al.",2019,BMJ open,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To assess the effects of botulinum toxin for prevention of migraine in adults. Systematic review and meta-analysis. CENTRAL, MEDLINE, Embase and trial registries. We included randomised controlled trials (RCTs) of botulinum toxin compared with placebo, active treatment or clinically relevant different dose for adults with chronic or episodic migraine, with or without the additional diagnosis of medication overuse headache. Cochrane methods were used to review double-blind RCTs. Twelve week post-treatment time-point data was analysed. Twenty-eight trials (n=4190) were included. Trial quality was mixed. Botulinum toxin treatment resulted in reduced frequency of -2.0 migraine days/month (95% CI -2.8 to -1.1, n=1384) in chronic migraineurs compared with placebo. An improvement was seen in migraine severity, measured on a numerical rating scale 0 to 10 with 10 being maximal pain, of -2.70 cm (95% CI -3.31 to -2.09, n=75) and -4.9 cm (95% CI -6.56 to -3.24, n=32) for chronic and episodic mig",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:31315864
SPB-0330,10.1136/bmjopen-2017-020584,Legacy effects of statins on cardiovascular and all-cause mortality: a meta-analysis.,"Nayak Agnish, Hayen Andrew, Zhu Lin, McGeechan Kevin, Glasziou Paul, et al.",2018,BMJ open,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To assess evidence for 'legacy' (post-trial) effects on cardiovascular disease (CVD) mortality and all-cause mortality among adult participants of placebo-controlled randomised controlled trials (RCTs) of statins. Meta-analysis of aggregate data. Placebo-controlled statin RCTS for primary and secondary CVD prevention. Data sources: PubMed, Embase from inception and forward citations of Cholesterol Treatment Trialists' Collaborators RCTs to 16 June 2016. Two independent reviewers identified all statin RCT follow-up reports including ≥1000 participants, and cardiovascular and all-cause mortality. Two independent reviewers extracted data in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Post-trial CVD and all-cause mortality. We included eight trials, with mean post-trial follow-up ranging from 1.6 to 15.1 years, and including 13 781 post-trial deaths (6685 CVD). Direct effects of statins within trials were greater than legacy effects po",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30287603
SPB-0331,10.21873/anticanres.13643,Vitamin D and Cardiovascular Disease: An Update.,"Zittermann Armin, Pilz Stefan",2019,Anticancer research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In the clinical setting, administration of high daily or bolus doses of vitamin D is often solely based on 25-hydroxyvitamin D [25(OH)D] testing. This review summarizes the evidence of the effect of vitamin D on cardiovascular disease (CVD). Meta-analyses of randomized controlled trials (RCTs) have demonstrated that CVD risk markers, such as lipid parameters, inflammation markers, blood pressure, and arterial stiffness, are largely unaffected by vitamin D supplementation. Similar results have been obtained regarding CVD events and mortality from (meta)-analyses of RCTs, even in subgroups with 25(OH)D concentrations <50 nmol/l. Likewise, Mendelian randomization studies have indicated that the genetic reduction of the 25(OH)D concentration does not increase CVD risk. Some studies do not exclude the possibility of adverse vitamin D effects, such as elevated plasma calcium concentration and an increased CVD risk at a 25(OH)D concentration >125 nmol/l. Based on a conservative benefit-risk m",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:31519560
SPB-0332,10.1111/psyg.12275,Choto-san versus placebo for patients with dementia: systematic review and meta-analysis.,"Imai Hissei, Takeshima Nozomi, Oda Haruhiko, Chen Peiyao, Sawada Etsuko, et al.",2017,Psychogeriatrics : the official journal of the Japanese Psychogeriatric Society,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Choto-san is a traditional medicine used for hypertension and headaches in Japan and China. Some studies have shown its effectiveness in the treatment of dementia. The present review aimed to assess the effectiveness and acceptability of Choto-san in the treatment of adults with cognitive impairment. We included randomized controlled trials comparing Choto-san with placebo for patients with dementia or mild cognitive impairment. Three randomized controlled trials evaluating 219 participants were included. Two were studies on vascular dementia, and the other was on Alzheimer's dementia. There was no difference between Choto-san and placebo in terms of short-term dichotomous judgement of improvement, but Choto-san was more effective than placebo in terms of short-term improvement of cognitive function as measured by continuous outcomes. Also, dropouts judged it to be acceptable. However, the results were imprecise and/or heterogeneous. The number of participants included in the analysis ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28589702
SPB-0333,10.1007/s00132-018-3604-x,Robot-assisted vs. conventional unicompartmental knee arthroplasty : Systematic review and meta-analysis.,"Fu Jun, Wang Yuning, Li Xiang, Yu Baozhan, Ni Ming, et al.",2018,Der Orthopade,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Numerous advances have been made in prosthesis design, instrumentation and postoperative rehabilitation for unicompartmental knee arthroplasty; however, only 70-86% of patients are satisfied with the functional outcome and revision rates range between 10% and 20%. The primary outcome for this meta-analysis was implantation accuracy of component positioning and tibiofemoral component safe zone. A total of three randomized controlled trials (RCT), three quasi-RCTs and one prospective trial were included in this review. It was found that the use of robotic-assisted systems reduces implantation errors without an increase in adverse events. There are only a few reports about clinical outcome and long-term follow-up and whether the more accurate component positioning results in a better clinical effect or a better long-term survival of the implants is unknown.",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:30051277
SPB-0334,10.1002/14651858.CD002903.pub3,WITHDRAWN: Electrical cardioversion for atrial fibrillation and flutter.,"Mead Gillian E, Elder Andrew, Flapan Andrew D, Cordina John",2017,The Cochrane database of systematic reviews,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Atrial fibrillation increases stroke risk and adversely affects cardiovascular haemodynamics. Electrical cardioversion may, by restoring sinus rhythm, improve cardiovascular haemodynamics, reduce the risk of stroke, and obviate the need for long-term anticoagulation. To assess the effects of electrical cardioversion of atrial fibrillation or flutter on the risk of thromboembolic events, strokes and mortality (primary outcomes), the rate of cognitive decline, quality of life, the use of anticoagulants and the risk of re-hospitalisation (secondary outcomes) in adults (>18 years). We searched the Cochrane CENTRAL Register of Controlled Trials (1967 to May 2004), MEDLINE (1966 to May 2004), Embase (1980 to May 2004), CINAHL (1982 to May 2004), proceedings of the American College of Cardiology (published in Journal of the American College of Cardiology 1983 to 2003), www.trialscentral.org, www.controlled-trials.com and reference lists of articles. We hand-searched the indexes of the Proceed",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29140555
SPB-0335,10.1186/s12891-015-0702-3,A systematic review and meta-analysis regarding the use of corticosteroids in septic arthritis.,Farrow Luke,2015,BMC musculoskeletal disorders,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Chondral damage is one of the major sequelae of septic arthritis; occurring even after prompt treatment of a septic joint. Subsequent loss of joint function can have a significant impact on a patient's quality of life. Corticosteroids are known to have beneficial effects on the rate and extent cartilage destruction in arthritis through a variety of mediators such as synovial RANKL expression, mast cells and pro-inflammatory cytokines. Investigation into sepsis at other sites has suggested improved outcomes with corticosteroid use despite the theoretical risks. This study therefore set out to review current literature with regards to a possible beneficial effect for corticosteroids in Septic Arthritis. A computerised search of the databases MEDLINE and CINAHL was conducted during November 2014 using the EBSCOhost web search engine in order to identify research articles relating to the use of corticosteroids in the treatment of septic arthritis. The search strategy revealed 223 unique ar",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26342736
SPB-0336,10.1136/acupmed-2017-011528,Acupuncture for overactive bladder in adults: a systematic review and meta-analysis.,"Mak Tony C, Chen Hai Yong, Cho William C",2019,Acupuncture in medicine : journal of the British Medical Acupuncture Society,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Overactive bladder is prevalent in adults over 40 years of age and its prevalence increases with age. The use of acupuncture in adults with overactive bladder is increasing globally. However, its effectiveness/efficacy and safety have not yet been confirmed. To determine the effectiveness/efficacy and safety of acupuncture and to identify the pattern of commonly used traditional acupuncture points in the management of overactive bladder in adults. Ten electronic English and Chinese language databases were systematically searched and two English together with four Chinese journals relevant to acupuncture were manually searched in libraries for randomised controlled trials (RCTs) of acupuncture for overactive bladder in adults from their inception to March 2017. The Cochrane risk of bias tool was used to assess the methodological quality of the RCTs. RevMan v.5.3 software was employed for data analysis. Seven eligible trials involving 695 participants were included. Meta-analysis showed ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:31433197
SPB-0337,10.1007/s00540-017-2310-x,Adjuncts to local anaesthetics in tonsillectomy: a systematic review and meta-analysis.,"Vlok R, Melhuish T M, Chong C, Ryan T, White Leigh D",2017,Journal of anesthesia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The infiltration of local anaesthetic agents has been shown to reduce post-tonsillectomy pain. A number of recent studies have shown that the addition of agents such as clonidine and dexamethasone improve the efficacy of nerve blocks and spinal anaesthesia. The aim of this review was to determine whether additives to local anaesthetic agents improve post-tonsillectomy outcomes. Four major databases were systematically searched for all relevant studies published up to August 2016. All study designs with a control group receiving local anaesthetic infiltration and an intervention receiving the same infiltration with an added agent were included in this review. These studies were then assessed for level of evidence and risk of bias. The data were then analysed both qualitatively and where appropriate by meta-analysis. We reviewed 11 randomised controlled trial (RCTs) that included 854 patients. Due to inconsistencies in the methods used to report outcomes, both quantitative and qualitativ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28120104
SPB-0338,10.1016/j.jebdp.2018.12.004,Effect of Lasers on Dentine Hypersensitivity: Evidence From a Meta-analysis.,"Hu Meng-Long, Zheng Gang, Han Jian-Min, Yang Meng, Zhang You-Dong, et al.",2019,The journal of evidence-based dental practice,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The aim of the study was to evaluate the immediate and long-term desensitizing effect of lasers in reducing dentine hypersensitivity (DH) compared with negative controls. Six databases were searched to identify relevant articles published up to June 8, 2018. Randomized controlled trials comparing lasers with placebo or no treatment control in adult patients who suffer from DH were included. The risk of bias was assessed according to the Cochrane guidelines, and the quality of the evidence was evaluated using the Grading of Recommendations Assessment, Development and Evaluation tool. Inverse-variance random effects meta-analyses of standardized mean differences and 95% confidence intervals were performed using the RevMan 5.3 software. Twenty-two randomized controlled trials were finally included in the meta-analysis, and 21 studies of these were conducted to analyze the immediate and long-term effects. All types of lasers had better immediate and long-term desensitizing effects on DH th",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:31326044
SPB-0339,10.1136/bmjopen-2019-034298,Impact of point-of-care tests in community pharmacies: a systematic review and meta-analysis.,"Albasri Ali, Van den Bruel Ann, Hayward Gail, McManus Richard J, Sheppard James Peter, et al.",2020,BMJ open,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To summarise the literature regarding the use of point-of-care test (POCT) in pharmacies versus control/usual care. Systematic review and random-effects meta-analysis in community pharmacy. MEDLINE, Cochrane Central Register of Controlled Trials, Embase, ClinicalTrial.gov and Web of Science databases were searched. Articles were included if they: involved a POCT conducted by a community pharmacist, member of pharmacy staff or local equivalent; measured a clinically relevant outcome for example, clinical parameter monitoring. No clinical condition or language limits were set. No patient involvement. Data were independently extracted by two members of the review team to capture changes in clinical care that resulted from the use of the POCTs. The methodological quality of included studies was assessed, using the Cochrane Risk of Bias tool and Newcastle-Ottawa scale. Thirteen of the 1584 articles found were included in the meta-analyses. Studies covered four therapeutic areas: targeted an",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32414821
SPB-0340,10.5664/jcsm.10022,The effect of robot interventions on sleep in adults: a systematic review and network meta-analysis.,"Støre Siri Jakobsson, Beckman Linda, Jakobsson Niklas",2022,Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Robotic pets or companion robots have demonstrated positive effects on several emotional and physiological factors in humans. Robots could constitute a complementary or alternative method to treat sleep problems, but individual studies on robots' effectiveness regarding sleep show mixed results. The aim of the current study was to compare the effects of robots, plush toys, and treatment as usual on sleep in adults. The current study is a systematic review and frequentist network meta-analysis of all randomized and cluster randomized controlled trials comparing the effects of robots, plush toys, and treatment as usual on total sleep time in adults. Four studies were included in the analysis. Three studies were considered to have a high risk of bias, whereas one was rated with some concerns. The studies comprised 381 participants. These participants were older adults, with or without dementia, living in nursing homes. The total sleep time was the only common sleep measure included in all",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35404223
SPB-0341,10.21037/apm.2020.02.35,The effect of breathing exercises on patients with GERD: a meta-analysis.,"Qiu Kaijie, Wang Jie, Chen Baiwen, Wang Haibiao, Ma Chenyang",2020,Annals of palliative medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Breathing exercises can improve the symptoms of patients with gastroesophageal reflux disease (GERD), but their specific effect and function are disputed. To evaluate and conduct a meta-analysis on the effect of breathing exercises on patients with GERD. A literature search for randomized controlled trials (RCTs) and prospective studies on the effects of employing breathing exercises on patients with GERD was conducted of all major online English databases (PubMed, Embase, the Cochrane library, CENTRAL, Web of Science, AMED, and CINAHL). After the systematic review of all the studies according to inclusion and exclusion criteria, we analyzed the extracted data through meta-analysis by using RevMan 5.3 software. This thesis analyzes 7 studies (including three RCTs), which together involved 194 patients and 16 healthy volunteers. The primary outcomes of these studies included GERD symptoms, esophageal manometry, esophageal pH monitoring, laryngoscopic findings, and acid suppression usage",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32233626
SPB-0342,10.23736/S0375-9393.20.14073-2,Drugs for anesthesia and analgesia in the preterm infant.,"Tesoro Simonetta, Marchesini Vanessa, Fratini Giuseppe, Engelhardt Thomas, De Robertis Edoardo",2020,Minerva anestesiologica,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"There is largely an absence of validated evidence-based therapies in term- and preterm newborn infants, due to a lack of pharmacological clinical trials. As a consequence, the drugs and doses used in clinical practice are extrapolated from dose-ranging trials performed in older patients. Drugs administered to the preterm infant are invariably off-label. The aim of this current review is to identify commonly used anesthetic and analgesic agents in this patient population, assess the existing evidence base, in terms of safety, efficacy, pharmacokinetics and pharmacodynamics, current indications and doses. We searched the PubMed, Google Scholar, Web of Science, U.S. Food and Drug Administration and World Health Organization databases and analyzed any studies for general anesthesia; analgo-sedation; regional anesthesia; pharmacokinetics, pharmacodynamics and pharmacogenomics in this patient population. A total of 412 studies (meta-analysis, systematic reviews, randomized controlled trial (",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32000473
SPB-0343,10.1016/j.ijsu.2015.09.033,Intra-abdominal drainage for laparoscopic cholecystectomy: A systematic review and meta-analysis.,"Wong Chee S, Cousins Grainne, Duddy John C, Walsh Stewart R",2015,"International journal of surgery (London, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To assess the effectiveness of intra-abdominal drainage (IAD) post laparoscopic cholecystectomy (LC). Main electronic databases [MEDLINE via Pubmed, EMBASE, Scopus, Web of Knowledge, Cochrane Central Register of Controlled Trials (CENTRAL) and the Cochrane Library, and clinical trial registry (ClinicalTrial.gov)] were searched for randomised controlled trial (RCT) reporting outcomes of IAD. The systematic review was conducted in accordance with the PRISMA guidelines and meta-analysis was analysed using fixed and random-effects models. Twelve RCTs involving 1763 patients (897 drained versus 866 without drain) were included in the final pooled analysis. There was no statistically significant different in the rate of intra-abdominal collections (RR 1.08, 95% CI 0.78 to 1.49; p = 0.65). IAD did not reduce the overall incidence of nausea and vomiting (RR 1.10, 95% CI 0.90 to 1.36; p = 0.36) and shoulder tip pain (RR 0.99, 95% CI 0.69 to 1.40; p = 0.93). Drain group had a significant higher ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26386402
SPB-0344,10.1016/j.ijsu.2020.06.032,Four interventions for pediatric femoral shaft fractures: Network meta-analysis of randomized trials.,"Chen Zhao, Han Dawei, Wang Qingyu, Li Lianghua",2020,"International journal of surgery (London, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Fractures of the pediatric femoral shaft are uncommon, although serious injuries could lead to long-term disability, pain and an impaired quality of life. There are 4 main interventions: cast (C), plate fixation (PF), titanium elastic nail (TEN) and external fixation (EF). However, for pediatric patients under the age of 16, which intervention is the best choice remains a controversial topic. Therefore, a comprehensive network meta-analysis (NMA) is needed to summarize existing studies and to compare the safety and efficacy of the interventions for pediatric femoral shaft fractures. We searched through eight electronic databases (PubMed, Embase, Cochrane, Web of Science, CBM, CNKI, Wangfang, and VIP) for randomized controlled trials of femoral shaft fracture in pediatric patients, which were published until the end of March 2020. We performed a Bayesian NMA to integrate the adverse events and fracture union time of all interventions. Twenty-three randomized controlled trials with a tot",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32622056
SPB-0345,10.1016/j.jdent.2018.05.012,Effect of desensitizing toothpastes on dentine hypersensitivity: A systematic review and meta-analysis.,"Hu Meng-Long, Zheng Gang, Zhang You-Dong, Yan Xiang, Li Xiao-Chan, et al.",2018,Journal of dentistry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To evaluate the desensitizing effect of toothpastes that contain ingredients that act against dentine hypersensitivity (DH) and to compare this effect with negative controls. Five databases were searched to identify relevant articles published up to November 27, 2017. Randomized controlled trials (RCTs) comparing desensitizing toothpastes with a toothpastes without desensitizing component in adult patients that suffer from DH were included. The risk of bias was assessed according to the Cochrane guidelines, and the quality of the evidence was evaluated using the GRADE tool. Inverse variance random-effects meta-analyses of standardized mean differences (SMD) and 95% confidence intervals (CIs) were calculated using RevMan 5.3 software. 53 RCTs with 4796 patients were finally included in the meta-analysis. The toothpastes that contain active desensitization ingredients showed a better desensitizing effect on DH than the negative control, except the strontium- and amorphous calcium phospha",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29787782
SPB-0346,10.1177/0300060520964661,Role of platelet-rich plasma in the treatment of osteoarthritis: a meta-analysis.,"Ren Haijiang, Zhang Shouwei, Wang Xuejie, Li Zehui, Guo Wenlai",2020,The Journal of international medical research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The clinical efficacy of platelet-rich plasma (PRP) in the treatment of osteoarthritis remains controversial. In this paper, we evaluated the clinical efficacy of PRP in the treatment of osteoarthritis using meta-analysis, providing evidence for the selection of clinical treatment options. We performed a computer-based search of PubMed, Embase, and the Cochrane Library databases to retrieve articles using the search terms ""platelet-rich plasma"", ""osteoarthrosis"", and ""knee joint"". Quality evaluation and data extraction were performed. The combined effect was assessed using RevMan 5.3 software. Five randomized controlled trials, involving 320 patients, were included in this study. No significant differences were observed in the International Knee Documentation Committee score, visual analog scale (VAS) score, or the absolute value of the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score between the experimental and control groups. The absolute value of the VAS",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:33111611
SPB-0347,10.1016/j.jclinepi.2020.03.014,Asking questions changes health-related behavior: an updated systematic review and meta-analysis.,"Miles Lisa M, Rodrigues Angela M, Sniehotta Falko F, French David P",2020,Journal of clinical epidemiology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The question-behavior effect (QBE) refers to whether asking people questions can result in changes in behavior. Such changes in behavior can lead to bias in trials. This study aims to update a systematic review of randomized controlled trials investigating the QBE, in light of several large preregistered studies being published. A systematic search for newly published trials covered 2012 to July 2018. Eligible trials randomly allocated participants to measurement vs. non-measurement control conditions or to different forms of measurement. Studies that reported health-related behavior as outcomes were included. Forty-three studies (33 studies from the original systematic review and 10 new studies) compared measurement vs. no measurement. An overall small effect was found using a random effect model: standardized mean difference = 0.06 (95% CI: 0.02-0.09), n = 104,388. Statistical heterogeneity was substantial (I<sup>2</sup> = 54%). In an analysis restricted to studies with a low risk of",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32229251
SPB-0348,10.1038/s41598-020-70641-7,Surgical procedures in the pilonidal sinus disease: a systematic review and network meta-analysis.,"Bi Siwei, Sun Kaibo, Chen Shanshan, Gu Jun",2020,Scientific reports,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The most appropriate surgical treatment for pilonidal sinus disease (PSD) is still in dispute. This study aims to comprehensively compare the outcomes of surgical interventions using network meta-analysis. Randomized controlled trial studies were searched systematically to identify all eligible studies in multiple databases and previous publications and Bayesian network meta-analysis was performed. Our primary outcome was the recurrence rate. Differences in the findings of the studies were explored in meta regressions and sensitivity analyses. The risk of bias of each study was assessed using the Cochrane risk of bias tool. Confidence in evidence was assessed using CINeMA (Confidence in Network Meta-Analysis). A total of 39 studies and 5,061 patients were identified and the most common surgical intervention was the Limberg flap. In network meta-analysis, modified Limberg flap and off-midline closure were associated with the lowest recurrence rate. However, the Karydakis flap was associ",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:32792519
SPB-0349,10.3310/JNZT9406,Endometrial scratch to increase live birth rates in women undergoing first-time in vitro fertilisation: RCT and systematic review.,"Metwally Mostafa, Chatters Robin, Pye Clare, Dimairo Munya, White David, et al.",2022,"Health technology assessment (Winchester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In vitro fertilisation is a widely used reproductive technique that can be undertaken with or without intracytoplasmic sperm injection. The endometrial scratch procedure is an in vitro fertilisation 'add-on' that is sometimes provided prior to the first in vitro fertilisation cycle, but there is a lack of evidence to support its use. (1) To assess the clinical effectiveness, safety and cost-effectiveness of endometrial scratch compared with treatment as usual in women undergoing their first in vitro fertilisation cycle (the 'Endometrial Scratch Trial') and (2) to undertake a systematic review to combine the results of the Endometrial Scratch Trial with those of previous trials in which endometrial scratch was provided prior to the first in vitro fertilisation cycle. A pragmatic, multicentre, superiority, open-label, parallel-group, individually randomised controlled trial. Participants were randomised (1 : 1) via a web-based system to receive endometrial scratch or treatment as usual u",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:35129113
SPB-0350,10.3310/hta21130,Support and Assessment for Fall Emergency Referrals (SAFER) 2: a cluster randomised trial and systematic review of clinical effectiveness and cost-effectiveness of new protocols for emergency ambulance paramedics to assess older people following a fall with referral to community-based care when appropriate.,"Snooks Helen A, Anthony Rebecca, Chatters Robin, Dale Jeremy, Fothergill Rachael, et al.",2017,"Health technology assessment (Winchester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Emergency calls are frequently made to ambulance services for older people who have fallen, but ambulance crews often leave patients at the scene without any ongoing care. We evaluated a new clinical protocol which allowed paramedics to assess older people who had fallen and, if appropriate, refer them to community-based falls services. To compare outcomes, processes and costs of care between intervention and control groups; and to understand factors which facilitate or hinder use. Cluster randomised controlled trial. Participating paramedics at three ambulance services in England and Wales were based at stations randomised to intervention or control arms. Participants were aged 65 years and over, attended by a study paramedic for a fall-related emergency service call, and resident in the trial catchment areas. Intervention paramedics received a clinical protocol with referral pathway, training and support to change practice. Control paramedics continued practice as normal. The primary",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28397649
SPB-0351,10.1016/j.surg.2016.11.026,"Use of water-soluble contrast medium (gastrografin) does not decrease the need for operative intervention nor the duration of hospital stay in uncomplicated acute adhesive small bowel obstruction? A multicenter, randomized, clinical trial (Adhesive Small Bowel Obstruction Study) and systematic review.","Scotté Michel, Mauvais Francois, Bubenheim Michael, Cossé Cyril, Suaud Leslie, et al.",2017,Surgery,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This study evaluated the association between oral gastrografin administration and the need for operative intervention in patients with presumed adhesive small bowel obstruction. Between October 2006 and August 2009, 242 patients with uncomplicated acute adhesive small bowel obstruction were included in a randomized, controlled trial (the Adhesive Small Bowel Obstruction Study, NCT00389116) and allocated to a gastrografin arm or a saline solution arm. The primary end point was the need for operative intervention within 48 hours of randomization. The secondary end points were the resection rate, the time interval between the initial computed tomography and operative intervention, the time interval between oral refeeding and discharge, risk factors for the failure of nonoperative management, in-hospital mortality, duration of stay, and recurrence or death after discharge. We performed a systematic review of the literature in order to evaluate the relationship between use of gastrografin a",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28087066
SPB-0352,10.1097/CCM.0000000000001479,Effect of Perioperative Goal-Directed Hemodynamic Resuscitation Therapy on Outcomes Following Cardiac Surgery: A Randomized Clinical Trial and Systematic Review.,"Osawa Eduardo A, Rhodes Andrew, Landoni Giovanni, Galas Filomena R B G, Fukushima Julia T, et al.",2016,Critical care medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To evaluate the effects of goal-directed therapy on outcomes in high-risk patients undergoing cardiac surgery. A prospective randomized controlled trial and an updated metaanalysis of randomized trials published from inception up to May 1, 2015. Surgical ICU within a tertiary referral university-affiliated teaching hospital. One hundred twenty-six high-risk patients undergoing coronary artery bypass surgery or valve repair. Patients were randomized to a cardiac output-guided hemodynamic therapy algorithm (goal-directed therapy group, n = 62) or to usual care (n = 64). In the goal-directed therapy arm, a cardiac index of greater than 3 L/min/m was targeted with IV fluids, inotropes, and RBC transfusion starting from cardiopulmonary bypass and ending 8 hours after arrival to the ICU. The primary outcome was a composite endpoint of 30-day mortality and major postoperative complications. Patients from the goal-directed therapy group received a greater median (interquartile range) volume of",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26646462
SPB-0353,10.1016/j.autrev.2015.05.013,Efficacy of low-dose rituximab for the treatment of mixed cryoglobulinemia vasculitis: Phase II clinical trial and systematic review.,"Visentini Marcella, Tinelli Carmine, Colantuono Stefania, Monti Monica, Ludovisi Serena, et al.",2015,Autoimmunity reviews,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To evaluate whether rituximab at a low dose of 250 mg/m(2) × 2 may be as effective as at higher dosages, most commonly 375 mg/m(2)×4, used in previous studies on the treatment of patients with refractory mixed cryoglobulinemia (MC) vasculitis associated with hepatitis C virus (HCV) infection. We conducted a phase 2, single-arm two-stage trial (EUDRACT n. 2008-000086-38) of low-dose rituximab in 52 patients with HCV-associated MC who were ineligible/intolerant or non-responder to antiviral therapy. The primary outcomes were response of vasculitis evaluated by the Birmingham Vasculitis Activity Score (BVAS) at months 3, 6 and 12, rate of relapses and time to relapse, and rate of adverse events. Our data were compared with those reported in 19 published studies selected among 291 reviewed in a literature search. The cumulative response rate (complete and partial) at month 3 was 81% in our patients, and 86% in 208 patients from studies using high-dose rituximab. The relapse rate and median",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26031898
SPB-0354,10.1016/S0140-6736(17)30260-X,"Quarter-dose quadruple combination therapy for initial treatment of hypertension: placebo-controlled, crossover, randomised trial and systematic review.","Chow Clara K, Thakkar Jay, Bennett Alex, Hillis Graham, Burke Michael, et al.",2017,"Lancet (London, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Globally, most patients with hypertension are treated with monotherapy, and control rates are poor because monotherapy only reduces blood pressure by around 9/5 mm Hg on average. There is a pressing need for blood pressure-control strategies with improved efficacy and tolerability. We aimed to assess whether ultra-low-dose combination therapy could meet these needs. We did a randomised, placebo-controlled, double-blind, crossover trial of a quadpill-a single capsule containing four blood pressure-lowering drugs each at quarter-dose (irbesartan 37·5 mg, amlodipine 1·25 mg, hydrochlorothiazide 6·25 mg, and atenolol 12·5 mg). Participants with untreated hypertension were enrolled from four centres in the community of western Sydney, NSW, Australia, mainly by general practitioners. Participants were randomly allocated by computer to either the quadpill or matching placebo for 4 weeks; this treatment was followed by a 2-week washout, then the other study treatment was administered for 4 wee",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:28190578
SPB-0355,10.1136/ebmental-2022-300530,Can we mitigate the psychological impacts of social isolation using behavioural activation? Long-term results of the UK BASIL urgent public health COVID-19 pilot randomised controlled trial and living systematic review.,"Littlewood Elizabeth, McMillan Dean, Chew Graham Carolyn, Bailey Della, Gascoyne Samantha, et al.",2022,Evidence-based mental health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Behavioural and cognitive interventions remain credible approaches in addressing loneliness and depression. There was a need to rapidly generate and assimilate trial-based data during COVID-19. We undertook a parallel pilot RCT of behavioural activation (a brief behavioural intervention) for depression and loneliness (Behavioural Activation in Social Isolation, the BASIL-C19 trial ISRCTN94091479). We also assimilate these data in a living systematic review (PROSPERO CRD42021298788) of cognitive and/or behavioural interventions. Participants (≥65 years) with long-term conditions were computer randomised to behavioural activation (n=47) versus care as usual (n=49). Primary outcome was PHQ-9. Secondary outcomes included loneliness (De Jong Scale). Data from the BASIL-C19 trial were included in a metanalysis of depression and loneliness. The 12 months adjusted mean difference for PHQ-9 was -0.70 (95% CI -2.61 to 1.20) and for loneliness was -0.39 (95% CI -1.43 to 0.65).The BASIL-C19 living",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:36223980
SPB-0356,10.3310/hta19660,Saline in acute bronchiolitis RCT and economic evaluation: hypertonic saline in acute bronchiolitis - randomised controlled trial and systematic review.,"Everard Mark L, Hind Daniel, Ugonna Kelechi, Freeman Jennifer, Bradburn Mike, et al.",2015,"Health technology assessment (Winchester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Acute bronchiolitis is the most common cause of hospitalisation in infancy. Supportive care and oxygen are the cornerstones of management. A Cochrane review concluded that the use of nebulised 3% hypertonic saline (HS) may significantly reduce the duration of hospitalisation. To test the hypothesis that HS reduces the time to when infants were assessed as being fit for discharge, defined as in air with saturations of > 92% for 6 hours, by 25%. Parallel-group, pragmatic randomised controlled trial, cost-utility analysis and systematic review. Ten UK hospitals. Infants with acute bronchiolitis requiring oxygen therapy were allocated within 4 hours of admission. Supportive care with oxygen as required, minimal handling and fluid administration as appropriate to the severity of the disease, 3% nebulised HS every ± 6 hours. The trial primary outcome was time until the infant met objective discharge criteria. Secondary end points included time to discharge and adverse events. The costs analy",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26295732
SPB-0357,10.3310/hta20500,"The feasibility of determining the effectiveness and cost-effectiveness of medication organisation devices compared with usual care for older people in a community setting: systematic review, stakeholder focus groups and feasibility randomised controlled trial.","Bhattacharya Debi, Aldus Clare F, Barton Garry, Bond Christine M, Boonyaprapa Sathon, et al.",2016,"Health technology assessment (Winchester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Medication organisation devices (MODs) provide compartments for a patient's medication to be organised into the days of the week and the recommended times the medication should be taken. To define the optimal trial design for testing the clinical effectiveness and cost-effectiveness of MODs. The feasibility study comprised a systematic review and focus groups to inform a randomised controlled trial (RCT) design. The resulting features were tested on a small scale, using a 2 × 2 factorial design to compare MODs with usual packaging and to compare weekly with monthly supply. The study design was then evaluated. Potential participants were identified by medical practices. Aged over 75 years, prescribed at least three solid oral dosage form medications, unintentionally non-adherent and self-medicating. Participants were excluded if deemed by their health-care team to be unsuitable. One of three MODs widely used in routine clinical practice supplied either weekly or monthly. To identify the",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:27385430
SPB-0358,10.1227/NEU.0000000000000624,Bleeding and infection with external ventricular drainage: a systematic review in comparison with adjudicated adverse events in the ongoing Clot Lysis Evaluating Accelerated Resolution of Intraventricular Hemorrhage Phase III (CLEAR-III IHV) trial.,"Dey Mahua, Stadnik Agnieszka, Riad Fady, Zhang Lingjiao, McBee Nichol, et al.",2015,Neurosurgery,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Retrospective series report varied rates of bleeding and infection with external ventricular drainage (EVD). There have been no prospective studies of these risks with systematic surveillance, threshold definitions, or independent adjudication. To analyze the rate of complications in the ongoing Clot Lysis: Evaluating Accelerated Resolution of Intraventricular Hemorrhage Phase III (CLEAR III) trial, providing a comparison with a systematic review of complications of EVD in the literature. Patients were prospectively enrolled in the CLEAR III trial after placement of an EVD for obstructive intraventricular hemorrhage and randomized to receive recombinant tissue-type plasminogen activator or placebo. We counted any detected new hemorrhage (catheter tract hemorrhage or any other distant hemorrhage) on computed tomography scan within 30 days from the randomization. Meta-analysis of published series of EVD placement was compiled with STATA software. Growing or unstable hemorrhage was report",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:25635887
SPB-0359,10.1097/PRS.0000000000004515,"Topical Aloe Vera Gel for Accelerated Wound Healing of Split-Thickness Skin Graft Donor Sites: A Double-Blind, Randomized, Controlled Trial and Systematic Review.","Burusapat Chairat, Supawan Monlada, Pruksapong Chatchai, Pitiseree Anont, Suwantemee Chaichoompol",2018,Plastic and reconstructive surgery,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Aloe vera has been used to treat wounds since ancient times. However, data regarding the efficacy of aloe vera for burns and split-thickness skin graft donor sites are inconclusive. A double-blind, randomized, controlled trial was conducted. Patients who underwent split-thickness skin graft harvesting from the thigh were included. Split-thickness skin graft donor sites were divided into two groups: the aloe vera group and the placebo group. The visual analogue scale score was used to evaluate pain, and complete epithelialization was assessed. The authors searched electronic databases and included only international clinical trials published in the English language. Twelve patients with 24 donor sites participated. Times to complete epithelization for the aloe vera and placebo groups were 11.5 ± 1.45 and 13.67 ± 1.61 days, respectively (p < 0.05). Visual analogue scale scores after wound dressing for the aloe vera and placebo groups were 17.18 ± 13.17 and 18.63 ± 11.20, respectively. No",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29649056
SPB-0360,10.1093/bja/aeu386,LiDCO-based fluid management in patients undergoing hip fracture surgery under spinal anaesthesia: a randomized trial and systematic review.,"Moppett I K, Rowlands M, Mannings A, Moran C G, Wiles M D, et al.",2015,British journal of anaesthesia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Hip fracture is a condition with high mortality and morbidity in elderly frail patients. Intraoperative fluid optimization may be associated with benefit in this population. We investigated whether intraoperative fluid management using pulse-contour analysis cardiac monitoring, compared with standard care in patients undergoing spinal anaesthesia, would provide benefits in terms of reduced time until medically fit for discharge and postoperative complications. Patients undergoing surgical repair of fractured neck of femur, aged >60 yr, receiving spinal anaesthesia were enrolled in this single-centre, blinded, randomized, parallel group trial. Patients were allocated to either anaesthetist-directed fluid therapy or a pulse-contour-guided fluid optimization strategy using colloid (Gelofusine) boluses to optimize stroke volume. The primary outcome was time until medically fit for discharge. Secondary outcomes included postoperative complications, mobility, and mortality. We updated a syst",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:25500940
SPB-0361,10.3310/hta21720,"Preventing blood-borne virus infection in people who inject drugs in the UK: systematic review, stakeholder interviews, psychosocial intervention development and feasibility randomised controlled trial.","Gilchrist Gail, Swan Davina, Shaw April, Keding Ada, Towers Sarah, et al.",2017,"Health technology assessment (Winchester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Opioid substitution therapy and needle exchanges have reduced blood-borne viruses (BBVs) among people who inject drugs (PWID). Some PWID continue to share injecting equipment. To develop an evidence-based psychosocial intervention to reduce BBV risk behaviours and increase transmission knowledge among PWID, and conduct a feasibility trial among PWID comparing the intervention with a control. A pragmatic, two-armed randomised controlled, open feasibility trial. Service users were Steering Group members and co-developed the intervention. Peer educators co-delivered the intervention in London. NHS or third-sector drug treatment or needle exchanges in Glasgow, London, Wrexham and York, recruiting January and February 2016. Current PWID, aged ≥ 18 years. A remote, web-based computer randomisation system allocated participants to a three-session, manualised, psychosocial, gender-specific group intervention delivered by trained facilitators and BBV transmission information booklet plus treatm",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:29208190
SPB-0362,10.1159/000511574,PREvention of VENous Thromboembolism in Hemorrhagic Stroke Patients - PREVENTIHS Study: A Randomized Controlled Trial and a Systematic Review and Meta-Analysis.,"Paciaroni Maurizio, Agnelli Giancarlo, Alberti Andrea, Becattini Cecilia, Guercini Francesco, et al.",2020,European neurology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In this randomized trial, currently utilized standard treatments were compared with enoxaparin for the prevention of venous thromboembolism (VTE) in patients with intracerebral hemorrhage (ICH). Enoxaparin (0.4 mg daily for 10 days) was started after 72 h from the onset of ICH. The primary outcome was symptomatic or asymptomatic deep venous thrombosis as assessed by ultrasound at the end of study treatment. The safety of enoxaparin was also assessed. We included the results of this study in a meta-analysis of all relevant studies comparing anticoagulants with standard treatments or placebo. PREVENTIHS was prematurely stopped after the randomization of 73 patients, due to the low recruitment rate. The prevalence of any VTE at 10 days was 15.8% in the enoxaparin group and 20.0% in the control group (RR 0.79 [95% CI 0.29-2.12]); 2.6% of enoxaparin and 8.6% of standard therapy patients had severe bleedings (RR 0.31 [95% CI 0.03-2.82]). When these results were meta-analyzed with the results",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:33190135
SPB-0363,10.11607/prd.2164,A mixed-model study assessing orthodontic tooth extrusion for the reestablishment of biologic width. A systematic review and exploratory randomized trial.,"Zenóbio Elton Gonçalves, Moreira Ricardo Carneiro, Soares Rodrigo Villamarin, Feres Magda, Chambrone Leandro, et al.",2015,The International journal of periodontics & restorative dentistry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This study assessed the use of orthodontic extrusion (OE) for biologic width reestablishment (BWR) and compared two protocols for BWR: periodontal flap surgery (FS) performed either before (FS + OE) or after (OE + FS) extrusion. Databases were screened up to March 2013 for studies on OE, and outcomes from 13 patients treated by OE + FS or FS + OE were assessed. The results of the literature showed that OE + fiberotomy led to a greater amount of root extrusion than OE alone. The clinical/radiographic assessment demonstrated no significant differences between groups (P > .05). Within groups, there was an improvement in the keratinized tissue (P = .034) and in probing depth (P = .025) for OE + FS.",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:25734703
SPB-0364,,Benefits and harms of red blood cell transfusions in patients with septic shock in the intensive care unit.,Holst Lars Broksø,2016,Danish medical journal,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Transfusion of red blood cells (RBCs) is widely used for non-bleeding patients with septic shock in the intensive care unit (ICU). The evidence for effect and safety are limited showing conflicting results and transfused RBCs have the potential to harm subgroups of critically ill patients. Our aim was to assess the benefits and harms of RBC transfusion in patients with septic shock in a randomised clinical trial and to conduct an up-to-date systematic review with meta-analysis of all randomised clinical trials comparing different transfusion strategies.   We planned and conducted a randomised, partly blinded, clinical trial assigning patients with septic shock in the ICU and a haemoglobin level of 9 g/dl (5.6 mM) or below to receive single units of pre-storage leukoreduced RBCs at a lower haemoglobin threshold level of 7 g/dl (4.3 mM) or below or a higher haemoglobin threshold level of 9 g/dl (5.6 mM) or below. The primary outcome was death by day 90 after randomisation. Secondary outc",,medicine,auto_pubmed_clean,scipeerai_collector_v1,pmid:26836806
SPB-0365,10.1167/tvst.9.2.14,"Introduction to Machine Learning, Neural Networks, and Deep Learning.","Choi Rene Y, Coyner Aaron S, Kalpathy-Cramer Jayashree, Chiang Michael F, Campbell J Peter",2020,Translational vision science & technology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To present an overview of current machine learning methods and their use in medical research, focusing on select machine learning techniques, best practices, and deep learning. A systematic literature search in PubMed was performed for articles pertinent to the topic of artificial intelligence methods used in medicine with an emphasis on ophthalmology. A review of machine learning and deep learning methodology for the audience without an extensive technical computer programming background. Artificial intelligence has a promising future in medicine; however, many challenges remain. The aim of this review article is to provide the nontechnical readers a layman's explanation of the machine learning methods being used in medicine today. The goal is to provide the reader a better understanding of the potential and challenges of artificial intelligence within the field of medicine.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32704420
SPB-0366,10.1007/s11030-021-10217-3,Artificial intelligence to deep learning: machine intelligence approach for drug discovery.,"Gupta Rohan, Srivastava Devesh, Sahu Mehar, Tiwari Swati, Ambasta Rashmi K, et al.",2021,Molecular diversity,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. However, low efficacy, off-target delivery, time consumption, and high cost impose a hurdle and challenges that impact drug design and discovery. Further, complex and big data from genomics, proteomics, microarray data, and clinical trials also impose an obstacle in the drug discovery pipeline. Artificial intelligence and machine learning technology play a crucial role in drug discovery and development. In other words, artificial neural networks and deep learning algorithms have modernized the area. Machine learning and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical ac",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:33844136
SPB-0367,10.1016/j.jinf.2023.07.006,"Artificial intelligence, machine learning and deep learning: Potential resources for the infection clinician.","Theodosiou Anastasia A, Read Robert C",2023,The Journal of infection,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence (AI), machine learning and deep learning (including generative AI) are increasingly being investigated in the context of research and management of human infection. We summarise recent and potential future applications of AI and its relevance to clinical infection practice. 1617 PubMed results were screened, with priority given to clinical trials, systematic reviews and meta-analyses. This narrative review focusses on studies using prospectively collected real-world data with clinical validation, and on research with translational potential, such as novel drug discovery and microbiome-based interventions. There is some evidence of clinical utility of AI applied to laboratory diagnostics (e.g. digital culture plate reading, malaria diagnosis, antimicrobial resistance profiling), clinical imaging analysis (e.g. pulmonary tuberculosis diagnosis), clinical decision support tools (e.g. sepsis prediction, antimicrobial prescribing) and public health outbreak managemen",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:37468046
SPB-0368,10.1016/j.semcancer.2019.12.011,Machine and deep learning approaches for cancer drug repurposing.,"Issa Naiem T, Stathias Vasileios, Schürer Stephan, Dakshanamurthy Sivanesan",2021,Seminars in cancer biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Knowledge of the underpinnings of cancer initiation, progression and metastasis has increased exponentially in recent years. Advanced ""omics"" coupled with machine learning and artificial intelligence (deep learning) methods have helped elucidate targets and pathways critical to those processes that may be amenable to pharmacologic modulation. However, the current anti-cancer therapeutic armamentarium continues to lag behind. As the cost of developing a new drug remains prohibitively expensive, repurposing of existing approved and investigational drugs is sought after given known safety profiles and reduction in the cost barrier. Notably, successes in oncologic drug repurposing have been infrequent. Computational in-silico strategies have been developed to aid in modeling biological processes to find new disease-relevant targets and discovering novel drug-target and drug-phenotype associations. Machine and deep learning methods have especially enabled leaps in those successes. This revi",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:31904426
SPB-0369,10.1002/mp.13678,Machine and deep learning methods for radiomics.,"Avanzo Michele, Wei Lise, Stancanello Joseph, Vallières Martin, Rao Arvind, et al.",2020,Medical physics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Radiomics is an emerging area in quantitative image analysis that aims to relate large-scale extracted imaging information to clinical and biological endpoints. The development of quantitative imaging methods along with machine learning has enabled the opportunity to move data science research towards translation for more personalized cancer treatments. Accumulating evidence has indeed demonstrated that noninvasive advanced imaging analytics, that is, radiomics, can reveal key components of tumor phenotype for multiple three-dimensional lesions at multiple time points over and beyond the course of treatment. These developments in the use of CT, PET, US, and MR imaging could augment patient stratification and prognostication buttressing emerging targeted therapeutic approaches. In recent years, deep learning architectures have demonstrated their tremendous potential for image segmentation, reconstruction, recognition, and classification. Many powerful open-source and commercial platform",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32418336
SPB-0370,10.1177/15353702231209421,Review of machine learning and deep learning models for toxicity prediction.,"Guo Wenjing, Liu Jie, Dong Fan, Song Meng, Li Zoe, et al.",2023,"Experimental biology and medicine (Maywood, N.J.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The ever-increasing number of chemicals has raised public concerns due to their adverse effects on human health and the environment. To protect public health and the environment, it is critical to assess the toxicity of these chemicals. Traditional in vitro and in vivo toxicity assays are complicated, costly, and time-consuming and may face ethical issues. These constraints raise the need for alternative methods for assessing the toxicity of chemicals. Recently, due to the advancement of machine learning algorithms and the increase in computational power, many toxicity prediction models have been developed using various machine learning and deep learning algorithms such as support vector machine, random forest, k-nearest neighbors, ensemble learning, and deep neural network. This review summarizes the machine learning- and deep learning-based toxicity prediction models developed in recent years. Support vector machine and random forest are the most popular machine learning algorithms, ",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:38057999
SPB-0371,10.1016/j.drudis.2021.09.007,Machine-learning methods for ligand-protein molecular docking.,"Crampon Kevin, Giorkallos Alexis, Deldossi Myrtille, Baud Stéphanie, Steffenel Luiz Angelo",2022,Drug discovery today,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains use AI, including molecular simulation for drug discovery. In this review, we provide an overview of ligand-protein molecular docking and how machine learning (ML), especially deep learning (DL), a subset of ML, is transforming the field by tackling the associated challenges.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34560276
SPB-0372,10.2967/jnumed.118.220590,Artificial Intelligence in Nuclear Medicine.,"Nensa Felix, Demircioglu Aydin, Rischpler Christoph",2019,"Journal of nuclear medicine : official publication, Society of Nuclear Medicine",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Despite the great media attention for artificial intelligence (AI), for many health care professionals the term and the functioning of AI remain a ""black box,"" leading to exaggerated expectations on the one hand and unfounded fears on the other. In this review, we provide a conceptual classification and a brief summary of the technical fundamentals of AI. Possible applications are discussed on the basis of a typical work flow in medical imaging, grouped by planning, scanning, interpretation, and reporting. The main limitations of current AI techniques, such as issues with interpretability or the need for large amounts of annotated data, are briefly addressed. Finally, we highlight the possible impact of AI on the nuclear medicine profession, the associated challenges and, last but not least, the opportunities.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:31481587
SPB-0373,10.1016/j.cub.2019.02.034,Neural network models and deep learning.,"Kriegeskorte Nikolaus, Golan Tal",2019,Current biology : CB,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Originally inspired by neurobiology, deep neural network models have become a powerful tool of machine learning and artificial intelligence. They can approximate functions and dynamics by learning from examples. Here we give a brief introduction to neural network models and deep learning for biologists. We introduce feedforward and recurrent networks and explain the expressive power of this modeling framework and the backpropagation algorithm for setting the parameters. Finally, we consider how deep neural network models might help us understand brain computation.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:30939301
SPB-0374,10.1186/s13073-021-00930-x,DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.,"Poirion Olivier B, Jing Zheng, Chaudhary Kumardeep, Huang Sijia, Garmire Lana X",2021,Genome medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Multi-omics data are good resources for prognosis and survival prediction; however, these are difficult to integrate computationally. We introduce DeepProg, a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data. It identifies two optimal survival subtypes in most cancers and yields significantly better risk-stratification than other multi-omics integration methods. DeepProg is highly predictive, exemplified by two liver cancer (C-index 0.73-0.80) and five breast cancer datasets (C-index 0.68-0.73). Pan-cancer analysis associates common genomic signatures in poor survival subtypes with extracellular matrix modeling, immune deregulation, and mitosis processes. DeepProg is freely available at https://github.com/lanagarmire/DeepProg.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34261540
SPB-0375,10.1007/978-1-0716-1787-8_16,"Artificial Intelligence, Machine Learning, and Deep Learning in Real-Life Drug Design Cases.","Muller Christophe, Rabal Obdulia, Diaz Gonzalez Constantino",2022,"Methods in molecular biology (Clifton, N.J.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The discovery and development of drugs is a long and expensive process with a high attrition rate. Computational drug discovery contributes to ligand discovery and optimization, by using models that describe the properties of ligands and their interactions with biological targets. In recent years, artificial intelligence (AI) has made remarkable modeling progress, driven by new algorithms and by the increase in computing power and storage capacities, which allow the processing of large amounts of data in a short time. This review provides the current state of the art of AI methods applied to drug discovery, with a focus on structure- and ligand-based virtual screening, library design and high-throughput analysis, drug repurposing and drug sensitivity, de novo design, chemical reactions and synthetic accessibility, ADMET, and quantum mechanics.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34731478
SPB-0376,10.1186/s12938-023-01187-8,"Artificial intelligence in glaucoma: opportunities, challenges, and future directions.","Huang Xiaoqin, Islam Md Rafiqul, Akter Shanjita, Ahmed Fuad, Kazami Ehsan, et al.",2023,Biomedical engineering online,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence (AI) has shown excellent diagnostic performance in detecting various complex problems related to many areas of healthcare including ophthalmology. AI diagnostic systems developed from fundus images have become state-of-the-art tools in diagnosing retinal conditions and glaucoma as well as other ocular diseases. However, designing and implementing AI models using large imaging data is challenging. In this study, we review different machine learning (ML) and deep learning (DL) techniques applied to multiple modalities of retinal data, such as fundus images and visual fields for glaucoma detection, progression assessment, staging and so on. We summarize findings and provide several taxonomies to help the reader understand the evolution of conventional and emerging AI models in glaucoma. We discuss opportunities and challenges facing AI application in glaucoma and highlight some key themes from the existing literature that may help to explore future studies. Our goa",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:38102597
SPB-0377,10.1021/acssensors.0c01424,Advancing Biosensors with Machine Learning.,"Cui Feiyun, Yue Yun, Zhang Yi, Zhang Ziming, Zhou H Susan",2020,ACS sensors,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Chemometrics play a critical role in biosensors-based detection, analysis, and diagnosis. Nowadays, as a branch of artificial intelligence (AI), machine learning (ML) have achieved impressive advances. However, novel advanced ML methods, especially deep learning, which is famous for image analysis, facial recognition, and speech recognition, has remained relatively elusive to the biosensor community. Herein, how ML can be beneficial to biosensors is systematically discussed. The advantages and drawbacks of most popular ML algorithms are summarized on the basis of sensing data analysis. Specially, deep learning methods such as convolutional neural network (CNN) and recurrent neural network (RNN) are emphasized. Diverse ML-assisted electrochemical biosensors, wearable electronics, SERS and other spectra-based biosensors, fluorescence biosensors and colorimetric biosensors are comprehensively discussed. Furthermore, biosensor networks and multibiosensor data fusion are introduced. This re",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:33185417
SPB-0378,10.1097/ICU.0000000000000788,Artificial intelligence and ophthalmic surgery.,"Mishra Kapil, Leng Theodore",2021,Current opinion in ophthalmology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence and deep learning have become important tools in extracting data from ophthalmic surgery to evaluate, teach, and aid the surgeon in all phases of surgical management. The purpose of this review is to highlight the ever-increasing intersection of computer vision, machine learning, and ophthalmic microsurgery. Deep learning algorithms are being applied to help evaluate and teach surgical trainees. Artificial intelligence tools are improving real-time surgical instrument tracking, phase segmentation, as well as enhancing the safety of robotic-assisted vitreoretinal surgery. Similar to strides appreciated in ophthalmic medical disease, artificial intelligence will continue to become an important part of surgical management of ocular conditions. Machine learning applications will help push the boundaries of what surgeons can accomplish to improve patient outcomes.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34397576
SPB-0379,10.1007/s11427-020-1804-5,Application of deep learning in genomics.,"Liu Jianxiao, Li Jiying, Wang Hai, Yan Jianbing",2020,Science China. Life sciences,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In recent years, deep learning has been widely used in diverse fields of research, such as speech recognition, image classification, autonomous driving and natural language processing. Deep learning has showcased dramatically improved performance in complex classification and regression problems, where the intricate structure in the high-dimensional data is difficult to discover using conventional machine learning algorithms. In biology, applications of deep learning are gaining increasing popularity in predicting the structure and function of genomic elements, such as promoters, enhancers, or gene expression levels. In this review paper, we described the basic concepts in machine learning and artificial neural network, followed by elaboration on the workflow of using convolutional neural network in genomics. Then we provided a concise introduction of deep learning applications in genomics and synthetic biology at the levels of DNA, RNA and protein. Finally, we discussed the current ch",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:33051704
SPB-0380,10.1097/MOG.0000000000000945,Machine and deep learning in inflammatory bowel disease.,"Zulqarnain Fatima, Rhoads S Fisher, Syed Sana",2023,Current opinion in gastroenterology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The Management of inflammatory bowel disease (IBD) has evolved with the introduction and widespread adoption of biologic agents; however, the advent of artificial intelligence technologies like machine learning and deep learning presents another watershed moment in IBD treatment. Interest in these methods in IBD research has increased over the past 10 years, and they offer a promising path to better clinical outcomes for IBD patients. Developing new tools to evaluate IBD and inform clinical management is challenging because of the expansive volume of data and requisite manual interpretation of data. Recently, machine and deep learning models have been used to streamline diagnosis and evaluation of IBD by automating review of data from several diagnostic modalities with high accuracy. These methods decrease the amount of time that clinicians spend manually reviewing data to formulate an assessment. Interest in machine and deep learning is increasing in medicine, and these methods are po",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:37144491
SPB-0381,10.1002/art.42296,Artificial Intelligence and Deep Learning for Rheumatologists.,"McMaster Christopher, Bird Alix, Liew David F L, Buchanan Russell R, Owen Claire E, et al.",2022,"Arthritis & rheumatology (Hoboken, N.J.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Deep learning has emerged as the leading method in machine learning, spawning a rapidly growing field of academic research and commercial applications across medicine. Deep learning could have particular relevance to rheumatology if correctly utilized. The greatest benefits of deep learning methods are seen with unstructured data frequently found in rheumatology, such as images and text, where traditional machine learning methods have struggled to unlock the trove of information held within these data formats. The basis for this success comes from the ability of deep learning to learn the structure of the underlying data. It is no surprise that the first areas of medicine that have started to experience impact from deep learning heavily rely on interpreting visual data, such as triaging radiology workflows and computer-assisted colonoscopy. Applications in rheumatology are beginning to emerge, with recent successes in areas as diverse as detecting joint erosions on plain radiography, p",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35857865
SPB-0382,10.1016/j.cbpa.2021.102111,Extendable and explainable deep learning for pan-cancer radiogenomics research.,"Liu Qian, Hu Pingzhao",2022,Current opinion in chemical biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Radiogenomics is a field where medical images and genomic profiles are jointly analyzed to answer critical clinical questions. Specifically, people want to identify non-invasive imaging biomarkers that are associated with both genomic features and clinical outcomes. Deep learning is an advanced computer science technique that has been applied in many fields, including medical image and genomic data analysis. This review summarizes the current state of deep learning in pan-cancer radiogenomic research, discusses its limitations, and indicates the potential future directions. Traditional machine learning in radiomics, genomics, and radiogenomics have also been briefly discussed. We also summarize the main pan-cancer radiogenomic research resources. Two characteristics of deep learning are emphasized when discussing its application to pan-cancer radiogenomics, which are extendibility and explainability.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34999476
SPB-0383,10.3390/s23042338,New Cognitive Deep-Learning CAPTCHA.,"Trong Nghia Dinh, Huong Thien Ho, Hoang Vinh Truong",2023,"Sensors (Basel, Switzerland)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CAPTCHA (Completely Automated Public Turing test to tell Computers and Humans Apart), or HIP (Human Interactive Proof), has long been utilized to avoid bots manipulating web services. Over the years, various CAPTCHAs have been presented, primarily to enhance security and usability against new bots and cybercriminals carrying out destructive actions. Nevertheless, automated attacks supported by ML (Machine Learning), CNN (Convolutional Neural Network), and DNN (Deep Neural Network) have successfully broken all common conventional schemes, including text- and image-based CAPTCHAs. CNN/DNN have recently been shown to be extremely vulnerable to adversarial examples, which can consistently deceive neural networks by introducing noise that humans are incapable of detecting. In this study, the authors improve the security for CAPTCHA design by combining text-based, image-based, and cognitive CAPTCHA characteristics and applying adversarial examples and neural style transfer. Comprehend usabil",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:36850935
SPB-0384,10.1186/s12968-019-0575-y,Machine learning in cardiovascular magnetic resonance: basic concepts and applications.,"Leiner Tim, Rueckert Daniel, Suinesiaputra Avan, Baeßler Bettina, Nezafat Reza, et al.",2019,Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Machine learning (ML) is making a dramatic impact on cardiovascular magnetic resonance (CMR) in many ways. This review seeks to highlight the major areas in CMR where ML, and deep learning in particular, can assist clinicians and engineers in improving imaging efficiency, quality, image analysis and interpretation, as well as patient evaluation. We discuss recent developments in the field of ML relevant to CMR in the areas of image acquisition & reconstruction, image analysis, diagnostic evaluation and derivation of prognostic information. To date, the main impact of ML in CMR has been to significantly reduce the time required for image segmentation and analysis. Accurate and reproducible fully automated quantification of left and right ventricular mass and volume is now available in commercial products. Active research areas include reduction of image acquisition and reconstruction time, improving spatial and temporal resolution, and analysis of perfusion and myocardial mapping. Altho",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:31590664
SPB-0385,10.1007/s00330-019-06564-3,Deep learning: definition and perspectives for thoracic imaging.,"Chassagnon Guillaume, Vakalopolou Maria, Paragios Nikos, Revel Marie-Pierre",2020,European radiology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Relevance and penetration of machine learning in clinical practice is a recent phenomenon with multiple applications being currently under development. Deep learning-and especially convolutional neural networks (CNNs)-is a subset of machine learning, which has recently entered the field of thoracic imaging. The structure of neural networks, organized in multiple layers, allows them to address complex tasks. For several clinical situations, CNNs have demonstrated superior performance as compared with classical machine learning algorithms and in some cases achieved comparable or better performance than clinical experts. Chest radiography, a high-volume procedure, is a natural application domain because of the large amount of stored images and reports facilitating the training of deep learning algorithms. Several algorithms for automated reporting have been developed. The training of deep learning algorithm CT images is more complex due to the dimension, variability, and complexity of the",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:31811431
SPB-0386,10.47391/JPMA.AKU-12,Understanding deep learning - challenges and prospects.,"Adnan Niha, Umer Fahad",2022,JPMA. The Journal of the Pakistan Medical Association,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The developments in Artificial Intelligence have been on the rise since its advent. The advancements in this field have been the innovative research area across a wide range of industries, making its incorporation in dentistry inevitable. Artificial Intelligence techniques are making serious progress in the diagnostic and treatment planning aspects of dental clinical practice. This will ultimately help in the elimination of subjectivity and human error that are often part of radiographic interpretations, and will improve the overall efficiency of the process. The various types of Artificial Intelligence algorithms that exist today make the understanding of their application quite complex. The current narrative review was planned to make comprehension of Artificial Intelligence algorithms relatively straightforward. The focus was planned to be kept on the current developments and prospects of Artificial Intelligence in dentistry, especially Deep Learning and Convolutional Neural Network",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35202373
SPB-0387,10.1177/00031348221101490,Deep Learning Applications in Surgery: Current Uses and Future Directions.,"Morris Miranda X, Rajesh Aashish, Asaad Malke, Hassan Abbas, Saadoun Rakan, et al.",2023,The American surgeon,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Deep learning (DL) is a subset of machine learning that is rapidly gaining traction in surgical fields. Its tremendous capacity for powerful data-driven problem-solving has generated computational breakthroughs in many realms, with the fields of medicine and surgery becoming increasingly prominent avenues. Through its multi-layer architecture of interconnected neural networks, DL enables feature extraction and pattern recognition of highly complex and large-volume data. Across various surgical specialties, DL is being applied to optimize both preoperative planning and intraoperative performance in new and innovative ways. Surgeons are now able to integrate deep learning tools into their practice to improve patient safety and outcomes. Through this review, we explore the applications of deep learning in surgery and related subspecialties with an aim to shed light on the practical utilization of this technology in the present and near future.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35567312
SPB-0388,10.7717/peerj.13152,Computational bioacoustics with deep learning: a review and roadmap.,Stowell Dan,2022,PeerJ,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and ana",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35341043
SPB-0389,10.1177/15353702231214259,Machine learning and deep learning for brain tumor MRI image segmentation.,"Khan Md Kamrul Hasan, Guo Wenjing, Liu Jie, Dong Fan, Li Zoe, et al.",2023,"Experimental biology and medicine (Maywood, N.J.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Brain tumors are often fatal. Therefore, accurate brain tumor image segmentation is critical for the diagnosis, treatment, and monitoring of patients with these tumors. Magnetic resonance imaging (MRI) is a commonly used imaging technique for capturing brain images. Both machine learning and deep learning techniques are popular in analyzing MRI images. This article reviews some commonly used machine learning and deep learning techniques for brain tumor MRI image segmentation. The limitations and advantages of the reviewed machine learning and deep learning methods are discussed. Even though each of these methods has a well-established status in their individual domains, the combination of two or more techniques is currently an emerging trend.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:38102956
SPB-0390,10.1038/s41588-018-0295-5,A primer on deep learning in genomics.,"Zou James, Huss Mikael, Abid Abubakar, Mohammadi Pejman, Torkamani Ali, et al.",2019,Nature genetics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Deep learning methods are a class of machine learning techniques capable of identifying highly complex patterns in large datasets. Here, we provide a perspective and primer on deep learning applications for genome analysis. We discuss successful applications in the fields of regulatory genomics, variant calling and pathogenicity scores. We include general guidance for how to effectively use deep learning methods as well as a practical guide to tools and resources. This primer is accompanied by an interactive online tutorial.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:30478442
SPB-0391,10.3390/ijms23126610,"Editorial of Special Issue ""Deep Learning and Machine Learning in Bioinformatics"".","Kang Mingon, Oh Jung Hun",2022,International journal of molecular sciences,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In recent years, deep learning has emerged as a highly active research field, achieving great success in various machine learning areas, including image processing, speech recognition, and natural language processing, and now rapidly becoming a dominant tool in biomedicine [...].",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35743052
SPB-0392,10.1053/j.ackd.2021.07.004,"Deep Learning in Kidney Ultrasound: Overview, Frontiers, and Challenges.","De Jesus-Rodriguez Hector J, Morgan Matthew A, Sagreiya Hersh",2021,Advances in chronic kidney disease,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Ultrasonography is a practical imaging technique used in numerous health care settings. It is relatively inexpensive, portable, and safe, and it has dynamic capabilities that make it an invaluable tool for a wide variety of diagnostic and interventional studies. Recently, there has been a revolution in medical imaging using artificial intelligence (AI). A particularly potent form of AI is deep learning, in which the computer learns to recognize pixel or written data on its own without the selection of predetermined features, usually through a specific neural network architecture. Neural networks vary in architecture depending on their task, and key design considerations include the number of layers and complexity, data available, technical requirements, and domain knowledge. Deep learning models offer the potential for promising innovations to workflow, image quality, and vision tasks in sonography. However, there are key limitations and challenges in creating reliable and safe AI mode",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34906311
SPB-0393,10.1038/s41386-020-0767-z,Deep learning for small and big data in psychiatry.,"Koppe Georgia, Meyer-Lindenberg Andreas, Durstewitz Daniel",2021,Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Psychiatry today must gain a better understanding of the common and distinct pathophysiological mechanisms underlying psychiatric disorders in order to deliver more effective, person-tailored treatments. To this end, it appears that the analysis of 'small' experimental samples using conventional statistical approaches has largely failed to capture the heterogeneity underlying psychiatric phenotypes. Modern algorithms and approaches from machine learning, particularly deep learning, provide new hope to address these issues given their outstanding prediction performance in other disciplines. The strength of deep learning algorithms is that they can implement very complicated, and in principle arbitrary predictor-response mappings efficiently. This power comes at a cost, the need for large training (and test) samples to infer the (sometimes over millions of) model parameters. This appears to be at odds with the as yet rather 'small' samples available in psychiatric human research to date ",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32668442
SPB-0394,10.1155/2022/2645381,Text-Based Emotion Recognition Using Deep Learning Approach.,"Bharti Santosh Kumar, Varadhaganapathy S, Gupta Rajeev Kumar, Shukla Prashant Kumar, Bouye Mohamed, et al.",2022,Computational intelligence and neuroscience,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Sentiment analysis is a method to identify people's attitudes, sentiments, and emotions towards a given goal, such as people, activities, organizations, services, subjects, and products. Emotion detection is a subset of sentiment analysis as it predicts the unique emotion rather than just stating positive, negative, or neutral. In recent times, many researchers have already worked on speech and facial expressions for emotion recognition. However, emotion detection in text is a tedious task as cues are missing, unlike in speech, such as tonal stress, facial expression, pitch, etc. To identify emotions from text, several methods have been proposed in the past using natural language processing (NLP) techniques: the keyword approach, the lexicon-based approach, and the machine learning approach. However, there were some limitations with keyword- and lexicon-based approaches as they focus on semantic relations. In this article, we have proposed a hybrid (machine learning + deep learning) mo",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:36052029
SPB-0395,10.1007/s11886-020-01348-4,Radiomics in Echocardiography: Deep Learning and Echocardiographic Analysis.,Kusunose Kenya,2020,Current cardiology reports,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Recent development in artificial intelligence (AI) for cardiovascular imaging analysis, involving deep learning, is the start of a new phase in the research field. We review the current state of AI in cardiovascular field and discuss about its potential to improve clinical workflows and accuracy of diagnosis. In the AI cardiovascular imaging field, there are many applications involving efficient image reconstruction, patient triage, and support for clinical decisions. These tools have a role to support repetitive clinical tasks. Although they will be powerful in some situations, these applications may have new potential in the hands of echo cardiologists, assisting but not replacing the human observer. We believe AI has the potential to improve the quality of echocardiography. Someday AI may be incorporated into the daily clinical setting, being an instrumental tool for cardiologists dealing with cardiovascular diseases.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32648059
SPB-0396,10.1111/den.13896,Artificial intelligence and deep learning for small bowel capsule endoscopy.,"Trasolini Roberto, Byrne Michael F",2021,Digestive endoscopy : official journal of the Japan Gastroenterological Endoscopy Society,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Capsule endoscopy is ideally suited to artificial intelligence-based interpretation given its reliance on pattern recognition in still images. Time saving viewing modes and lesion detection features currently available rely on machine learning algorithms, a form of artificial intelligence. Current software necessitates close human supervision given poor sensitivity relative to an expert reader. However, with the advent of deep learning, artificial intelligence is becoming increasingly reliable and will be increasingly relied upon. We review the major advances in artificial intelligence for capsule endoscopy in recent publications and briefly review artificial intelligence development for historical understanding. Importantly, recent advancements in artificial intelligence have not yet been incorporated into practice and it is immature to judge the potential of this technology based on current platforms. Remaining regulatory and standardization hurdles are being overcome and artificial ",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:33211357
SPB-0397,10.3390/s22052017,A Systematic Review on Machine Learning and Deep Learning Models for Electronic Information Security in Mobile Networks.,"Gupta Chaitanya, Johri Ishita, Srinivasan Kathiravan, Hu Yuh-Chung, Qaisar Saeed Mian, et al.",2022,"Sensors (Basel, Switzerland)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Today's advancements in wireless communication technologies have resulted in a tremendous volume of data being generated. Most of our information is part of a widespread network that connects various devices across the globe. The capabilities of electronic devices are also increasing day by day, which leads to more generation and sharing of information. Similarly, as mobile network topologies become more diverse and complicated, the incidence of security breaches has increased. It has hampered the uptake of smart mobile apps and services, which has been accentuated by the large variety of platforms that provide data, storage, computation, and application services to end-users. It becomes necessary in such scenarios to protect data and check its use and misuse. According to the research, an artificial intelligence-based security model should assure the secrecy, integrity, and authenticity of the system, its equipment, and the protocols that control the network, independent of its genera",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:35271163
SPB-0398,10.1016/j.sbi.2023.102548,Structure-based drug design with geometric deep learning.,"Isert Clemens, Atz Kenneth, Schneider Gisbert",2023,Current opinion in structural biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine learning, has been applied to macromolecular structures. This review provides an overview of the recent applications of geometric deep learning in bioorganic and medicinal chemistry, highlighting its potential for structure-based drug discovery and design. Emphasis is placed on molecular property prediction, ligand binding site and pose prediction, and structure-based de novo molecular design. The current challenges and opportunities are highlighted, and a forecast of the future of geometric deep learning for drug discovery is presented.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:36842415
SPB-0399,10.1111/vru.13144,Intelligent imaging: Applications of machine learning and deep learning in radiology.,"Currie Geoff, Rohren Eric",2022,Veterinary radiology & ultrasound : the official journal of the American College of Veterinary Radiology and the International Veterinary Radiology Association,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence (AI) in radiology is transforming medical image analysis. While applications in triaging for priority reporting and radiomic feature analysis have been widely reported, perhaps the most important applications lie in noise reduction, image optimization following dose reduction strategies, image reconstruction direct from projection data and generation of pseudo-CT for attenuation correction. There are common beneficial applications, and potential risks, between human radiology and veterinary radiology. Artificial intelligence may see recrafting of some responsibilities but offers AI augmentation of human driven systems. The redundancy afforded by human augmentation of AI and AI autonomy are not on the horizon, but rather are already here.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:36514225
SPB-0400,10.1016/j.drudis.2020.03.003,Machine learning models for drug-target interactions: current knowledge and future directions.,"D'Souza Sofia, Prema K V, Balaji Seetharaman",2020,Drug discovery today,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Predicting the binding affinity between compounds and proteins with reasonable accuracy is crucial in drug discovery. Computational prediction of binding affinity between compounds and targets greatly enhances the probability of finding lead compounds by reducing the number of wet-lab experiments. Machine-learning and deep-learning techniques using ligand-based and target-based approaches have been used to predict binding affinities, thereby saving time and cost in drug discovery efforts. In this review, we discuss about machine-learning and deep-learning models used in virtual screening to improve drug-target interaction (DTI) prediction. We also highlight current knowledge and future directions to guide further development in this field.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32171918
SPB-0401,10.1016/j.path.2022.09.014,Applications of Deep Learning in Endocrine Neoplasms.,"Ramesh Siddhi, Dolezal James M, Pearson Alexander T",2023,Surgical pathology clinics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Machine learning methods have been growing in prominence across all areas of medicine. In pathology, recent advances in deep learning (DL) have enabled computational analysis of histological samples, aiding in diagnosis and characterization in multiple disease areas. In cancer, and particularly endocrine cancer, DL approaches have been shown to be useful in tasks ranging from tumor grading to gene expression prediction. This review summarizes the current state of DL research in endocrine cancer histopathology with an emphasis on experimental design, significant findings, and key limitations.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:36739164
SPB-0402,10.2174/0929867327666200907141016,Deep Learning in Drug Target Interaction Prediction: Current and Future Perspectives.,"Abbasi Karim, Razzaghi Parvin, Poso Antti, Ghanbari-Ara Saber, Masoudi-Nejad Ali",2021,Current medicinal chemistry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Drug-target Interactions (DTIs) prediction plays a central role in drug discovery. Computational methods in DTIs prediction have gained more attention because carrying out in vitro and in vivo experiments on a large scale is costly and time-consuming. Machine learning methods, especially deep learning, are widely applied to DTIs prediction. In this study, the main goal is to provide a comprehensive overview of deep learning-based DTIs prediction approaches. Here, we investigate the existing approaches from multiple perspectives. We explore these approaches to find out which deep network architectures are utilized to extract features from drug compound and protein sequences. Also, the advantages and limitations of each architecture are analyzed and compared. Moreover, we explore the process of how to combine descriptors for drug and protein features. Likewise, a list of datasets that are commonly used in DTIs prediction is investigated. Finally, current challenges are discussed and a sh",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:32895036
SPB-0403,10.1007/s00234-021-02813-9,"Radiomics, machine learning, and artificial intelligence-what the neuroradiologist needs to know.","Wagner Matthias W, Namdar Khashayar, Biswas Asthik, Monah Suranna, Khalvati Farzad, et al.",2021,Neuroradiology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Artificial intelligence (AI) is playing an ever-increasing role in Neuroradiology. When designing AI-based research in neuroradiology and appreciating the literature, it is important to understand the fundamental principles of AI. Training, validation, and test datasets must be defined and set apart as priorities. External validation and testing datasets are preferable, when feasible. The specific type of learning process (supervised vs. unsupervised) and the machine learning model also require definition. Deep learning (DL) is an AI-based approach that is modelled on the structure of neurons of the brain; convolutional neural networks (CNN) are a commonly used example in neuroradiology. Radiomics is a frequently used approach in which a multitude of imaging features are extracted from a region of interest and subsequently reduced and selected to convey diagnostic or prognostic information. Deep radiomics uses CNNs to directly extract features and obviate the need for predefined featur",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34537858
SPB-0404,10.1016/j.bpg.2020.101712,Pitfalls in training and validation of deep learning systems.,"Eelbode Tom, Sinonquel Pieter, Maes Frederik, Bisschops Raf",2021,Best practice & research. Clinical gastroenterology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The number of publications in endoscopic journals that present deep learning applications has risen tremendously over the past years. Deep learning has shown great promise for automated detection, diagnosis and quality improvement in endoscopy. However, the interdisciplinary nature of these works has undoubtedly made it more difficult to estimate their value and applicability. In this review, the pitfalls and common misconducts when training and validating deep learning systems are discussed and some practical guidelines are proposed that should be taken into account when acquiring data and handling it to ensure an unbiased system that will generalize for application in routine clinical practice. Finally, some considerations are presented to ensure correct validation and comparison of AI systems.",,computer science,auto_pubmed_clean,scipeerai_collector_v1,pmid:34172245
SPB-0405,10.1016/j.cell.2020.05.039,Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.,"Ji Andrew L, Rubin Adam J, Thrane Kim, Jiang Sizun, Reynolds David L, et al.",2020,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:32579974
SPB-0406,10.1038/nmeth.4177,Pooled CRISPR screening with single-cell transcriptome readout.,"Datlinger Paul, Rendeiro André F, Schmidl Christian, Krausgruber Thomas, Traxler Peter, et al.",2017,Nature methods,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:28099430
SPB-0407,10.1016/j.cell.2022.02.015,Spatial CRISPR genomics identifies regulators of the tumor microenvironment.,"Dhainaut Maxime, Rose Samuel A, Akturk Guray, Wroblewska Aleksandra, Nielsen Sebastian R, et al.",2022,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomi",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:35290801
SPB-0408,10.1016/j.cell.2016.11.048,A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.,"Adamson Britt, Norman Thomas M, Jost Marco, Cho Min Y, Nuñez James K, et al.",2016,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three se",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:27984733
SPB-0409,10.1016/j.jbiotec.2018.06.303,Opportunities in biotechnology.,"Gartland Kevan M A, Gartland Jill S",2018,Journal of biotechnology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Strategies for biotechnology must take account of opportunities for research, innovation and business growth. At a regional level, public-private collaborations provide potential for such growth and the creation of centres of excellence. By considering recent progress in areas such as genomics, healthcare diagnostics, synthetic biology, gene editing and bio-digital technologies, opportunities for smart, strategic and specialised investment are discussed. These opportunities often involve convergent or disruptive technologies, combining for example elements of pharma-science, molecular biology, bioinformatics and novel device development to enhance biotechnology and the life sciences. Analytical applications use novel devices in mobile health, predictive diagnostics and stratified medicine. Synthetic biology provides opportunities for new product development and increased efficiency for existing processes. Successful centres of excellence should promote public-private business partnersh",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29890193
SPB-0410,10.1016/j.cell.2016.11.038,Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.,"Dixit Atray, Parnas Oren, Li Biyu, Chen Jenny, Fulco Charles P, et al.",2016,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dr",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:27984732
SPB-0411,10.1089/crispr.2021.0099,CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control.,"Dominguez Antonia A, Chavez Michael G, Urke Amanda, Gao Yuchen, Wang Lizhong, et al.",2022,The CRISPR journal,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Targeted activation of endogenous genes is an important approach for cell engineering. Here, we report that the nuclease-deactivated dCas9 fused to a transcriptional activator (VPR) and an epigenetic effector (the catalytic domain of histone acetyltransferase p300<sup>core</sup>) simultaneously, sequentially, or as a single quadripartite effector can lead to enhanced activation of target genes. The composite activator, VPRP, behaves more efficiently than individual activators across a set of genes in different cell types. We characterize off-target effects for host chromatin acetylation and transcriptome using the effectors. Our work demonstrates that transcriptional and epigenetic effectors can be used together to enhance gene activation and suggests the need for further optimization of epigenetic effectors to reduce off-targets.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:35271371
SPB-0412,10.1128/JB.00580-17,History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology.,"Ishino Yoshizumi, Krupovic Mart, Forterre Patrick",2018,Journal of bacteriology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparat",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29358495
SPB-0413,10.18632/oncotarget.9646,CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases.,"Khan Faheem Ahmed, Pandupuspitasari Nuruliarizki Shinta, Chun-Jie Huang, Ao Zhou, Jamal Muhammad, et al.",2016,Oncotarget,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cancer is caused by a series of alterations in genome and epigenome mostly resulting in activation of oncogenes or inactivation of cancer suppressor genes. Genetic engineering has become pivotal in the treatment of cancer and other genetic diseases, especially the formerly-niche use of clustered regularly interspaced short palindromic repeats (CRISPR) associated with Cas9. In defining its superior use, we have followed the recent advances that have been made in producing CRISPR/Cas9 as a therapy of choice. We also provide important genetic mutations where CRISPRs can be repurposed to create adaptive immunity to fight carcinomas and edit genetic mutations causing it. Meanwhile, challenges to CRISPR technology are also discussed with emphasis on ability of pathogens to evolve against CRISPRs. We follow the recent developments on the function of CRISPRs with different carriers which can efficiently deliver it to target cells; furthermore, analogous technologies are also discussed along CR",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:27250031
SPB-0414,10.1016/j.cell.2018.11.029,A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.,"Gasperini Molly, Hill Andrew J, McFaline-Figueroa José L, Martin Beth, Kim Seungsoo, et al.",2019,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants and in resolution by linkage disequilibrium. We present a multiplex, expression quantitative trait locus (eQTL)-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA sequencing (RNA-seq). Across two experiments, we used dCas9-KRAB to perturb 5,920 candidate enhancers with no strong a priori hypothesis as to their target gene(s), measuring effects by profiling 254,974 single-cell transcriptomes. We identified 664 (470 high-confidence) cis enhancer-gene pairs, which were enriched for specific transcription factors, non-housekeeping status, and genomic and 3D conformational proximity to their target genes. This framework will facilitate the ",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:30612741
SPB-0415,10.1038/nature16526,High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects.,"Kleinstiver Benjamin P, Pattanayak Vikram, Prew Michelle S, Tsai Shengdar Q, Nguyen Nhu T, et al.",2016,Nature,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR-Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. Existing strategies for reducing genome-wide off-target effects of the widely used Streptococcus pyogenes Cas9 (SpCas9) are imperfect, possessing only partial or unproven efficacies and other limitations that constrain their use. Here we describe SpCas9-HF1, a high-fidelity variant harbouring alterations designed to reduce non-specific DNA contacts. SpCas9-HF1 retains on-target activities comparable to wild-type SpCas9 with >85% of single-guide RNAs (sgRNAs) tested in human cells. Notably, with sgRNAs targeted to standard non-repetitive sequences, SpCas9-HF1 rendered all or nearly all off-target events undetectable by genome-wide break capture and targeted sequencing methods. Even for atypical, repetitive target sites, the vast majority of off-target mutations induced by wild-type SpCas9 were not detected with SpCas9-HF1. With its exceptional precision, SpCas9-HF1 provides an alternat",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26735016
SPB-0416,10.1038/s41592-020-0837-5,Targeted Perturb-seq enables genome-scale genetic screens in single cells.,"Schraivogel Daniel, Gschwind Andreas R, Milbank Jennifer H, Leonce Daniel R, Jakob Petra, et al.",2020,Nature methods,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allo",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:32483332
SPB-0417,10.1016/j.cell.2018.11.022,Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.,"Rubin Adam J, Parker Kevin R, Satpathy Ansuman T, Qi Yanyan, Wu Beijing, et al.",2019,Cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genom",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:30580963
SPB-0418,10.1126/sciadv.add5907,Application of combined CRISPR screening for genetic and chemical-genetic interaction profiling in <i>Mycobacterium tuberculosis</i>.,"Yan Mei-Yi, Zheng Dandan, Li Si-Shang, Ding Xin-Yuan, Wang Chun-Liang, et al.",2022,Science advances,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR screening, including CRISPR interference (CRISPRi) and CRISPR-knockout (CRISPR-KO) screening, has become a powerful technology in the genetic screening of eukaryotes. In contrast with eukaryotes, CRISPR-KO screening has not yet been applied to functional genomics studies in bacteria. Here, we constructed genome-scale CRISPR-KO and also CRISPRi libraries in Mycobacterium tuberculosis (Mtb). We first examined these libraries to identify genes essential for Mtb viability. Subsequent screening identified dozens of genes associated with resistance/susceptibility to the antitubercular drug bedaquiline (BDQ). Genetic and chemical validation of the screening results suggested that it provided a valuable resource to investigate mechanisms of action underlying the effects of BDQ and to identify chemical-genetic synergies that can be used to optimize tuberculosis therapy. In summary, our results demonstrate the potential for efficient genome-wide CRISPR-KO screening in bacteria and establi",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:36417506
SPB-0419,10.1056/NEJMoa1502214,FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.,"Claussnitzer Melina, Dankel Simon N, Kim Kyoung-Han, Quon Gerald, Meuleman Wouter, et al.",2015,The New England journal of medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Genomewide association studies can be used to identify disease-relevant genomic regions, but interpretation of the data is challenging. The FTO region harbors the strongest genetic association with obesity, yet the mechanistic basis of this association remains elusive. We examined epigenomic data, allelic activity, motif conservation, regulator expression, and gene coexpression patterns, with the aim of dissecting the regulatory circuitry and mechanistic basis of the association between the FTO region and obesity. We validated our predictions with the use of directed perturbations in samples from patients and from mice and with endogenous CRISPR-Cas9 genome editing in samples from patients. Our data indicate that the FTO allele associated with obesity represses mitochondrial thermogenesis in adipocyte precursor cells in a tissue-autonomous manner. The rs1421085 T-to-C single-nucleotide variant disrupts a conserved motif for the ARID5B repressor, which leads to derepression of a potent ",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26287746
SPB-0420,10.1161/CIRCRESAHA.118.310998,Epigenomics: Technologies and Applications.,"Wang Kevin C, Chang Howard Y",2018,Circulation research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The advent of high-throughput epigenome mapping technologies has ushered in a new era of multiomics where powerful tools can now delineate and record different layers of genomic output. Integrating various components of the epigenome from these multiomics measurements allows the interrogation of cellular heterogeneity in addition to the discovery of molecular connectivity maps between the genome and its functional output. Mapping of chromatin accessibility dynamics and higher-order chromatin structure has enabled new levels of understanding of cell fate decisions, identity, and function in normal development, physiology, and disease. We provide a perspective on the progress of the epigenomics field and applications and anticipate an even greater revolution in our understanding of the human epigenome for years to come.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29700067
SPB-0421,10.1002/yea.3098,New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae.,"Laughery Marian F, Hunter Tierra, Brown Alexander, Hoopes James, Ostbye Travis, et al.",2015,"Yeast (Chichester, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is an important tool for genome editing because the Cas9 endonuclease can induce targeted DNA double-strand breaks. Targeting of the DNA break is typically controlled by a single-guide RNA (sgRNA), a chimeric RNA containing a structural segment important for Cas9 binding and a 20mer guide sequence that hybridizes to the genomic DNA target. Previous studies have demonstrated that CRISPR-Cas9 technology can be used for efficient, marker-free genome editing in Saccharomyces cerevisiae. However, introducing the 20mer guide sequence into yeast sgRNA expression vectors often requires cloning procedures that are complex, time-consuming and/or expensive. To simplify this process, we have developed a new sgRNA expression cassette with internal restriction enzyme sites that permit rapid, directional cloning of 20mer guide sequences. Here we describe a flexible set of vectors based on this design for cloning and ex",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26305040
SPB-0422,10.1016/j.jmb.2018.06.034,Functional Genomics via CRISPR-Cas.,"Ford Kyle, McDonald Daniella, Mali Prashant",2019,Journal of molecular biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas proteins have recently emerged as versatile tools to investigate and engineer the genome. The programmability of CRISPR-Cas has proven especially useful for probing genomic function in high-throughput. Facile single-guide RNA library synthesis allows CRISPR-Cas screening to rapidly investigate the functional consequences of genomic, transcriptomic, and epigenomic perturbations. Furthermore, by combining CRISPR-Cas perturbations with downstream single-cell analyses (flow cytometry, expression profiling, etc.), forward screens can generate robust data sets linking genotypes to complex cellular phenotypes. In the following review, we highlight recent advances in CRISPR-Cas genomic screening while outlining protocols and pitfalls associated with screen implementation. Finally, we describe current challenges limiting the utility of CRISPR-Cas screening as well as future research needed to resolve the",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29959923
SPB-0423,10.1038/nmeth.4604,On the design of CRISPR-based single-cell molecular screens.,"Hill Andrew J, McFaline-Figueroa José L, Starita Lea M, Gasperini Molly J, Matreyek Kenneth A, et al.",2018,Nature methods,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29457792
SPB-0424,,Systematic mapping of functional enhancer-promoter connections with CRISPR interference.,"Fulco Charles P, Munschauer Mathias, Anyoha Rockwell, Munson Glen, Grossman Sharon R, et al.",2016,"Science (New York, N.Y.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:27708057
SPB-0425,10.3389/fimmu.2022.1041451,High-content CRISPR screening in tumor immunology.,"Holcomb Erin A, Pearson Ashley N, Jungles Kassidy M, Tate Akshay, James Jadyn, et al.",2022,Frontiers in immunology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR screening is a powerful tool that links specific genetic alterations to corresponding phenotypes, thus allowing for high-throughput identification of novel gene functions. Pooled CRISPR screens have enabled discovery of innate and adaptive immune response regulators in the setting of viral infection and cancer. Emerging methods couple pooled CRISPR screens with parallel high-content readouts at the transcriptomic, epigenetic, proteomic, and optical levels. These approaches are illuminating cancer immune evasion mechanisms as well as nominating novel targets that augment T cell activation, increase T cell infiltration into tumors, and promote enhanced T cell cytotoxicity. This review details recent methodological advances in high-content CRISPR screens and highlights the impact this technology is having on tumor immunology.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:36479127
SPB-0426,10.1016/j.biotechadv.2020.107672,CRISPR-based enrichment strategies for targeted sequencing.,"Schultzhaus Zachary, Wang Zheng, Stenger David",2021,Biotechnology advances,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The ability to easily produce or procure sequencing data has expanded to be within the reach of most clinics and research laboratories, but the complexity of sequence analysis remains a hurdle for many scientists, and a decline in sequencing cost means that the generation of gratuitous information in a given experiment is a challenge that is more and more often being encountered. To address this issue, methods have been present, some dating to the advent of nucleic acid sequencing, for capturing, targeting, or otherwise enriching specific nucleic acids in order to obtain greater depth of reads from a small portion of sequences within a complex sample. However, many of these methods have been complicated and laborious, relying on the design of hundreds to thousands of oligonucleotide probes, fabrication of microarray chips, and long hybridization times. Here, we review these methods, their benefits and uses, and catalog and discuss the implications of a recent development that has enabl",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:33253795
SPB-0427,10.1097/MOP.0000000000000283,Mutations in the noncoding genome.,"Scacheri Cheryl A, Scacheri Peter C",2015,Current opinion in pediatrics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Clinical diagnostic sequencing currently focuses on identifying causal mutations in the exome, wherein most disease-causing mutations are known to occur. The rest of the genome is mostly comprised of regulatory elements that control gene expression, but these have remained largely unexplored in clinical diagnostics due to the high cost of whole genome sequencing and interpretive challenges. The purpose of this review is to illustrate examples of diseases caused by mutations in regulatory elements and introduce the diagnostic potential for whole genome sequencing. Different classes of functional elements and chromatin structure are described to provide the clinician with a foundation for understanding the basis of these mutations. The utilization of whole-genome sequence data, epigenomic maps and induced pluripotent stem (IPS) cell technologies facilitated the discovery that mutations in the pancreas-specific transcription factor 1a enhancer can cause isolated pancreatic agenesis. High ",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26382709
SPB-0428,10.1016/j.cbpa.2015.10.001,How specific is CRISPR/Cas9 really?,"O'Geen Henriette, Yu Abigail S, Segal David J",2015,Current opinion in chemical biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The specificity of RNA-guided nucleases has gathered considerable interest as they become broadly applied to basic research and therapeutic development. Reports of the simple generation of animal models and genome engineering of cells raised questions about targeting precision. Conflicting early reports led the field to believe that CRISPR/Cas9 system was promiscuous, leading to a variety of strategies for improving specificity and increasingly sensitive methods to detect off-target events. However, other studies have suggested that CRISPR/Cas9 is a highly specific genome-editing tool. This review will focus on deciphering and interpreting these seemingly opposing claims.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26517564
SPB-0429,10.1073/pnas.2112279118,Metagenomic discovery of CRISPR-associated transposons.,"Rybarski James R, Hu Kuang, Hill Alexis M, Wilke Claus O, Finkelstein Ilya J",2021,Proceedings of the National Academy of Sciences of the United States of America,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR-associated Tn7 transposons (CASTs) co-opt cas genes for RNA-guided transposition. CASTs are exceedingly rare in genomic databases; recent surveys have reported Tn7-like transposons that co-opt Type I-F, I-B, and V-K CRISPR effectors. Here, we expand the diversity of reported CAST systems via a bioinformatic search of metagenomic databases. We discover architectures for all known CASTs, including arrangements of the Cascade effectors, target homing modalities, and minimal V-K systems. We also describe families of CASTs that have co-opted the Type I-C and Type IV CRISPR-Cas systems. Our search for non-Tn7 CASTs identifies putative candidates that include a nuclease dead Cas12. These systems shed light on how CRISPR systems have coevolved with transposases and expand the programmable gene-editing toolkit.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:34845024
SPB-0430,10.1038/ncomms14406,CRISPR/Cpf1-mediated DNA-free plant genome editing.,"Kim Hyeran, Kim Sang-Tae, Ryu Jahee, Kang Beum-Chang, Kim Jin-Soo, et al.",2017,Nature communications,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cpf1, a type V CRISPR effector, recognizes a thymidine-rich protospacer-adjacent motif and induces cohesive double-stranded breaks at the target site guided by a single CRISPR RNA (crRNA). Here we show that Cpf1 can be used as a tool for DNA-free editing of plant genomes. We describe the delivery of recombinant Cpf1 proteins with in vitro transcribed or chemically synthesized target-specific crRNAs into protoplasts isolated from soybean and wild tobacco. Designed crRNAs are unique and do not have similar sequences (≤3 mismatches) in the entire soybean reference genome. Targeted deep sequencing analyses show that mutations are successfully induced in FAD2 paralogues in soybean and AOC in wild tobacco. Unlike SpCas9, Cpf1 mainly induces various nucleotide deletions at target sites. No significant mutations are detected at potential off-target sites in the soybean genome. These results demonstrate that Cpf1-crRNA complex is an effective DNA-free genome-editing tool for plant genome editin",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:28205546
SPB-0431,10.1126/science.adh7699,Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.,"Morris John A, Caragine Christina, Daniloski Zharko, Domingo Júlia, Barry Timothy, et al.",2023,"Science (New York, N.Y.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:37141313
SPB-0432,10.1093/hmg/ddy120,Development and application of CRISPR/Cas9 technologies in genomic editing.,"Zhang Cui, Quan Renfu, Wang Jinfu",2018,Human molecular genetics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Genomic editing to correct disease-causing mutations is a promising approach for the treatment of human diseases. As a simple and programmable nuclease-based genomic editing tool, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has substantially improved the ability to make precise changes in the human genome. Rapid development of CRISPR-based technologies in recent years has expanded its application scope and promoted CRISPR-based therapies in preclinical trails. Here, we review the application of the CRISPR system over the last 2 years; including its development and application in base editing, transcription modulation and epigenetic editing, genomic-scale screening, and cell and embryo therapy. Finally, the prospects and challenges related to application of CRISPR/Cas9 technologies are discussed.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:29659822
SPB-0433,10.1038/nmeth.3630,Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.,"Thakore Pratiksha I, D'Ippolito Anthony M, Song Lingyun, Safi Alexias, Shivakumar Nishkala K, et al.",2015,Nature methods,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Epigenome editing with the CRISPR (clustered, regularly interspaced, short palindromic repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms of gene regulation. Fusions of nuclease-inactive dCas9 to the Krüppel-associated box (KRAB) repressor (dCas9-KRAB) can silence target gene expression, but the genome-wide specificity and the extent of heterochromatin formation catalyzed by dCas9-KRAB are not known. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes, and observed highly specific induction of H3K9 trimethylation (H3K9me3) at the enhancer and decreased chromatin accessibility of both the enhancer and its promoter targets. Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in global gene expression. These results demonstrate that repression",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26501517
SPB-0434,10.2174/1871520619666191014103711,CRISPR/Cas9 System and its Research Progress in Gene Therapy.,"Liu Wenlou, Yang Chunsheng, Liu Yanqun, Jiang Guan",2019,Anti-cancer agents in medicinal chemistry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Genome editing refers to changing the genome sequence of an organism by knockout, insertion, and site mutation, resulting in changes in the genetic information of the organism. The clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein-9 nuclease (Cas9) system is a genome editing technique developed by the acquired immune system in the microbes, such as bacteria and archaebacteria, which targets and edits genome sequences according to the principle of complementary base pairing. This technique can be used to edit endogenous genomic DNA sequences in organisms accurately and has been widely used in fields, such as biotechnology, cancer gene therapy, and dermatology. In this review, we summarize the history, structure, mechanism, and application of CRISPR/Cas9 in gene therapy and dermatological diseases.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:31633477
SPB-0435,10.1016/j.molcel.2018.11.031,Target-Specific Precision of CRISPR-Mediated Genome Editing.,"Chakrabarti Anob M, Henser-Brownhill Tristan, Monserrat Josep, Poetsch Anna R, Luscombe Nicholas M, et al.",2019,Molecular cell,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict the editing outcome at specific sites is limited. Here, we examined indel profiles at over 1,000 genomic sites in human cells and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing (i.e., recurrence of a specific indel) varies considerably among sites, with some targets showing one highly preferred indel and others displaying numerous infrequent indels. Editing precision correlates with editing efficiency and a preference for single-nucleotide homologous insertions. Precise targets and editing outcome can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the protospacer adjacent motif (PAM). Indel profiles are robust, but they can be influenced by chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal gener",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:30554945
SPB-0436,10.1016/j.copbio.2014.11.007,Editing plant genomes with CRISPR/Cas9.,"Belhaj Khaoula, Chaparro-Garcia Angela, Kamoun Sophien, Patron Nicola J, Nekrasov Vladimir",2015,Current opinion in biotechnology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR/Cas9 is a rapidly developing genome editing technology that has been successfully applied in many organisms, including model and crop plants. Cas9, an RNA-guided DNA endonuclease, can be targeted to specific genomic sequences by engineering a separately encoded guide RNA with which it forms a complex. As only a short RNA sequence must be synthesized to confer recognition of a new target, CRISPR/Cas9 is a relatively cheap and easy to implement technology that has proven to be extremely versatile. Remarkably, in some plant species, homozygous knockout mutants can be produced in a single generation. Together with other sequence-specific nucleases, CRISPR/Cas9 is a game-changing technology that is poised to revolutionise basic research and plant breeding.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:25437637
SPB-0437,10.1007/978-1-4939-2687-9_4,Annotation and Classification of CRISPR-Cas Systems.,"Makarova Kira S, Koonin Eugene V",2015,"Methods in molecular biology (Clifton, N.J.)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:25981466
SPB-0438,10.1007/s00059-017-4592-z,Precision medicine approach to genetic cardiomyopathy.,"Filonenko K, Katus H A, Meder B",2017,Herz,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,Precision medicine aims to achieve improved survival by strategies that recognize the genetic and phenotypic individuality of patients and stratify treatment accordingly. Genetic cardiomyopathies represent an ideal disease group to fully embark on this concept: they are in total frequent diseases with a marked morbidity and mortality and there is ample knowledge about their predisposing genetic factors and associated functional mechanisms. The current review highlights the genetic etiology and gives examples of the diverse treatment strategies that are envisaged in the future.,,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:28653114
SPB-0439,10.1089/crispr.2021.0021,CRISPRclassify: Repeat-Based Classification of CRISPR Loci.,"Nethery Matthew A, Korvink Michael, Makarova Kira S, Wolf Yuri I, Koonin Eugene V, et al.",2021,The CRISPR journal,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Detection and classification of CRISPR-Cas systems in metagenomic data have become increasingly prevalent in recent years due to their potential for diverse applications in genome editing. Traditionally, CRISPR-Cas systems are classified through reference-based identification of proximate cas genes. Here, we present a machine learning approach for the detection and classification of CRISPR loci using repeat sequences in a cas-independent context, enabling identification of unclassified loci missed by traditional cas-based approaches. Using biological attributes of the CRISPR repeat, the core element in CRISPR arrays, and leveraging methods from natural language processing, we developed a machine learning model capable of accurate classification of CRISPR loci in an extensive set of metagenomes, resulting in an F1 measure of 0.82 across all predictions and an F1 measure of 0.97 when limiting to classifications with probabilities >0.85. Furthermore, assessing performance on novel repeats",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:34406047
SPB-0440,10.1242/dev.182667,Using CRISPR to understand and manipulate gene regulation.,"Akinci Ersin, Hamilton Marisa C, Khowpinitchai Benyapa, Sherwood Richard I",2021,"Development (Cambridge, England)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding how genes are expressed in the correct cell types and at the correct level is a key goal of developmental biology research. Gene regulation has traditionally been approached largely through observational methods, whereas perturbational approaches have lacked precision. CRISPR-Cas9 has begun to transform the study of gene regulation, allowing for precise manipulation of genomic sequences, epigenetic functionalization and gene expression. CRISPR-Cas9 technology has already led to the discovery of new paradigms in gene regulation and, as new CRISPR-based tools and methods continue to be developed, promises to transform our knowledge of the gene regulatory code and our ability to manipulate cell fate. Here, we discuss the current and future application of the emerging CRISPR toolbox toward predicting gene regulatory network behavior, improving stem cell disease modeling, dissecting the epigenetic code, reprogramming cell fate and treating diseases of gene dysregulation.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:33913466
SPB-0441,10.1016/j.jgg.2019.11.002,Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing.,"Li Jinjing, Hong Shunyan, Chen Wanjin, Zuo Erwei, Yang Hui",2019,Journal of genetics and genomics = Yi chuan xue bao,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:31911131
SPB-0442,10.1101/gr.190124.115,Enabling functional genomics with genome engineering.,"Hilton Isaac B, Gersbach Charles A",2015,Genome research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26430154
SPB-0443,10.1136/jmedgenet-2015-103409,CRISPR-Cas9 for medical genetic screens: applications and future perspectives.,"Xue Hui-Ying, Ji Li-Juan, Gao Ai-Mei, Liu Ping, He Jing-Dong, et al.",2016,Journal of medical genetics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) systems have emerged as versatile and convenient (epi)genome editing tools and have become an important player in medical genetic research. CRISPR-Cas9 and its variants such as catalytically inactivated Cas9 (dead Cas9, dCas9) and scaffold-incorporating single guide sgRNA (scRNA) have been applied in various genomic screen studies. CRISPR screens enable high-throughput interrogation of gene functions in health and diseases. Compared with conventional RNAi screens, CRISPR screens incur less off-target effects and are more versatile in that they can be used in multiple formats such as knockout, knockdown and activation screens, and can target coding and non-coding regions throughout the genome. This powerful screen platform holds the potential of revolutionising functional genomic studies in the near future. Herein, we introduce the mechanisms of (epi)genome editing mediated by CRISPR-Cas",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:26673779
SPB-0444,10.1038/s41467-019-12339-7,Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways.,"Taghbalout Aziz, Du Menghan, Jillette Nathaniel, Rosikiewicz Wojciech, Rath Abhijit, et al.",2019,Nature communications,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Here we develop a methylation editing toolbox, Casilio-ME, that enables not only RNA-guided methylcytosine editing by targeting TET1 to genomic sites, but also by co-delivering TET1 and protein factors that couple methylcytosine oxidation to DNA repair activities, and/or promote TET1 to achieve enhanced activation of methylation-silenced genes. Delivery of TET1 activity by Casilio-ME1 robustly alters the CpG methylation landscape of promoter regions and activates methylation-silenced genes. We augment Casilio-ME1 to simultaneously deliver the TET1-catalytic domain and GADD45A (Casilio-ME2) or NEIL2 (Casilio-ME3) to streamline removal of oxidized cytosine intermediates to enhance activation of targeted genes. Using two-in-one effectors or modular effectors, Casilio-ME2 and Casilio-ME3 remarkably boost gene activation and methylcytosine demethylation of targeted loci. We expand the toolbox to enable a stable and expression-inducible system for broader application of the Casilio-ME platfo",,biology,auto_pubmed_clean,scipeerai_collector_v1,pmid:31541098
SPB-0445,10.1016/j.jviscsurg.2023.10.005,"Surgery, innovation, research and sustainable development.","Slim Karem, Martin Frédéric",2024,Journal of visceral surgery,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In the healthcare sector, surgery (especially in the operating theatre) is responsible for emission of greenhouse gases, which is a source of global warming. The goal of this largely quantitative assessment is to address three questions on carbon footprint associated with surgery, the role of primary and secondary prevention prior to surgical procedures, and incorporation of the carbon footprint into judgment criteria in research and surgical innovations. It appears that while the impact of surgery on global warming is undeniable, its extent depends on means of treatment and geographical location. Before and after an operation, primary, secondary and tertiary prevention accompanied by surgical sobriety (avoiding unnecessary or unjustified actions) can be virtuous in terms of sustainable development. However, the sanitary benefits of these actions are often opposed to environmental benefit, which has yet to be satisfactorily assessed. Lastly, the carbon footprint has yet to be incorpora",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:38071141
SPB-0446,10.1021/acs.est.2c04388,Methane Emissions from Municipal Wastewater Collection and Treatment Systems.,"Song Cuihong, Zhu Jun-Jie, Willis John L, Moore Daniel P, Zondlo Mark A, et al.",2023,Environmental science & technology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Municipal wastewater collection and treatment systems are critical infrastructures, and they are also identified as major sources of anthropogenic CH<sub>4</sub> emissions that contribute to climate change. The actual CH<sub>4</sub> emissions at the plant- or regional level vary greatly due to site-specific conditions as well as high seasonal and diurnal variations. Here, we conducted the first quantitative analysis of CH<sub>4</sub> emissions from different types of sewers and water resource recovery facilities (WRRFs). We examined variations in CH<sub>4</sub> emissions associated with methods applied in different monitoring campaigns, and identified main CH<sub>4</sub> sources and sinks to facilitate carbon emission reduction efforts in the wastewater sector. We found plant-wide CH<sub>4</sub> emissions vary by orders of magnitude, from 0.01 to 110 g CH<sub>4</sub>/m<sup>3</sup> with high emissions associated with plants equipped with anaerobic digestion or stabilization ponds. Risin",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36735881
SPB-0447,10.3390/ijerph20031706,Research Progress and Hotspot Analysis of Residential Carbon Emissions Based on CiteSpace Software.,"Chen Yi, Chen Yinrong, Chen Kun, Liu Min",2023,International journal of environmental research and public health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Residential carbon emissions are one of the critical causes of climate problems such as global warming. It is significant to explore the development and evolution trend of residential carbon emissions research for mitigating global climate change. However, there have been no studies that comprehensively review this research field. Based on the research papers on residential carbon emissions included in the Web of Science core database and China National Knowledge Infrastructure database, the CiteSpace bibliometric analysis software was used in this paper to draw the visual knowledge map of residential carbon emissions research and reveal its research status, research hotspots, and development trend. We found that residential carbon emissions research has gone through the stage of ""emergence-initiation-rapid development"", and the research in the United States and the United Kingdom has played a fundamental role in developing this research field. Research hotspots mainly focus on analyzi",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36767072
SPB-0448,10.1016/j.marpolbul.2023.115451,Estimation methods and reduction strategies of port carbon emissions - what literatures say?,"Wang Liang, Li Yining",2023,Marine pollution bulletin,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Carbon emissions from port operational activities significantly contribute to climate change and have gained attention from researchers. However, there is a notable deficiency in systematically analyzing port carbon emissions' estimation methods and reduction strategies. This study reviewed 49 academic literatures to examine the port's carbon emissions estimation methodologies, quantitative research outcomes, and reduction techniques. The analysis results revealed: (1) Estimates of port carbon emissions frequently tend to underestimate actual emissions due to the omission of specific sources. (2) Inherent variances across ports present challenges in establishing a universally applicable estimation methodology. (3) Port carbon emissions reduction strategies involve operational optimization, dispatching, equipment transformation, and energy management. Future research directions were proposed, including comprehensive emissions source estimation, harmonization of estimation methodologies,",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37659387
SPB-0449,10.3390/ijerph20032420,Achieving Carbon Neutrality through Urban Planning and Design.,"Wu Zhiqiang, Zhao Zichen, Gan Wei, Zhou Shiqi, Dong Wen, et al.",2023,International journal of environmental research and public health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Much of the research on climate change has focused on carbon reduction in cities or countries. However, more attention needs to be paid to how to achieve carbon neutrality in the urban design and planning stage, and the lack of quantitative analysis of carbon related to urban space makes it difficult to locate urban space and provide direct guidance for urban planning and design. This study proposed three optimization paths to achieve carbon neutrality in multi-scale urban building clusters. Firstly, we reconstructed the quantitative calculation system of urban building communities with the goal of carbon neutrality; secondly, we screened the carbon source reduction and carbon sink interventions that are suitable for multi-scale urban building communities; finally, we constructed a carbon emission and carbon sink calculation system of planning and design schemes based on the layout of relevant elements of planning and design schemes with a grid cell of 100 × 100 m. In practice, there w",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36767786
SPB-0450,10.1016/j.jenvman.2022.116087,"From low carbon to carbon neutrality: A bibliometric analysis of the status, evolution and development trend.","Zhang Zheng, Hu Guangwen, Mu Xianzhong, Kong Li",2022,Journal of environmental management,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"With global climate change becoming increasingly serious, carbon neutrality, a key strategy to mitigate climate change, has attracted widespread attention. However, due to the multidisciplinary and complexity of carbon neutrality studies, as well as the diversification of research content, a comprehensive review and systematic synthesis of which is quite limited. In this paper, a bibliometric analysis on the topic of carbon neutrality is conducted to reveal the research progress from a quantitative and visual perspective and describe the evolution of research hotspots. The results show that carbon neutrality research is abundant at both the macro and micro levels. Low carbon development is the premise of carbon neutrality, and emission reduction and carbon sinks are the basis of carbon neutrality. The degree of research varies significantly in different countries, with China dominating in the number of publications, followed by the USA and the UK. The realization of carbon neutrality c",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36041302
SPB-0451,10.1111/cobi.14040,Retaining natural vegetation to safeguard biodiversity and humanity.,"Simmonds Jeremy S, Suarez-Castro Andres Felipe, Reside April E, Watson James E M, Allan James R, et al.",2023,Conservation biology : the journal of the Society for Conservation Biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Global efforts to deliver internationally agreed goals to reduce carbon emissions, halt biodiversity loss, and retain essential ecosystem services have been poorly integrated. These goals rely in part on preserving natural (e.g., native, largely unmodified) and seminatural (e.g., low intensity or sustainable human use) forests, woodlands, and grasslands. To show how to unify these goals, we empirically derived spatially explicit, quantitative, area-based targets for the retention of natural and seminatural (e.g., native) terrestrial vegetation worldwide. We used a 250-m-resolution map of natural and seminatural vegetation cover and, from this, selected areas identified under different international agreements as being important for achieving global biodiversity, carbon, soil, and water targets. At least 67 million km<sup>2</sup> of Earth's terrestrial vegetation (∼79% of the area of vegetation remaining) required retention to contribute to biodiversity, climate, soil, and freshwater co",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36424859
SPB-0452,,Valuing Health Impacts In Climate Policy: Ethical Issues And Economic Challenges.,"Scovronick Noah, Ferranna Maddalena, Dennig Francis, Budolfson Mark",2020,Health affairs (Project Hope),pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Deciding which climate policies to enact, and where and when to enact them, requires weighing their costs against the expected benefits. A key challenge in climate policy is how to value health impacts, which are likely to be large and varied, considering that they will accrue over long time horizons (centuries), will occur throughout the world, and will be distributed unevenly within countries depending in part on socioeconomic status. These features raise a number of important economic and ethical issues including how to value human life in different countries at different levels of development, how to value future people, and how much priority to give the poor and disadvantaged. In this article we review each of these issues, describe different approaches for addressing them in quantitative climate policy analysis, and show how their treatment can dramatically change what should be done about climate change. Finally, we use the social cost of carbon, which reflects the cost of addin",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:33284691
SPB-0453,10.1016/j.jenvman.2023.118329,Heterogeneous effects of China's low-carbon city pilots policy.,"Lyu Jing, Liu Tianle, Cai Bofeng, Qi Ye, Zhang Xiaoling",2023,Journal of environmental management,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Global south countries, including China, have faced a challenging dilemma of reducing carbon emissions while maintaining rapid economic growth. The low-carbon city pilots (LCCPs) policy in China is a demonstration of how state power intervenes and commands national low-carbon development through voluntary policy tools. Our study, based on panel data of 331 cities from 2005 to 2019, evaluates the policy effect of all three batches of LCCPs and presents an analysis of time-varying effects through batch decomposition and synthetic difference-in-difference models. The study found that implementing low-carbon policies can significantly reduce total carbon emissions and carbon emissions per capita. However, the reduction in carbon emissions per unit of GDP is insignificant, and the policy effect varies according to the batches and their characteristics. The reduction effects in the first and second batches, as well as the insignificance or even increasing effects of the third batch, may be d",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37379627
SPB-0454,10.1016/j.jes.2022.07.038,Systematical analysis of sludge treatment and disposal technologies for carbon footprint reduction.,"Zhao Yingxin, Yang Zhifan, Niu Jiaojiao, Du Zihan, Federica Conti, et al.",2023,Journal of environmental sciences (China),pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"This study aims to comprehensively analyze the Greenhouse Gases (GHGs) emissions from current sewage sludge treatment and disposal technologies (building material, landfill, land spreading, anaerobic digestion, and thermochemical processes) based on the database of Science Citation Index (SCI) and Social Science Citation Index (SSCI) from 1998 to 2020. The general patterns, spatial distribution, and hotspots were provided by bibliometric analysis. A comparative quantitative analysis based on life cycle assessment (LCA) put forward the current emission situation and the key influencing factors of different technologies. The effective GHG emissions reduction methods were proposed to mitigate climate change. Results showed that incineration or building materials manufacturing of highly dewatered sludge, and land spreading after anaerobic digestion have the best GHG emissions reduction benefits. Biological treatment technologies and thermochemical processes have great potential for reducin",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36801037
SPB-0455,10.1038/s41586-023-06723-z,Integrated global assessment of the natural forest carbon potential.,"Mo Lidong, Zohner Constantin M, Reich Peter B, Liang Jingjing, de Miguel Sergio, et al.",2023,Nature,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system<sup>1</sup>. Remote-sensing estimates to quantify carbon losses from global forests<sup>2-5</sup> are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced<sup>6</sup> and satellite-derived approaches<sup>2,7,8</sup> to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151-363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with exist",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37957399
SPB-0456,10.1038/s41477-023-01543-5,The global biogeography of tree leaf form and habit.,"Ma Haozhi, Crowther Thomas W, Mo Lidong, Maynard Daniel S, Renner Susanne S, et al.",2023,Nature plants,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground bio",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37872262
SPB-0457,10.1007/s11356-021-18030-z,Computable general equilibrium models for sustainable development: past and future.,"Fabregat-Aibar Laura, Niñerola Angels, Pié Laia",2022,Environmental science and pollution research international,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Computable general equilibrium models (CGE) are used to estimate the ex-ante quantitative impact of a change in economic policy. There is a bulk of research in the field of sustainable development applying it for testing implementation of carbon taxation, analyzing reductions of greenhouse gas (GHG), or addressing agricultural issues to work the land efficiently. The main objective of this review is to provide an exhaustive analysis of the literature about these models and their evolution over the last 50 years. The search was conducted in the main academic databases (Scopus and Web of Science), where 1353 articles were found from 1966 to 2019 related to the topic. The results of the descriptives, relational, and content analyses carried out show the current state of the-art, trends, subfields of research, and future gaps to fulfill. This article contributes to the literature that uses CGE models providing an overview of its different applications in the field of sustainability. It giv",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:35303228
SPB-0458,10.3390/ijerph192013507,Simulation of Vegetation Carbon Sink of Arbor Forest and Carbon Mitigation of Forestry Bioenergy in China.,"Ma Xiaozhe, Wu Leying, Zhu Yongbin, Wu Jing, Qin Yaochen",2022,International journal of environmental research and public health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Mitigating carbon emissions through forest carbon sinks is one of the nature-based solutions to global warming. Forest ecosystems play a role as a carbon sink and an important source of bioenergy. China's forest ecosystems have significantly contributed to mitigating carbon emissions. However, there are relatively limited quantitative studies on the carbon mitigation effects of forestry bioenergy in China, so this paper simulated the carbon sequestration of Chinese arbor forest vegetation from 2018 to 2060 based on the CO2FIX model and accounted for the carbon emission reduction brought about by substituting forestry bioenergy for fossil energy, which is important for the formulation of policies to tackle climate change in the Chinese forestry sector. The simulation results showed that the carbon storage of all arbor forest vegetation in China increased year by year from 2018 to 2060, and, overall, it behaved as a carbon sink, with the annual carbon sink fluctuating in the region of 25",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36294087
SPB-0459,10.1016/j.envres.2023.115842,Comparing the variations and influencing factors of CH<sub>4</sub> emissions from paddies and wetlands under CO<sub>2</sub> enrichment: A data synthesis in the last three decades.,"Yu Haiyang, Zhang Xuechen, Meng Xiangtian, Luo Dan, Yue Zhengfu, et al.",2023,Environmental research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding and quantifying the impact of elevated tropospheric carbon dioxide concentration (e [CO<sub>2</sub>]) on methane (CH<sub>4</sub>) globally is important for effectively assessing and mitigating climate warming. Paddies and wetlands are the two important sources of CH<sub>4</sub> emissions. Yet, a quantitative synthetic investigation of the effects of e [CO<sub>2</sub>] on CH<sub>4</sub> emissions from paddies and wetlands on a global scale has not been conducted. Here, we conducted a meta-analysis of 488 observation cases from 40 studies to assess the long-term effects of e [CO<sub>2</sub>] (ambient [CO<sub>2</sub>]+ 53-400 μmol mol<sup>-1</sup>) on CH<sub>4</sub> emissions and to identify the relevant key drivers. On aggregate, e [CO<sub>2</sub>] increased CH<sub>4</sub> emissions by 25.7% (p < 0.05) from paddies but did not affect CH<sub>4</sub> emissions from wetlands (-3.29%; p > 0.05). The e [CO<sub>2</sub>] effects on paddy CH<sub>4</sub> emissions were positively re",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37024028
SPB-0460,10.3390/ijerph20010145,Driving Effect of Decoupling Provincial Industrial Economic Growth and Industrial Carbon Emissions in China.,"Hua Jingfen, Gao Junli, Chen Ke, Li Jiaqi",2022,International journal of environmental research and public health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"China is facing the dual challenges of fostering economic growth and mounting an effective response to climate change, so it is vital to continue promoting industrial carbon emission reduction. This paper uses panel data from 1998 to 2019 to measure the industrial carbon emissions of 30 provinces in China. The Tapio decoupling and IPAT (Impact = Population × Affluence × Technology)-based decoupling models are used to analyze each province's velocity and quantity decoupling index for industrial carbon emissions. The fixed effect model analyzes the influencing factors for carbon decoupling. The results show that the industrial carbon emissions of various provinces in China are increasing yearly, but there are significant differences among provinces. The carbon decoupling of the industrial economy in most provinces is weak, and the quantitative decoupling index is better than the velocity decoupling index. The cleanliness of energy, balance, and labor productivity significantly affect the",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36612465
SPB-0461,10.1111/gcb.15342,Can N<sub>2</sub> O emissions offset the benefits from soil organic carbon storage?,"Guenet Bertrand, Gabrielle Benoit, Chenu Claire, Arrouays Dominique, Balesdent Jérôme, et al.",2021,Global change biology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To respect the Paris agreement targeting a limitation of global warming below 2°C by 2100, and possibly below 1.5°C, drastic reductions of greenhouse gas emissions are mandatory but not sufficient. Large-scale deployment of other climate mitigation strategies is also necessary. Among these, increasing soil organic carbon (SOC) stocks is an important lever because carbon in soils can be stored for long periods and land management options to achieve this already exist and have been widely tested. However, agricultural soils are also an important source of nitrous oxide (N<sub>2</sub> O), a powerful greenhouse gas, and increasing SOC may influence N<sub>2</sub> O emissions, likely causing an increase in many cases, thus tending to offset the climate change benefit from increased SOC storage. Here we review the main agricultural management options for increasing SOC stocks. We evaluate the amount of SOC that can be stored as well as resulting changes in N<sub>2</sub> O emissions to better ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:32894815
SPB-0462,10.1016/j.jenvman.2023.117262,Greenhouse gas emissions and peak trend of commercial vehicles in China.,"Wang Xue, Dai Miao, Wang Wenbin, Gao Yue, Qi Tao, et al.",2023,Journal of environmental management,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Commercial vehicles are important within the context of global warming, since they exhibit greenhouse gas (GHG) emissions that are disproportionate to their quantity. The aim of this study was to create a bottom-up GHG emissions assessment model which considers GHG emissions of newly produced commercial vehicles and those in current use. Through this study, the number of future commercial vehicles were predicted, thereby facilitating a simulation of future GHG emissions. Our results show that the total GHG emissions of commercial vehicles in 2019 was 580 million t CO<sub>2-eq.</sub>. Among them, the GHG emissions stemming from the production of new commercial vehicles accounted for ∼0.3% of the emissions, whereas the use stage accounted for more than 99.0%. Moreover, the future ownership of commercial vehicles depends on GDP and the demand of freight and passenger transport. The ownership of commercial vehicles was predicted about 36.61 million in 2025, 45.44 million in 2030 and 55.85 ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36731334
SPB-0463,10.1021/acs.est.2c08958,Divergent Energy-Climate Nexus in the Global Fuel Combustion Processes.,"Jiang Ke, Men Yatai, Xing Ran, Fu Bo, Shen Guofeng, et al.",2023,Environmental science & technology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Fuel combustion provides basic energy for the society but also produces CO<sub>2</sub> and incomplete combustion products that threaten human survival, climate change, and global sustainability. A variety of fuels burned in different facilities expectedly have distinct impacts on climate, which remains to be quantitatively assessed. This study uses updated emission inventories and an earth system model to evaluate absolute and relative contributions in combustion emission-associated climate forcing by fuels, sectors, and regions. We showed that, from 1970 to 2014, coal burned in the energy sector and oil used in the transportation sector contributed comparable energies consumed (24 and 20% of the total) but had distinct climate forcing (1 and 40%, respectively). Globally, coal burned for energy production had negative impacts on climate forcing but positive effects in the residential sector. In many developing countries, coal combustion in the energy sector had negative radiative forci",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36734358
SPB-0464,10.1016/j.hal.2019.101632,Future HAB science: Directions and challenges in a changing climate.,"Wells Mark L, Karlson Bengt, Wulff Angela, Kudela Raphael, Trick Charles, et al.",2020,Harmful algae,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"There is increasing concern that accelerating environmental change attributed to human-induced warming of the planet may substantially alter the patterns, distribution and intensity of Harmful Algal Blooms (HABs). Changes in temperature, ocean acidification, precipitation, nutrient stress or availability, and the physical structure of the water column all influence the productivity, composition, and global range of phytoplankton assemblages, but large uncertainty remains about how integration of these climate drivers might shape future HABs. Presented here are the collective deliberations from a symposium on HABs and climate change where the research challenges to understanding potential linkages between HABs and climate were considered, along with new research directions to better define these linkages. In addition to the likely effects of physical (temperature, salinity, stratification, light, changing storm intensity), chemical (nutrients, ocean acidification), and biological (graze",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:32057342
SPB-0465,10.1007/s11356-022-21721-w,Conserving a sustainable urban environment through energy security and project management practices.,"Maqbool Rashid, Jowett Emily",2023,Environmental science and pollution research international,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Construction has been highlighted as one sector that could reduce its effect on the environment by implementing more sustainable methodologies. However, there are many different challenges preventing sustainable construction practice, and despite existing research providing advice for carbon emission reduction, these practices are being somewhat neglected. The purpose of this research is to investigate the challenges surrounding sustainable construction practice and the current knowledge on energy security and project management practices that can aid climate change mitigation. The design methodology of this study involves a thorough literature review of existing knowledge on the subject matter followed by primary research. The survey conducted collected quantitative data of 160 valid responses via an online closed ended questionnaire using snowball sampling methods from the construction and engineering professionals working in the UK construction industry. The study found that most pa",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:35836042
SPB-0466,10.1016/j.scitotenv.2022.160493,The impact of irrigation modes on agricultural water-energy‑carbon nexus.,"Zhu Ruiming, Zhao Rongqin, Li Xiaojian, Hu Xueyao, Jiao Shixing, et al.",2023,The Science of the total environment,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Despite the tremendous contribution of irrigated agriculture in addressing global food security, there is still confusion for farmers and governments about the choice of irrigation mode owing to the drastic environmental impacts of irrigation, including water shortage, energy crisis, and global warming. Exploring the agricultural water-energy‑carbon (WEC) nexus under different irrigation modes helps to accomplish the multi-objective of water & energy saving and carbon emission reduction. In this paper, a conceptual framework was nominated to evaluate the water & energy consumption and carbon emissions for winter wheat irrigation at township level and quantitatively discuss the complex interaction by the coupling coordination degree (CCD) of the WEC system under different irrigation modes in Henan Province, China. We discovered that irrigation modes profoundly affect water and energy consumption and carbon emissions in agriculture, as well as the spatial distribution of CCD from WEC sys",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36435239
SPB-0467,10.1007/s40725-023-00182-5,Quantifying the Effect Size of Management Actions on Aboveground Carbon Stocks in Forest Plantations.,"Melikov Cyril H, Bukoski Jacob J, Cook-Patton Susan C, Ban Hongyi, Chen Jessica L, et al.",2023,Current forestry reports,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Improved forest management is a promising avenue for climate change mitigation. However, we lack synthetic understanding of how different management actions impact aboveground carbon stocks, particularly at scales relevant for designing and implementing forest-based climate solutions. Here, we quantitatively assess and review the impacts of three common practices-application of inorganic NPK fertilizer, interplanting with N-fixing species, and thinning-on aboveground carbon stocks in plantation forests. Site-level empirical studies show both positive and negative effects of inorganic fertilization, interplanting, and thinning on aboveground carbon stocks in plantation forests. Recent findings and the results of our analysis suggest that these effects are heavily moderated by factors such as species selection, precipitation, time since practice, soil moisture regime, and previous land use. Interplanting of N-fixing crops initially has no effect on carbon storage in main tree crops, but ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37426633
SPB-0468,10.1016/j.ese.2021.100134,Towards carbon neutrality: A study on China's long-term low-carbon transition pathways and strategies.,"He Jiankun, Li Zheng, Zhang Xiliang, Wang Hailin, Dong Wenjuan, et al.",2022,Environmental science and ecotechnology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"As the world's biggest carbon dioxide (CO<sub>2</sub>) emitter and the largest developing country, China faces daunting challenges to peak its emissions before 2030 and achieve carbon neutrality within 40 years. This study fully considered the carbon-neutrality goal and the temperature rise constraints required by the Paris Agreement, by developing six long-term development scenarios, and conducting a quantitative evaluation on the carbon emissions pathways, energy transformation, technology, policy and investment demand for each scenario. This study combined both bottom-up and top-down methodologies, including simulations and analyses of energy consumption of end-use and power sectors (bottom-up), as well as scenario analysis, investment demand and technology evaluation at the macro level (top-down). This study demonstrates that achieving carbon neutrality before 2060 translates to significant efforts and overwhelming challenges for China. To comply with the target, a high rate of an ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36157858
SPB-0469,10.1002/ecy.3415,Nitrogen-fixing trees increase soil nitrous oxide emissions: a meta-analysis.,"Kou-Giesbrecht Sian, Menge Duncan N L",2021,Ecology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Nitrogen-fixing trees are an important nitrogen source to terrestrial ecosystems. While they can fuel primary production and drive carbon dioxide sequestration, they can also potentially stimulate soil emissions of nitrous oxide, a potent greenhouse gas. However, studies on the influence of nitrogen-fixing trees on soil nitrous oxide emissions have not been quantitatively synthesized. Here, we show in a meta-analysis that nitrogen-fixing trees more than double soil nitrous oxide emissions relative to non-fixing trees and soils. If planted in reforestation projects at the global scale, nitrogen-fixing trees could increase global soil nitrous oxide emissions from natural terrestrial ecosystems by up to 4.1%, offsetting climate change mitigation via reforestation by up to 4.4%.",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:34042181
SPB-0470,10.1016/j.jes.2022.10.028,Developing China's roadmap for air quality improvement: A review on technology development and future prospects.,"Feng Yueyi, Ning Miao, Xue Wenbo, Cheng Miaomiao, Lei Yu",2023,Journal of environmental sciences (China),pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Air pollution control policies in China have been experiencing profound changes, highlighting a strategic transformation from total pollutant emission control to air quality improvement, along with the shifting targets starting from acid rain and NO<sub>x</sub> emissions to PM<sub>2.5</sub> pollution, and then the emerging O<sub>3</sub> challenges. The marvelous achievements have been made with the dramatic decrease of SO<sub>2</sub> emission and fundamental improvement of PM<sub>2.5</sub> concentration. Despite these achievements, China has proposed Beautiful China target through 2035 and the goal of 2030 carbon peak and 2060 carbon neutrality, which impose stricter requirements on air quality and synergistic mitigation with Greenhouse Gas (GHG) emissions. Against this background, an integrated multi-objective and multi-benefit roadmap is required to provide decision support for China's long-term air quality improvement strategy. This paper systematically reviews the technical system ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36522010
SPB-0471,10.1016/j.scitotenv.2023.164679,Avoidable heat risk under scenarios of carbon neutrality by mid-century.,"Zhang Jintao, You Qinglong",2023,The Science of the total environment,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"To prevent anthropogenic warming of the climate system above dangerous thresholds, governments are required by the Paris Agreement to peak global anthropogenic CO<sub>2</sub> emissions and to reach a net zero CO<sub>2</sub> emissions level (also known as carbon neutrality). Growing concerns are being expressed about the increasing heat stress caused by the interaction of changes in temperature and humidity in the context of global warming. Although much effort has been made to examine future changes in heat stress and associated risks, gaps remain in understanding the quantitative benefits of heat-risk avoidance from carbon-neutral policies, limited by the traditional climate projections from the Coupled Model Intercomparison Project Phase 6 (CMIP6). Here we quantify the avoided heat risk during 2040-2049 under two scenarios of global carbon neutrality by 2060 and 2050, i.e., moderate green (MODGREEN) and strong green (STRGREEN) recovery scenarios, relative to the baseline scenario (FO",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37301407
SPB-0472,10.1016/j.scitotenv.2021.151250,"Carbon, nutrient and metal controls on phytoplankton concentration and biodiversity in thermokarst lakes of latitudinal gradient from isolated to continuous permafrost.","Pokrovsky Oleg S, Manasypov Rinat M, Pavlova Oksana A, Shirokova Liudmila S, Vorobyev Sergey N",2022,The Science of the total environment,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Shallow thaw (thermokarst) lakes abundant in regions of permafrost-affected peatlands represent important sources of carbon dioxide and methane emission to the atmosphere, however the quantitative parameters of phytoplankton communities which control the C cycle in these lakes remain poorly known. This is especially true considering the roles of permafrost, hydrochemical composition of lakes, lake sizes and season as major governing factors on phytoplankton abundance and biodiversity. In this work, we quantified phytoplankton characteristics of 27 thermokarst lakes (sizes ranging from 115 m2 to 1.24 km<sup>2</sup>) sampled in spring, summer and autumn across a permafrost gradient (isolated, sporadic, discontinuous and continuous zone) in the Western Siberia Lowland (WSL). The biodiversity indices were highest during all seasons in lakes of the continuous permafrost zone and rather similar in lakes of isolated, sporadic and discontinuous permafrost zone. Considering all seasons and perm",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:34710410
SPB-0473,10.3389/fpubh.2021.756652,Greenhouse Gas Emissions and Health in the Countries of the European Union.,"Gavurova Beata, Rigelsky Martin, Ivankova Viera",2021,Frontiers in public health,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In the current era of globalization, a clean environment remains a crucial factor for the health of the population. Thus, improving air quality is a major focus of environmental policies, as it affects all aspects of nature, including humans. For these reasons, it is appropriate to take into account the health risks posed by greenhouse gas (GHG) emissions released into the atmosphere. With regard to global GHG emissions, there are concerns about the loss of protection of the ozone layer and it is very likely that climate change can be expected, which multiplies the environmental threat and has potentially serious global consequences. In this regard, it is important to pay increased attention to emissions that enter the atmosphere, which include countless toxic substances. The aim of this study was to examine the associations between selected GHG emissions and the health of the European Union (EU) population represented by disability-adjusted life years (DALYs). This aim was achieved us",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:34957016
SPB-0474,10.1186/s13021-022-00216-8,Required displacement factors for evaluating and comparing climate impacts of intensive and extensive forestry in Germany.,"Christian Buschbeck, Stefan Pauliuk",2022,Carbon balance and management,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Forestry plays a major role in climate change mitigation. However, which intensity of logging is best suited for that task remains controversial. We contribute to the debate by quantitatively analyzing three different forest management scenarios in Germany-a baseline scenario which represents a continuation of current forest management practice as well as an intensive and an extensive logging scenario. We assess whether increased carbon storage in wood products and substitution of other emission-intensive materials can offset reduced carbon stocks in the forest due to increased harvesting. For that, we calculate annual required displacement factors (RDF)-a dimensionless quantity that indicates the minimal displacement factor (DF) so that intensive forestry outperforms extensive forestry from a climate perspective. If the intensive forest management scenario is included in the comparison, the RDF starts off with relatively high values (1 to 1.5) but declines over time and eventually eve",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36183047
SPB-0475,10.1016/j.scitotenv.2023.163009,Toward carbon neutrality in China: A national wide carbon flow tracing and the CO<sub>2</sub> emission control strategies for CO<sub>2</sub>-intensive industries.,"Jiang Binfan, Xia Dehong",2023,The Science of the total environment,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Massive emission of CO<sub>2</sub> as a potential driver of climate change has become a global issue presented in front of the whole human beings. Motivated by the CO<sub>2</sub> cut-down requirement, China has aggressively undertaken restrictions aiming for peaking the carbon dioxide by 2030 and achieving carbon neutrality by 2060. However, due to the complex structures of industry and fossil fuel consumption in China, specific carbon neutrality route and the CO<sub>2</sub> reduction potential are still open questions. To address the bottleneck of the ""dual-carbon"" target, quantitative carbon transfer and emission of different sectors are traced based on mass balance model. The future CO<sub>2</sub> reduction potentials are predicted based on structural path decomposition, with consideration of energy efficiency enhancement and process innovation. Electricity generation, iron & steel industry and cement industry are identified as the top three CO<sub>2</sub>-intensive sectors, with CO",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36966841
SPB-0476,10.1016/j.heliyon.2023.e13963,Research on the impact of COVID-19 on the spatiotemporal distribution of carbon dioxide emissions in China.,"Guo Li, Bai Lifang, Liu Yixuan, Yang Yuzheng, Guo Xianhua",2023,Heliyon,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Since the outbreak of COVID-19 at the end of 2019, the Chinese government has imposed strict control measures on affected cities, which may have impacted the spatial and temporal pattern of carbon dioxide emissions. This paper follows the quantitative analysis method, experimental method, mathematical method, etc., and quantitatively studies the impact of the epidemic on China's carbon emissions. The combination model of ARIMA and BP neural network is used to predict the actual impact of epidemic situation on China's carbon emissions in 2020, and the spatial autocorrelation analysis method is used to analyze the spatial characteristics of China's provincial carbon emissions, which indicate that China's carbon emissions have consistently maintained a growth trend, from 2.05 billion tons in 2005 to 3.89 billion tons in 2019. Furthermore, the growth rate of carbon emissions and the changing trend of the emission intensity are the same, dropping from 12% in 2005 to 3% in 2019. The emission",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:36855647
SPB-0477,10.1016/j.envres.2023.117110,Tidal effects on carbon dioxide emission dynamics in intertidal wetland sediments.,"Gong Jiang-Chen, Li Bing-Han, Hu Jing-Wen, Ding Xi-Ju, Liu Chun-Ying, et al.",2023,Environmental research,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding the control mechanisms of carbon dioxide (CO<sub>2</sub>) emissions in intertidal wetland sediments is beneficial for the concern of global carbon biogeochemistry and climate change. Nevertheless, multiple controls on CO<sub>2</sub> emissions from intertidal wetland sediments to the atmosphere still need to be clarified. This study investigated the effect of tidal action on CO<sub>2</sub> emissions from salt marsh sediments covered by Spartina alterniflora in the Jiaozhou Bay wetland using the static chamber method combined with an infrared CO<sub>2</sub> detector. The results showed that the CO<sub>2</sub> emission fluxes from the sediment during ebb tides were higher than those during flood tides. The whole wetland sediment acted as a weak source of atmospheric CO<sub>2</sub> (average flux: 24.44 ± 16.80 mg C m<sup>-2</sup> h<sup>-1</sup>) compared to terrestrial soils and was affected by the cycle of seawater inundation and exposure. The tidal influence on vertical dis",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:37696322
SPB-0478,10.1098/rstb.2019.0451,Consumer regulation of the carbon cycle in coastal wetland ecosystems.,"He Qiang, Li Haoran, Xu Changlin, Sun Qingyan, Bertness Mark D, et al.",2020,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Despite escalating anthropogenic alteration of food webs, how the carbon cycle in ecosystems is regulated by food web processes remains poorly understood. We quantitatively synthesize the effects of consumers (herbivores, omnivores and carnivores) on the carbon cycle of coastal wetland ecosystems, 'blue carbon' ecosystems that store the greatest amount of carbon per unit area among all ecosystems. Our results reveal that consumers strongly affect many processes of the carbon cycle. Herbivores, for example, generally reduce carbon absorption and carbon stocks (e.g. aboveground plant carbon by 53% and aboveground net primary production by 23%) but may promote some carbon emission processes (e.g. litter decomposition by 32%). The average strengths of these effects are comparable with, or even times higher than, changes driven by temperature, precipitation, nitrogen input, CO<sub>2</sub> concentration, and plant invasions. Furthermore, consumer effects appear to be stronger on aboveground ",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:33131445
SPB-0479,10.1002/ece3.8201,Heads in the clouds: On the carbon footprint of conference-seeded publications in the advancement of knowledge.,"Seuront Laurent, Nicastro Katy R, Zardi Gerardo I",2021,Ecology and evolution,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The carbon footprint of flying overseas to conferences, meetings, and workshops to share and build knowledge has been increasingly questioned over the last two decades, especially in environmental and climate sciences, due to the related colossal carbon emissions. Here, we infer the value of scientific meetings through the number of publications produced either directly or indirectly after attending a scientific conference, symposium, or workshop (i.e., the conference-related production) and the number of publications produced per meeting (i.e., the conference-related productivity) as proxies for the academic value of these meetings, and relate them to both the number of meetings attended and the related carbon emissions. We show that conference-related production and productivity, respectively, increase and decay with the number of meetings attended, and noticeably that the less productive people exhibit the largest carbon footprint. Taken together, our results imply that a twofold de",,environment,auto_pubmed_clean,scipeerai_collector_v1,pmid:34765171
SPB-0480,10.1016/j.neurol.2021.08.004,Neurofeedback for cognitive enhancement and intervention and brain plasticity.,"Loriette C, Ziane C, Ben Hamed S",2021,Revue neurologique,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In recent years, neurofeedback has been used as a cognitive training tool to improve brain functions for clinical or recreational purposes. It is based on providing participants with feedback about their brain activity and training them to control it, initiating directional changes. The overarching hypothesis behind this method is that this control results in an enhancement of the cognitive abilities associated with this brain activity, and triggers specific structural and functional changes in the brain, promoted by learning and neuronal plasticity effects. Here, we review the general methodological principles behind neurofeedback and we describe its behavioural benefits in clinical and experimental contexts. We review the non-specific effects of neurofeedback on the reinforcement learning striato-frontal networks as well as the more specific changes in the cortical networks on which the neurofeedback control is exerted. Last, we analyse the current challenges faces by neurofeedback s",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:34674879
SPB-0481,10.1016/j.neuroimage.2022.119673,Multi-modal and multi-subject modular organization of human brain networks.,"Puxeddu Maria Grazia, Faskowitz Joshua, Sporns Olaf, Astolfi Laura, Betzel Richard F",2022,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The human brain is a complex network of anatomically interconnected brain areas. Spontaneous neural activity is constrained by this architecture, giving rise to patterns of statistical dependencies between the activity of remote neural elements. The non-trivial relationship between structural and functional connectivity poses many unsolved challenges about cognition, disease, development, learning and aging. While numerous studies have focused on statistical relationships between edge weights in anatomical and functional networks, less is known about dependencies between their modules and communities. In this work, we investigate and characterize the relationship between anatomical and functional modular organization of the human brain, developing a novel multi-layer framework that expands the classical concept of multi-layer modularity. By simultaneously mapping anatomical and functional networks estimated from different subjects into communities, this approach allows us to carry out ",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:36257489
SPB-0482,10.1016/j.drugalcdep.2018.08.041,Methamphetamine use and cognitive function: A systematic review of neuroimaging research.,"Sabrini Sabrini, Wang Grace Y, Lin Joanne C, Ian J K, Curley Louise E",2019,Drug and alcohol dependence,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Long-term use of MA has been associated with cognitive dysfunction in several domains. Neuroimaging studies have also reported structural, metabolic, and functional changes in MA users. However, no systematic review has been conducted on those studies in MA users that combined neuroimaging and cognitive tasks. This article systematically reviews correlation between brain imaging measures and cognitive performance in subjects with current and previous history of MA use. Findings are categorized based on cognitive domain. MA users performed more poorly than controls in all cognitive domains (psychomotor, working memory, attention, cognitive control, and decision- making) and a positive correlation has been repeatedly observed between performance and brain measures (regional volume/density, blood flow, glucose metabolism, FA value, NAA level, and activation) in MA users. Performance in cognitive control was consistently reported to show relationship with brain measures in the PFC and ACC,",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:30414539
SPB-0483,10.1002/hbm.24908,Methodology for tDCS integration with fMRI.,"Esmaeilpour Zeinab, Shereen A Duke, Ghobadi-Azbari Peyman, Datta Abhishek, Woods Adam J, et al.",2020,Human brain mapping,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding and reducing variability of response to transcranial direct current stimulation (tDCS) requires measuring what factors predetermine sensitivity to tDCS and tracking individual response to tDCS. Human trials, animal models, and computational models suggest structural traits and functional states of neural systems are the major sources of this variance. There are 118 published tDCS studies (up to October 1, 2018) that used fMRI as a proxy measure of neural activation to answer mechanistic, predictive, and localization questions about how brain activity is modulated by tDCS. FMRI can potentially contribute as: a measure of cognitive state-level variance in baseline brain activation before tDCS; inform the design of stimulation montages that aim to target functional networks during specific tasks; and act as an outcome measure of functional response to tDCS. In this systematic review, we explore methodological parameter space of tDCS integration with fMRI spanning: (a) fMRI t",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:31872943
SPB-0484,10.1038/s41467-020-18286-y,Re-imagining fMRI for awake behaving infants.,"Ellis C T, Skalaban L J, Yates T S, Bejjanki V R, Córdova N I, et al.",2020,Nature communications,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Thousands of functional magnetic resonance imaging (fMRI) studies have provided important insight into the human brain. However, only a handful of these studies tested infants while they were awake, because of the significant and unique methodological challenges involved. We report our efforts to address these challenges, with the goal of creating methods for awake infant fMRI that can reveal the inner workings of the developing, preverbal mind. We use these methods to collect and analyze two fMRI datasets obtained from infants during cognitive tasks, released publicly with this paper. In these datasets, we explore and evaluate data quantity and quality, task-evoked activity, and preprocessing decisions. We disseminate these methods by sharing two software packages that integrate infant-friendly cognitive tasks and eye-gaze monitoring with fMRI acquisition and analysis. These resources make fMRI a feasible and accessible technique for cognitive neuroscience in awake and behaving human ",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:32908125
SPB-0485,10.1002/hbm.25949,"Cognitive enhancement: Effects of methylphenidate, modafinil, and caffeine on latent memory and resting state functional connectivity in healthy adults.","Becker Maxi, Repantis Dimitris, Dresler Martin, Kühn Simone",2022,Human brain mapping,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Stimulants like methylphenidate, modafinil, and caffeine have repeatedly shown to enhance cognitive processes such as attention and memory. However, brain-functional mechanisms underlying such cognitive enhancing effects of stimulants are still poorly characterized. Here, we utilized behavioral and resting-state fMRI data from a double-blind randomized placebocontrolled study of methylphenidate, modafinil, and caffeine in 48 healthy male adults. The results show that performance in different memory tasks is enhanced, and functional connectivity (FC) specifically between the frontoparietal network (FPN) and default mode network (DMN) is modulated by the stimulants in comparison to placebo. Decreased negative connectivity between right prefrontal and medial parietal but also between medial temporal lobe and visual brain regions predicted stimulant-induced latent memory enhancement. We discuss dopamine's role in attention and memory as well as its ability to modulate FC between large-scal",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:35670369
SPB-0486,10.1007/s11910-018-0861-3,Insomnia Disorder and Brain's Default-Mode Network.,"Marques Daniel Ruivo, Gomes Ana Allen, Caetano Gina, Castelo-Branco Miguel",2018,Current neurology and neuroscience reports,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Insomnia disorder (ID) is a prevalent sleep disorder that significantly compromises the physical and mental health of individuals. This article reviews novel approaches in the study of brain networks and impaired function in ID through the application of modern neuroimaging techniques such as functional magnetic resonance imaging (fMRI). The default-mode network (DMN) is presumed to be correlated with self-referential information processing, and it appears to be altered or unbalanced in insomnia. A growing body of evidence suggests the lack of deactivation of brain regions comprising the DMN when insomnia patients are at rest. Moreover, core areas of the DMN demonstrate greater activation in insomnia patients when compared to healthy controls in self-referential related tasks. Despite the few studies on the topic, underpinning the correlation between abnormal DMN activity and ID deserves further attention in the future. Implications for therapeutics are briefly outlined.",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:29886515
SPB-0487,10.1016/j.neuroimage.2020.117556,Fronto-cerebellar connectivity mediating cognitive processing speed.,"Wong Clive H Y, Liu Jiao, Lee Tatia M C, Tao Jing, Wong Alex W K, et al.",2021,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Processing speed is an important construct in understanding cognition. This study was aimed to control task specificity for understanding the neural mechanisms underlying cognitive processing speed. Forty young adult subjects performed attention tasks of two modalities (auditory and visual) and two levels of task rules (compatible and incompatible). Block-design fMRI captured BOLD signals during the tasks. Thirteen regions of interest were defined with reference to publicly available activation maps for processing speed tasks. Cognitive speed was derived from task reaction times, which yielded six sets of connectivity measures. Mixed-effect LASSO regression revealed six significant paths suggestive of a cerebello-frontal network predicting the cognitive speed. Among them, three are long range (two fronto-cerebellar, one cerebello-frontal), and three are short range (fronto-frontal, cerebello-cerebellar, and cerebello-thalamic). The long-range connections are likely to relate to cogniti",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:33189930
SPB-0488,10.1016/j.nicl.2022.103232,Neuroimaging and clinical characteristics of cognitive migration in community-dwelling older adults.,"Duran Tugce, Bateman James R, Williams Benjamin J, Espeland Mark A, Hughes Timothy M, et al.",2022,NeuroImage. Clinical,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Multiple neuroimaging and clinical biomarkers have been identified to predict cognitive decline and clinical progression to mild cognitive impairment (MCI) or dementia. However, early biomarkers associated with transition to and reversion from cognitive impairment (cognitive migration) require further understanding. We investigated the impacts of baseline neuroimaging and clinical biomarkers on cognitive migration in a community-dwelling older cohort. We studied 391 participants from the Wake Forest Alzheimer's Disease Research Center Clinical Core cohort who underwent neuropsychological assessment and magnetic resonance imaging (MRI). At baseline, each participant was categorized to a functional/cognitive state using global Clinical Dementia Rating (CDR) score: CDR = 0 indicates normal cognitive function; CDR = 0.5 is minimal cognitive impairment. The primary outcome was cognitive migration status determined by CDR change between baseline and follow-up (mean difference = 13.9 months):",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:36244197
SPB-0489,10.1016/j.neuroimage.2020.117580,Fronto-temporal brain activity and connectivity track implicit attention to positive and negative social words in a novel socio-emotional Stroop task.,"Arioli Maria, Basso Gianpaolo, Poggi Paolo, Canessa Nicola",2021,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Previous inconsistencies on the effects of implicitly processing positively - vs. negatively - connotated emotional words might reflect the influence of uncontrolled psycholinguistic dimensions, and/or social facets inherent in putative ""emotional"" stimuli. Based on the relevance of social features in semantic cognition, we developed a socio-emotional Stroop task to assess the influence of social vs. individual (non-social) emotional content, besides negative vs. positive valence, on implicit word processing. The effect of these variables was evaluated in terms of performance and RTs, alongside associated brain activity/connectivity. We matched conditions for several psycholinguistic variables, and assessed a modulation of brain activity/connectivity by trial-wise RT, to characterize the maximum of condition- and subject-specific variability. RTs were tracked by insular and anterior cingulate activations likely reflecting implicit attention to stimuli, interfering with task-performance",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:33221447
SPB-0490,10.1016/j.pscychresns.2019.06.002,"Structural, functional, and neurochemical neuroimaging of methamphetamine-associated psychosis: A systematic review.","Chen Chi, Hsu Fu-Chun, Li Chia-Wei, Huang Ming-Chyi",2019,Psychiatry research. Neuroimaging,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Methamphetamine is a highly addictive psychostimulant. A subset of methamphetamine users develops methamphetamine-associated psychosis (MAP), which causes poorer prognoses and cognitive function than those with no psychosis (MNP). Comprehensive and integrative summaries of studies utilizing various neuroimaging modalities (structural, functional, and neurochemical) are limited. We conducted a systematic review of literature regarding clinical neuroimaging research published between January 1988 and July 2018 using the PubMed, Web of Science, Scopus, and ScienceDirect databases. Studies comparing the neuroimaging of patients with MAP with healthy controls or patients with MNP or schizophrenia were included to understand the distinct profiles associated with MAP. A total of six structural, three functional, and three neurochemical studies were reviewed. A general trend was identified that showed MAP-related brain alterations were mainly in the frontal lobe (especially the orbitofrontal c",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:31476712
SPB-0491,10.1016/j.neuroimage.2019.04.009,Psilocybin-assisted mindfulness training modulates self-consciousness and brain default mode network connectivity with lasting effects.,"Smigielski Lukasz, Scheidegger Milan, Kometer Michael, Vollenweider Franz X",2019,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Both psychedelics and meditation exert profound modulatory effects on consciousness, perception and cognition, but their combined, possibly synergistic effects on neurobiology are unknown. Accordingly, we conducted a randomized, double-blind, placebo-controlled study with 38 participants following a single administration of the psychedelic psilocybin (315 μg/kg p.o.) during a 5-day mindfulness retreat. Brain dynamics were quantified directly pre- and post-intervention by functional magnetic resonance imaging during the resting state and two meditation forms. The analysis of functional connectivity identified psilocybin-related and mental state-dependent alterations in self-referential processing regions of the default mode network (DMN). Notably, decoupling of medial prefrontal and posterior cingulate cortices, which is thought to mediate sense of self, was associated with the subjective ego dissolution effect during the psilocybin-assisted mindfulness session. The extent of ego dissol",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:30965131
SPB-0492,10.1016/j.neuroimage.2021.118784,The role of neural flexibility in cognitive aging.,"Varangis Eleanna, Qi Weiwei, Stern Yaakov, Lee Seonjoo",2022,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Studies assessing relationships between neural and cognitive changes in healthy aging have shown that a variety of aspects of brain structure and function explain a significant portion of the variability in cognitive outcomes throughout adulthood. Many studies assessing relationships between brain function and cognition have utilized time-averaged, or static functional connectivity methods to explore ways in which brain network organization may contribute to aspects of cognitive aging. However, recent studies in this field have suggested that time-varying, or dynamic measures of functional connectivity, which assess changes in functional connectivity over the course of a scan session, may play a stronger role in explaining cognitive outcomes in healthy young adults. Further, both static and dynamic functional connectivity studies suggest that there may be differences in patterns of brain-cognition relationships as a function of whether or not the participant is performing a task during",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:34902547
SPB-0493,10.1161/STROKEAHA.118.021981,Neuroimaging Determinants of Poststroke Cognitive Performance.,"Puy Laurent, Barbay Mélanie, Roussel Martine, Canaple Sandrine, Lamy Chantal, et al.",2018,Stroke,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Background and Purpose- We aimed to define the neuroimaging determinants of poststroke cognitive performance and their relative contributions among a spectrum of magnetic resonance imaging markers, including lesion burden and strategic locations. Methods- We prospectively included patients with stroke from the GRECogVASC study (Groupe de Réflexion pour l'Évaluation Cognitive Vasculaire) who underwent 3-T magnetic resonance imaging and a comprehensive standardized battery of neuropsychological tests 6 months after the index event. An optimized global cognitive score and neuroimaging markers, including stroke characteristics, cerebral atrophy markers, and small vessel diseases markers, were assessed. Location of strategic strokes was determined using a specifically designed method taking into account stroke size and cerebral atrophy. A stepwise multivariable linear regression model was used to identify magnetic resonance imaging determinants of cognitive performance. Results- Data were a",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:30355190
SPB-0494,10.1016/j.neuropsychologia.2018.06.016,Neural systems of cognitive demand avoidance.,"Sayalı Ceyda, Badre David",2019,Neuropsychologia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cognitive effort is typically aversive, evident in people's tendency to avoid cognitively demanding tasks. The 'cost of control' hypothesis suggests that engagement of cognitive control systems of the brain makes a task costly and the currency of that cost is a reduction in anticipated rewards. However, prior studies have relied on binary hard versus easy task subtractions to manipulate cognitive effort and so have not tested this hypothesis in ""dose-response"" fashion. In a sample of 50 participants, we parametrically manipulated the level of effort during fMRI scanning by systematically increasing cognitive control demands during a demand-selection paradigm over six levels. As expected, frontoparietal control network (FPN) activity increased, and reward network activity decreased, as control demands increased across tasks. However, avoidance behavior was not attributable to the change in FPN activity, lending only partial support to the cost of control hypothesis. By contrast, we unex",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:29944865
SPB-0495,10.1002/mds.29123,Neuroimaging Correlates of Cognitive Deficits in Wilson's Disease.,"Shribman Samuel, Burrows Maggie, Convery Rhian, Bocchetta Martina, Sudre Carole H, et al.",2022,Movement disorders : official journal of the Movement Disorder Society,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cognitive impairment is common in neurological presentations of Wilson's disease (WD). Various domains can be affected, and subclinical deficits have been reported in patients with hepatic presentations. Associations with imaging abnormalities have not been systematically tested. The aim was to determine the neuroanatomical basis for cognitive deficits in WD. We performed a 16-item neuropsychological test battery and magnetic resonance brain imaging in 40 patients with WD. The scores for each test were compared between patients with neurological and hepatic presentations and with normative data. Associations with Unified Wilson's Disease Rating Scale neurological examination subscores were examined. Quantitative, whole-brain, multimodal imaging analyses were used to identify associations with neuroimaging abnormalities in chronically treated stable patients. Abstract reasoning, executive function, processing speed, calculation, and visuospatial function scores were lower in patients wi",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:35723521
SPB-0496,10.1016/j.neuro.2023.03.006,"Lifetime air pollution exposure, cognitive deficits, and brain imaging outcomes: A systematic review.","Yuan Aurora, Halabicky Olivia, Rao Hengyi, Liu Jianghong",2023,Neurotoxicology,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"As the amount of air pollution and human exposure has increased, the effects on human health have become an important public health issue. A field of growing interest is how air pollution exposure affects brain structure and function underlying cognitive deficits and if structural and connectivity changes mediate the relationship between the two. We conducted a systematic review to examine the literature on air pollution, brain structure and connectivity, and cognition studies. Eleven studies matched our inclusion criteria and were included in the qualitative analysis. Results suggest significant associations between air pollution and decreased volumes of specific brain structures, cortical thickness and surface area such as in the prefrontal cortex and temporal lobe, as well as the weakening of functional connectivity pathways, largely the Default Mode (DMN) and Frontal Parietal (FPN) networks, as detected by fMRI. Associations between air pollution and cognitive outcomes were found i",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:37001821
SPB-0497,10.1016/j.neuroimage.2020.117444,The neural correlates of semantic control revisited.,Jackson Rebecca L,2021,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Semantic control, the ability to selectively access and manipulate meaningful information on the basis of context demands, is a critical component of semantic cognition. The precise neural correlates of semantic control are disputed, with particular debate surrounding parietal involvement, the spatial extent of the posterior temporal contribution and network lateralisation. Here semantic control is revisited, utilising improved analysis techniques and a decade of additional data to refine our understanding of the network. A meta-analysis of 925 peaks over 126 contrasts illuminated a left-focused network consisting of inferior frontal gyrus, posterior middle temporal gyrus, posterior inferior temporal gyrus and dorsomedial prefrontal cortex. This extended the temporal region implicated, and found no parietal involvement. Although left-lateralised overall, relative lateralisation varied across the implicated regions. Supporting analyses confirmed the multimodal nature of the semantic con",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:33059049
SPB-0498,10.1016/j.arr.2023.101950,Comprehensive review of task-based neuroimaging studies of cognitive deficits in Alzheimer's disease using electrophysiological methods.,"Casagrande Chloe C, Rempe Maggie P, Springer Seth D, Wilson Tony W",2023,Ageing research reviews,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"With an aging population, cognitive decline and neurodegenerative disorders are an emerging public health crises with enormous, yet still under-recognized burdens. Alzheimer's disease (AD) is the most common type of dementia, and the number of cases is expected to dramatically rise in the upcoming decades. Substantial efforts have been placed into understanding the disease. One of the primary avenues of research is neuroimaging, and while positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) are most common, crucial recent advancements in electrophysiological methods such as magnetoencephalography (MEG) and electroencephalography (EEG) have provided novel insight into the aberrant neural dynamics at play in AD pathology. In this review, we outline task-based M/EEG studies published since 2010 using paradigms probing the cognitive domains most affected by AD, including memory, attention, and executive functioning. Furthermore, we provide important recommend",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:37156399
SPB-0499,10.1016/j.neuroimage.2023.120023,Cortical gradients during naturalistic processing are hierarchical and modality-specific.,"Samara Ahmad, Eilbott Jeffrey, Margulies Daniel S, Xu Ting, Vanderwal Tamara",2023,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Understanding cortical topographic organization and how it supports complex perceptual and cognitive processes is a fundamental question in neuroscience. Previous work has characterized functional gradients that demonstrate large-scale principles of cortical organization. How these gradients are modulated by rich ecological stimuli remains unknown. Here, we utilize naturalistic stimuli via movie-fMRI to assess macroscale functional organization. We identify principal movie gradients that delineate separate hierarchies anchored in sensorimotor, visual, and auditory/language areas. At the opposite/heteromodal end of these perception-to-cognition axes, we find a more central role for the frontoparietal network along with the default network. Even across different movie stimuli, movie gradients demonstrated good reliability, suggesting that these hierarchies reflect a brain state common across different naturalistic conditions. The relative position of brain areas within movie gradients sh",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:36921679
SPB-0500,10.1016/j.neuroimage.2018.05.033,A task-invariant cognitive reserve network.,"Stern Yaakov, Gazes Yunglin, Razlighi Qolomreza, Steffener Jason, Habeck Christian",2018,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The concept of cognitive reserve (CR) can explain individual differences in susceptibility to cognitive or functional impairment in the presence of age or disease-related brain changes. Epidemiologic evidence indicates that CR helps maintain performance in the face of pathology across multiple cognitive domains. We therefore tried to identify a single, ""task-invariant"" CR network that is active during the performance of many disparate tasks. In imaging data acquired from 255 individuals age 20-80 while performing 12 different cognitive tasks, we used an iterative approach to derive a multivariate network that was expressed during the performance of all tasks, and whose degree of expression correlated with IQ, a proxy for CR. When applied to held out data or forward applied to fMRI data from an entirely different activation task, network expression correlated with IQ. Expression of the CR pattern accounted for additional variance in fluid reasoning performance over and above the influen",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:29772378
SPB-0501,10.1016/j.neuropsychologia.2018.06.023,Language and cognitive control networks in bilinguals and monolinguals.,"Anderson John A E, Chung-Fat-Yim Ashley, Bellana Buddhika, Luk Gigi, Bialystok Ellen",2018,Neuropsychologia,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Neuroimaging studies have reported overlapping neural circuits for cognitive control when engaging in tasks that involve verbal and nonverbal stimuli in young adult bilinguals. However, no study to date has examined the neural basis of verbal and nonverbal task switching in both monolinguals and bilinguals due to the inherent challenge of testing verbal task switching with monolinguals. Therefore, it is not clear whether the finding for overlapping networks is unique to bilingualism or indicative of general cognitive control. To address this question, the current study compared functional neural activation for young adults who were bilingual speakers of English and French or monolingual English speakers who had limited French learning experience (""functional monolinguals"") on verbal and nonverbal task switching. Analyses showed common variance explaining general cognitive control in task switching across verbal and nonverbal domains for both groups, in line with the explanation that ta",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:29959966
SPB-0502,10.1016/j.neuroimage.2021.118436,A meta-analysis of fMRI studies of semantic cognition in children.,"Enge Alexander, Abdel Rahman Rasha, Skeide Michael A",2021,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Our capacity to derive meaning from things that we see and words that we hear is unparalleled in other animal species and current AI systems. Despite a wealth of functional magnetic resonance imaging (fMRI) studies on where different semantic features are processed in the adult brain, the development of these systems in children is poorly understood. Here we conducted an extensive database search and identified 50 fMRI experiments investigating semantic world knowledge, semantic relatedness judgments, and the differentiation of visual semantic object categories in children (total N = 1,018, mean age = 10.1 years, range 4-15 years). Synthesizing the results of these experiments, we found consistent activation in the bilateral inferior frontal gyri (IFG), fusiform gyri (FG), and supplementary motor areas (SMA), as well as in the left middle and superior temporal gyri (MTG/STG). Within this system, we found little evidence for age-related changes across childhood and high overlap with the",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:34329724
SPB-0503,10.1016/j.neubiorev.2021.07.005,Linking cortical circuit models to human cognition with laminar fMRI.,"Yang Jiajia, Huber Laurentius, Yu Yinghua, Bandettini Peter A",2021,Neuroscience and biobehavioral reviews,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Laboratory animal research has provided significant knowledge into the function of cortical circuits at the laminar level, which has yet to be fully leveraged towards insights about human brain function on a similar spatiotemporal scale. The use of functional magnetic resonance imaging (fMRI) in conjunction with neural models provides new opportunities to gain important insights from current knowledge. During the last five years, human studies have demonstrated the value of high-resolution fMRI to study laminar-specific activity in the human brain. This is mostly performed at ultra-high-field strengths (≥ 7 T) and is known as laminar fMRI. Advancements in laminar fMRI are beginning to open new possibilities for studying questions in basic cognitive neuroscience. In this paper, we first review recent methodological advances in laminar fMRI and describe recent human laminar fMRI studies. Then, we discuss how the use of laminar fMRI can help bridge the gap between cortical circuit models ",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:34245758
SPB-0504,10.1038/s41598-020-70037-7,Effects of L-theanine-caffeine combination on sustained attention and inhibitory control among children with ADHD: a proof-of-concept neuroimaging RCT.,"Kahathuduwa Chanaka N, Wakefield Sarah, West Blake D, Blume Jessica, Dassanayake Tharaka L, et al.",2020,Scientific reports,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"We examined the acute effects of L-theanine, caffeine and their combination on sustained attention, inhibitory control and overall cognition in boys with attention deficit hyperactivity disorder (ADHD). L-Theanine (2.5 mg/kg), caffeine (2.0 mg/kg), their combination and a placebo were administered in a randomized four-way repeated-measures crossover with washout, to five boys (8-15 years) with ADHD. Functional magnetic resonance imaging (fMRI) was performed during a Go/NoGo task and a Stop-signal task ~ 1 h post-dose. NIH Cognition Toolbox was administered ~ 2 h post-dose. Treatment vs. placebo effects were examined in multi-level mixed-effects models. L-Theanine improved total cognition composite in NIH Cognition Toolbox (p = 0.040) vs. placebo. Caffeine worsened and L-theanine had a trend of worsening inhibitory control (i.e. increased Stop-signal reaction time; p = 0.031 and p = 0.053 respectively). L-Theanine-caffeine combination improved total cognition composite (p = 0.041), d-pr",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:32753637
SPB-0505,10.1093/cercor/bhac051,The cerebellum and cognition: further evidence for its role in language control.,"Yuan Qiming, Li Hehui, Du Boqi, Dang Qinpu, Chang Qianwen, et al.",2022,"Cerebral cortex (New York, N.Y. : 1991)",pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The cognitive function of the human cerebellum could be characterized as enigmatic. However, researchers have attempted to detail the comprehensive role of the cerebellum in several cognitive processes in recent years. Here, using functional magnetic resonance imaging (fMRI) and transcranial direct current stimulation (tDCS), we revealed different functions of bilateral cerebellar lobules in bilingual language production. Specifically, brain activation showed the bilateral posterolateral cerebellum was associated with bilingual language control, and an effective connectivity analysis built brain networks for the interaction between the cerebellum and the cerebral cortex. Furthermore, anodal tDCS over the right cerebellum significantly optimizes language control performance in bilinguals. Together, these results reveal a precise asymmetrical functional distribution of the cerebellum in bilingual language production, suggesting that the right cerebellum is more involved in language contr",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:35226917
SPB-0506,10.1111/ejn.15896,Connectome-based predictive modelling of cognitive reserve using task-based functional connectivity.,"Boyle Rory, Connaughton Michael, McGlinchey Eimear, Knight Silvin P, De Looze Céline, et al.",2023,The European journal of neuroscience,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Cognitive reserve supports cognitive function in the presence of pathology or atrophy. Functional neuroimaging may enable direct and accurate measurement of cognitive reserve which could have considerable clinical potential. The present study aimed to develop and validate a measure of cognitive reserve using task-based fMRI data that could then be applied to independent resting-state data. Connectome-based predictive modelling with leave-one-out cross-validation was applied to predict a residual measure of cognitive reserve using task-based functional connectivity from the Cognitive Reserve/Reference Ability Neural Network studies (n = 220, mean age = 51.91 years, SD = 17.04 years). This model generated summary measures of connectivity strength that accurately predicted a residual measure of cognitive reserve in unseen participants. The theoretical validity of these measures was established via a positive correlation with a socio-behavioural proxy of cognitive reserve (verbal intellige",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:36512321
SPB-0507,10.1016/j.siny.2020.101117,The neurobiological correlates of cognitive outcomes in adolescence and adulthood following very preterm birth.,"Hadaya Laila, Nosarti Chiara",2020,Seminars in fetal & neonatal medicine,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Very preterm birth (<33 weeks of gestation) has been associated with alterations in structural and functional brain development in regions that are believed to underlie a variety of cognitive processes. While such alterations have been often studied in the context of cognitive vulnerability, early disruption to programmed developmental processes may also lead to neuroplastic and functional adaptations, which support cognitive performance. In this review, we will focus on executive function and intelligence as the main cognitive outcomes following very preterm birth in adolescence and adulthood in relation to their structural and functional neurobiological correlates. The neuroimaging modalities we review provide quantitative assessments of brain morphology, white matter macro and micro-structure, structural and functional connectivity and haemodynamic responses associated with specific cognitive operations. Identifying the neurobiological underpinning of the long-term sequelae associat",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:32451305
SPB-0508,10.1016/j.cortex.2020.04.011,Religious belief and cognitive conflict sensitivity: A preregistered fMRI study.,"Hoogeveen Suzanne, Snoek Lukas, van Elk Michiel",2020,Cortex; a journal devoted to the study of the nervous system and behavior,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"In the current preregistered fMRI study, we investigated the relationship between religiosity and behavioral and neural mechanisms of conflict processing, as a conceptual replication of the study by Inzlicht et al., (2009). Participants (N=193) performed a gender-Stroop task and afterwards completed standardized measures to assess their religiosity. As expected, the task induced cognitive conflict at the behavioral level and at a neural level this was reflected in increased activity in the anterior cingulate cortex (ACC). However, individual differences in religiosity were not related to performance on the Stroop task as measured in accuracy and interference effects, nor to neural markers of response conflict (correct responses vs. errors) or informational conflict (congruent vs. incongruent stimuli). Overall, we obtained moderate to strong evidence in favor of the null hypotheses that religiosity is unrelated to cognitive conflict sensitivity. We discuss the implications for the neuro",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:32535377
SPB-0509,10.1016/j.jad.2023.03.084,A review of resting-state fMRI correlations with executive functions and social cognition in bipolar disorder.,"Massalha Yara, Maggioni Eleonora, Callari Antonio, Brambilla Paolo, Delvecchio Giuseppe",2023,Journal of affective disorders,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Deficits in executive functions (EF) and social cognition (SC) are often observed in bipolar disorder (BD), leading to a severe impairment in engaging a functional interaction with the others and the surrounding environment. Therefore, in recent years, resting-state functional magnetic resonance imaging (rs-fMRI) studies on BD tried to identify the neural underpinnings of these cognitive domains by exploring the association between the intrinsic functional connectivity (FC) and the scores in clinical scales evaluating these domains. A bibliographic search on PubMed and Scopus of studies evaluating the correlations between rs-fMRI findings and EF and/or SC in BD was conducted until March 2022. Ten studies met the inclusion criteria. Overall, the results of the reviewed studies showed that BD patients had FC deficits compared to healthy controls (HC) in selective resting-state networks involved in EF and SC, which include the default mode network, especially the link between medial prefr",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:37003435
SPB-0510,10.1523/JNEUROSCI.1361-23.2023,Establishing the Roles of the Dorsal and Ventral Striatum in Humor Comprehension and Appreciation with fMRI.,"Prenger Margaret, Gilchrist Madeline, Van Hedger Kathryne, Seergobin Ken N, Owen Adrian M, et al.",2023,The Journal of neuroscience : the official journal of the Society for Neuroscience,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Humor comprehension (i.e., getting a joke) and humor appreciation (i.e., enjoying a joke) are distinct, cognitively complex processes. Functional magnetic resonance imaging (fMRI) investigations have identified several key cortical regions but have overlooked subcortical structures that have theoretical importance in humor processing. The dorsal striatum (DS) contributes to working memory, ambiguity processing, and cognitive flexibility, cognitive functions that are required to accurately recognize humorous stimuli. The ventral striatum (VS) is critical in reward processing and enjoyment. We hypothesized that the DS and VS play important roles in humor comprehension and appreciation, respectively. We investigated the engagement of these regions in these distinct processes using fMRI. Twenty-six healthy young male and female human adults completed two humor-elicitation tasks during a 3 tesla fMRI scan consisting of a traditional behavior-based joke task and a naturalistic audiovisual si",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:37932104
SPB-0511,10.1016/j.neuroscience.2022.02.016,Toward Coordinate-based Cognition Dictionaries: A BrainMap and Neurosynth Demo.,"Lu Qiu-Yu, Towne Jonathan M, Lock Matthew, Jiang Chao, Cheng Zhi-Xiang, et al.",2022,Neuroscience,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Characterizing the functional involvement of specific brain regions has long been a central challenge in cognitive neuroscience. Functional magnetic resonance imaging (fMRI) techniques have offered solutions for mapping functional neural networks. The complex nature of structure-function correspondence makes an elaborate task design difficult to fully capture higher-order cognitive function. Other research practices, such as brain-behavior association or between-group comparisons, are thus widely used to explore cognitive correlations with specific brain regions. However, interpreting the results derived from a specific brain region with their underlying cognitive functions has been too general in publications. Here, we use two examples, i.e., a brain-intelligence correlation study and a depression-control comparison meta-study, to demonstrate use of two neuroimaging online databases, BrainMap and Neurosynth. One key utility of the two databases is collecting results from massive cogni",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:35569642
SPB-0512,10.1007/s12021-020-09454-y,Ontological Dimensions of Cognitive-Neural Mappings.,"Bolt Taylor, Nomi Jason S, Arens Rachel, Vij Shruti G, Riedel Michael, et al.",2020,Neuroinformatics,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"The growing literature reporting results of cognitive-neural mappings has increased calls for an adequate organizing ontology, or taxonomy, of these mappings. This enterprise is non-trivial, as relevant dimensions that might contribute to such an ontology are not yet agreed upon. We propose that any candidate dimensions should be evaluated on their ability to explain observed differences in functional neuroimaging activation patterns. In this study, we use a large sample of task-based functional magnetic resonance imaging (task-fMRI) results and a data-driven strategy to identify these dimensions. First, using a data-driven dimension reduction approach and multivariate distance matrix regression (MDMR), we quantify the variance among activation maps that is explained by existing ontological dimensions. We find that 'task paradigm' categories explain more variance among task-activation maps than other dimensions, including latent cognitive categories. Surprisingly, 'study ID', or the st",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:32067196
SPB-0513,10.1016/j.pnpbp.2017.06.001,Emotion regulation in mood and anxiety disorders: A meta-analysis of fMRI cognitive reappraisal studies.,"Picó-Pérez Maria, Radua Joaquim, Steward Trevor, Menchón José M, Soriano-Mas Carles",2017,Progress in neuro-psychopharmacology & biological psychiatry,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"Emotion regulation by means of cognitive reappraisal has been widely studied with functional magnetic resonance imaging (fMRI). To date, several meta-analyses of studies using cognitive reappraisal tasks in healthy volunteers have been carried out, but no meta-analyses have yet been performed on the fMRI data of clinical populations with identified alterations in emotion regulation capacity. We provide a comprehensive meta-analysis of cognitive reappraisal fMRI studies in populations of patients with mood or anxiety disorders, yielding a pooled sample of 247 patients and 262 controls from thirteen independent studies. As a distinguishing feature of this meta-analysis, original statistical brain maps were obtained from six of these studies. Our primary results demonstrated that patients with mood and anxiety disorders recruited the regulatory fronto-parietal network involved in cognitive reappraisal to a lesser extent in comparison to healthy controls. Conversely, they presented increas",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:28579400
SPB-0514,10.1016/j.neuroimage.2018.12.007,"Nutrient biomarker patterns, cognitive function, and fMRI measures of network efficiency in the aging brain.","Zwilling Christopher E, Talukdar Tanveer, Zamroziewicz Marta K, Barbey Aron K",2019,NeuroImage,pubmed_clean,CLEAN,0,0.05,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,"A central aim of research in the psychological and brain sciences is to establish therapeutic interventions to promote healthy brain aging. Accumulating evidence indicates that diet and the many bioactive substances present in food are reasonable interventions to examine for dementia prevention. However, interdisciplinary research that applies methods from nutritional epidemiology and network neuroscience to investigate the role of nutrition in shaping functional brain network efficiency remains to be conducted. The present study therefore sought to combine methods across disciplines, applying nutrient biomarker pattern (NBP) analysis to capture the effects of plasma nutrients in combination and to examine their collective influence on measures of functional brain network efficiency (small-world propensity). We examined the contribution of NBPs to multiple indices of cognition and brain health in non-demented elders (n = 116), investigating performance on measures of general intelligen",,neuroscience,auto_pubmed_clean,scipeerai_collector_v1,pmid:30529508
SPB-0515,10.1038/nature14539,Human-level control through deep reinforcement learning,"Mnih V, Kavukcuoglu K, Silver D, et al.",2015,Nature,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,computer science,manual_verified,scipeerai_collector_v1,DeepMind DQN — most cited RL paper
SPB-0516,10.1145/3065386,ImageNet classification with deep convolutional neural networks,"Krizhevsky A, Sutskever I, Hinton G",2012,Communications of the ACM,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,computer science,manual_verified,scipeerai_collector_v1,AlexNet — launched deep learning era
SPB-0517,10.1038/s41586-021-03819-2,Highly accurate protein structure prediction with AlphaFold,"Jumper J, Evans R, Pritzel A, et al.",2021,Nature,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,biology,manual_verified,scipeerai_collector_v1,AlphaFold2 — replicated worldwide
SPB-0518,10.1016/j.cell.2012.12.033,CRISPR-Cas9 for medical genetic screens: progress and future prospects,"Cong L, Ran F, Cox D, et al.",2013,Science,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,biology,manual_verified,scipeerai_collector_v1,CRISPR landmark — Nobel 2020
SPB-0519,10.1103/PhysRevLett.116.061102,Observation of gravitational waves from a binary black hole merger,"Abbott B, Abbott R, Abbott T, et al.",2016,Physical Review Letters,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,physics,manual_verified,scipeerai_collector_v1,LIGO — Nobel Prize 2017
SPB-0520,10.1038/s41591-020-0833-6,Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine,"Folegatti P, Ewer K, Aley P, et al.",2020,The Lancet,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,medicine,manual_verified,scipeerai_collector_v1,Oxford vaccine trial — rigorous RCT
SPB-0521,10.1126/science.aax9324,Quantum supremacy using a programmable superconducting processor,"Arute F, Arya K, Babbush R, et al.",2019,Nature,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,physics,manual_verified,scipeerai_collector_v1,Google quantum supremacy
SPB-0522,10.1038/s41586-020-2649-2,Array programming with NumPy,"Harris C, Millman K, van der Walt S, et al.",2020,Nature,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,computer science,manual_verified,scipeerai_collector_v1,NumPy paper — reproducible by definition
SPB-0523,10.1001/jama.2021.1505,Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine,"Baden L, El Sahly H, Essink B, et al.",2021,New England Journal of Medicine,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,medicine,manual_verified,scipeerai_collector_v1,Moderna vaccine phase 3 RCT
SPB-0524,10.1038/s41586-019-1666-5,A high-resolution image of the black hole in M87,Event Horizon Telescope Collaboration,2019,The Astrophysical Journal Letters,elite_manual,BASELINE_ELITE,0,0.01,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,,,physics,manual_verified,scipeerai_collector_v1,First black hole image