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Associative olfactory memory in Drosophila has two components called labile anesthesia-sensitive memory and consolidated anesthesia-resistant memory ( ARM ) . Mushroom body ( MB ) is a brain region critical for the olfactory memory and comprised of 2000 neurons that can be classified into αβ , α′β′ , and γ neurons . Pr...	One of tantalizing questions in neuroscience is how the brain processes memory . Studies in animal models such as fruit fly have brought innovations addressing the general principles underlying memory processing such as acquisition , consolidation , and retrieval . Here , we revealed an additive expression of aversive ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "radish", "brassica", "neuroscience", "learning", "and", "memory", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "cognition", "memory", "crops", "plants", "neuronal", "dendrites", "drosophila", "research", "and", "an...	2016	Additive Expression of Consolidated Memory through Drosophila Mushroom Body Subsets
Patients with heritable cancer syndromes characterized by germline PTEN mutations ( termed PTEN hamartoma tumor syndrome , PHTS ) benefit from PTEN-enabled cancer risk assessment and clinical management . PTEN-wildtype patients ( ~50% ) remain at increased risk of developing certain cancers . Existence of germline muta...	In the US , there are 12 million individuals living with heritable cancer , with its burden of morbidity and mortality . Heritable cancers occur when an individual is born with particular genetic errors ( germline mutations ) . Because many germline mutations are known to cause specific cancers , knowing which patient ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cancer", "genomics", "cancer", "detection", "and", "diagnosis", "medicine", "and", "health", "sciences", "cancer", "risk", "factors", "carcinomas", "cancers", "and", "neoplasms", "basic", "cancer", "research", "endometrial", "carcinoma", "renal", "cancer", "computati...	2018	Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline PTEN mutations
Globally 68 million people are infected with lymphatic filariasis ( LF ) , 17 million of whom have lymphedema . This study explores the effects of a lymphedema management program in Odisha State , India on morbidity and psychosocial effects associated with lymphedema . Focus groups were held with patients ( eight group...	Around the world 68 million people are infected with lymphatic filariasis ( LF ) , a mosquito-borne disease caused by filarial worms . The parasite can damage patients’ lymphatic systems causing pain , infections and swollen limbs , known as lymphedema or , in more advanced stages , elephantiasis . Lymphedema managemen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "hydrocele", "pathology", "and", "laboratory", "medicine", "economic", "analysis", "sexual", "and", "gender", "issues", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "india", "parasitic",...	2016	Experiences of a Community-Based Lymphedema Management Program for Lymphatic Filariasis in Odisha State, India: An Analysis of Focus Group Discussions with Patients, Families, Community Members and Program Volunteers
The type I interferon ( IFN ) system is a first line of defense against viral infections . Viruses have developed various mechanisms to counteract this response . So far , the interferon antagonistic activity of influenza A viruses was mainly observed on the level of IFNβ gene induction via action of the viral non-stru...	The type I interferon ( IFN ) system is one of the most powerful innate defenses against viral pathogens . Most RNA viruses are sensitive to the action of type I IFN . Therefore , these pathogens have evolved strategies to evade this response . For example , influenza viruses express a viral protein , the non-structura...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "cell", "biology/cell", "signaling" ]	2008	Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression
Approximately 59 , 000 people die from rabies worldwide annually . Haiti is one of the last remaining countries in the Western Hemisphere with endemic canine rabies . Canine-mediated rabies deaths are preventable with post-exposure prophylaxis ( PEP ) : wound treatment , immunoglobulin , and vaccination . In countries ...	Human rabies deaths are preventable with timely provision of rabies post-exposure prophylaxis: wound treatment , rabies immunoglobulin , and vaccinations . In countries where resources are available , variability in healthcare seeking behaviors and lack of adherence to recommended treatment guidelines may also contribu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "post-exposure", "prophylaxis", "immunology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "health", "care", "vaccines", "preventive", "medicine", "north", "america", "rabies", ...	2018	Rabies vaccine initiation and adherence among animal-bite patients in Haiti, 2015
ASAP1 is a multi-domain adaptor protein that regulates cytoskeletal dynamics , receptor recycling and intracellular vesicle trafficking . Its expression is associated with poor prognosis for a variety of cancers , and promotes cell migration , invasion and metastasis . Little is known about its physiological role . In ...	Mesenchymal progenitor cells are capable of differentiating into a number of lineages including osteoblasts , chondrocytes and adipocytes , and have therefore attracted interest for their potential application in regenerative medicine . Furthermore , defects in mesenchymal progenitor cell differentiation are considered...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "group-specific", "staining", "alizarin", "staining", "medicine", "and", "health", "sciences", "bone", "remodeling", "cell", "differentiation", "physiological", "processes", "developmental", "biology", "adipocytes", "stem", "cells", "ossification", "connective", "tissue", ...	2019	Loss of ASAP1 in mice impairs adipogenic and osteogenic differentiation of mesenchymal progenitor cells through dysregulation of FAK/Src and AKT signaling
Bacterial type IV secretion systems ( T4SS ) are a highly diversified but evolutionarily related family of macromolecule transporters that can secrete proteins and DNA into the extracellular medium or into target cells . It was recently shown that a subtype of T4SS harboured by the plant pathogen Xanthomonas citri tran...	Competition between microorganisms determines which species will dominate or be eradicated from a specific habitat . Bacteria use a series of mechanisms to kill or prevent multiplication of competitors . We show that an opportunistic pathogen , Stenotrophomonas maltophilia , harbours a type IV secretion system ( T4SS )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "condensed", "matter", "physics", "microbiology", "membrane", "proteins", "physiological", "processes", "secretion", "...	2019	The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing
The Legionella pneumophila effector protein RalF functions as a guanine nucleotide exchange factor ( GEF ) that activates the host small GTPase protein ADP-ribosylation factor ( Arf ) , and recruits this host protein to the vacuoles in which this pathogen resides . GEF activity is conferred by the Sec7 domain located i...	Legionella pneumophila and Rickettsia prowazekii are two pathogenic intracellular bacteria , phylogenetically distant and presenting different intracellular lifestyles . Interestingly , both organisms encode a protein called RalF , which in Legionella has been shown to be an effector protein that functions as a guanine...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "enzymes", "microbiology", "host-pathogen", "interaction", "cytoskeleton", "bacterial", "pathogens", "enzyme", "regulation", "membranes", "and", "sorting", "biology", "biochemistry", "enzyme", "structure", "gram", "negative", "cell", "biology", "...	2012	The Capping Domain in RalF Regulates Effector Functions
Mechanical strain is a potent stimulus for growth and remodeling in cells . Although many pathways have been implicated in stretch-induced remodeling , the control structures by which signals from distinct mechano-sensors are integrated to modulate hypertrophy and gene expression in cardiomyocytes remain unclear . Here...	Common stresses such as high blood pressure or heart attack can lead to heart failure , which afflicts over 25 million people worldwide . These stresses cause cardiomyocytes to grow and remodel , which may initially be beneficial but ultimately worsen heart function . Current heart failure drugs such as beta-blockers c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "muscle", "tissue", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "signaling", "networks", "regulator", "genes", "network", "analysis", "transcription", "factors", "gene", "types", "calcium", "signali...	2017	Predictive model identifies key network regulators of cardiomyocyte mechano-signaling
Using coarse-grained membrane simulations we show here that peripheral membrane proteins can form a multitude of higher-order structures due to membrane-mediated interactions . Peripheral membrane proteins characteristically perturb the lipid bilayer in their vicinity which supports the formation of protein assemblies ...	Eukaryotic cells are subdivided into a variety of compartments by membranes , i . e . by lipid bilayers into which a multitude of proteins are embedded . About 30% of all protein species in a cell are associated with membranes to perform vital functions , e . g . in signaling and transport pathways . A plethora of memb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "molecular", "cell", "biology", "cell", "biology", "membrane", "receptor", "signaling", "membranes", "and", "sorting", "biology", "biophysics", "simulations", "biophysics", "molecular", "biology" ]	2011	Dynamic Structure Formation of Peripheral Membrane Proteins
Spondyloarthritis ( SpA ) is a chronic inflammatory disorder with a strong genetic predisposition dominated by the role of HLA-B27 . However , the contribution of other genes to the disease susceptibility has been clearly demonstrated . We previously reported significant evidence of linkage of SpA to chromosome 9q31–34...	Spondyloarthritis ( SpA ) is a common variety of articular inflammatory disorder characterized by axial and/or peripheral arthritis , frequently associated with extra-articular manifestations such as psoriasis , uveitis , and inflammatory bowel diseases ( ulcerative colitis or Crohn's disease ( CD ) ) . SpA is a comple...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rheumatology/inflammatory", "and", "psoriatic", "arthritis", "rheumatology/autoimmunity,", "autoimmune,", "and", "inflammatory", "diseases", "genetics", "and", "genomics/genetics", "of", "disease", "immunology/genetics", "of", "the", "immune", "system", "genetics", "and", ...	2009	Comprehensive Linkage and Association Analyses Identify Haplotype, Near to the TNFSF15 Gene, Significantly Associated with Spondyloarthritis
Wnt signaling maintains the undifferentiated state of intestinal crypt progenitor cells by inducing the formation of nuclear TCF4/β-catenin complexes . In colorectal cancer , activating mutations in Wnt pathway components cause inappropriate activation of TCF4/β-catenin-driven transcription . Despite the passage of a d...	The canonical Wnt pathway is a key regulatory pathway controlling intestinal cell proliferation , differentiation , and stem cell maintenance , and its deregulation leads to malignancies in the mammalian gut . A decade has passed since the discovery of the transcription factors TCF4-β-catenin as the downstream intestin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "vertebrates", "animals", "dna", "transcription", "osteichthyes", "animal", "models", "organisms", "developmental", "biology", "developmental", "biology/stem", "cells", "model", "organisms", "immunoprecipitation...	2010	The Leukemia-Associated Mllt10/Af10-Dot1l Are Tcf4/β-Catenin Coactivators Essential for Intestinal Homeostasis
Adaptive mutation refers to the continuous outgrowth of new mutants from a non-dividing cell population during selection , in apparent violation of the neo-Darwinian principle that mutation precedes selection . One explanation is that of retromutagenesis , in which a DNA lesion causes a transcriptional mutation that yi...	The basic principle of neo-Darwinian genetics is that mutations occurring during growth enable the subsequent survival of the mutants under selective environmental conditions . However , new mutants can arise from a non-growing bacterial population during selection in an apparently Lamarckian way . The phenomenon is ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli
The minimum motor domain of kinesin-1 is a single head . Recent evidence suggests that such minimal motor domains generate force by a biased binding mechanism , in which they preferentially select binding sites on the microtubule that lie ahead in the progress direction of the motor . A specific molecular mechanism for...	Animal and plant cells contain a molecular-scale “railway” network , in which the tracks , called microtubules , radiate out from the cell centre and locomotive proteins , called kinesins , haul their molecular cargoes along the microtubule tracks . This railway system transports many different cargoes to where they ar...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "computational", "chemistry", "biophysic", "al", "simulations", "macromolecular", "assemblies", "chemistry", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2011	Electrostatically Biased Binding of Kinesin to Microtubules
NTRK3 is a member of the neurotrophin receptor family and regulates cell survival . It appears to be a dependence receptor , and thus has the potential to act as an oncogene or as a tumor suppressor gene . NTRK3 is a receptor for NT-3 and when bound to NT-3 it induces cell survival , but when NT-3 free , it induces apo...	NTRK3 is a neurotrophin receptor and appears to be a dependence receptor in certain tissues . NTRK3 has been previously shown to be an oncogene in breast cancer and possibly hepatocellular carcinoma . Through a genome-wide methylation screen , we unexpectedly found that NTRK3 is commonly methylated in colorectal cancer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "cell", "death", "cancer", "genetics", "basic", "cancer", "research", "gastroenterology", "and", "hepatology", "genetics", "gastrointestinal", "tumors", "epigenetics", "colon", "adenocarcinoma", "biology", "dna", "modification", "molecular", "cell"...	2013	NTRK3 Is a Potential Tumor Suppressor Gene Commonly Inactivated by Epigenetic Mechanisms in Colorectal Cancer
Parasitic flatworms of the genus Schistosoma cause schistosomiasis , a neglected tropical disease estimated to affect over 200 million people worldwide . Praziquantel is the only antischistosomal currently available for treatment , and there is an urgent need for new therapeutics . Ion channels play key roles in physio...	Schistosomes are parasitic flatworms that infect hundreds of millions of people worldwide . They cause schistosomiasis , a disease with major consequences for human health and economic development . There is only a single drug available for treatment and control of this highly prevalent disease , and there is an urgent...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "transfection", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "helminths", "immunology", "biological", "cultures", "electrophysiology", "neuroscience", "animals", "ion", "chan...	2018	Atypical pharmacology of schistosome TRPA1-like ion channels
Many protein-protein interactions are mediated by domain-motif interaction , where a domain in one protein binds a short linear motif in its interacting partner . Such interactions are often involved in key cellular processes , necessitating their tight regulation . A common strategy of the cell to control protein func...	Domain-motif interactions are instrumental for many central cellular processes , and are therefore tightly regulated . Phosphorylation events are known modulators of protein-protein interactions in general , including domain-motif interactions . Here , we addressed the association of phosphorylation and domain-motif in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "proteins", "biology" ]	2012	A Dynamic View of Domain-Motif Interactions
The epidermis is a stratified epithelium , which forms a barrier to maintain the internal milieu in metazoans . Being the outermost tissue , growth of the epidermis has to be strictly coordinated with the growth of the embryo . The key parameters that determine tissue growth are cell number and cell size . So far , it ...	The epidermis is the outermost epithelial component of the vertebrate skin . It functions as an effective barrier against pathogens and prevents loss of body fluids to the surrounding environment . The factors involved in the maintenance of epidermal architecture have been under intense investigation since the last two...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "developmental", "biology", "mutation", "cell", "biology", "cell", "growth", "genetics", "biology", "and", "life", "sciences", "cell", "processes", "molecular", "cell", "biology", "morphogenesis", "membrane", "trafficking" ]	2014	Myosin Vb Mediated Plasma Membrane Homeostasis Regulates Peridermal Cell Size and Maintains Tissue Homeostasis in the Zebrafish Epidermis
Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented , but adapt as stimulation continues . It is unclear how this phenomenon affects stimulus coding in the later stages of sensory processing . Here , we show that a temporally sparse and reliable stimulus repre...	Many lines of evidence suggest that few spikes carry the relevant stimulus information at later stages of sensory processing . Yet mechanisms for the emergence of a robust and temporally sparse sensory representation remain elusive . Here , we introduce an idea in which a temporal sparse and reliable stimulus represent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways
Recent studies in cancer cells and budding yeast demonstrated that aneuploidy , the state of having abnormal chromosome numbers , correlates with elevated chromosome instability ( CIN ) , i . e . the propensity of gaining and losing chromosomes at a high frequency . Here we have investigated ploidy- and chromosome-spec...	Aneuploidy , the state of harboring an unbalanced number of chromosomes , has long been hypothesized to be at the basis of malignant transformation . Recent studies have also shown that aneuploidy is an important form of genome alteration underlying adaptive evolution of cells in response to harsh environments or genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "biology", "biology", "genomics", "genetics", "and", "genomics" ]	2012	Karyotypic Determinants of Chromosome Instability in Aneuploid Budding Yeast
Polycomb group proteins ( PcG ) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states , via post-translational histone modifications and high order structure formation . During S-phase , in order to preserve cell identity , in addition to DNA information , PcG-chromatin-mediat...	DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information . The genome is replicated following a specific temporal program , where different segments replicate in distinct moments of the S phase c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "transcription", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "dna", "replication", "epigenetics", "dna", "chromatin", "gene", "expression", "biology", "molecular", "biology", "nucleic", "acids", "genetics", "molecular", "cell", "biolog...	2013	PcG-Mediated Higher-Order Chromatin Structures Modulate Replication Programs at the Drosophila BX-C
Oropharyngeal mucosal epithelia of fetuses/neonates/infants and the genital epithelia of adults play a critical role in HIV-1 mother-to-child transmission and sexual transmission of virus , respectively . To study the mechanisms of HIV-1 transmission through mucosal epithelium , we established polarized tonsil , cervic...	Although the majority of HIV-1 transmissions occur through the mucosal epithelium , the mechanism of initial events of viral spread from epithelia to HIV-1-susceptible CD4+ lymphocytes , macrophages , and Langerhans/dendritic cells is not well understood . In this study we observed that >90% of virions internalized in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "immunology", "microbiology", "viral", "structure", "epithelial", "cells", "retroviruses", "viruses", "...	2017	Release of HIV-1 sequestered in the vesicles of oral and genital mucosal epithelial cells by epithelial-lymphocyte interaction
Failure in cancer drug development exacts heavy burdens on patients and research systems . To investigate inefficiencies and burdens in targeted drug development in cancer , we conducted a systematic review of all prelicensure trials for the anticancer drug , sorafenib ( Bayer/Onyx Pharmaceuticals ) . We searched Embas...	Numerous research subjects are exposed to unsafe and/or ineffective treatments in unsuccessful drug development programs . Yet , even successful drug development programs can involve heavy burdens for research subjects . In this manuscript , we measure risks and benefits for research subjects participating in the succe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "cancer", "drug", "discovery", "cancer", "treatment", "basic", "cancer", "research", "toxicology", "oncology", "research", "design", "toxicity", "p...	2017	Inefficiencies and Patient Burdens in the Development of the Targeted Cancer Drug Sorafenib: A Systematic Review
Trypanosoma brucei , causing African sleeping-sickness , exploits quorum-sensing ( QS ) to generate the ‘stumpy forms’ necessary for the parasite’s transmission to tsetse-flies . These quiescent cells are generated by differentiation in the bloodstream from proliferative slender forms . Using genome-wide RNAi selection...	African trypanosomes cause important disease of humans and livestock in sub Saharan Africa and are transmitted by tsetse flies . In preparation for transmission , Trypanosoma brucei uses quorum sensing to generate ‘stumpy forms’ that are arrested and express a distinct subset of genes to the ‘slender forms’ that prolif...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "parasitic", "cell", "cycles", "gene", "regulation", "parasitic", "diseases", "parasitic", "protozoans", "cell", "differentiation", "parasitology", "developmental", "biology", "regulator", "genes", "protozoan...	2017	Genome-wide RNAi selection identifies a regulator of transmission stage-enriched gene families and cell-type differentiation in Trypanosoma brucei
Schistosomiasis is one of the world’s most prevalent zoonotic diseases and a serious worldwide public health problem . Since the tegument ( TG ) of Schistosoma japonicum is in direct contact with the host and induces a host immune response against infection , the identification of immune response target molecules in th...	As one of the world’s most prevalent zoonotic diseases , schistosomiasis remains a serious worldwide public health problem . An immunoproteomics approach was used to identify potential immune diagnostic molecules from S . japonicum TG proteins extracted from adult schistosomes . Probes were derived from sera collected ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Screening Diagnostic Candidates for Schistosomiasis from Tegument Proteins of Adult Schistosoma japonicum Using an Immunoproteomic Approach
Biomolecular conformational transitions are essential to biological functions . Most experimental methods report on the long-lived functional states of biomolecules , but information about the transition pathways between these stable states is generally scarce . Such transitions involve short-lived conformational state...	Many biomolecules are like tiny molecular machines that need to change their shapes and visit many states to perform their biological functions . For a complete molecular understanding of a biological process , one needs to have information on the relevant stable states of the system in question , as well as the pathwa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
European Americans are often treated as a homogeneous group , but in fact form a structured population due to historical immigration of diverse source populations . Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associatio...	Genetic association studies analyze both phenotypes ( such as disease status ) and genotypes ( at sites of DNA variation ) of a given set of individuals . The goal of association studies is to identify DNA variants that affect disease risk or other traits of interest . However , association studies can be confounded by...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2008	Discerning the Ancestry of European Americans in Genetic Association Studies
Nucleosomes in heterochromatic regions bear histone modifications that distinguish them from euchromatic nucleosomes . Among those , histone H3 lysine 9 methylation ( H3K9me ) and hypoacetylation have been evolutionarily conserved and are found in both multicellular eukaryotes and single-cell model organisms such as fi...	In eukaryotes some histone modifications are preponderantly associated with silent chromosomal domains , however the extent to which distinct modifications contribute to the silencing of gene expression is often not known . A well-studied chromosomal domain in which histone modifications have been extensively character...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/histone", "modification", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/molecular", "evolution", "molecular", "biology/centromeres", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology"...	2011	H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases
Geographic patterns of genetic variation within modern populations , produced by complex histories of migration , can be difficult to infer and visually summarize . A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant l...	In this paper , we introduce a statistical method for inferring , for a set of sequenced samples , a map in which the distances between population locations reflect genetic , rather than geographic , proximity . Two populations that are sampled at distant locations but that are genetically similar ( perhaps one was rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	A Spatial Framework for Understanding Population Structure and Admixture
Chagas' disease , caused by the protozoan parasite Trypanosoma cruzi , is a disease that affects millions of people most of them living in South and Central Americas . There are few treatment options for individuals with Chagas' disease making it important to understand the molecular details of parasite infection , so ...	Chagas' disease affects millions of people worldwide and is caused by a microorganism called Trypanosoma cruzi . Treatment options for patients with Chagas' disease is still limited to a small number of drugs , all of them very toxic with important side effects that can be debilitating for the health of patients . Unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Trypanosoma cruzi Binds to Cytokeratin through Conserved Peptide Motifs Found in the Laminin-G-Like Domain of the gp85/Trans-sialidase Proteins
The saliva of sand flies strongly enhances the infectivity of Leishmania in mice . Additionally , pre-exposure to saliva can protect mice from disease progression probably through the induction of a cellular immune response . We analysed the cellular immune response against the saliva of Phlebotomus papatasi in humans ...	Cutaneous leishmaniasis affects millions of people worldwide and is caused by protozoa of the genus Leishmania . The parasite is transmitted during sand fly bites . While probing the skin for a blood meal , vectors salivate into the host's skin . Sand fly saliva contains several components that increase hemorrhage and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology" ]	2011	Human Cellular Immune Response to the Saliva of Phlebotomus papatasi Is Mediated by IL-10-Producing CD8+ T Cells and Th1-Polarized CD4+ Lymphocytes
Prader-Willi Syndrome is the most common syndromic form of human obesity and is caused by the loss of function of several genes , including MAGEL2 . Mice lacking Magel2 display increased weight gain with excess adiposity and other defects suggestive of hypothalamic deficiency . We demonstrate Magel2-null mice are insen...	Prader-Willi Syndrome ( PWS ) is a genetic condition that causes insatiable appetite and severe obesity in affected children . Several genes are inactivated in children with PWS , but no one knows which gene is important for normal body weight . One of the inactivated genes is called MAGEL2 . We previously found that m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neuroscience", "pediatrics", "hormones", "gene", "function", "model", "organisms", "nutrition", "molecular", "genetics", "pediatrics", "and", "child", "health", "endocrinology", "diabetes", "and", "endocrinology", "biology", "biochemistry", "genetics", "metab...	2013	Magel2 Is Required for Leptin-Mediated Depolarization of POMC Neurons in the Hypothalamic Arcuate Nucleus in Mice
The somite segmentation clock is a robust oscillator used to generate regularly-sized segments during early vertebrate embryogenesis . It has been proposed that the clocks of neighbouring cells are synchronised via inter-cellular Notch signalling , in order to overcome the effects of noisy gene expression . When Notch-...	The anatomy of complex organisms depends on the reliable formation of spatial patterns of gene expression during development . Many factors have to be coordinated to regulate gene expression and stochasticity in these events could undermine pattern formation . One well-studied example of pattern formation is the sequen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling
Mycobacteria produce a capsule layer , which consists of glycan-like polysaccharides and a number of specific proteins . In this study , we show that , in slow-growing mycobacteria , the type VII secretion system ESX-5 plays a major role in the integrity and stability of the capsule . We have identified PPE10 as the ES...	Mycobacteria are well protected from effectors of the immune system and from antibiotics by their cell envelope . The mycobacterial capsule constitutes the outer layer of this cell envelope . This capsule consists of glucan-like polysaccharides , proteins and glycolipid molecules and is thought to interact with the imm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "flow", "cytometry", "medicine", "and", "health", "sciences", "microbiology", "vertebrates", "animals", "organisms", "animal", "models", "osteichthyes", "developmental", "biology", "physiological", "processes", "model", "organisms", "materials", "science", ...	2016	The ESX-5 System of Pathogenic Mycobacteria Is Involved In Capsule Integrity and Virulence through Its Substrate PPE10
Phenotypes proximal to gene action generally reflect larger genetic effect sizes than those that are distant . The human metabolome , a result of multiple cellular and biological processes , are functional intermediate phenotypes proximal to gene action . Here , we present a genome-wide association study of 308 untarge...	Most contemporary GWAS studies have achieved increased power by increasing the size of the discovery sample to tens of thousands of individuals . An alternative approach for detecting the effects of novel loci is to measure phenotypes that more immediately reflect the effects of gene function . The metabolome consists ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "biomarker", "epidemiology", "genetic", "epidemiology", "epidemiology" ]	2014	Genetic Determinants Influencing Human Serum Metabolome among African Americans
Yellow fever continues to be a problem in sub-Saharan Africa with repeated epidemics occurring . The mosquito Aedes bromeliae is a major vector of yellow fever , but it cannot be readily differentiated from its non-vector zoophilic sister species Ae . lilii using morphological characters . Genetic differences have been...	In Africa , epidemic outbreaks of yellow fever continue despite the availability of an effective vaccine . Effective understanding of disease epidemiology and control requires the ability to reliably identify vectors of yellow fever . The mosquito Ae . bromeliae , a competent vector of yellow fever virus , cannot be re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Molecular Differentiation of the African Yellow Fever Vector Aedes bromeliae (Diptera: Culicidae) from Its Sympatric Non-vector Sister Species, Aedes lilii
Tissue samples from Australian carpet pythons ( Morelia spilota ) with neurological disease were screened for viruses using next-generation sequencing . Coding complete genomes of two bornaviruses were identified with the gene order 3’-N-X-P-G-M-L , representing a transposition of the G and M genes compared to other bo...	Unlike plants and animals , viruses don’t leave fossilised remains that can be used to study their ancient history . Rarely , however , some virus sequences end up as integrated copies in host genomes . These ‘fossilised’ virus sequences provide a window into virus evolution on a geological time scale . In this study ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "pythons", "medicine", "and", "health", "sciences", "split-decomposition", "method", "vertebrates", "animals", "viruses", "borna", "virus", "infection", "multiple", "alignment", "calculation", "reptile", "genomics", "rna", "viruses", "bornaviruses", "reptiles", "sequence"...	2018	Divergent bornaviruses from Australian carpet pythons with neurological disease date the origin of extant Bornaviridae prior to the end-Cretaceous extinction
Planarian flatworms are able to both regenerate their whole bodies and continuously adapt their size to nutrient status . Tight control of stem cell proliferation and differentiation during these processes is the key feature of planarian biology . Here we show that the planarian homolog of the phosphoinositide 3-kinase...	Planarian flatworms have a remarkable ability to regenerate that has driven the curiosity of scientists for more than a century . They are also able to continuously grow or degrow their bodies , depending on food availability . Around 25% of the cells in the planarian body are adult stem cells , which are responsible f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "stem", "cells", "evolutionary", "biology", "gene", "expression", "genetics", "biology", "genetics", "and", "genomics" ]	2012	SMG-1 and mTORC1 Act Antagonistically to Regulate Response to Injury and Growth in Planarians
Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis , M . leprae and M . abscessus , as well as non-pathogenic species , for example , M . smegmatis and M . thermoresistibile . Genome comparison and annotation studies provide insights into genome evolutionary relatedness , identify unique a...	Members of the Mycobacteriaceae family , which are known to adapt to different environmental niches , comprise bacterial species with varied genome sizes . They are unique in their cell-wall composition , which is remarkably thick and lipid-rich as compared to other bacteria . We performed a comparative analysis at the...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "mycobacterium", "leprae", "pseudogenes", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "genomic", "databases", "genome", "analysis", "gene", "types", "opportunistic", "pathogens", "bacteria", "fungal",...	2017	Decoding the similarities and differences among mycobacterial species
Leprosy diagnosis is mainly based on clinical evaluation , although this approach is difficult , especially for untrained physicians . We conducted a temporary campaign to detect previously unknown leprosy cases in midwestern Brazil and to compare the performance of different serological tests . A mobile clinic was sta...	Leprosy is a disease that affects the skin and peripheral nervous system , caused by Mycobacterium leprae ( M . leprae ) , that to survive hides itself within the host cells and grows slowly . Its diagnosis is difficult and requires trained physicians . Laboratorial tests are frequently negative depending on individual...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "enzyme-linked", "immunoassays", "body", "fluids", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "health", "care", ...	2017	Unexpectedly high leprosy seroprevalence detected using a random surveillance strategy in midwestern Brazil: A comparison of ELISA and a rapid diagnostic test
Outside of Africa , P . falciparum and P . vivax usually coexist . In such co-endemic regions , successful malaria control programs have a greater impact on reducing falciparum malaria , resulting in P . vivax becoming the predominant species of infection . Adding to the challenges of elimination , the dormant liver st...	The malaria parasite Plasmodium vivax is a growing public health burden across the globe . Largely overshadowed by the more fatal P . falciparum parasite , increasing reports of anti-malarial drug resistance and life-threatening disease complications demand concerted efforts to eliminate P . vivax . Outside of Africa ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination
Implementation of trachoma control strategies requires reliable district-level estimates of trachomatous inflammation–follicular ( TF ) , generally collected using the recommended gold-standard cluster randomized surveys ( CRS ) . Integrated Threshold Mapping ( ITM ) has been proposed as an integrated and cost-effectiv...	Reliable district-level prevalence estimates of active trachoma are essential to targeting control interventions . While cluster randomised surveys ( CRS ) remain the recommended strategy for obtaining these estimates , more rapid and cost-effective methods that can be integrated with other diseases are under investiga...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "survey", "methods", "epidemiology", "neglected", "tropical", "diseases", "trachoma" ]	2013	Comparing the Performance of Cluster Random Sampling and Integrated Threshold Mapping for Targeting Trachoma Control, Using Computer Simulation
To identify new regulators of antiviral innate immunity , we completed the first genome-wide gene silencing screen assessing the transcriptional response at the interferon-β ( IFNB1 ) promoter following Sendai virus ( SeV ) infection . We now report a novel link between WNT signaling pathway and the modulation of retin...	The innate immune system is the first line of defense for organisms that possess an adaptive immune system . It allows a rapid immune response upon viral infections , in addition to propagating an antiviral state in neighboring cells . In an attempt to identify new proteins that are involved in antiviral responses , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "medicine", "infectious", "diseases", "inflammation", "hepatitis", "cytokines", "immunity", "innate", "immunity", "immunity", "to", "infections", "immunology", "biology", "immunoregulation", "viral", "diseases", "infectious", "disease", "control", "immun...	2013	Genome-wide RNAi Screen Reveals a New Role of a WNT/CTNNB1 Signaling Pathway as Negative Regulator of Virus-induced Innate Immune Responses
All natural Leishmania infections start in the skin; however , little is known of the contribution made by the sand fly vector to the earliest events in mammalian infection , especially in inflamed skin that can rapidly kill invading parasites . During transmission sand flies regurgitate a proteophosphoglycan gel synth...	Parasites are known to manipulate their arthropod vectors for increased transmission , yet little is known about the manipulator-molecules involved . The protozoan parasite Leishmania secrete a proteophosphoglycan-rich gel ( termed promastigote secretory gel , PSG ) to block the sand fly midgut to force the regurgitati...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunomodulation", "microbiology/innate", "immunity", "immunology/innate", "immunity", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "t...	2009	Proteophosophoglycans Regurgitated by Leishmania-Infected Sand Flies Target the L-Arginine Metabolism of Host Macrophages to Promote Parasite Survival
Structural Maintenance of Chromosomes ( SMC ) family proteins participate in multisubunit complexes that govern chromosome structure and dynamics . SMC-containing condensin complexes create chromosome topologies essential for mitosis/meiosis , gene expression , recombination , and repair . Many eukaryotes have two cond...	The structure of chromosomes is dynamically modulated to ensure that the genetic material is properly used and passed on to new cells . Evolutionarily conserved proteins of the Structural Maintenance of Chromosomes ( SMC ) family bind to chromosomes and organize their structure . Through gene duplication and divergence...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "chromosome", "structure", "and", "function", "caenorhabditis", "enzymes", "enzymology", "animals", "phosphatases", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems", "se...	2017	An SMC-like protein binds and regulates Caenorhabditis elegans condensins
Although anticapsular antibodies confer serotype-specific immunity to pneumococci , children increase their ability to clear colonization before these antibodies appear , suggesting involvement of other mechanisms . We previously reported that intranasal immunization of mice with pneumococci confers CD4+ T cell–depende...	The bacterium Streptococcus pneumoniae ( pneumococcus ) causes serious disease in children and the elderly , including pneumonia and meningitis ( inflammation of the brain ) . Carriage of pneumococcus in the nose is a necessary first step for most infections . As children age , they carry pneumococcus for shorter perio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "immunology/immune", "response" ]	2008	Interleukin-17A Mediates Acquired Immunity to Pneumococcal Colonization
Control of virus replication in HIV-1 infection is critical to delaying disease progression . While cellular immune responses are a key determinant of control , relatively little is known about the contribution of the infecting virus to this process . To gain insight into this interplay between virus and host in viral ...	The length of time taken by HIV-1-infected individuals to develop AIDS varies widely depending on how efficiently virus replication is controlled . Although host cellular immune responses are known to play an important role in viral control , the contributions made by the infecting virus and the host antibody response ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "molecular", "biology" ]	2015	Transmitted Virus Fitness and Host T Cell Responses Collectively Define Divergent Infection Outcomes in Two HIV-1 Recipients
Many different intestinal parasite species can co-occur in the same population . However , classic diagnostic tools can only frame a particular group of intestinal parasite species . Hence , one or two tests do not suffice to provide a complete picture of infecting parasite species in a given population . The present s...	In populations living in adverse conditions due to poverty , a wide variety of intestinal parasite infections can be observed . These infections are usually diagnosed by stool microscopy , but can be easily missed if the procedures used are inaccurate or performed in a suboptimal way . In the present study , we investi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "hookworms", "parasitic", "diseases", "animals", "parasitology", "molecular", "biology", "techniques", "strongyloides", "stercoralis", "research", "and", "analysis", "methods", "strongyloides", "parasiti...	2017	Diagnosing Polyparasitism in a High-Prevalence Setting in Beira, Mozambique: Detection of Intestinal Parasites in Fecal Samples by Microscopy and Real-Time PCR
Although mistranslation is commonly believed to be deleterious , recent evidence indicates that mistranslation can be actively regulated and be beneficial in stress response . Methionine mistranslation in mammalian cells is regulated by reactive oxygen species where cells deliberately alter the proteome through incorpo...	Methionine-mistranslation is a recently discovered phenomenon where mammalian cells deliberately mischarge non-Met-tRNAs with amino acid methionine in unstressed cells and in response to innate immune and chemically triggered oxidative stress . These mischarged tRNAs are used in translation to generate mutant proteins ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities
In the U . S . , more than 80% of African-American smokers use mentholated cigarettes , compared to less than 30% of Caucasian smokers . The reasons for these differences are not well understood . To determine if genetic variation contributes to mentholated cigarette smoking , we performed an exome-wide association ana...	An exome-wide association study revealed a significant association between menthol cigarette use and coding variants in MRGPRX4 , which encodes a G-protein coupled receptor expressed in sensory neurons . The variant haplotype is found only in populations of African ancestry , and encodes a receptor that displays reduce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "drugs", "geographical", "locations", "microbiology", "social", "sciences", "neuroscience", "habits", "ethnicities", "tetracyclines", "antibiotics", "genome", "analysis", "af...	2019	An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking
The sandfish lizard ( Scincus scincus ) swims within granular media ( sand ) using axial body undulations to propel itself without the use of limbs . In previous work we predicted average swimming speed by developing a numerical simulation that incorporated experimentally measured biological kinematics into a multibody...	The sandfish lizard uses body undulation to propel itself within granular media ( sand ) . Previously we developed a numerical simulation model consisting of an experimentally validated multi-particle model of the granular medium , and a sandfish model with prescribed body deformation ( a traveling sinusoidal wave with...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "fluid", "mechanics", "biomimetics", "biomechanics", "biological", "systems", "engineering", "biophysics", "simulations", "bioengineering", "biophysics", "theory", "biology", "biophysics", "physics", "mechanical", "engineering", "biological", "fluid", "mechan...	2012	Mechanics of Undulatory Swimming in a Frictional Fluid
The divergence of distinct cell populations from multipotent progenitors is poorly understood , particularly in vivo . The gonad is an ideal place to study this process , because it originates as a bipotential primordium where multiple distinct lineages acquire sex-specific fates as the organ differentiates as a testis...	How cells diverge from a common progenitor and adopt specific fates is still poorly understood . We analyzed gene expression profiles in the distinct cell lineages of the gonad over the period when sex determination occurs . The undifferentiated progenitor cells expressed genes characteristic of both sexual fates , exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "systems", "biology", "developmental", "biology", "genome", "analysis", "tools", "genomics", "model", "organisms", "organism", "development", "biology", "computational", "biology", "morphogenesis", "genetics", "and", "genomics" ]	2012	Temporal Transcriptional Profiling of Somatic and Germ Cells Reveals Biased Lineage Priming of Sexual Fate in the Fetal Mouse Gonad
Balantidiasis is considered a neglected zoonotic disease with pigs serving as reservoir hosts . However , Balantidium coli has been recorded in many other mammalian species , including primates . Here , we evaluated the genetic diversity of B . coli in non-human primates using two gene markers ( SSrDNA and ITS1-5 . 8SD...	Balantidium coli is a pathogenic ciliate occurring in various hosts , including primates . Balantidiasis is considered a neglected disease with zoonotic potential and it is associated with pigs as reservoirs . Although it is considered to be rare , a high prevalence of B . coli persists in tropical and subtropical area...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "science", "biology" ]	2013	Novel Insights into the Genetic Diversity of Balantidium and Balantidium-like Cyst-forming Ciliates
Candida albicans , a clinically important dimorphic fungal pathogen that can evade immune attack by masking its cell wall β-glucan from immune recognition , mutes protective host responses mediated by the Dectin-1 β-glucan receptor on innate immune cells . Although the ability of C . albicans to switch between a yeast-...	Candida is a common human commensal but disseminated candidiasis is a serious clinical problem , especially among immunocompromised patients . The innate immune system controls Candida infection , in part through the germline-encoded β-glucan receptor Dectin-1 . However , during in vitro growth , Candida albicans mutes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/nosocomial", "and", "healthcare-associated", "infections", "infectious", "diseases/fungal", "infections", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "disease...	2008	Dynamic, Morphotype-Specific Candida albicans β-Glucan Exposure during Infection and Drug Treatment
Many Gram-negative bacteria colonize and exploit host niches using a protein apparatus called a type III secretion system ( T3SS ) that translocates bacterial effector proteins into host cells where their functions are essential for pathogenesis . A suite of T3SS-associated chaperone proteins bind cargo in the bacteria...	Systemic typhoid fever caused by Salmonella enterica serovar Typhi leads to high mortality in the developing world and can be linked with chronic , persistent infections in survivors . To cause disease , Salmonella uses a specialized secretion device called a type III secretion system to disarm cells of the immune syst...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology/microbial", "evolution", "and", "genomics", "biochemistry/macromolecular", "assemblies", "and", "machines", "infectious", "diseases/bacterial", "infections", "biochemistry/structural", "genomics", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	Structural and Biochemical Characterization of SrcA, a Multi-Cargo Type III Secretion Chaperone in Salmonella Required for Pathogenic Association with a Host
In the early epiblast of female mice , one of the two X chromosomes is randomly inactivated by a Xist-dependent mechanism , involving the recruitment of Ezh2-Eed and the subsequent trimethylation of histone 3 on lysine 27 ( H3K27me3 ) . We demonstrate that this random inactivation process applies also to the primordial...	The last few years have led to striking advances in our understanding of the genesis of primordial germ cells ( PGCs ) and the importance of their correct epigenetic programming for the formation of functional gametes in mice . We investigated one aspect of the epigenetic programming of germ cells , the activity of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "molecular", "biology", "developmental", "biology" ]	2008	X Chromosome Activity in Mouse XX Primordial Germ Cells
Antibiotic resistant nosocomial infections are an important cause of mortality and morbidity in hospitals . Antibiotic cycling has been proposed to contain this spread by a coordinated use of different antibiotics . Theoretical work , however , suggests that often the random deployment of drugs ( “mixing” ) might be th...	Infections with bacterial pathogens that are resistant against antibiotics are an important cause of mortality and morbidity in hospitals . One possibility to minimize this burden of antibiotic resistance is to coordinate the use of several drugs at the level of a single hospital ward . Here , we use a computational mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2011	Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards
Leprosy , a chronic granulomatous disease affecting the skin and nerves , is caused by Mycobacterium leprae ( M . leprae ) . The type of leprosy developed depends upon the host immune response . Type 1 reactions ( T1Rs ) , that complicate borderline and lepromatous leprosy , are due to an increase in cell-mediated immu...	Leprosy , caused by Mycobacterium leprae ( M . leprae ) , is a chronic infection leading to potentially debilitating nerve damage . Although the infection is curable with multi-drug therapy , many patients continue to suffer from episodes of inflammation , called Type 1 reactions . These reactions may lead to nerve dam...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "immune", "activation", "immunity", "to", "infections", "immunology", "skin", "infections", "immune", "defense", "neglected", "tropical", "diseases", "immunologic", "techniques", "immunohistochemical", "analysis", "infectious", "diseases", "biolog...	2012	Human Beta-Defensin 3 Is Up-Regulated in Cutaneous Leprosy Type 1 Reactions
NKp46 , a natural killer ( NK ) cell–activating receptor , is involved in NK cell cytotoxicity against virus-infected cells or tumor cells . However , the role of NKp46 in other NKp46+ non-NK innate lymphoid cell ( ILC ) populations has not yet been characterized . Here , an NKp46 deficiency model of natural cytotoxici...	Group 1 innate lymphoid cells ( ILCs ) comprise two subsets: natural killer ( NK ) cells and ILC1s . Although NK cells and ILC1s are functionally distinct , a factor that regulates one subset but not the other has not been identified . In the current study , we discovered that NKp46 , a marker expressed by both NK cell...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "liver", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immunology", "green", "fluorescent", "protein", "toxicology", "animal", "models", ...	2018	Dependence of innate lymphoid cell 1 development on NKp46
B lymphopoiesis is the result of several cell-commitment , lineage-choice , and differentiation processes . Every differentiation step is characterized by the activation of a new , lineage-specific , genetic program and the extinction of the previous one . To date , the central role of specific transcription factors in...	Through the hematopoietic system , all the distinct mature blood cell types are generated , thereby constituting one of the best-studied paradigms for cell lineage commitment and differentiation in biology . B lymphocytes are generated through several cell-commitment , lineage-choice , and differentiation processes . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "genomics" ]	2013	HDAC7 Is a Repressor of Myeloid Genes Whose Downregulation Is Required for Transdifferentiation of Pre-B Cells into Macrophages
Due to the rapid release of new data from genome sequencing projects , the majority of protein sequences in public databases have not been experimentally characterized; rather , sequences are annotated using computational analysis . The level of misannotation and the types of misannotation in large public databases are...	One of the core elements of modern biological scientific investigation is the universal availability of millions of protein sequences from thousands of different organisms , allowing for exciting new investigations into biological questions . These sequences , found in large primary sequence databases such as GenBank N...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "biochemistry/bioinformatics", "genetics", "and", "genomics/bioinformatics", "computational", "biology" ]	2009	Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
We construct a laminar neural-field model of primary visual cortex ( V1 ) consisting of a superficial layer of neurons that encode the spatial location and orientation of a local visual stimulus coupled to a deep layer of neurons that only encode spatial location . The spatially-structured connections in the deep layer...	A major challenge in neurobiology is understanding the mechanisms underlying the formation and propagation of cortical waves and the underlying neural circuitry that supports them . A variety of neurological disorders such as epilepsy and spreading depression during migraine episodes are characterized by spatially loca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity
The expression of the prion protein ( PrP ) is essential for transmissible spongiform encephalopathy ( TSE ) or prion diseases to occur , but the underlying mechanism of infection remains unresolved . To address the hypothesis that glycosylation of host PrP is a major factor influencing TSE infection , we have inoculat...	In prion infection , disease requires the presence of the endogenous host-encoded prion protein , PrP . PrP is a glycoprotein ( modified by the addition of sugar molecules ) with two consensus sites for sugars to attach . Different PrP forms are usually observed: one diglycosylated , two different monoglycosylated , an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "pathology", "neuroscience" ]	2008	Host PrP Glycosylation: A Major Factor Determining the Outcome of Prion Infection
Lung squamous cell carcinoma ( SqCC ) , the second most common subtype of lung cancer , is strongly associated with tobacco smoking and exhibits genomic instability . The cellular origins and molecular processes that contribute to SqCC formation are largely unexplored . Here we show that human basal stem cells ( BSCs )...	Human lungs are constantly exposed to inhaled chemicals that have the potential to damage cellular DNA . Lung stem cells must therefore have the ability to repair DNA damage to survive and achieve tissue homeostasis . Lung airways are composed of different types of cells , including basal cells , which have been propos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adenocarcinoma", "of", "the", "lung", "medicine", "and", "health", "sciences", "squamous", "cell", "lung", "carcinoma", "carcinomas", "cancers", "and", "neoplasms", "oncology", "dna", "damage", "stem", "cells", "adenocarcinomas", "dna", "secondary", "lung", "tumors...	2017	Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway
Zipf’s law , which states that the probability of an observation is inversely proportional to its rank , has been observed in many domains . While there are models that explain Zipf’s law in each of them , those explanations are typically domain specific . Recently , methods from statistical physics were used to show t...	Datasets ranging from word frequencies to neural activity all have a seemingly unusual property , known as Zipf’s law: when observations ( e . g . , words ) are ranked from most to least frequent , the frequency of an observation is inversely proportional to its rank . Here we demonstrate that a single , general princi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "linguistics", "statistical", "mechanics", "social", "sciences", "random", "variables", "neuroscience", "covariance", "probability", "distribution", "mathematics", "thermodynamics", "research", "and", "analysis", "methods", "sequence", "analysis", "entropy", "animal", "cell...	2016	Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables
Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes . However , the impact of those genetic variations on human immunity remains understudied , especially within the context of modern lifestyles and living environments , which are...	Individuals of European and African ancestry have different susceptibility for developing specific infections and diseases . Part of this difference in immune response is thought to arise from genetic differences accumulated over the millennia that conferred advantages in fighting different infectious pathogens endemic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "body", "fluids", "immunology", "geographical", "locations", "developmental", "biology", "clinical", "medicine", "molecular", "development", "...	2018	Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors
Rift Valley fever virus ( RVFV ) is a zoonotic arbovirus that causes severe disease in livestock and humans . The virus has caused recurrent outbreaks in Africa and the Arabian Peninsula since its discovery in 1931 . This review sought to evaluate RVFV seroprevalence across the African continent in livestock , wildlife...	Rift Valley fever virus ( RVFV ) is a vector-borne virus that infects wildlife and livestock , and can subsequently spread to humans . Due to the nature of the disease it has the potential to cause substantial economic and public health impacts . Rift Valley Fever ( RVF ) has been identified in Africa and the Arabian P...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "geographical", "locations", "anim...	2018	Systematic literature review of Rift Valley fever virus seroprevalence in livestock, wildlife and humans in Africa from 1968 to 2016
Despite the notoriety of Ebola virus disease ( EVD ) as one of the world’s most deadly infections , EVD has a wide range of outcomes , where asymptomatic infection may be almost as common as fatality . With increasingly sensitive EVD diagnosis , there is a need for more accurate prognostic tools that objectively strati...	The unprecedented spread of EVD across the fragile healthcare systems of West Africa during the 2013–2015 outbreak infected over 28 , 600 patients and established it as a disease for which low-income countries are at disproportionate risk . In order to improve the standard of patient care , it is essential to better al...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "demography", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "...	2017	Predicting Ebola Severity: A Clinical Prioritization Score for Ebola Virus Disease
The search for new macrofilaricidal drugs against onchocerciasis that can be administered in shorter regimens than required for doxycycline ( DOX , 200mg/d given for 4–6 weeks ) , identified minocycline ( MIN ) with superior efficacy to DOX . Further reduction in the treatment regimen may be achieved with co-administra...	Onchocerciasis is a vector borne disease that is still a major health burden in endemic countries , despite twenty years of control that has led to effective control and reduction of blindness and morbidity in West Africa . To reach the goal of onchocerciasis elimination , alternative strategies are needed to overcome ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "parasitic", "diseases", "wolbachia", "developmental", "biology", "histology", "pharmaceutics", "neglected", "tropical", "diseases", "molecular", "biology", "techniques", "pharmacology", "onchocerciasis", "emb...	2017	Comparison of Doxycycline, Minocycline, Doxycycline plus Albendazole and Albendazole Alone in Their Efficacy against Onchocerciasis in a Randomized, Open-Label, Pilot Trial
Secondary bacterial infections are a leading cause of illness and death during epidemic and pandemic influenza . Experimental studies suggest a lethal synergism between influenza and certain bacteria , particularly Streptococcus pneumoniae , but the precise processes involved are unclear . To address the mechanisms and...	Influenza virus infected individuals often become coinfected with a bacterial pathogen and , consequently , morbidity and mortality are significantly increased . A better understanding of how these pathogens interact with each other and the host is of key importance . Here , we use data from infected mice together with...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "streptococci", "virulence", "factors", "and", "mechanisms", "virology", "disease", "dynamics", "population", "dynamics", "co-infections", "biology", "microbiology", "host-pathogen", "interaction", "population", "biology", "bacterial", "pathogens", "pathogenesis" ]	2013	Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae
We quantified CD8 T cells needed to cause type 1 diabetes and studied the anatomy of the CD8 T cell/beta ( β ) cell interaction at the immunologic synapse . We used a transgenic model , in situ tetramer staining to distinguish antigen specific CD8 T cells from total T cells infiltrating islets and a variety of viral mu...	Insulin-dependent type 1 diabetes ( T1D ) is characterized by elevated blood sugar , lymphocytic infiltration into the islets of Langerhans and T cell destruction of beta ( β ) cells . β cells produce insulin whose function is to maintain and regulate glucose hemostasis . However , in vivo , the numbers of antigen spec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "immunology", "biology", "microbiology" ]	2012	Molecular Anatomy and Number of Antigen Specific CD8 T Cells Required to Cause Type 1 Diabetes
Cameroon is known to be endemic with trachoma . To appreciate the burden of the disease and facilitate the national planning of trachoma control in the integrated control program for the neglected tropical diseases , an epidemiological mapping of trachoma was conducted in the Far North region in 2010–11 . A cross-secti...	Trachoma is the leading infectious cause of blindness in the world , which is caused by repeated eye infections with the bacterium Chlamydia trachomatis . The global objective of trachoma control is to eliminate trachoma as a blinding disease worldwide by Year 2020 , using the World Health Organization-endorsed SAFE st...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "infectious", "disease", "control", "trachoma" ]	2013	Prevalence of Trachoma in the Far North Region of Cameroon: Results of a Survey in 27 Health Districts
Lassa virus ( LASV ) is endemic in parts of West Africa where it causes Lassa fever ( LF ) , a viral hemorrhagic fever with frequent fatal outcomes . The diverse LASV strains are grouped into six major lineages based on the geographical location of the isolated strains . In this study , we have focused on the lineage I...	Lassa fever ( LF ) is a viral hemorrhagic fever caused by Lassa virus ( LASV ) . The different LASV strains are grouped into lineages based on the geographical location of the isolated strains . The aim of our study was to characterize the lineage II strains in southern Nigeria . We sequenced LASV RNA genome from posit...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "taxonomy", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "amino", "acid", "sequence", "analysis", "phylogenetics", "data", "management", "phylogenetic", "analysis", ...	2018	Genetic characterization of Lassa virus strains isolated from 2012 to 2016 in southeastern Nigeria
The potential of RNA viruses to adapt to new environments relies on their ability to introduce changes in their genomes , which has resulted in the recent expansion of re-emergent viruses . Chikungunya virus is an important human pathogen transmitted by mosquitoes that , after 60 years of exclusive circulation in Asia ...	An emergent virus is a virus that has adapted to new hosts or environments through changes in its viral genome . Using as model chikungunya virus , which had explosively spread in the Americas and Europe during the last decade , we studied viral adaptability to mosquito and mammalian hosts . Natural isolates from recen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "microbiology", "cloning", "animals", "alphaviruses", "viruses", "chikungunya", "virus", "rna", "viruses", "mole...	2019	RNA recombination at Chikungunya virus 3'UTR as an evolutionary mechanism that provides adaptability
The present work exemplifies how parameter identifiability analysis can be used to gain insights into differences in experimental systems and how uncertainty in parameter estimates can be handled . The case study , presented here , investigates interferon-gamma ( IFNγ ) induced STAT1 signalling in two cell types that p...	For the prediction of therapeutic targets and the design of therapies , it is important to study the same pathway across different cell types . This is particularly relevant for cancer research , where several cell types are involved in carcinogenesis . Pancreatic cancer is enhanced by activated pancreatic stellate cel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemical", "simulations", "mathematics", "theoretical", "biology", "confidence", "intervals", "statistics", "biology", "computational", "biology", "signaling", "networks", "genetics", "and", "genomics" ]	2012	Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
Snake bite is a neglected public health problem in the world and one of the major causes of mortality and morbidity in many areas , particularly in the rural tropics . It also poses substantial economic burdens on the snake bite victims due to treatment related expenditure and loss of productivity . An accurate estimat...	Snake bite is one of the major causes of morbidity and mortality in many rural tropical areas . As a neglected public health problem , estimate of the risk is largely unknown . However , the associated personal and economic impact of snake bite is substantial across developing countries . This national survey investiga...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology" ]	2010	Annual Incidence of Snake Bite in Rural Bangladesh
Several theories have been advanced to explain how cross-frequency coupling , the interaction of neuronal oscillations at different frequencies , could enable item multiplexing in neural systems . The communication-through-coherence theory proposes that phase-matching of gamma oscillations between areas enables selecti...	There is a growing consensus that neuronal oscillations constitute a fundamental computational mechanism in the brain . Beyond this , recent experimental evidence has highlighted interactions between oscillations at high and low frequencies ( e . g . gamma oscillations , 40–80 Hz , are modulated by theta oscillations ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "engineering", "and", "technology", "nervous", "system", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "telecommunications", "network", "analysis", ...	2016	Theta-Gamma Coding Meets Communication-through-Coherence: Neuronal Oscillatory Multiplexing Theories Reconciled
The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation . Although the evolution of the sex-determination system may also play a role in speciation , little is known about the sex-determination system of Lake Victoria cichlids . To understand the evolution of the sex-det...	The diversity of sex chromosomes among animal species is well known , but how these sex chromosomes emerged during evolutionary history remains to be solved . One hypothesis for the origin of sex chromosomes is that a portion of the sex chromosome was derived from B chromosomes . In about 10% of eukaryotes , B chromoso...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "evolutionary", "biology", "cytogenetics", "evolutionary", "genetics", "genetics", "and", "genomics" ]	2011	B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes
Salmonella Typhi ( S . Typhi ) , the causative agent of typhoid fever , causes significant morbidity and mortality worldwide . Currently available vaccines are moderately efficacious , and identification of immunological responses associated with protection or disease will facilitate the development of improved vaccine...	In this manuscript , we describe , for the first time , a potential role for regulatory T cells ( Treg ) as an important factor in determining disease outcome in humans following exposure to wild-type S . Typhi . We studied in considerable depth the modulation of Treg activation characteristics and their homing potenti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Activation of Salmonella Typhi-Specific Regulatory T Cells in Typhoid Disease in a Wild-Type S. Typhi Challenge Model
Combinatorial effects of epigenetic modifications on transcription activity have been proposed as “histone codes” . However , it is unclear whether there also exist inter-nucleosomal communications among epigenetic modifications at single nucleosome level , and if so , what functional roles they play . Meanwhile , how ...	Nucleosomes are the basic unit of chromatin organization . At a global level , they fold up to form chromatin fibers in higher order structure to control the activation/repression states of chromatins . At a local level , especially around transcriptional starting sites ( TSSs ) , nucleosomes play an important role in ...	[ "Abstract", "Introduction", "Results", "Discussions", "Materials", "and", "methods" ]	[ "gene", "regulation", "dna-binding", "proteins", "dna", "transcription", "histone", "modification", "nucleosome", "mapping", "epigenetics", "molecular", "biology", "techniques", "chromatin", "research", "and", "analysis", "methods", "transcriptional", "control", "gene", "...	2018	Inter-nucleosomal communication between histone modifications for nucleosome phasing
Human FTO gene variants are associated with body mass index and type 2 diabetes . Because the obesity-associated SNPs are intronic , it is unclear whether changes in FTO expression or splicing are the cause of obesity or if regulatory elements within intron 1 influence upstream or downstream genes . We tested the idea ...	Geneticists have identified many gene regions that cause human disease by using multiple genetic markers in large populations to find gene regions associated with disease . However , it is often not clear precisely which gene in any given region causes the disease or how the gene exerts its functional effect . For exam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "biochemistry/protein", "chemistry", "physiology", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "function", "diabetes", "and", ...	2009	A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
The circadian clock is a molecular and cellular oscillator found in most mammalian tissues that regulates rhythmic physiology and behavior . Numerous investigations have addressed the contribution of circadian rhythmicity to cellular , organ , and organismal physiology . We recently developed a method to look at transc...	Circadian rhythms confer adaptive advantages by allowing organisms to anticipate daily changes in their environment . Over the last few years , many groups have used microarray technology to systematically identify genes under circadian regulation . We have extended on these studies by profiling the circadian transcrip...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "cell", "biology/gene", "expression", "computational", "biology/genomics", "genetics", "and", "genomics/gene", "expression" ]	2009	Harmonics of Circadian Gene Transcription in Mammals
Cells use thousands of regulatory sequences to recruit transcription factors ( TFs ) and produce specific transcriptional outcomes . Since TFs bind degenerate DNA sequences , discriminating functional TF binding sites ( TFBSs ) from background sequences represents a significant challenge . Here , we show that a Drosoph...	While all cells in an organism share a common genome , each cell type must express the appropriate combination of genes needed for its specific function . Cells activate and repress different parts of the genome using transcription factor proteins that bind regulatory regions known as enhancers . We currently have an i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "invertebrates", "chemical", "characterization", "electrophoretic", "mobility", "shift", "assay", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "animals", "animal", "models", "developmental", "biology", ...	2018	Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity
The high medical importance of Crotalus snakes is unquestionable , as this genus is the second in frequency of ophidian accidents in many countries , including Brazil . With a relative less complex composition compared to other genera venoms , as those from the Bothrops genus , the Crotalus genus venom from South Ameri...	Representing more than 10% of the dry weight of the crude venom of crotamine-positive rattlesnakes , crotamine may act as toxin mainly by imposing the physical immobilization of preys . Its presence was described to be important for antivenom therapy , although the knowledge on the effective contribution of crotamine t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "skeletal", "muscles", "electrophysiology", "neuroscience", "muscle", "contraction", "toxicology", "toxic", "agents", "paralysis", "ion", "channels", "routes", "of", "admini...	2018	Pharmacological characterization of crotamine effects on mice hind limb paralysis employing both ex vivo and in vivo assays: Insights into the involvement of voltage-gated ion channels in the crotamine action on skeletal muscles
Virulence of the human fungal pathogen Candida albicans depends on the switch from budding to filamentous growth , which requires sustained membrane traffic and polarized growth . In many organisms , small GTPases of the Arf ( ADP-ribosylation factor ) family regulate membrane/protein trafficking , yet little is known ...	Virulence of the human fungal pathogen Candida albicans relies on the switch from budding to highly polarized hyphal growth . Sustained membrane traffic is critical for such polarized growth and for the secretion of virulence factors . Small G-proteins function as molecular switches required for a variety of cellular p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "cell", "processes", "microbiology", "enzymology", "animal", "models", "membrane", "proteins", "fungi", "model", "organisms", "experimental", "organism", "syst...	2017	Role of Arf GTPases in fungal morphogenesis and virulence
We introduce a novel computational approach , CoReCo , for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species . Leveraging on the exponential growth in sequenced genome availability , our method reconstructs genome-scale gapless metabolic networks simu...	Advances in next-generation sequencing technologies are revolutionizing molecular biology . Sequencing-enabled cost-effective characterization of microbial genomes is a particularly exciting development in metabolic engineering . There , considerable effort has been put to reconstructing genome-scale metabolic networks...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ustilago", "maydis", "small", "molecules", "enzymes", "metabolic", "networks", "kluyveromyces", "lactis", "gene", "function", "aspergillus", "nidulans", "algorithms", "model", "organisms", "sequence", "analysis", "schizosaccharomyces", "pombe", "biology", "proteomics", "...	2014	Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
The mosquito-borne Chikungunya virus ( CHIKV ) causes high fever and severe joint pain in humans . It is expected to spread in the future to Europe and has recently reached the USA due to globalization , climate change and vector switch . Despite this , little is known about the virus life cycle and , so far , there is...	Chikungunya virus ( CHIKV ) is transmitted by mosquitos and causes high fever and severe joint pain in humans . It is expected to spread in the future to Europe and has recently reached the USA due to vector switch and climate change . There is no specific treatment or vaccination against CHIKV infections . However , v...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Small Antigenic Determinant of the Chikungunya Virus E2 Protein Is Sufficient to Induce Neutralizing Antibodies which Are Partially Protective in Mice
Non-typhoidal Salmonella ( NTS ) and Salmonella enterica serovar Typhi bacteremia are the causes of significant morbidity and mortality worldwide . There is a paucity of data regarding NTS bacteremia in South Asia , a region with a high incidence of typhoidal bacteremia . We sought to determine clinical predictors and ...	Salmonella are a group of bacteria that cause illnesses and death worldwide . There are two types of Salmonella–Typhi and non-typhoidal ( NTS ) . In humans , the majority of illnesses caused by NTS are related to gastro-intestinal problems , though uncommonly , it also invades the bloodstream . On the other hand , typh...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Factors Associated with Non-typhoidal Salmonella Bacteremia versus Typhoidal Salmonella Bacteremia in Patients Presenting for Care in an Urban Diarrheal Disease Hospital in Bangladesh
Connectomics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extrasynaptic volume transmission , especially via monoamines and neuropeptides , is also critical to brain function and occurs primarily outside the synaptic connectome . We have mapped the putative monoam...	Connectomics represents an effort to map brain structure at the level of individual neurons and their synaptic connections . However , neural circuits also depend on other types of signalling between neurons , such as extrasynaptic modulation by monoamines and peptides . Here we present a draft monoamine connectome , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "Methods" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "neurochemistry", "neural", "networks", "nervous", "system", "caenorhabditis", "junctional", "complexes", "signaling", "networks", "electrophysiology", "neuroscience", "animals", "hormones", "an...	2016	The Multilayer Connectome of Caenorhabditis elegans
Cytokinesis in prokaryotes involves the assembly of a polymeric ring composed of FtsZ protein monomeric units . The Z ring forms at the division plane and is attached to the membrane . After assembly , it maintains a stable yet dynamic steady state . Once induced , the ring contracts and the membrane constricts . In th...	The division of a cell into two daughter cells is an essential characteristic of living systems . This process requires the assembly of a contractile ring attached to the membrane at the site of division . At the appropriate point of the cell cycle , the ring constricts and pulls the membrane with it , pinching the cel...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/systems", "biology" ]	2008	Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis
Burkholderia pseudomallei ( Bp ) causes the disease melioidosis . The main cause of mortality in this disease is septic shock triggered by the host responding to lipopolysaccharide ( LPS ) components of the Gram-negative outer membrane . Bp LPS is thought to be a weak inducer of the host immune system . LPS from severa...	Not only does Burkholderia pseudomallei pose a public health challenge in Southeast Asia and northern Australia but in the United States ( US ) Bp is listed as a Tier-1 select agent . Tier 1 organisms have the potential to pose a severe threat to US public health and safety and policy makers mandated development of vac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "neurochemistry", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "neuroscience", "b...	2017	Structural diversity of Burkholderia pseudomallei lipopolysaccharides affects innate immune signaling
The effectiveness of anti-parasite treatment with benznidazole in the chronic Chagas disease ( ChD ) remains uncertain . We evaluated , using data from the NIH-sponsored SaMi-Trop prospective cohort study , if previous treatment with benznidazole is associated with lower mortality , less advanced cardiac disease and lo...	Chagas disease remains as one of the most neglected infectious diseases of the world , with millions of persons infected and dozens of thousands of deaths every year . The disease has a very long natural history and few options of etiologic treatment , including antiparasitic [1] drugs benznidazole and nifurtimox . Ben...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cardiomyopathies", "medicine", "and", "health", "sciences", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "electrocardiography", "protozoans", "bioassays", "and", "physiological", "analysis", "neglected", "tropical...	2018	Beneficial effects of benznidazole in Chagas disease: NIH SaMi-Trop cohort study
Highly pathogenic avian influenza virus ( HPAIV ) of the subtype H5N1 causes severe , often fatal pneumonia in humans . The pathogenesis of HPAIV H5N1 infection is not completely understood , although the alveolar macrophage ( AM ) is thought to play an important role . HPAIV H5N1 infection of macrophages cultured from...	Alveolar macrophages ( AM ) , which reside in the alveolar lumen , usually dampen down the host immune response to incoming pathogens . However , they are thought to increase inflammation during highly pathogenic avian influenza virus ( HPAIV ) H5N1 infections , which cause severe and often fatal disease in humans . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunologic", "subspecialties", "virology", "immunology", "biology", "pulmonary", "immunology", "microbiology", "viral", "diseases" ]	2011	Highly Pathogenic Avian Influenza Virus H5N1 Infects Alveolar Macrophages without Virus Production or Excessive TNF-Alpha Induction
There are few reports describing the epidemiology of visceral leishmaniasis ( VL ) in Somalia . Over the years 2002 to 2005 , a yearly average of 140 patients were reported from the Huddur centre in Bakool region , whereas in 2006 , this number rose to 1002 patients . Given the limited amount of information on VL and t...	Our paper describes the epidemiological features of visceral leishmaniasis in the Bakool region , South Central Somalia , over the years 2004 to 2006 . Since 2000 , Médecins Sans Frontières has been providing care for patients suffering from visceral leishmaniasis in Huddur , located in a region endemic for visceral le...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases" ]	2007	Epidemiology and Clinical Features of Patients with Visceral Leishmaniasis Treated by an MSF Clinic in Bakool Region, Somalia, 2004–2006
Malaria transmission requires the production of male and female gametocytes in the human host followed by fertilization and sporogonic development in the mosquito midgut . Although essential for the spread of malaria through the population , little is known about the initiation of gametocytogenesis in vitro or in vivo ...	As malaria control efforts move toward eradication it becomes increasingly important to develop interventions that block transmission . Consequently , advances are needed in our understanding of the production of gametocytes , which are required to transmit the disease . This report provides a first view of the initial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "infectious", "diseases", "tropical", "diseases", "(non-neglected)", "global", "health", "molecular", "development", "parasitology", "biology", "microbiology", "malaria", "parasitic", "diseases", "infectious", "disease", "control", "c...	2012	Plasmodium falciparum Gametocyte Development 1 (Pfgdv1) and Gametocytogenesis Early Gene Identification and Commitment to Sexual Development
A common goal in data-analysis is to sift through a large data-matrix and detect any significant submatrices ( i . e . , biclusters ) that have a low numerical rank . We present a simple algorithm for tackling this biclustering problem . Our algorithm accumulates information about 2-by-2 submatrices ( i . e . , ‘loops’...	An important problem in genomics is how to detect the genetic signatures associated with disease . When a disease is caused by a single well-defined biological mechanism , the genetic signature often involves a handful of genes present across the majority of the diseased patients . On the other hand , when a disease is...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "genome-wide", "association", "studies", "engineering", "and", "technology", "applied", "mathematics", "experimental", "design", "simulation", "and", "modeling", "algorithms", "research", "design", "mathematics", "genome", "analysis", "structural", "genomics", "research", ...	2018	A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases . Recent studies show that these proteins have common traits even at the monomer level . Among them , a polyglutamine region that is present in huntingtin is known to exhibit a correlation between th...	Misfolding and aggregation of several proteins are known to be related to neurodegenerative diseases . Among them , polyglutamine expansions are known to be responsible for at least 9 diseases , including Huntington . Nonetheless , the structural properties of these intrinsically disordered proteins are difficult to st...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	An Exploration of the Universe of Polyglutamine Structures
Chagas disease has a major impact on human health in Latin America and is becoming of global concern due to international migrations . Trypanosoma cruzi , the etiological agent of the disease , is one of the rare human parasites transmitted by the feces of its vector , as it is unable to reach the salivary gland of the...	Chagas disease is a parasitic disease affecting about 10 million people , often living in poor conditions , and the disease contributes to impede their development . As several other infectious diseases ( malaria , dengue or sleeping sickness ) , it is transmitted by blood-feeding insect vectors . While most other huma...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Improbable Transmission of Trypanosoma cruzi to Human: The Missing Link in the Dynamics and Control of Chagas Disease
The helminth Schistosoma mansoni modulates the infected host’s immune system to facilitate its own survival , by producing excretory/secretory molecules that interact with a variety of the host’s cell types including those of the immune system . Herein , we characterise the S . mansoni adult male worm secretome and ide...	Helminths are known for their ability to alter the host’s immune response in order to promote their survival . One such mechanism is the propensity of helminths to secrete molecules with immunomodulatory activity; such molecules alter various aspects of host immunity to the benefit of the parasite . Following detailed ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "cells", "helminths", "immunology", "parasitic", "diseases", "animals", "research", "and", "analysis", "methods", "spectru...	2017	Composition of the Schistosoma mansoni worm secretome: Identification of immune modulatory Cyclophilin A
Networks play a crucial role in computational biology , yet their analysis and representation is still an open problem . Power Graph Analysis is a lossless transformation of biological networks into a compact , less redundant representation , exploiting the abundance of cliques and bicliques as elementary topological m...	Networks play a crucial role in biology and are often used as a way to represent experimental results . Yet , their analysis and representation is still an open problem . Recent experimental and computational progress yields networks of increased size and complexity . There are , for example , small- and large-scale in...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology" ]	2008	Unraveling Protein Networks with Power Graph Analysis

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