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Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas , yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers . Biomedical researchers who embrace cloud computing can reap reward...	Cloud computing has revolutionized the tech sector , but academia is slow to adopt . These 11 quick tips are geared towards helping academic researchers and their teams harness the power of cloud computing by utilizing the design patterns that have evolved in the past decade . Cloud computing can increase reproducibili...	[ "Abstract", "Introduction", "Templatize", "infrastructure", "with", "version", "control", "Embrace", "ephemerality:", "Image", "data", "and", "software", "Use", "containers", "Manage", "security", "and", "privacy", "as", "code", "Use", "managed", "services", "instead"...	[ "cloud", "computing", "education", "engineering", "and", "technology", "computer", "hardware", "data", "management", "scientists", "science", "and", "technology", "workforce", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "compu...	2018	Eleven quick tips for architecting biomedical informatics workflows with cloud computing
While the recognition of microbial infection often occurs at the cell surface via Toll-like receptors , the cytosol of the cell is also under surveillance for microbial products that breach the cell membrane . An important outcome of cytosolic recognition is the induction of IFNα and IFNβ , which are critical mediators...	Bacterial and viral infection stimulates production of several cytokines and chemokines that are thought to protect the host against infection . The bacterial strain known to cause tuberculosis elicits production of type I interferons , yet it was unclear how the bacteria isolated within the cell was capable of stimula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity" ]	2009	NOD2, RIP2 and IRF5 Play a Critical Role in the Type I Interferon Response to Mycobacterium tuberculosis
Cells in organ primordia undergo active proliferation at an early stage to generate sufficient number , before exiting proliferation and entering differentiation . However , how the actively proliferating cells are developmentally reprogrammed to acquire differentiation potential during organ maturation is unclear . He...	Cells in a young organ primordium proliferate to generate sufficient number , before they exit division cycle and enter differentiation programme at later stages . While factors that drive cell cycle progression have been identified and studied in detail in diverse eukaryotic species , developmental factors that promot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "classical", "mechanics", "pavement", "cells", "gene", "regulation", "plant", "cell", "biology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "regulatory", "proteins", "dna-binding", "proteins", "cell", "differentiation", "hormo...	2019	The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways
Next to the two-component and quorum sensing systems , cell-surface signaling ( CSS ) has been recently identified as an important regulatory system in Pseudomonas aeruginosa . CSS systems sense signals from outside the cell and transmit them into the cytoplasm . They generally consist of a TonB-dependent outer membran...	Pseudomonas aeruginosa is a versatile pathogen; these bacteria are able to cause an infection in humans and other mammals , zebrafish , insects , nematodes and even plants . P . aeruginosa evolved an impressive amount of gene regulation systems to be able to express the right virulence genes under the right circumstanc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	A Novel Extracytoplasmic Function (ECF) Sigma Factor Regulates Virulence in Pseudomonas aeruginosa
Signal transducer and activator of transcription 3 ( Stat3 ) transduces signals of many peptide hormones from the cell surface to the nucleus and functions as an oncoprotein in many types of cancers , yet little is known about how it achieves its native folded state within the cell . Here we show that Stat3 is a novel ...	Stat3 is a multidomain transcription factor that contributes to many cellular functions by transmitting signals for over 40 peptide hormones from the cell surface to the nucleus . Understanding how multidomain proteins achieve their fully folded and functional state is of substantial biological interest . As Stat3 sign...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "signal", "transduction", "cell", "biology", "proteins", "chaperone", "proteins", "biology", "and", "life", "sciences", "molecular", "cell", "biology" ]	2014	Modulation of STAT3 Folding and Function by TRiC/CCT Chaperonin
Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads . In the SCAR/WAVE ( Suppressor of cAMP receptor defect/WASP family verpolin homologous protein ) actin regulatory complex , the conserved N...	Characterization of Lotus japonicus mutants defective for nodule infection by rhizobia led to the identification of a gene we named SCARN . Two of the five alleles caused formation of branched root-hairs in uninoculated seedlings , suggesting SCARN plays a role in the microtubule and actin-regulated polar growth of roo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation
Regions of the genome that have been the target of positive selection specifically along the human lineage are of special importance in human biology . We used high throughput sequencing combined with methods to enrich human genomic samples for particular targets to obtain the sequence of 22 chromosomal samples at high...	The search for functional regions in the human genome , beyond the protein-coding portion , often relies on signals of conservation across species . The Human Accelerated Regions ( HARs ) are strongly conserved elements , ranging in size from 100–400 bp , that show an unexpected number of human-specific changes . This ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2010	GC-Biased Evolution Near Human Accelerated Regions
During online speech processing , our brain tracks the acoustic fluctuations in speech at different timescales . Previous research has focused on generic timescales ( for example , delta or theta bands ) that are assumed to map onto linguistic features such as prosody or syllables . However , given the high intersubjec...	How we comprehend speech—and how the brain encodes information from a continuous speech stream—is of interest for neuroscience , linguistics , and research on language disorders . Previous work that examined dynamic brain activity has addressed the issue of comprehension only indirectly , by contrasting intelligible sp...	[ "Abstract", "Results", "Discussion", "Materials", "and", "methods" ]	[ "syllables", "linguistics", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "nervous", "system", "signal", "processing", "social", "sciences", "neuroscience", "brain", "mapping", "neuroimaging", "research", "and", "analysis", "methods", "syn...	2018	Perceptually relevant speech tracking in auditory and motor cortex reflects distinct linguistic features
Membrane-protein design is an exciting and increasingly successful research area which has led to landmarks including the design of stable and accurate membrane-integral proteins based on coiled-coil motifs . Design of topologically more complex proteins , such as most receptors , channels , and transporters , however ...	Membrane proteins comprise a third of the genome and have essential roles as intermediaries between the cell and its environment . Despite exciting recent progress in membrane-protein modelling and design , however , these fields lag far behind advances in soluble proteins , chiefly because of inaccurate modelling of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "membrane", "potential", "electrophysiology", "membrane", "proteins", "mutation", "protein", "structure", "prediction", "protein", "structure", "sequence", "motif", "analysis", "cellular", "structures", "and", "organelles", "resear...	2019	A lipophilicity-based energy function for membrane-protein modelling and design
With the antibiotic development pipeline running dry , many fear that we might soon run out of treatment options . High-density infections are particularly difficult to treat due to their adaptive multidrug-resistance and currently there are no therapies that adequately address this important issue . Here , a large-sca...	There has been enormous publicity about the inexorable rise of resistance and the dearth of new therapies . However less attention has been placed on adaptively multidrug-resistant high density bacterial infections for which antibiotics are highly used but no effective therapies currently exist . Here we have provided ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "biotechnology", "antimicrobials", "synthetic", "biotechnology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "drugs", "synthetic", "biology", "microbiology", "staphylococcus", "aureu...	2018	Synergy between conventional antibiotics and anti-biofilm peptides in a murine, sub-cutaneous abscess model caused by recalcitrant ESKAPE pathogens
Impairment of the intestinal barrier and subsequent microbial translocation ( MT ) may be involved in chronic immune activation , which plays a central role in HIV pathogenesis . Th17 cells are critical to prevent MT . The aim of the study was to investigate , in patients with primary HIV infection ( PHI ) , the early ...	Generalized immune activation is pivotal in the pathogenesis of HIV disease . Impairment in the gut mucosal barrier allows the translocation of microbial flora from the gut towards the circulation . Translocated microbial products , together with HIV replication , contribute to chronic immune activation . Th17 cells ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "cytokines", "monocytes", "clinical", "immunology", "immunity", "hiv", "innate", "immunity", "immune", "activation", "t", "cells", "immunity", "to", "infections", "immunology", "biology", "immunoregulation", "vira...	2013	The Th17/Treg Ratio, IL-1RA and sCD14 Levels in Primary HIV Infection Predict the T-cell Activation Set Point in the Absence of Systemic Microbial Translocation
The WHO has established the disability-adjusted life year ( DALY ) as a metric for measuring the burden of human disease and injury globally . However , most DALY estimates have been calculated as national totals . We mapped spatial variation in the burden of human African trypanosomiasis ( HAT ) in Uganda for the year...	Since the 1990s the World Health Organisation has established the disability-adjusted life year ( DALY ) as a metric for the burden of human disease and injury . However , disease burden has primarily been estimated at the national scale , which does not account for sub-country variations in burden levels . We used the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "disease", "mapping", "geography", "social", "and", "behavioral", "sciences", "global", "health", "epidemiology", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "spatial", "analysis", "human", "geography" ]	2014	Incorporating Scale Dependence in Disease Burden Estimates: The Case of Human African Trypanosomiasis in Uganda
This model-based design of experiments ( MBDOE ) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study . The ideal global solution for this experiment design problem...	Many mathematical models that have been developed for biological systems are limited because the complex systems are not well understood , the parameters are not known , and available data is limited and noisy . On the other hand , experiments to support model development are limited in terms of costs and time , feasib...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty
Nematode-trapping fungi are “carnivorous” and attack their hosts using specialized trapping devices . The morphological development of these traps is the key indicator of their switch from saprophytic to predacious lifestyles . Here , the genome of the nematode-trapping fungus Arthrobotrys oligospora Fres . ( ATCC24927...	The fungus Arthrobotrys oligospora has multiple lifestyles . It's not only a nematode pathogen , but also a saprophyte , a pathogen of other fungi , and a colonizer of plant roots . As a nematode pathogen , A . oligospora forms adhesive networks to capture nematodes and is a model organism for understanding the interac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology", "host-pathogen", "interaction", "gene", "function", "genome", "sequencing", "fungi", "sequence", "analysis", "mycology", "gene", "expression", "microbial", "pathogens", "comparative", "genomics", "biology", "proteomics", "pathogenesis", "biochemistry", "gene...	2011	Genomic and Proteomic Analyses of the Fungus Arthrobotrys oligospora Provide Insights into Nematode-Trap Formation
Chikungunya virus ( CHIKV ) is an emerging arbovirus , belonging to the Togaviridae family , Alphavirus genus , transmitted by Aedes spp . mosquitoes . Since 2007 , two different CHIKV strains ( E1-226A and E1-226V ) have been responsible for outbreaks in European countries , including Italy , sustained by Ae . albopic...	Aedes albopictus is a proven vector of more than 20 different arboviruses and , as demonstrated by experimental infections , is an efficient vector of chikungunya virus ( CHIKV ) in several countries . In Italy this widespread species caused the first outbreak of CHIKV in Europe in 2007 ( Emilia-Romagna region ) and re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "european", "union", "landforms", "pathogens", "italian", "people", "topography", "tropica...	2018	Vector competence of Italian Aedes albopictus populations for the chikungunya virus (E1-226V)
Interleukin-1 ( IL-1 ) is a large cytokine family closely related to innate immunity and inflammation . IL-1 proteins are key players in signaling pathways such as apoptosis , TLR , MAPK , NLR and NF-κB . The IL-1 pathway is also associated with cancer , and chronic inflammation increases the risk of tumor development ...	Structural pathways are important because they provide insight into signaling mechanisms; help understand the mechanism of disease-related mutations; and help in drug discovery . While extremely useful , common pathway diagrams lacking structural data are unable to provide mechanistic insight to explain oncogenic mutat...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "protein", "interactions", "proteins", "protein", "structure", "biology", "computational", "biology" ]	2014	The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer
The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain . Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins . Despite these advantages , many proteins...	High prevalence of multi-domain proteins in proteomes has been attributed to higher stability and functional and folding advantages of the multi-domain proteins . Influence of tethering of domains on the overall properties of proteins has been well studied but its influence on the properties of the constituent domains ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "molecular", "dynamics", "condensed", "matter", "physics", "dna-binding", "proteins", "probability", "distribution", "mathematics", "polymerases", "network", "analysis", "protein", "structure", "crystallography", "crystallization", "research", "and", "analysis", "methods", ...	2018	Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
Protein aggregation into amyloid fibrils and protofibrillar aggregates is associated with a number of the most common neurodegenerative diseases . We have established , using a computational approach , that knowledge of the primary sequences of proteins is sufficient to predict their in vitro aggregation propensities ....	A wide range of diseases , including diabetes and common brain diseases of old age , are characterised by the deposition of protein in the affected tissues . Alzheimer disease , the most common neurodegenerative disorder , is caused by the aggregation and deposition of a peptide called Aβ in the brain . We have previou...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "neurological", "disorders", "computational", "biology", "biophysics" ]	2007	Systematic In Vivo Analysis of the Intrinsic Determinants of Amyloid β Pathogenicity
Aging and longevity are considered to be highly complex genetic traits . In order to gain insight into aging as a polygenic trait , we employed an outbred Saccharomyces cerevisiae model , generated by crossing a vineyard strain RM11 and a laboratory strain S288c , to identify quantitative trait loci that control chrono...	Dietary restriction promotes longevity in many species , ranging from yeast to primates , and delays aging-related pathologies including cancer in rodent models . There is considerable interest in understanding how nutrient limitation mediates these beneficial effects . Much of what we have learned about the genetics o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "dna", "replication", "dna", "metabolic", "pathways", "biology", "molecular", "biology", "systems", "biology", "biochemistry", "nitrogen", "metabolism", "nucleic", "acids", "genetics", "molecular", "cell", "biology", "metabolism", "genetics", "and", ...	2011	Natural Polymorphism in BUL2 Links Cellular Amino Acid Availability with Chronological Aging and Telomere Maintenance in Yeast
Enterovirus A71 ( EV-A71 ) is an important emerging pathogen causing large epidemics of hand , foot and mouth disease ( HFMD ) in children . In Malaysia , since the first EV-A71 epidemic in 1997 , recurrent cyclical epidemics have occurred every 2–3 years for reasons that remain unclear . We hypothesize that this cycli...	Enterovirus A71 ( EV-A71 ) is a major cause of hand , foot , and mouth disease ( HFMD ) in children . Since the first outbreak in Malaysia in 1997 , EV-A71 epidemics have occurred every 2–3 years , in 2000 , 2003 , 2006 , 2008/2009 , and 2012 . As the reasons for this cyclical pattern are not known , we hypothesize tha...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "immune", "physiology", "infectious", "disease", "epidemiology", "immunology", "geographical", "locations", "age", "groups", "antibodies", "families", "genetic", "epidemiology", "immune", "system", "proteins", "infectio...	2016	Cyclical Patterns of Hand, Foot and Mouth Disease Caused by Enterovirus A71 in Malaysia
Members of the phylum Apicomplexa , which include the malaria parasite Plasmodium , share many features in their invasion mechanism in spite of their diverse host cell specificities and life cycle characteristics . The formation of a moving junction ( MJ ) between the membranes of the invading apicomplexan parasite and...	Malaria arises from infection of erythrocytes by single-cell parasites belonging to the genus Plasmodium , the species P . falciparum causing the most severe forms of the disease . The formation of a moving junction ( MJ ) between the membranes of the parasite and its host cell is essential for invasion . Two important...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "cell", "biology", "protein", "interactions", "proteins", "protein", "structure", "biology", "microbiology", "parasitology" ]	2012	Structural and Functional Insights into the Malaria Parasite Moving Junction Complex
Among the natural compounds , terpenoids play an important role in the drug discovery process for tropical diseases . The aim of the present work was to isolate antiprotozoal compounds from Ambrosia elatior and A . scabra . The sesquiterpene lactone ( STL ) cumanin was isolated from A . elatior whereas two other STLs ,...	In addition to the primary metabolism necessary for life , plants have a secondary metabolism that generates compounds , which aid in their growth and development . A common role of secondary metabolites is defense mechanisms to fight off animals , pest and pathogens . Pharmacognosy takes advantage of the rich source o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Natural Terpenoids from Ambrosia Species Are Active In Vitro and In Vivo against Human Pathogenic Trypanosomatids
Barley ( Hordeum vulgare L . ) Mla alleles encode coiled-coil ( CC ) , nucleotide binding , leucine-rich repeat ( NB-LRR ) receptors that trigger isolate-specific immune responses against the powdery mildew fungus , Blumeria graminis f . sp . hordei ( Bgh ) . How Mla or NB-LRR genes in grass species are regulated at po...	Plants rely on cell-surface and intracellular immune receptors to sense pathogen invasion and to mediate defense responses . However , uncontrolled activation of immune responses is harmful to plant growth and development . Small RNAs have recently been shown to fine-tune the expression of intracellular immune receptor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "micrornas", "plant", "science", "plant", "disease", "resistance", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "plant", "pathology" ]	2014	The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling
Enhancing brown fat activity and promoting white fat browning are attractive therapeutic strategies for treating obesity and associated metabolic disorders . To provide a comprehensive picture of the gene regulatory network in these processes , we conducted a series of transcriptome studies by RNA sequencing ( RNA-seq ...	Fat accumulation is a major health problem in many countries , but unlike white fat—which stores calories—brown fat is packed with mitochondria to burn energy . Therefore , promoting “browning” of white fat and enhancing brown fat activity are seen as promising therapeutic strategies to fight obesity . Long noncoding R...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "brown", "adipose", "tissue", "messenger", "rna", "long", "non-coding", "rnas", "cell", "differentiation", "developmental", "biology", "adipocytes", "connective", "tissue", "cells", "genome", "analysis", "adipocyte", "differentia...	2017	Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators
West Nile virus is globally wide-spread and causes significant disease in humans and animals . The evolution of West Nile virus Kunjin subtype in Australia ( WNVKUN ) was investigated using archival samples collected over a period of 50 years . Based on the pattern of fixed amino acid substitutions and time-stamped mol...	West Nile virus is endemic in Australia , and is considered benign in relation to strains that circulate globally . In 2011 , a more pathogenic variant emerged which caused disease in horses . To understand the evolution of the virus , and as a background to the emergence of the pathogenic strain , we used high through...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "organismal", "evolution", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "australia", "organic", "compounds", "viruses", ...	2016	Archival Isolates Confirm a Single Topotype of West Nile Virus in Australia
The World Bank Loan Project ( WBLP ) for controlling schistosomiasis in China was implemented during 1992–2001 . Its short-term impact has been assessed from non-spatial perspective , but its long-term impact remains unclear and a spatial evaluation has not previously been conducted . Here we compared the spatial distr...	Schistosomiasis japonica is an important disease in China with a documented history of more than 2 , 100 years . The World Bank Loan Project ( WBLP ) implemented during 1992–2001 contributed greatly to China's schistosomiasis control . This study shows that the long-term impact of WBLP strategy on schistosomiasis contr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Long-Term Impact of the World Bank Loan Project for Schistosomiasis Control: A Comparison of the Spatial Distribution of Schistosomiasis Risk in China
Staphylococcal enterotoxins ( SEs ) produced by Staphylococcus aureus are known as causative agents of emetic food poisoning . We previously demonstrated that SEA binds with submucosal mast cells and evokes mast cell degranulation in a small emetic house musk shrew model . Notably , primates have been recognized as the...	Staphylococcal enterotoxin A ( SEA ) is a bacterial toxin that has been recognized as a leading causative agent of staphylococcal food poisoning since 1930 . The primary symptoms of staphylococcal food poisoning are nausea and emesis , which develop up to 1–6 h after ingestion of the causative foods contaminated by the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "mast", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "vomiting", "vertebrates", "marmosets", "neuroscience", "animals", "mammals", "organic", "compounds", ...	2019	Histamine release from intestinal mast cells induced by staphylococcal enterotoxin A (SEA) evokes vomiting reflex in common marmoset
Endoreplication is a cell cycle variant that entails cell growth and periodic genome duplication without cell division , and results in large , polyploid cells . Cells switch from mitotic cycles to endoreplication cycles during development , and also in response to conditional stimuli during wound healing , regeneratio...	Endoreplication is a cell cycle variant that entails cell growth and periodic genome duplication without cell division , and results in large , polyploid cells . Cells switch from mitotic division cycles to endoreplication cycles during development , and also in response to conditional stimuli during wound healing , re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cloning", "departures", "from", "diploidy", "animals", "animal", "models", "mitosis", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "cytokines...	2019	A Cyclin A—Myb-MuvB—Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles
Dengue is a growing problem both in its geographical spread and in its intensity , and yet current global distribution remains highly uncertain . Challenges in diagnosis and diagnostic methods as well as highly variable national health systems mean no single data source can reliably estimate the distribution of this di...	Previous attempts to map the current global distribution of dengue virus transmission have produced variable results , particularly in Africa , reflecting the lack of accuracy in both diagnostic and locational information of reported dengue cases . In this study , instead of excluding these less informed points we incl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "dengue", "fever", "neglected", "tropical", "diseases", "dengue", "viral", "diseases", "epidemiological", "methods", "disease", "in...	2012	Refining the Global Spatial Limits of Dengue Virus Transmission by Evidence-Based Consensus
The assembly of the mitotic centromere has been extensively studied in recent years , revealing the sequence and regulation of protein loading to this chromosome domain . However , few studies have analyzed centromere assembly during mammalian meiosis . This study specifically targets this approach on mouse spermatocyt...	The centromere is a chromosome domain essential for the correct partitioning of chromosomes during mitotic and meiotic cell divisions . The characterization of the centromeric proteins and their sequential assembly have been extensively studied in mammalian mitosis , since defective chromosome segregation is associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/nuclear", "structure", "and", "function", "cell", "biology", "genetics", "and", "genomics/chromosome", "biology" ]	2009	Sequential Assembly of Centromeric Proteins in Male Mouse Meiosis
Cell stress and infection promote the formation of ubiquitinated aggregates in both non-immune and immune cells . These structures are recognised by the autophagy receptor p62/sequestosome 1 and are substrates for selective autophagy . The intracellular growth of Salmonella enterica occurs in a membranous compartment ,...	Ubiquitination can target substrates to a number of fates , including autophagy , the essential cellular process that allows cells to degrade cytosolic material . Although Salmonella enterica resides in a vacuolar compartment during infection , it translocates several virulence proteins into the host cell cytoplasm . W...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology" ]	2012	The Salmonella Deubiquitinase SseL Inhibits Selective Autophagy of Cytosolic Aggregates
Children affected by Specific Language Impairment ( SLI ) fail to acquire age appropriate language skills despite adequate intelligence and opportunity . SLI is highly heritable , but the understanding of underlying genetic mechanisms has proved challenging . In this study , we use molecular genetic techniques to inves...	Children affected by Specific Language Impairment ( SLI ) have unexpected problems learning to talk and understand language , despite developing normally in all other areas . This disorder runs in families but we do not understand how the genetic contributions work , or which genetic mechanisms might be important . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment
It has been proposed that in wild ecosystems viruses are often plant mutualists , whereas agroecosystems favour pathogenicity . We seek evidence for virus pathogenicity in wild ecosystems through the analysis of plant-virus coevolution , which requires a negative effect of infection on the host fitness . We focus on th...	Plant-virus coevolution has not been demonstrated in any wild system , and it has been proposed that viruses often would be mutualistic symbionts , rather than pathogens , in wild plant ecosystems . We analyse if viruses are virulent pathogens of plants in wild ecosystems and , consequently , plants have evolved defenc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "population", "genetics", "brassica", "plant", "science", "model", "organisms", "coevolution", "experimental", "organism", "systems", "plant", "pathology", "popula...	2019	Cucumber mosaic virus infection as a potential selective pressure on Arabidopsis thaliana populations
The maternally inherited intracellular bacteria Wolbachia can manipulate host reproduction in various ways that foster frequency increases within and among host populations . Manipulations involving cytoplasmic incompatibility ( CI ) , where matings between infected males and uninfected females produce non-viable embry...	Wolbachia are bacteria that live within the cells of arthropod hosts and are widespread in many groups of insects . These bacteria can rapidly spread through a population through a process of cytoplasmic incompatibility whereby females uninfected by Wolbachia show embryo death when they mate with males carrying the bac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "biology", "model", "organisms" ]	2013	Rapid Sequential Spread of Two Wolbachia Variants in Drosophila simulans
Regulation of cell cycle progression is fundamental to cell health and reproduction , and failures in this process are associated with many human diseases . Much of our knowledge of cell cycle regulators derives from loss-of-function studies . To reveal new cell cycle regulatory genes that are difficult to identify in ...	All cells require proper cell cycle regulation; failure leads to numerous human diseases . Cell cycle mechanisms are broadly conserved across eukaryotes , with many key regulatory genes known . Nonetheless , our knowledge of regulators is incomplete . Many classic studies have analyzed yeast loss-of-function mutants to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/dna", "replication", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "function", "cell", "biology/gene", "expression" ]	2008	Mechanisms of Cell Cycle Control Revealed by a Systematic and Quantitative Overexpression Screen in S. cerevisiae
After infection with T . brucei AnTat 1 . 1 , C57BL/6 mice lost splenic B2 B cells and lymphoid follicles , developed poor parasite-specific antibody responses , lost weight , became anemic and died with fulminating parasitemia within 35 days . In contrast , infected C57BL/6 mice lacking the cytotoxic granule pore-form...	Trypanosomiasis-susceptible mammals that are infected with African trypanosomes develop anemia , lose weight , lose immune competence and have an increased susceptibility to secondary infections . Our earlier studies in the T . b . brucei AnTat 1 . 1 mouse model of African trypanosomiasis show that infection-induced lo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "protozoans", "antibodies", "quantitative"...	2016	Trypanosoma brucei Co-opts NK Cells to Kill Splenic B2 B Cells
FoxP3+ regulatory CD4 T cells ( Tregs ) help to maintain the delicate balance between pathogen-specific immunity and immune-mediated pathology . Prior studies suggest that Tregs are induced by P . falciparum both in vivo and in vitro; however , the factors influencing Treg homeostasis during acute and chronic infection...	In malaria endemic regions , immunity is slow to develop and does not provide substantial protection against reinfection . Rather , following repeated exposure , older children and adults eventually develop protection from most symptomatic manifestations of the infection . This may be due in part to the induction of im...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Decline of FoxP3+ Regulatory CD4 T Cells in Peripheral Blood of Children Heavily Exposed to Malaria
Trachoma is the most common cause of infectious blindness . Hot , dry climates , dust and water scarcity are thought to be associated with the distribution of trachoma but the evidence is unclear . The aim of this study was to evaluate the epidemiological evidence regarding the extent to which climatic factors explain ...	Trachoma – the leading cause of infectious blindness – is spread through contact with infected persons by hands and towels , and by ‘eye-seeking flies . ’ Trachoma prevalence is high in areas characterised by poverty , inadequate water supply , and poor sanitation . Trachoma is controlled by the SAFE strategy: S = surg...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	The Impact of Climatic Risk Factors on the Prevalence, Distribution, and Severity of Acute and Chronic Trachoma
Genome-wide association studies ( GWASs ) have recently revealed many genetic associations that are shared between different diseases . We propose a method , disPCA , for genome-wide characterization of shared and distinct risk factors between and within disease classes . It flips the conventional GWAS paradigm by anal...	Epidemiological studies have revealed distinct diseases that tend to co-occur in individuals . As genome-wide association studies ( GWASs ) have increased in numbers , more evidence regarding the genetic nature of this shared disease etiology is revealed . Here , we present a novel method that utilizes principal compon...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "genetic", "association", "studies", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "human", "genetics" ]	2014	Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
A common complementary strategy in Genome-Wide Association Studies ( GWAS ) is to perform Gene Set Analysis ( GSA ) , which tests for the association between one phenotype of interest and an entire set of Single Nucleotide Polymorphisms ( SNPs ) residing in selected genes . While there exist many tools for performing G...	Researchers are frequently interested in the association between a biologically related set of genes—for example , a particular immune response pathway—and a complex phenotype . Such associations are often explored by applying various gene set analysis methods to genotype data from genome-wide association studies . How...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "breast", "tumors", "volcanology", "magma", "statistics", "cancers", "and", "neoplasms", "oncology", "developmental", "biology", "mathematics", "test", "statistics", "genome", "analysis", ...	2019	Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
Inter-individual variation in gene regulatory elements is hypothesized to play a causative role in adverse drug reactions and reduced drug activity . However , relatively little is known about the location and function of drug-dependent elements . To uncover drug-associated elements in a genome-wide manner , we perform...	Drug response varies between individuals and can be caused by genetic factors . Nucleotide variation in gene regulatory elements can have a significant effect on drug response , but due to the difficulty in identifying these elements , they remain understudied . Here , we used various genomic assays to analyze human li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "functional", "genomics", "health", "care", "genome", "analysis", "genetic", "elements", "dna", "gene", "regions", "molecular", "genetics", "pharmacoeconomics", "health", "economics", "gene", "expression", "bioch...	2014	Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cutaneous mechanoreceptors transduce different tactile stimuli into neural signals that produce distinct sensations of touch . The Pacinian corpuscle ( PC ) , a cutaneous mechanoreceptor located deep within the dermis of the skin , detects high frequency vibrations that occur within its large receptive field . The PC i...	We performed computer simulations of the mechanical behavior of the Pacinian corpuscle ( PC ) , a sensory receptor in the skin that helps detect short-term contact and high-frequency vibration . The PC is composed of a series of tissue layers , and we found that this characteristic structure may explain the response of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Multiscale Mechanical Model of the Pacinian Corpuscle Shows Depth and Anisotropy Contribute to the Receptor’s Characteristic Response to Indentation
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis ( HAT ) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga . In Uganda , Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well...	Northern Uganda is an epidemiologically important region affected by human African trypanosomiasis ( HAT ) because it harbors both forms of the HAT disease ( T . b . gambiense and T . b . rhodesiense ) . The geographic location of this region creates the risk that these distinct foci could merge , which would complicat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "mitochondrial", "dna", "population", "genetics", "geographical", "locations", "uganda", "genetic", "mapping", "aquatic", "environments", "forms", "of", "dna", "bodie...	2017	Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control
There is heterogeneity in invariant natural killer T ( iNKT ) cells based on the expression of CD4 and the IL-17 receptor B ( IL-17RB ) , a receptor for IL-25 which is a key factor in TH2 immunity . However , the development pathway and precise function of these iNKT cell subtypes remain unknown . IL-17RB+ iNKT cells a...	T cells are a diverse group of immune cells involved in cell-mediated acquired immunity . One subset of T cells is the innate-like invariant natural killer T ( iNKT ) cells that recognize glycolipid ligands on target cells instead of peptides . We know that functionally distinct subtypes of iNKT cells are involved in s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "clinical", "immunology", "immunology", "biology" ]	2012	Development and Function of Invariant Natural Killer T Cells Producing TH2- and TH17-Cytokines
Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research . One example is the discovery of transcription factor binding motifs that are inferred from ChIP–chip ( chromatin immuno-precipitation on a microarray ...	A computational problem with many applications in molecular biology is to identify short DNA sequence patterns ( motifs ) that are significantly overrepresented in a target set of genomic sequences relative to a background set of genomic sequences . One example is a target set that contains DNA sequences to which a spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mathematics", "saccharomyces", "homo", "(human)", "computational", "biology" ]	2007	Discovering Motifs in Ranked Lists of DNA Sequences
Seasonal-long larvicide treatments and/or outdoor space-spray applications of insecticides are frequently applied to reduce Aedes albopictus nuisance in urban areas of temperate regions , where the species has become a permanent pest affecting people’s quality of life and health . However , assessments of the effective...	Due to the considerable nuisance created by the aggressive day-time biting behaviour of the “tiger mosquito , ” insecticide treatments are largely employed in urban areas of temperate regions where this tropical species has become a permanent pest . These include treatments of catch basins with lethal products for mosq...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "larvicides", "invertebrates", "medicine", "and", "health", "sciences", "demography", "population", "dynamics", "binomials", "animals", "age", "groups", "adults", "mathematics", "algebra", "pest", "control", "population", "biology", "insect", "vectors"...	2016	Assessment of the Effectiveness of a Seasonal-Long Insecticide-Based Control Strategy against Aedes albopictus Nuisance in an Urban Area
The human β2-adrenergic receptor ( β2AR ) , a member of the G-protein coupled receptor ( GPCR ) family , is expressed in bronchial smooth muscle cells . Upon activation by agonists , β2AR causes bronchodilation and relief in asthma patients . The N-terminal polymorphism of β2AR at the 16th position , Arg16Gly , has war...	The human β2-adrenergic receptor ( β2AR ) is an important member of the GPCR family and a mutation at the 16th position , Arg16Gly , is commonly found in the population . This variation in asthma patients is linked to differential ( good/bad ) response to the drug albuterol , an agonist of the β2AR . To date , the coor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "biochemistry", "biochemical", "simulations", "medicine", "and", "health", "sciences", "pharmacogenetics", "biology", "and", "life", "sciences", "pharmacology", "computational", "biology", "biophysics", "pharmacogenomics", "biophysical", "simulations" ]	2014	Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β2-Adrenergic Receptor
Mutations in the human LMNA gene cause muscular dystrophy by mechanisms that are incompletely understood . The LMNA gene encodes A-type lamins , intermediate filaments that form a network underlying the inner nuclear membrane , providing structural support for the nucleus and organizing the genome . To better understan...	Mutations in the human LMNA gene cause muscular dystrophy that is often accompanied by heart disease . The LMNA gene makes proteins that form a network on the inner side of the nuclear envelope , a structure that reinforces the cell nucleus . How mutations in the LMNA gene cause muscle disease is not well understood . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Myopathic Lamin Mutations Cause Reductive Stress and Activate the Nrf2/Keap-1 Pathway
It has been suggested that HIV-1 has evolved its set-point virus load to be optimized for transmission . Previous epidemiological models and studies into the heritability of set-point virus load confirm that this mode of adaptation within the human population is feasible . However , during the many cycles of replicatio...	HIV-1 is a relatively young virus , being introduced in the human population somewhere between 1884 and 1924 . Yet , previous studies suggest that the virus has already evolved to be efficiently transmitted among humans . Efficient transmission occurs when the set-point virus load , the semi-stable number of virus part...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "immunology", "microbiology", "synthetic", "bioengineering", "immunodeficiency", "viruses", "protein", "engineering", "plant", "science", "sexually", "transmitted", "diseases", ...	2014	Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution
A major goal of genetics is to define the relationship between phenotype and genotype , while a major goal of ecology is to identify the rules that govern community assembly . Achieving these goals by analyzing natural systems can be difficult , as selective pressures create dynamic fitness landscapes that vary in both...	The variability of natural systems makes it difficult to deduce how organisms' genotypes manifest as phenotypes , and how communities of interacting organisms arise . Using laboratory experimental evolution we can control this variation . We previously showed that a population of E . coli that originated from a single ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "population", "genetics", "microbiology", "escherichia", "coli", "mutation", "coevolution", "evolutionary", "adaptation", "bacterial", "pathogens", "genetic", "polymorphism", "medical", "microbiology", "microbial", "pathogens", "evolutionary", "genetics...	2014	Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community
The morphology of synapses is of central interest in neuroscience because of the intimate relation with synaptic efficacy . Two decades of gene manipulation studies in different animal models have revealed a repertoire of molecules that contribute to synapse development . However , since such studies often assessed onl...	Altered synapse function underlies cognitive disorders such as intellectual disability , autism and schizophrenia . The morphology of synapses is crucial for their function but is often described using only a small number of parameters or categories . As a consequence , it is still unknown how different aspects of syna...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "nervous", "system", "electrophysiology", "neuroscience", "animals", "animal", "models", "multivariate", "analysis", "drosophila", "melanogaster", "model", "organisms", "mathematics", "morphome...	2016	A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry
Directional mechanoreception by hair cells is transmitted to the brain via afferent neurons to enable postural control and rheotaxis . Neuronal tuning to individual directions of mechanical flow occurs when each peripheral axon selectively synapses with multiple hair cells of identical planar polarization . How such me...	Mechanosensory systems are essential for maintaining posture , gaze , and body orientation during locomotion . Such stability requires a coherent representation in the brain of the location and movement of mechanical stimuli . In fishes , mechanical stimuli at a given position activate direction-sensitive receptors cal...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "fish", "nervous", "system", "vertebrates", "electrophysiology", "green", "fluorescent", "protein", "neuroscience", "animals", "cell", "polarity", "animal", "models", "osteichthyes", "developmental", "biology"...	2018	Hair cell identity establishes labeled lines of directional mechanosensation
Most chronic viral infections are managed with small molecule therapies that inhibit replication but are not curative because non-replicating viral forms can persist despite decades of suppressive treatment . There are therefore numerous strategies in development to eradicate all non-replicating viruses from the body ....	Innovative new approaches are being developed to eradicate viral infections that until recently were considered incurable . We are interested in engineering DNA cleavage enzymes that can cut and incapacitate persistent viruses . One hurdle is that these enzymes must be delivered to infected cells as genes within viral ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "antivirals", "infectious", "diseases", "mechanisms", "of", "resistance", "and", "susceptibility", "genomics", "hepatitis", "mathematics", "hepatitis", "b", "viral", "persistence", "and", "latency", "gene", "therapy", "virology", "microbiology", "biology", "...	2013	Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach
Functional recovery from cutaneous injury requires not only the healing and regeneration of skin cells but also reinnervation of the skin by somatosensory peripheral axon endings . To investigate how sensory axon regeneration and wound healing are coordinated , we amputated the caudal fins of zebrafish larvae and image...	Touch-sensing neurons project axonal processes that branch extensively within the outer layers of skin to detect touch stimuli . Recovering from skin injuries thus requires not only repair of damaged skin tissue but also regeneration of the sensory axons innervating it . To study whether skin wound healing is coordinat...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "neuroscience/sensory", "systems", "cell", "biology/cell", "signaling", "cell", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/developmental", "molecular", "mechanisms", "cell", "biology/neu...	2011	Hydrogen Peroxide Promotes Injury-Induced Peripheral Sensory Axon Regeneration in the Zebrafish Skin
Prediction of compounds that are active against a desired biological target is a common step in drug discovery efforts . Virtual screening methods seek some active-enriched fraction of a library for experimental testing . Where data are too scarce to train supervised learning models for compound prioritization , initia...	In the early stages of drug discovery efforts , computational models are used to predict activity and prioritize compounds for experimental testing . New targets commonly lack the data necessary to build effective models , and the screening needed to generate that experimental data can be costly . We seek to improve th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "data", "acquisition", "statistics", "enzymes", "enzymology", "mathematics", "forecasting", "pharmacology", "molecular", "biology", "techniques", "enzyme", "inhibitors", "research", "and", "analysis", "methods", "computer", "and", ...	2019	Predicting kinase inhibitors using bioactivity matrix derived informer sets
Autologous transplantation and engraftment of HIV-resistant cells in sufficient numbers should recapitulate the functional cure of the Berlin Patient , with applicability to a greater number of infected individuals and with a superior safety profile . A robust preclinical model of suppressed HIV infection is critical i...	Over the past decade , multiple strategies have been investigated for HIV Cure . Especially notable are cell-based approaches , inspired by the cure of the Berlin Patient , who was transplanted with hematopoietic stem cells from a donor that carried a mutation at the CCR5 locus . This mutation renders cells resistant t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "urology", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "...	2018	Differential impact of transplantation on peripheral and tissue-associated viral reservoirs: Implications for HIV gene therapy
To avoid crashing onto the floor , a free falling fly needs to trigger its wingbeats quickly and control the orientation of its thrust accurately and swiftly to stabilize its pitch and hence its speed . Behavioural data have suggested that the vertical optic flow produced by the fall and crossing the visual field plays...	On the basis of vision-based feedback control of optic flow occurring during insects’ flight , we developed a dynamic model that accounts for the pitch orientation and speed in plummeting flies . We compared the hoverflies’ responses with our model and showed that an optic-flow based control strategy can be used to cor...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "acceleration", "invertebrates", "medicine", "and", "health", "sciences", "classical", "mechanics", "social", "sciences", "neuroscience", "insect", "flight", "biological", "locomotion", "animals", "flight", "(biology)", "simulation", "and", "modeling", "animal", "anatomy"...	2018	Modeling visual-based pitch, lift and speed control strategies in hoverflies
Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance , commonly called isolation-by-distance . Despite the prevalence of isolation-by-distance in nature , to date few studies have empirically demonstrated the processes that generate ...	Dispersal is a fundamental component of the life history of most organisms and therefore influences many biological processes . Dispersal is particularly important in creating genetic structure on the landscape . We often observe a pattern of decreased genetic relatedness between individuals as geographic distances inc...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "methods" ]	[ "united", "states", "biogeography", "ecology", "and", "environmental", "sciences", "animal", "genetics", "z", "chromosomes", "population", "dynamics", "population", "genetics", "geographical", "locations", "north", "america", "animal", "behavior", "mathematics", "bird", ...	2017	Deconstructing isolation-by-distance: The genomic consequences of limited dispersal
Australia is currently canine rabies free . However , communities located on the northern coastline–such as the Northern Peninsula Area ( NPA ) , Queensland–are at risk of an incursion due to their large populations of susceptible free-roaming dogs and proximity to rabies-infected Indonesian islands . A rabies-spread m...	Australia is currently free of canine rabies . However , northern communities are at risk of an incursion . The free-roaming dogs in the at-risk communities of the Northern Peninsula Area , Queensland , Australia , display various roaming behaviours which affect how they interact with each other and subsequently affect...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "australia", "domestic", "animals", "pets", "and", "companion", "animals", "dogs", "animals", "mammals", "simulation", "and", ...	2019	Modelling targeted rabies vaccination strategies for a domestic dog population with heterogeneous roaming patterns
Pregnancy and parturition are intricately regulated to ensure successful reproductive outcomes . However , the factors that control gestational length in humans and other anthropoid primates remain poorly defined . Here , we show the endogenous retroviral long terminal repeat transposon-like human element 1B ( THE1B ) ...	The proper timing of delivery is critical during pregnancy; if too early or too late , the baby will be at risk of serious health problems and even death . Corticotropin-releasing hormone ( CRH ) is a protein that can be detected in maternal blood , and its concentration correlates with the timing of birth . In humans ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "reproductive", "system", "vertebrates", "animals", "mammals", "animal", "models", "primates", "developmental", "biology", "model", "organisms", "experimental", "organism", "systems", "genetic", "element...	2018	Anthropoid primate–specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length
Cyclic-di-GMP ( c-di-GMP ) is a ubiquitous bacterial signaling molecule that regulates a variety of complex processes through a diverse set of c-di-GMP receptor proteins . We have utilized a systematic approach to identify c-di-GMP receptors from the pathogen Vibrio cholerae using the Differential Radial Capillary Acti...	Cyclic-di-GMP ( c-di-GMP ) is a ubiquitous bacterial signaling molecule that regulates important bacterial functions , including virulence , antibiotic resistance , biofilm formation and cell division . The list of known c-di-GMP receptors is clearly incomplete . Here we utilized a systematic and unbiased biochemical a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems
New promising avenues for the pharmacological treatment of skeletal and heart muscle diseases rely on direct sarcomeric modulators , which are molecules that can directly bind to sarcomeric proteins and either inhibit or enhance their activity . A recent breakthrough has been the discovery of the myosin activator omeca...	Cardiac myosin is a motor protein responsible for the contraction of the heart muscle . New strategies for the cure of heart diseases are currently being developed by using myosin modulators , which are small molecules that can interact with myosin and modify its activity . The advantage of this approach over tradition...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "simulation", "and", "modeling", "multivariate", "analysis", "molecular", "motors", "actin", "motors", "mathematics", "statistics", "(mathematics)", "pharmaceutics", "motor", "proteins", "research", "and", "analysis", "methods", ...	2017	Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
We resequenced and phased 27 kb of DNA within 580 kb of the MHC class II region in 158 population chromosomes , most of which were conserved extended haplotypes ( CEHs ) of European descent or contained their centromeric fragments . We determined the single nucleotide polymorphism and deletion-insertion polymorphism al...	The human major histocompatibility complex ( MHC ) is a gene-dense region highly enriched in immune response genes . MHC genetic variation is among the highest in the human genome and is associated with both tissue transplant compatibility and many genetic disorders . Long-range ( 1–3 Mb ) MHC haplotypes of essentially...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "haplotypes", "medicine", "and", "health", "sciences", "major", "histocompatibility", "complex", "genetic", "polymorphism", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "genetics", "biology", "and", "life", "sciences", "population", "genetics",...	2014	Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from HLA-DQA2 to DAXX
Maize leafbladeless1 ( lbl1 ) encodes a key component in the trans-acting short-interfering RNA ( ta-siRNA ) biogenesis pathway . Correlated with a great diversity in ta-siRNAs and the targets they regulate , the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species . Mutat...	Mutations in maize leafbladeless1 ( lbl1 ) that disrupt ta-siRNA biogenesis give rise to plants with thread-like leaves that have lost top/bottom polarity . We used genomic approaches to identify lbl1-dependent small RNAs and their targets to determine the basis for these polarity defects . This revealed substantial di...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "genomes", "developmental", "biology", "plant", "science", "organism", "development", "plant", "development", "leaf", "development", "meristem", "development", "plant", "growth", "and", "development", "plant", "genomics", "genetics", "biology", ...	2014	Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development
Food choice and eating behavior affect health and longevity . Large-scale research efforts aim to understand the molecular and social/behavioral mechanisms of energy homeostasis , body weight , and food intake . Honey bees ( Apis mellifera ) could provide a model for these studies since individuals vary in food-related...	Food choice , food handling , and eating are aspects of food-related behavior that can become pathological , as seen in the public health problems of obesity and diabetes . Thus , the insight that molecules from the body can bind to brain cells and signal and change food-related behavior is of biomedical interest . One...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "diabetes", "and", "endocrinology/obesity", "ecology/behavioral", "ecology", "genetics", "and", "genomics/functional", "genomics" ]	2010	Down-Regulation of Honey Bee IRS Gene Biases Behavior toward Food Rich in Protein
Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease ( PD ) . We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1 , 458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium ( NGRC ) , a...	Parkinson's disease ( PD ) , like most common disorders , involves interactions between genetic make-up and environmental exposures that are unique to each individual . Caffeinated-coffee consumption may protect some people from developing PD , although not all benefit equally . In a genome-wide search , we discovered ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2011	Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee
The structure and composition of bacterial communities can compromise antibiotic efficacy . For example , the secretion of β-lactamase by individual bacteria provides passive resistance for all residents within a polymicrobial environment . Here , we uncover that collective resistance can also develop via intracellular...	Antibiotic-resistant bacterial infections are on the rise and pose a serious threat to society . The influence of genetic resistance mechanisms on antibiotic therapy is well described . However , other factors , such as epigenetic resistance or the impact of the environment on antibiotic therapy , are less well underst...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "pathogens", "drugs", "microbiology", "staphylococcus", "aureus", "electromagnetic", "radiation", "antibiotic", "resistance", "antibiotics", "pharmacology"...	2016	Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation
The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap , NprR , PlcR , and PrgX proteins that are regulated by imported oligopeptide autoinducers . Rap proteins are phosphatases and transcriptional anti-activators , and NprR , PlcR , and PrgX pr...	The bacterial cell–cell communication process known as quorum sensing regulates important social behaviors including antibiotic production , motility , virulence , biofilm formation , sporulation , bioluminescence , and genetic competence . Gram-positive bacteria secrete oligopeptide quorum-sensing signals that bind to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "enzyme", "structure", "protein", "interactions", "proteins", "enzymes", "protein", "structure", "macromolecular", "assemblies", "genetics", "biology", "microbiology", "biophysics", "genetics", "and", "genomics" ]	2013	Conformational Change-Induced Repeat Domain Expansion Regulates Rap Phosphatase Quorum-Sensing Signal Receptors
Systemic lupus erythematosus ( SLE ) is an inflammatory autoimmune disease with a strong genetic component . African-Americans ( AA ) are at increased risk of SLE , but the genetic basis of this risk is largely unknown . To identify causal variants in SLE loci in AA , we performed admixture mapping followed by fine map...	African-Americans ( AA ) are at increased risk of systemic lupus erythematosus ( SLE ) , but the genetic basis of this risk increase is largely unknown . We used admixture mapping to localize disease-causing genetic variants that differ in frequency across populations . This approach is advantageous for localizing susc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "gene", "expression", "genetics", "molecular", "genetics", "biology", "population", "genetics", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2013	Admixture Mapping in Lupus Identifies Multiple Functional Variants within IFIH1 Associated with Apoptosis, Inflammation, and Autoantibody Production
Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases . Further , the efficacy of smoking cessation pharmacotherapy is dependent on the rate of nicotine metabolism . Our objective was to use nicotine metabolite ratio ( NMR ) , an established biomarker o...	Nicotine metabolism rate significantly varies between individuals and affects smoking behavior . Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases . Further , the efficacy of smoking cessation pharmacotherapy is dependent on nicotine metabolism rate...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism
SARS-coronavirus ( SARS-CoV ) replication and transcription are mediated by a replication/transcription complex ( RTC ) of which virus-encoded , non-structural proteins ( nsps ) are the primary constituents . The 16 SARS-CoV nsps are produced by autoprocessing of two large precursor polyproteins . The RTC is believed t...	The SARS-coronavirus ( SARS-CoV ) , which causes the life-threatening severe acute respiratory syndrome , replicates in the cytoplasm of infected host cells . A critical early step in the SARS-CoV life cycle is the formation of a replication/transcription complex ( RTC ) that drives viral genome replication and subgeno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/viral", "infections", "biochemistry/macromolecular", "assemblies", "and", "machines", "molecular", "biology" ]	2008	SARS-Coronavirus Replication/Transcription Complexes Are Membrane-Protected and Need a Host Factor for Activity In Vitro
Herpes simplex virus-1 ( HSV-1 ) causes lifelong infection affecting between 50 and 90% of the global population . In addition to causing dermal lesions , HSV-1 is a leading cause of blindness resulting from recurrent corneal infection . Corneal disease is characterized by loss of corneal immunologic privilege and exte...	Herpes simplex virus-type 1 is the leading cause of infectious corneal blindness in the industrialized world . Most of the morbidity associated with the virus is due to the host response to episodic reactivation of latent virus . Corneal immunologic privilege is associated with a number of factors including the absence...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	The Herpes Simplex Virus-1 Transactivator Infected Cell Protein-4 Drives VEGF-A Dependent Neovascularization
Insertion sequences ( IS ) are the simplest and most abundant form of transposable DNA found in bacterial genomes . When present in multiple copies , it is thought that they can promote genomic plasticity and genetic exchange , thus being a major force of evolutionary change . The main processes that determine IS conte...	Insertion sequences ( IS ) are mobile genetic elements found in most prokaryotic genomes . They are able to autonomously change position and proliferate in chromosomes . The nature of the coevolutionary dynamics of IS with the genome that hosts them is a matter of debate: Do IS proliferate to the point of causing the e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mobile", "genetic", "elements", "genome", "complexity", "computer", "and", "information", "sciences", "systems", "science", "mathematics", "genome", "evolution", "statistics", "(mathematics)", "population", "modeling", "genetic", "elements", "genetics", "transposable", "...	2014	Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes
Spinal muscular atrophy is a severe motor neuron disease caused by inactivating mutations in the SMN1 gene leading to reduced levels of full-length functional SMN protein . SMN is a critical mediator of spliceosomal protein assembly , and complete loss or drastic reduction in protein leads to loss of cell viability . H...	The identification of mutations in the Survival Motor Neuron ( SMN ) gene as the cause of the severe motor neuron disorder spinal muscular atrophy is one of a number of discoveries implicating selective motor neuron vulnerability to defects in processing of RNA and its associated ribonucleoprotein complexes . An unreso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/neuromuscular", "diseases", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "neuroscience/neurodevelopment", "neurological", "disorders/neurogene...	2009	Alternative Splicing Events Are a Late Feature of Pathology in a Mouse Model of Spinal Muscular Atrophy
Target Product Profiles ( TPPs ) are process tools providing product requirements to guide researchers , developers and manufacturers in their efforts to develop effective and useful products such as biologicals , drugs or diagnostics . During a WHO Stakeholders Meeting on Taenia solium diagnostics , several TPPs were ...	Diagnosing the different manifestations of Taenia solium ( taeniasis and neurocysticercosis in humans , and pig cysticercosis ) presents many challenges . The current paper describes the Optimal and Minimal attributes of the diagnostic tests that would be fit for a variety of diagnostic purposes , presented in the form...	[ "Abstract", "Introduction", "Methodology", "Results", "and", "discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "neurocysticercosis", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "neuroscience", "neglected", "tropical", "diseases", "infectious", "disease", "control", "neuroimaging", "research", "and", ...	2017	Target product profiles for the diagnosis of Taenia solium taeniasis, neurocysticercosis and porcine cysticercosis
Allele age has long been a focus of population genetic research , primarily because it can be an important clue to the fitness effects of an allele . By virtue of their effects on fitness , alleles under directional selection are expected to be younger than neutral alleles of the same frequency . We developed a new coa...	We developed a way to estimate the time when a copy of a gene most recently shared ancestry with other copies of that gene . This is also an estimate of the upper bound of when a mutation has arisen , and it can be used to study the ages of alleles that are found in a population . The method can be applied to the very ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Web", "resources" ]	[ "alleles", "genetic", "mapping", "simulation", "and", "modeling", "mutation", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "gene", "mapping", "bioinformatics", "sequence", "alignment", "chromosome", "biology", "...	2019	An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations
Circumstances that compromise efficient DNA replication , such as disruptions to replication fork progression , cause a state known as DNA replication stress ( RS ) . Whereas normally proliferating cells experience low levels of RS , excessive RS from intrinsic or extrinsic sources can trigger cell cycle arrest and sen...	Duplication of the genome by DNA replication is essential for cell proliferation . DNA replication is initiated from many sites ( “origins” ) along chromosomes that are bound by replication licensing proteins , including MCM2-7 . They are also core components of the replication helicase complex that unwinds double stra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation
Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways . Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network . The plant immune si...	When a plant detects pathogen attack , this information is conveyed through a molecular signaling network to turn on a large variety of immune responses . We investigated how this plant immune signaling network was organized using the model plant Arabidopsis . Wild type and mutant plants with defects in immune signalin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "plant", "biology/plant", "genetics", "and", "gene", "expression", "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation" ]	2010	Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling
Chloroquine ( CQ ) and other quinoline-containing antimalarials are important drugs with many therapeutic benefits as well as adverse effects . However , the molecular targets underlying most such effects are largely unknown . By taking a novel functional genomics strategy , which employs a unique combination of genome...	By using a novel SL/DS methodology in the model organism yeast , we discovered that the antimalarial drug CQ inhibits thiamine transporters and consequently causes thiamine ( vitamin B1 ) deficiency and growth defects . This mechanism of action ( MOA ) is conserved in human cells and possibly also in other organisms . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "biology" ]	2012	Discovering Thiamine Transporters as Targets of Chloroquine Using a Novel Functional Genomics Strategy
Eosinophils are effectors in immunity to tissue helminths but also induce allergic immunopathology . Mechanisms of eosinophilia in non-mucosal tissues during infection remain unresolved . Here we identify a pivotal function of tissue macrophages ( Mϕ ) in eosinophil anti-helminth immunity using a BALB/c mouse intra-per...	Helminths parasitize approximately one quarter of the global population . Medically-important helminths , including filariae responsible for elephantiasis and river blindness , are targeted for elimination as a public health problem . Currently there are no vaccines or immunotherapeutics available for filarial worms or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "helminths", "immunology", "parasitic", "diseases", "animals", "nematode", "infections", "brugia", "white", "blood", "cells", "animal", "cells", "eosinophilia", "hematology", ...	2018	Interleukin-4 activated macrophages mediate immunity to filarial helminth infection by sustaining CCR3-dependent eosinophilia
Epstein-Barr virus ( EBV ) is a γ-herpesvirus that may cause infectious mononucleosis in young adults . In addition , epidemiological and molecular evidence links EBV to the pathogenesis of lymphoid and epithelial malignancies . EBV has the unique ability to transform resting B cells into permanently proliferating , la...	Epstein-Barr virus is an oncogenic γ-herpesvirus that may cause infectious mononucleosis in young adults and fatal lymphoproliferative disorders in immunocompromised patients and is associated with the pathogenesis of Burkitt's lymphoma , nasopharyngeal and gastric carcinoma . Epstein-Barr virus nuclear antigen 2 ( EBN...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	The EBNA-2 N-Terminal Transactivation Domain Folds into a Dimeric Structure Required for Target Gene Activation
In mammals , the suprachiasmatic nucleus ( SCN ) of the hypothalamus constitutes the central circadian pacemaker . The SCN receives light signals from the retina and controls peripheral circadian clocks ( located in the cortex , the pineal gland , the liver , the kidney , the heart , etc . ) . This hierarchical organiz...	In order to adapt to their cycling environment , virtually all living organisms have developed an internal timer , the circadian clock . In mammals , the circadian pacemaker is composed of about 20 , 000 neurons , called the suprachiasmatic nucleus ( SCN ) located in the hypothalamus . The SCN receives light signals fr...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "systems", "biology", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus
The liver and pancreas originate from overlapping embryonic regions , and single-cell lineage tracing in zebrafish has shown that Bone morphogenetic protein 2b ( Bmp2b ) signaling is essential for determining the fate of bipotential hepatopancreatic progenitors towards the liver or pancreas . Despite its pivotal role ,...	Lineage-specific multipotent progenitors play crucial roles in embryonic development , regeneration in adult tissues , and diseases such as cancer . Bone morphogenetic protein ( Bmp ) signaling is critical for regulating the cell fate choice of liver versus pancreas , two essential organs of body metabolism . Through t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "in", "situ", "hybridization", "bmp", "signaling", "molecular", "probe", "techniques", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "molecular", "biology", "techn...	2016	Four and a Half LIM Domains 1b (Fhl1b) Is Essential for Regulating the Liver versus Pancreas Fate Decision and for β-Cell Regeneration
lin-28 is a conserved regulator of cell fate succession in animals . In Caenorhabditis elegans , it is a component of the heterochronic gene pathway that governs larval developmental timing , while its vertebrate homologs promote pluripotency and control differentiation in diverse tissues . The RNA binding protein enco...	As tissues form , different cell types are generated from a common pool of undifferentiated cells . The mechanisms that control this developmental timing are largely unknown . In the nematode Caenorhabditis elegans , the heterochronic genes control a succession of cell fates in progressively differentiating tissues of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "model", "organisms", "genetics", "biology", "genetics", "and", "genomics" ]	2012	lin-28 Controls the Succession of Cell Fate Choices via Two Distinct Activities
Cartilage and endochondral bone development require SOX9 activity to regulate chondrogenesis , chondrocyte proliferation , and transition to a non-mitotic hypertrophic state . The restricted and reciprocal expression of the collagen X gene , Col10a1 , in hypertrophic chondrocytes and Sox9 in immature chondrocytes epito...	Chondrogenic differentiation is a key process in the formation of endochondral bone . Despite the wealth of information about gene expression patterns and signaling pathways important for this process , it is not clear how differentiation state-specificity of transcription is controlled . The transcription factor SOX9 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	SOX9 Governs Differentiation Stage-Specific Gene Expression in Growth Plate Chondrocytes via Direct Concomitant Transactivation and Repression
Diagnosis and treatment for visceral leishmaniasis ( VL ) is considered to be delayed amongst poor , rural women in highly endemic districts of Bihar and Jharkhand . The objective of this study was to assess and understand barriers to VL diagnosis and treatment for women in endemic districts with a high burden of VL . ...	India bears the greatest burden of a fatal parasitic disease called visceral leishmaniasis ( VL ) , popularly known as Kala Azar . The disease is confined mostly to hot spots in Bihar and Jharkhand in the eastern part of the country . Amongst factors hampering efforts to eliminate VL are delays from the onset of sympto...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "medical", "doctors", "pathology", "and", "laboratory", "medicine", "medical", "personnel", "tropical", "diseases", "parasitic", "diseases", "health", "care", "health", "care", "providers", "women's", "health", "si...	2019	“It’s just a fever”: Gender based barriers to care-seeking for visceral leishmaniasis in highly endemic districts of India: A qualitative study
N-terminal acetylation ( N-Ac ) is a highly abundant eukaryotic protein modification . Proteomics revealed a significant increase in the occurrence of N-Ac from lower to higher eukaryotes , but evidence explaining the underlying molecular mechanism ( s ) is currently lacking . We first analysed protein N-termini and th...	Small chemical groups are commonly attached to proteins in order to control their activity , localization , and stability . An abundant protein modification is N-terminal acetylation , in which an N-terminal acetyltransferase ( NAT ) catalyzes the transfer of an acetyl group to the very N-terminal amino acid of the pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "model", "organisms", "molecular", "cell", "biology", "genetics", "biology", "genomics", "evolutionary", "biology", "proteomics" ]	2011	NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation
Through as yet undefined proteins and pathways , the SUMO-targeted ubiquitin ligase ( STUbL ) suppresses genomic instability by ubiquitinating SUMO conjugated proteins and driving their proteasomal destruction . Here , we identify a critical function for fission yeast STUbL in suppressing spontaneous and chemically ind...	The failure of cellular DNA repair mechanisms can lead to cancer , neurodegeneration , or premature aging . Although much is known about specific DNA repair mechanisms , an understanding of how these processes are critically orchestrated by post-translational modifiers such as SUMO and ubiquitin is in its infancy . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "genetics", "and", "genomics/chromosome", "biology" ]	2011	SUMO-Targeted Ubiquitin Ligase, Rad60, and Nse2 SUMO Ligase Suppress Spontaneous Top1–Mediated DNA Damage and Genome Instability
Given the continued successes of the world’s lymphatic filariasis ( LF ) elimination programs and the growing successes of many malaria elimination efforts , the necessity of low cost tools and methodologies applicable to long-term disease surveillance is greater than ever before . As many countries reach the end of th...	As a non-invasive method of indirectly monitoring insect-borne disease , molecular xenomonitoring ( MX ) , the molecular testing of insects for the presence of a pathogen , can provide important information about disease prevalence without the need for human sampling . However , given the successes of tropical disease ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "parasitic", "diseases", "animals", "parasitic", "protozoans", "parasitology", "apicomplexa", "brugia", "protozoans", "molecular", "biology", "techniques", "ins...	2016	A Novel Xenomonitoring Technique Using Mosquito Excreta/Feces for the Detection of Filarial Parasites and Malaria
Schistosomiasis is a neglected tropical disease that is responsible for almost 300 , 000 deaths annually . Mass drug administration ( MDA ) is used worldwide for the control of schistosomiasis , but chemotherapy fails to prevent reinfection with schistosomes , so MDA alone is not sufficient to eliminate the disease , a...	Schistosomiasis is a neglected tropical disease that kills as many as 300 , 000 people each year . Mass drug administration is widely used to control schistosomiasis , but fails to prevent rapid reinfection in endemic areas . There is a desperate need for a prophylactic vaccine; however , very few candidates have been ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "helminth", "infections", "infectious", "diseases", "schistosomiasis", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	An Immunomics Approach to Schistosome Antigen Discovery: Antibody Signatures of Naturally Resistant and Chronically Infected Individuals from Endemic Areas
Cytomegalovirus ( CMV ) causes a persistent , lifelong infection . CMV persists in a latent state and undergoes intermittent subclinical viral reactivation that is quelled by ongoing T cell responses . While T cells are critical to maintain control of infection , the immunological factors that promote CMV persistence r...	Cytomegalovirus ( CMV ) infection in both mice and humans is normally initially contained by a vigorous adaptive immune response that drives the virus into latency in multiple tissues . However , the immunologic mechanisms that control latency are not well understood . In this report , we have examined the role of regu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "cytotoxic", "t", "cells", "viral", "load", "research", "and", "analysis", "met...	2017	Tissue-specific control of latent CMV reactivation by regulatory T cells
Pseudomonas aeruginosa infection can be disastrous in chronic lung diseases such as cystic fibrosis and chronic obstructive pulmonary disease . Its toxic effects are largely mediated by secreted virulence factors including pyocyanin , elastase and alkaline protease ( AprA ) . Efficient functioning of the endoplasmic re...	Pseudomonas aeruginosa causes a devastating infection when it affects patients with cystic fibrosis or other chronic lung diseases . It often causes chronic infection due to its resistance to antibiotic treatment and its ability to form biofilms in these patients . The toxic effects of P . aeruginosa are largely mediat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Virulence Factors of Pseudomonas aeruginosa Induce Both the Unfolded Protein and Integrated Stress Responses in Airway Epithelial Cells
The membrane proximal external region ( MPER ) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10 . To date , no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies . We immunized llamas with gp41-MPER proteoliposomes and selecte...	Due to the absence of an effective vaccine or cure for acquired immunodeficiency syndrome ( AIDS ) , HIV-1 infections still result in high mortality . Two antibodies , 2F5 and 4E10 , previously isolated from HIV-1 infected patients , prevent infections by binding to the MPER of gp41 , a part of the virus that is diffic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand", "interactions", "viral", "vaccines", "macromolecular", "assemblies", "microbiology", "viral", "structure", "immunodeficiency", "viruses", "adaptive", "immunity", "immunizations", "microbial", "pathogens", "biology", "biophysics", "viral", "envelope", ...	2013	A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition
A homologue of the ecdysone receptor has previously been identified in human filarial parasites . As the ecdysone receptor is not found in vertebrates , it and the regulatory pathways it controls represent attractive potential chemotherapeutic targets . Administration of 20-hydroxyecdysone to gerbils infected with B . ...	The human filarial parasites are the causative agents of two neglected tropical diseases targeted for elimination by the international community . The current elimination programs rely upon the mass distribution of a limited number of drugs , leaving the programs open to failure in the event that resistance develops . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "transfection", "invertebrates", "medicine", "and", "health", "sciences", "transient", "transfection", "assay", "membrane", "potential", "electrophysiology", "cloning", "parasitic", "diseases", "animals", "physiological", "processes", "developmental", "biology", "receptor", ...	2016	Identification of Ecdysone Hormone Receptor Agonists as a Therapeutic Approach for Treating Filarial Infections
Activation of Notch1 signaling in neural progenitor cells ( NPCs ) induces self-renewal and inhibits neurogenesis . Upon neuronal differentiation , NPCs overcome this inhibition , express proneural genes to induce Notch ligands , and activate Notch1 in neighboring NPCs . The molecular mechanism that coordinates Notch1 ...	Early during development , neural progenitor cells ( NPCs ) can either proliferate or differentiate into neurons . Thus , generation of the correct number of neurons is governed by a tightly regulated balance between proliferation and differentiation , and disruption of this balance can result in severe developmental d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/stem", "cells", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "neuroscience/neuronal", "and", "glial", "cell", "biology", "neuroscience/neuronal", "signaling", "mechanisms", "developmental", "biology/molecular", "development",...	2010	Prox1 Regulates the Notch1-Mediated Inhibition of Neurogenesis
Despite the well-documented role of remote enhancers in controlling developmental gene expression , the mechanisms that allocate enhancers to genes are poorly characterized . Here , we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo , using a series of engineered ch...	The specificity of enhancer-gene interactions is fundamental to the execution of gene regulatory programs underpinning embryonic development and cell differentiation . However , our understanding of the mechanisms conferring specificity to enhancers and target gene interactions is limited . In this study , we character...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "chromosome", "biology", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "chromatin" ]	2015	A Discrete Transition Zone Organizes the Topological and Regulatory Autonomy of the Adjacent Tfap2c and Bmp7 Genes
The let-7 microRNA ( miRNA ) regulates cellular differentiation across many animal species . Loss of let-7 activity causes abnormal development in Caenorhabditis elegans and unchecked cellular proliferation in human cells , which contributes to tumorigenesis . These defects are due to improper expression of protein-cod...	In the past decade , microRNAs ( miRNAs ) have become recognized as key regulators of gene expression in many biological pathways . These small , non-coding RNAs target specific protein-coding genes for repression . The specificity is mediated by partial base-pairing interactions between the 22 nucleotide miRNA and seq...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Functional Genomic Analysis of the let-7 Regulatory Network in Caenorhabditis elegans
Out of all the complex phenomena displayed in the behaviour of animal groups , many are thought to be emergent properties of rather simple decisions at the individual level . Some of these phenomena may also be explained by random processes only . Here we investigate to what extent the interaction dynamics of a populat...	From the synchronised beauty of fish schools to the rigorous hierarchy of ant colonies , animals often display awe-inspiring collective behaviour . In recent years , principles of statistical physics have helped to unveil some simple mechanisms behind the emergence of such collective dynamics . Among the most elementar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "stochastic", "processes", "animal", "behavior", "mathematics", "statistical", "mechanics", "ecology", "evolutionary", "biology", "biology", "probability", "theory", "behavioral", "ecology" ]	2012	How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population
The drug molecule PTC124 ( Ataluren ) has been described as a read-through agent , capable of suppressing premature termination codons ( PTCs ) and restoring functional protein production from genes disrupted by nonsense mutations . Following the discovery of PTC124 there was some controversy regarding its mechanism of...	Ten percent of all single-gene hereditary diseases are caused by nonsense mutations . These are alterations in the DNA sequence of a protein-coding gene that cause the ribosome to prematurely finish translating the gene transcript before a full-length , active protein can be produced . In 2007 a drug was developed call...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "genetic", "mutation", "mutation", "types", "drug", "research", "and", "development", "drugs", "and", "devices", "small", "molecules", "genetics", "biology", "chemical", "biology", "drug", "discovery" ]	2013	A Lack of Premature Termination Codon Read-Through Efficacy of PTC124 (Ataluren) in a Diverse Array of Reporter Assays
The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast , systematic and cost-effective way . Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious ev...	One of the most profound outcomes of fast , reliable genome sequencing is the ability to tailor drug therapy to an individual’s genotype . This ‘personalized’ or ‘precision medicine’ is the realization of a decades-long effort to maximize drug effect and limit unwanted side effects . An undesirable consequence of such ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "drugs", "population", "genetics", "alleles", "gene", "pool", "mutation", "pharmacology", "population", "biology", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "seque...	2016	Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions

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