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Testing for genetic effects on mean values of a quantitative trait has been a very successful strategy . However , most studies to date have not explored genetic effects on the variance of quantitative traits as a relevant consequence of genetic variation . In this report , we demonstrate that , under plausible scenari...	Finding gene–gene and gene–environment interactions is a major challenge in genetics . In this report , we propose a novel method to help detect these interactions . This method works by first identifying a subset of genetic variants more likely to be involved in genetic interactions and then testing these variants for...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "diabetes", "and", "endocrinology/obesity", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/bioinformatics" ]	2010	On the Use of Variance per Genotype as a Tool to Identify Quantitative Trait Interaction Effects: A Report from the Women's Genome Health Study
Human antibodies ( Abs ) elicited by influenza viruses often bind with a high affinity to past influenza virus strains , but paradoxically , do not bind to the viral strain actually eliciting the response . This phenomena is called ‘original antigenic sin’ ( OAS ) since this can occur at the expense of generating new d...	Humans are continuously exposed to antigenically distinct influenza virus strains . Influenza virus infections early in life elicit immune responses that are subsequently recalled upon exposures with different influenza virus strains . Antibodies elicited against older influenza strains can dominate immune responses el...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "microbial", "mutation", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immune", "cells", "influenza", "pathogens", "biological", "cultures", "immunology", ...	2016	Antibodies with ‘Original Antigenic Sin’ Properties Are Valuable Components of Secondary Immune Responses to Influenza Viruses
Visceral leishmaniasis has now emerged as an important opportunistic disease in patients coinfected with human immunodeficiency virus type-1 ( HIV-1 ) . Although the effectiveness of HIV-1 protease inhibitors , such as nelfinavir , in antiretroviral therapies is well documented , little is known of the impact of these ...	Visceral leishmaniasis is the most severe form of disease caused by the parasite Leishmania . It is a major concern in South America , Africa , India and the Middle East . Additionally , it has now emerged as an important opportunistic disease in patients coinfected with HIV-1 . This is due , in part , to the increasin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "virology/immunodeficiency", "viruses", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/protozoal", ...	2010	Nelfinavir, an HIV-1 Protease Inhibitor, Induces Oxidative Stress–Mediated, Caspase-Independent Apoptosis in Leishmania Amastigotes
Homology-dependent repair of DNA double-strand breaks ( DSBs ) by gene conversion involves short tracts of DNA synthesis and limited loss of heterozygosity ( LOH ) . For DSBs that present only one end , repair occurs by invasion into a homologous sequence followed by replication to the end of the chromosome resulting i...	DNA double-strand breaks ( DSBs ) can occur spontaneously in cells by defective DNA replication or are induced by various types of DNA damaging agents , such as those used in chemo- or radiation therapy . Failure to repair DSBs , or inappropriate repair , can result in chromosome loss or chromosome rearrangements , eve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "molecular", "biology/recombination", "genetics", "and", "genomics/chromosome", "biology", "biochemistry/replication", "and", "repair", "molecular", "biology/dna", "repair" ]	2010	Extensive DNA End Processing by Exo1 and Sgs1 Inhibits Break-Induced Replication
We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets , in order to understand the biological roles of transcription factors . We develop a computational framework for this task , whose features include a new statistical score for motif scanning ...	We develop a computational pipeline for predicting the functions of transcription factor motifs , through DNA sequence analysis . The pipeline is applied to the newly sequenced genome of the jewel wasp , Nasonia vitripennis . It exploits the wealth of molecular data available in another insect species , the fruitfly Dr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/comparative", "sequence", "analysis", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2010	Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances
Borrelia burgdorferi , the causative agent of Lyme disease , is transmitted to humans by bite of Ixodes scapularis ticks . The mechanisms by which the bacterium is transmitted from vector to host are poorly understood . In this study , we show that the F ( ab ) 2 fragments of BBE31 , a B . burgdorferi outer-surface lip...	Lyme disease , the most common tick-borne illness in North America , is caused by Borrelia burgdorferi . Currently , spirochete and tick molecules that facilitate Borrelia migration within the vector , a key step for mammalian infection by tick-transmitted spirochetes , have not yet been identified . In this study , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "lyme", "disease" ]	2011	Molecular Interactions that Enable Movement of the Lyme Disease Agent from the Tick Gut into the Hemolymph
River blindness and lymphatic filariasis are two filarial diseases that globally affect millions of people mostly in impoverished countries . Current mass drug administration programs rely on drugs that primarily target the microfilariae , which are released from adult female worms . The female worms can live for sever...	Safe and effective macrofilaricidal drugs are critically needed to treat onchocerciasis and lymphatic filariasis , which affect over 54 million people worldwide . Flubendazole ( FBZ ) in its current commercial formulations is an effective anthelminthic for intestinal soil transmitted helminth ( STH ) infections but not...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "parasitic", "diseases", "animals", "nematode", "infections", "developmental", "biology", "routes", "of", "administration", "brugia", "filariasis", "neglected", "tropical",...	2019	Efficacy of subcutaneous doses and a new oral amorphous solid dispersion formulation of flubendazole on male jirds (Meriones unguiculatus) infected with the filarial nematode Brugia pahangi
Epstein-Barr virus ( EBV ) and related lymphocryptoviruses ( LCV ) from non-human primates infect B cells , transform their growth to facilitate life-long viral persistence in the host , and contribute to B cell oncogenesis . Co-evolution of LCV with their primate hosts has led to species-specificity so that LCVs prefe...	Co-evolution of viruses and their natural hosts often results in barriers limiting the ability of viruses to infect hosts from other species . Understanding the nature of these species barriers has provided important insights into different aspects of viral life cycles , from virus entry into cells to host factors rest...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "immunology", "cell", "processes", "microbiology", "immunoblotting", "plasm...	2017	Species-specific functions of Epstein-Barr virus nuclear antigen 2 (EBNA2) reveal dual roles for initiation and maintenance of B cell immortalization
Acetylation of histone H3 lysine 56 is a covalent modification best known as a mark of newly replicated chromatin , but it has also been linked to replication-independent histone replacement . Here , we measured H3K56ac levels at single-nucleosome resolution in asynchronously growing yeast cultures , as well as in yeas...	Wrapping of eukaryotic genomes by the histone proteins impacts virtually all known DNA templates processes . Covalent modification of the histone proteins has emerged as a key mechanism for regulation of transcription and other processes . Here , we report high-resolution genomic mapping of a relatively recently descri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromatin", "structure" ]	2008	Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast
Driven by oncogenic signaling , glutamine addiction exhibited by cancer cells often leads to severe glutamine depletion in solid tumors . Despite this nutritional environment that tumor cells often experience , the effect of glutamine deficiency on cellular responses to DNA damage and chemotherapeutic treatment remains...	Cancer cells residing within the intratumoral microenvironment are subject to severe glutamine shortages . Herein , we provide mechanistic insight by which glutamine deficiency leads to cellular sensitivity to alkylating agents . We find that glutamine deficiency inhibits the DNA repair activity of the ALKBH enzymes , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "chemical", "compounds", "molecular", "probe", "techniques", "cancer", "treatment", "immunoblotting", "enzymology", "cell", "metabolism", "organic", "compounds", "oncology", "dna", "damage", "acidic", "amino...	2017	Glutamine deficiency induces DNA alkylation damage and sensitizes cancer cells to alkylating agents through inhibition of ALKBH enzymes
The link between object perception and neural activity in visual cortical areas is a problem of fundamental importance in neuroscience . Here we show that electrical potentials from the ventral temporal cortical surface in humans contain sufficient information for spontaneous and near-instantaneous identification of a ...	We describe a new technique for decoding perception from electrical potentials measured from the human brain surface . All previous attempts have focused on the identification of classes of stimuli or behavior where the timing of experimental parameters is known or pre- designated . However , real world experience is s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change
Upon nutrient limitation , budding yeasts like Saccharomyces cerevisiae can be induced to adopt alternate filament-like growth patterns called diploid pseudohyphal or invasive haploid growth . Here , we report a novel constitutive pseudohyphal growth state , sharing some characteristics with classic forms of filamentou...	Many pathogenic fungi alternate between unicellular and multicellular filamentous forms , which is often critical for host-cell attachment , tissue invasion , and virulence . Certain strains of the nonpathogenic budding yeast Saccharomyces cerevisiae are also capable of forming invasive pseudohyphal filaments in nutrie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Stable Pseudohyphal Growth in Budding Yeast Induced by Synergism between Septin Defects and Altered MAP-kinase Signaling
We demonstrate that both Hepatitis C virus ( HCV ) and Bovine Viral Diarrhea virus ( BVDV ) contain regions in their 5’ UTRs that stall and repress the enzymatic activity of the cellular 5’-3’ exoribonuclease XRN1 , resulting in dramatic changes in the stability of cellular mRNAs . We used biochemical assays , virus in...	Understanding how a persistent virus like Hepatitis C Virus ( HCV ) interfaces with the cellular machinery during infection can provide significant insights into mechanisms of pathogenesis . We demonstrate that while trying to degrade HCV transcripts , a major cellular exonuclease called XRN1 stalls and gets repressed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	XRN1 Stalling in the 5’ UTR of Hepatitis C Virus and Bovine Viral Diarrhea Virus Is Associated with Dysregulated Host mRNA Stability
Protein-ligand recognition plays key roles in many biological processes . One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism , which often results from a combination of induced fit and conformational selection . In this study , we have developed a three-pron...	Molecular recognition plays important roles in numerous biological processes including gene regulation , cell signaling and enzymatic activity . It has been suggested that molecular recognition employs a variety of mechanisms , ranging from induced fit to conformational selection . In many realistic systems , conformat...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biophysics", "computational", "biology", "biology", "and", "life", "sciences", "biophysical", "simulations" ]	2014	Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
Recognizing the life cycle of an organism is key to understanding its biology and ecological impact . Emiliania huxleyi is a cosmopolitan marine microalga , which displays a poorly understood biphasic sexual life cycle comprised of a calcified diploid phase and a morphologically distinct biflagellate haploid phase . Di...	This study assesses the interplay between the globally distributed microalga Emiliania huxleyi and its specific lytic viruses , EhV , which drive the termination of vast oceanic blooms . E . huxleyi is characterized by a biphasic life cycle that alternates between morphologically dissimilar diploid and haploid cells . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "meiosis", "ecology", "and", "environmental", "sciences", "viral", "transmission", "and", "infection", "diplobiontic", "life", "cycle", "cell", "cycle", "and", "cell", "division", "cell", "processes", "population", "genetics", "microbiology", "plo...	2017	Morphological switch to a resistant subpopulation in response to viral infection in the bloom-forming coccolithophore Emiliania huxleyi
Given sufficient large protein families , and using a global statistical inference approach , it is possible to obtain sufficient accuracy in protein residue contact predictions to predict the structure of many proteins . However , these approaches do not consider the fact that the contacts in a protein are neither ran...	Here , we introduce a novel protein contact prediction method PconsC2 that , to the best of our knowledge , outperforms earlier methods . PconsC2 is based on our earlier method , PconsC , as it utilizes the same set of contact predictions from plmDCA and PSICOV . However , in contrast to PconsC , where each residue pai...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "machine", "learning", "algorithms", "protein", "interactions", "applied", "mathematics", "neuroscience", "simulation", "and", "modeling", "algorithms", "mathematics", "protein", "structure", "prediction", "artificial", "intelligence", "protein", "folding", "protein", "stru...	2014	Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
Extradenticle ( Exd ) and Homothorax ( Hth ) function as positive transcriptional cofactors of Hox proteins , helping them to bind specifically their direct targets . The posterior Hox protein Abdominal-B ( Abd-B ) does not require Exd/Hth to bind DNA; and , during embryogenesis , Abd-B represses hth and exd transcript...	Hox genes encode transcription factors necessary to achieve the morphological differences between anterior and posterior regions of the body . These genes have been functionally conserved during animal evolution , and similar classes can be recognized in vertebrates and invertebrates . To bind DNA and regulate many of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2013	Antagonism Versus Cooperativity with TALE Cofactors at the Base of the Functional Diversification of Hox Protein Function
Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery . Although there are numerous papers on the prediction of interaction sites using information derived from structure , there are only...	In their active state , proteins—the workhorses of a living cell—need to have a defined 3D structure . The majority of functions in the living cell are performed through protein interactions that occur through specific , often unknown , residues on their surfaces . We can study protein interactions either qualitatively...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology" ]	2009	Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests
Dengue is the most prevalent arthropod-borne viral human disease in tropical and subtropical regions , caused by four dengue virus ( DENV ) serotypes . In spite of the increasing global incidence , no specific antiviral therapy is available . Cells of the mononuclear phagocyte lineage are the main targets either for di...	Dengue is currently a widespread viral disease transmitted to human by mosquitoes , with very high prevalence in tropical and subtropical regions of América and Asia . Approximately 2 . 5 billion people are living in endemic areas and it is estimated that 350 million apparent and inapparent infections occur each year ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "viral", "transmission", "and", "infection", "pathogens", "drugs", "cell", "processes", "microbiology", "viral", "structure", "bone", "ma...	2018	Blockade of dengue virus entry into myeloid cells by endocytic inhibitors in the presence or absence of antibodies
In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification ( LAMP ) assay for the rapid detection of Brugia genomic DNA . Amplification was detected using turbidity or fluorescence as readouts . Reactions generated a turbidity threshold value or a clear visual positive within ...	Brugian filariasis is a debilitating neglected tropical disease caused by infection with the filarial parasites Brugia malayi or Brugia timori . Adult worms live in the lymphatic system and produce large numbers of microfilariae that predominantly circulate in the blood at night . Bloodsucking mosquitoes spread the dis...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "diagnostic", "medicine", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Diagnosis of Brugian Filariasis by Loop-Mediated Isothermal Amplification
Telomere-binding proteins constituting the shelterin complex have been studied primarily for telomeric functions . However , mounting evidence shows non-telomeric binding and gene regulation by shelterin factors . This raises a key question—do telomeres impact binding of shelterin proteins at distal non-telomeric sites...	Telomeres ( special DNA-protein assemblies that protect chromosome ends ) affect ageing and diseases such as cancer . Although this has been recognized for many years , biological processes that connect telomeres to ageing , cancer and other cellular functions remain to be fully understood . Certain proteins , believed...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "chromosome", "structure", "and", "function", "biological", "cultures", "dna", "transcription", "histone", "modification", "ht1080", "cells", "telomeres", "epigenetics", "chromatin", "research", "and", "analysis", "methods", "tel...	2018	Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends
Klebsiella ( K . ) pneumoniae is a common cause of pneumonia-derived sepsis . Myeloid related protein 8 ( MRP8 , S100A8 ) and MRP14 ( S100A9 ) are the most abundant cytoplasmic proteins in neutrophils . They can form MRP8/14 heterodimers that are released upon cell stress stimuli . MRP8/14 reportedly exerts antimicrobi...	Neutrophils are phagocytes that are well known for their capacity to engulf and kill microbial pathogens . It has become increasingly clear that neutrophils also kill or inhibit growth extracellularly by releasing neutrophil extracellular traps ( NETs ) , chromatin fibers decorated with neutrophil derived proteins . MR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "klebsiella", "infections", "bloodstream", "infections", "clinical", "immunology", "immunity", "innate", "immunity", "immunity", "to", "infections", "klebsiella", "pneumonia", "immunology" ]	2012	Myeloid-Related Protein-14 Contributes to Protective Immunity in Gram-Negative Pneumonia Derived Sepsis
Why do some individuals need more sleep than others ? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration , revealing mutants that convey very long or short sleep . Whether such extreme long or short sleep could exist in natural populations was un...	One of the biggest mysteries in biology is the need to sleep . Sleep duration has an underlying genetic basis , suggesting that very long and short sleep times could be bred for experimentally . How far can sleep duration be driven up or down ? Here we achieved extremely long and short night sleep duration by subjectin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "sleep", "deprivation", "sleep", "artificial", "selection", "computational", "biology", "alleles", "physiological", "processes", "genome", "analysis", "chronobiology", "mapk", "signaling", "...	2017	Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep
Lassa fever is a viral hemorrhagic fever endemic in West Africa . The reservoir host of the virus is a multimammate rat , Mastomys natalensis . Prevalence estimates of Lassa virus antibodies in humans vary greatly between studies , and the main modes of transmission of the virus from rodents to humans remain unclear . ...	Lassa fever is a viral haemorrhagic fever endemic in West Africa , mainly transmitted to humans by multimammate rats . Several modes of virus transmission are suspected: aerosolisation of the virus , contact with infected rodent excreta , and consumption of rodent meat . Person-to-person transmission also occurs via co...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/nosocomial", "and", "healthcare-associated", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epide...	2009	Prevalence and Risk Factors of Lassa Seropositivity in Inhabitants of the Forest Region of Guinea: A Cross-Sectional Study
Autosomal dominant polycystic kidney disease ( ADPKD ) is characterized by formation of renal cysts that destroy the kidney . Mutations in PKD1 and PKD2 , encoding polycystins-1 and -2 , cause ADPKD . Polycystins are thought to function in primary cilia , but it is not well understood how these and other proteins are t...	ADPKD , the most common potentially lethal monogenetic disorder , is caused by mutations in PKD1 and PKD2 . We are beginning to appreciate the important roles these gene products , and others , play in cilia , which are thin rod-like organelles projecting from the cell surface . Defects in cilia function are associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "cell", "biology/membranes", "and", "sorting", "nephrology/hereditary,", "genetic,", "and", "development", "nephrology" ]	2011	The Exocyst Protein Sec10 Interacts with Polycystin-2 and Knockdown Causes PKD-Phenotypes
Stem cells in tissues reside in and receive signals from local microenvironments called niches . Understanding how multiple signals within niches integrate to control stem cell function is challenging . The Drosophila testis stem cell niche consists of somatic hub cells that maintain both germline stem cells and somati...	Stem cells adhere to niches , or local microenvironments , which provide essential maintenance cues . In the Drosophila testis niche , quiescent hub cells maintain adjacent germline and somatic stem cells ( or cyst stem cells , CySCs ) via local JAK-STAT signaling . Here , we show that the Slit-Robo and JAK-STAT pathwa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "cell", "biology", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	Coordinate Regulation of Stem Cell Competition by Slit-Robo and JAK-STAT Signaling in the Drosophila Testis
The Chlamydiae are a highly successful group of obligate intracellular bacteria , whose members are remarkably diverse , ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa . While their infective developmental stage , the elementary body ( EB ) , has long been accepted to be complete...	The Chlamydiae are a group of bacteria that strictly rely on eukaryotic host cells as a niche for intracellular growth . This group includes major pathogens of humans and animals as well as symbionts of protists . Unlike most other bacteria , chlamydiae alternate between two distinct developmental stages . Here we prov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "biology", "microbiology", "bacterial", "pathogens" ]	2013	Metabolic Features of Protochlamydia amoebophila Elementary Bodies – A Link between Activity and Infectivity in Chlamydiae
Chronic persistent infections have been associated with T lymphocytes functional impairment . The aim of this study was to compare the activation status , the proliferative potential and the expression of CD28 and CD3ζ chain on T lymphocytes between chronic chagasic patients and uninfected controls . Forty-two chronic ...	In Chagas disease , caused by Trypanosoma cruzi , there is an acute onset from which most of the individuals recover if a competent immune response develops . Patients can remain asymptomatic ( indeterminate ) for many years , but near 30% can develop specific organ damage , mainly the heart . The pathogenesis of chron...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "parasitic", "diseases", "chagas", "disease", "immune", "cells", "t", "cells", "parasitology", "immunology", "biology", "microbiology", "neglected", "tropical", "diseases", "immunomodulation", "immune", "response" ]	2013	T Lymphocytes from Chagasic Patients Are Activated but Lack Proliferative Capacity and Down-Regulate CD28 and CD3ζ
Severe acute respiratory syndrome coronavirus ( SARS-CoV ) infection often caused severe end stage lung disease and organizing phase diffuse alveolar damage , especially in the elderly . The virus-host interactions that governed development of these acute end stage lung diseases and death are unknown . To address this ...	The SARS coronavirus is a highly pathogenic respiratory virus that caused the first epidemic of the 21st century . During the epidemic ∼10% of those infected died and the elderly were particularly vulnerable . Severe cases developed acute lung injury with pulmonary fibrosis and Acute Respiratory Distress Syndrome ( ARD...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/host", "antiviral", "responses", "virology/animal", "models", "of", "infection", "immunology/innate", "immunity" ]	2010	SARS-CoV Pathogenesis Is Regulated by a STAT1 Dependent but a Type I, II and III Interferon Receptor Independent Mechanism
Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains ( TADs ) . From a visual examination of the chromosomal contact map , however , it is clear that the organization of the domains is not simple or ob...	The accommodation of the roughly 2m of DNA in the nuclei of mammalian cells results in an intricate structure , in which the topologically associating domains ( TADs ) formed by densely interacting genomic regions emerge as a fundamental structural unit . Identification of TADs is essential for understanding the role o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "applied", "mathematics", "regulatory", "proteins", "dna-binding", "proteins", "simulation", "and", "modeling", "algorithms", "histone", "modification", "optimization", "mutation", "chromosome", "mapping", "mathematics", "transcription", "factors", "ep...	2017	MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
Alternative splicing of precursor messenger RNA ( pre-mRNA ) is common in mammalian cells and enables the production of multiple gene products from a single gene , thus increasing transcriptome and proteome diversity . Disturbance of splicing regulation is associated with many human diseases; however , key splicing fac...	The production of functional spermatozoa is an extraordinarily complex process that transforms a conventional round cell into the highly specialised sperm cell . These events require the coordinated activation of thousands of genes . It is likely that this complexity contributes to the large number of idiopathic infert...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "networks", "animal", "genetics", "genetic", "mutation", "gene", "regulation", "cell", "differentiation", "gene", "function", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "molecular", "genetics", "gene", "expr...	2013	RBM5 Is a Male Germ Cell Splicing Factor and Is Required for Spermatid Differentiation and Male Fertility
To eliminate blinding trachoma , the World Health Organization emphasizes implementing the SAFE strategy , which includes annual mass drug administration ( MDA ) with azithromycin to the whole population of endemic districts . Prevalence surveys to assess impact at the district level are recommended after at least 3 ye...	Trachoma , the leading cause of preventable blindness , is targeted for “elimination as a public health problem” by the year 2020 . National programs are implementing the recommended strategy of surgery , antibiotics , facial cleanliness , and environmental improvements ( SAFE ) to meet this target . Many programs are ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ophthalmology", "medicine", "public", "health", "trachoma" ]	2014	Prevalence of Trachoma at Sub-District Level in Ethiopia: Determining When to Stop Mass Azithromycin Distribution
Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles . In plants , genomic imprinting has mainly been observed in the endosperm , an ephemeral triploid tissue derived after fertilization of the diploid central cell wit...	Genomic imprinting poses a violation to the Mendelian rules of inheritance , which state functional equality of maternally and paternally inherited alleles . Imprinted genes are expressed dependent on their parent-of-origin , implicating an epigenetic asymmetry of maternal and paternal alleles . Genomic imprinting occu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "plant", "biology", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm
Epstein-Barr virus ( EBV ) causes infectious mononucleosis and is associated with various malignancies , including Burkitt's lymphoma and nasopharyngeal carcinoma . Like all herpesviruses , the EBV life cycle alternates between latency and lytic replication . During latency , the viral genome is largely silenced by hos...	γ herpesviruses are characterized by their life-long persistence in the infected host . This is due in part to their ability to establish latency in infected cells . Epstein-Barr virus ( EBV ) is almost ubiquitous within the human population . The virus establishes latency in B-lymphocytes and is thought to reactivate ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "biochemistry/protein", "folding", "virology", "infectious", "diseases/viral", "infections", "virology/viruses", "and", "cancer", "biochemistry/transcription", "and", "translation" ]	2008	Methylated DNA Recognition during the Reversal of Epigenetic Silencing Is Regulated by Cysteine and Serine Residues in the Epstein-Barr Virus Lytic Switch Protein
Interactions with flying foxes pose disease transmission risks to volunteer rehabilitators ( carers ) who treat injured , ill , and orphaned bats . In particular , Australian bat lyssavirus ( ABLV ) can be transmitted directly from flying foxes to humans in Australia . Personal protective equipment ( PPE ) and rabies v...	Wildlife rehabilitators can encounter risks when handling animals , such as physical harm and exposure to infectious diseases . In Australia , rehabilitators that care for fruit bats may be exposed to Australian bat lyssavirus if bitten or scratched , which is fatal to people not vaccinated against rabies . We initiate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "viruses", "preventive", ...	2016	Disease Risk Perception and Safety Practices: A Survey of Australian Flying Fox Rehabilitators
Seroprevalence survey is the most practical method for accurately estimating infection attack rate ( IAR ) in an epidemic such as influenza . These studies typically entail selecting an arbitrary titer threshold for seropositivity ( e . g . microneutralization [MN] 1∶40 ) and assuming the probability of seropositivity ...	Seroprevalence studies have been regarded as the most practical method for accurately estimating the number of infections in influenza epidemics and pandemics . However , methods for inferring the number of infections from seroprevalence data in previous studies have mostly been based on conventional practice instead o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "medicine", "and", "health", "sciences", "population", "modeling", "influenza", "immunology", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "computational", "biology", "vir...	2014	Inferring Influenza Infection Attack Rate from Seroprevalence Data
The mitotic checkpoint ( also called spindle assembly checkpoint ) is a signaling pathway that ensures faithful chromosome segregation . Mitotic checkpoint proteins inhibit the anaphase-promoting complex ( APC/C ) and its activator Cdc20 to prevent precocious anaphase . Checkpoint signaling leads to a complex of APC/C ...	Cell division is a fundamental event in the life of cells . It requires that a mother cell gives rise to two daughters which carry the same genetic material of their mother . Thus , during each cell cycle the genetic material needs to be replicated , compacted into chromosomes and redistributed to the two daughter cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "anaphase", "engineering", "and", "technology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "mathematical", "models", "simulation", "and", "modeling", "signal", "inhibition", "network", "analysis", "chemical", "dissociation", "research", "and", "a...	2018	Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex
Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation . Here , we present a genomic survey of recent local selective sweeps , especially aimed at those nearly or recently completed . A novel approach was developed for such signals...	The evolution of new functions and adaptation to new environments occurs by positive selection , whereby beneficial mutations increase in frequency and eventually become fixed in a population . Detecting such selection in humans is crucial for understanding the importance of past genetic adaptations and their role in c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology", "evolutionary", "biology", "homo", "(human)", "genetics", "and", "genomics" ]	2007	A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
Following almost 30 years of relative silence , chikungunya fever reemerged in Kenya in 2004 . It subsequently spread to the islands of the Indian Ocean , reaching Southeast Asia in 2006 . The virus was first detected in Cambodia in 2011 and a large outbreak occurred in the village of Trapeang Roka Kampong Speu Provinc...	During the recent resurgence of chikungunya , the scale of imported cases into previously unaffected countries has caused great concern due to the presence of a competent vector ( Aedes albopictus ) in many of these regions . This study describes a mathematical model for a chikungunya outbreak in the rural Cambodian vi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "population", "biology", "medicine", "and", "health", "sciences", "epidemiology" ]	2014	A Model for a Chikungunya Outbreak in a Rural Cambodian Setting: Implications for Disease Control in Uninfected Areas
Coordinated transcriptional and epigenetic mechanisms that direct development of the later differentiating second heart field ( SHF ) progenitors remain largely unknown . Here , we show that a novel zebrafish histone deacetylase 1 ( hdac1 ) mutant allele cardiac really gone ( crg ) has a deficit of ventricular cardiomy...	Congenital heart defects are the most common malformations found in newborns , with many of these defects disrupting development of the outflow tract , the structure where blood is expelled from the heart . Despite their frequency , we do not have a grasp of the molecular and genetic mechanisms that underlie most conge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "cardiac", "ventricles", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "heart", "experimental", "organism", "systems", "epigenet...	2019	HDAC1-mediated repression of the retinoic acid-responsive gene ripply3 promotes second heart field development
There are only few assays available for the detection of Crimean-Congo Hemorrhagic Fever Virus ( CCHFV ) -specific antibodies in animals , and data about diagnostic sensitivity and specificity are incompletely documented for most of these tests . This is unfortunate since CCHFV antibodies in animals can be used as indi...	Crimean-Congo hemorrhagic fever virus ( CCHFV ) infections in humans can cause a deadly hemorrhagic fever with high fatality rates . Most humans are infected by ticks or by contact with blood . No vaccine prophylaxis or therapeutic interventions are available . Ticks of the genus Hyalomma function as vector of CCHFV . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Circulation of Crimean-Congo Hemorrhagic Fever Virus in the Former Yugoslav Republic of Macedonia Revealed by Screening of Cattle Sera Using a Novel Enzyme-linked Immunosorbent Assay
A fundamental task of a sensory system is to infer information about the environment . It has long been suggested that an important goal of the first stage of this process is to encode the raw sensory signal efficiently by reducing its redundancy in the neural representation . Some redundancy , however , would be expec...	Studies of the computational principles of sensory coding have largely focused on the redundancy reduction hypothesis , which posits that a neural population should encode the raw sensory signal efficiently by reducing its redundancy . Models based on this idea , however , have not taken into account some important asp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "visual", "system", "computational", "neuroscience", "biology", "and", "life", "sciences", "sensory", "systems", "computational", "biology", "neuroscience", "coding", "mechanisms" ]	2014	A Simple Model of Optimal Population Coding for Sensory Systems
Tri-methylation on histone H3 lysine 4 ( H3K4me3 ) is associated with active gene expression but its regulatory role in transcriptional activation is unclear . Here we used Caenorhabditis elegans to investigate the connection between H3K4me3 and gene expression regulation during aging . We uncovered around 30% of H3K4m...	Histone modifications , the specific chemical modifications on histone proteins , are key for regulating the packing of DNA , and thus have important influence on diverse biological processes . An intensely studied function of histone modifications is their contribution to regulating gene expression . Recent studies in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "rna", "interference", "caenorhabditis", "gene", "regulation", "dna-binding", "proteins", "animals", "dna", "transcription", "histone", "modification", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "syste...	2018	Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells
DNA methylation regulates gene expression in many organisms . In eukaryotes , DNA methylation is associated with gene repression , while it exerts both activating and repressive effects in the Proteobacteria through largely locus-specific mechanisms . Here , we identify a critical DNA methyltransferase in M . tuberculo...	Tuberculosis is a disease with a devastating impact on public health , killing over 1 . 5 million people each year around the globe . Tuberculosis is caused by the bacterium Mycobacterium tuberculosis , which over millennia has evolved the ability to survive and persist for decades in the harsh environment inside its h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "tuberculosis", "gene", "expression", "genetics", "gene", "regulation", "epigenetics", "molecular", "genetics", "biology", "dna", "modification", "microbiology", "gram", "positive", "microbial", "pathogens", "...	2013	DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis
Heterozygous LIS1 mutations are the most common cause of human lissencephaly , a human neuronal migration defect , and DCX mutations are the most common cause of X-linked lissencephaly . LIS1 is part of a protein complex including NDEL1 and 14-3-3ε that regulates dynein motor function and microtubule dynamics , while D...	Neuronal migration is a biological process that ensures proper organization of the cerebral cortex during development . Failure of this process leads to lissencephaly , a neuronal migration defect in humans and an important cause of mental retardation and intractable epilepsy . To study these defects , we generated mou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "cell", "biology/neuronal", "signaling", "mechanisms", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics...	2011	Global Developmental Gene Expression and Pathway Analysis of Normal Brain Development and Mouse Models of Human Neuronal Migration Defects
Envenomations by the snake Bothrops asper represent a serious medical problem in Central America and parts of South America . These envenomations concur with drastic local tissue pathology , including a prominent edema . Since lymph flow plays a role in the maintenance of tissue fluid balance , the effect of B . asper ...	Envenomations by snakes of the family Viperidae ( pit vipers ) induce severe pathological alterations at the site of venom injection , such as edema , necrosis , hemorrhage , and blistering , which may lead to permanent tissue damage and disability . Edema is a prominent and common manifestation in these envenomations ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "pathology/histopathology", "biochemistry/protein", "chemistry", "pathology/cellular", "pathology", "pathology/pathophysiology" ]	2008	Effects of Bothrops asper Snake Venom on Lymphatic Vessels: Insights into a Hidden Aspect of Envenomation
The enormous toll on human life during the 1918–1919 Spanish influenza pandemic is a constant reminder of the potential lethality of influenza viruses . With the declaration by the World Health Organization of a new H1N1 influenza virus pandemic , and with continued human cases of highly pathogenic H5N1 avian influenza...	The world is currently experiencing a pandemic caused by a new type of H1N1 influenza virus that originated in swine . Although it is too early to tell how virulent this new virus may be , some influenza viruses can cause severe disease . The 1918 pandemic , also caused by an H1N1 virus , resulted in over 50 million de...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology/animal", "models", "of", "infection", "virology" ]	2009	Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes
Meiotic nuclear oscillations in the fission yeast Schizosaccharomyces pombe are crucial for proper chromosome pairing and recombination . We report a mechanism of these oscillations on the basis of collective behavior of dynein motors linking the cell cortex and dynamic microtubules that extend from the spindle pole bo...	A key aspect of life is sexual reproduction , which involves the mixing of genetic material during meiosis . In fission yeast and other organisms , the successful mixing and recombining of the chromosomes requires concerted movement of the nucleus . This phenomenon is driven by molecular motors that move the nucleus ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "cell", "biology" ]	2009	Self-Organization of Dynein Motors Generates Meiotic Nuclear Oscillations
The yellow fever mosquito Aedes aegypti is the major vector of arboviruses , causing numerous devastating human diseases , such as dengue and yellow fevers , Chikungunya and Zika . Female mosquitoes need vertebrate blood for egg development , and repeated cycles of blood feeding are tightly linked to pathogen transmiss...	Female mosquitoes transmit numerous devastating human diseases . The mosquito gut , in addition to its primary function as a site of blood digestion , represents the entry point for pathogen colonization in mosquito vectors . The conserved microRNA , miR-275 , was shown to be required for blood digestion and egg develo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "body", "fluids", "gene", "regulation", "messenger", "rna", "animals", "notch", "signaling", "micrornas", "insect", "vectors", "cellular", "structures", "and", "organelles", "cytoskeleto...	2017	MicroRNA-275 targets sarco/endoplasmic reticulum Ca2+ adenosine triphosphatase (SERCA) to control key functions in the mosquito gut
Cells are often exposed to physical or chemical stresses that can damage the structures of essential biomolecules . Stress-induced cellular damage can become deleterious if not managed appropriately . Rapid and adaptive responses to stresses are therefore crucial for cell survival . In eukaryotic cells , different stre...	Cells have evolved complex stress responses to cope with environmental challenges that could otherwise inflict severe damage on the molecules essential for life . Stress responses must ameliorate the immediate damage caused by stress exposure and also adjust metabolic capacity , gene expression output , and other cellu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Dynamic Sumoylation of a Conserved Transcription Corepressor Prevents Persistent Inclusion Formation during Hyperosmotic Stress
Bartonella bacilliformis is the aetiological agent of human bartonellosis , a potentially life threatening infection of significant public health concern in the Andean region of South America . Human bartonellosis has long been recognised in the region but a recent upsurge in the number of cases of the disease and an a...	Bartonellosis ( Carrion's disease ) is caused by the bacterium Bartonella bacilliformis and is encountered across the Andean cordillera , particularly in Peru . B . bacilliformis is transmitted by arthropods , probably sandflies , and exploits humans as a reservoir host , establishing chronic infections characterized b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "biology", "microbiology", "population", "biology", "genetics", "and", "genomics" ]	2011	Multi-Locus Sequence Analysis Reveals Profound Genetic Diversity among Isolates of the Human Pathogen Bartonella bacilliformis
In this communication , we demonstrate that galectin ( Gal ) -9 acts to constrain CD8+ T cell immunity to Herpes Simplex Virus ( HSV ) infection . In support of this , we show that animals unable to produce Gal-9 , because of gene knockout , develop acute and memory responses to HSV that are of greater magnitude and be...	Adaptive immune responses to foreign antigens require precise regulation , otherwise excessive bystander damage to host tissues may occur and responses to other antigens could be compromised . Some galectin proteins binding to receptors on cells of the immune system form part of the regulatory system , although this to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "immunology/immunity", "to", "infections" ]	2010	Galectin-9/TIM-3 Interaction Regulates Virus-Specific Primary and Memory CD8+ T Cell Response
A fundamental challenge to contemporary genetics is to distinguish rare missense alleles that disrupt protein functions from the majority of alleles neutral on protein activities . High-throughput experimental tools to securely discriminate between disruptive and non-disruptive missense alleles are currently missing . ...	Exome sequencing has proven powerful to identify protein-coding variation across the human genome , unravel the basis of monogenic diseases and discover rare alleles that confer risk for complex disease . Nevertheless , two key challenges limit its application to complex phenotypes: first , most alleles identified in a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction
Leishmaniasis is a neglected disease caused by Leishmania , an intracellular protozoan parasite which possesses a unique thiol metabolism based on trypanothione . Trypanothione is used as a source of electrons by the tryparedoxin/tryparedoxin peroxidase system ( TXN/TXNPx ) to reduce the hydroperoxides produced by macr...	Leishmania spp . are protozoa responsible for Leishmaniases , neglected diseases killing up to 60 , 000 people every year . Current therapies rely mainly on antimonial drugs that are inadequate due to poor drug efficacy and safety , combined with increasing drug resistance . To overcome these problems , there is an urg...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biochemistry", "biology", "biophysics" ]	2012	The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural Determinants of Leishmania Detoxification Pathway
The immune mechanisms that recognize inhaled Aspergillus fumigatus conidia to promote their elimination from the lungs are incompletely understood . FleA is a lectin expressed by Aspergillus fumigatus that has twelve binding sites for fucosylated structures that are abundant in the glycan coats of multiple plant and an...	Inhaled Aspergillus fumigatus conidia are effectively eliminated from the lung by the coordinated actions of mucociliary clearance and macrophage killing , but the mechanisms of attachment of Aspergillus fumigatus ( A . fumigatus ) conidia to the airway mucus gel are unknown . In addition , the mechanisms of phagocytos...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "invertebrates", "aspergillus", "fumigatus", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "aspergillus", "pathogens", "immunology", "cell", "processes", "microbiology", "animals", "fungi", "f...	2016	FleA Expression in Aspergillus fumigatus Is Recognized by Fucosylated Structures on Mucins and Macrophages to Prevent Lung Infection
Dengue viruses ( DENVs ) are among the most rapidly and efficiently spreading arboviruses . WHO recently estimated that about half of the world’s population is now at risk for DENV infection . There is no specific treatment or vaccine available to treat or prevent DENV infections . Here , we report the development of a...	Among the flavivirus family , dengue virus ( DENV ) represents the most important public health issue , affecting a large area of the world . The incidence rate of DENV infections is increasing every year . In lieu of the uncontrolled mosquito vector and the lack of specific treatments for DENV disease , an effective d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Immunogenic Properties of a BCG Adjuvanted Chitosan Nanoparticle-Based Dengue Vaccine in Human Dendritic Cells
Infectious diseases often spread as spatial epidemic outbreak waves . A number of model studies have shown that such spatial pattern formation can have important consequences for the evolution of pathogens . Here , we show that such spatial patterns can cause cyclic evolutionary dynamics in selection for the length of ...	Parasites are commonly believed to evolve to make as many infections as possible . In large scale simulations of disease spread , however , natural selection can instead act to maximize outbreak frequency . Here , pathogens that cause short infections can be rewarded for their prudence by a rapid subsequent outbreak . ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "infectious", "diseases", "evolutionary", "biology/evolutionary", "ecology" ]	2010	Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens , such as Mycobacterium leprae , the main causative agent of leprosy . Leprosy is one of the oldest recorded and most stigmatizing diseases in human history . The disease was prevalent in Europe until the 16th century and is still end...	Many controversies surround leprosy , which is one of the oldest recorded diseases of humankind . The origin and past spread of its main causative agent , Mycobacterium leprae , remain unknown although many attempts have been made to reconstruct its past from historical and archeological sources . Analysis of ancient M...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "osteology", "genome", "analysis", "paleontology", "neglected", "tropical", "diseases", "molecular", "genetics", "paleogenetics"...	2018	Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe
In bacterial , yeast , and human cells , stress-induced mutation mechanisms are induced in growth-limiting environments and produce non-adaptive and adaptive mutations . These mechanisms may accelerate evolution specifically when cells are maladapted to their environments , i . e . , when they are are stressed . One me...	Mutational processes are being discovered in which bacterial , yeast , and human cells under various stresses activate programs that increase mutagenesis , often under the control of cellular stress responses . These programs may potentially increase genetic variability in populations specifically when they are maladap...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "molecular", "biology/dna", "repair", "molecular", "biology/molecular", "evolution", "microbiology/microbial", "evolution", "and", "ge...	2008	Mutability and Importance of a Hypermutable Cell Subpopulation that Produces Stress-Induced Mutants in Escherichia coli
Recent theoretical studies have proposed that the redundant motor system in humans achieves well-organized stereotypical movements by minimizing motor effort cost and motor error . However , it is unclear how this optimization process is implemented in the brain , presumably because conventional schemes have assumed a ...	It is thought that the brain can optimize motor commands to produce efficient movements; however , it is unknown how this optimization process is implemented in the brain . Here we examine a biologically plausible hypothesis in which slight forgetting in the motor learning process plays an important role in the optimiz...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "anatomy", "and", "physiology", "neuroscience", "learning", "and", "memory", "motor", "systems", "computational", "neuroscience", "neurological", "system", "coding", "mechanisms", "robotics", "musculoskeletal", "system", "biology", "central", "nervou...	2012	Learning with Slight Forgetting Optimizes Sensorimotor Transformation in Redundant Motor Systems
Centromeres , the specialized chromatin structures that are responsible for equal segregation of chromosomes at mitosis , are epigenetically maintained by a centromere-specific histone H3 variant ( CenH3 ) . However , the mechanistic basis for centromere maintenance is unknown . We investigated biochemical properties o...	The octameric structure of eukaryotic nucleosomes is universally accepted as the basic unit of chromatin . This is certainly the case for the vast bulk of nucleosomes; however , there have been no reports of the in vivo structure of nucleosomes associated with centromeres . Though centromeres make up only a minute frac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "drosophila", "genetics", "and", "genomics", "insects" ]	2007	Tetrameric Structure of Centromeric Nucleosomes in Interphase Drosophila Cells
The phenotype and function of immune cells infiltrating the conjunctiva in scarring trachoma have yet to be fully characterized . We assessed tissue morphology and immunophenotype of cellular infiltrates found in trachomatous scarring compared to control participants . Clinical assessments and conjunctival biopsy sampl...	Trachoma is initiated by repeated infection of the conjunctiva throughout childhood by the bacterium Chlamydia trachomatis ( Ct ) . Conjunctival inflammation and scarring progress throughout the lives of many adults even in the absence of Ct infection , causing the eyelashes to turn inwards ( trichiasis ) and damage th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chlamydia", "trachomatis", "pathogens", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "signs", "and", "symptoms"...	2016	Immunohistochemical Analysis of Scarring Trachoma Indicates Infiltration by Natural Killer and Undefined CD45 Negative Cells
The agents of sleeping sickness disease , Trypanosoma brucei complex parasites , are transmitted to mammalian hosts through the bite of an infected tsetse . Information on tsetse-trypanosome interactions in the salivary gland ( SG ) tissue , and on mammalian infective metacyclic ( MC ) parasites present in the SG , is ...	Tsetse flies transmit the causative agents of African sleeping sickness and nagana in sub-Saharan Africa . The parasites are acquired when tsetse flies feed on an infected host , undergo multiplication in the fly gut and migrate to the salivary glands ( SG ) . The cycle resumes once this infected fly transmits the para...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "microbiology", "genomics", "veterinary", "science" ]	2014	Insights into the Trypanosome-Host Interactions Revealed through Transcriptomic Analysis of Parasitized Tsetse Fly Salivary Glands
Progeny particles of non-enveloped lytic parvoviruses were previously shown to be actively transported to the cell periphery through vesicles in a gelsolin-dependent manner . This process involves rearrangement and destruction of actin filaments , while microtubules become protected throughout the infection . Here the ...	Previously , it was thought that non-enveloped lytic parvoviruses were released through a lytic burst of cells at the end of infection . However , recent work demonstrated that these small non-enveloped single-stranded DNA viruses are actively transported through vesicles from the nucleus , the site of replication and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Vesicular Transport of Progeny Parvovirus Particles through ER and Golgi Regulates Maturation and Cytolysis
Viral attachment to specific host receptors is the first step in viral infection and serves an essential function in the selection of target cells . Mammalian reoviruses are highly useful experimental models for studies of viral pathogenesis and show promise as vectors for oncolytics and vaccines . Reoviruses engage ce...	Mammalian orthoreoviruses ( reoviruses ) are useful models for studies of virus–receptor interactions and viral pathogenesis . They are closely related in structure to adenoviruses and share similar mechanisms of cell attachment and entry . The receptor for reovirus , junctional adhesion molecule-A ( JAM-A ) , is a com...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/viral", "infections", "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines", "cell", "biology/cell", "adhesion...	2008	Structure of Reovirus σ1 in Complex with Its Receptor Junctional Adhesion Molecule-A
The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated process . Signaling cascades triggered by different environmental and physiological signals converge to control HilD , an AraC regulator that coordinates the expression of several virulence factors . The expression o...	Salmonella enterica serovar Typhimurium is a foodborne pathogen that causes gastroenteritis in humans . To successfully trigger infection , S . Typhimurium invades epithelial cells , a process that requires the coordinated expression of a set of genes . HilD is a pivotal regulator of S . Typhimurium pathogenicity , as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "dna", "transcription", "epithelial", "cells", "bacterial", "diseases", "regulator", "genes", "enterobacteriaceae", "gene", "types", ...	2017	Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar Typhimurium
Evidence from recent studies assessing the impact of school water , sanitation and hygiene ( WASH ) interventions on child health has been mixed . Self-reports of disease are subject to bias , and few WASH impact evaluations employ objective health measures to assess reductions in disease and exposure to pathogens . We...	Water , sanitation , and hygiene ( WASH ) in schools is promoted as an intervention to improve child health in low-resource settings . However , evidence of the impact of school WASH interventions on child health is mixed . One reason could be that most studies rely on self-reported disease symptoms , which are prone t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "education", "pathogens", "sociology", "immunology", "microbiology", "social", "sciences", "factor", "analysis", "health", "care", "viruses", "mathematics", "r...	2018	The impact of school water, sanitation, and hygiene improvements on infectious disease using serum antibody detection
XX and XY fetal gonads are initially bipotential , poised between the ovary and testis fate . Multiple lines of evidence suggest that commitment to testis fate requires the repression of genes associated with ovary fate . It was previously shown that loss of CBX2 , the subunit of the Polycomb Repressive Complex 1 ( PRC...	During development , the bipotential fetal gonad can commit to the testis fate or to the ovary fate . Mutation of the epigenetic regulator CBX2 leads to ovary development in XY embryos , suggesting a critical role for chromatin remodeling during sex determination . However , the epigenetic mechanisms that regulate the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "epithelial", "cells", "sertoli", "cells", "developmental", "biology", "stem", "cells", "epigenetics", "morphogenesis", "chromatin", "animal", "cells", "chromosome", "biology", "gene", "express...	2019	CBX2 is required to stabilize the testis pathway by repressing Wnt signaling
The current standard of care for hepatitis C virus ( HCV ) infection – combination therapy with pegylated interferon and ribavirin – elicits sustained responses in only ∼50% of the patients treated . No alternatives exist for patients who do not respond to combination therapy . Addition of ribavirin substantially impro...	The treatment of HCV infection poses a major global health-care challenge today . The current standard of care , combination therapy with interferon and ribavirin , works in only about half of the patients treated . Because no alternatives are available yet for patients in whom combination therapy fails , identifying w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "infectious", "diseases/viral", "infections", "hematology/anemias", "computational", "biology", "pharmacology/adverse", "reactions" ]	2011	Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy
Hypersaline environments pose major challenges to their microbial residents . Microorganisms have to cope with increased osmotic pressure and low water activity and therefore require specific adaptation mechanisms . Although mechanisms have already been thoroughly investigated in the green alga Dunaliella salina and so...	Salinity is one of the strongest abiotic factors in nature and can have harmful effects on organisms . When a cell is placed in a high-salt environment , osmotic pressure pulls unbound water molecules out of the cell , leaving behind a highly concentrated cytoplasm , which impairs cell function and can cause cell death...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "chemical", "compounds", "aliphatic", "amino", "acids", "absorption", "spectroscopy", "enzymes", "nmr", "spectroscopy", "extremophiles", "enzymology", "organic", "compounds", "amino", "acids", "cellular", "structures", "and",...	2018	Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum
The yeast Saccharomyces cerevisiae undergoes a dramatic growth transition from its unicellular form to a filamentous state , marked by the formation of pseudohyphal filaments of elongated and connected cells . Yeast pseudohyphal growth is regulated by signaling pathways responsive to reductions in the availability of n...	Eukaryotic cells respond to nutritional and environmental stress through complex regulatory programs controlling cell metabolism , growth , and morphology . In the budding yeast Saccharomyces cerevisiae , conditions of limited nitrogen and/or glucose can initiate a dramatic growth transition wherein the yeast cells for...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "spectrometric", "identification", "of", "proteins", "model", "organisms", "functional", "genomics", "yeast", "and", "fungal", "models", "biology", "genomics", "saccharomyces", "cerevisiae", "proteomics" ]	2014	The Yeast Sks1p Kinase Signaling Network Regulates Pseudohyphal Growth and Glucose Response
Genetic screening is becoming possible on an unprecedented scale . However , its utility remains controversial . Although most variant genotypes cannot be easily interpreted , many individuals nevertheless attempt to interpret their genetic information . Initiatives such as the Personal Genome Project ( PGP ) and Illum...	The Personal Genome Project ( PGP ) is an emerging community whose goal is to collect and publicly share genomes , environmental data , medical records , and clinical traits from tens of thousands of volunteers . This information may enable computer software to establish the relationships between patterns of alteration...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "analysis", "biology", "and", "life", "sciences", "genomics", "statistics", "computational", "biology" ]	2014	A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
Non-homologous end joining ( NHEJ ) is the major mechanism of double-strand break repair ( DSBR ) in mammalian cells . NHEJ has traditionally been inferred from experimental systems involving induced double strand breaks ( DSBs ) . Whether or not the spectrum of repair events observed in experimental NHEJ reflects the ...	Changes to DNA sequence are the major source of variation in evolution . Those changes often arise from damage to DNA that is repaired in a way that fails to restore the original sequence . One type of DNA damage is a chromosomal double-strand break . Such breaks are mostly studied experimentally in model systems , bec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/replication", "and", "repair", "biochemistry/bioinformatics", "evolutionary", "biology/genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Numt-Mediated Double-Strand Break Repair Mitigates Deletions during Primate Genome Evolution
Since 1996 , there have been several case reports of autochthonous visceral leishmaniasis in Thailand . Here we report a case in a 52-year-old Thai male from northern Thailand , who presented with subacute fever , huge splenomegaly and pancytopenia . Bone marrow aspiration revealed numerous amastigotes within macrophag...	Visceral leishmaniasis is a potentially life threatening parasitic disease that is found in many tropical and subtropical regions of the world . We report a case of visceral leishmaniasis in northern Thailand caused by a recently described new species of Leishmania parasite , Leishmania martiniquensis . By comparing DN...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "leishmaniasis", "parasitology", "biology", "and", "life", "sciences", "vector-borne", "diseases", "protozoan", "infections", "pa...	2014	First Isolation of Leishmania from Northern Thailand: Case Report, Identification as Leishmania martiniquensis and Phylogenetic Position within the Leishmania enriettii Complex
Bacterial diversification is often observed , but underlying mechanisms are difficult to disentangle and remain generally unknown . Moreover , controlled diversification experiments in ecologically relevant environments are lacking . We studied bacterial diversification in the mammalian gut , one of the most complex ba...	The mechanisms generating the huge biodiversity on earth are not entirely understood . Bacterial populations are powerful models to explore the mechanisms of evolution , owing to their big population size , rapid growth , and high mutation rate . One of the more complex bacterial community is the mammalian gut microbio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Trade-Off between Bile Resistance and Nutritional Competence Drives Escherichia coli Diversification in the Mouse Gut
Epstein-Barr virus ( EBV ) is associated with human malignancies , especially those affecting the B cell compartment such as Burkitt lymphoma . The virally encoded homolog of the mammalian pro-survival protein Bcl-2 , BHRF1 contributes to viral infectivity and lymphomagenesis . In addition to the pro-apoptotic BH3-only...	Altruistic suicide of infected host cells is a key defense mechanism to combat viral infection . To ensure their own survival and proliferation , certain viruses , including Epstein-Barr virus ( EBV ) , have mechanisms to subvert apoptosis , including the expression of homologs of the mammalian pro-survival protein Bcl...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "biochemistry/biomacromolecule-ligand", "interactions", "virology/viruses", "and", "cancer", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus BHRF1
To understand visual cognition , it is imperative to determine when , how and with what information the human brain categorizes the visual input . Visual categorization consistently involves at least an early and a late stage: the occipito-temporal N170 event related potential related to stimulus encoding and the parie...	How the brain uses visual information to construct representations of categories is a central question of cognitive neuroscience . With our methods we visualize how the brain transforms its representations of facial expressions . Using electroencephalographic data , we analyze how representations change over the first ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "computational", "biology/computational", "neuroscience", "neuroscience/psychology", "neuroscience/experimental", "psychology", "neuroscience/natural", "and", "synthetic", "vision" ]	2009	Dynamics of Trimming the Content of Face Representations for Categorization in the Brain
Chikungunya virus ( CHIKV ) has resulted in several outbreaks in the past six decades . The clinical symptoms of Chikungunya infection include fever , skin rash , arthralgia , and an increasing incidence of encephalitis . The re-emergence of CHIKV with more severe pathogenesis highlights its potential threat on our hum...	Polarized cells are found in many parts of the human body and are characterized by the presence of two distinct plasma membrane domains: the apical domain facing the lumen and the basolateral domain facing the underlying tissues . Polarized epithelial cells line the major cavities of our body , while polarized endothel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virulence", "factors", "and", "mechanisms", "virology", "biology", "microbiology" ]	2014	A Polarized Cell Model for Chikungunya Virus Infection: Entry and Egress of Virus Occurs at the Apical Domain of Polarized Cells
Identifying the physiological functions of microRNAs ( miRNAs ) is often challenging because miRNAs commonly impact gene expression under specific physiological conditions through complex miRNA::mRNA interaction networks and in coordination with other means of gene regulation , such as transcriptional regulation and pr...	MicroRNAs ( miRNAs ) are important in the regulation of gene expression and are present in many organisms . To identify specific biological processes that are regulated by miRNAs , we disturbed total miRNA function under a certain genetic background and searched for defects . Interestingly , we found a prominent develo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Functional Analysis of Neuronal MicroRNAs in Caenorhabditis elegans Dauer Formation by Combinational Genetics and Neuronal miRISC Immunoprecipitation
Transcription activator-like ( TAL ) effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen . The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues ( RVDs...	While it had already been discovered that transcription activator-like ( TAL ) effectors from Xanthomonas pathogens act as transcription factors in the host plant , deciphering the modular code of DNA binding specificity of TAL effectors in 2009 fascinated the scientific community . This modular code opens the possibil...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "plant", "biology", "statistics", "gene", "regulation", "microbiology", "host-pathogen", "interaction", "crop", "genetics", "dna", "transcription", "plant", "science", "mathematics", "crops", "plant", "pathology", "molecular", "genetics", "bacterial", "pathogens", "sequen...	2013	Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites
The transmissible agent of prion disease consists of a prion protein in its abnormal , β-sheet rich state ( PrPSc ) , which is capable of replicating itself according to the template-assisted mechanism . This mechanism postulates that the folding pattern of a newly recruited polypeptide chain accurately reproduces that...	The transmissible agent of prion disease consists of a prion protein in its abnormal conformation ( PrPSc ) , which replicates itself according to the template-assisted mechanism . This mechanism postulates that the folding pattern of a newly recruited polypeptide chain accurately reproduces that of a PrPSc . The curre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "histology", "neurobiology", "of", "disease", "and", "regeneration", "infectious", "diseases", "proteins", "protein", "folding", "neurology", "neurodegenerative", "diseases", "neurological", "disorders", "biology", "biophysics", "neuroscience", "...	2011	Genesis of Mammalian Prions: From Non-infectious Amyloid Fibrils to a Transmissible Prion Disease
Trans/cis prolyl isomerisation is involved in several biological processes , including the development of numerous diseases . In the HIV-1 capsid protein ( CA ) , such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A ( CypA ) . Here , we use metadynamics simulations...	Peptidyl prolyl isomerases are ubiquitous enzymes whose actions are crucial in several biological processes , such as , for instance , in cellular signalling and in the onset of several diseases , e . g . , HIV infection . Therefore , these isomerases are promising targets for the design of new drugs . For this purpose...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/molecular", "dynamics", "biophysics/biocatalysis" ]	2009	Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
Synchronization of neural oscillations as a mechanism of brain function is attracting increasing attention . Neural oscillation is a rhythmic neural activity that can be easily observed by noninvasive electroencephalography ( EEG ) . Neural oscillations show the same frequency and cross-frequency synchronization for va...	In this paper , we propose an estimation method to identify a dynamical system from rhythmic time-series data . Rhythmic activities have been observed frequently and are synchronized in various fields , and synchronization is an important topic in nonlinear science . It is well known that such synchronization can be de...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "syllables", "medicine", "and", "health", "sciences", "linguistics", "engineering", "and", "technology", "electrical", "circuits", "electronic", "circuits", "signal", "processing", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "sig...	2018	A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data
Faces transmit a wealth of social information . How this information is exchanged between face-processing centers and brain areas supporting social cognition remains largely unclear . Here we identify these routes using resting state functional magnetic resonance imaging in macaque monkeys . We find that face areas fun...	Primates have evolved to transmit social information through their faces . Where and how the brain processes facial information received by the eyes we now understand quite well . Yet we do not know how this information is made available to other brain areas so that a face can evoke an emotion , activate the memory of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Face Patch Resting State Networks Link Face Processing to Social Cognition
Multiple positions within the SWI/SNF chromatin remodeling complex can be filled by mutually exclusive subunits . Inclusion or exclusion of these proteins defines many unique forms of SWI/SNF and has profound functional consequences . Often this complex is studied as a single entity within a particular cell type and we...	The SWI/SNF chromatin remodeling complex is made of multiple subunits , and the inclusion of different mutually exclusive subunits allows potentially many biochemically distinct forms of SWI/SNF . Members of this complex are among the most frequently mutated genes in cancer . Here , we present the first genome-wide loc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
The mechanisms by which different microbes colonize the healthy human gut versus other body sites , the gut in disease states , or other environments remain largely unknown . Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis . We approach th...	Why do certain microbes and not others colonize our gut , and why do they differ between healthy and sick people ? One explanation is the genes in their genomes . If we can find microbial genes involved in gut adaptation , we may be able to keep out pathogens and encourage the growth of beneficial microbes . One could ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "gut", "bacteria", "microbiome", "crohn's", "disease", "immunology", "microbiology", "species", "delimitation", "bacteroides", "animal", "phylogenetics", "phylogenetics", "data", "management", "clinical", "medicine", "m...	2018	Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Ser/thr phosphatases dephosphorylate their targets with high specificity , yet the structural and sequence determinants of phosphosite recognition are poorly understood . Calcineurin ( CN ) is a conserved Ca2+/calmodulin-dependent ser/thr phosphatase and the target of immunosuppressants , FK506 and cyclosporin A ( CSA ...	Transplantation medicine was revolutionized by the introduction of the immunosuppressant drugs cyclosporin A and FK506 that prevent rejection of transplanted organs by the recipient's immune system . These drugs work by inhibiting calcineurin , a conserved protein phosphatase . Calcineurin regulates the immune response...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "protein", "interactions", "enzymes", "immunology", "chemical", "biology", "biophysics", "simulations", "enzyme", "classes", "enzyme", "regulation", "biology", "proteomics", "biophysics", "drug", "discovery", "immune", "system", "b...	2013	The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin
Hematopoietic stem cells ( HSCs ) are rare quiescent cells that continuously replenish the cellular components of the peripheral blood . Observing that the ataxia-associated gene Ataxin-1-like ( Atxn1L ) was highly expressed in HSCs , we examined its role in HSC function through in vitro and in vivo assays . Mice lacki...	Our labs , working separately on brain function and blood stem cells , noticed that a particular gene involved in movement disorders was also expressed in the blood system . We discovered through bone marrow transplantation experiments that this gene , called Ataxin-1-like , normally plays a role in restricting the num...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "immunology", "biology", "neuroscience" ]	2013	Ataxin1L Is a Regulator of HSC Function Highlighting the Utility of Cross-Tissue Comparisons for Gene Discovery
The growth potential of the tumor-like Echinococcus multilocularis metacestode ( causing alveolar echinococcosis , AE ) is directly linked to the nature/function of the periparasitic host immune-mediated processes . We previously showed that Fibrinogen-like-protein 2 ( FGL2 ) , a novel CD4+CD25+ Treg effector molecule ...	In larval E . multilocularis infection causing alveolar echinococcosis ( AE ) in humans as well as mice , immune tolerance and/or down-regulation of protective immunity is a marked characteristic of this chronic disease . Our study provides a comprehensive evidence for a major involvement of the recently identified CD4...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Deletion of Fibrinogen-like Protein 2 (FGL-2), a Novel CD4+ CD25+ Treg Effector Molecule, Leads to Improved Control of Echinococcus multilocularis Infection in Mice
The paramyxoviruses are a family of negative-sense RNA viruses that includes many important human and animal pathogens . Paramyxovirus RNA synthesis requires the viral phosphoprotein ( P ) and the large ( L ) protein . Phosphorylation of P is thought to regulate viral gene expression , though direct proof remains elusi...	The paramyxoviruses are a family of negative-sense RNA viruses that includes many important human and animal pathogens . Paramyxovirus RNA synthesis requires the viral phosphoprotein ( P ) and the large ( L ) protein . Phosphorylation of P is thought to regulate viral gene expression , though direct proof remains elusi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/antivirals,", "including", "modes", "of", "action", "and", "resista...	2009	PLK1 Down-Regulates Parainfluenza Virus 5 Gene Expression
One of the hallmarks of biological organisms is their ability to integrate disparate information sources to optimize their behavior in complex environments . How this capability can be quantified and related to the functional complexity of an organism remains a challenging problem , in particular since organismal funct...	Intelligent behavior encompasses appropriate navigation in complex environments that is achieved through the integration of sensorial information and memory of past events to create purposeful movement . This behavior is often described as “complex” , but universal ways to quantify such a notion do not exist . Promisin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complex", "systems", "cognitive", "neuroscience", "mathematics", "cognition", "computational", "neuroscience", "evolutionary", "modeling", "consciousness", "decision", "making", "applied", "mathematics", "biology", "computational", "biology", "neuroscience" ]	2011	Integrated Information Increases with Fitness in the Evolution of Animats
Even in the steady-state , the number of biomolecules in living cells fluctuates dynamically , and the frequency spectrum of this chemical fluctuation carries valuable information about the dynamics of the reactions creating these biomolecules . Recent advances in single-cell techniques enable direct monitoring of the ...	Recent advances in single-cell experimental techniques enable direct visualization of dynamic fluctuations of the biomolecular concentration in each cell; however , a robust , quantitative understanding of the stochastic dynamics of the chemical noise in living cells has yet to be achieved . To understand how the frequ...	[ "Abstract", "Introduction", "Results/discussion", "Methods" ]	[ "genetic", "networks", "enzymes", "gene", "regulation", "messenger", "rna", "enzymology", "dna", "transcription", "network", "analysis", "reaction", "dynamics", "physical", "chemistry", "computer", "and", "information", "sciences", "proteins", "gene", "expression", "che...	2019	Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics
During spermatogenesis , the blood-testis barrier ( BTB ) segregates the adluminal ( apical ) and basal compartments in the seminiferous epithelium , thereby creating a privileged adluminal environment that allows post-meiotic spermatid development to proceed without interference of the host immune system . A key featu...	Mammalian spermatogenesis takes place within a sheltered environment , whereby somatic Sertoli cells protect and guide germ cells as they mature and differentiate . A key structure generated by the protective Sertoli cell epithelium is the blood-testis barrier ( BTB ) , a composite of junctional and cytoskeletal elemen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "development", "biology", "and", "life", "sciences", "adhesion", "molecules", "developmental", "biology" ]	2014	N-WASP Is Required for Structural Integrity of the Blood-Testis Barrier
Constraint-based approaches have been used for integrating data in large-scale metabolic networks to obtain insights into metabolism of various organisms . Due to the underlying steady-state assumption , these approaches are usually not suited for making predictions about metabolite levels . Here , we ask whether we ca...	Organisms are usually exposed to changing environments and balance these perturbations by altering their metabolic state . Gaining a deeper understanding of metabolic adjustment to varying external conditions is important for the development of advanced engineering strategies for microorganisms as well as for higher pl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "plant", "science", "model", "organisms", "theoretical", "biology", "synthetic", "biology", "biology", "and", "life", "sciences", "computational", "biology", "research", "and", "analysis", "methods" ]	2014	Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses
Cutaneous leishmaniasis ( CL ) is a disfiguring disease that confronts clinicians with a quandary: leave patients untreated or engage in a complex or toxic treatment . Topical treatment of CL offers a practical and safe option . Accordingly , the treatment of CL with WR279 , 396 , a formulation of paromomycin and genta...	Cutaneous leishmaniasis is due to a small parasite ( Leishmania ) that creates disfiguring sores , and affects more than one million persons ( mainly children ) each year . Treating lesions with a cream—instead of with injections as currently done—would greatly improve the well-being of affected patients . No cream for...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/skin", "infections", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2009	WR279,396, a Third Generation Aminoglycoside Ointment for the Treatment of Leishmania major Cutaneous Leishmaniasis: A Phase 2, Randomized, Double Blind, Placebo Controlled Study
The activity of polymerase γ is complicated , involving both correct and incorrect DNA polymerization events , exonuclease activity , and the disassociation of the polymerase:DNA complex . Pausing of pol-γ might increase the chance of deletion and depletion of mitochondrial DNA . We have developed a stochastic simulati...	As a polymerase copies a DNA strand , it may briefly pause . The pauses of the polymerase are important factors in the formation of large-scale deletions in mitochondrial DNA , a major cause of pathogenicity in mitochondrial diseases . To investigate these pauses , we have developed a simulation of the function of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "enzymes", "mathematics", "dna", "replication", "dna", "bioenergetics", "enzyme", "kinetics", "stochastic", "processes", "biophysics", "simulations", "mitochondrial", "diseases", "theoretical", "biology", "biochemistry", "simulations", "biology", "biophysics", "probability", ...	2011	Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study
Many neurons have epochs in which they fire action potentials in an approximately periodic fashion . To see what effects noise of relatively small amplitude has on such repetitive activity we recently examined the response of the Hodgkin-Huxley ( HH ) space-clamped system to such noise as the mean and variance of the a...	Many neurons , especially those found in subcortical nuclei , often exhibit repetitive approximately periodic firing of action potentials . We have previously demonstrated how weak noise may inhibit repetitive activity in the Hodgkin-Huxley point model and in pairs of coupled type 1 model neurons . Here we investigated...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Weak Noise in Neurons May Powerfully Inhibit the Generation of Repetitive Spiking but Not Its Propagation
Cortical maps , consisting of orderly arrangements of functional columns , are a hallmark of the organization of the cerebral cortex . However , the microorganization of cortical maps at the level of single neurons is not known , mainly because of the limitations of available mapping techniques . Here , we used bulk lo...	Mice depend on their whiskers to explore their environment . Tactile receptors at the base of each whisker relay sensory information to a brain area called the barrel cortex . This somatosensory area consists of an orderly array of cortical columns , each containing clusters of neurons whose responses are driven primar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "mus", "(mouse)" ]	2007	The Functional Microarchitecture of the Mouse Barrel Cortex
The functional principle of the vertebrate brain is often paralleled to a computer: information collected by dedicated devices is processed and integrated by interneuron circuits and leads to output . However , inter- and motorneurons present in today's vertebrate brains are thought to derive from neurons that combined...	The brains of vertebrates consist mainly of interneurons—neurons processing information coming from other neurons . Light information is believed to enter the brain through dedicated photoreceptor cells that are distinct from these processing cells , and motorneurons then relay the information to the musculature . Here...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "visual", "system", "zebrafish", "model", "organisms", "molecular", "cell", "biology", "neurons", "cellular", "types", "sensory", "systems", "biology", "evolutionary", "biology", "neuroscience", "evolutionary", "developmental", "biology" ]	2013	Co-Expression of VAL- and TMT-Opsins Uncovers Ancient Photosensory Interneurons and Motorneurons in the Vertebrate Brain
Melioidosis is a frequently fatal infectious disease caused by the soil dwelling Gram-negative bacterium Burkholderia pseudomallei . Environmental sampling is important to identify geographical distribution of the organism and related risk of infection to humans and livestock . The aim of this study was to evaluate spa...	Melioidosis is a severe infection caused by the environmental bacterium Burkholderia pseudomallei . Soil sampling is important to identify geographic regions where humans and animals are at risk of exposure . The purpose of this study was to examine a factor that has a major bearing on the accuracy of soil sampling: th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/spatial", "and", "landscape", "ecology", "infectious", "diseases/bacterial", "infections" ]	2010	Burkholderia pseudomallei Is Spatially Distributed in Soil in Northeast Thailand

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