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Bacterial outer membrane vesicle ( OMV ) -mediated delivery of proteins to host cells is an important mechanism of host-pathogen communication . Emerging evidence suggests that OMVs contain differentially packaged short RNAs ( sRNAs ) with the potential to target host mRNA function and/or stability . In this study , we...	Pseudomonas aeruginosa is a gram-negative , opportunistic pathogen that accounts for about 10% of all hospital-acquired infections in the US and primarily infects immunocompromised hosts , including patients with chronic obstructive pulmonary disease and cystic fibrosis . Gram-negative bacteria like P . aeruginosa prod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "rna", "extraction", "microbiology", "pseudo...	2016	A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles
Opacification of the ocular lens , termed cataract , is a common cause of blindness . To become transparent , lens fiber cells undergo degradation of their organelles , including their nuclei , presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing towa...	Besides associated with aging , the eye disease cataract can occur early in life because of defects in lens development . Lens fiber cells degrade their nuclei to achieve lens transparency , which poses a fundamental question: how is differentiation regulated in a cell progressing toward compromised transcriptional pot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "engineering", "and", "technology", "lens", "disorders", "ocular", "anatomy", "messenger", "rna", "vertebrates", "animals", "cell", "differentiation", "animal", "models", "osteichthyes", "developmental", "biology", "model...	2018	The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development
Chikungunya virus ( CHIKV ) has emerged as one of the most important arboviruses of public health significance in the past decade . The virus is mainly maintained through human-mosquito-human cycle . Other routes of transmission and the mechanism of maintenance of the virus in nature are not clearly known . Vertical tr...	Although vertical transmission of arboviruses has been recognized for nearly a century , rates of transmission in laboratory experiments are low and their significance in terms of survival of virus during periods of low transmission appears debatable . Recently , major urban outbreaks of chikungunya have been recorded ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "virology", "biology", "and", "life", "sciences", "microbiology", "viral", "diseases" ]	2014	Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti
Ticks are considered the second vector of human and animal diseases after mosquitoes . Therefore , identification of ticks and associated pathogens is an important step in the management of these vectors . In recent years , Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry ( MALDI-TOF MS ) ha...	Ticks are among the most important vectors and reservoirs of several animal and human pathogens such as viruses , bacteria and protozoa . However , very few studies have been done on ticks in Mali . At present , little information is available about tick species infesting livestock or human tick-borne diseases transmit...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "legs", "ixodes", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "limbs", "(anatomy)", "animals", "organic", "compounds", "rickettsia", "ticks", "alcohols", "b...	2017	Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali
Tsetse flies are vectors of the protozoan parasite African trypanosomes , which cause sleeping sickness disease in humans and nagana in livestock . Although there are no effective vaccines and efficacious drugs against this parasite , vector reduction methods have been successful in curbing the disease , especially for...	Infections with the parasitic bacterium Wolbachia are widespread in insects and cause a number of reproductive modifications , including cytoplasmic incompatibility ( CI ) . There is growing interest in Wolbachia , as CI may be able to drive desired phenotypes such as disease resistance traits , into natural population...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "applied", "mathematics", "biology", "microbiology" ]	2011	Wolbachia Symbiont Infections Induce Strong Cytoplasmic Incompatibility in the Tsetse Fly Glossina morsitans
Mathematical models of scientific data can be formally compared using Bayesian model evidence . Previous applications in the biological sciences have mainly focussed on model selection in which one first selects the model with the highest evidence and then makes inferences based on the parameters of that model . This “...	Bayesian model comparison provides a formal method for evaluating different computational models in the biological sciences . Emerging application domains include dynamical models of neuronal and biochemical networks based on differential equations . Much previous work in this area has focussed on selecting the single ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/transcriptional", "regulation", "computational", "biology/computational", "neuroscience", "computational", "biology/metabolic", "networks", "mathematics/statistics", "computati...	2010	Comparing Families of Dynamic Causal Models
Rare copy number variants ( CNVs ) are frequently associated with common neurological disorders such as mental retardation ( MR; learning disability ) , autism , and schizophrenia . CNV screening in clinical practice is limited because pathological CNVs cannot be distinguished routinely from benign CNVs , and because g...	Mental retardation ( MR; also known as learning disability ) affects 1%–3% of people and is often associated with the presence of genomic copy number variations ( CNVs ) such as deletions and duplications . Most of these CNVs are rare and they often involve tens , sometimes hundreds , of genes . Pinpointing exactly whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/cognitive", "neurology", "and", "dementia", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders/neuropsychiatric", ...	2009	Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models
The olfactory organ of vertebrates receives chemical cues present in the air or water and , at the same time , they are exposed to invading pathogens . Nasal-associated lymphoid tissue ( NALT ) , which serves as a mucosal inductive site for humoral immune responses against antigen stimulation in mammals , is present al...	The olfactory organ is a vitally important chemosensory organ in vertebrates but it is also continuously stimulated by pathogenic microorganisms in the external environment . In mammals and birds , nasopharynx-associated lymphoid tissue ( NALT ) is considered one of the first lines of immune defense against inhaled ant...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "fish", "immune", "cells", "body", "fluids", "immune", "physiology", "immunology", "vertebrates", "parasitic", "diseases", "animals", "olfactory", "organs", "osteichthyes", "respiratory", "system", "antibodies",...	2018	Mucosal immunoglobulins protect the olfactory organ of teleost fish against parasitic infection
Single-stranded polyanions ≥40 bases in length facilitate the formation of hamster scrapie prions in vitro , and polyanions co-localize with PrPSc aggregates in vivo [1] , [2] . To test the hypothesis that intact polyanionic molecules might serve as a structural backbone essential for maintaining the infectious conform...	Prions are unorthodox infectious agents whose composition remains undetermined . Previous experiments have shown that long , negatively charged polymers such as nucleic acid and carbohydrate molecules promote the formation of purified prions in test tube chemical reactions . Various classes of negatively charged polyme...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "veterinary", "diseases", "zoonotic", "diseases", "veterinary", "science", "prion", "diseases" ]	2011	In Situ Photodegradation of Incorporated Polyanion Does Not Alter Prion Infectivity
The DNA damage response is a signaling pathway found throughout biology . In many bacteria the DNA damage checkpoint is enforced by inducing expression of a small , membrane bound inhibitor that delays cell division providing time to repair damaged chromosomes . How cells promote checkpoint recovery after sensing succe...	Prokaryotes and eukaryotes coordinate cell division to genome integrity using DNA damage checkpoints . Many bacteria express a small , membrane binding protein to slow cell division when obstacles to DNA replication are encountered . Cell division inhibitors of this class have been identified in several bacterial speci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "serum", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "enzymes", "cell", "cycle", "and", "cell", "division", "pathogens", "cell", "processes", "bacillus", "enzymology", "microbiology", "gene", "reg...	2018	Discovery of a dual protease mechanism that promotes DNA damage checkpoint recovery
Social determinants can affect the transmission of leprosy and its progression to disease . Not much is known about the effectiveness of welfare and primary health care policies on the reduction of leprosy occurrence . The aim of this study is to evaluate the impact of the Brazilian cash transfer ( Bolsa Família Progra...	Leprosy is considered a poverty related disease . Not much is known about the effectiveness of welfare and primary health care policies on reduction of leprosy occurrence . We conducted a study to evaluate the impact of the Brazilian conditional cash transfer ( Bolsa Família Program ) and the Primary Health Care ( Fami...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "social", "epidemiology", "bacterial", "diseases", "infectious", "diseases", "public", "and", "occupational", "health", "plant", "science", "medicine", "and", "health", "sciences", "primary", "care", "infectious", "disease", "epidemiology", "epidemiology", "plant", "pat...	2014	Effect of the Brazilian Conditional Cash Transfer and Primary Health Care Programs on the New Case Detection Rate of Leprosy
Many recurrent chromosome translocations in cancer result in the generation of fusion genes that are directly implicated in the tumorigenic process . Precise modeling of the effects of cancer fusion genes in mice has been inaccurate , as constructs of fusion genes often completely or partially lack the correct regulato...	Many cancers carry recurrent chromosome translocations , which often result in the formation of fusion genes that are directly involved in the tumorigenic process . Alveolar rhabdomyosarcoma , a muscle tumor in children , is typified by a translocation that fuses the PAX3 gene on chromosome 2 to the FOXO1 gene on chrom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Modeling of the Human Alveolar Rhabdomyosarcoma Pax3-Foxo1 Chromosome Translocation in Mouse Myoblasts Using CRISPR-Cas9 Nuclease
We recently demonstrated that the respiratory syncytial virus ( RSV ) NS1 protein , an antagonist of host type I interferon ( IFN-I ) production and signaling , has a suppressive effect on the maturation of human dendritic cells ( DC ) that was only partly dependent on released IFN-I . Here we investigated whether NS1 ...	Respiratory syncytial virus ( RSV ) is a leading cause of pediatric lower respiratory tract disease . RSV has two IFN-I antagonist proteins , NS1 and NS2 . In this study , we infected primary human dendritic cells with recombinant RSV from which the NS1 and/or the NS2 genes were deleted , and evaluated effects on the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "infectious", "diseases", "immunology/immune", "response", "immunology/innate", "immunity", "virology", "infectious", "diseases/viral", "infections", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "incl...	2011	Respiratory Syncytial Virus Interferon Antagonist NS1 Protein Suppresses and Skews the Human T Lymphocyte Response
Bordetella adenylate cyclase toxin-hemolysin ( CyaA ) penetrates the cytoplasmic membrane of phagocytes and employs two distinct conformers to exert its multiple activities . One conformer forms cation-selective pores that permeabilize phagocyte membrane for efflux of cytosolic potassium . The other conformer conducts ...	The adenylate cyclase toxin ( CyaA ) of pathogenic Bordetellae eliminates the first line of host innate immune defense by inhibiting the oxidative burst and complement-mediated opsonophagocytic killing of bacteria . The toxin penetrates myeloid phagocytes , such as neutrophil , macrophage or dendritic cells , and subve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "cell", "biology", "proteins", "biology", "microbiology", "bacterial", "pathogens", "toxicology" ]	2012	Calcium Influx Rescues Adenylate Cyclase-Hemolysin from Rapid Cell Membrane Removal and Enables Phagocyte Permeabilization by Toxin Pores
The network of native non-covalent residue contacts determines the three-dimensional structure of a protein . However , not all contacts are of equal structural significance , and little knowledge exists about a minimal , yet sufficient , subset required to define the global features of a protein . Characterisation of ...	A protein structure can be visualized as a network of non-covalent contacts existing between amino acids . But not all such contacts are important structural determinants of a protein . We have attempted to identify a subset of amino acid contacts that are essential for reconstructing protein structures . Initially , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/protein", "structure", "prediction", "computational", "biology/macromolecular", "structure", "analysis", "computational", "biology/protein", "homology", "detection", "computational", "biology" ]	2009	Defining an Essence of Structure Determining Residue Contacts in Proteins
Several brain diseases are characterized by abnormally strong neuronal synchrony . Coordinated Reset ( CR ) stimulation was computationally designed to specifically counteract abnormal neuronal synchronization processes by desynchronization . In the presence of spike-timing-dependent plasticity ( STDP ) this may lead t...	Abnormally strong neuronal synchronization is found in a number of brain disorders . To specifically counteract abnormal neuronal synchrony and , hence , related symptoms , Coordinated Reset ( CR ) stimulation was developed . CR stimulation employs basic plasticity and dynamic self-organization principles of the nervou...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "neurodegenerative", "diseases", "membrane", "potential", "signaling", "networks", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "synaptic",...	2018	How stimulation frequency and intensity impact on the long-lasting effects of coordinated reset stimulation
The yeast prion [SWI+] , formed of heritable amyloid aggregates of the Swi1 protein , results in a partial loss of function of the SWI/SNF chromatin-remodeling complex , required for the regulation of a diverse set of genes . Our genetic analysis revealed that [SWI+] propagation is highly dependent upon the action of m...	Yeast prions are heritable genetic elements , formed spontaneously by aggregation of a single protein . Prions can thus generate diverse phenotypes in a dominant , non-Mendelian fashion , without a corresponding change in chromosomal gene structure . Since the phenotypes caused by the presence of a prion are thought to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "microbiology/microbial", "growth", "and", "development", "genetics", "and", "genomics/gene", "function" ]	2011	[SWI+], the Prion Formed by the Chromatin Remodeling Factor Swi1, Is Highly Sensitive to Alterations in Hsp70 Chaperone System Activity
Despite their importance in maintaining the integrity of all cellular pathways , the role of mutations on protein-protein interaction ( PPI ) interfaces as cancer drivers has not been systematically studied . Here we analyzed the mutation patterns of the PPI interfaces from 10 , 028 proteins in a pan-cancer cohort of 5...	Until now , most efforts in cancer genomics have focused on identifying genes and pathways driving tumor development . Although this has been unquestionably a success , as evidenced by the fact that we now have an extensive catalogue of cancer driver genes and pathways , there is still a poor understanding of why patie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
Interest in larval source management ( LSM ) as an adjunct intervention to control and eliminate malaria transmission has recently increased mainly because long-lasting insecticidal nets ( LLINs ) and indoor residual spray ( IRS ) are ineffective against exophagic and exophilic mosquitoes . In Amazonian Peru , the iden...	The most efficient malaria vector in the Latin American region is Nyssorhynchus darlingi ( formerly Anopheles darlingi ) . In Amazonian Peru , where malaria is endemic , Ny . darlingi feeds both indoors and outdoors ( endophagy , exophagy ) , depending on the local environment , and rests outdoors ( exophily ) . LLINs ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "surface", "water", "rivers", "engineering", "and", "technology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "cameras", ...	2019	High-accuracy detection of malaria vector larval habitats using drone-based multispectral imagery
Myriapods ( e . g . , centipedes and millipedes ) display a simple homonomous body plan relative to other arthropods . All members of the class are terrestrial , but they attained terrestriality independently of insects . Myriapoda is the only arthropod class not represented by a sequenced genome . We present an analys...	Arthropods are the most abundant animals on earth . Among them , insects clearly dominate on land , whereas crustaceans hold the title for the most diverse invertebrates in the oceans . Much is known about the biology of these groups , not least because of genomic studies of the fruit fly Drosophila , the water flea Da...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "genome", "sequencing", "organismal", "evolution", "genome", "complexity", "genomics", "genome", "evolution", "molecular", "biology", "animal", "evolution", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular...	2014	The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
Killed , oral cholera vaccines have proven safe and effective , and several large-scale mass cholera vaccination efforts have demonstrated the feasibility of widespread deployment . This study uses a mathematical model of cholera transmission in Bangladesh to examine the effectiveness of potential vaccination strategie...	Bangladesh has a high burden of cholera and may become the first country to use cholera vaccine on a large scale . Mass cholera vaccination may be hard to justify to international funding agencies because of the modest efficacy of existing vaccines and their limited duration of protection . However , mass cholera vacci...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "vaccines", "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "cholera", "cholera", "vaccines", "population", "modeling", "neglected", "tropical", "diseases", "immunology", "biology", "and", "life", "sciences", "infectious", "di...	2014	Comparative Effectiveness of Different Strategies of Oral Cholera Vaccination in Bangladesh: A Modeling Study
C . elegans undergoes periods of behavioral quiescence during larval molts ( termed lethargus ) and as adults . Little is known about the circuit mechanisms that establish these quiescent states . Lethargus and adult locomotion quiescence is dramatically reduced in mutants lacking the neuropeptide receptor NPR-1 . Here...	Animals switch between periods of behavioral arousal and quiescence in response to environmental , developmental , and circadian cues . Little is known about the circuit mechanisms that produce these behavioral states . During larval molts , C . elegans exhibits a sleep-like state ( termed lethargus ) that is character...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Sensory Neurons Arouse C. elegans Locomotion via Both Glutamate and Neuropeptide Release
Human African Trypanosomiasis is a vector-borne disease of sub-Saharan Africa that causes significant morbidity and mortality . Current therapies have many drawbacks , and there is an urgent need for new , better medicines . Ideally such new treatments should be fast-acting cidal agents that cure the disease in as few ...	Trypanosoma brucei is a protozoan parasite causing African sleeping sickness . Current treatments for this disease have significant limitations , underlining the need for better and safer drugs . To identify new chemical starting points for drug development , large compound collections are screened against the parasite...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "infectious", "diseases", "african", "trypanosomiasis", "parasitology", "neglected", "tropical", "diseases", "biology", "microbiology", "drug", "discovery" ]	2012	A Static-Cidal Assay for Trypanosoma brucei to Aid Hit Prioritisation for Progression into Drug Discovery Programmes
Dosage compensation has been thought to be a ubiquitous property of sex chromosomes that are represented differently in males and females . The expression of most X-borne genes is equalized between XX females and XY males in therian mammals ( marsupials and “placentals” ) by inactivating one X chromosome in female soma...	Dosage compensation equalizes the expression of genes found on sex chromosomes so that they are equally expressed in females and males . In placental and marsupial mammals , this is accomplished by silencing one of the two X chromosomes in female cells . In birds , dosage compensation seems not to be strictly required ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/epigenetics" ]	2008	The Status of Dosage Compensation in the Multiple X Chromosomes of the Platypus
Decoding models , such as those underlying multivariate classification algorithms , have been increasingly used to infer cognitive or clinical brain states from measures of brain activity obtained by functional magnetic resonance imaging ( fMRI ) . The practicality of current classifiers , however , is restricted by tw...	Neurological and psychiatric spectrum disorders are typically defined in terms of particular symptom sets , despite increasing evidence that the same symptom may be caused by very different pathologies . Pathophysiological classification and effective treatment of such disorders will increasingly require a mechanistic ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "computer", "science", "computer", "modeling", "mathematics", "neurological", "disorders", "statistics", "neurology", "statistical", "methods", "neuroimaging" ]	2011	Generative Embedding for Model-Based Classification of fMRI Data
Protein aggregation , arising from the failure of the cell to regulate the synthesis or degradation of aggregation-prone proteins , underlies many neurodegenerative disorders . However , the balance between the synthesis , clearance , and assembly of misfolded proteins into neurotoxic aggregates remains poorly understo...	Alzheimer's disease is thought to be a result of neuronal damage caused by toxic aggregated forms of the Aβ peptide in the brain . There is no cure and existing treatments are ineffective in reversing or preventing disease progression . Here we describe a novel strategy that makes use of an engineered “Affibody” protei...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology/protein", "chemistry", "and", "proteomics", "biochemistry/protein", "folding", "biochemistry/protein", "chemistry", "biotechnology/protein", "chemistry", "and", "proteomics" ]	2010	Sequestration of the Aβ Peptide Prevents Toxicity and Promotes Degradation In Vivo
Whole-chromosome imbalances affect over half of early human embryos and are the leading cause of pregnancy loss . While these errors frequently arise in oocyte meiosis , many such whole-chromosome abnormalities affecting cleavage-stage embryos are the result of chromosome missegregation occurring during the initial mit...	By day 3 of development , more than half of human embryos contain at least one cell that deviates from the typical 46-chromosome complement . These whole-chromosome abnormalities include polyploidies , which affect the entire chromosome set , as well as aneuploidies , which involve gains and losses of particular chromo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evidence of Selection against Complex Mitotic-Origin Aneuploidy during Preimplantation Development
Schistosomiasis japonica is a zoonotic parasitic disease . After nearly 70 years of control efforts in China , Schistosomiasis transmission has been reduced to a much lower level . The absence or near absence of infections in humans or livestock , based on traditional fecal and serological tests , has made the targets ...	With the continued activities of the prevention and control programme in China , the prevalence and intensity of Schistosoma japonicum infection have been reduced to low levels . This makes it impossible to detect any infections in humans or livestock using the traditional approach of fecal and serological testing , so...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "livestock", "medicine", "and", "health", "sciences", "helminths", "china", "statistics", "metaanalysis", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "gastropods", "mathematics", "neglected", "trop...	2019	A meta-analysis of infection rates of Schistosoma japonicum in sentinel mice associated with infectious waters in mainland China over last 40 years
Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks . Evolutionary innovations and adaptations often require rapid changes of such networks . It has long been hypothesized that transposable elements ( TE ) might contribute to the rewiring of regulat...	Evolutionary innovations and adaptations often require rapid changes in gene regulation . Transposable elements constitute the most dynamic part of eukaryotic genomes . Insertions of transposable elements can influence the expression of surrounding genes by donating new regulatory elements . A longstanding hypothesis p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2010	Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements
Synthetic biology efforts have largely focused on small engineered gene networks , yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge . Here we present the design , system integration , and analysis of several large scale synthetic gene circuits...	Over the last decade several relatively small synthetic gene networks have been successfully implemented and characterized , including oscillators , toggle switches , and intercellular communication systems . However , the ability to engineer large-scale synthetic gene networks for controlling multicellular systems wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "synthetic", "biology", "biology", "computational", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
Consecutive repetition of actions is common in behavioral sequences . Although integration of sensory feedback with internal motor programs is important for sequence generation , if and how feedback contributes to repetitive actions is poorly understood . Here we study how auditory feedback contributes to generating re...	Repetitions are common in animal vocalizations . Songs of many songbirds contain syllables that repeat a variable number of times , with non-Markovian distributions of repeat counts . The neural mechanism underlying such syllable repetitions is unknown . In this work , we show that auditory feedback plays an important ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition
The notion of attractor networks is the leading hypothesis for how associative memories are stored and recalled . A defining anatomical feature of such networks is excitatory recurrent connections . These “attract” the firing pattern of the network to a stored pattern , even when the external input is incomplete ( patt...	A type of neural network called an “attractor network” is thought to underlie memory associations . Importantly , when such a network is presented with part of a memory , the network activity is attracted to the complete memory . However , it has been difficult to obtain clear experimental evidence for such attractor n...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "neural", "networks", "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "learning", "and", "memory" ]	2014	A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus
Ankylosing spondylitis ( AS ) is a highly heritable immune-mediated arthritis common in Turkish and Iranian populations . Familial Mediterranean Fever ( FMF ) is an autosomal recessive autoinflammatory disease most common in people of Mediterranean origin . MEFV , an FMF-associated gene , is also a candidate gene for A...	Ankylosing spondylitis ( AS ) is a highly heritable immune-mediated arthritis . To identify new genetic associations with AS , we performed genome-wide association studies in Turkish and Iranian AS patients and controls . We identified a novel rare coding MEFV variant associated with AS . Rare polymorphisms of MEFV , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "statistics", "immunology", "variant", "genotypes", "alleles", "genetic", "mapping", "multivariate", "analysis", "clinical", "medicine", "linkage", "disequilibrium", "mathematics", "genome", ...	2019	Genome-wide association study in Turkish and Iranian populations identify rare familial Mediterranean fever gene (MEFV) polymorphisms associated with ankylosing spondylitis
A goal of many sensorimotor studies is to quantify the stimulus-behavioral response relation for specific organisms and specific sensory stimuli . This is especially important to do in the context of painful stimuli since most animals in these studies cannot easily communicate to us their perceived levels of such noxio...	A doctor assesses pain by asking her patient to “rate your pain on the scale of 1 to 10 . ” She may then prescribe some drugs and later ask the question again to see if they worked . New drugs are often developed using animal models , but we cannot ask an animal , especially a small invertebrate animal , to rate , simi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "velocity", "invertebrates", "somatosensory", "system", "medicine", "and", "health", "sciences", "classical", "mechanics", "engineering", "and", "technology", "caenorhabditis", "nociception", "lasers", "social", "sciences", "random", "variables", "neuroscience", "animals", ...	2016	Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level
The neurosteroid dehydroepiandrosterone ( DHEA ) , produced by neurons and glia , affects multiple processes in the brain , including neuronal survival and neurogenesis during development and in aging . We provide evidence that DHEA interacts with pro-survival TrkA and pro-death p75NTR membrane receptors of neurotrophi...	Dehydroepiandrosterone ( DHEA ) and its sulphate ester are the most abundant steroid hormones in humans , and DHEA was described as the first neurosteroid produced in the brain . DHEA is known to participate in multiple events in the brain , including neuronal survival and neurogenesis . However , to date no specific c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cell", "death", "molecular", "neuroscience", "neuroscience", "membrane", "receptor", "signaling", "signaling", "pathways", "signaling", "in", "cellular", "processes", "endocrinology", "diabetes", "and", "endocrinology", "biology", "neuroendocrinology", "molecul...	2011	Neurosteroid Dehydroepiandrosterone Interacts with Nerve Growth Factor (NGF) Receptors, Preventing Neuronal Apoptosis
Conserved noncoding elements ( CNCs ) are an abundant feature of vertebrate genomes . Some CNCs have been shown to act as cis-regulatory modules , but the function of most CNCs remains unclear . To study the evolution of CNCs , we have developed a statistical method called the “shared rates test” to identify CNCs that ...	Conservation of DNA sequences across evolutionary history is a highly informative signal for identifying regions with important biological functions . In particular , conserved noncoding regions have been shown to be good candidates for containing regulatory elements that have roles in gene regulation . Recent studies ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "genetics", "and", "genomics", "mammals", "computational", "biology" ]	2007	Adaptive Evolution of Conserved Noncoding Elements in Mammals
We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera . Applying comprehensive forward and reverse geneti...	More than 1 , 000 microbial genomes have been sequenced to date , containing millions of predicted genes . While the broad functional category of many of these individual genes can be reliably predicted using sequence homology , sequence information alone is often insufficient to assign a gene a specific cellular funct...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "microbiology/environmental", "microbiology", "biochemistry/biocatalysis", "physiology/sensory", "systems", "physiology/genomics", "cell", "biology/cell", "growth", "and", "division", "microbiology/microbial", "evolution", "and", "genomics", "molecular", "biology", "molecular", "...	2008	Genetic and Computational Identification of a Conserved Bacterial Metabolic Module
The nature of toxic effects exerted on neurons by misfolded proteins , occurring in a number of neurodegenerative diseases , is poorly understood . One approach to this problem is to measure effects when such proteins are expressed in heterologous neurons . We report on effects of an ALS-associated , misfolding-prone m...	A new animal model of the human neurodegenerative disease amyotrophic lateral sclerosis ( ALS; Lou Gehrig's Disease ) is presented . Two percent of ALS cases result from heritable mutations affecting the abundant enzyme superoxide dismutase ( SOD1 ) . Such mutations have been indicated to impair the folding and stabili...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "biochemistry", "cell", "biology", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "function", "genetics", "and",...	2009	An ALS-Linked Mutant SOD1 Produces a Locomotor Defect Associated with Aggregation and Synaptic Dysfunction When Expressed in Neurons of Caenorhabditis elegans
The rate of mutation is central to evolution . Mutations are required for adaptation , yet most mutations with phenotypic effects are deleterious . As a consequence , the mutation rate that maximizes adaptation will be some intermediate value . Here , we used digital organisms to investigate the ability of natural sele...	Natural selection is shortsighted and therefore does not necessarily drive populations toward improved long-term performance . Some traits may evolve because they provide immediate gains , even though they are less successful in the long run than some alternatives . Here , we use digital organisms to analyze the abilit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology" ]	2008	Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
The evolutionarily conserved nature of the few well-known anti-aging interventions that affect lifespan , such as caloric restriction , suggests that aging-related research in model organisms is directly relevant to human aging . Since human lifespan is a complex trait , a systems-level approach will contribute to a mo...	Aging leads to changes in the activity of genes , but these changes are much more subtle than those between health and disease . This makes finding the genes involved in aging difficult . We have combined two ways to improve information on the involvement of genes in aging . First , important gene activity tends to be ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "genetic", "networks", "skeletal", "muscles", "brain", "physiological", "processes", "developmental", "biology", "organism", "development", "network", "analysis", "genome", "analysis", "musc...	2019	Cross-species functional modules link proteostasis to human normal aging
Since 2001 , Haiti’s National Program for the Elimination of Lymphatic Filariasis ( NPELF ) has worked to reduce the transmission of lymphatic filariasis ( LF ) through annual mass drug administration ( MDA ) with diethylcarbamazine and albendazole . The NPELF reached full national coverage with MDA for LF in 2012 , an...	Lymphatic filariasis and malaria are mosquito-borne parasitic infections that are endemic in Haiti . Soil-transmitted helminths are also present in Haiti , infecting large numbers of people every year . Since 2001 , Haiti’s National Program for the Elimination of Lymphatic Filariasis ( NPELF ) has worked to reduce the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "children", "medicine", "and", "health", "sciences", "body", "fluids", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "parasitic", "protozoans", "north", "america", "age", "groups", "protozoa...	2017	Partnering for impact: Integrated transmission assessment surveys for lymphatic filariasis, soil transmitted helminths and malaria in Haiti
Despite dengue dynamics being driven by complex interactions between human hosts , mosquito vectors and viruses that are influenced by climate factors , an operational model that will enable health authorities to anticipate the outbreak risk in a dengue non-endemic area has not been developed . The objectives of this s...	With the continuously high levels of worldwide dengue transmission , predicting dengue outbreaks in advance of their occurrence or identifying specific locations where outbreak risks are highest is of critical importance . However , only few studies have been conducted in dengue non-endemic countries to evaluate the as...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Re-assess Vector Indices Threshold as an Early Warning Tool for Predicting Dengue Epidemic in a Dengue Non-endemic Country
Telomeres , the ends of linear eukaryotic chromosomes , have a specialized chromatin structure that provides a stable chromosomal terminus . In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomere length . Here we show that binding of multiple Rap1 proteins stimulates DNA double-str...	Telomere length is maintained primarily through equilibrium between telomerase-mediated lengthening and the loss of telomeric sequence through the end-replication problem . In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomerase recruitment in a dosage-dependent manner . In this p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Binding of Multiple Rap1 Proteins Stimulates Chromosome Breakage Induction during DNA Replication
The Toxin Complex ( TC ) is a large multi-subunit toxin encoded by a range of bacterial pathogens . The best-characterized examples are from the insect pathogens Photorhabdus , Xenorhabdus and Yersinia . They consist of three large protein subunits , designated A , B and C that assemble in a 5∶1∶1 stoichiometry . Oral ...	The Toxin Complex ( TC ) is a large multimeric protein complex first identified in the insect pathogens Photorhabdus and Xenorhabdus . TC isolates from these pathogens exhibit oral toxicity to a diverse range of insects . As such there is significant interest in developing them as candidates for crop protection strateg...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Role of TcdB and TccC Subunits in Secretion of the Photorhabdus Tcd Toxin Complex
Post-mortem brains from Down syndrome ( DS ) and Alzheimer's disease ( AD ) patients show an upregulation of the Down syndrome critical region 1 protein ( DSCR1 ) , but its contribution to AD is not known . To gain insights into the role of DSCR1 in AD , we explored the functional interaction between DSCR1 and the amyl...	Alzheimer's disease ( AD ) is a debilitating neurodegenerative disease characterized by gradual neuronal cell loss and memory decline . Importantly , Down syndrome ( DS ) individuals over 40 years of age almost always develop neuropathological features of AD , although most do not develop dementia until at least two de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Nebula/DSCR1 Upregulation Delays Neurodegeneration and Protects against APP-Induced Axonal Transport Defects by Restoring Calcineurin and GSK-3β Signaling
Root vacuolar sequestration is one of the best-conserved plant strategies to cope with heavy metal toxicity . Here we report that zinc ( Zn ) tolerance in Arabidopsis requires the action of a novel Major Facilitator Superfamily ( MFS ) transporter . We show that ZIF2 ( Zinc-Induced Facilitator 2 ) localises primarily a...	Alternative splicing , which generates multiple messenger RNAs ( mRNAs ) from the same gene , is a key posttranscriptional regulatory mechanism in higher eukaryotes whose functional relevance in plants remains poorly understood . The sequestration of metal ions inside the vacuole of root cells is an important strategy ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "science", "cell", "biology", "gene", "expression", "plant", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "plant", "genetics", "molecular", "cell", "biology", "plant", "physiology", "genetic", "engineering", "gene", ...	2014	Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis
Control of arbovirus transmission remains focused on vector control through application of insecticides directly to the environment . However , these insecticide applications are often reactive interventions that can be poorly-targeted , inadequate for localized control during outbreaks , and opposed due to environment...	West Nile virus ( WNV ) is a mosquito-borne virus that causes significant disease and death every year in humans , domesticated animals , and wildlife . Control of WNV transmission is focused on controlling the mosquito vector through applications of insecticides directly to the environment . In this study , we evaluat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "diet", "animals", "viruses", "nutritio...	2019	Evaluation of a novel West Nile virus transmission control strategy that targets Culex tarsalis with endectocide-containing blood meals
Antimicrobial resistance ( AMR ) is currently one of the most important challenges to the treatment of bacterial infections . A critical issue to combat AMR is to restrict its spread . In several instances , bacterial plasmids are involved in the global spread of AMR . Plasmids belonging to the incompatibility group ( ...	Dissemination of antimicrobial resistance ( AMR ) among different bacterial populations occurs due to mainly the presence of plasmids that encode AMR determinants . IncHI plasmids are one of the groups of bacterial plasmids that confer AMR to several enterobacteria . Recently , resistance to one of the last-resort anti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "plasmids", "immunology", "microbiology", "plasmid", "construction", "bacterial", "diseases", "antibiotic", "resistance", "enterobacter...	2019	Expression of a novel class of bacterial Ig-like proteins is required for IncHI plasmid conjugation
It is widely accepted for humans and higher animals that vision is an active process in which the organism interprets the stimulus . To find out whether this also holds for lower animals , we designed an ambiguous motion stimulus , which serves as something like a multi-stable perception paradigm in Drosophila behavior...	Vision is considered an active process in humans and higher animals in which the stimulus is interpreted by the subject and can be perceived in different ways if it is ambiguous . We aimed to find out whether this also holds for lower animals , such as the fruit fly Drosophila melanogaster . To provide ambiguity , we e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "velocity", "invertebrates", "classical", "mechanics", "social", "sciences", "neuroscience", "animals", "animal", "models", "perception", "drosophila", "melanogaster", "model", "organisms", "cognitive", "psychology", "experimental", "organism", "systems", "vision", "drosoph...	2018	Multi-stability with ambiguous visual stimuli in Drosophila orientation behavior
Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract . In the Drosophila midgut , Upd3 is a major cytokine , which is induced in enterocytes ( EC ) and enteroblasts ( EB ) upon oral infection , and initiates intestinal stem cell ( ISC ) depende...	Tissue regeneration is a fundamental process that maintains the integrity of the intestinal epithelium when faced with chemical or microbial stresses . In both healthy and diseased conditions , pro-regenerative cytokines function as central coordinators of gut renewal , linking inflammation to stem cell activity . In D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "rna", "interference", "immune", "physiology", "cytokines", "gene", "regulation", "immunology", "cell", "processes", "animals", "animal", "models", "developmental", ...	2017	Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection
X chromosome inactivation in female mammals results in dosage compensation of X-linked gene products between the sexes . In humans there is evidence that a substantial proportion of genes escape from silencing . We have carried out a large-scale analysis of gene expression in lymphoblastoid cell lines from four human p...	The males and females of many species are distinguished by their inheritance of different sets of sex chromosomes . This creates a significant imbalance in gene number between the sexes . Dosage compensation is the correction for this imbalance and is achieved by regulating gene activity across entire sex chromosomes ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2008	Large-Scale Population Study of Human Cell Lines Indicates that Dosage Compensation Is Virtually Complete
Visceral leishmaniasis ( VL ) is a neglected tropical disease and is fatal if untreated . There is no vaccine available against leishmaniasis . The majority of patients with cutaneous leishmaniasis ( CL ) or VL develop a long-term protective immunity after cure from infection , which indicates that development of an ef...	Leishmaniasis is a disease with a wide spectrum of clinical manifestations caused by different species of protozoa belonging to the Leishmania genus that are transmitted by sand fly vectors . Visceral infections of Leishmania cause significant mortality and morbidity and development of a vaccine to prevent leishmaniasi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Intradermal Immunization of Leishmania donovani Centrin Knock-Out Parasites in Combination with Salivary Protein LJM19 from Sand Fly Vector Induces a Durable Protective Immune Response in Hamsters
Intervertebral disc metabolic transport is essential to the functional spine and provides the cells with the nutrients necessary to tissue maintenance . Disc degenerative changes alter the tissue mechanics , but interactions between mechanical loading and disc transport are still an open issue . A poromechanical finite...	Low back pain is a very common pathology in industrialized countries , often due to bad posture . It is also highly related to intervertebral disc aging . Aging of the disc is a normal process characterized by series of changes in its structure and function . The events that convert normal aging into degenerative disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "bioengineering", "biomedical", "engineering", "engineering" ]	2011	The Effect of Sustained Compression on Oxygen Metabolic Transport in the Intervertebral Disc Decreases with Degenerative Changes
The evolution of sterile worker castes in eusocial insects was a major problem in evolutionary theory until Hamilton developed a method called inclusive fitness . He used it to show that sterile castes could evolve via kin selection , in which a gene for altruistic sterility is favored when the altruism sufficiently be...	The evolution of sterile worker castes in social insects has fascinated biologists ever since Darwin; how can selection favor a trait that decreases reproductive fitness ? W . D . Hamilton solved this dilemma in the 1960s with a theory showing that reproductive altruism could evolve if it increased the worker’s inclusi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Relatedness, Conflict, and the Evolution of Eusociality
microRNAs ( miRNAs ) are important post-transcriptional regulators , but the extent of this regulation is uncertain , both with regard to the number of miRNA genes and their targets . Using an algorithm based on intragenomic matching of potential miRNAs and their targets coupled with support vector machine classificati...	microRNAs ( miRNAs ) are small RNA molecules that regulate gene expression by complementary basepairing to mRNAs . In plants , this base-pairing is almost perfect along the whole length of miRNAs . This long stretch of complementarity makes it relatively easy to make computational predictions of the targets for known m...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "populus", "oryza", "plant", "biology", "arabidopsis", "computational", "biology" ]	2007	Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants
Protein interactions play a vital part in the function of a cell . As experimental techniques for detection and validation of protein interactions are time consuming , there is a need for computational methods for this task . Protein interactions appear to form a network with a relatively high degree of local clusterin...	For understanding the complex activities within an organism , a complete and error-free network of protein interactions which occur in the organism would be a significant step forward . The large amount of experimentally derived data now available has provided us with a chance to study the complicated behaviour of prot...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/systems", "biology", "computational", "biology" ]	2008	Predicting and Validating Protein Interactions Using Network Structure
Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection . To date , the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication . To investigate positive selection on ...	Identification of the genomic regions under selection during dog domestication is extremely challenging because the demographic fluctuations associated with domestication can produce signals in polymorphism data that mimic those imposed by selective sweeps . We perform the first analysis of selection on the dog lineage...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "types", "demography", "domestic", "animals", "population", "genetics", "wolves", "vertebrates", "pets", "and", "companion", "animals", "dogs", "mammals", "animals", "mammalian", "genomics", "population", "biology", "zoology", "animal", "genomics", "people", ...	2016	Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs
The frequency of the most common sporadic Apert syndrome mutation ( C755G ) in the human fibroblast growth factor receptor 2 gene ( FGFR2 ) is 100–1 , 000 times higher than expected from average nucleotide substitution rates based on evolutionary studies and the incidence of human genetic diseases . To determine if thi...	Some human disease mutations occur 100–1 , 000 times more frequently than would be predicted from genome wide studies of mutation in different species . In Apert syndrome , for example , two-thirds of all new causal mutations occur at only one base in the affected gene . This unusually high frequency suggests that some...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "homo", "(human)", "computational", "biology", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	The Molecular Anatomy of Spontaneous Germline Mutations in Human Testes
Diarrheal disease remains among the leading causes of global mortality in children younger than 5 years . Exposure to domestic animals may be a risk factor for diarrheal disease . The objectives of this study were to identify animal-related exposures associated with cases of moderate-to-severe diarrhea ( MSD ) in child...	Diarrheal disease is one of the leading causes of death worldwide in children younger than 5 years . Exposure to animals in homes may be a risk factor for diarrhea in children . To test this , we studied a subset of children in the Global Enteric Multicenter Study ( GEMS ) in rural western Kenya , whose caretakers repo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "livestock", "medicine", "and", "health", "sciences", "zoonotic", "pathogens", "animal", "pathogens", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "domestic", "animals", "vertebrates", "animals", "mammals", "diarrhea", "sign...	2017	Animal-related factors associated with moderate-to-severe diarrhea in children younger than five years in western Kenya: A matched case-control study
The stress-induced mutagenesis hypothesis postulates that in response to stress , bacteria increase their genome-wide mutation rate , in turn increasing the chances that a descendant is able to better withstand the stress . This has implications for antibiotic treatment: exposure to subinhibitory doses of antibiotics h...	The effect of environmental stress on bacterial mutagenesis has been a paradigm-shift discovery . Recent developments include evidence that various antibiotics increase mutation rates in bacteria when used at subinhibitory concentrations . It is therefore suggested that such treatments promote resistance evolution beca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "death", "rates", "antimicrobials", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "population", "dynamics", "drugs", "population", "genetics", "cell", "processes", "microbiology", "cell", "cycle", "and", "cell", "division", "a...	2018	Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
The highly pathogenic avian influenza ( HPAI ) H5N1 influenza virus has been a public health concern for more than a decade because of its frequent zoonoses and the high case fatality rate associated with human infections . Severe disease following H5N1 influenza infection is often associated with dysregulated host inn...	Some avian influenza viruses , including highly pathogenic H5N1 virus , cause severe disease in humans and in experimental animal models associated with excessive cytokine production . We aimed to understand the virological mechanism behind the cytokine storm , and particularly the contribution of internal gene segment...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "epithelial", "cells", "viruses", "bone", "marrow", "...	2018	Internal genes of a highly pathogenic H5N1 influenza virus determine high viral replication in myeloid cells and severe outcome of infection in mice
Persistent non-participation of children in mass drug administration ( MDAs ) for trachoma may reduce program impact . Risk factors that identify families where participation is a problem or program characteristics that foster non-participation are poorly understood . We examined risk factors for households with at lea...	The World Health Organization advocates at least three mass drug administrations ( MDAs ) with antibiotics when the prevalence of follicular trachoma ( TF ) is greater than 10% in children under age ten . Full child participation is necessary for maximizing the impact of trachoma control programs . The present paper id...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "ophthalmology", "neglected", "tropical", "diseases", "public", "health" ]	2012	Azithromycin Mass Treatment for Trachoma Control: Risk Factors for Non-Participation of Children in Two Treatment Rounds
Nipah virus ( NiV ) is a member of the genus Henipavirus ( family Paramyxoviridae ) that causes severe and often lethal respiratory illness and encephalitis in humans with high mortality rates ( up to 92% ) . NiV can cause Acute Lung Injury ( ALI ) in humans , and human-to-human transmission has been observed in recent...	Nipah virus ( NiV ) is a highly pathogenic zoonotic virus that causes fatal disease in humans and a variety of other mammalian hosts including pigs . Given the lack of effective therapeutics and vaccines , this virus is considered a public health and agricultural concern , and listed as category C priority pathogen for...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "infectious", "diseases", "veterinary", "diseases", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "veterinary", "virology...	2014	A Human Lung Xenograft Mouse Model of Nipah Virus Infection
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture , in which all cells have equal access to nutrients . In the real world , bacteria are more likely to live in physically structured habitats as colonies , within which individual cells vary ...	The vast majority of theoretical and experimental studies assume that bacteria exist as planktonic cells in well-mixed liquid cultures , all with equal access to nutrients , wastes , toxins , antibiotics , bacterial viruses , and each other . However , in the real world , bacteria are more often found in physically str...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "death", "rates", "classical", "mechanics", "chemical", "compounds", "fluid", "mechanics", "demography", "microbiology", "carbohydrates", "geometry", "organic", "compounds", "glucose", "mathematical", "models", "developmental", "biology", "mathematics", "statistics", "(math...	2017	Growth of bacteria in 3-d colonies
Holoprosencephaly ( HPE ) is a severe human genetic disease affecting craniofacial development , with an incidence of up to 1/250 human conceptions and 1 . 3 per 10 , 000 live births . Mutations in the Sonic Hedgehog ( SHH ) gene result in HPE in humans and mice , and the Shh pathway is targeted by other mutations that...	Holoprosencephaly ( HPE ) is a devastating genetic disease affecting human brain development . HPE affects more than 1/8 , 000 live births and up to 1/250 conceptions . Several genetic loci are associated with HPE , and the mutated genes have been identified at some . We have analyzed the role of the TGIF1 gene , which...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "developmental", "biology", "model", "organisms", "molecular", "development", "genetics", "biology", "human", "genetics", "morphogenesis", "genetics", "and", "genomics", "clinical", "genetics" ]	2012	Loss of Tgif Function Causes Holoprosencephaly by Disrupting the Shh Signaling Pathway
Coregulator proteins ( CoRegs ) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression . In this study we analyzed data from 3 , 290 immuno-precipitations ( IP ) followed by mass spectrometry ( MS ) applied to human cell lines aimed a...	In response to various extracellular stimuli , protein complexes are transiently assembled within the nucleus of cells to regulate gene transcription in a context dependent manner . Here we analyzed data from 3 , 290 proteomics experiments that used as bait different member proteins from regulatory complexes with diffe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "spectrometric", "identification", "of", "proteins", "biochemistry", "mathematics", "protein", "interactions", "protein", "abundance", "statistics", "regulatory", "networks", "biology", "computational", "biology", "signaling", "networks", "proteomics", ...	2011	Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes
In an inflammatory setting , macrophages can be polarized to an inflammatory M1 phenotype or to an anti-inflammatory M2 phenotype , as well as existing on a spectrum between these two extremes . Dysfunction of this phenotypic switch can result in a population imbalance that leads to chronic wounds or disease due to unr...	Using experimental data and mathematical analysis , we develop a model for the inflammatory response that includes macrophage polarization between M1 and M2 phenotypes . Dysfunction of this phenotypic switch can disrupt the timely influx and egress of immune cells during the healing process and lead to chronic wounds o...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "inflammatory", "diseases", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "cell", "processes", "signs", "and", "symptoms", "neutrophils", "white", "blood", "...	2019	Identifying important parameters in the inflammatory process with a mathematical model of immune cell influx and macrophage polarization
A recently published transcriptional oscillator associated with the yeast cell cycle provides clues and raises questions about the mechanisms underlying autonomous cyclic processes in cells . Unlike other biological and synthetic oscillatory networks in the literature , this one does not seem to rely on a constitutive ...	Technologies such as gene arrays enable acquisition of large amounts of data on gene expression variations , which reveal the structures of gene regulatory networks that govern the metabolic and developmental machinery in the cell . We study a model of an oscillatory gene regulatory network that has been recently sugge...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "physics/interdisciplinary", "physics", "computational", "biology/transcriptional", "regulation" ]	2010	Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator
T-cell proliferation and generation of protective memory during chronic infections depend on Interleukin-7 ( IL-7 ) availability and receptivity . Regulation of IL-7 receptor ( IL-7R ) expression and signalling are key for IL-7-modulated T-cell functions . Aberrant expression of soluble ( s ) and membrane-associated ( ...	IL-7 is important for the development and homeostasis of T cells and promotes antigen-specific T-cell responses . Aberrant expression of plasma IL-7 and soluble IL-7R are found in autoimmune diseases and chronic viral infections . In AIDS patients—especially those who fail to reconstitute T-cell numbers during therapy—...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "phosphorylation", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "cloning", "bacterial", "diseases", "developmental...	2017	Aberrant plasma IL-7 and soluble IL-7 receptor levels indicate impaired T-cell response to IL-7 in human tuberculosis
Uropathogenic Escherichia coli ( UPEC ) is a leading etiological agent of bacteremia in humans . Virulence mechanisms of UPEC in the context of urinary tract infections have been subjected to extensive research . However , understanding of the fitness mechanisms used by UPEC during bacteremia and systemic infection is ...	Uropathogenic E . coli is a major cause of bacterial bloodstream infections in humans . Dissemination of E . coli into the bloodstream during urinary tract infections may lead to potentially fatal complications . This pathogen is becoming increasingly resistant to currently used antibiotics . To develop additional tool...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic Infection
Meiotic recombination normally takes place between allelic sequences on homologs . This process can also occur between non-allelic homologous sequences . Such ectopic interaction events can lead to chromosome rearrangements and are normally avoided . However , much remains unknown about how these ectopic interaction ev...	Meiosis is a special type of cell division that generates gametes for sexual reproduction . During meiosis , recombination not only occurs between allelic sequences on homologs , but also between non-allelic homologous sequences at dispersed loci . Such ectopic recombination is the main cause of chromosomal alterations...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	OsHUS1 Facilitates Accurate Meiotic Recombination in Rice
CD8+ T cells play a key role in the in vivo control of HIV-1 replication via their cytolytic activity as well as their ability to secrete non-lytic soluble suppressive factors . Although the chemokines that naturally bind CCR5 ( CCL3/MIP-1α , CCL4/MIP- 1β , CCL5/RANTES ) are major components of the CD8-derived anti-HIV...	Although HIV , the causative agent of AIDS , establishes a lifelong infection that cannot be eradicated even with effective treatment , the host immune system has the ability to contain its replication for many years in which the disease remains asymptomatic . Key players in HIV control are CD8+ T cells , specialized i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The CD8-Derived Chemokine XCL1/Lymphotactin Is a Conformation-Dependent, Broad-Spectrum Inhibitor of HIV-1
Dengue is one of the most serious mosquito-borne infectious diseases in the world . Aedes albopictus is the most invasive mosquito and one of the primary vectors of dengue . Vector control using insecticides is the only viable strategy to prevent dengue virus transmission . In Guangzhou , after the 2014 pandemic , mass...	Guangzhou is the most epidemic area of dengue in China . Massive insecticides have been used to control the vector mosquito Ae . albopictus , as no specific vaccines are available for dengue . Regular monitoring of insecticide susceptibility is essential for insecticide resistance management . In this study , the insec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "malathion", "animals", "organic", "compounds", "developmental", "biology", "organophosphates", "ddt", "mutation", "population", "biology", "insect", "vectors", "agrochemi...	2019	Fast emerging insecticide resistance in Aedes albopictus in Guangzhou, China: Alarm to the dengue epidemic
An ultimate goal of genetic research is to understand the connection between genotype and phenotype in order to improve the diagnosis and treatment of diseases . The quantitative genetics field has developed a suite of statistical methods to associate genetic loci with diseases and phenotypes , including quantitative t...	Many recent efforts to understand the genetic origins of complex diseases utilize statistical approaches to analyze phenotypic traits measured in genetically well-characterized populations . While these quantitative genetics methods are powerful , their success is limited by sampling biases and other confounding factor...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "function", "computational", "biology/genomics" ]	2010	Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations
GDNF signaling through the Ret receptor tyrosine kinase ( RTK ) is required for ureteric bud ( UB ) branching morphogenesis during kidney development in mice and humans . Furthermore , many other mutant genes that cause renal agenesis exert their effects via the GDNF/RET pathway . Therefore , RET signaling is believed ...	Kidney development requires the secreted protein GDNF , which signals via its cellular receptor RET to promote growth and branching of the ureteric bud , the progenitor of the collecting duct system . The transcription factors ETV4 and ETV5 regulate gene expression in response to GDNF . We report that deleting Spry1 , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "developmental", "biology", "developmental", "biology/morphogenesis", "and", "cell", "biology", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/gene", "function", "developmental", "biology/organo...	2010	Kidney Development in the Absence of Gdnf and Spry1 Requires Fgf10
The unfolded protein response ( UPR ) is a conserved mechanism that mitigates accumulation of unfolded proteins in the ER . The yeast UPR is subject to intricate post-transcriptional regulation , involving recruitment of the RNA encoding the Hac1 transcription factor to the ER and its unconventional splicing . To inves...	The unfolded protein response ( UPR ) , which allows eukaryotic cells to cope with stresses that impair their ability to properly fold and assemble their membrane and secreted proteins , is implicated in many human diseases such as diabetes , neurodegeneration , and cancer . In yeast , the HAC1 gene encodes a transcrip...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "mechanisms", "of", "signal", "transduction", "gene", "regulation", "rna", "stability", "gene", "function", "crosstalk", "biological", "transport", "molecular", "genetics", "stress", "signaling", "cascade", "gene", "expression", "biolo...	2012	The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA
Spatial arrangement of neurite branching is instructed by both attractive and repulsive cues . Here we show that in C . elegans , the Wnt family of secreted glycoproteins specify neurite branching sites in the PLM mechanosensory neurons . Wnts function through MIG-1/Frizzled and the planar cell polarity protein ( PCP )...	Extrinsic cues instruct neurite branching patterns through cytoskeletal remodeling at precise locations . We show that the Wnt glycoproteins signal through the Frizzled receptor and the Planar Cell Polarity ( PCP ) protein VANG-1 to instruct neurite branching in the nematode C . elegans , by restricting F-actin assembl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "nervous", "system", "cell", "processes", "electrophysiology", "neurites", "neuroscience", "animals", "animal", "models", "caenorhabditis", "elegans", "signal", "inhibition", "model", "organisms", ...	2017	A Wnt-planar polarity pathway instructs neurite branching by restricting F-actin assembly through endosomal signaling
The intestinal immune system must be able to respond to a wide variety of infectious organisms while maintaining tolerance to non-pathogenic microbes and food antigens . The Vitamin A metabolite all-trans-retinoic acid ( atRA ) has been implicated in the regulation of this balance , partially by regulating innate lymph...	Innate lymphoid cells ( ILCs ) are emerging as important regulators of immune responses at barrier sites such as the intestine . However , the molecular mechanisms that control this are not well described . In the intestine , the Vitamin A metabolite all-trans-retinoic acid ( atRA ) has been shown to be an important co...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cell-mediated", "immunity", "diet", "physiological", "processes", "bacterial", "diseases", "infectious", "disease", "immunology", "clinical", "medicine", "nutrition", "homeostasis...	2018	HIC1 links retinoic acid signalling to group 3 innate lymphoid cell-dependent regulation of intestinal immunity and homeostasis
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians , crustaceans , fish and insects , resulting in major losses in aquaculture and damage to aquatic ecosystems . We have sequenced the 63 Mb genome of the fresh water fish pathogen , Saprolegn...	Fish are an increasingly important source of animal protein globally , with aquaculture production rising dramatically over the past decade . Saprolegnia is a fungal-like oomycete and one of the most destructive fish pathogens , causing millions of dollars in losses to the aquaculture industry annually . Saprolegnia ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "sequencing", "genome", "expression", "analysis", "genome", "databases", "emerging", "infectious", "diseases", "microbial", "pathogens", "comparative", "genomics", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "parasitology", "pathogenesis" ...	2013	Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica
The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival . The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail , but lacking is knowledge of the pote...	Vision begins when an image is focused on the neural retina where rod and cone photoreceptors convert light into the electrical signals of the brain . The 4 cone subtypes in retinas of the majority of fishes , lizards and birds , provide rich color vision . In contrast , retinas of most mammals are better adapted for d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "ocular", "anatomy", "social", "sciences", "vertebrates", "neuroscience", "animals", "alleles", "cell", "differentiation", "animal", "models", "osteichthyes", "mi...	2016	Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish
Heme is a cofactor in proteins that function in almost all sub-cellular compartments and in many diverse biological processes . Heme is produced by a conserved biosynthetic pathway that is highly regulated to prevent the accumulation of heme—a cytotoxic , hydrophobic tetrapyrrole . Caenorhabditis elegans and related pa...	Heme is an iron-containing cofactor for proteins involved in many critical cellular processes . However , free heme is toxic to cells , suggesting that heme synthesis , acquisition , and transport is highly regulated . Efforts to understand heme trafficking in multicellular organisms have failed primarily due to the in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/neglected", "tropical", "diseases", "biochemistry/chemical", "biology", "of", "the", "cell", "cell", "biology/membranes", "and", "sorting", "infe...	2010	Genome-Wide Analysis Reveals Novel Genes Essential for Heme Homeostasis in Caenorhabditis elegans
Transcriptional/translational feedback loops drive daily cycles of expression in clock genes and clock-controlled genes , which ultimately underlie many of the overt circadian rhythms manifested by organisms . Moreover , phosphorylation of clock proteins plays crucial roles in the temporal regulation of clock protein a...	Circadian clocks are synchronized to local time by daily cycles in light-dark and temperature . Although light is generally thought to be the most dominant entraining cue in nature , daily cycles in temperature are sufficient to synchronize clocks in a large range of organisms . In Drosophila , dCLOCK is a master circa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biochemistry", "biology", "and", "life", "sciences", "chronobiology" ]	2014	Phosphorylation of a Central Clock Transcription Factor Is Required for Thermal but Not Photic Entrainment
Schistosomiasis is a major disease of the developing world for which no vaccine has been successfully commercialized . While numerous Schistosoma mansoni worm antigens have been identified that elicit antibody responses during natural infections , little is known as to the identities of the schistosome antigens that ar...	Schistosomiasis is caused by blood flukes residing in the veins of infected individuals and afflicts millions of people in the developing world . The schistosome worms can remain healthy in the bloodstream for more than 10 years , implying an extraordinary ability to evade host immune damage . Scientists are seeking to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "physiology", "helminths", "immunology", "animals", "antibodies", "extraction", "techniques", "research", "and", "analysis", "methods", "immune", "system", "protei...	2017	Schistosoma mansoni Infection of Mice, Rats and Humans Elicits a Strong Antibody Response to a Limited Number of Reduction-Sensitive Epitopes on Five Major Tegumental Membrane Proteins
The Gambia’s National Eye Health Programme has made a concerted effort to reduce the prevalence of trachoma . The present study had two objectives . The first was to conduct surveillance following mass drug administrations to determine whether The Gambia has reached the World Health Organization’s ( WHO ) criteria for ...	Trachoma , the world’s leading infectious cause of blindness , is caused by ocular infection with the bacterium Chlamydia trachomatis . The Gambia , situated in West Africa , has implemented all facets of the World Health Organization-recommended SAFE strategy for trachoma control including surgery to correct the in-tu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "census", "surgical", "and", "invasive", "medical", "procedures", "bacterial", "diseases", "research", "design", "eye", "diseases", "sexually", "transmitted", "diseases", "glob...	2016	Cross-Sectional Surveys of the Prevalence of Follicular Trachoma and Trichiasis in The Gambia: Has Elimination Been Reached?
The four Rep proteins of adeno-associated virus ( AAV ) orchestrate all aspects of its viral life cycle , including transcription regulation , DNA replication , virus assembly , and site-specific integration of the viral genome into the human chromosome 19 . All Rep proteins share a central SF3 superfamily helicase dom...	Viruses have to optimize the limited size of their genomes in order to generate the proteins required for infection and replication . Several mechanisms are used to accomplish this including the use of multiple promoters and alternative splicing . These processes generate gene products with diverse functions through th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "enzymes", "macromolecular", "assemblies", "viral", "enzymes", "microbiology", "viral", "preintegration", "complex", "proteins", "biology", "viral", "replication", "complex", "viral", "replication", "biophysics", "biochemistry", "vir...	2012	The Interdomain Linker of AAV-2 Rep68 Is an Integral Part of Its Oligomerization Domain: Role of a Conserved SF3 Helicase Residue in Oligomerization
Leptospirosis is an important zoonotic disease worldwide . Humans usually present a mild non-specific febrile illness , but a proportion of them develop more severe outcomes , such as multi-organ failure , lung hemorrhage and death . Such complications are thought to depend on several factors , including the host immun...	Leptospirosis is zoonotic disease of global importance , with over a million cases and nearly 60 , 000 deaths annually . Symptomatic disease presentation ranges from a mild febrile disease with non-specific symptoms to severe forms , characterized by multi-organ failure , lung hemorrhage , and death . Factors driving s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "leptospira", "pathology", "and", "laboratory", "medicine", "acute", "phase", "proteins", "pathogens", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "neglected", "tropical", ...	2017	Distinct antibody responses of patients with mild and severe leptospirosis determined by whole proteome microarray analysis
Studying aneuploidy during organism development has strong limitations because chronic mitotic perturbations used to generate aneuploidy usually result in lethality . We developed a genetic tool to induce aneuploidy in an acute and time-controlled manner during Drosophila development . This is achieved by reversible de...	Aneuploidy—the presence of an abnormal number of chromosomes in a cell—is a hallmark of cancer and developmental disorders . However , it is notoriously difficult to study in a living organism . We have thus developed a new genetic tool that allows for the inducible generation of aneuploidy in the fruit fly Drosophila ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "cellular", "stress", "responses", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "chromatids", "departures", "from", "diploidy", "animals", "animal", "models", "developmental", "biology", ...	2019	Induced aneuploidy in neural stem cells triggers a delayed stress response and impairs adult life span in flies
The determinants of transcriptional regulation in malaria parasites remain elusive . The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of pa...	Development of the malaria parasite , Plasmodium falciparum , in the blood is driven by a number of different genes expressed at different times and at different levels . Exactly what influences such transcriptional changes remains elusive , particularly in regard to important phenotypes like drug resistance . Using cD...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics" ]	2008	Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation
Autism spectrum disorders ( ASD ) are neurodevelopmental disorders with phenotypic and genetic heterogeneity . Recent studies have reported rare and de novo mutations in ASD , but the allelic architecture of ASD remains unclear . To assess the role of common and rare variations in ASD , we constructed a gene co-express...	Autism spectrum disorders ( ASD ) are neurodevelopmental syndromes with a strong genetic basis , but are influenced by many different genes . Recent studies have identified multiple genetic risk factors , including rare mutations and genetic variations common in the population . To identify possible connections between...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "medicine", "mental", "health", "genetics", "biology", "genomics", "neuroscience", "genetics", "and", "genomics" ]	2012	Networks of Neuronal Genes Affected by Common and Rare Variants in Autism Spectrum Disorders
The stabilization of the replisome complex is essential in order to achieve highly processive DNA replication and preserve genomic integrity . Conversely , it would also be advantageous for the cell to abrogate replisome functions to prevent inappropriate replication when fork progression is adversely perturbed . Howev...	Replication stress interferes with the normal progression of the replication fork . Under these conditions , cells activate the replication checkpoint to coordinate DNA repair with cell cycle arrest . The current understanding is that , in response to replication block , this checkpoint stabilizes replication forks and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "division", "dna", "replication", "nucleic", "acids", "cell", "biology", "genetics", "dna", "biology", "molecular", "cell", "biology", "dna", "repair", "molecular", "biology", "genetics", "and", "genomics" ]	2013	Coordinated Degradation of Replisome Components Ensures Genome Stability upon Replication Stress in the Absence of the Replication Fork Protection Complex
Arbovirus infections are a serious concern in tropical countries due to their high levels of transmission and morbidity . With the outbreaks of chikungunya ( CHIKV ) in surrounding regions in recent years and the fact that the environment in Vietnam is suitable for the vectors of CHIKV , the possibility of transmission...	In recent years , the reemergence of chikungunya has gained global attention and threatened to become a global outbreak . Although the epidemiology of chikungunya is known globally , the viral activity in Vietnam has not been thoroughly investigated . In this paper , we used information from a systematic review and ser...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "geographical", "locations", "microbiology", "tropical", "diseases", "alphaviruses", "viruses", "age", "groups", "chikungunya", "...	2018	Evidence of previous but not current transmission of chikungunya virus in southern and central Vietnam: Results from a systematic review and a seroprevalence study in four locations
Gene order is not random in eukaryotic chromosomes , and co-regulated genes tend to be clustered . The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional ( 3D ) organization are still unclear however . Here we have adapted a recently described meth...	Prokaryotic operons normally comprise functionally related genes whose expression is coordinated . Even though operons do not exist in most eukaryotes , results from the last fifteen years indicate that gene order is nonetheless not random in eukaryotes , and that coexpressed genes tend to be grouped in the genome . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "breast", "tumors", "reproductive", "system", "cancers", "and", "neoplasms", "basic", "cancer", "research", "human", "genomics", "oncology", "chromosome", "mapping", "molecular", "biology", "techniques", "...	2017	Analysis of the relationship between coexpression domains and chromatin 3D organization
Intellectual disability and seizures are frequently associated with hypomagnesemia and have an important genetic component . However , to find the genetic origin of intellectual disability and seizures often remains challenging because of considerable genetic heterogeneity and clinical variability . In this study , we ...	Mental retardation affects 1–3% of the population and has a strong genetic etiology . Consequently , early identification of the genetic causes of mental retardation is of significant importance in the diagnosis of the disease , as predictor of the progress of the disease and for the determination of treatment . In thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mineral", "metabolism", "and", "the", "kidney", "epilepsy", "medicine", "and", "health", "sciences", "neurology", "developmental", "and", "pediatric", "neurology", "nephrology" ]	2014	CNNM2 Mutations Cause Impaired Brain Development and Seizures in Patients with Hypomagnesemia
Convergent morphologies have arisen in plants multiple times . In non-vascular and vascular land plants , convergent morphology in the form of roots , stems , and leaves arose . The morphology of some green algae includes an anchoring holdfast , stipe , and leaf-like fronds . Such morphology occurs in the absence of mu...	Plants include both the green algae and land plants . Multiple times , root , stem , and leaf-like structures arose independently in plant lineages . In some instances , such as the siphonous algae , these structures arose in the absence of multicellularity . It has been argued by some that the morphology of multicellu...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "plant", "growth", "and", "development", "plant", "cell", "biology", "marine", "biology", "developmental", "biology", "plant", "science", "plant", "morphology", "molecular", "cell", "biology", "organism", "development", "morphogenesis", "cellu...	2015	An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia
Cellular senescence is a driver of various aging-associated disorders , including osteoarthritis . Here , we identified a critical role for Yes-associated protein ( YAP ) , a major effector of Hippo signaling , in maintaining a younger state of human mesenchymal stem cells ( hMSCs ) and ameliorating osteoarthritis in m...	Stem cell aging contributes to aging-associated degenerative diseases . Studies aiming to characterize the mechanisms of stem cell aging are critical for obtaining a comprehensive understanding of the aging process and developing novel strategies to treat aging-related diseases . As a prevalent aging-associated chronic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "rheumatology", "medicine", "and", "health", "sciences", "senescence", "forkhead", "box", "green", "fluorescent", "protein", "physiological", "processes", "developmental", "biology", "luminescent", "proteins", "organism", "development", "stem", ...	2019	Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritis
The MYC oncogene has been implicated in the regulation of up to thousands of genes involved in many cellular programs including proliferation , growth , differentiation , self-renewal , and apoptosis . MYC is thought to induce cancer through an exaggerated effect on these physiologic programs . Which of these genes are...	The targeted inactivation of oncogenes may be a specific and effective treatment of cancer . However , how oncogene inactivation leads to tumor regression is not clear . Previously , we have shown that even the brief inactivation of the MYC oncogene can result in the sustained regression of at least some tumors . To un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/cancer", "genetics" ]	2008	Combined Analysis of Murine and Human Microarrays and ChIP Analysis Reveals Genes Associated with the Ability of MYC To Maintain Tumorigenesis
Floral organs display tremendous variation in their exterior that is essential for organogenesis and the interaction with the environment . This diversity in surface characteristics is largely dependent on the composition and structure of their coating cuticular layer . To date , mechanisms of flower organ initiation a...	The cuticular layer that covers all aerial parts of plants plays a vital role not only in the interaction with environment but also in plant development and growth . Despite the recent significant achievements in the identification of structural genes involved in cuticle biosynthesis and secretion , little is known reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "growth", "and", "development", "plant", "biology/plant", "genetics", "and", "gene", "expression", "plant", "biology/plant", "biochemistry", "and", "physiology" ]	2011	SHINE Transcription Factors Act Redundantly to Pattern the Archetypal Surface of Arabidopsis Flower Organs
Vaccines that activate strong specific Th1-predominant immune responses are critically needed for many intracellular pathogens , including Leishmania . The requirement for sustained and efficient vaccination against leishmaniasis is to formulate the best combination of immunopotentiating adjuvant with the stable antige...	Visceral leishmaniasis ( VL ) , a vector-transmitted disease caused by Leishmania donovani , is potentially fatal if left untreated . Vaccination against VL has received limited attention compared with cutaneous leishmaniasis , although the need for an effective vaccine is pressing for the control of the disease . Earl...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunity", "immunology", "biology", "immune", "response" ]	2011	Potentiating Effects of MPL on DSPC Bearing Cationic Liposomes Promote Recombinant GP63 Vaccine Efficacy: High Immunogenicity and Protection
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other . Three main competition systems have been described: type six secretion systems ( T6SS ) ; contact dependent inhibition ( CDI ) ; and bacteriocins . Unlike T6SS and CDI systems , bacteriocins do not require contact between ba...	Bacteria deploy a variety of antimicrobials to kill competing bacteria . Nuclease bacteriocins are a miscellaneous group of protein toxins that target closely related species , cleaving nucleic acids in the cytoplasm . It has proved difficult to establish how widespread bacteriocins are in bacterial populations due to ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "nucleases", "deoxyribonucleases", "enzymes", "pathogens", "dna-binding", "proteins", "enzymology", "microbiology", "toxic", "agents", "toxicology", "pseudomonas", "aeruginosa",...	2017	Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models
Many plant cells can be reprogrammed into a pluripotent state that allows ectopic organ development . Inducing totipotent states to stimulate somatic embryo ( SE ) development is , however , challenging due to insufficient understanding of molecular barriers that prevent somatic cell dedifferentiation . Here we show th...	Somatic embryogenesis provides the strongest support for plant cell totipotency but reprogramming of non-reproductive tissue is problematic or even impossible in many plant species . Here we show that the activity of Polycomb Repressive Complex 2 ( PRC2 ) constitutes a major barrier to hormone-mediated establishment of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "growth", "and", "development", "gene", "regulation", "regulatory", "proteins", "brassica", "dna-binding", "proteins", "hormones", "developmental", "biology", "plant", "science", "model", "organisms", "plant", "hormones", "experimental", "organism", "systems", ...	2017	PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana

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