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Dehydroepiandrosterone sulphate ( DHEAS ) is the most abundant circulating steroid secreted by adrenal glands—yet its function is unknown . Its serum concentration declines significantly with increasing age , which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-r...	Dehydroepiandrosterone sulphate ( DHEAS ) , mainly secreted by the adrenal gland , is the most abundant circulating steroid in humans . It shows a significant physiological decline after the age of 25 and diminishes about 95% by the age of 85 years , which has led to speculation that a relative DHEAS deficiency may con...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "geriatrics", "epidemiology", "endocrinology", "genetics", "biology", "genomics", "diabetes", "and", "endocrinology", "genetics", "and", "genomics" ]	2011	Eight Common Genetic Variants Associated with Serum DHEAS Levels Suggest a Key Role in Ageing Mechanisms
Decision making has been studied with a wide array of tasks . Here we examine the theoretical structure of bandit , information sampling and foraging tasks . These tasks move beyond tasks where the choice in the current trial does not affect future expected rewards . We have modeled these tasks using Markov decision pr...	Numerous choice tasks have been used to study decision processes . Some of these choice tasks , specifically n-armed bandit , information sampling and foraging tasks , pose choices that trade-off immediate and future reward . Specifically , the best choice may not be the choice that pays off the highest reward immediat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Theory of Choice in Bandit, Information Sampling and Foraging Tasks
Migratory waterfowl of the world are the natural reservoirs of influenza viruses of all known subtypes . However , it is unknown whether these waterfowl perpetuate highly pathogenic ( HP ) H5 and H7 avian influenza viruses . Here we report influenza virus surveillance from 2001 to 2006 in wild ducks in Alberta , Canada...	Influenza surveillance in wild migratory birds has been done at two sites in North America: 1 ) in Alberta , Canada , for the past 31 years , and 2 ) along Delaware Bay , United States , for the past 22 years . These studies support the concept that wild migratory birds are the reservoirs of all influenza A viruses and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "influenza", "virology" ]	2007	Influenza in Migratory Birds and Evidence of Limited Intercontinental Virus Exchange
The basidiomycete Ustilago maydis causes smut disease in maize . Colonization of the host plant is initiated by direct penetration of cuticle and cell wall of maize epidermis cells . The invading hyphae are surrounded by the plant plasma membrane and proliferate within the plant tissue . We identified a novel secreted ...	For many fungi that infect plants , successful invasion is coupled to a series of differentiation steps that are necessary to breach the plant cuticle . Such fungi form specialized infection structures which allow direct penetration of the plant cuticle . The smut fungus Ustilago maydis establishes a biotrophic interac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/gene", "expression" ]	2009	Pep1, a Secreted Effector Protein of Ustilago maydis, Is Required for Successful Invasion of Plant Cells
Computational neutralization fingerprinting , NFP , is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection . Here , we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologi...	HIV-1 remains a significant global health threat , with no effective vaccine against the virus currently available . Since traditional vaccine design efforts have had limited success , much effort in recent years has focused on gaining a better understanding of the ways select individuals are able to effectively neutra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "applied", "mathematics", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "algorithms", "simulation", "and", ...	2017	Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting
In Caenorhabditis elegans and Drosophila melanogaster , the aging of the soma is influenced by the germline . When germline-stem cells are removed , aging slows and lifespan is increased . The mechanism by which somatic tissues respond to loss of the germline is not well-understood . Surprisingly , we have found that a...	The reproductive status and longevity of animals are strongly interlinked . Increasing age influences the reproductive capacities of most animals . However , little is known about how reproductive status might affect lifespan . Experiments in worms and flies have shown that removing cells that give rise to gametes , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology/stem", "cells", "molecular", "biology/transcription", "initiation", "and", "activation", "developmental", "biology/aging", "molecular", "biology/transcription", "elongation", "developmental", "biology/developmental...	2009	A Transcription Elongation Factor That Links Signals from the Reproductive System to Lifespan Extension in Caenorhabditis elegans
The ecological success of social insects is often attributed to an increase in efficiency achieved through division of labor between workers in a colony . Much research has therefore focused on the mechanism by which a division of labor is implemented , i . e . , on how tasks are allocated to workers . However , the im...	Social insects , including ants , bees , and termites , may make up 75% of the world's insect biomass . This success is often attributed to their complex colony organization . Each individual is thought to specialize in a particular task and thus become an “expert” for this task . Researchers have long assumed that the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "ecology" ]	2008	Specialization Does Not Predict Individual Efficiency in an Ant
Toxoplasmosis is an important , widespread , parasitic infection caused by Toxoplasma gondii . The chronic infection in immunocompetent patients , usually considered as asymptomatic , is now suspected to be a risk factor for various neurological disorders , including epilepsy . We aimed to conduct a systematic review a...	Toxoplasmosis is a common parasitic infection and affects one-third of the global population . The burden this figure represents clearly signifies the public health relevance of toxoplasmosis . Epilepsy , another chronic condition , is often caused by a variety of infections that affect numerous low- and middle-income ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Toxoplasmosis and Epilepsy — Systematic Review and Meta Analysis
The pathogenic non-cultivable treponemes include three subspecies of Treponema pallidum ( pallidum , pertenue , endemicum ) , T . carateum , T . paraluiscuniculi , and the unclassified Fribourg-Blanc treponeme ( Simian isolate ) . These treponemes are morphologically indistinguishable and antigenically and genetically ...	Pathogenic treponemes include three subspecies of Treponema pallidum ( pallidum , pertenue , endemicum ) , T . carateum , T . paraluiscuniculi , and the unclassified Fribourg-Blanc treponeme . Although they share morphology and have very similar antigenic profiles , they have traditionally been distinguished by mode of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "emerging", "infectious", "diseases", "gene", "identification", "and", "analysis", "genetics", "microbial", "pathogens", "molecular", "genetics", "host-pathogen", "interaction", "biology", "microbiology", "pathogenesis" ]	2013	Fine Analysis of Genetic Diversity of the tpr Gene Family among Treponemal Species, Subspecies and Strains
Epstein–Barr virus ( EBV ) is considered a ubiquitous herpesvirus with the ability to cause latent infection in humans worldwide . EBV-association is evidently linked to different types of human malignancies , mainly of epithelial and lymphoid origin . Of interest is the EBV nuclear antigen 3C ( EBNA3C ) which is criti...	EBV is associated with a broad range of human cancers . EBV-encoded nuclear antigen 3C ( EBNA3C ) is one of the essential latent antigens important for deregulating the functions of numerous host transcription factors which play vital roles in B-cell immortalization . The family of E2F transcription factors are involve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "affinity", "chromatography", "gene", "regulation", "regulatory", "proteins", "immunology", "cell", "processes", "dna-binding", "proteins", "plasmid", "construction", "dna", "transcription", "...	2016	EBV Nuclear Antigen 3C Mediates Regulation of E2F6 to Inhibit E2F1 Transcription and Promote Cell Proliferation
There is clear empirical evidence that environmental conditions can influence Ascaris spp . free-living stage development and host reinfection , but the impact of these differences on human infections , and interventions to control them , is variable . A new model framework reflecting four key stages of the A . lumbric...	Soil-transmitted helminth infections affect 1 . 5 billion people worldwide and mass drug adminstration ( MDA ) is one of the key public health measures for reducing the burden of infection . A number of experimental studies have demonstrated links between temperature and the dynamics of Ascaris spp . eggs , which are e...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "helminths", "geographical", "locations", "parasitic", "diseases", "animals", "parasitology", "seasons", "developmental", "biology", "ascaris", "ascaris", "lumbricoides", "population", "biology", ...	2018	Seasonally timed treatment programs for Ascaris lumbricoides to increase impact—An investigation using mathematical models
Cell water permeability and cell wall properties are critical to survival of plant cells during freezing , however the underlying molecular mechanisms remain elusive . Here , we report that a specifically cold-induced nuclear protein , Tolerant to Chilling and Freezing 1 ( TCF1 ) , interacts with histones H3 and H4 and...	Cold acclimation is a well-known adaptive process through which plants can dramatically increase their tolerance to freezing temperature . Modifications of cell wall have been recognized as a key characteristic during plant acclimation to low temperature . However , the molecular mechanism responsible for such cellular...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis
APOBEC3G ( A3G ) is a potent antiretroviral deoxycytidine deaminase that , when incorporated into HIV virions , hypermutates nascent viral DNA formed during reverse transcription . HIV Vif counters the effect of A3G by depleting intracellular stores of the enzyme , thereby blocking its virion incorporation . Through pu...	APOBEC3G ( A3G ) is a cellular enzyme that promotes DNA mutagenesis and can restrict infection by HIV-1 . However , HIV counters the antiviral effects of A3G through the action of its Vif protein . In the absence of Vif , A3G is effectively incorporated into virions , where it mutagenizes the first DNA copy ( cDNA ) ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "biochemistry", "infectious", "diseases", "virology", "in", "vitro" ]	2007	Newly Synthesized APOBEC3G Is Incorporated into HIV Virions, Inhibited by HIV RNA, and Subsequently Activated by RNase H
Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures . The formation of fruiting bodies is a result of collective cell movement on a solid surface . In the course of development , groups o...	Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures . The formation of fruiting bodies is a result of collective cell movement on a solid surface . Since collective cell motility during b...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Supporting", "Information" ]	[]	2015	Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations
Juvenile hormones ( JHs ) play a major role in controlling development and reproduction in insects and other arthropods . Synthetic JH-mimicking compounds such as methoprene are employed as potent insecticides against significant agricultural , household and disease vector pests . However , a receptor mediating effects...	Juvenile hormones ( JHs ) play critical roles in the development of arthropods , comprising half the animal biomass of the oceans and over a million insect species , which have an enormous impact on ecosystems , agriculture ( pollinators and pests ) and health of mankind ( disease vectors ) . Despite decades of researc...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genetic Evidence for Function of the bHLH-PAS Protein Gce/Met As a Juvenile Hormone Receptor
Structurally segregated and functionally specialized regions of the human cerebral cortex are interconnected by a dense network of cortico-cortical axonal pathways . By using diffusion spectrum imaging , we noninvasively mapped these pathways within and across cortical hemispheres in individual human participants . An ...	In the human brain , neural activation patterns are shaped by the underlying structural connections that form a dense network of fiber pathways linking all regions of the cerebral cortex . Using diffusion imaging techniques , which allow the noninvasive mapping of fiber pathways , we constructed connection maps coverin...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "neuroscience" ]	2008	Mapping the Structural Core of Human Cerebral Cortex
The extraction of accurate self-motion information from the visual world is a difficult problem that has been solved very efficiently by biological organisms utilizing non-linear processing . Previous bio-inspired models for motion detection based on a correlation mechanism have been dogged by issues that arise from th...	Building artificial vision systems that work robustly in a variety of environments has been difficult , with systems often only performing well under restricted conditions . In contrast , animal vision operates effectively under extremely variable situations . Many attempts to emulate biological vision have met with li...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "computer", "science/natural", "and", "synthetic", "vision", "neuroscience/natural", "and", "synthetic", "vision", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2009	Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology
Type IV pili are dynamic cell surface appendages found throughout the bacteria . The ability of these structures to undergo repetitive cycles of extension and retraction underpins their crucial roles in adhesion , motility and natural competence for transformation . In the best-studied systems a dedicated retraction AT...	Bacteria interact with their surroundings using micrometre scale polymers called type IV pili . They allow bacteria to physically sense , attach and move on surfaces , and even to take up DNA . Consequently they represent important mechanisms of environmental survival and pathogenesis . The versatility of type IV pili ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "chitin", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "vibrio", "enzymology", "microbiology", "pili", "and", "fimbriae", "phosphatases", "pseudomonas", "aeruginosa", "vibrio", "cholerae", "materials", "s...	2019	The type IV pilus protein PilU functions as a PilT-dependent retraction ATPase
Sporadic adrenocortical carcinomas ( ACC ) are rare endocrine neoplasms with a dismal prognosis . By contrast , benign tumors of the adrenal cortex are common in the general population . Whether benign tumors represent a separate entity or are in fact part of a process of tumor progression ultimately leading to an ACC ...	A sequential acquisition of genetic events is critical in tumorigenesis , and a dysregulation of a limited set of pathways has been demonstrated as sufficient to progressively transform normal cells into tumor cells in several human tissues . However , in the case of adrenocortical tumorigenesis , whether benign tumors...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	Acquisition Order of Ras and p53 Gene Alterations Defines Distinct Adrenocortical Tumor Phenotypes
Neural crest cells ( NCC ) are a transient migratory cell population that generates diverse cell types such as neurons and glia of the enteric nervous system ( ENS ) . Via an insertional mutation screen for loci affecting NCC development in mice , we identified one line—named TashT—that displays a partially penetrant a...	Hirschsprung’s disease ( also known as aganglionic megacolon ) is a severe congenital defect of the enteric nervous system ( ENS ) resulting in complete failure to pass stools . It is characterized by the absence of neural ganglia ( aganglionosis ) in the distal gut due to incomplete colonization of the embryonic intes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Male-Biased Aganglionic Megacolon in the TashT Mouse Line Due to Perturbation of Silencer Elements in a Large Gene Desert of Chromosome 10
The prospects for the success of malaria control depend , in part , on the basic reproductive number for malaria , R0 . Here , we estimate R0 in a novel way for 121 African populations , and thereby increase the number of R0 estimates for malaria by an order of magnitude . The estimates range from around one to more th...	Each year malaria results in more than a million deaths . Controlling this disease involves understanding its transmission . For all infectious disease , the basic reproductive number , R0 , describes the most important aspects of transmission . This is the expected number of hosts that can trace their infection direct...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "health", "and", "epidemiology", "ecology", "plasmodium", "anopheles", "homo", "(human)" ]	2007	Revisiting the Basic Reproductive Number for Malaria and Its Implications for Malaria Control
HIV infection can be effectively controlled by anti-retroviral therapy ( ART ) in most patients . However therapy must be continued for life , because interruption of ART leads to rapid recrudescence of infection from long-lived latently infected cells . A number of approaches are currently being developed to ‘purge’ t...	During treatment of HIV infection the virus persists in infected cells in a quiescent or ‘latent’ state . If treatment is stopped , then virus rebounds to detectable levels usually within 2–3 weeks . This is thought to occur due to release of infectious virus from a reservoir of long-lived latently infected cells . Red...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	HIV Reactivation from Latency after Treatment Interruption Occurs on Average Every 5-8 Days—Implications for HIV Remission
It is a long-established fact that neuronal plasticity occupies the central role in generating neural function and computation . Nevertheless , no unifying account exists of how neurons in a recurrent cortical network learn to compute on temporally and spatially extended stimuli . However , these stimuli constitute the...	The world is not perceived as a chain of segmented sensory still lifes . Instead , it appears that the brain is capable of integrating the temporal dependencies of the incoming sensory stream with the spatial aspects of that input . It then transfers the resulting whole in a useful manner , in order to reach a coherent...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "mathematics", "neural", "homeostasis", "neural", "networks", "computational", "neuroscience", "biology", "nonlinear", "dynamics", "neuroscience", "learning", "and", "memory" ]	2014	Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations
Two lineages of Salmonella enterica serovar Typhimurium ( S . Typhimurium ) of multi-locus sequence type ST313 have been linked with the emergence of invasive Salmonella disease across sub-Saharan Africa . The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage . We analyse...	Salmonella enterica is a diverse species , isolates of which can colonise or infect many different animals , including humans and can cause different disease syndromes . S . enterica can be sub-typed using serology into serovars . Isolates from some serovars , known as generalists , can infect multiple hosts ( e . g . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa
Cellular and systemic responses to low oxygen levels are principally mediated by Hypoxia Inducible Factors ( HIFs ) , a family of evolutionary conserved heterodimeric transcription factors , whose alpha- and beta-subunits belong to the bHLH-PAS family . In normoxia , HIFα is hydroxylated by specific prolyl-4-hydroxylas...	Sufficient oxygen supply is essential for animal survival . When cells or organisms are exposed to low oxygen levels ( hypoxia ) , a complex molecular response is triggered , enabling adaptation to this stressful condition . A key mediator of this response is HIF , a transcription factor that induces the expression of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "rna", "interference", "gene", "regulation", "oxygen", "animals", "animal", "models", "developmental", "biology", "micrornas", "model", "organisms", "drosophila", "melanogaster", "hypoxia", "molecular", "biology", "techniques", "epigenetics", "embryos", "...	2016	miR-190 Enhances HIF-Dependent Responses to Hypoxia in Drosophila by Inhibiting the Prolyl-4-hydroxylase Fatiga
Elevated plasma triglyceride ( TG ) levels are an established risk factor for type-2 diabetes ( T2D ) . However , recent studies have hinted at the possibility that genetic risk for TG may paradoxically protect against T2D . In this study , we examined the association of genetic risk for TG with incident T2D , and the ...	An elevated triglyceride level is generally considered a risk factor for the development of type-2 diabetes . However , recent studies suggest , somewhat paradoxically , that genetic risk for elevated triglycerides may protect against type-2 diabetes . In this study , we test the relationship of triglyceride-associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Triglyceride-Increasing Alleles Associated with Protection against Type-2 Diabetes
Hereditary hearing loss is a clinically and genetically heterogeneous disorder . More than 80 genes have been implicated to date , and with the advent of targeted genomic enrichment and massively parallel sequencing ( TGE+MPS ) the rate of novel deafness-gene identification has accelerated . Here we report a family seg...	The most frequent sensory disorder worldwide is hearing impairment . It impacts over 5% of the world population ( 360 million persons ) , and is characterized by extreme genetic heterogeneity . Over 80 genes have been implicated in isolated ( also referred to as ‘non-syndromic’ ) hearing loss , and abundant evidence su...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	HOMER2, a Stereociliary Scaffolding Protein, Is Essential for Normal Hearing in Humans and Mice
Tetherin , an interferon-inducible membrane protein , inhibits the release of nascent enveloped viral particles from the surface of infected cells . However , the mechanisms underlying virion retention have not yet been fully delineated . Here , we employ biochemical assays and engineered tetherin proteins to demonstra...	The cellular restriction factor , tetherin , prevents HIV-1 and other enveloped virus particles from being disseminated into the extracellular milieu by infiltrating their envelopes and by physically crosslinking them to the cell surface . It is known that tetherin consists of pairs of membrane anchors , situated at ei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "virology", "biology", "microbiology" ]	2013	Mechanism of HIV-1 Virion Entrapment by Tetherin
At the crossroad between the NF-κB and the MAPK pathways , the ternary complex composed of p105 , ABIN2 and TPL2 is essential for the host cell response to pathogens . The matrix protein ( M ) of field isolates of rabies virus was previously shown to disturb the signaling induced by RelAp43 , a NF-κB protein close to R...	Rabies virus is a recurring zoonosis responsible for about 60 , 000 deaths per year . A key feature of rabies virus is its stealth , allowing it to spread within the host and escape the immune response . To do so , rabies virus developed several mechanisms , including a thorough interference with cell signaling pathway...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "protein", "interaction", "networks", "immunology", "microbiology", "enzymology", "viruses", "rna", "viruses", "network"...	2017	Regulation of NF-κB by the p105-ABIN2-TPL2 complex and RelAp43 during rabies virus infection
Prompt therapy with high-dose intravenous benzylpenicillin for a prolonged period is critical for neurosyphilis patients to avoid irreversible sequelae . However , life-threatening neutropenia has been reported as a complication of prolonged therapy with high doses of benzylpenicillin when treating other diseases . Thi...	High-dose intravenous benzylpenicillin is an effective treatment for neurosyphilis although it can cause potentially life-threatening drug-induced neutropenia . We investigated the incidence , presentation , management and prognosis of benzylpenicillin-induced neutropenia among neurosyphilis patients treated over a thr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "inflammatory", "diseases", "urology", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "maternal", "health", "blood", "counts", "immunology", "tropical", "diseases", "throat"...	2017	Neutropenia induced by high-dose intravenous benzylpenicillin in treating neurosyphilis: Does it really matter?
Rab proteins are small GTPases that act as essential regulators of vesicular trafficking . 44 subfamilies are known in humans , performing specific sets of functions at distinct subcellular localisations and tissues . Rab function is conserved even amongst distant orthologs . Hence , the annotation of Rabs yields funct...	Intracellular compartmentalisation via membrane-delimited organelles is a fundamental feature of the eukaryotic cell . Understanding its origins and specialisation into functionally distinct compartments is a major challenge in evolutionary cell biology . We focus on the Rab enzymes , critical organisers of the traffic...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computer", "applications", "genome", "expression", "analysis", "cellular", "structures", "subcellular", "organelles", "genome", "evolution", "evolutionary", "biology", "molecular", "genetics", "information", "technology", "sequence", "analysis", "comparative", "genomics", ...	2011	Thousands of Rab GTPases for the Cell Biologist
High-throughput drug screening has facilitated the discovery of drug combinations in cancer . Many existing studies adopted a full matrix design , aiming for the characterization of drug pair effects for cancer cells . However , the full matrix design may be suboptimal as it requires a drug pair to be combined at multi...	Cancer is one of the main causes of death worldwide . Although new treatment strategies have been achieved , they still have limited efficacy as cancer cells can easily develop drug resistance . To achieve more sustainable therapies to treat cancer , we need multi-targeted drug combinations that can inhibit cancer cell...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "oncology", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "machine", "learning", "drug", "research", "and", "development", "pharmaceutics", "artificial", "intelligence", "cancer", "drug", "discovery", "dose", "prediction", "metho...	2019	Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer
Patterns of spontaneous activity in the developing retina , LGN , and cortex are necessary for the proper development of visual cortex . With these patterns intact , the primary visual cortices of many newborn animals develop properties similar to those of the adult cortex but without the training benefit of visual exp...	Before many animals first open their eyes , neurons in the retina , thalamus , and visual cortex fire spontaneously in highly structured , patterned ways . Experimental manipulations have demonstrated that this activity is necessary for proper function , but it is difficult to answer certain fundamental questions about...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2008	Innate Visual Learning through Spontaneous Activity Patterns
Unexplained cardiac arrest ( UCA ) with documented ventricular fibrillation ( VF ) is a major cause of sudden cardiac death . Abnormal sympathetic innervations have been shown to be a trigger of ventricular fibrillation . Further , adequate expression of SEMA3A was reported to be critical for normal patterning of cardi...	Unexplained cardiac arrest with documented ventricular fibrillation ( UCA ) is defined as spontaneous ventricular fibrillation ( VF ) that is not associated with known structural or electrical heart diseases and is one of the major causes of sudden cardiac death . Identification of the genes responsible for UCA may fur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "arrhythmias", "neurology", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "autonomic", "nervous", "system", "cardiovascular" ]	2013	A Nonsynonymous Polymorphism in Semaphorin 3A as a Risk Factor for Human Unexplained Cardiac Arrest with Documented Ventricular Fibrillation
Leptospirosis is a worldwide zoonotic bacterial disease caused by infection with leptospires . Leptospirosis in humans and livestock is an endemic and epidemic disease in Thailand . Livestock may act as reservoirs for leptospires and source for human infection . Data on leptospirosis infection in humans and livestock (...	Leptospirosis is an important worldwide zoonotic disease , particularly in tropical and subtropical countries . The infection in humans is caused by either direct contact with products of infected animals , mainly urine , or by indirect contact via a contaminated environment . The animal hosts are thus considered reser...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "tropical", "diseases", "buffaloes", "animals", "mammals", "bacterial", ...	2017	Investigation on predominant Leptospira serovars and its distribution in humans and livestock in Thailand, 2010-2015
In August 2014 , the National Institute for Communicable Diseases ( NICD ) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory ( SA FEDL ) near Freetown , Sierra Leone in response to the rapidly increasing number of Ebola virus disease ( EVD ) cases . The SA FEDL operated in the Weste...	In response to Ebola virus disease outbreak in West Africa , the National Institute for Communicable Diseases in South Africa established a modular high-biosafety field Ebola diagnostic laboratory ( FEDL ) near Freetown , Sierra Leone . This was the sole diagnostic capacity available to respond to the overwhelming dema...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2017	South African Ebola diagnostic response in Sierra Leone: A modular high biosafety field laboratory
Human African trypanosomiasis ( HAT ) is an important public health problem in sub-Saharan Africa , affecting hundreds of thousands of individuals . An urgent need exists for the discovery and development of new , safe , and effective drugs to treat HAT , as existing therapies suffer from poor safety profiles , difficu...	Human African trypanosomiasis ( HAT ) is caused by infection with the parasite Trypanosoma brucei and is an important public health problem in sub-Saharan Africa . New , safe , and effective drugs are urgently needed to treat HAT , particularly stage 2 disease where the parasite infects the brain . Existing therapies f...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicinal", "chemistry", "chemical", "biology", "chemistry", "biology", "microbiology", "parasitology", "parasite", "physiology" ]	2011	SCYX-7158, an Orally-Active Benzoxaborole for the Treatment of Stage 2 Human African Trypanosomiasis
Severe malaria occurs predominantly in young children and immunity to clinical disease is associated with cumulative exposure in holoendemic settings . The relative contribution of immunity against various stages of the parasite life cycle that results in controlling infection and limiting disease is not well understoo...	Human malaria infections resulting in serious complications and death occur predominantly in young children , and resistance is gradually acquired with repeated exposure . Malaria parasites have two major stages within the human host during its life cycle: an initial liver stage , and the subsequent blood stage , where...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "population", "modeling", "biology", "computational", "biology", "infectious", "disease", "modeling" ]	2012	The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection
Urinary tract infections ( UTIs ) afflict over 9 million women in America every year , often necessitating long-term prophylactic antibiotics . One risk factor for UTI is frequent sexual intercourse , which dramatically increases the risk of UTI . The mechanism behind this increased risk is unknown; however , bacteriur...	Urinary tract infections ( UTIs ) affect millions of women each year resulting in substantial morbidity and lost wages . Approximately 1 . 5 million women are referred to urology clinics suffering from chronic recurrent UTI on a yearly basis necessitating the use of prophylactic antibiotics . Frequent and recent sexual...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "women's", "health", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "superinfection", "microbio...	2015	Uropathogenic Escherichia coli Superinfection Enhances the Severity of Mouse Bladder Infection
Filarial diseases represent a significant social and economic burden to over 120 million people worldwide and are caused by endoparasites that require the presence of symbiotic bacteria of the genus Wolbachia for fertility and viability of the host parasite . Targeting Wolbachia for elimination is a therapeutic approac...	Infection with the filarial endoparasites Brugia malayi and its symbiotic bacteria Wolbachia represent a significant burden to both humans and animals . Current treatment protocols include use of multiple drugs over a course of months to years , resulting in high costs , undesirable side effects , and poor patient comp...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Polyanhydride Nanoparticle Delivery Platform Dramatically Enhances Killing of Filarial Worms
Age-related defects in stem cells can limit proper tissue maintenance and hence contribute to a shortened lifespan . Using highly purified hematopoietic stem cells from mice aged 2 to 21 mo , we demonstrate a deficit in function yet an increase in stem cell number with advancing age . Expression analysis of more than 1...	Aging is marked by a decline in function of the entire organism . The effect of age on the regenerative capacity of adult stem cells , which should rejuvenate tissues throughout life , is poorly understood . Bone marrow stem cells , also known as hematopoietic stem cells ( HSCs ) , continuously regenerate the cells tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "immunology", "mus", "(mouse)", "hematology" ]	2007	Aging Hematopoietic Stem Cells Decline in Function and Exhibit Epigenetic Dysregulation
The Middle East respiratory syndrome coronavirus ( MERS-CoV ) is a zoonotic betacoronavirus that was first detected in humans in 2012 as a cause of severe acute respiratory disease . As of July 28 , 2017 , there have been 2 , 040 confirmed cases with 712 reported deaths . While many infections have been fatal , there h...	New Zealand white rabbits display an increase in lung inflammation following reinfection with MERS-CoV that is associated with non-neutralizing antibodies and complement proteins . The development of neutralizing antibodies resulted in protection from infection . These findings may have implications for individuals tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "complement", "system", "medicine", "and", "health", "sciences", "coronaviruses", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pathogens", "immunology", "microbiology", "rabbits", "verte...	2017	Enhanced inflammation in New Zealand white rabbits when MERS-CoV reinfection occurs in the absence of neutralizing antibody
Although bacteria are unicellular organisms , they have the ability to act in concert by synthesizing and detecting small diffusing autoinducer molecules . The phenomenon , known as quorum sensing , has mainly been proposed to serve as a means for cell-density measurement . Here , we use a cell-based model of growing b...	Unicellular organisms have the ability to communicate with each other via signaling molecules , leading to correlated behaviors resembling that of higher organisms . This process , called quorum sensing , allows the cells to monitor the population size or density in a decentralized fashion and perform a common task whe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2010	A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies
The globally distributed ectoparasite Varroa destructor is a vector for viral pathogens of the Western honeybee ( Apis mellifera ) , in particular the Iflavirus Deformed Wing Virus ( DWV ) . In the absence of Varroa low levels DWV occur , generally causing asymptomatic infections . Conversely , Varroa-infested colonies...	Honeybees are the most important managed pollinating insect , contributing billions of dollars to annual global agricultural production . Over the last century a parasitic mite , Varroa , has spread worldwide , with significant impacts on honeybee colony health as a consequence of its transmission of a cocktail of viru...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "epizootics", "sequencing", "techniques", "genome", "evolution", "parasite", "evolution", "rna", "analysis", "nucleic", "acid", "sequencing", "parasitology", "phylogenetic", "analysis", "genome", "analysis", "molecular", "biology", "techniques", "veterinary", "science", "...	2014	A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission
In many human fungal pathogens , genes required for disease remain largely unannotated , limiting the impact of virulence gene discovery efforts . We tested the utility of a cross-species genetic interaction profiling approach to obtain clues to the molecular function of unannotated pathogenicity factors in the human p...	HIV/AIDS patients , cancer chemotherapy patients , and organ transplant recipients are highly susceptible to infection by opportunistic fungal pathogens , organisms common in the environment that are harmless to normal individuals . Understanding how these pathogens cause disease requires the identification of genes re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	Approaching the Functional Annotation of Fungal Virulence Factors Using Cross-Species Genetic Interaction Profiling
During embryonic development , signalling molecules known as morphogens act in a concentration-dependent manner to provide positional information to responding tissues . In the early zebrafish embryo , graded signalling by members of the nodal family induces the formation of mesoderm and endoderm , thereby patterning t...	One of the earliest events in vertebrate embryonic development is the patterning of the embryo into three germ layers: the ectoderm , mesoderm , and endoderm . Morphogens are signalling molecules that act in a concentration-dependent manner to induce the formation of different cell types . Members of the nodal family a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "developmental", "biology" ]	2009	Visualisation and Quantification of Morphogen Gradient Formation in the Zebrafish
Codon pair bias deoptimization ( CPBD ) has enabled highly efficient and rapid attenuation of RNA viruses . The technique relies on recoding of viral genes by increasing the number of codon pairs that are statistically underrepresented in protein coding genes of the viral host without changing the amino acid sequence o...	Codon pair bias deoptimization ( CPBD ) enables highly efficient attenuation of viruses . In contrast to other methods , live attenuated virus vaccine candidates can be rationally designed and produced within days . The technique involves recoding of viral genes , while preserving their codon bias and amino acid sequen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "sequencing", "techniques", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "bac", "cloning", "pathogens", "microbiology", "vertebrates", "cloning", "animals", "vector", "cloning", "viruses", "rna...	2018	Attenuation of a very virulent Marek's disease herpesvirus (MDV) by codon pair bias deoptimization
Little is known about the natural history of dengue in Papua New Guinea ( PNG ) . We assessed dengue virus ( DENV ) -specific neutralizing antibody profiles in serum samples collected from northern and southern coastal areas and the highland region of New Guinea between 1959 and 1963 . Neutralizing antibodies were demo...	Dengue is a mosquito-borne disease caused by infection with any of the four dengue virus serotypes ( DENV-1 –DENV-4 ) , which are transmitted in more than 100 tropical and subtropical countries . The current global dengue burden , and dengue mortality , is greatest in the southeast Asian and western Pacific region wher...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "invertebrates", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "geographical", "locations", "microbiology", "tropical", "diseases", "spatial", "epidemiology", "a...	2017	Serological evidence for transmission of multiple dengue virus serotypes in Papua New Guinea and West Papua prior to 1963
In vertebrates , the conserved Wnt signalling cascade promotes the stabilization and nuclear accumulation of β-catenin , which then associates with the lymphoid enhancer factor/T cell factor proteins ( LEF/TCFs ) to activate target genes . Wnt/β -catenin signalling is essential for T cell development and differentiatio...	In vertebrates the canonical Wnt signalling culminates in β-catenin moving into the nucleus where it activates transcription of target genes . Wnt/β-catenin signalling is essential for the thymic maturation and differentiation of naïve T cells . Here we show that SATB1 , a T cell lineage-enriched chromatin organizer an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "cell", "biology/nuclear", "structure", "and", "function", "cell", "biology/cell", "signaling", "immunology/leukocyte", "signaling", "and", "gene", "expression", "cell", "biology/gene", "expression" ]	2010	Global Regulator SATB1 Recruits β-Catenin and Regulates TH2 Differentiation in Wnt-Dependent Manner
In eukaryotes , the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome . Because viral RNAs often lack canonical caps or poly-A tails , they can also be vulnerable to degradation by these host exonucleases . Yeast lack sophisticated mechanisms of innate and adaptive immunity , but do use ...	Like other eukaryotes , Saccharomyces cerevisiae is chronically infected with viruses . It is fascinating to consider how S . cerevisiae deals with viral infection , because yeast have limited mechanisms of immunity . Our paper focuses on Xrn1p , an enzyme that is important for the destruction of irregular cellular RNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "rna", "extraction", "microbiology", "cloning", "fungi", "model", "organisms", "fungal", "evolution", "microbial", "evolution", "molecular", "biology", "tec...	2016	XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts
Staphylococcus aureus , a pathogen responsible for hospital and community-acquired infections , expresses many virulence factors under the control of numerous regulatory systems . Here we show that one of the small pathogenicity island RNAs , named SprD , contributes significantly to causing disease in an animal model ...	Bacteria possess numerous and diverse means of gene regulation using RNA molecules , including small RNAs ( sRNAs ) . Here we show that one sRNA is essential for a major human bacterial pathogen , Staphylococcus aureus , to cause a disease in an animal model of infection . Our study provides evidence that this RNA regu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/rna", "structure", "microbiology/immunity", "to", "infections", "infectious", "diseases/bacterial", "infections", "biochemistry/transcription", "and", "translation", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	A Staphylococcus aureus Small RNA Is Required for Bacterial Virulence and Regulates the Expression of an Immune-Evasion Molecule
Somitogenesis is a process common to all vertebrate embryos in which repeated blocks of cells arise from the presomitic mesoderm ( PSM ) to lay a foundational pattern for trunk and tail development . Somites form in the wake of passing waves of periodic gene expression that originate in the tailbud and sweep posteriorl...	The vertebral column is a characteristic structure of all vertebrates . Individual vertebrae , together with ribs and attached muscles , develop from repeated embryonic structures called somites . The somite pattern forms in the embryo during somitogenesis . We know that this process uses periodic gene expression ( a b...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "mathematics", "developmental", "biology/pattern", "formation", "biophysics/biomacromolecule-ligand", "interactions", "developmental", "biology/developmental", "molecular", "mechanisms", "computational", "biology/systems", "biology" ]	2010	Somitogenesis Clock-Wave Initiation Requires Differential Decay and Multiple Binding Sites for Clock Protein
Gene silencing is a natural antiviral defense mechanism in plants . For effective infection , plant viruses encode viral silencing suppressors to counter this plant antiviral response . The geminivirus-encoded C4 protein has been identified as a gene silencing suppressor , but the underlying mechanism of action has not...	Geminiviruses are single-stranded DNA ( ssDNA ) viruses that infect a wide range of plant species and are responsible for substantial crop damage worldwide . However , how geminiviruses inhibit plant antiviral gene silencing defense is unclear . Here , we report that a single geminiviral protein CLCuMuV C4 inhibits bot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "chemical", "compounds", "gene", "regulation", "nucleotides", "organic", "compounds", "mutation", "plant", "science", "pyrimidines", "amino", "acids", "epigenetics", "dna", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "res...	2018	Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase
PML nuclear bodies ( PML-NBs ) are enigmatic structures of the cell nucleus that act as key mediators of intrinsic immunity against viral pathogens . PML itself is a member of the E3-ligase TRIM family of proteins that regulates a variety of innate immune signaling pathways . Consequently , viruses have evolved effecto...	Research of the last few years has revealed that microbial infections are not only controlled by innate and adaptive immune mechanisms , but also by cellular restriction factors , which give cells the capacity to resist pathogens . PML nuclear bodies ( PML-NBs ) are dot-like nuclear structures representing multiprotein...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immediate-early", "promoter", "medicine", "and", "health", "sciences", "immunology", "microbiology", "infectious", "disease", "immunology", "protein", "structure", "nuclear", "bodies", "cellular", "structures", "and", "organelles", "immune", "system", "proteins", "protei...	2014	Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions
Plasmodium undergoes one round of multiplication in the liver prior to invading erythrocytes and initiating the symptomatic blood phase of the malaria infection . Productive hepatocyte infection by sporozoites leads to the generation of thousands of merozoites capable of erythrocyte invasion . Merozoites are released f...	The malaria parasite Plasmodium undergoes one large round of multiplication in the liver before beginning the blood phase of the life cycle , the phase that causes the typical episodes of fever and chills . Using intravital microscopy and fluorescent parasites , we studied the mode and dynamics of parasite release from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "plasmodium", "gastroenterology", "and", "hepatology", "in", "vitro", "immunology", "microbiology", "mus", "(mouse)" ]	2007	Release of Hepatic Plasmodium yoelii Merozoites into the Pulmonary Microvasculature
Nosocomial infections are increasingly being recognised as a major patient safety issue . The modern hospital environment and associated health care practices have provided a niche for the rapid evolution of microbial pathogens that are well adapted to surviving and proliferating in this setting , after which they can ...	Hospital infections are increasingly being recognised as a major patient safety issue with the hospital environment providing a niche for the rapid evolution of microbial pathogens that are well adapted to infecting susceptible patients . The spore-forming Clostridium difficile is one such bacterium , which causes dise...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	The Anti-Sigma Factor TcdC Modulates Hypervirulence in an Epidemic BI/NAP1/027 Clinical Isolate of Clostridium difficile
The mechanisms by which adaptive phenotypes spread within an evolving population after their emergence are understood fairly well . Much less is known about the factors that influence the evolutionary accessibility of such phenotypes , a pre-requisite for their emergence in a population . Here , we investigate the infl...	Adaptation involves the discovery by mutation and spread through populations of traits ( or “phenotypes” ) that have high fitness under prevailing environmental conditions . While the spread of adaptive phenotypes through populations is mediated by natural selection , the likelihood of their discovery by mutation depen...	[ "Abstract", "Introduction", "Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/metabolic", "networks", "computational", "biology/systems", "biology" ]	2009	On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network
Endoglin is an auxiliary receptor for members of the TGF-β superfamily and plays an important role in the homeostasis of the vessel wall . Mutations in endoglin gene ( ENG ) or in the closely related TGF-β receptor type I ACVRL1/ALK1 are responsible for a rare dominant vascular dysplasia , the Hereditary Hemorrhagic Te...	Endoglin is a transmembrane protein and an auxiliary receptor for TGF-β with an important role in the homeostasis of the vessel wall . However , endoglin was originally identified as a human cell surface antigen expressed in a pre-B leukemic cell line . Mutations in ENG are responsible for the Hereditary Hemorrhagic Te...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immunology", "opportunistic", "infections", "animal", "models", "model", "organisms", "signs", "and", ...	2016	Mice Lacking Endoglin in Macrophages Show an Impaired Immune Response
Herpesviruses are large DNA viruses which depend on many nuclear functions , and therefore on host transport factors to ensure specific nuclear import of viral and host components . While some import cargoes bind directly to certain transport factors , most recruit importin β1 via importin α . We identified importin α1...	Nuclear pore complexes are highly selective gateways that penetrate the nuclear envelope for bidirectional trafficking between the cytoplasm and the nucleoplasm . Viral and host cargoes have to engage specific transport factors to achieve active nuclear import and export . Like many human and animal DNA viruses , herpe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nuclear", "import", "gene", "regulation", "cell", "processes", "microbiology", "light", "microscopy", "viral", "structure", "neuroscience", "virus", "effects", "on", "host", "gene", "expression", "microscopy", "research", "and", "analysis", "methods", "small", "inter...	2018	Importin α1 is required for nuclear import of herpes simplex virus proteins and capsid assembly in fibroblasts and neurons
Through high coverage whole-genome sequencing and imputation of the identified variants into a large fraction of the Icelandic population , we found four independent signals in the low density lipoprotein receptor gene ( LDLR ) that associate with levels of non-high density lipoprotein cholesterol ( non-HDL-C ) and cor...	Cholesterol levels in the bloodstream , in particular elevated low-density lipoprotein cholesterol ( LDL-C ) , are strong risk factors for cardiovascular disease , and LDL-C reduction reduces mortality in people at risk . One of the major determinants of plasma LDL-C levels is the low density lipoprotein receptor ( LDL...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Splice Region Variant in LDLR Lowers Non-high Density Lipoprotein Cholesterol and Protects against Coronary Artery Disease
An epistatic interaction between two genes occurs when the phenotypic impact of one gene depends on another gene , often exposing a functional association between them . Due to experimental scalability and to evolutionary significance , abundant work has been focused on studying how epistasis affects cellular growth ra...	An epistatic interaction between two genes occurs when the phenotypic impact of one gene is dependent on the other . While different phenotypes have been used to uncover epistasis in different contexts , little is known about how cell-scale genetic interaction networks vary across multiple phenotypes . Here we use a ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/functional", "genomics", "computational", "biology/metabolic", "networks", "microbiology/microbial", "physi...	2011	Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes
Different neuronal types within brain motor areas contribute to the generation of complex motor behaviors . A widely studied songbird forebrain nucleus ( HVC ) has been recognized as fundamental in shaping the precise timing characteristics of birdsong . This is based , among other evidence , on the stretching and the ...	The study of the neuronal mechanisms that give rise to the complex behavior of singing in birds has been hotly debated lately . Many models have been tested and novel tools have been developed to try to understand the role of a key brain nucleus in the song pathway: HVC . It is believed that it is highly responsible fo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "nervous", "system", "membrane", "potential", "vertebrates", "electrophysiology", "neuroscience", "animals", "physiological", "parameters", "body", "temperature",...	2017	Temperature manipulation of neuronal dynamics in a forebrain motor control nucleus
Histone posttranslational modifications ( HPTMs ) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis ( SMB ) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions ( nutrient-rich ) but are activated whe...	In this work we monitored by proteomic analysis and ChIP-seq the genome-wide distribution of several key modifications on histone H3 in the model fungus Aspergillus nidulans cultivated either under optimal physiological conditions ( active growth ) or less favourable conditions which are known to promote the production...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "aspergillus", "fungal", "genetics", "gene", "regulation", "dna-binding", "proteins", "dna", "transcription", "aspergillus", "nidulans", "fungi", "model", "organisms", "epigenetics", "chromatin", "research", "and", "analysis", "methods", "mycology", "genomics", "chromosom...	2016	KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans
Dengue fever is an increasingly significant arthropod-borne viral disease , with at least 50 million cases per year worldwide . As with other viral pathogens , dengue virus is dependent on its host to perform the bulk of functions necessary for viral survival and replication . To be successful , dengue must manipulate ...	Dengue virus ( DENV ) represents a major disease burden in tropical and subtropical regions of the world , and has shown an increase in the number of cases in recent years . DENV is transmitted to humans through the bite of an infected mosquito , typically Aedes aegypti , after which it begins the infection and replica...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "virology/immune", "evasion", "virology/viral", "replication", "and", "gene", "regulation", "infectious", "diseases/neglected", "tropical", "diseases", "computational", "biology/protein", "homology", "detection", "molecular", "biology/bioinformatics", "infectious", "diseases/vira...	2011	Mapping Protein Interactions between Dengue Virus and Its Human and Insect Hosts
Advances in time-lapse fluorescence microscopy have enabled us to directly observe dynamic cellular phenomena . Although the techniques themselves have promoted the understanding of dynamic cellular functions , the vast number of images acquired has generated a need for automated processing tools to extract statistical...	Morphological change is a key indicator of various cellular functions such as migration and construction of specific structures . Time-lapse image microscopy permits the visualization of changes in morphology and spatio-temporal protein activity related to dynamic cellular functions . However , an unsolved problem is t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "molecular", "biology/bioinformatics", "biotechnology/bioengineering", "computational", "biology/molecular", "dynamics", "cell", "biology/cytoskeleton" ]	2008	Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking
Peroxisome proliferator-activated receptor ( PPAR ) γ is a global transcriptional regulator associated with anti-inflammatory actions . It is highly expressed in alveolar macrophages ( AMs ) , which are unable to clear the intracellular pathogen Mycobacterium tuberculosis ( M . tb ) . Although M . tb infection induces ...	The bacterium Mycobacterium tuberculosis is the causative agent of the disease tuberculosis ( TB ) , which is a global health problem and a leading cause of death world-wide . There is a clear need for better therapies for this disease , the design of which is predicated on better understanding of how M . tuberculosis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "gene", "regulation", "granulomas", "enzymes", "immunology", "cell", "processes", "enzymology", "tropical", "diseases", "bacterial", "diseases", "bacteria", "s...	2018	PPARγ is critical for Mycobacterium tuberculosis induction of Mcl-1 and limitation of human macrophage apoptosis
In order to analyse large complex stochastic dynamical models such as those studied in systems biology there is currently a great need for both analytical tools and also algorithms for accurate and fast simulation and estimation . We present a new stochastic approximation of biological oscillators that addresses these ...	Many cellular and molecular systems such as the circadian clock and the cell cycle are oscillators that are modelled using nonlinear dynamical systems . Moreover , oscillatory systems are ubiquitous elsewhere in science . There is an extensive theory for perfectly noise-free dynamical systems and very effective algorit...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "invertebrates", "applied", "mathematics", "animals", "circadian", "oscillators", "simulation", "and", "modeling", "algorithms", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "probability", "distribution", "mathematics", "experimental", "organism", ...	2017	Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference
Plants are associated with a complex microbiota that contributes to nutrient acquisition , plant growth , and plant defense . Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals , including maize . We studied an indigenous landrace of maize grown in nitrogen...	Nitrogen is an essential nutrient for plants , and for many nonlegume crops , the requirement for nitrogen is primarily met by the use of inorganic fertilizers . These fertilizers are produced from fossil fuel by energy-intensive processes that are estimated to use 1% to 2% of the total global energy supply and produce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "microbiome", "chemical", "compounds", "split-decomposition", "method", "microbiology", "plant", "physiology", "diazo", "compounds", "organic", "compounds", "multiple", "alignment", "calculation", "cereal", "crops", "plant", ...	2018	Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota
Mycobacterium tuberculosis , the etiological agent of TB , possesses a cholesterol catabolic pathway implicated in pathogenesis . This pathway includes an iron-dependent extradiol dioxygenase , HsaC , that cleaves catechols . Immuno-compromised mice infected with a ΔhsaC mutant of M . tuberculosis H37Rv survived 50% lo...	Mycobacterium tuberculosis , the etiological agent of TB , is the most devastating infectious agent of mortality worldwide: it is carried by one-third of all humans and kills nearly two million people annually . Recent work has established that the pathogen metabolizes cholesterol , although the role of this metabolism...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/biocatalysis", "biochemistry/biomacromolecule-ligand", "interactions", "infectious", "diseases/bacterial", "infections", "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Studies of a Ring-Cleaving Dioxygenase Illuminate the Role of Cholesterol Metabolism in the Pathogenesis of Mycobacterium tuberculosis
Cutaneous leishmaniasis ( CL ) is a parasitic disease causing chronic , ulcerating skin lesions . Most humans infected with the causative Leishmania protozoa are asymptomatic . Leishmania spp . are usually introduced by sand flies into the dermis of mammalian hosts in the presence of bacteria from either the host skin ...	Cutaneous leishmaniasis ( CL ) is a vector-borne ulcerating skin disease affecting several million people worldwide . The causative Leishmania spp . protozoa are transmitted by infected phlebotomine sand flies . During a sand fly bite , bacteria can be coincidentally inoculated into the dermis with the parasite . Staph...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "ears", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "staphylococcus", "aureus", "animal", "models", "otology", "model", ...	2019	Coinfection with Leishmania major and Staphylococcus aureus enhances the pathologic responses to both microbes through a pathway involving IL-17A
Assembly of kinetochore complexes , involving greater than one hundred proteins , is essential for chromosome segregation and genome stability . Neocentromeres , or new centromeres , occur when kinetochores assemble de novo , at DNA loci not previously associated with kinetochore proteins , and they restore chromosome ...	The accurate segregation of chromosomes during cell division is essential for maintaining genome integrity . The centromere is the DNA region on each chromosome where assembly of a large protein complex , the kinetochore , is required to maintain proper chromosome segregation . In addition , active centromeres exhibit ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chromosome", "structure", "and", "function", "centromeres", "pathogens", "microbiology", "dna", "transcription", "fungi", "model", "organisms", "genome", "analysis", "fungal", "patho...	2016	Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome
Advances in high-throughput genotyping and the International HapMap Project have enabled association studies at the whole-genome level . We have constructed whole-genome genotyping panels of over 550 , 000 ( HumanHap550 ) and 650 , 000 ( HumanHap650Y ) SNP loci by choosing tag SNPs from all populations genotyped by the...	Advances in high-throughput genotyping technology and the International HapMap Project have enabled genetic association studies at the whole-genome level . Our paper describes two genome-wide SNP panels that contain tag SNPs derived from the International HapMap Project . Tag SNPs are proxies for groups of highly corre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2007	Power to Detect Risk Alleles Using Genome-Wide Tag SNP Panels
Pregnant women with sporotrichosis should not receive systemic antifungal therapy except in severe cases when amphotericin B is recommended . Thermotherapy is the most reported treatment described in this group of patients . It entails weeks of daily self-application of heat to the lesions , requires that the patient f...	Sporotrichosis is a cosmopolitan disease , considered the most important subcutaneous mycosis in Latin America . Since 1998 , there is an ongoing cat-transmitted zoonotic epidemic of sporotrichosis occurring in Rio de Janeiro , Brazil . Pregnant women are a vulnerable population occasionally affected that require speci...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "drugs", "geographical", "locations", "microbiology", "antifungals", "surgical", "and", "invasive", "medical",...	2018	Cryosurgery for the treatment of cutaneous sporotrichosis in four pregnant women
The ability of specific neurons to regenerate their axons after injury is governed by cell-intrinsic regeneration pathways . In Caenorhabditis elegans , the JNK and p38 MAPK pathways are important for axon regeneration . Axonal injury induces expression of the svh-2 gene encoding a receptor tyrosine kinase , stimulatio...	An axon’s ability to regenerate after injury is governed by cell-intrinsic regeneration pathways . In C . elegans , the JNK and p38 MAPK pathways play an important role in axon regeneration . The JNK pathway is activated by growth factor SVH-1 , which signals through its receptor SVH-2 . It is known that expression of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Axon Regeneration Is Regulated by Ets–C/EBP Transcription Complexes Generated by Activation of the cAMP/Ca2+ Signaling Pathways
Cyclophilin B ( CyPB ) , encoded by PPIB , is an ER-resident peptidyl-prolyl cis-trans isomerase ( PPIase ) that functions independently and as a component of the collagen prolyl 3-hydroxylation complex . CyPB is proposed to be the major PPIase catalyzing the rate-limiting step in collagen folding . Mutations in PPIB c...	Osteogenesis imperfecta ( OI ) , or brittle bone disease , is characterized by susceptibility to fractures from minimal trauma and growth deficiency . Deficiency of components of the collagen prolyl 3-hydroxylation complex , CRTAP , P3H1 and CyPB , cause recessive types VII , VIII and IX OI , respectively . We have pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "model", "organisms", "genetics", "biology", "and", "life", "sciences", "research", "and", "analysis", "methods", "clinical", "genetics" ]	2014	Abnormal Type I Collagen Post-translational Modification and Crosslinking in a Cyclophilin B KO Mouse Model of Recessive Osteogenesis Imperfecta
The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology . Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point , or measures of dissimilarity between pai...	Microbes colonize the human body soon after birth and propagate to form rich ecosystems . These ecosystems play essential roles in health and disease . Recent advances in DNA sequencing technologies make possible comprehensive studies of the time-dependent behavior of microbes throughout the body . Sophisticated comput...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "small", "intestine", "clinical", "research", "design", "biota", "statistics", "microbiology", "algorithms", "metagenomics", "mathematics", "gastroenterology", "and", "hepatology", "genetics", "and", "genomics", "computer", "inferencing", "ecological", "metrics"...	2012	Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems
We have sequenced the complete mitochondrial genome of the extinct American mastodon ( Mammut americanum ) from an Alaskan fossil that is between 50 , 000 and 130 , 000 y old , extending the age range of genomic analyses by almost a complete glacial cycle . The sequence we obtained is substantially different from previ...	We determined the complete mitochondrial genome of the mastodon ( Mammut americanum ) , a recently extinct relative of the living elephants that diverged about 26 million years ago . We obtained the sequence from a tooth dated to 50 , 000–130 , 000 years ago , increasing the specimen age for which such palaeogenomic an...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "mammals" ]	2007	Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup
Lassa virus ( LASV ) is responsible for a viral hemorrhagic fever in humans and the death of 3 , 000 to 5 , 000 people every year . The immune response to LASV is poorly understood , but type I interferon ( IFN-I ) and T-cell responses appear to be critical for the host . We studied the response of myeloid dendritic ce...	Lassa fever is a viral hemorrhagic fever and a major public health issue in West Africa . Lassa virus , the causative agent of Lassa fever , is listed by the World Health Organization as one of the emerging pathogens likely to cause severe outbreaks in the near future . Indeed , there is currently no vaccine and no tre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "gene", "regulation", "antigen-presenting", "cells", "drugs", "immunology", "microbiology", "immunosuppressives", "dendritic", "cells", "cytotoxic", "t", "cells", "phar...	2018	Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells
While it is known that a large fraction of vertebrate genes are under the control of a gene regulatory network ( GRN ) forming a clock with circadian periodicity , shorter period oscillatory genes like the Hairy-enhancer-of split ( Hes ) genes are discussed mostly in connection with the embryonic process of somitogenes...	During vertebrate embryonic development , the segmented structure of the axial skeleton is laid down by the process of somitogenesis . Periodically , blocks of cells separate at the anterior end of a mesenchymal tissue ( PSM ) on either side of the neural tube and develop later into spinal vertebrae . Cellular oscillat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "theoretical", "biology", "biology", "and", "life", "sciences", "developmental", "biology", "computational", "biology" ]	2014	Fast Synchronization of Ultradian Oscillators Controlled by Delta-Notch Signaling with Cis-Inhibition
Genes with male- and testis-enriched expression are under-represented on the Drosophila melanogaster X chromosome . There is also an excess of retrotransposed genes , many of which are expressed in testis , that have “escaped” the X chromosome and moved to the autosomes . It has been proposed that inactivation of the X...	During spermatogenesis , the X chromosome is inactivated in the male germline ( sperm cells ) , thereby silencing , or inactivating , genes residing on the X chromosome . X chromosome silencing is thought to be common among species with XY sex determination and has important implications for genome evolution . For exam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "genetics", "and", "genomics", "evolutionary", "biology" ]	2007	X Chromosome Inactivation during Drosophila Spermatogenesis
The Gram-positive , spore-forming pathogen Clostridium difficile is the leading definable cause of healthcare-associated diarrhea worldwide . C . difficile infections are difficult to treat because of their frequent recurrence , which can cause life-threatening complications such as pseudomembranous colitis . The spore...	C . difficile is the leading cause of healthcare-associated infectious diarrhea in the United States in large part because of its ability to form spores . Since spores are resistant to most disinfectants and antibiotics , C . difficile infections frequently recur and are easily spread . Despite the importance of spores...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "infectious", "diseases", "genetics", "biology", "microbiology" ]	2013	Global Analysis of the Sporulation Pathway of Clostridium difficile
The world's oceans contain a complex mixture of micro-organisms that are for the most part , uncharacterized both genetically and biochemically . We report here a metagenomic study of the marine planktonic microbiota in which surface ( mostly marine ) water samples were analyzed as part of the Sorcerer II Global Ocean ...	Marine microbes remain elusive and mysterious , even though they are the most abundant life form in the ocean , form the base of the marine food web , and drive energy and nutrient cycling . We know so little about the vast majority of microbes because only a small percentage can be cultivated and studied in the lab . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "archaea", "ecology", "virology", "microbiology", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
The adaptive cytotoxic T lymphocyte ( CTL ) -mediated immune response is critical for clearance of many viral infections . These CTL recognize naturally processed short viral antigenic peptides bound to human leukocyte antigen ( HLA ) class I molecules on the surface of infected cells . This specific recognition allows...	The arboviral pathogen Chikungunya virus ( CHIKV ) is a serious threat to global health , and is considered a priority re-emerging virus . This pathogen causes acute febrile infection in patients , leading to debilitating arthralgia and arthritis . In recent years , CHIKV has spread quickly in tropical and subtropical ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "antigen", "presentation", "lysosomes", "immune", "cells", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "enzymes", "pathogens", "immunolo...	2017	Complex antigen presentation pathway for an HLA-A*0201-restricted epitope from Chikungunya 6K protein
Species barriers , expressed as hybrid inviability and sterility , are often due to epistatic interactions between divergent loci from two lineages . Theoretical models indicate that the strength , direction , and complexity of these genetic interactions can strongly affect the expression of interspecific reproductive ...	A characteristic feature of new species is their inability to produce fertile or viable hybrids with other lineages . This post-zygotic reproductive isolation is caused by dysfunctional interactions between genes that have newly evolved changes in the diverging lineages . Whether these interactions occur between pairs ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "pollen", "epistasis", "plant", "anatomy", "plant", "science", "fitness", "epistasis", "cell", "biology", "quantitative", "trait", "loci", "chromosome", "biology", "heredity", "genetics", "biology", "and", "life", "sciences", "introgression", "evolutionary", "biology", ...	2017	Pervasive antagonistic interactions among hybrid incompatibility loci
We are using the fungus Neurospora crassa as a model organism to study the circadian system of eukaryotes . Although the FRQ/WCC feedback loop is said to be central to the circadian system in Neurospora , rhythms can still be seen under many conditions in FRQ-less ( frq knockout ) strains . To try to identify component...	All eukaryotes ( including humans ) , and some bacteria , have evolved internal biological clocks that control activity and physiology in a daily ( circadian ) cycle . The molecular oscillators that drive these circadian rhythms are said to depend on rhythmic expression and feedback regulation of a small set of “clock ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetic", "mutation", "neurospora", "crassa", "genetics", "yeast", "and", "fungal", "models", "biology", "microbial", "growth", "and", "development", "microbiology", "genetics", "and", "genomics" ]	2011	A New Mutation Affecting FRQ-Less Rhythms in the Circadian System of Neurospora crassa
The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not . Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites , involving a nucleosome-free region ( NFR ) flanked b...	Within the last five years , knowledge about nucleosome organization on the genome has grown dramatically . To a large extent , this has been achieved by an increasing number of experimental studies determining nucleosome positions at high resolution over entire genomes . Particular attention has been paid to promoter ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/chromatin", "structure", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/chromosome", "biology" ]	2010	Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites
Reciprocal chromosomal translocations ( RCTs ) leading to the formation of fusion genes are important drivers of hematological cancers . Although the general requirements for breakage and fusion are fairly well understood , quantitative support for a general mechanism of RCT formation is still lacking . The aim of this...	A common genetic lesion leading to hematological cancer is the creation of fusion genes as a result of reciprocal translocations between chromosomes . Such translocations are non-random , in the sense that certain genes are more likely to be fused than others , and they appear to be tissue-specific . Current models ten...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Note", "added", "in", "proof" ]	[ "hematologic", "cancers", "and", "related", "disorders", "oncology", "medicine", "genomics", "chromosome", "biology", "basic", "cancer", "research", "genetics", "genetics", "and", "genomics", "biology", "computational", "biology", "gene", "networks", "hematology" ]	2012	Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer
Although autism has a clear genetic component , the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes . We used homozygosity analysis to identify probands from nonconsanguineous families that showed evidence of distant shared ancestry , suggesting potentially rece...	Autism spectrum disorders are neurodevelopmental disorders that are genetically highly heterogeneous , with no single gene accounting for more than 1% of cases . In order to identify recessive mutations , we selected probands from an outbred population based on abundance of homozygosity in their genomes . We interrogat...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2012	Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism
Despite significant , steady progress in schistosomiasis control in the People's Republic of China over the past 50 years , available data suggest that the disease has re-emerged with several outbreaks of acute infections in the early new century . In response , a new integrated strategy was introduced . This retrospec...	A retrospective study on the incidence of acute schistosomiasis in the People's Republic of China ( P . R . China ) was performed , in order to assess the new integrated control strategy that was implemented through the national control program from 2005 to 2012 . The lake and marshland regions have been identified as ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "malacology", "spatial", "epidemiology", "tropical", "diseases", "parasitic", "diseases", "parasitology", "global", "health", "neglected", "tro...	2014	Reduction Patterns of Acute Schistosomiasis in the People's Republic of China
The CDTI model is known to have enhanced community participation in planning and resource mobilization toward the control of onchocerciasis . These effects were expected to translate into better individual acceptance of the intervention and hence high Treatment Coverage , leading to a sustainable community-led strategy...	River blindness is caused by a very tiny , thread-like worm . The disease is better controlled when affected communities are included in the planning and carrying out of distribution of Ivermectin used to treat the disease . For a community to be able to prevent people from getting this disease , members must take Iver...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "transportation", "tropical", "diseases", "geographical", "locations", "social", "sciences", "census", "parasitic", "diseases", "research", "design", "neglected", "tropical", "diseases", "onchoce...	2017	Programmatic factors associated with the limited impact of Community-Directed Treatment with Ivermectin to control Onchocerciasis in three drainage basins of South West Cameroon
During pancreatic development , transcription factor cascades gradually commit precursor populations to the different endocrine cell fate pathways . Although mutational analyses have defined the functions of many individual pancreatic transcription factors , the integrative transcription factor networks required to reg...	Diabetes mellitus is a family of metabolic diseases that can result from either destruction or dysfunction of the insulin-producing beta cells of the pancreas . Recent studies have provided hope that generating insulin-producing cells from alternative cell sources may be a possible treatment for diabetes; this includes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "histology", "genetics", "biology", "genetics", "and", "genomics" ]	2013	Regulation of Neurod1 Contributes to the Lineage Potential of Neurogenin3+ Endocrine Precursor Cells in the Pancreas
The ApoE ε4 allele is the most significant genetic risk factor for late-onset Alzheimer disease . The risk conferred by ε4 , however , differs across populations , with populations of African ancestry showing lower ε4 risk compared to those of European or Asian ancestry . The cause of this heterogeneity in risk effect ...	The strongest risk gene identified for late-onset Alzheimer disease is ApoE . However , the risk for Alzheimer disease due to ApoE is not consistent across populations . For example , individuals with African ancestry experience less risk from ApoE ε4 than individuals of European or Asian ancestry . The cause of the di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "european", "union", "evolutionary", "biology", "neurodegenerative", "diseases", "population", "genetics", "geographical", "locations", "genetic", "mapping", "ethnicities", "african", "american", "people", "population", "biology", ...	2018	Ancestral origin of ApoE ε4 Alzheimer disease risk in Puerto Rican and African American populations
Understanding microbial nutritional requirements is a key challenge in microbiology . Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements , which we apply to thousands of species to study the relat...	Understanding microbial nutrition is critical for understanding microbial life , and thus has a major influence in many areas of biology . In recent years , the traditional methods of studying microbial nutrition , which rely on culturing bacteria and assessing their nutritional needs through extensive experiments , ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "systems", "ecology", "computer", "and", "information", "sciences", "ecology", "network", "analysis", "metabolic", "pathways", "biology", "and", "life", "sciences", "metabolic", "networks", "microbiology", "metabolism", "microbial", ...	2014	A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness
We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals . We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8 . 4% . Using a j...	Viral loads of Human Immunodeficiency Virus infections are correlated between the donor and the recipient of the transmission pair . Similarly , human genetic factors may modulate viral load . In this study we estimate the extents to which viral load is heritable either via the viral genotype ( from donor to recipient ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "viral", "transmission", "and", "infection", "pathogens", "population", "genetics", "microbiology", "retroviruses", "...	2017	Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control
Most pairwise and multiple sequence alignment programs seek alignments with optimal scores . Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides . For local pairwise alignment , substitution scores are implicitly of log-odds form . We now extend the log-odds ...	Multiple sequence alignment is a fundamental tool of biological research , widely used to identify important regions of DNA or protein molecules , to infer their biological functions , to reconstruct ancestries , and in numerous other applications . The effectiveness and accuracy of sequence comparison programs depends...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/protein", "homology", "detection", "computational", "biology/sequence", "motif", "analysis", "computational", "biology" ]	2010	The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
In veterinary parasitology samples are often pooled for a rapid assessment of infection intensity and drug efficacy . Currently , studies evaluating this strategy in large-scale drug administration programs to control human soil-transmitted helminths ( STHs; Ascaris lumbricoides , Trichuris trichiura , and hookworm ) ,...	Since the last decade , growing awareness of the control of neglected tropical diseases ( NTDs ) has resulted in worldwide increased pledges of drug donations . However , health care decision makers have a limited repertoire of strategies for a rapid assessment of infection intensity and for checking of drug resistance...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "epidemiology", "drugs", "and", "devices", "public", "health" ]	2013	Comparison of Individual and Pooled Stool Samples for the Assessment of Soil-Transmitted Helminth Infection Intensity and Drug Efficacy
Telomeric repeats preserve genome integrity by stabilizing chromosomes , a function that appears to be important for both cancer and aging . In view of this critical role in genomic integrity , the telomere's own integrity should be of paramount importance to the cell . Ultraviolet light ( UV ) , the preeminent risk fa...	Telomeres consist of a repeated sequence located at each end of each chromosome . This repeated sequence is required for chromosomal stability and integrity , a function important for both cancer and aging . The DNA sequence of human telomeres is 5–10 kb of a repeated double-strand hexamer ( 5′TTAGGG/5′CCCTAA ) . In th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "cell", "biology/cellular", "death", "and", "stress", "responses", "dermatology/skin", "cancers,", "including", "melanoma", "and", "lymphoma", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", ...	2010	Human Telomeres Are Hypersensitive to UV-Induced DNA Damage and Refractory to Repair
Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation . These studies have identified a number of evolutionary regularities: ( 1 ) phenotypes occupy only a small subspace of possible phenotypes , ( 2 ) the influence of...	At the very end of his On the Origin of Species , Charles Darwin wrote , “from so simple a beginning endless forms most beautiful and most wonderful have been , and are being , evolved . ” Nature truly displays a bewildering variety of shapes and forms . Yet , with all its magnificence , this diversity still represents...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "computational", "biology/transcriptional", "regulation", "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/developmental", "evolution" ]	2008	An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
A hallmark of the G1/S transition in budding yeast cell cycle is the proteolytic degradation of the B-type cyclin-Cdk stoichiometric inhibitor Sic1 . Deleting SIC1 or altering Sic1 degradation dynamics increases genomic instability . Certain key facts about the parts of the G1/S circuitry are established: phosphorylati...	In eukaryotic organisms , genome replication starts simultaneously from many sites on the DNA , called origins of replication . In budding yeast , these origins are activated by a kinase , Clb5/6-Cdk1 . Until the start of S-phase , when the replication origins are activated , this kinase is kept inactive by an inhibito...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Design Principles of the Yeast G1/S Switch
From computational simulations of a serotonin 2A receptor ( 5-HT2AR ) model complexed with pharmacologically and structurally diverse ligands we identify different conformational states and dynamics adopted by the receptor bound to the full agonist 5-HT , the partial agonist LSD , and the inverse agonist Ketanserin . T...	The 5-HT2A receptor for the neurotransmitter serotonin ( 5-HT ) belongs to family A ( rhodopsin-like ) G-protein coupled receptors ( GPCRs ) , one of the most important classes of membrane proteins that are targeted by an extensive and diverse collection of external stimuli . Recently we learned that different ligands ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mechanisms", "of", "signal", "transduction", "membrane", "proteins", "membrane", "structures", "biophysics", "simulations", "cell", "membrane", "cytochemistry", "proteins", "biophysics", "theory", "biology", "biophysics", "molecular", "biology", "biochemistry", "signal", ...	2012	Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties

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