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Down syndrome ( DS ) , with trisomy of chromosome 21 ( HSA21 ) , is the commonest human aneuploidy . Pre-leukemic myeloproliferative changes in DS foetal livers precede the acquisition of GATA1 mutations , transient myeloproliferative disorder ( DS-TMD ) and acute megakaryocytic leukemia ( DS-AMKL ) . Trisomy of the Er...	An excess number of genes in trisomy on human chromosome 21 leads to the development of specific diseases in human Down syndrome . An excess copy of the gene , ERG , an ETS family transcription factor , has been implicated in abnormal blood system development in Down syndrome . In this study we show how trisomy of Erg ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Semen is a major vector for HIV transmission , but the semen HIV RNA viral load ( VL ) only correlates moderately with the blood VL . Viral shedding can be enhanced by genital infections and associated inflammation , but it can also occur in the absence of classical pathogens . Thus , we hypothesized that a dysregulate...	The classical paradigm of HIV infectivity centers on the blood HIV RNA viral load . However , while other fluid compartments such as semen and cerebrospinal fluid can have distinct viral loads from blood , the causes of localized HIV shedding are not fully understood . Since the semen viral load is an independent predi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "urology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "microbiology", "immunodeficiency", "viruses", "urologic", "infections", "infectious", "diseases", "medical", "microbiology", "hiv", "microbial", "pathogens", "...	2014	The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection
Lymphatic filariasis ( LF ) and podoconiosis are neglected tropical diseases ( NTDs ) that pose a significant physical , social and economic burden to endemic communities . Patients affected by the clinical conditions of LF ( lymphoedema and hydrocoele ) and podoconiosis ( lymphoedema ) need access to morbidity managem...	Patients affected by the clinical conditions of lymphatic filariasis ( lymphoedema and hydrocoele ) and podoconiosis ( lymphoedema ) require access to a minimum package of care to prevent progression of the disease , and to improve their quality of life . Clear estimates of the number and location of these patients is ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "legs", "tropical", "diseases", "geographical", "locations", "limbs", "(anatomy)", "parasitic", "diseases", "health", "care", "ethnicities", "age", "groups", "neglected", "tropical", "diseases", "ethiopia", "supervisors", "africa...	2018	Integrated morbidity mapping of lymphatic filariasis and podoconiosis cases in 20 co-endemic districts of Ethiopia
We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites . The model includes the chemical potential of the transcription factor , non-specific binding affinity of the protein for DNA , as well as sequence-specific parameters that ma...	The DNA binding sites of transcription factors that control gene expression are often predicted based on a collection of known or selected binding sites . The most commonly used methods for inferring the binding site pattern , or sequence motif , assume that the sites are selected in proportion to their affinity for th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation" ]	2009	Inferring Binding Energies from Selected Binding Sites
A recent paper by Karin et al . introduced a mathematical notion called dynamical compensation ( DC ) of biological circuits . DC was shown to play an important role in glucose homeostasis as well as other key physiological regulatory mechanisms . Karin et al . went on to provide a sufficient condition to test whether ...	A recently introduced mathematical notion called dynamical compensation of biological circuits was shown to play an important role in glucose homeostasis and other key physiological regulatory mechanisms . This paper explains how dynamical compensation can be formulated in terms of a well-known concept in systems biolo...	[ "Abstract", "Introduction", "Results", "Examples", "from", "the", "paper", "[", "Discussion", "Methods" ]	[ "control", "theory", "chemical", "compounds", "engineering", "and", "technology", "integrative", "physiology", "carbohydrates", "organic", "compounds", "glucose", "control", "engineering", "systems", "science", "mathematics", "algebra", "polynomials", "computer", "and", "...	2017	Dynamic compensation, parameter identifiability, and equivariances
Circulating levels of adiponectin , a hormone produced predominantly by adipocytes , are highly heritable and are inversely associated with type 2 diabetes mellitus ( T2D ) and other metabolic traits . We conducted a meta-analysis of genome-wide association studies in 39 , 883 individuals of European ancestry to identi...	Serum adiponectin levels are highly heritable and are inversely correlated with the risk of type 2 diabetes ( T2D ) , coronary artery disease , stroke , and several metabolic traits . To identify common genetic variants associated with adiponectin levels and risk of T2D and metabolic traits , we conducted a meta-analys...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "clinical", "research", "design", "genetics", "molecular", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits: A Multi-Ethnic Meta-Analysis of 45,891 Individuals
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the etiologic agent of three human malignancies , the endothelial cell cancer Kaposi’s sarcoma , and two B cell cancers , Primary Effusion Lymphoma and multicentric Castleman’s disease . KSHV has latent and lytic phases of the viral life cycle , and while both contrib...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the causative agent of three human malignancies . KSHV establishes latent infection but can be reactivated from latency to the lytic phase of the viral life cycle to propagate . KSHV reactivation from latency is controlled by epigenetic changes at the promoter of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vero", "cells", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "biological", "cultures", "dna-binding", "proteins", "microbiology", "viruses", "dna", "viruses", "epigenetics", "herpesviruses", "chromatin", "research", ...	2018	Chromatin remodeling controls Kaposi's sarcoma-associated herpesvirus reactivation from latency
Genetic variation at the Human Leucocyte Antigen ( HLA ) genes is associated with many autoimmune and infectious disease phenotypes , is an important element of the immunological distinction between self and non-self , and shapes immune epitope repertoires . Determining the allelic state of the HLA genes ( HLA typing )...	Determining an individual’s HLA type ( the sequence of the exons of the HLA genes ) is important in many areas of biomedical research . For example , HLA types shape immune epitope repertoires , which are relevant in cancer immunotherapy , and influence autoimmune and infectious disease risk . Whole-genome sequencing d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "infographics", "split-decomposition", "method", "population", "genetics", "computational", "biology", "alleles", "multiple", "alignment", "calculation", "platinum", "genome", "analysis", "molecular", "biology", "techniques", "population", "biology...	2016	High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs
The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV . Numerous strategies are being explored to eliminate this reservoir . To translate these efforts into clinical trials , there is a strong need for validated biomarkers that can monitor the reservoir over time...	Current HIV-1 research aims to find a cure for HIV-1 , either by pursuing viral eradication or by attempting to attain an immune-mediated functional cure . For the purpose of interpreting the findings of these eradication strategies , a validated representative biomarker of the replication-competent latent HIV-1 reserv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "biological", "cultures", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "rna", "viruses", "...	2016	Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth
Rhythmical activity patterns are ubiquitous in nature . We study an oscillatory biological system: collective activity cycles in ant colonies . Ant colonies have become model systems for research on biological networks because the interactions between the component parts are visible to the naked eye , and because the t...	Many complex biological systems , from cardiac tissues to entire animal populations , exhibit rhythmical oscillations . Here we studied a textbook example of a complex living system–colonies of Leptothorax ants , which exhibit short ( 15 minute ) collective activity cycles . In ant colonies , information , food , and c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "sociology", "signaling", "networks", "social", "sciences", "animals", "circadian", "oscillators", "simulation", "...	2017	Short-term activity cycles impede information transmission in ant colonies
Osteogenesis imperfecta ( OI ) is a hereditary disease occurring in humans and dogs . It is characterized by extremely fragile bones and teeth . Most human and some canine OI cases are caused by mutations in the COL1A1 and COL1A2 genes encoding the subunits of collagen I . Recently , mutations in the CRTAP and LEPRE1 g...	Osteogenesis imperfecta ( OI ) is a genetic condition of humans and dogs characterized by extremely fragile bones and teeth . Most human OI cases are caused by defects in one of two collagen genes . Mutations in two other genes related to collagen maturation can also lead to OI in some patients . We studied Dachshunds ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics", "genetics", "and", "genomics/medical", "genetics" ]	2009	A Missense Mutation in the SERPINH1 Gene in Dachshunds with Osteogenesis Imperfecta
Kaposi's sarcoma ( KS ) is a highly disseminated angiogenic tumor of endothelial cells linked to infection by Kaposi's sarcoma-associated herpesvirus ( KSHV ) . KSHV encodes more than two dozens of miRNAs but their roles in KSHV-induced tumor dissemination and metastasis remain unknown . Here , we found that ectopic ex...	Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma ( KS ) . KS is a highly disseminated tumor often involved with visceral organs . Experimentally , KSHV infection induces the invasiveness of endothelial cells . KSHV encodes twelve precursor miRNAs ( pre-miRNAs ) , which are p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A KSHV microRNA Directly Targets G Protein-Coupled Receptor Kinase 2 to Promote the Migration and Invasion of Endothelial Cells by Inducing CXCR2 and Activating AKT Signaling
CD4+ T cells are essential for the control of Yersinia enterocolitica ( Ye ) infection in mice . Ye can inhibit dendritic cell ( DC ) antigen uptake and degradation , maturation and subsequently T-cell activation in vitro . Here we investigated the effects of Ye infection on splenic DCs and T-cell proliferation in an e...	Dendritic cells ( DCs ) are crucial in promoting immune responses against pathogens . Mouse DCs consist of different subpopulations but their role in immunity to pathogens and immune evasion is largely unclear . The enteric pathogen Yersinia enterocolitica ( Ye ) was shown to evade DC functions in bone marrow-derived D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/antigen", "processing", "and", "recognition", "immunology/leukocyte", "development", "cell", "biology/cell", "signaling", "immunology/immunomodulation", "immunology/immune", "response", "immunology/innate", "...	2010	Immune Evasion by Yersinia enterocolitica: Differential Targeting of Dendritic Cell Subpopulations In Vivo
Equine arteritis virus ( EAV ) has the unique ability to establish long-term persistent infection in the reproductive tract of stallions and be sexually transmitted . Previous studies showed that long-term persistent infection is associated with a specific allele of the CXCL16 gene ( CXCL16S ) and that persistence is m...	A distinctive feature of equine arteritis virus ( EAV ) is its ability to establish long-term persistent infection in the stallion reproductive tract in the presence of strong immune and inflammatory responses . The data presented herein provides insight into the molecular signature of the inflammatory response during ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "microbiology", "signs", "and", "sy...	2019	Equine arteritis virus long-term persistence is orchestrated by CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis
Poverty has long been considered a risk factor for leprosy and is related to nutritional deficiencies . In this study , we aim to investigate the association between poverty-related diet and nutrition with leprosy . In rural leprosy-endemic areas in Indonesia , we conducted a household-based case-control study using tw...	Despite the suggestion that nutritional deficiencies may impair host immune responses against Mycobacterium leprae , there has not been any systematic study on how various aspects of poverty interact and associate with nutrition and leprosy . In poor rural areas in Indonesia that have the highest proportion of multibac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "diet", "anemia", "health", "care", "bacterial", "diseases", "physiological", "processes", "nutrition", "neglected", "tropical", "diseases", "public", "and", "occupational", "health", "infectious", "diseas...	2018	Dietary diversity and poverty as risk factors for leprosy in Indonesia: A case-control study
Recurrent connections play an important role in cortical function , yet their exact contribution to the network computation remains unknown . The principles guiding the long-term evolution of these connections are poorly understood as well . Therefore , gaining insight into their computational role and into the mechani...	The recurrent interactions among cortical neurons shape the representation of incoming information but the principles governing their evolution are yet unclear . We investigate the computational role of recurrent connections in the context of sensory processing . Specifically , we study a neuronal network model in whic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "medicine", "and", "health", "sciences", "neural", "networks", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "cognitive", "psychology", "network", "analysis", "hallucinations", "vision", "neuronal", "tuning", "computer", "and", ...	2016	Optimal Information Representation and Criticality in an Adaptive Sensory Recurrent Neuronal Network
In vertebrates , left-right ( LR ) axis specification is determined by a ciliated structure in the posterior region of the embryo . Fluid flow in this ciliated structure is responsible for the induction of unilateral left-sided Nodal activity in the lateral plate mesoderm , which in turn regulates organ laterality . Bm...	Although vertebrates are bilaterally symmetric when observed from the outside , inside the body cavity the organs are positioned asymmetrically with respect to the left and right sides . Cases where all the organs are mirror imaged , known as situs inversus , are not associated with any medical defects . Severe medical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "model", "organisms", "genetics", "biology", "genetics", "and", "genomics", "cardiovascular" ]	2011	Bmp and Nodal Independently Regulate lefty1 Expression to Maintain Unilateral Nodal Activity during Left-Right Axis Specification in Zebrafish
Leprosy is a disease of skin and peripheral nerves . The process of nerve injury occurs gradually through the course of the disease as well as acutely in association with reactions . The INFIR ( ILEP Nerve Function Impairment and Reactions ) Cohort was established to identify clinically relevant neurological and immuno...	Leprosy is a disease of skin and peripheral nerves . The skin changes aid early detection and diagnosis , while the nerve damage leads to progressive impairment and disability . The aim of this study was to identify new risk factors at diagnosis and during follow-up that would predict which patients would develop nerve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunity", "to", "infections", "neurological", "disorders" ]	2009	Predicting Neuropathy and Reactions in Leprosy at Diagnosis and Before Incident Events—Results from the INFIR Cohort Study
Podoconiosis , affects lower limb , is an entirely preventable non-communicable tropical disease common in low income countries . Globally it is estimated that there are 4 million peoples with podoconiosis and nationally it is estimated that there are 1 . 56 million cases of podoconiosis . Even though nationwide mappin...	Podoconiosis ( endemic non-filarial elephantiasis ) is one of a disabling and stigmatizing neglected tropical disease ( NTD ) which affects the lower limb found mostly in low income countries . Even though there were mostly prevalence studies and disease mapping , there was no report , especially on factors associated ...	[ "Abstract", "Introduction", "Methods", "and", "materials", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "legs", "feet", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "filariasis", "signs", "and", "symptoms", "neglected", "tropical", "diseases", "ethiopia"...	2019	Community based cross sectional study of podoconiosis and associated factors in Dano district, Central Ethiopia
Epstein-Barr virus ( EBV ) infection causes B cell lymphomas in humanized mouse models and contributes to a variety of different types of human lymphomas . T cells directed against viral antigens play a critical role in controlling EBV infection , and EBV-positive lymphomas are particularly common in immunocompromised ...	EBV is a human herpesvirus that remains in the host for life , but is normally well controlled by the host immune response . Nevertheless , EBV causes lymphomas in certain individuals , particularly when T cell function is impaired . Antibodies against two different inhibitory receptors on T cells , PD-1 and CTLA-4 , h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "cancer", "treatment", "immunology", "cancers", "and", "neoplasms", "oncology", "hematologic", "cancers", "and", "related", "disorders", "animal", "models", "model", "org...	2016	PD-1/CTLA-4 Blockade Inhibits Epstein-Barr Virus-Induced Lymphoma Growth in a Cord Blood Humanized-Mouse Model
Virulent Agrobacterium tumefaciens strains integrate their T-DNA into the plant genome where the encoded agrobacterial oncogenes are expressed and cause crown gall disease . Essential for crown gall development are IaaH ( indole-3-acetamide hydrolase ) , IaaM ( tryptophan monooxygenase ) and Ipt ( isopentenyl transfera...	Crown gall development requires the expression of agrobacterial genes in the plant host . These genes are transferred by the T-DNA of the plant pathogen Agrobacterium tumefaciens and include the oncogenes IaaH , IaaM and Ipt , which , according to the tumor-inducing principle , are essential for crown gall development ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Regulation of Oncogene Expression in T-DNA-Transformed Host Plant Cells
Entamoeba histolytica is an intestinal protozoan parasite that causes amoebiasis , including amebic dysentery and liver abscesses . E . histolytica invades host tissues by adhering onto cells and phagocytosing them depending on the adaptation and expression of pathogenic factors , including Gal/GalNAc lectin . We have ...	Amebiasis , a neglected tropical disease caused by the protozoan parasite Entamoeba histolytica , is the second leading cause of death from protozoan diseases . Vaccination is considered as an effective strategy against amebiasis; however , clinical vaccines have yet to be developed . We previously reported that the in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "innate", "immune", "system", "immune", "physiology", "cytokines", "enzyme-linked", "immunoassays", "complement", "system", "spleen", "immunology", "vertebrates", "animals", "mammals", "parasit...	2016	Evaluation of the C-Terminal Fragment of Entamoeba histolytica Gal/GalNAc Lectin Intermediate Subunit as a Vaccine Candidate against Amebic Liver Abscess
Cell death plays a major role during C . elegans oogenesis , where over half of the oogenic germ cells die in a process termed physiological apoptosis . How germ cells are selected for physiological apoptosis , or instead become oocytes , is not understood . Most oocytes produce viable embryos when apoptosis is blocked...	Many germ cells die by apoptosis during the development of animal oocytes , including more than half of all germ cells in the model system C . elegans . How individual germ cells are selected for apoptosis , or survival , is not known . Here we study the cell biology of apoptosis . The C . elegans gonad is a syncytium ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "caenorhabditis", "cell", "processes", "animals", "germ", "cells", "animal", "models", "caenorhabditis", "elegans", "oocytes", "model", "organisms", "experimen...	2018	Binucleate germ cells in Caenorhabditis elegans are removed by physiological apoptosis
In numerous species , the formation of meiotic crossovers is largely under the control of a group of proteins known as ZMM . Here , we identified a new ZMM protein , HEI10 , a RING finger-containing protein that is well conserved among species . We show that HEI10 is structurally and functionally related to the yeast Z...	During meiosis two successive chromosomal divisions follow a single S phase , resulting in the formation of four haploid cells , each with half of the parental genetic material . This ploidy reduction occurs during the first meiotic division , when homologous chromosomes ( paternal and maternal ) are separated from eac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "molecular", "cell", "biology", "cell", "biology", "chromosome", "biology", "genetics", "plant", "genetics", "biology", "genetics", "and", "genomics", "gene", "function" ]	2012	The Arabidopsis HEI10 Is a New ZMM Protein Related to Zip3
The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution . Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new , promiscuous activity is often accompanied by only a mild reduction of t...	Understanding how enzymes evolve is a fundamental question that can help us decipher not only the mechanisms of evolution on a higher level , i . e . , whole organisms , but also advances our knowledge of sequence-structure-function relationships as a guide to artificial evolution in the test tube . An important yet un...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "enzymes", "enzymology", "epistasis", "mutation", "substitution", "mutation", "proteins", "molecular", "evolution", "chemistry", "evolutionary", "genetics", "biochemistry", "point", "mutation", "hydrolysis", "heredity", "genetics", "biology", "and", ...	2016	Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity
Post-transcriptional control is nowadays considered a main checking point for correct gene regulation during development , and RNA binding proteins actively participate in this process . Arabidopsis thaliana FLOWERING LOCUS WITH KH DOMAINS ( FLK ) and PEPPER ( PEP ) genes encode RNA-binding proteins that contain three ...	Unlike animals , angiosperms ( flowering plants ) lack a germline that is set-aside early in embryo development . Contrariwise , reproductive success relies on the formation of flowers during adult life , which provide the germ cells and the means for fertilization . Therefore , timing of flowering and flower organ mor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	K-homology Nuclear Ribonucleoproteins Regulate Floral Organ Identity and Determinacy in Arabidopsis
Kaposi's sarcoma herpesvirus ( KSHV ) encodes a cluster of twelve micro ( mi ) RNAs , which are abundantly expressed during both latent and lytic infection . Previous studies reported that KSHV is able to inhibit apoptosis during latent infection; we thus tested the involvement of viral miRNAs in this process . We foun...	MiRNAs are small , non-coding RNAs that regulate gene expression post-transcriptionally via binding to complementary sites in target mRNAs . This evolutionary conserved regulatory system is present in most eukaryotes , and it has recently been shown that certain viruses have evolved to express their own miRNAs . Due to...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "cell", "death", "rna", "interference", "viruses", "and", "cancer", "microbiology", "host-pathogen", "interaction", "gene", "expression", "biology", "molecular", "biology", "rna", "cell", "biology", "nucleic", "acids", "virology", "molecular", "cell", "biology" ]	2011	Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis
Of the over 250 Aspergillus species , Aspergillus fumigatus accounts for up to 80% of invasive human infections . A . fumigatus produces galactosaminogalactan ( GAG ) , an exopolysaccharide composed of galactose and N-acetyl-galactosamine ( GalNAc ) that mediates adherence and is required for full virulence . Less path...	The ubiquitous mold A . fumigatus is isolated in over 80% of all patients with invasive aspergillosis ( IA ) . A . nidulans is a relatively non-pathogenic species that rarely causes IA except in patients with chronic granulomatous disease ( CGD ) , a hereditary disease characterized by impaired neutrophil function due ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Fungal Exopolysaccharide Galactosaminogalactan Mediates Virulence by Enhancing Resistance to Neutrophil Extracellular Traps
West Nile virus ( WNV ) is transmitted to vertebrate hosts by mosquitoes as they take a blood meal . The amount of WNV inoculated by mosquitoes as they feed on a live host is not known . Previous estimates of the amount of WNV inoculated by mosquitoes ( 101 . 2–104 . 3 PFU ) were based on in vitro assays that do not al...	Since it was first introduced into the United States in 1999 , West Nile virus ( WNV ) has caused significant disease in humans , horses , and other animals . WNV is transmitted to humans and other vertebrate hosts by female mosquitoes as they take a blood meal . Currently , the amount of virus inoculated by mosquitoes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "infectious", "diseases", "public", "health", "and", "epidemiology", "virology", "mus", "(mouse)", "insects" ]	2007	Mosquitoes Inoculate High Doses of West Nile Virus as They Probe and Feed on Live Hosts
An estimated 60 , 000 people die of rabies annually . The vast majority of cases of human rabies develop following a bite from an infected dog . Rabies can be controlled in both human and canine populations through widespread vaccination of dogs . Rabies is particularly problematic in Malawi , costing the country an es...	Rabies is a devastating disease that is estimated to result in the death of approximately 60 , 000 people every year . Most humans contract rabies following a bite from an infected dog and it has been demonstrated that provided a large enough proportion of the dog population is vaccinated; rabies incidence can be marke...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "social", "sciences", "malawi", "dogs", "animals", "mammals", "cell", "phones", "vaccines", "preventive", "medi...	2016	The Vaccination of 35,000 Dogs in 20 Working Days Using Combined Static Point and Door-to-Door Methods in Blantyre, Malawi
Cholera infection continues to be a threat to global public health . The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century . Thirty-eight V . cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characteri...	Vibrio cholerae is a diarrheal pathogen that is responsible for substantial morbidity and mortality worldwide . Historically , seven pandemics of cholera have been recognized , with classical biotype strains associated with the sixth and the El Tor biotype with the seventh ( current ) pandemic . Recently multi-drug res...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "genomics", "computational", "biology" ]	2014	The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India
Chronic infections with human viruses , such as HIV and HCV , or mouse viruses , such as LCMV or Friend Virus ( FV ) , result in functional exhaustion of CD8+ T cells . Two main mechanisms have been described that mediate this exhaustion: expression of inhibitory receptors on CD8+ T cells and expansion of regulatory T ...	A loss of function , the so-called ‘exhaustion’ of CD8+ T cells , is a hallmark of many chronic infections . The T cell exhaustion is mediated by two main mechanisms , the expression of inhibitory receptors on CD8+ T cells and virus-induced expansion of regulatory T cells ( Tregs ) , which suppress CD8+ T cell activity...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2013	Combining Regulatory T Cell Depletion and Inhibitory Receptor Blockade Improves Reactivation of Exhausted Virus-Specific CD8+ T Cells and Efficiently Reduces Chronic Retroviral Loads
At least 25 inherited disorders in humans result from microsatellite repeat expansion . Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however , cis-elements and trans-factors regulating the instability process remain undefined . Genomic fragments from the human...	The human genome contains many repetitive sequences . In 1991 , we discovered that excessive lengthening of a three-nucleotide ( trinucleotide ) repeat sequence could cause a human genetic disease . We now know that this unique type of genetic mutation , known as a “repeat expansion , ” occurs in at least 25 different ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/epigenetics", "neurological", "disorders/neurogenetics", "genetics", "and", "genomics/medical", "genetics" ]	2008	CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination
Standard treatment of cutaneous leishmaniasis ( CL ) in Suriname entails three injections of pentamidine isethionate ( PI ) 4 mg/kg per injection in 7 days ( 7 day regimen ) . Compliance to treatment is low and may contribute to increasing therapy failure . A 3 day regimen , including 2 injections of 7 mg/kg in 3 days ...	Cutaneous Leishmaniasis ( CL ) , caused by the single cellular protozoan parasite of the genus Leishmania , is treated in Suriname with pentamidine isethionate ( PI ) . Standard treatment consists of 3 intramuscular injections of 4 mg per kg bodyweight given in 7 days . Compliance to treatment is low which may lead to ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Randomized Single-Blinded Non-inferiority Trial Of 7 mg/kg Pentamidine Isethionate Versus 4 mg/kg Pentamidine Isethionate for Cutaneous Leishmaniaisis in Suriname
Cell division in Escherichia coli starts with assembly of FtsZ protofilaments into a ring-like structure , the Z-ring . Positioning of the Z-ring at midcell is thought to be coordinated by two regulatory systems , nucleoid occlusion and the Min system . In E . coli , nucleoid occlusion is mediated by the SlmA proteins ...	Cell division in Escherichia coli begins with the assembly of FtsZ proteins into a ring-like structure , the Z-ring . Remarkably , the Z-ring localizes with very high precision at midcell . Currently , two molecular systems , nucleoid occlusion and the Min system , are known to localize the Z-ring . Here , we explore w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "complexes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "escherichia", "coli", "prokaryotic", "models", "model", "organisms", "cytokinesis", "bacterial", "pathogens", "research", "and", "analysis", "methods", "medical",...	2014	Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in Escherichia coli
The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year , causing up to a third of all AIDS-related deaths . Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied , yet increasingly impo...	Cryptococcus neoformans is a species complex of often highly pathogenic fungi that cause significant disease in humans . Cryptococcus is notable in the degree that virulence differs amongst genotypes , and highly-virulent emerging lineages are changing patterns of disease in time and space . Cryptococcus neoformans var...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "molecular", "biology", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2011	Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin
It is now clearly established that the transfusion of blood from variant CJD ( v-CJD ) infected individuals can transmit the disease . Since the number of asymptomatic infected donors remains unresolved , inter-individual v-CJD transmission through blood and blood derived products is a major public health concern . Cur...	In the UK , several v-CJD cases have been identified in patients that received blood or blood-derived products prepared from incubating asymptomatic donors . Since there is no screening test to identify infected donors , procedural risk reduction measures remain the only protection against v-CJD transfusion risk . Thes...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "prion", "diseases" ]	2012	Highly Efficient Prion Transmission by Blood Transfusion
A five-year citywide control program based on regular application of temephos significantly reduced Aedes aegypti larval indices but failed to maintain them below target levels in Clorinda , northern Argentina . Incomplete surveillance coverage and reduced residuality of temephos were held as the main putative causes l...	Dengue is currently the most important viral disease of humans transmitted by arthropods worldwide . Aedes aegypti , a human-biting mosquito dwelling in artificial domestic containers , is the main vector of dengue . Ae . aegypti larval control programs are frequently based on the application of the insecticide temepho...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/social", ...	2011	Water Use Practices Limit the Effectiveness of a Temephos-Based Aedes aegypti Larval Control Program in Northern Argentina
Until recently , the Chagas disease vector , Triatoma infestans , was widespread in Arequipa , Perú , but as a result of a decades-long campaign in which over 70 , 000 houses were treated with insecticides , infestation prevalence is now greatly reduced . To monitor for T . infestans resurgence , the city is currently ...	Chagas disease is a serious infection that is spread by blood-sucking insects called ‘kissing bugs . ’ These bugs live in and around human homes , and until recently , they infested thousands of human homes throughout Arequipa , the second largest city in Perú . However , a decades-long control campaign drastically red...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "neuroscience", "cognitive", "psychology", "cognition", "neglected", "tropical", "diseases", "infectious", "disease", "control", "informat...	2018	Integrating evidence, models and maps to enhance Chagas disease vector surveillance
Mating and gametogenesis are two essential components of animal reproduction . Gametogenesis must be modulated by the need for gametes , yet little is known of how mating , a process that utilizes gametes , may modulate the process of gametogenesis . Here , we report that mating stimulates female germline stem cell ( G...	In many animals , gametogenesis is supported by germline stem cells ( GSCs ) . Since GSCs are the fundamental cell population for successful reproduction , how such special GSCs are precisely proliferated is a long-standing question in biology . In the fruit fly Drosophila melanogaster , it is known that gametogenesis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "rna", "interference", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "stem", "cells", "membrane", "receptor", "signaling", "hormone", ...	2016	Mating-Induced Increase in Germline Stem Cells via the Neuroendocrine System in Female Drosophila
We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections . We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence . Comprehensive analysis of mixed RNA pop...	To establish infection and colonize within a host , infecting pathogens have to cope with a variety of destructive surroundings . The food-borne pathogen Y . pseudotuberculosis can cause persistent infection in mice . Upon infection , Y . pseudotuberculosis passes the anti-microbial gastrointestinal milieu and finally ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis
Typhoid fever is endemic across sub-Saharan Africa . However , estimates of the burden of typhoid are undermined by insufficient blood volumes and lack of sensitivity of blood culture . Here , we aimed to address this limitation by exploiting pre-enrichment culture followed by PCR , alongside routine blood culture to i...	There are increasing reports of typhoid fever epidemics in sub-Saharan Africa frequently affecting young adults and children aged between 5 and 16 years . In Asia where typhoid is hyperendemic , children aged 0 to 4 years also have a high burden of typhoid fever . Diagnosis of typhoid in young children is particularly ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "salmonella", "typhi", "health", "care", "organisms", "bacterial", "diseases", "signs", "and", "symptoms", "enterobacteriaceae", "conval...	2019	Ascertaining the burden of invasive Salmonella disease in hospitalised febrile children aged under four years in Blantyre, Malawi
Transitions at CpG dinucleotides , referred to as “CpG substitutions” , are a major mutational input into vertebrate genomes and a leading cause of human genetic disease . The prevalence of CpG substitutions is due to their mutational origin , which is dependent on DNA methylation . In comparison , other single nucleot...	Mutations are raw materials of evolution . Earlier studies have shown that mutations occur at different frequencies in different genomic regions . By investigating the patterns and causes of such “regional” variation of mutations , we can better understand the mechanisms of underlying mutagenesis . In the human and oth...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "analysis", "evolutionary", "biology/genomics", "genetics",...	2008	Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation
There is a need for sensitive and specific rapid diagnostic tests ( RDT ) for canine visceral leishmaniasis . The aims of this study were to evaluate the diagnostic performance of immunochromatographic dipstick RDTs using rK39 antigen for canine visceral leishmaniasis by ( i ) investigating the sensitivity of RDTs to d...	Canine visceral leishmaniasis is a vector-borne disease caused by the intracellular parasite Leishmania infantum . It is an important veterinary disease , and dogs are also the main animal reservoir for human infection . The disease is widespread in the Mediterranean area , and parts of Asia and South and Central Ameri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "veterinary", "diseases", "diagnostic", "medicine", "veterinary", "parasitology", "veterinary", "diagnostics", "leishmaniasis", "neglected", "tropical", "diseases", "quantitative", "parasitology", "veterinary", "scie...	2013	Evaluation of rK39 Rapid Diagnostic Tests for Canine Visceral Leishmaniasis: Longitudinal Study and Meta-Analysis
Most organisms use 24-hr circadian clocks to keep temporal order and anticipate daily environmental changes . In Drosophila melanogaster CLOCK ( CLK ) and CYCLE ( CYC ) initiates the circadian system by promoting rhythmic transcription of hundreds of genes . However , it is still not clear whether high amplitude transc...	Circadian clocks allow organisms to predict daily environmental changes . These clocks time the sleep/wake cycles and many other physiological and cellular pathways to 24hs rhythms . The current model states that circadian clocks keep time by the use of biochemical feedback loops . These feedback loops are responsible ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "molecular", "neuroscience", "neuroscience", "animals", "dna", "transcription", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "drosophila", "research", "and", "analysis", "methods", "gene", "expression", "insects", "arthropoda", ...	2014	Synergistic Interactions between the Molecular and Neuronal Circadian Networks Drive Robust Behavioral Circadian Rhythms in Drosophila melanogaster
Little is currently known about bacterial pathogen evolution and adaptation within the host during acute infection . Previous studies of Burkholderia pseudomallei , the etiologic agent of melioidosis , have shown that this opportunistic pathogen mutates rapidly both in vitro and in vivo at tandemly repeated loci , maki...	While both viral and bacterial pathogens have been shown to undergo genetic changes over the course of a chronic infection , this phenomenon has not been studied during an acute infection and as such is not well understood . Here , we examined within-host evolution of the pathogen Burkholderia pseudomallei during acute...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/microbial", "evolution", "and", "genomics" ]	2010	Within-Host Evolution of Burkholderia pseudomallei in Four Cases of Acute Melioidosis
The biofilm matrix , composed of exopolysaccharides , proteins , nucleic acids and lipids , plays a well-known role as a defence structure , protecting bacteria from the host immune system and antimicrobial therapy . However , little is known about its responsibility in the interaction of biofilm cells with host tissue...	Staphylococcus aureus is a pathogen responsible for a wide variety of infections , some of which become chronic due to the capacity of this bacteria to form multicellular communities that grow embedded in a self-produced extracellular matrix , referred to as biofilms . Numerous evidences have demonstrated that growing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "bacterial", "biofilms", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction" ]	2012	Bap, a Biofilm Matrix Protein of Staphylococcus aureus Prevents Cellular Internalization through Binding to GP96 Host Receptor
Maintaining balanced growth in a changing environment is a fundamental systems-level challenge for cellular physiology , particularly in microorganisms . While the complete set of regulatory and functional pathways supporting growth and cellular proliferation are not yet known , portions of them are well understood . I...	A major challenge for living organisms is the regulation of cellular growth in a fluctuating environment . Sudden changes in nutrient availability or the presence of stress factors typically require rapid adjustments of cellular growth . The misregulation of growth control in higher organisms is a major factor in the d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/cell", "growth", "and", "division", "computational", "biology/genomics", "mathematics/statistics", "cell", "biology/gene", "expression" ]	2009	Predicting Cellular Growth from Gene Expression Signatures
We report on atomistic simulation of the folding of a natively-knotted protein , MJ0366 , based on a realistic force field . To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology . By using the d...	It has been recently observed that the native structure of proteins can contain knots . These are formed during the folding process and are tightened in a specific ( i . e . native ) location , along the poly-peptide chain . The existence of knots hence implies a high degree coordination of local and global conformatio...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "physics", "protein", "folding", "biophysics", "theory", "biophysics" ]	2013	Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
DNA replication is a key process in living organisms . DNA polymerase α ( Polα ) initiates strand synthesis , which is performed by Polε and Polδ in leading and lagging strands , respectively . Whereas loss of DNA polymerase activity is incompatible with life , viable mutants of Polα and Polε were isolated , allowing t...	Three DNA polymerases replicate DNA in Eukaryotes . DNA polymerase α ( Polα ) initiates strand synthesis , which is performed by Polε and Polδ in leading and lagging strands , respectively . Not only the information encoded in the DNA , but also the inheritance of chromatin states is essential during development . Loss...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Arabidopsis DNA Polymerase δ Has a Role in the Deposition of Transcriptionally Active Epigenetic Marks, Development and Flowering
The neuronal mechanisms underlying the emergence of orientation selectivity in the primary visual cortex of mammals are still elusive . In rodents , visual neurons show highly selective responses to oriented stimuli , but neighboring neurons do not necessarily have similar preferences . Instead of a smooth map , one ob...	It is not yet fully clear how sensory information is being processed when it arrives in primary cortical areas . We studied this general question in the context of rodent vision . We focused on the example of orientation selectivity , namely the selectivity of cortical neurons for specific orientations of an elongated ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "visual", "system", "computational", "neuroscience", "biology", "and", "life", "sciences", "sensory", "systems", "computational", "biology", "neuroscience", "neuronal", "tuning", "coding", "mechanisms" ]	2015	Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics
Plants use the energy in sunlight for photosynthesis , but as a consequence are exposed to the toxic effect of UV radiation especially on DNA . The UV-induced lesions on DNA affect both transcription and replication and can also have mutagenic consequences . Here we investigated the regulation and the function of the r...	Recent research revealed strong links between Cullin4 ( CUL4 ) –based cullin-RING ubiquitin ligases ( CRLs ) and chromatin biology , including DNA replication and DNA repair . During Nucleotide Excision Repair ( NER ) , CUL4 together with DDB1 ( DNA Damage Binding protein 1 ) ubiquitylate an increasingly large number o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "genetics", "and", "gene", "expression", "molecular", "biology/dna", "repair", "cell", "biology/cell", "signaling" ]	2008	Regulation and Role of Arabidopsis CUL4-DDB1A-DDB2 in Maintaining Genome Integrity upon UV Stress
Grid cells in the entorhinal cortex encode the position of an animal in its environment with spatially periodic tuning curves with different periodicities . Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing . Here we develop a theory for efficient c...	Grid cells encode a mammal’s estimate of position by firing in multiple locations . These locations are arranged on the vertices of a triangular lattice . Lattices vary in spacing and therefore represent position over different spatial scales . We suggest that grid cells encode position while taking into account the sp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "brain", "electrophysiology", "mathematical", "models", "neuroscience", "optimization", "mathematics", "computational", "neuroscience", "neuronal", "tuning", "coding", "mechanisms", "r...	2017	An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules
ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy , positioning , and composition . In vitro , Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30–85 bp of extranucleosomal DNA to reposition nucleosomes , but linker DNA in S . cerevisiae averages <20 bp . To addre...	Eukaryotic genomes are compacted into chromatin , which restricts access to DNA . In order for cells to transcribe , replicate , and repair DNA , chromatin structure must be altered . Eukaryotes have evolved chromatin remodeling enzymes that use energy derived from ATP hydrolysis to modulate chromatin structure . In vi...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "chromosome", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "genomics", "yeast", "and", "fungal", "models", "saccharomyces", "cerevisiae", "chromatin", "genetics", "and", "genomics", "microbiology", "dna", "transcription" ]	2013	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
Pneumonic plague is the most rapid and lethal form of Yersinia pestis infection . Increasing evidence suggests that Y . pestis employs multiple levels of innate immune evasion and/or suppression to produce an early “pre-inflammatory” phase of pulmonary infection , after which the disease is highly inflammatory in the l...	Inhalation of respiratory droplets containing Yersinia pestis results in a rapidly developing and lethal pneumonia . Interestingly , early interactions between Y . pestis and host cells in the lung contribute to significant immune evasion , but also ultimately result in severe innate immune activation . Our results dem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Yersinia pestis Activates Both IL-1β and IL-1 Receptor Antagonist to Modulate Lung Inflammation during Pneumonic Plague
Early detection of cancer-associated genomic instability is crucial , particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis . Currently used methods require the presence of already established neoplastic cells because they only detect clonal mutations . I...	In hereditary non-polyposis colorectal cancer ( HNPCC ) , a germline mutation in one allele of a gene responsible for repairing DNA damage predisposes the host to cancer , because subsequent somatic inactivation of the one wild-type allele leads to genomic instability that favours tumourigenesis . Nonneoplastic tissues...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology/gastrointestinal", "cancers", "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/comparative", "genomics", "molecular", "biology/dna", "repair" ]	2010	Ultradeep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability
Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission . However , they are currently excluded from control programmes . Molecular phylogenetic studies have provided insights into the evolutionary origins and transmis...	Many pre-school children in sub-Saharan Africa are infected with the parasite Schistosoma mansoni , which causes intestinal schistosomiasis . However , there has been no work published on the molecular epidemiology of Schistosoma in children under six or the role that these children play in parasite transmission . We a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers
In oral squamous cell carcinoma ( OSCC ) , metastasis to lymph nodes is associated with a 50% reduction in 5-year survival . To identify a metastatic gene set based on DNA copy number abnormalities ( CNAs ) of differentially expressed genes , we compared DNA and RNA of OSCC cells laser-microdissected from non-metastati...	Neck lymph node metastasis is the most important prognostic factor in oral squamous cell carcinoma ( OSCC ) . To identify genes associated with this critical step of OSCC progression , we compared DNA copy number aberrations and gene expression differences between tumor cells found in metastatic lymph nodes versus thos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "functional", "genomics", "molecular", "cell", "biology", "metastasis", "dna", "modification", "basic", "cancer", "research", "gene", "expression", "biology", "genomics", "molecular", "biology", "genetics", "and", "genomics" ]	2013	Integrative Genomics in Combination with RNA Interference Identifies Prognostic and Functionally Relevant Gene Targets for Oral Squamous Cell Carcinoma
Plants constantly adjust their growth , development and metabolism to the ambient light environment . Blue light is sensed by the Arabidopsis photoreceptors CRY1 and CRY2 which subsequently initiate light signal transduction by repressing the COP1/SPA E3 ubiquitin ligase . While the interaction between cryptochromes an...	Plants sense ambient light conditions through several photoreceptors that induce a complex signaling cascade to vastly alter gene expression , growth and development . Blue light activates two cryptochrome photoreceptors which subsequently inactivate an E3 ubiquitin ligase consisting of COP1 and SPA proteins . While CO...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "yeast", "two-hybrid", "assays", "protein", "interactions", "social", "sciences", "neuroscience", "fungi", "protein", "interaction", "assays", "immunoprecipitation", "seedlings", "co-immunoprecipitation", "molecular", "biology", "techniques", "plants", "res...	2017	The blue light-induced interaction of cryptochrome 1 with COP1 requires SPA proteins during Arabidopsis light signaling
Prions arise when the cellular prion protein ( PrPC ) undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrPSc . Frequently , PrPSc is protease-resistant but protease-sensitive ( s ) prions have been isolated in humans and other animals . We report here that protease-se...	Prions are infectious proteins that cause heritable , sporadic , and transmissible diseases in humans and other mammals . These infectious proteins arise when the normal form of the prion protein ( PrP ) adopts a self-perpetuating conformation . This disease-causing PrP form is frequently distinguished from normal PrP ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/prion", "diseases" ]	2010	Protease-Sensitive Synthetic Prions
Emerging and re-emerging arthropod-borne viruses ( arboviruses ) cause human and animal disease globally . Field and laboratory investigation of mosquito-borne arboviruses requires analysis of mosquito samples , either individually , in pools , or a body component , or secretion such as saliva . We assessed the applica...	Testing for the presence of arboviruses in mosquitoes used in laboratory experiments or surveillance usually involves collecting samples , from pools of hundreds of mosquitoes to the legs and wings of an individual mosquito and testing them by different methods . These methods can be labour intensive and costly and req...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "laboratory", "equipment", "engineering", "and", "technology", "pathogens", ...	2018	Mosquito excreta: A sample type with many potential applications for the investigation of Ross River virus and West Nile virus ecology
Urogenital schistosomiasis is a tropical disease infecting more than 100 million people in sub-Saharan Africa . Individuals in endemic areas endure repeated infections with long-lived schistosome worms , and also encounter larval and egg stages of the life cycle . Protective immunity against infection develops slowly w...	Urogenital schistosomiasis is a tropical infectious disease caused by schistosome blood flukes , infecting more than 100 million people in sub-Saharan Africa . Protective immunity develops against schistosomes , but takes many years to do so , with children acquiring multiple infections with long-lived parasites . It i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "immunity", "to", "infections", "immunology", "parasitic", "diseases", "mathematics", "infectious", "diseases", "epidemiology", "biology", "infectious", ...	2011	Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis
Retinal ganglion cells are commonly classified as On-center or Off-center depending on whether they are excited predominantly by brightening or dimming within the receptive field . Here we report that many ganglion cells in the salamander retina can switch from one response type to the other , depending on stimulus eve...	The eye communicates to the brain all the information needed for vision in the form of electrical pulses , or spikes , on optic nerve fibers . These spikes are produced by retinal ganglion cells , the output neurons of the retina . In a popular view of retinal function , each ganglion cell responds to a small region of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "vertebrates", "neuroscience", "animals" ]	2007	Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On
Understanding the cell-specific binding patterns of transcription factors ( TFs ) is fundamental to studying gene regulatory networks in biological systems , for which ChIP-seq not only provides valuable data but is also considered as the gold standard . Despite tremendous efforts from the scientific community to condu...	Transcription factors play a central role in regulating various cellular processes . They bind to DNA in a cell-specific way . To study where a TF would bind to DNA , ChIP-seq experiment has been developed and widely adopted by the science community to study genome-wide in vivo protein-DNA interactions . However , for ...	[ "Abstract", "Introduction", "Models", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "chemical", "characterization", "neural", "networks", "nucleases", "engineering", "and", "technology", "deoxyribonucleases", "enzymes", "signal", "processing", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins"...	2017	Imputation for transcription factor binding predictions based on deep learning
Intrinsically disordered regions have been associated with various cellular processes and are implicated in several human diseases , but their exact roles remain unclear . We previously defined two classes of conserved disordered regions in budding yeast , referred to as “flexible” and “constrained” conserved disorder ...	A protein's cellular and molecular function is typically determined by its folded structure . However , a large fraction of proteomes lack stably folded structure . These regions are referred to as intrinsically disordered . Protein disorder has largely been understudied , although it is emerging to have numerous impor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "systems", "biology", "genome", "expression", "analysis", "genomics", "protein", "interactions", "proteins", "biology", "computational", "biology", "structural", "genomics" ]	2013	Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
A priority for biomedical research is to understand the causes of variation in susceptibility to infection . To investigate genetic variation in a model system , we used flies collected from single populations of three different species of Drosophila and artificially selected them for resistance to the parasitoid wasp ...	We have found that three species of fruit fly evolve resistance to parasitic wasps ( parasitoids ) by increasing investment in their immune defences but they achieve this in different ways . Resistance always involved increases in the number of the circulating hemocytes , which are the blood cells that kill parasitoids...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "immune", "cells", "parasite", "evolution", "immunology", "parasitic", "diseases", "animals", "parasitology", "animal", "models", "developmental", ...	2017	Parallel and costly changes to cellular immunity underlie the evolution of parasitoid resistance in three Drosophila species
The tails of histone proteins are central players for all chromatin-mediated processes . Whereas the N-terminal histone tails have been studied extensively , little is known about the function of the H2A C-terminus . Here , we show that the H2A C-terminal tail plays a pivotal role in regulating chromatin structure and ...	Histones are the main protein components of chromatin . The N-terminal tails of histones stick out from the nucleosomes , the building blocks of chromatin , and are involved in the regulation of all DNA–dependent processes . Only Histone H2A has an additional C-terminal tail and currently very little is known about the...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "biochemistry", "molecular", "biology/chromatin", "structure" ]	2010	Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
Toxoplasma gondii establishes a chronic infection by forming cysts preferentially in the brain . This chronic infection is one of the most common parasitic infections in humans and can be reactivated to develop life-threatening toxoplasmic encephalitis in immunocompromised patients . Host-pathogen interactions during t...	A large portion of people worldwide are chronically infected with T . gondii . Chronic infection with this parasite is characterized by formation of tissue cysts . Bradyzoites slowly replicate within cysts during the chronic stage of infection leading to a corresponding increase in cyst size . Cysts occasionally ruptur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection
Stem cells are crucial in morphogenesis in plants and animals . Much is known about the mechanisms that maintain stem cell fates or trigger their terminal differentiation . However , little is known about how developmental time impacts stem cell fates . Using Arabidopsis floral stem cells as a model , we show that stem...	Stem cells have the capacity to self renew while producing daughter cells that undergo differentiation . While some stem cells remain as stem cells throughout the life of an organism , others are programmed to terminate within developmental contexts . It is presumed that stem cell termination is simply the differentiat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "developmental", "biology/plant", "growth", "and", "development", "developmental", "biology/stem", "cells" ]	2011	ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis
In response to a 2011 cholera outbreak in Papua New Guinea , the Government of the Solomon Islands initiated a cholera prevention program which included cholera disease prevention and treatment messaging , community meetings , and a pre-emptive cholera vaccination campaign targeting 11 , 000 children aged 1–15 years in...	We assessed knowledge , attitudes and practices of diarrhea and cholera disease and prevention in two areas of the Solomon Islands near Papua New Guinea . Both areas were ‘at risk’ for cholera disease and received messages about cholera prevention . Later , one of the areas also received vaccination against cholera . T...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "solomon", "islands", "ecology", "and", "environmental", "sciences", "water", "resources", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "geographical", "locations", "health", "care", "vaccin...	2016	Knowledge, Attitudes, and Practices regarding Diarrhea and Cholera following an Oral Cholera Vaccination Campaign in the Solomon Islands
Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy . However , tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression . We therefore developed a novel ...	Identifying genes that contribute to cancer biology is complicated partly because cancers can have dozens of somatic mutations and thousands of germline variants . Somatic mutations are gene variants that arise after conception in an organism while germline variants are gene variants present at conception in an organis...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Human immunodeficiency virus ( HIV-1 ) enters cells following sequential activation of the high-potential-energy viral envelope glycoprotein trimer by target cell CD4 and coreceptor . HIV-1 variants differ in their requirements for CD4; viruses that can infect coreceptor-expressing cells that lack CD4 have been generat...	Human immunodeficiency virus ( HIV-1 ) , the cause of acquired immunodeficiency syndrome ( AIDS ) , enters cells by attaching its major surface component , the envelope glycoprotein spike , to a receptor protein on the target cell called CD4 . This attachment promotes cell entry by allowing the envelope protein to bind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "humoral", "immunity", "immunity", "to", "infections", "immunology", "microbiology", "viral", "structure", "immunodeficiency", "viruses", "mechanisms", "of", "resistance", "and", "susceptibility", "viral", "immune", "evasion", "bio...	2011	Contribution of Intrinsic Reactivity of the HIV-1 Envelope Glycoproteins to CD4-Independent Infection and Global Inhibitor Sensitivity
Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation . We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C . elegans . In this organism , the dosage compensation complex ...	DNA isolated from the nucleus of a single human cell , if stretched out , would be 3 meters long . This amount of DNA must be packaged into a nucleus , which is orders of magnitude smaller . DNA of active genes tends to be loosely packed and localized internally within the nucleus , while DNA of inactive genes tends to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "chromosome", "structure", "and", "function", "gene", "regulation", "cell", "differentiation", "developmental", "biology", "epigenetics", "sex", "chromosomes", "chromosome", "biology", "genetic", "interference", "gene", "expression", "x", "chromosom...	2016	Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression
Investigating the complex systems dynamics of the aging process requires integration of a broad range of cellular processes describing damage and functional decline co-existing with adaptive and protective regulatory mechanisms . We evolve an integrated generic cell network to represent the connectivity of key cellular...	The global process of aging disturbs a broad range of cellular mechanisms in a complex fashion and is not well understood . One important goal of computational approaches in aging is to develop integrated models in terms of a unifying aging theory , predicting progression of aging phenotypes grounded on molecular mecha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "computational", "biology", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2010	Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses
Schistosoma haematobium and Schistosoma mansoni are blood flukes that cause urogenital and intestinal schistosomiasis , respectively . In Côte d′Ivoire , both species are endemic and control efforts are being scaled up . Accurate knowledge of the geographical distribution , including delineation of high-risk areas , is...	Two types of blood-dwelling parasitic worms that cause schistosomiasis ( i . e . , Schistosoma haematobium and Schistosoma mansoni ) are endemic in Côte d′Ivoire , West Africa . Reliable information on their geographical distribution is needed to plan and guide the national control program . Recently , control efforts ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "medicine", "and", "health", "sciences", "simulation", "and", "modeling", "biology", "and", "life", "sciences", "parasitology", "research", "and", "analysis", "methods" ]	2014	Bayesian Risk Mapping and Model-Based Estimation of Schistosoma haematobium–Schistosoma mansoni Co-distribution in Côte d′Ivoire
Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease . To decipher the mechanism underlying the formation of tau aggregates , we developed a novel approach for constructing models of natively unfolded proteins . The method , energy-minima mapping and ...	Alzheimer's disease pathology is characterized by two types of protein aggregates that are found in the brain—amyloid plaques and neurofibrillary tangles . Several studies suggest that these aggregates also play an active role in the disease process . Thus , an understanding of disease pathogenesis may be facilitated b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/protein", "folding" ]	2008	The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau
Efforts are underway to eliminate trachoma as a public health problem by 2020 . Programmatic guidelines are based on clinical signs that correlate poorly with Chlamydia trachomatis ( Ct ) infection in post-treatment and low-endemicity settings . Age-specific seroprevalence of anti Ct Pgp3 antibodies has been proposed a...	Trachoma is caused by the bacterium Chlamydia trachomatis ( Ct ) . Individuals who have previously been infected with Ct carry specific antibodies in their blood . Recent studies have suggested that these antibodies may be a good way to estimate the intensity of transmission of this bacterium in a population . Among pe...	[ "Abstract", "Introduction", "Methods", "and", "Materials", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "immunology", "tropical", "diseases", "geographical", "locations", "uganda", "bacterial", "diseases", "eye", ...	2017	Defining Seropositivity Thresholds for Use in Trachoma Elimination Studies
Blocking neurotransmission , botulinum neurotoxin is the most poisonous biological substance known to mankind . Despite its infamy as the scourge of the food industry , the neurotoxin is increasingly used as a pharmaceutical to treat an expanding range of muscle disorders . Whilst neurotoxin expression by the spore-for...	Botulinum neurotoxin produced by the spore-forming bacterium Clostridium botulinum is the most poisonous biological substance known to mankind . By blocking neurotransmission , the neurotoxin causes a flaccid paralysis called botulism which may to lead to death upon respiratory muscle collapse . Despite its infamy as t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "botulism", "microbial", "pathogens", "biology", "microbiology", "bacterial", "pathogens", "gram", "positive" ]	2013	Two-Component Signal Transduction System CBO0787/CBO0786 Represses Transcription from Botulinum Neurotoxin Promoters in Clostridium botulinum ATCC 3502
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide . One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals . Soils and surface waters also host a high diversity of non-pathogenic...	Leptospirosis which is an emerging zoonotic disease worldwide , is transmitted to humans through contact with soils or surface waters contaminated with the urine of reservoir animals . Species of Leptospira , which include infectious and non-infectious strains , are ubiquitous in the environment . In this study we have...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "bacterial", "diseases", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genome", "ana...	2019	Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
Terrestrial arthropods are commonly infected with maternally inherited bacterial symbionts that cause cytoplasmic incompatibility ( CI ) . In CI , the outcome of crosses between symbiont-infected males and uninfected females is reproductive failure , increasing the relative fitness of infected females and leading to sp...	Many arthropods are infected with bacterial symbionts that are maternally transmitted and have a great impact on their hosts' biology , ecology , and evolution . One of the most common phenotypes of facultative symbionts appears to be cytoplasmic incompatibility ( CI ) , a type of reproductive failure in which bacteria...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genomics", "microbial", "evolution", "biology", "evolutionary", "biology", "comparative", "genomics", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics" ]	2012	Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii
Cells decode information of signaling activation at a scale of tens of minutes by downstream gene expression with a scale of hours to days , leading to cell fate decisions such as cell differentiation . However , no system identification method with such different time scales exists . Here we used compressed sensing te...	The key points of this study are two-fold: The first point is the decoding mechanism for cell differentiation . We previously demonstrated the encoding mechanism of cell fate decision information by transient and sustained ERK activation in PC12 cells , and also identified the decoding genes essential for cell differen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "applied", "mathematics", "neurites", "neuroscience", "cell", "differentiation", "simulation", "and", "modeling", "algorithms", "developmental", "biology", "systems", "science", "mathematics", "signaling", "cascades", "neuronal", "dendrites", "research", "and", "analysis", ...	2017	System identification of signaling dependent gene expression with different time-scale data
The elimination of infectious diseases requires reducing transmission below a certain threshold . The Visceral Leishmaniasis ( VL ) Elimination Initiative in Southeast Asia aims to reduce the annual VL incidence rate below 1 case per 10 , 000 inhabitants in endemic areas by 2015 via a combination of case management and...	Visceral leishmaniasis is suspected to be the second largest parasitic killer in the world after malaria . On the Indian subcontinent , the vector-borne disease is caused by the protozoan flagellate Leishmania donovani and transmitted by the sand fly Phlebotomus argentipes . The regional elimination programme has sugge...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "mathematics", "infectious", "disease", "epidemiology", "epidemiology", "applied", "mathematics", "biology", "and", "life", "sciences", "population", "biology", "physical", "sciences" ]	2014	Model-Based Investigations of Different Vector-Related Intervention Strategies to Eliminate Visceral Leishmaniasis on the Indian Subcontinent
The type III secretion system ( TTSS ) is a key mechanism for host cell interaction used by a variety of bacterial pathogens and symbionts of plants and animals including humans . The TTSS represents a molecular syringe with which the bacteria deliver effector proteins directly into the host cell cytosol . Despite the ...	Many Gram-negative bacteria live closely associated with humans , animals , or plants . The pathogenic or symbiotic interactions between bacteria and host are often mediated by the secretion of bacterial proteins into the host cells . The Type III secretion system ( TTSS ) is one of the best studied cellular machinerie...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "computational", "biology/sequence", "motif", "analysis", "microbiology/microbial", "evolution", "and", "genomics", "molecular", "biology/bioinformatics", "public", "health", "and", "epidemiology/infectious", "diseases", "computational",...	2009	Sequence-Based Prediction of Type III Secreted Proteins
Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease ( IBD ) , and dozens of IBD genetic variants have been identified in genome-wide association studies . However , the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility remains uncle...	In this study , we used observational data to explore associations between host genetics and the commensal microbiome in inflammatory bowel disease cases . Our analysis identified four associations involving two genes and four bacterial taxa and replicated two of these associations in independent cohorts . Then , we de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "microbiome", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "ulcerative", "colitis", "social", "sciences", "colitis", "gastroenterology", "and", "hepatology", "bacterial", "genetics", "i...	2019	Genetic effects on the commensal microbiota in inflammatory bowel disease patients
Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning . We introduce network schemas to elucidate shared mechanisms within interactomes . Network schemas specify descriptions of proteins and the topology of interactions among them . We develop...	Large-scale networks of protein-protein interactions provide a view into the workings of the cell . However , these interaction maps do not come with a key for interpreting them , so it is necessary to develop methods that shed light on their functioning and organization . We propose the language of network schemas for...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science", "computational", "biology/systems", "biology", "computational", "biology/signaling", "networks" ]	2008	Organization of Physical Interactomes as Uncovered by Network Schemas
Epigenetic mechanisms and chromatin structure play an important role in development . Their impact is therefore expected to be strong in parasites with complex life cycles and multiple , strikingly different , developmental stages , i . e . developmental plasticity . Some studies have already described how the chromati...	Schistosoma mansoni is a parasitic flatworm and causative agent of intestinal schistosomiasis , a neglected tropical disease affecting 67 million people worldwide . The parasite has a complex life cycle involving two consecutive obligate hosts ( a poikilotherm snail and a homeotherm mammal ) and two transitions between...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "helminths", "gene", "regulation", "dna-binding", "proteins", "animals", "parasitology", "dna", "transcription", "developmental", "biology", "sporocysts", "epigenetics", "chromatin", "transcriptional", "control", "chro...	2018	Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni
In a developing embryo , the spatial distribution of a signaling molecule , or a morphogen gradient , has been hypothesized to carry positional information to pattern tissues . Recent measurements of morphogen distribution have allowed us to subject this hypothesis to rigorous physical testing . In the early Drosophila...	In the early stages of development , an embryo must establish the beginnings of a body plan in order to grow organs and limbs in the right places . Across the fruit fly embryo , proteins known as morphogens cause chain reactions that eventually lead to the growth of many different body parts . One specific morphogen , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient
Intelligence is our ability to learn appropriate responses to new stimuli and situations . Neurons in association cortex are thought to be essential for this ability . During learning these neurons become tuned to relevant features and start to represent them with persistent activity during memory delays . This learnin...	Working memory is a cornerstone of intelligence . Most , if not all , tasks that one can imagine require some form of working memory . The optimal solution of a working memory task depends on information that was presented in the past , for example choosing the right direction at an intersection based on a road-sign so...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[]	2015	How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks
Leptospirosis is one of the most widespread zoonotic diseases , which is of global medical and veterinary importance , and also a re-emerging infectious disease . The main tracks of transmission are known; however , the relative importance of each of the components and the respective environmental risk factors are uncl...	Leptospirosis is a bacterial disease passed from animals to people—either through direct contact with animals or indirectly via the environment . The disease can be found worldwide but is more important in tropical and subtropical countries . Due to their sheer genetic diversity , virtually all mammals can be infected ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Environmental and Behavioural Determinants of Leptospirosis Transmission: A Systematic Review
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions , symbiosis , virus vectoring , and the developmental causes of extreme phenotypic plasticity . Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum . This first published whole g...	Aphids are common pests of crops and ornamental plants . Facilitated by their ancient association with intracellular symbiotic bacteria that synthesize essential amino acids , aphids feed on phloem ( sap ) . Exploitation of a diversity of long-lived woody and short-lived herbaceous hosts by many aphid species is a resu...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics" ]	2010	Genome Sequence of the Pea Aphid Acyrthosiphon pisum
Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci ( QTLs ) . Many studies have found a large proportion of quantitative trait variation can be attrib...	There has been a great amount of debate over the relative importance of additivity and non-additivity in quantitative trait variation . The main argument supporting the importance of additivity is the observation that the additive component of genetic variance is much greater than non-additive variance components , whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "epistasis", "genetic", "dominance", "genetic", "polymorphism", "quantitative", "trait", "loci", "phenotypes", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "quantitative", "traits", "evolutionary", "biolo...	2016	The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis
The natural infection of sand flies by Leishmania was examined in the Department of Huanuco of Peru , where cutaneous leishmaniasis caused by a hybrid of Leishmania ( Viannia ) braziliensis/L . ( V . ) peruviana is endemic . A total of 2 , 997 female sand flies were captured by CDC light traps and Shannon traps , of wh...	Leishmaniasis is a protozoan disease caused by members of the genus Leishmania , which are distributed worldwide , especially in tropical and subtropical areas . More than 20 species of Leishmania are described as causative agents of human leishmaniases and clinical features are largely associated with the infective sp...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	First Evidence of a Hybrid of Leishmania (Viannia) braziliensis/L. (V.) peruviana DNA Detected from the Phlebotomine Sand Fly Lutzomyia tejadai in Peru
The organization of computations in networks of spiking neurons in the brain is still largely unknown , in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain . In principle there exists a powerful co...	It is well-known that neurons communicate with short electric pulses , called action potentials or spikes . But how can spiking networks implement complex computations ? Attempts to relate spiking network activity to results of deterministic computation steps , like the output bits of a processor in a digital computer ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2011	Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons
Mammalian nuclear receptors broadly influence metabolic fitness and serve as popular targets for developing drugs to treat cardiovascular disease , obesity , and diabetes . However , the molecular mechanisms and regulatory pathways that govern lipid metabolism remain poorly understood . We previously found that the Cae...	Mammalian nuclear receptors are actively targeted for treatment of a range of cardiovascular diseases and obesity . However , effective drug development still depends on a more exhaustive characterization of how different nuclear receptors mediate their different physiological effects in vivo . Taking advantage of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Coordinate Regulation of Lipid Metabolism by Novel Nuclear Receptor Partnerships
The endoplasmic-reticulum quality-control ( ERQC ) system shuttles misfolded proteins for degradation by the proteasome through the well-defined ER-associated degradation ( ERAD ) pathway . In contrast , very little is known about the role of autophagy in ERQC . Macro-autophagy , a collection of pathways that deliver p...	ER-quality control ( ERQC ) ensures delivery of “native” proteins through the secretory pathway . Currently , ER-associated degradation ( ERAD ) , which delivers misfolded proteins for degradation by the proteasome , is considered a major ERQC pathway , with autophagy as its backup . Until now , the role of autophagy ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Role for Macro-ER-Phagy in ER Quality Control
A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations . Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at differe...	Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time . However , ancient DNA studies are often based on DNA extracted from only one or a few individuals and , therefore , do not lend the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "molecular", "biology", "genetics", "and", "genomics/population", "genetics" ]	2009	Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool
The ability of mice to resist infection with the protozoan parasite , Toxoplasma gondii , depends in large part on the function of members of a complex family of atypical large GTPases , the interferon-gamma-inducible immunity-related GTPases ( IRG proteins ) . Nevertheless , some strains of T . gondii are highly virul...	Toxoplasma gondii is an intracellular parasitic protozoan infecting about a third of humankind . Humans , however , are unlikely to be important hosts in terms of the evolution of the parasite because , for completion of the parasite sexual cycle , the infected animal must be eaten by a cat . Therefore , important inte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parasite", "evolution", "enzymes", "immunology", "microbiology", "host-pathogen", "interaction", "parasitology", "animal", "models", "model", "organisms", "enzyme", "regulation", "protozoan", "models", "biology", "mouse", "biochemistry", "enzyme", "structure", "immunity", ...	2012	A Toxoplasma gondii Pseudokinase Inhibits Host IRG Resistance Proteins
Emergence of a new influenza strain leads to a rapid global spread of the virus due to minimal antibody immunity . Pre-existing CD8+ T-cell immunity directed towards conserved internal viral regions can greatly ameliorate the disease . However , mutational escape within the T cell epitopes is a substantial issue for vi...	Introduction of a new influenza strain into human circulation leads to a rapid global spread of the virus due to minimal antibody immunity . Established T-cell immunity towards conserved viral regions provides some protection against influenza and promotes rapid recovery . However , influenza viruses mutate to escape t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunity", "to", "infections", "immunology/immune", "response" ]	2010	Protective Efficacy of Cross-Reactive CD8+ T Cells Recognising Mutant Viral Epitopes Depends on Peptide-MHC-I Structural Interactions and T Cell Activation Threshold
A global strategy of mass drug administration ( MDA ) has greatly reduced the burden of lymphatic filariasis ( LF ) in endemic countries . In Madagascar , the National Programme to eliminate LF has scaled-up annual MDA of albendazole and diethylcarbamazine across the country in the last decade , but its impact on LF tr...	Lymphatic filariasis is a neglected disease with chronic disabling consequences . Endemic countries have reduced lymphatic filariasis transmission through a strategy of annual rounds of mass drug administration ( MDA ) , but the impact of such strategy has not yet been reported for Madagascar . In this study we conduct...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cancer", "detection", "and", "diagnosis", "children", "medicine", "and", "health", "sciences", "lymphatic", "mapping", "education", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "oncology", "age", "grou...	2018	Towards elimination of lymphatic filariasis in southeastern Madagascar: Successes and challenges for interrupting transmission
Vision is the dominant sensory modality in many organisms for foraging , predator avoidance , and social behaviors including mate selection . Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye . Sensitivity to individual colors , i . e . , peak s...	Vertebrate color vision is possible when cone visual pigments with distinct peak spectral sensitivities ( λmax ) are expressed in separate cone populations and provide differential input to downstream neurons . The λmax is a function of the type of chromophore ( such as 11-cis retinal ) and the amino acid sequence of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "molecular", "dynamics", "vertebrates", "social", "sciences", "pigments", "animals", "neuroscience", "animal", "models", "osteichthyes", "model", "organisms", "mathematics", "forecasting", "statistics", "(mathematics)", "materials", "science", "experimental", "organ...	2018	Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

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