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Rift Valley fever ( RVF ) is a mosquito-borne viral zoonosis of ruminants and humans that causes outbreaks in Africa and the Arabian Peninsula with significant public health and economic consequences . Humans become infected through mosquito bites and contact with infected livestock . The virus is maintained between ou...	Rift Valley fever ( RVF ) is a mosquito-borne disease caused by the Rift Valley fever virus ( RVFV ) transmitted by diverse species of mosquitoes broadly classified into primary vectors and secondary vectors . Primary vectors consist of floodwater Aedes ( e . g Ae . mcintoshi , Ae . ochraceus , Ae . sudanensis , Ae . d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "geographical", "locations", "microbiology", "animals", "vi...	2017	Distribution and abundance of key vectors of Rift Valley fever and other arboviruses in two ecologically distinct counties in Kenya
In the presence of oxygen ( O2 ) the model bacterium Escherichia coli is able to conserve energy by aerobic respiration . Two major terminal oxidases are involved in this process - Cyo has a relatively low affinity for O2 but is able to pump protons and hence is energetically efficient; Cyd has a high affinity for O2 b...	The model bacterium Escherichia coli has a modular electron transport chain that allows it to successfully compete in environments with differing oxygen ( O2 ) availabilities . It has two well-characterized terminal oxidases , Cyd and Cyo . Cyd has a very high affinity for O2 , whereas Cyo has a lower affinity , but is...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "systems", "biology", "computer", "and", "information", "sciences", "network", "analysis", "regulatory", "networks", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli
Electrocorticography ( ECoG ) is becoming more prevalent due to improvements in fabrication and recording technology as well as its ease of implantation compared to intracortical electrophysiology , larger cortical coverage , and potential advantages for use in long term chronic implantation . Given the flexibility in ...	Electrocorticography ( ECoG ) is a type of electrophysiological monitoring that uses electrodes placed directly on the exposed surface of the brain . ECoG is a promising technique for studying the brain , and EcoG signals can be used to control brain-computer interfaces . Advances have made it possible to record simult...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "statistics", "electronics", "random", "variables", "electrophysiology", "neuroscience", "covariance", "multivariate", "analysis", "mathematics", "brain", "mapping", "membrane", "electrophysiology", ...	2019	Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components
Recombination , complementation and competition profoundly influence virus evolution and epidemiology . Since viruses are intracellular parasites , the basic parameter determining the potential for such interactions is the multiplicity of cellular infection ( cellular MOI ) , i . e . the number of viral genome units th...	Viruses are fast evolving organisms for which changes in fitness and virulence are driven by interactions between genomes such as recombination , functional complementation , and competition . Viruses being intra-cellular parasites , one basic parameter determines the potential for such interactions: the cellular multi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "virology", "plant", "biology" ]	2010	Dynamics of the Multiplicity of Cellular Infection in a Plant Virus
We have investigated the immunogenicity in rabbits of native-like , soluble , recombinant SOSIP . 664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 ( HIV-1 ) ; specifically BG505 ( clade A ) , B41 ( clade B ) , CZA97 ( clade C ) and DU422 ( clade C ) . The various trimers were d...	Native-like SOSIP trimers are a platform for development of immunogens aimed at inducing broadly neutralizing antibodies and , hence , a possible vaccine against HIV-1 infection . No previous study has reported on immune responses to more than one such trimer . Here , we assess how rabbits respond to immunization with ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "rabbits", "cloning", "animals", "mammals", "retroviruses", "animal", ...	2016	Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C
In mammals , mothers are the primary caregiver , programmed , in part , by hormones produced during pregnancy . High-quality maternal care is essential for the survival and lifelong health of offspring . We previously showed that the paternally silenced imprinted gene pleckstrin homology-like domain family A member 2 (...	Female mammals are primed during pregnancy for their new role as a mother caring for their newborn . Indirect evidence suggests that this behaviour is , in part , instructed by hormones produced by the foetally derived placenta . We previously reported that the Phlda2 gene controls the size of the placental endocrine c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "maternal", "health", "obstetrics", "and", "gynecology", "brain", "vertebrates", "animals", "mammals", "hormones", "endocrine", "physiology", "reproductive", "physiology", "developmental", "biology", "wome...	2018	Maternal care boosted by paternal imprinting in mammals
Accumulating evidence indicates that the capacity to integrate information in the brain is a prerequisite for consciousness . Integrated Information Theory ( IIT ) of consciousness provides a mathematical approach to quantifying the information integrated in a system , called integrated information , Φ . Integrated inf...	Integrated Information Theory ( IIT ) of consciousness attracts scientists who investigate consciousness owing to its explanatory and predictive powers for understanding the neural properties of consciousness . IIT predicts that the levels of consciousness are related to the quantity of information integrated in the br...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "vertebrates", "random", "variables", "neuroscience", "covariance", "animals", "mammals", "primates", "regression", "analysis", "cognitive", "neuroscience", "probability", "distribution", "mathematics", "statistics", "(mathematics)", "thermodynamics", "research", "and", "anal...	2016	Measuring Integrated Information from the Decoding Perspective
Despite the clinical ubiquity of anesthesia , the molecular basis of anesthetic action is poorly understood . Amongst the many molecular targets proposed to contribute to anesthetic effects , the voltage gated sodium channels ( VGSCs ) should also be considered relevant , as they have been shown to be sensitive to all ...	The molecular mechanisms mediating the pharmacologically induced state of general anesthesia are , in general , poorly understood . Modulation of voltage gated sodium channels is thought to play a major role in anesthesia , as several members of this class of channels show a significant response to general anesthetics ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "anesthetic", "mechanisms", "medicine", "biophysic", "al", "simulations", "general", "anesthesia", "anesthesiology", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2013	Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation
We systematically determined which spectrotemporal modulations in speech are necessary for comprehension by human listeners . Speech comprehension has been shown to be robust to spectral and temporal degradations , but the specific relevance of particular degradations is arguable due to the complexity of the joint spec...	The sound signal of speech is rich in temporal and frequency patterns . These fluctuations of power in time and frequency are called modulations . Despite their acoustic complexity , spoken words remain intelligible after drastic degradations in either time or frequency . To fully understand the perception of speech an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology", "neuroscience/psychology", "neuroscience/experimental", "psychology" ]	2009	The Modulation Transfer Function for Speech Intelligibility
The large variability in mRNA and protein levels found from both static and dynamic measurements in single cells has been largely attributed to random periods of transcription , often occurring in bursts . The cell cycle has a pronounced global role in affecting transcriptional and translational output , but how this i...	There is an astonishing amount of variation in the number of mRNA and protein molecules generated from particular genes between genetically identical single cells grown in the same environment . Particularly for mRNA , the large variation seen from these “noisy” genes is consistent with the idea of transcriptional burs...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "cell", "growth", "gene", "expression", "genetics", "biology", "computational", "biology", "molecular", "cell", "biology" ]	2013	Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression
The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus ( eQTL ) mapping . While trait-associated variants may operate in a cell-type specific manner , eQTL datasets for such cell-types may not always be available . We performed a genome-environment interact...	Many variants in the genome , including variants associated with disease , affect the expression of genes . These so-called expression quantitative trait loci ( eQTL ) can be used to gain insight in the downstream consequences of disease . While it has been shown that many disease-associated variants alter gene express...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cell Specific eQTL Analysis without Sorting Cells
The Nrf family of transcription factors mediates adaptive responses to stress and longevity , but the identities of the crucial Nrf targets , and the tissues in which they function in multicellular organisms to promote survival , are not known . Here , we use whole transcriptome RNA sequencing to identify 810 genes who...	Organisms have evolved mechanisms to protect themselves at the cellular level in response to a variety of environmental stresses . Oxidative stress , caused by an imbalance in the cellular production of free radicals and endogenous antioxidant defenses , can be particularly detrimental to the nervous system . Indeed , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "caenorhabditis", "elegans", "cellular", "stress", "responses", "model", "organisms", "biology", "molecular", "cell", "biology" ]	2014	Regulation of Synaptic nlg-1/Neuroligin Abundance by the skn-1/Nrf Stress Response Pathway Protects against Oxidative Stress
Switching of the Variant Surface Glycoprotein ( VSG ) in Trypanosoma brucei provides a crucial host immune evasion strategy that is catalysed both by transcription and recombination reactions , each operating within specialised telomeric VSG expression sites ( ES ) . VSG switching is likely triggered by events focused ...	All pathogens must survive eradication by the host immune response in order to continue infections and be passed on to a new host . Changes in the proteins expressed on the surface of the pathogen , or on the surface of the cells the pathogen infects , is a widely used strategy to escape immune elimination . Understand...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "serum", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "nucleases", "molecular", "probe", "techniques", "enzymes", "immunology", "dna-binding", "proteins", "enzymology", "antigenic", "variation", "parasitic", "protozoans", "...	2018	Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion
The clinical outcomes of human infections by Plasmodium falciparum remain highly unpredictable . A complete understanding of the complex interactions between host cells and the parasite will require in vitro experimental models that simultaneously capture diverse host–parasite interactions relevant to pathogenesis . He...	With over 500 million clinical cases and 1 million deaths per year , malaria presents a devastating global health problem . Samples from patients with severe disease suggest that binding of malaria-infected red blood cells ( iRBCs ) to host mammalian cells plays an important role in precipitating blood vessel blockages...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology", "cell", "biology", "pathology", "plasmodium", "in", "vitro", "immunology", "microbiology", "eukaryotes", "chemical", "biology", "hematology" ]	2007	Microfluidic Modeling of Cell−Cell Interactions in Malaria Pathogenesis
In the dark , etiolated seedlings display a long hypocotyl , the growth of which is rapidly inhibited when the seedlings are exposed to light . In contrast , the phytohormone ethylene prevents hypocotyl elongation in the dark but enhances its growth in the light . However , the mechanism by which light and ethylene sig...	It is well known that light suppresses hypocotyl growth in seedlings , while the phytohormone ethylene and its precursor 1-aminocyclopropane-1-carboxylate ( ACC ) enhance hypocotyl growth in the light . However , the mechanism by which light and ethylene oppositely affect this process at the protein level is unclear . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Ethylene Promotes Hypocotyl Growth and HY5 Degradation by Enhancing the Movement of COP1 to the Nucleus in the Light
Infectious diseases impose considerable burden on society , despite significant advances in technology and medicine over the past century . Advanced warning can be helpful in mitigating and preparing for an impending or ongoing epidemic . Historically , such a capability has lagged for many reasons , including in parti...	Despite advanced and widely accessible health care , a large number of annual deaths in the United States are attributable to infectious diseases like influenza . Many of these cases could be easily prevented if sufficiently advanced warning was available . This is the main goal of epidemiological forecasting , a relat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "epidemiological", "statistics", "infectious", "diseases", "medicine", "and", "health", "sciences", "mathematics", "forecasting", "statistics", "(mathematics)", "chikungunya", "infection", "epidemiology", "mathematical", "and", "statistical", "techniques", "influenza", "negle...	2017	A human judgment approach to epidemiological forecasting
A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation , but identifying loci subject to positive selection has been a challenge . Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations . We mapped natura...	Local adaptation is thought to be a driving force in population differentiation and the formation of new species . Yet , there are few examples of ecologically relevant phenotypes that have been mapped to individual genes , making it difficult to know what drives the evolution of such genes and contributes to the molec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/genomics", "evolutionary", "biology/evolutionary", "ecology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2010	Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations
The Calsequestrin ( Csq ) transgenic mouse model of cardiomyopathy exhibits wide variation in phenotypic progression dependent on genetic background . Seven heart failure modifier ( Hrtfm ) loci modify disease progression and outcome . Here we report Tnni3k ( cardiac Troponin I-interacting kinase ) as the gene underlyi...	Heart failure is the common final outcome of many forms of acute and chronic heart disease . The prognosis of heart disease is highly variable between patients , and these differences in the phenotypic expression ( symptoms , course , and final outcome ) are in part due to genetic factors that have proven difficult to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "discovery" ]	2009	Tnni3k Modifies Disease Progression in Murine Models of Cardiomyopathy
When selective pressures differ between males and females , the genes experiencing these conflicting evolutionary forces are said to be sexually antagonistic . Although the phenotypic effect of these genes has been documented in both wild and laboratory populations , their identity , number , and location remains unkno...	Males and females of many species are different: many of these differences are thought to have evolved because the sexes often have needs and strategies that do not coincide . For example , in fruit-flies , females may do best by concentrating their efforts in acquiring resources to be able to lay more eggs , while mal...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/evolutionary", "ecology", "evolutionary", "biology/sexual", "behavior", "genetics", "and", "genomics/complex", "traits", "evolutionary", "biology/genomics" ]	2010	The Sexually Antagonistic Genes of Drosophila melanogaster
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 ( APOBEC3 ) proteins are cell-encoded cytidine deaminases , some of which , such as APOBEC3G ( A3G ) and APOBEC3F ( A3F ) , act as potent human immunodeficiency virus type-1 ( HIV-1 ) restriction factors . These proteins require packaging into HIV-1 ...	APOBEC3 proteins are cell-encoded restriction factors that counteract infections , particularly by retroviruses such as HIV-1 , and retrotransposons . When packaged into HIV-1 particles , APOBEC3G and APOBEC3F both inhibit reverse transcription and induce destructive hypermutation in viral DNA . The mechanism of APOBEC...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
In sub-Saharan Africa , over 200 million individuals are estimated to be infected with urinary and intestinal schistosomiasis . In a bid to lay a foundation for effective future control programme , this study was carried out with the aim of assessing the diagnostic efficacy of some questionnaire-based rapid assessment ...	Schistosomiasis is a water-borne neglected infectious disease of poverty that has consistently plagued over 200 million helpless inhabitants of the tropics , particularly , sub-Sahara Africa . Under the auspices of different nomenclatures and affiliations , many control programmes based on Praziquantel have been inaugu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "education", "helminths", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "parasitology", "urine", "physiological", "processes", "negl...	2017	Rapid mapping of urinary schistosomiasis: An appraisal of the diagnostic efficacy of some questionnaire-based indices among high school students in Katsina State, northwestern Nigeria
Obesity is a worldwide health problem that is closely linked to many metabolic disorders . Regular physical exercise has been found to attenuate the genetic predisposition to obesity . However , it remains unknown what kinds of exercise can modify the genetic risk of obesity . This study included 18 , 424 unrelated Han...	The complex interplay of genetics and lifestyle makes obesity a challenging issue . Previous studies have found performing regular physical exercise could blunt the genetic effects on body mass index ( BMI ) . However , BMI does not take into account lean body mass or identify central obesity . Moreover , it remains un...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "body", "weight", "medicine", "and", "health", "sciences", "swimming", "education", "sociology", "sports", "and", "exercise", "medicine", "social", "sciences", "physical", "activity", "biological", "locomotion", "physiological", "parameters", "obesity", "public", "and",...	2019	Performing different kinds of physical exercise differentially attenuates the genetic effects on obesity measures: Evidence from 18,424 Taiwan Biobank participants
The Warburg effect - a classical hallmark of cancer metabolism - is a counter-intuitive phenomenon in which rapidly proliferating cancer cells resort to inefficient ATP production via glycolysis leading to lactate secretion , instead of relying primarily on more efficient energy production through mitochondrial oxidati...	Cancer cells , as opposed to normal cells , produce a substantial amount of energy inefficiently via aerobic glycolysis , even in the presence of sufficient oxygen to support mitochondrial respiration . Despite the fact that this phenomenon , called the Warburg effect , has already been discovered back in 1924 , its ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "molecular", "cell", "biology", "cell", "biology", "cell", "growth", "biology", "computational", "biology", "metabolic", "networks", "genetics", "and", "genomics" ]	2011	Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect
The mechanistic target of rapamycin ( mTOR ) is an established therapeutic target in renal cell carcinoma ( RCC ) . Mechanisms of secondary resistance to rapalog therapy in RCC have not been studied previously . We identified six patients with metastatic RCC who initially responded to mTOR inhibitor therapy and then pr...	Mammalian target of rapamycin ( mTOR ) inhibitors , everolimus and temsirolimus , are FDA-approved for treatment of metastatic renal cell carcinoma ( mRCC ) , but molecular mechanisms of acquired or secondary resistance to these agents are unknown . We evaluated six mRCC patients with available pre-treatment specimens ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "renal", "cell", "carcinoma", "medicine", "and", "health", "sciences", "cancer", "treatment", "carcinomas", "drugs", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "microbiology", "alleles", "antimalarials", "oncology", "mutation", ...	2018	Mechanisms of acquired resistance to rapalogs in metastatic renal cell carcinoma
Identification and characterization of CD8+ and CD4+ T-cell epitopes elicited by HIV therapeutic vaccination is key for elucidating the nature of protective cellular responses and mechanism of the immune evasion of HIV . Here , we report the characterization of HIV-specific T-cell responses in cART ( combination antire...	Improvement of therapeutic vaccine strategies in the perspective of HIV cure is warranted and one of the determinant factors for elucidating the nature of protective cellular responses is the identification and characterization of CD8+ and CD4+ T-cell epitopes elicited by the vaccine . However , fine characterization o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunode...	2019	Anti-HIV potency of T-cell responses elicited by dendritic cell therapeutic vaccination
Lymphedema related to lymphatic filariasis ( LF ) is a disabling condition that commonly manifests in adolescence . Fifty-three adolescents , 25 LF infected and 28 LF non-infected , in age and sex-matched groups , using the Binax ICT rapid card test for filarial antigen were recruited to the study . None of the partici...	The effects of lymphatic filariasis ( LF ) on the lymphatic system often become apparent during adolescence when the lower limb swells due to lymphedema and males develop hydrocele . Currently there is no simple or mobile field method to identify those at greatest risk of developing lymphedema or those with early subcl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "diagnostic", "medicine", "public", "health" ]	2011	Lymphatic Filariasis: A Method to Identify Subclinical Lower Limb Change in PNG Adolescents
Cutaneous beta human papillomavirus ( HPV ) types are suspected to be involved , together with ultraviolet ( UV ) radiation , in the development of non-melanoma skin cancer ( NMSC ) . Studies in in vitro and in vivo experimental models have highlighted the transforming properties of beta HPV E6 and E7 oncoproteins . Ho...	Many epidemiological and biological findings support the hypothesis that beta HPV types cooperate with UV radiation in the induction of NMSC , the most common form of human cancer . We have previously shown that K14 HPV38 E6/E7 Tg mice , when exposed to long-term UV radiation , developed NMSC , whereas WT animals subje...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "keratinocytes", "pathology", "and", "laboratory", "medicine", "ultraviolet", "radiation", "light", "electromagnetic", "radiation", "epithelial", "cells", "radiation", "animal", "models", "oncology", "mutation", "model", "organisms...	2018	Beta HPV38 oncoproteins act with a hit-and-run mechanism in ultraviolet radiation-induced skin carcinogenesis in mice
Adenoviruses infect epithelial cells lining mucous membranes to cause acute diseases in people . They are also utilized as vectors for vaccination and for gene and cancer therapy , as well as tools to discover mechanisms of cancer due to their tumorigenic potential in experimental animals . The adenovirus E4-ORF1 gene ...	Adenoviruses cause acute illnesses in people , and are additionally utilized both as vehicles to cure genetic diseases , fight cancer , and deliver vaccines , and as tools to discover how cancers develop due to a capacity to generate tumors in experimental animals . The adenovirus E4-ORF1 protein reprograms cell metabo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "protein", "interactions", "enzymes", "regulatory", "proteins", "enzymology", "microbiology", "basic", "cancer", "research", "oncology", "model", "organisms", "population", "modeling", "enzyme", "chemistry", "research", "and", "a...	2014	The Human Adenovirus E4-ORF1 Protein Subverts Discs Large 1 to Mediate Membrane Recruitment and Dysregulation of Phosphatidylinositol 3-Kinase
Trichomonas vaginalis is a causative agent of Trichomoniasis , a leading non-viral sexually transmitted disease worldwide . In the current study , we show Heat shock protein 90 is essential for its growth . Upon genomic analysis of the parasite , it was found to possess seven ORFs which could potentially encode Hsp90 i...	Hsp90 is an essential chaperone in eukaryotes and it is often described as a master regulator of cellular homeostasis . In addition to its well-known functions inside the cell , extracellular Hsp90 has also been implicated in migration and invasion of tumor cells . We have , for the first time , identified the presence...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzymes", "endoplasmic", "reticulum", "cell", "processes", "enzymology", "phosphatases", "physiological", "processes", "sequence", "motif", "analysis", "trichomonas", "cellular", "structures", "and", "organelles", "research", "and...	2018	A secreted Heat shock protein 90 of Trichomonas vaginalis
Ebola virus ( EBOV ) causes severe and often fatal hemorrhagic fever in humans and nonhuman primates ( NHPs ) . Currently , there are no licensed vaccines or therapeutics for human use . Recombinant vesicular stomatitis virus ( rVSV ) -based vaccine vectors , which encode an EBOV glycoprotein in place of the VSV glycop...	Ebola viruses ( EBOV ) , of which there are five species , are categorized as Category A Priority Pathogens and Tier 1 Select Agents by several US Government agencies as a result of their high mortality rates and potential for use as agents of bioterrorism . Currently , there are no vaccines or therapeutics approved fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Vesicular Stomatitis Virus-Based Vaccines Protect Nonhuman Primates against Bundibugyo ebolavirus
Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut , infecting approximately 1 billion individuals worldwide . Although Blastocystis has been linked to intestinal disorders , its pathogenicity remains controversial because most carriers are asymptomatic . Here , the genome sequence of Blasto...	Blastocystis are unicellular eukaryotic organisms related to algae and some plant pathogens . They are common constituents of the human gut microbial community , colonizing approximately 1 billion humans worldwide . Whether their presence is harmful or not continues to be hotly debated . Part of the uncertainty stems f...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods", "and", "materials" ]	[ "methods", "and", "resources", "enzymes", "enzymology", "parasitic", "protozoans", "genomic", "databases", "protozoans", "genome", "analysis", "energy-producing", "organelles", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "research", "and"...	2017	Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Yeast RNA polymerase II ( Pol II ) terminates transcription of coding transcripts through the polyadenylation ( pA ) pathway and non-coding transcripts through the non-polyadenylation ( non-pA ) pathway . We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components...	Transcription termination is an important regulatory event for both non-coding and coding transcripts . Using high-throughput sequencing , we have mapped RNA Polymerase II's position in the genome after depletion of termination factors from the nucleus . We found that depletion of Ysh1 and Sen1 cause build up of polyme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "machines", "molecular", "complexes", "genetic", "elements", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "molecular", "biology", "techniques", "molecular", "biology" ]	2014	Genome-Wide Mapping of Yeast RNA Polymerase II Termination
Cells use surface receptors to estimate concentrations of external ligands . Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species . However , the environment typically contains many ligands , which can bind to the same receptors with different affinities , resulting...	Cells live in chemically complex environments with many different chemical ligands around them . Can cells estimate concentrations of more ligands than they have receptor types ? In this paper , we show that , surprisingly , the answer is “yes” , and the estimation can be implemented with simple biochemical components ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "enzymology", "social", "sciences", "neuroscience", "immune", "receptor", "signaling", "membrane", "receptor", "signaling", "sequence", "motif", "analysis", "enzyme", "kinetics", "research", "and"...	2017	Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor
Cell-to-cell transmission of vaccinia virus can be mediated by enveloped virions that remain attached to the outer surface of the cell or those released into the medium . During egress , the outer membrane of the double-enveloped virus fuses with the plasma membrane leaving extracellular virus attached to the cell surf...	Traversing the plasma membrane of the host cell is a significant challenge for many viruses during the infection cycle , and the efficiency of detachment from the host cell and subsequent release can have implications in pathogenesis . Vaccinia virus exits cells through the loss of an outer membrane but remains attache...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "envelope", "molecular", "cell", "biology", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology", "viral", "structure", "host-pathogen", "interaction" ]	2013	A36-dependent Actin Filament Nucleation Promotes Release of Vaccinia Virus
While major inroads have been made in identifying the genetic causes of rare Mendelian disorders , little progress has been made in the discovery of common gene variations that predispose to complex diseases . The single gene variants that have been shown to associate reproducibly with complex diseases typically have s...	Complex diseases are common disorders that are believed to have many causes . Examples include Alzheimer disease , diabetes mellitus , nicotine and alcohol dependence , and several cancers . This study represents a paradigm shift from single gene to pathway studies of complex diseases . We present the example of Parkin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "cell", "biology", "neurological", "disorders", "neuroscience", "homo", "(human)", "genetics", "and", "genomics" ]	2007	A Genomic Pathway Approach to a Complex Disease: Axon Guidance and Parkinson Disease
Recent work has shown that functional connectivity among cortical neurons is highly varied , with a small percentage of neurons having many more connections than others . Also , recent theoretical developments now make it possible to quantify how neurons modify information from the connections they receive . Therefore ...	We recorded the electrical activity of hundreds of neurons simultaneously in brain tissue from mice and we analyzed these signals using state-of-the-art tools from information theory . These tools allowed us to ascertain which neurons were transmitting information to other neurons and to characterize the computations p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "membrane", "potential", "sociology", "signaling", "networks", "social", "sciences", "electrophysiology", "neuroscience", "network", "analysis", "thermodynamics", "computer", "and", "in...	2016	High-Degree Neurons Feed Cortical Computations
Histone H3 di- and trimethylation on lysine 4 are major chromatin marks that correlate with active transcription . The influence of these modifications on transcription itself is , however , poorly understood . We have investigated the roles of H3K4 methylation in Saccharomyces cerevisiae by determining genome-wide exp...	In eukaryotes , DNA is packaged together with histones into nucleosomes . This packaging has a repressive role on gene expression . The N-termini of histones are subject to multiple modifications that affect DNA–dependent processes . The histone modification that has been predominantly linked with active transcription ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "gene", "regulation", "microbiology", "dna", "transcription", "histone", "modification", "model", "organisms", "epigenetics", "molecular", "genetics", "chromatin", "gene", "expression", "biology", "molecular", ...	2012	Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription
Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals . Although its population structure was long described as clonal , based on high linkage disequilibrium between loci typed by enzyme electrophoresis , recent examination of gene sequences has revealed that re...	Salmonella enterica is a species of bacteria that causes severe diseases in humans and animals . We sequenced about a tenth of the genome from a broadly sampled collection of S . enterica . By comparing these genetic sequences , we were able to partially reconstruct the ancestry of this sample . We identified five line...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "bacterial", "evolution", "genomics", "biology", "computational", "biology", "comparative", "genomics", "microbiology", "salmonella", "bacterial", "pathogens" ]	2011	Recombination and Population Structure in Salmonella enterica
Nuclear receptors were originally defined as endocrine sensors in humans , leading to the identification of the nuclear receptor superfamily . Despite intensive efforts , most nuclear receptors have no known ligand , suggesting new ligand classes remain to be discovered . Furthermore , nuclear receptors are encoded in ...	Zinc is an essential nutrient for all life forms , and maintaining zinc homeostasis is critical for survival . However , little is known about how animals sense changes in zinc availability and make adjustments to maintain homeostasis . In particular , logic dictates there must be a mechanism for zinc sensing , but it ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "invertebrates", "medicine", "and", "health", "sciences", "affinity", "chromatography", "caenorhabditis", "messenger", "rna", "dna-binding", "proteins", "animals", "dna", "transcription", "animal", "models", "physiological", "processes", "caenorhabditis", "...	2017	The Nuclear Receptor HIZR-1 Uses Zinc as a Ligand to Mediate Homeostasis in Response to High Zinc
Our previous studies showed that Trichinella spiralis paramyosin ( TsPmy ) is an immunomodulatory protein that inhibits complement C1q and C8/C9 to evade host complement attack . Vaccination with recombinant TsPmy protein induced protective immunity against T . spiralis larval challenge . Due to the difficulty in produ...	Trichinellosis is one of the most important food-borne parasitic zoonoses , and a serious public health issue worldwide . Developing a vaccine is an alternative approach to control the disease . TsPmy is a paramyosin expressed by Trichinella spiralis to bind and neutralize human complement and a vaccine antigen . We ma...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "spleen", "immunology", "animal", "models", "preventive", "medicine", "developmental", "biology", "model", "organisms", "vaccination", "and", "immunization", "immunologic", "...	2016	Oral Vaccination with Attenuated Salmonella typhimurium-Delivered TsPmy DNA Vaccine Elicits Protective Immunity against Trichinella spiralis in BALB/c Mice
Signaling of the cytokine interleukin-6 ( IL-6 ) via its soluble IL-6 receptor ( sIL-6R ) is responsible for the proinflammatory properties of IL-6 and constitutes an attractive therapeutic target , but how the sIL-6R is generated in vivo remains largely unclear . Here , we use liquid chromatography–mass spectrometry t...	Interleukin-6 ( IL-6 ) is a cytokine secreted by our body upon infection or trauma to stimulate the immune system response . IL-6 is partially responsible for fever and triggers inflammation in many diseases . It activates its target cells via the membrane-bound IL-6 receptor ( IL-6R ) , and soluble forms of this recep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "enzymes", "metabolic", "processes", "enzymology", "plasmid", "construction", "physiological", "processes", "dna", "construction", "glycosylation", "molecular", "biology", "techni...	2017	Proteolytic Origin of the Soluble Human IL-6R In Vivo and a Decisive Role of N-Glycosylation
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms . In this study , we applied metabolic labeling of newly transcribed RNA with 4-thiouridine ( 4sU-tagging ) to dissect the real-time kinetics of cellular and viral transcriptional activity dur...	Cytomegaloviruses are large DNA viruses , which establish life-long latent infections , leaving the infected individual at risk of reactivation and disease . Here , we applied 4-thiouridine- ( 4sU ) -tagging of newly transcribed RNA to monitor the real-time kinetics of transcriptional activity of both cellular and vira...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "infectious", "disease", "modeling", "viral", "diseases" ]	2012	Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection
The rapid evolution of RNA-encoded viruses such as HIV presents a major barrier to infectious disease control using conventional pharmaceuticals and vaccines . Previously , it was proposed that defective interfering particles could be developed to indefinitely control the HIV/AIDS pandemic; in individual patients , the...	A major obstacle to effective antimicrobial therapy campaigns is the rapid evolution of drug resistance . Given the static nature of current pharmaceuticals and vaccines , natural selection inevitably drives pathogens to mutate into drug-resistant variants that can resume productive replication . Further , these drug-r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "organismal", "evolution", "hiv", "infections", "medicine", "and", "health", "sciences", "hiv", "prevention", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "parasite", "evolution", "pathogens", "microbiology", "parasitology", ...	2016	Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals
In HIV/SIV-infected humans and rhesus macaques ( RMs ) , a severe depletion of intestinal CD4+ T-cells producing interleukin IL-17 and IL-22 associates with loss of mucosal integrity and chronic immune activation . However , little is known about the function of IL-17 and IL-22 producing cells during lentiviral infecti...	Persistent immune activation and inflammation are key features and strong predictors of morbidity/mortality in HIV infection . A specific quantitative loss of Th17 and Th22 CD4+ T-cells , which are crucial to maintaining the mucosal immunity , has been shown to directly associate with microbial translocation , systemic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "hiv", "infections", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "body", "fluids", "immune", "activation", "pathogens", ...	2016	Loss of Function of Intestinal IL-17 and IL-22 Producing Cells Contributes to Inflammation and Viral Persistence in SIV-Infected Rhesus Macaques
Multilayered defense responses ensure that plants are hosts to only a few adapted pathogens in the environment . The host range of a plant pathogen depends on its ability to fully overcome plant defense barriers , with failure at any single step sufficient to prevent life cycle completion of the pathogen . Puccinia str...	Plants are constantly exposed to a multitude of potential pathogens but remain immune to most of these due to a multilayered immune system . Pathogens have specialized by adapting to certain host plants and their defense barriers . Most of our understanding of plant-pathogen interactions stems from these highly special...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "quantitative", "trait", "loci", "population", "genetics", "developmental", "biology", "plant", "science", "plant", "pathology", "molecular", "biology", "techniques", "population", "biology", "research", "and", "analysis", "methods", "gene", "mapping...	2018	The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates
Throughout evolution , cytomegaloviruses ( CMVs ) have been capturing genes from their hosts , employing the derived proteins to evade host immune defenses . We have recently reported the presence of a number of CD48 homologs ( vCD48s ) encoded by different pathogenic viruses , including several CMVs . However , their ...	In order to evade detection and destruction by cytotoxic lymphocytes and successfully persist within their hosts , cytomegalovirus ( CMVs ) have evolved a number of genes dedicated to block immune recognition . Certain CMVs and other large DNA viruses encode homologs of the cell-surface molecule CD48 , a ligand of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "cell", "physiology", "cell", "binding", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "nervous", "system", "immunology", "biological", "culture...	2019	Subversion of natural killer cell responses by a cytomegalovirus-encoded soluble CD48 decoy receptor
Our understanding of persistence and plasticity of IL-17A+ memory T cells is clouded by conflicting results in models analyzing T helper 17 cells . We studied memory IL-17A+ CD8+ T-cell ( Tc17 ) homeostasis , persistence and plasticity during fungal vaccine immunity . We report that vaccine-induced memory Tc17 cells pe...	CD4+ T-cell deficient patients such as those with AIDS and idiopathic CD4+ T-cell lymphopenia are vulnerable to systemic fungal infections . We previously showed that CD8+ T cells can be exploited in CD4+ T cell deficient hosts for vaccine immunity against lethal fungal pneumonia in mice and that IL-17A production by t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "antimicrobials", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "drugs", "immunology", "microbiology", "antifungals", "neuroscience", "learning", "and", "memory", "prevent...	2017	Antifungal Tc17 cells are durable and stable, persisting as long-lasting vaccine memory without plasticity towards IFNγ cells
Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology ( e . g . identifying motor-related proteins ) and clinical research ( e . g . identification of cancer biomarkers ) . Here we describe the design of a system that provid...	Determining the subcellular location of all proteins is a critical but daunting task for systems biologists , especially when variation between different cell types is considered . Fluorescence microscopy is the main source of information about subcellular location , but large collections of fluorescence images for man...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules
Acetylcholine is the canonical excitatory neurotransmitter of the mammalian neuromuscular system . However , in the trematode parasite Schistosoma mansoni , cholinergic stimulation leads to muscle relaxation and a flaccid paralysis , suggesting an inhibitory mode of action . Information about the pharmacological mechan...	Schistosomiasis is a widespread , chronic disease affecting over 200 million people in developing countries . Currently , there is no vaccine available and treatment depends on the use of a single drug , praziquantel . Reports of reduced praziquantel efficacy , as well as its ineffectiveness against larval schistosomul...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "signal", "transduction", "infectious", "diseases", "medicine", "and", "health", "sciences", "neurochemistry", "helminth", "infections", "schistosomiasis", "cell", "biology", "membrane", "receptor", "signaling", "neurochemicals", "mechanisms", "of", "signal"...	2014	Functional Characterization of a Novel Family of Acetylcholine-Gated Chloride Channels in Schistosoma mansoni
Melioidosis , caused by bioterror treat agent Burkholderia pseudomallei , is an important cause of community-acquired Gram-negative sepsis in Southeast Asia and Northern Australia . New insights into the pathogenesis of melioidosis may help improve treatment and decrease mortality rates from this dreadful disease . We ...	Melioidosis , caused by bioterror threat agent Burkholderia pseudomallei , is an important cause of community-acquired sepsis in Southeast Asia and Northern Australia . Recently , it has been predicted that the annual burden of melioidosis is much higher than previously thought , with 165 . 000 human cases from which 8...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "death", "rates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "demography", "melioidosis", "diabetes", "mellitus", "bacterial", "diseases", "physiological", "processes", "sepsis", "endocrine"...	2017	Increased Von Willebrand factor, decreased ADAMTS13 and thrombocytopenia in melioidosis
Paracoccidioidomycosis ( PCM ) is a neglected disease present in Latin America with difficulty in treatment and occurrence of serious sequelae . Thus , the development of alternative therapies is imperative . In the current work , two oxadiazole compounds ( LMM5 and LMM11 ) presented fungicidal activity against Paracoc...	Paracoccidioidomycosis ( PCM ) is a granulomatous fungal infection with clinically severe forms and serious pulmonary sequelae . The current limited arsenal and prolonged treatment regimen demonstrate the need for new antifungals . This study reveals two fungicidal oxadiazole compounds for PCM treatment . The in vitro ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "fungicides", "tropical", "diseases", "microbiology", "light", "microscopy", "immunology", "antifungals", "fungal", "structure", "toxicology", "toxicity", "fu...	2019	Antifungal activity of two oxadiazole compounds for the paracoccidioidomycosis treatment
Candida albicans can stochastically switch between two phenotypes , white and opaque . Opaque cells are the sexually competent form of C . albicans and therefore undergo efficient polarized growth and mating in the presence of pheromone . In contrast , white cells cannot mate , but are induced – under a specialized set...	Candida albicans is the predominant fungal pathogen afflicting humans , where many infections arise due to its proclivity to form biofilms . Biofilms are complex multicellular communities in which cells exhibit distinct properties to those grown in suspension . They are particularly relevant in the development of devic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "microbiology", "gene", "function", "epigenetics", "molecular", "genetics", "mycology", "cell", "adhesion", "gene", "expression", "microbial", "pathogens", "biology", "pathogenesis", "cell", "biology", "genetics", "genomics", "molecular...	2013	Genetic Control of Conventional and Pheromone-Stimulated Biofilm Formation in Candida albicans
Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous defense against viral infections . Viral recognition determinants in intrinsic immunity genes are expected to evolve rapidly as host genes adapt to changing viruses , resulting in a signature of adaptive evolution . Zinc-fing...	Host–virus interactions are a classic example of genetic conflict in which both entities try to gain an evolutionary advantage over the other . This “back-and-forth” evolution is predicted to result in rapid changes of both host and viral proteins , which results in an evolutionary signature of positive selection , esp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primates", "viruses", "virology", "evolutionary", "biology", "homo", "(human)", "rattus", "(rat)" ]	2008	Positive Selection and Increased Antiviral Activity Associated with the PARP-Containing Isoform of Human Zinc-Finger Antiviral Protein
The multifunctional NS1 protein of influenza A viruses suppresses host cellular defense mechanisms and subverts other cellular functions . We report here on a new role for NS1 in modifying cell-cell signaling via the Hedgehog ( Hh ) pathway . Genetic epistasis experiments and FRET-FLIM assays in Drosophila suggest that...	The NS1 protein produced by influenza A viruses alters host cellular defense mechanisms . We report here on a new role for NS1 in modifying cell-cell communication via the Hedgehog ( Hh ) signaling pathway . Genetic and microscopy studies in flies indicate that NS1 alters the transcriptional read-out of Hh targets by i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", ...	2017	Influenza NS1 directly modulates Hedgehog signaling during infection
Motivation: Recently , copy number variation ( CNV ) has gained considerable interest as a type of genomic variation that plays an important role in complex phenotypes and disease susceptibility . Since a number of CNV detection methods have recently been developed , it is necessary to help investigators choose suitabl...	As an important type of genomic structural variation , CNVs are associated with complex phenotypes because they change the number of copies of genes in cells , affecting coding sequences and playing an important role in the susceptibility or resistance to human diseases . To identify CNVs , several experimental methods...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "applied", "mathematics", "genomic", "library", "construction", "simulation", "and", "modeling", "algorithms", "genome", "sequencing", "genomic", "databases", "mathematics", "genome", "analysis", "copy", "number", "variation", "molecular", "bio...	2019	Comprehensively benchmarking applications for detecting copy number variation
How do we use our memories of the past to guide decisions we've never had to make before ? Although extensive work describes how the brain learns to repeat rewarded actions , decisions can also be influenced by associations between stimuli or events not directly involving reward — such as when planning routes using a c...	We are always learning regularities in the world around us: where things are , and in what order we might find them . Our knowledge of these contingencies can be relied upon if we later want to use them to make decisions . However , there is little agreement about the neurobiological mechanism by which learned continge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Cortical and Hippocampal Correlates of Deliberation during Model-Based Decisions for Rewards in Humans
Protein or DNA motifs are sequence regions which possess biological importance . These regions are often highly conserved among homologous sequences . The generation of multiple sequence alignments ( MSAs ) with a correct alignment of the conserved sequence motifs is still difficult to achieve , due to the fact that th...	The most important functional parts of proteins are often small—but very specific—sequence motifs . Moreover , these motifs tend to be strongly conserved during evolution due to their functional role . Nevertheless , when trying to align protein sequences of the same family , it is often very difficult to align such mo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "split-decomposition", "method", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "multiple", "alignment", "calculation", "rna", "viruses", "protein"...	2018	Motif-Aware PRALINE: Improving the alignment of motif regions
In the event of a new infectious disease outbreak , mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic . In the early stages of such outbreaks , substantial parameter uncertainty may limit the ability of models to provide...	Mathematical and simulation models may be used to inform policy in the early stages of an infectious disease outbreak by evaluating which control strategies will minimize the impact of the epidemic . In these early stages , significant uncertainty can limit the ability of models to provide accurate predictions , and po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "livestock", "medicine", "and", "health", "sciences", "animal", "diseases", "foot", "and", "mouth", "disease", "ruminants", "immunology", "vertebrates", "animals", "mammals", "simulation", "and", "modeling", "preventive", "medicine", "infectious", "disease", "control", ...	2018	Real-time decision-making during emergency disease outbreaks
The World Health Organization has recently reemphasized the importance of providing preventive chemotherapy to women of reproductive age in countries endemic for soil-transmitted helminthiasis as they are at heightened risk of associated morbidity . The Demographic and Health Surveys ( DHS ) Program is responsible for ...	Soil-transmitted helminths are intestinal worms that cause significant suffering among the poorest communities in the world . They are transmitted via contaminated water , food or soil , all of which result from poor sanitation . Children and women of reproductive age are at heightened risk of related morbidities such ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cognitive", "neurology", "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "united", "nations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "neuroscience", "political", "science", "health", "car...	2019	Provision of deworming intervention to pregnant women by antenatal services in countries endemic for soil-transmitted helminthiasis
Recognition of viruses by pattern recognition receptors ( PRRs ) causes interferon-β ( IFN-β ) induction , a key event in the anti-viral innate immune response , and also a target of viral immune evasion . Here the vaccinia virus ( VACV ) protein C6 is identified as an inhibitor of PRR-induced IFN-β expression by a fun...	A key event in the innate immune response to virus infection is the detection of pathogen-associated molecular patterns ( PAMPs ) such as viral DNA and RNA by cellular pattern recognition receptors ( PRRs ) . This leads to expression of interferon-β ( IFN-β ) by an infected cell . Many viruses have evolved mechanisms t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "molecular", "cell", "biology", "viral", "immune", "evasion", "immunity", "virology", "innate", "immunity", "biology", "microbiology", "molecular", "biology" ]	2011	Vaccinia Virus Protein C6 Is a Virulence Factor that Binds TBK-1 Adaptor Proteins and Inhibits Activation of IRF3 and IRF7
Mitochondrial dysfunction activates the mitochondrial retrograde signaling pathway , resulting in large scale changes in gene expression . Mitochondrial retrograde signaling in neurons is poorly understood and whether retrograde signaling contributes to cellular dysfunction or is protective is unknown . We show that in...	Loss of mitochondrial function activates the mitochondrial retrograde signaling pathway resulting in large scale changes in nuclear gene transcription . Very little is known about retrograde signaling in the nervous system and how the transcriptional changes affect neuronal function . Here we identify Ras-ERK-ETS signa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "neuroscience", "biological", "locomotion", "animals", "motor", "neurons", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "mito...	2018	Ras-ERK-ETS inhibition alleviates neuronal mitochondrial dysfunction by reprogramming mitochondrial retrograde signaling
Prions adopt alternative , self-replicating protein conformations and thereby determine novel phenotypes that are often irreversible . Nevertheless , dominant-negative prion mutants can revert phenotypes associated with some conformations . These observations suggest that , while intervention is possible , distinct inh...	Prion proteins adopt alternative conformations and assemble into amyloid fibers , which have been associated with human disease . These fibers are highly stable and self-replicate , leading to their persistence and resulting in a set of progressive and often fatal disorders . Inhibitors have been shown to interfere wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "diseases", "medicine", "and", "health", "sciences", "molecular", "probe", "techniques", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunoblotting", "light", "microscopy", "cell", "disruption", "fungi", "animal", "prion", "diseases", ...	2017	A dominant-negative mutant inhibits multiple prion variants through a common mechanism
In many organisms , dietary restriction appears to extend lifespan , at least in part , by down-regulating the nutrient-sensor TOR ( Target Of Rapamycin ) . TOR inhibition elicits autophagy , the large-scale recycling of cytoplasmic macromolecules and organelles . In this study , we asked whether autophagy might contri...	Dietary restriction ( limited food intake ) increases lifespan in many organisms . However , the cellular processes underlying this fascinating phenomenon are still poorly understood . When an animal is starved , it degrades and recycles its organelles and other cellular components in a process called autophagy ( liter...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "developmental", "biology", "caenorhabditis", "molecular", "biology", "genetics", "and", "genomics" ]	2008	A Role for Autophagy in the Extension of Lifespan by Dietary Restriction in C. elegans
DNA damage checkpoint activation can be subdivided in two steps: initial activation and signal amplification . The events distinguishing these two phases and their genetic determinants remain obscure . TopBP1 , a mediator protein containing multiple BRCT domains , binds to and activates the ATR/ATRIP complex through it...	DNA structure–dependent checkpoint activation and the amplification of checkpoint signals are carefully modulated to allow the checkpoint kinases to delay mitosis and regulate DNA metabolism . While much work has gone into understanding how this checkpoint functions , the mechanism by which the checkpoint signal is amp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	The Rad4TopBP1 ATR-Activation Domain Functions in G1/S Phase in a Chromatin-Dependent Manner
Dimorphism or morphogenic conversion is exploited by several pathogenic fungi and is required for tissue invasion and/or survival in the host . We have identified a homolog of a master regulator of this morphological switch in the plant pathogenic fungus Fusarium oxysporum f . sp . lycopersici . This non-dimorphic fung...	Plant pathogenic fungi have evolved many ways to infect their hosts and can have devastating effects on commercial crop production . Dissecting their infection strategies and understanding the molecular pathways involved in pathogenesis have been and continue to be the subject of intensive research . New insights gaine...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "pathology/molecular", "pathology" ]	2009	The Nuclear Protein Sge1 of Fusarium oxysporum Is Required for Parasitic Growth
Aurora kinases constitute a family of enzymes that play a key role during metazoan cells division , being involved in events like centrosome maturation and division , chromatin condensation , mitotic spindle assembly , control of kinetochore-microtubule attachments , and cytokinesis initiation . In this work , three Au...	The cell cycle is a complex and highly regulated cellular process in which different checkpoints are coordinated and a unique pattern of protein activities is present . In trypanosomatids , this process is even more complex because of the presence of the kinetoplast , a network of circular DNA inside a large mitochondr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "parasitic", "cell", "cycles", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "enzymology", "parasitic", "protozoans", "protozoan", "life", "cycles", "parasitology", "developmental", "biology", "trypomastigotes", "protozoans", ...	2019	Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins . Two models that explain this increase in complexity are: 1 ) adaptive changes after gene duplication , such as resolution of adaptive conflicts , and 2 ) non-adaptive processes such as dupli...	Parallel evolution of protein domain organization following gene duplication has been demonstrated in the spindle checkpoint pathway leading to the hypothesis that this organization is likely to be adaptive . We test this hypothesis by reconstructing budding yeast strains with a spindle checkpoint pathway containing a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "green", "fluorescent", "protein", "fungi", "luminescent", "proteins", "model", "organisms", "fungal", "evolution", "experimental", "organism", "systems", "sequence", "motif", "analysis", "saccharomyces", "research", "and", "analysis", "methods", "sequence", "analysis", ...	2017	Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments
The formation of species in the absence of geographic barriers ( i . e . sympatric speciation ) remains one of the most controversial topics in evolutionary biology . While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible , only a handful of accepted empirical e...	Speciation is the main driver of biological diversity and how species arise is a central question in evolutionary biology . For speciation to occur in sexually reproducing organisms the exchange of genetic material ( gene flow ) between populations has to be reduced . Ultimately this has to be due to genetically determ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "species", "colonization", "ecology", "and", "environmental", "sciences", "demography", "population", "genetics", "aquatic", "environments", "phylogenetic", "analysis", "speciation", "bodies", "of", "water", "molecular", "biology", "techniques", "population", "biology", "...	2016	Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids
Single-molecule techniques for protein sequencing are making headway towards single-cell proteomics and are projected to propel our understanding of cellular biology and disease . Yet , single cell proteomics presents a substantial unmet challenge due to the unavailability of protein amplification techniques , and the ...	Macromolecules identification methods are central for most biological and biomedical studies , and while the field of genomics advanced to single-molecule resolution , the proteomic field still relies on bulk and costly techniques . We describe a solution for single protein identification , based on the analysis of opt...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "transport", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "chemical", "compounds", "particle", "physics", "energy", "transfer", "cell", "processes", "immunology", "organic", "compounds", "developm...	2019	Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification
Zic3 regulates early embryonic patterning in vertebrates . Loss of Zic3 function is known to disrupt gastrulation , left-right patterning , and neurogenesis . However , molecular events downstream of this transcription factor are poorly characterized . Here we use the zebrafish as a model to study the developmental rol...	The Zic3 transcription factor regulates early embryonic patterning , and the loss of its function leads to defects in left-right body asymmetry . Previous studies have only identified a small number of Zic3 targets , which renders the molecular mechanism underlying its activity insufficiently understood . Utilizing two...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome Wide Analysis Reveals Zic3 Interaction with Distal Regulatory Elements of Stage Specific Developmental Genes in Zebrafish
Horizontal gene transfer ( HGT ) in bacteria generates variation and drives evolution , and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species . We previously described a novel form of chromosomal conjugation in mycobacteria that does not confor...	Bacteria reproduce by binary fission , generating two clones of the original; this restricts the genomic diversity of the population , which brings with it inherent evolutionary drawbacks . This problem can be eased by conjugation , which transfers DNA from a donor to a recipient bacterium . Understanding the potential...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "evolution", "microbiology", "genome", "sequencing", "prokaryotic", "models", "model", "organisms", "molecular", "cell", "biology", "microbial", "evolution", "molecular", "genetics", "microbial", "pathogens", "comparative",...	2013	Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus
The human immunity-related GTPase M ( IRGM ) has been shown to be critically involved in regulating autophagy as a means of disposing cytosolic cellular structures and of reducing the growth of intracellular pathogens in vitro . This includes Mycobacterium tuberculosis , which is in agreement with findings indicating t...	Autophagy is a process in which cell components are degraded by the lysosomal machinery . It has recently been described that activation of autophagy reduces the viability of M . tuberculosis in phagosomes due to an intimate autophagy-phagocytosis interaction . M . tuberculosis may also be directly accessible to autoph...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics", "microbiology/microbial", "evolution", "and", "genomics" ]	2009	Autophagy Gene Variant IRGM −261T Contributes to Protection from Tuberculosis Caused by Mycobacterium tuberculosis but Not by M. africanum Strains
The standard approach for identifying gene networks is based on experimental perturbations of gene regulatory systems such as gene knock-out experiments , followed by a genome-wide profiling of differential gene expressions . However , this approach is significantly limited in that it is not possible to perturb more th...	A complete understanding of how gene regulatory networks are wired in a biological system is important in many areas of biology and medicine . The most popular method for investigating a gene network has been based on experimental perturbation studies , where the expression of a gene is experimentally manipulated to ob...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "regulatory", "networks", "population", "genetics", "biology", "computational", "biology" ]	2014	Learning Gene Networks under SNP Perturbations Using eQTL Datasets
How cells communicate to initiate a regenerative response after damage has captivated scientists during the last few decades . It is known that one of the main signals emanating from injured cells is the Reactive Oxygen Species ( ROS ) , which propagate to the surrounding tissue to trigger the replacement of the missin...	One of the early events that occur after tissue damage consists on the production of Reactive Oxygen Species ( ROS ) , that signal to the surrounding tissue to initiate wound healing and regeneration . Many signaling pathways , such as JNK and p38 , respond to oxidative stress and are necessary for regenerative growth ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "redox", "signaling", "cell", "processes", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "organism", "development", "experimental", "organism", "systems", "morphogenesis", "...	2019	Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila
Although social behaviour can bring many benefits to an individual , there are also costs that may be incurred whenever the members of a social group interact . The formation of dominance hierarchies could offer a means of reducing some of the costs of social interaction , but individuals within the hierarchy may end u...	Dominance hierarchies could offer interacting animals a quick way to settle disputes without having to use too much effort . However , individuals may pay a price for acknowledging their position within the hierarchy , which could influence how they choose to behave within the group . Consequently , the actions of the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "game", "theory", "computer", "science", "evolutionary", "ecology", "computer", "modeling", "animal", "behavior", "mathematics", "theoretical", "biology", "ecology", "evolutionary", "biology", "applied", "mathematics", "theoretical", "ecology", "biology", "behavioral", "e...	2011	The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers
Cystic echinococcosis ( CE ) is a neglected parasitic zoonosis with considerable socioeconomic impact on affected pastoral communities . CE is endemic throughout the Mediterranean , including Morocco , where the Mid Atlas is the most prevalent area for both human and animal infection . The highest hospital annual incid...	Cystic Echinococcosis ( CE ) is a parasitic infection whose natural domestic cycle develops between dogs and sheep ( and other livestock ) . Human infection is endemic in pastoral communities , where close contact with the dog-sheep cycle occurs . In humans , as well as in livestock , the parasite develops as fluid-fil...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "livestock", "morocco", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "vertebrates", "parasitic", "diseases", "dogs", "mammals", "animals", "pets", "and", ...	2017	Human cystic echinococcosis in Morocco: Ultrasound screening in the Mid Atlas through an Italian-Moroccan partnership
Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world . These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions , such as redox homeostasis and nucleot...	Neglected tropical diseases caused by parasites of the genera Trypanosoma and Leishmania affect millions of people , primarily in the developing world . Due to a historical lack of incentive or interest , few new drugs have been developed to treat these conditions . Numerous efforts have targeted the metabolism of tryp...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "enzymology", "microbiology", "parasitic", "protozoans", "protozoans", "sequence", "motif", "analysis", "pharmacology", "enzyme", "inhibitors", "research", "and", "analysis", "methods", "sequence", "analysis", "bioinformatics", "bi...	2017	Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions
Invasive Non-typhoidal Salmonella ( iNTS ) are an important cause of bacteraemia in children and HIV-infected adults in sub-Saharan Africa . Previous research has shown that iNTS strains exhibit a pattern of gene loss that resembles that of host adapted serovars such as Salmonella Typhi and Paratyphi A . Salmonella ent...	Bacteraemia and meningitis caused by non-typhoidal Salmonella ( including serovars Typhimurium , Enteritidis and Bovismorbificans ) are a serious health issue in sub-Saharan Africa , particularly in young children and HIV-infected adults . Previous work has indicated that a distinct S . Typhimurium sequence type , ST31...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2013	Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi
Understanding the evolution of a protein , including both close and distant relationships , often reveals insight into its structure and function . Fast and easy access to such up-to-date information facilitates research . We have developed a hierarchical evolutionary classification of all proteins with experimentally ...	Protein structural domain databases offer a vital resource for structural bioinformatics . These databases provide functional inference for homologous structures , supply templates for structural prediction experiments , and differentiate between homologs and analogs . The rate of structure determination and deposition...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "protein", "structure", "comparison", "biochemistry", "proteins", "protein", "structure", "protein", "structure", "databases", "biology", "and", "life", "sciences", "protein", "domains" ]	2014	ECOD: An Evolutionary Classification of Protein Domains
The brain constantly infers the causes of the inputs it receives and uses these inferences to generate statistical expectations about future observations . Experimental evidence for these expectations and their violations include explicit reports , sequential effects on reaction times , and mismatch or surprise signals...	We explore the possibility that the computation of time-varying transition probabilities may be a core building block of sequence knowledge in humans . Humans may then use these estimates to predict future observations . Expectations derived from such a model should conform to several properties . We list six such prop...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "reaction", "time", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "mag...	2016	Human Inferences about Sequences: A Minimal Transition Probability Model
Elimination of kala-azar is planned for South Asia requiring good surveillance along with other strategies . We assessed surveillance in Gaffargaon upazila ( a subdistrict of 13 unions ) of Mymensingh district , Bangladesh highly endemic for kala-azar . In 4703 randomly sampled households , within nine randomly sampled...	Visceral leishmaniasis , a parasitic disease transmitted by sandflies , is known as kala-azar in South Asia , and has been targeted for elimination in that region . The aim is to reduce its incidence to a low level so that it is no longer a public health problem . Elimination strategies include good surveillance for oc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Performance of Kala-Azar Surveillance in Gaffargaon Subdistrict of Mymensingh, Bangladesh
Mitochondrial DNA ( mtDNA ) encodes proteins essential for ATP production . Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging , genetic diseases , and sensitivity to environmental agents . We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mut...	Thousands of mitochondrial DNA ( mtDNA ) per cell are necessary to maintain energy required for cellular survival in humans . Interfering with the mtDNA polymerase can result in mitochondrial diseases and mitochondrial toxicity . Therefore , it is important to explore new genetic and environmental mechanisms that alter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutagenesis", "biochemistry", "mitochondrial", "genetics", "medicine", "and", "health", "sciences", "dna", "polymerase", "polymerases", "dna", "replication", "proteins", "mitochondrial", "dna", "forms", "of", "dna", "genetics", "biology", "and", "life", "sciences", "...	2014	MMS Exposure Promotes Increased MtDNA Mutagenesis in the Presence of Replication-Defective Disease-Associated DNA Polymerase γ Variants
Our investigations show that nonlethal concentrations of nitric oxide ( NO ) abrogate the antibiotic activity of β-lactam antibiotics against Burkholderia pseudomallei , Escherichia coli and nontyphoidal Salmonella enterica serovar Typhimurium . NO protects B . pseudomallei already exposed to β-lactams , suggesting tha...	β-lactam drugs that inhibit peptidoglycan biosynthesis are often used in the treatment of bacterial infections , including melioidosis . Independent of their antibiotic activity , we have noted that submicromolar concentrations of β-lactams potentiate the killing of intracellular B . pseudomallei supported by NO genera...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medical", "microbiology", "microbiology" ]	2014	Nitric Oxide from IFNγ-Primed Macrophages Modulates the Antimicrobial Activity of β-Lactams against the Intracellular Pathogens Burkholderia pseudomallei and Nontyphoidal Salmonella
Embryonic development is tightly regulated by transcription factors and chromatin-associated proteins . H3K4me3 is associated with active transcription and H3K27me3 with gene repression , while the combination of both keeps genes required for development in a plastic state . Here we show that deletion of the H3K4me2/3 ...	Histone modifications are involved in transcriptional regulation and thus affect cellular identity , differentiation , and development . We study the histone demethylase Jarid1b ( Kdm5b/Plu1 ) , as it has been reported to be highly expressed in several human cancers and therefore might present a novel target for anti-c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3
Copy-number variations ( CNVs ) constitute very common differences between individual humans and possibly all genomes and may therefore be important fuel for evolution , yet how they form remains elusive . In starving Escherichia coli , gene amplification is induced by stress , controlled by the general stress response...	Much of the difference between individual humans is in the number of copies of genes and lengths of genome . The mechanisms by which copy number variation arises are not well understood . We sought information on copy number change mechanisms by extensive use of array comparative genomic hybridization of whole genomes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cancer", "genetics", "genetics", "molecular", "genetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2011	Global Chromosomal Structural Instability in a Subpopulation of Starving Escherichia coli Cells
Paracoccidioides brasiliensis and Paracoccidioides lutzii are the etiological agents of Paracoccidioidomycosis ( PCM ) , and are easily isolated from human patients . However , due to human migration and a long latency period , clinical isolates do not reflect the spatial distribution of these pathogens . Molecular det...	Paracoccidioides brasiliensis and Paracoccidioides lutzii are the fungal species responsible for one of the most important mycoses of Latin America , Paracoccidioidomycosis ( PCM ) . These fungi can grow in soil from forests , deforested areas , sugarcane , coffee , and rice plantations , as well as pasturelands , and ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "in", "situ", "hybridization", "molecular", "probe", "techniques", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "xenarthra", "fungi", "materials", "science", "spe...	2016	Environmental Mapping of Paracoccidioides spp. in Brazil Reveals New Clues into Genetic Diversity, Biogeography and Wild Host Association
A relatively small number of signals are responsible for the variety and pattern of cell types generated in developing embryos . In part this is achieved by exploiting differences in the concentration or duration of signaling to increase cellular diversity . In addition , however , changes in cellular competence—tempor...	During embryonic development different cell types arise at different times and places . This diversity is produced by a relatively small number of signals and depends , at least in part , on changes in the way cells respond to each signal . One example of this so-called change in “competence” is found in the vertebrate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "cell", "fate", "determination", "developmental", "biology" ]	2014	Integration of Signals along Orthogonal Axes of the Vertebrate Neural Tube Controls Progenitor Competence and Increases Cell Diversity
The Haemophilus influenzae HMW1 adhesin is a high-molecular weight protein that is secreted by the bacterial two-partner secretion pathway and mediates adherence to respiratory epithelium , an essential early step in the pathogenesis of H . influenzae disease . In recent work , we discovered that HMW1 is a glycoprotein...	Decoration of proteins with carbohydrates has an important impact on protein function throughout biology and has been recognized increasingly in pathogenic bacteria . Haemophilus influenzae is a common cause of both bacterial respiratory tract disease and bacterial invasive disease and initiates infection by colonizing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "biochemistry/biocatalysis" ]	2010	The Haemophilus influenzae HMW1C Protein Is a Glycosyltransferase That Transfers Hexose Residues to Asparagine Sites in the HMW1 Adhesin
Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells . The exact nature of these interactions , which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryo...	We elucidate by computational means the processes by which the development of the mammalian embryo during its first four to five days occurs , as it is transformed from a single stem cell into hundreds of cells of different tissue types . We are interested in understanding the fundamental processes of how gene expressi...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "developmental", "biology/embryology", "developmental", "biology/stem", "cells", "developmental", "biology/morphogenesis", "and", "cell", "biology", "computational", "biology/transcriptional", "regulation", "biophysics/theory", "and", "simulation" ]	2011	Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo
Allergic reactions can be considered as maladaptive IgE immune responses towards environmental antigens . Intriguingly , these mechanisms are observed to be very similar to those implicated in the acquisition of an important degree of immunity against metazoan parasites ( helminths and arthropods ) in mammalian hosts ....	Allergy is an increasingly widespread clinical problem that leads to various conditions such as allergic asthma and susceptibility to anaphylactic shock . These conditions arise from exposure to a range of environmental and food proteins ( ‘allergens’ ) that are recognised by a form of immune system antibody called IgE...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity
Resistance of the snail Biomphalaria glabrata to the trematode Schistosoma mansoni is correlated with allelic variation at copper-zinc superoxide dismutase ( sod1 ) . We tested whether there is a fitness cost associated with carrying the most resistant allele in three outbred laboratory populations of snails . These th...	Driving resistance genes into vector populations remains a promising but underused method for reducing transmission of vector-borne diseases . Understanding the genetic mechanisms governing resistance and how resistance is maintained in vector populations is essential for the development of resistant vectors as a means...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "of", "disease", "trait", "locus", "heredity", "genetics", "biology", "evolutionary", "biology", "evolutionary", "selection", "genetic", "determinism", "evolutionary", "processes", "genetics", "and", "genomics" ]	2012	Effects of Cu/Zn Superoxide Dismutase (sod1) Genotype and Genetic Background on Growth, Reproduction and Defense in Biomphalaria glabrata
Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging . In this study we utilized the budding yeast , Saccharomyces cerevisiae , in a large-scale screen for genes that function in the regulation of chronological lifespan , which is defined by the n...	The aging process is associated with the onset of several age-associated diseases including diabetes and cancer . In rodent model systems , the dietary regimen known as caloric restriction ( CR ) is known to delay or prevent these diseases and to extend lifespan . As a result , there is a great deal of interest in unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics", "molecular", "biology" ]	2010	A Microarray-Based Genetic Screen for Yeast Chronological Aging Factors
Soil may serve as an environmental reservoir for prion infectivity and contribute to the horizontal transmission of prion diseases ( transmissible spongiform encephalopathies [TSEs] ) of sheep , deer , and elk . TSE infectivity can persist in soil for years , and we previously demonstrated that the disease-associated f...	Transmissible spongiform encephalopathies ( TSEs ) are a group of incurable neurological diseases likely caused by a misfolded form of the prion protein . TSEs include scrapie in sheep , bovine spongiform encephalopathy ( “mad cow” disease ) in cattle , chronic wasting disease in deer and elk , and Creutzfeldt-Jakob di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology", "mathematics", "none", "science", "policy", "neurological", "disorders", "gastroenterology", "and", "hepatology", "in", "vitro", "mus", "(mouse)", "mammals" ]	2007	Oral Transmissibility of Prion Disease Is Enhanced by Binding to Soil Particles
A common theoretical view is that attractor-like properties of neuronal dynamics underlie cognitive processing . However , although often proposed theoretically , direct experimental support for the convergence of neural activity to stable population patterns as a signature of attracting states has been sparse so far ,...	For understanding how neural processes give rise to cognitive operations , it is essential to understand how aspects of the underlying neural network dynamics reconstructed from neurophysiological measurements relate to behavior . For instance , different actions may be represented by neural states characterized by sta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "biology", "computational", "biology", "neuroscience" ]	2011	Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making
The models in statistical physics such as an Ising model offer a convenient way to characterize stationary activity of neural populations . Such stationary activity of neurons may be expected for recordings from in vitro slices or anesthetized animals . However , modeling activity of cortical circuitries of awake anima...	Simultaneous analysis of large-scale neural populations is necessary to understand coding principles of neurons because they concertedly process information . Methods of thermodynamics and statistical mechanics are useful to understand collective phenomena of the interacting elements , and they have been successfully u...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "applied", "mathematics", "population", "dynamics", "membrane", "potential", "electrophysiology", "random", "variables", "neuroscience", "covariance", "simulation", "and", "modeling", "...	2017	Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
Diagnosis of leptospirosis by the gold standard serologic assay , the microscopic agglutination test ( MAT ) , requires paired sera and is not widely available . We developed a rapid assay using immunodominant Leptospira immunoglobulin-like ( Lig ) proteins in a Dual Path Platform ( DPP ) . This study aimed to evaluate...	Leptospirosis is an important cause of acute fever in the tropics and the mortality rate may exceed 15% in patients with severe disease manifestations . The gold standard serological test for diagnosing leptospirosis , the microagglutination test or MAT , requires significant laboratory resources and results are not ti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "immunology", "bacterial", "diseases", "test", "evaluation", "clinical", "epidemiology", "global", "health", "neglected", "tropical", "diseases", "immunologic", "techniques", "infectious", "diseases", "epidemiology", ...	2012	Accuracy of a Dual Path Platform (DPP) Assay for the Rapid Point-of-Care Diagnosis of Human Leptospirosis
The information processing abilities of neural circuits arise from their synaptic connection patterns . Understanding the laws governing these connectivity patterns is essential for understanding brain function . The overall distribution of synaptic strengths of local excitatory connections in cortex and hippocampus is...	The computations that brain circuits can perform depend on their wiring . While a wiring diagram is still out of reach for major brain structures such as the neocortex and hippocampus , data on the overall distribution of synaptic connection strengths and the temporal fluctuations of individual synapses have recently b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "computational", "neuroscience", "biology", "neuroscience" ]	2013	Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex
Positive strand RNA viruses , such as dengue virus type 2 ( DENV2 ) expand and structurally alter ER membranes to optimize cellular communication pathways that promote viral replicative needs . These complex rearrangements require significant protein scaffolding as well as changes to the ER chemical composition to supp...	Dengue viruses are aggressive mosquito-borne viruses causing over 350 million infections annually . There are no antivirals to combat infection and the only vaccine available is suboptimal . Here , we have investigated how these viruses hijack critical metabolic pathways in cells to convert the host environment to supp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "oleic", "acid", "gene", "regulation", "rna", "extraction", "microbiology", "viral", "structure", "viruses", "rna", "viruses", "extraction", "techniques", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "lipids", "gene", "expression", "viral"...	2018	Stearoly-CoA desaturase 1 differentiates early and advanced dengue virus infections and determines virus particle infectivity
Ion homeostasis is essential for plant growth and environmental adaptation , and maintaining ion homeostasis requires the precise regulation of various ion transporters , as well as correct root patterning . However , the mechanisms underlying these processes remain largely elusive . Here , we reported that a choline t...	Ion transporters play a key role in mineral nutrients uptake and transport of plants . Their cellular and subcellular localization is essential for fulfilling their functions and are therefore generally fine-tuned . However , the molecular mechanisms underlying this process remain largely unclear . In this study , we a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "transport", "b", "vitamins", "cell", "physiology", "plant", "anatomy", "medicine", "and", "health", "sciences", "vesicles", "chemical", "compounds", "cell", "processes", "green", "fluorescent", "protein", "organic", "compounds", "cholines", "physiological", ...	2017	A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis
Previous studies in Saccharomyces cerevisiae established that depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds of genes . To probe the mechanism of this transcriptional de-repression , we depleted nucleosomes in vivo by conditional repression of histone H3 transcription . We ...	Chromatin is formed by wrapping 146 bp of DNA around a disc-shaped complex of proteins called histones . These protein–DNA structures are known as nucleosomes . Nucleosomes help to regulate gene transcription , because nucleosomes compete with transcription factors for access to DNA . The precise positioning and level ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "genomics", "functional", "genomics", "molecular", "cell", "biology", "molecular", "biology", "gene", "regulation", "gene", "expression", "molecular", "genetics", "biology", "computational", "biology", "chromatin", "genetics", "and", ...	2012	In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae

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