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In all mammals , tissue inflammation leads to pain and behavioral sensitization to thermal and mechanical stimuli called hyperalgesia . We studied pain mechanisms in the African naked mole-rat , an unusual rodent species that lacks pain-related neuropeptides ( e . g . , substance P ) in cutaneous sensory fibers . Naked...	Chemicals such as capsaicin and acid are considered noxious because they cause irritation and pain when applied to the skin . Acid is , for example , a very noxious stimulus and can cause intense pain . Indeed , acid is both noxious and painful to all animals including amphibians and fish . Here we describe a member of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physiology", "evolutionary", "biology", "neuroscience" ]	2008	Selective Inflammatory Pain Insensitivity in the African Naked Mole-Rat (Heterocephalus glaber)
Parasitic nematodes of humans , other animals and plants continue to impose a significant public health and economic burden worldwide , due to the diseases they cause . Promising antiparasitic drug and vaccine candidates have been discovered from excreted or secreted ( ES ) proteins released from the parasite and expos...	Excretory-secretory ( ES ) proteins are an important class of proteins in many organisms , spanning from bacteria to human beings , and are potential drug targets for several diseases . In this study , we first developed a software platform , EST2Secretome , comprised of carefully selected computational tools to identi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "infectious", "diseases/helminth", "infections", "biochemistry/bioinformatics", "computational", "biology/genomics", "genetics", "and", "genomics", "biochemistry/drug", "discovery" ]	2008	Needles in the EST Haystack: Large-Scale Identification and Analysis of Excretory-Secretory (ES) Proteins in Parasitic Nematodes Using Expressed Sequence Tags (ESTs)
In a prebiotic RNA world , parasitic behaviour may be favoured because template dependent replication happens in trans , thus being altruistic . Spatially extended systems are known to reduce harmful effects of parasites . Here we present a spatial system to show that evolution of replication is ( indirectly ) enhanced...	The RNA world is a stage of evolution that preceded cellular life . In this world , RNA molecules would both replicate other RNAs and behave as templates for replication . A known evolutionary problem of this world is that selection should favour parasitic templates that do not replicate others , because they would be ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "parasite", "replication", "parasite", "evolution", "population", "dynamics", "parasitology", "developmental", "biology", "speciation", "theoretical", "ecology", "population", "biology", "waves", "morphogenesis", "pattern", "fo...	2016	Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation
Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes . However , most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level . We have bridged these two methodologies with a multiscale mutation clustering algorithm that...	Identifying driver mutations in cancer has been a major challenge in cancer research , with the ultimate goal of understanding the detailed molecular origins of cancer and providing genetically personalized treatments . For decades , the cancer research community has known that mutations in certain genes—such as tumor ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusion", "Methods" ]	[ "medicine", "and", "health", "sciences", "applied", "mathematics", "carcinomas", "endometrial", "carcinoma", "cancers", "and", "neoplasms", "simulation", "and", "modeling", "oncology", "algorithms", "mutation", "mathematics", "clustering", "algorithms", "nonsense", "mutat...	2017	Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
The balance between T helper ( Th ) 1 and Th2 cell responses is a major determinant of the outcome of experimental leishmaniasis , but polarized Th1 or Th2 responses are not sufficient to account for healing or nonhealing . Here we show that high arginase activity , a hallmark of nonhealing disease , is primarily expre...	Leishmania parasites are obligate intracellular pathogens that predominantly invade macrophages . Instruction of macrophages by T cell-derived signals is required to control parasite growth . Here we show that arginase , an enzyme induced in Leishmania-infected macrophages , is highly expressed at the site of pathology...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2009	Local Suppression of T Cell Responses by Arginase-Induced L-Arginine Depletion in Nonhealing Leishmaniasis
Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization . Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species . Using compar...	To understand how the cell performs the required biological functions and reacts to changes in the environment , scientists have been studying how cellular components interact . In recent years , new experimental methods have immensely increased our ability to map out these connections . However , it is important to ke...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "molecular", "biology", "caenorhabditis", "eukaryotes", "computational", "biology", "evolutionary", "biology", "drosophila", "saccharomyces" ]	2007	Specificity and Evolvability in Eukaryotic Protein Interaction Networks
αβ-tubulin dimers need to convert between a ‘bent’ conformation observed for free dimers in solution and a ‘straight’ conformation required for incorporation into the microtubule lattice . Here , we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations , emphasizing implications for m...	Microtubules are composed of αβ-tubulins that play an instrumental role in regulating intracellular trafficking and formation of the mitotic spindle during mitosis and cell division . Structural studies have shown that tubulin exists in a “straight” conformation compatible with that in the microtubule lattice and a “be...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "physics", "biochemistry", "computer", "science", "computer", "modeling", "chemistry", "theoretical", "chemistry", "biology", "computational", "chemistry", "computerized", "simulations", "biophysics" ]	2014	The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery
The circadian clock coordinates physiology and metabolism . mTOR ( mammalian/mechanistic target of rapamycin ) is a major intracellular sensor that integrates nutrient and energy status to regulate protein synthesis , metabolism , and cell growth . Previous studies have identified a key role for mTOR in regulating phot...	The circadian clock coordinates daily physiology and metabolism in animals . There has been considerable interest in identifying mechanisms that link metabolic signals to circadian time keeping . mTOR ( mammalian/mechanistic target of rapamycin ) is a major intracellular sensor that integrates nutrient and energy statu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "liver", "vertebrates", "mice", "cell", "metabolism", "animals", "electromagnetic", "radiation", "mammals", "circadian", "oscillators", "fibroblasts", "connective", "tissue", "cells", "chronobiology", "animal"...	2018	mTOR signaling regulates central and peripheral circadian clock function
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus . This has raised fundamental questions concerning speciation , selection and transmission of the genetic make-up to next generations . Although this conc...	Endomycorrhizal fungi are known for their symbiosis with the vast majority of land plants . The fungus penetrates the root and facilitates uptake of nutrients for the plant . For a long time it was hypothesized that endomycorrhizal fungi have a complex genetic makeup , as they are asexual organisms . Their hyphae do no...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "agroecology", "genetics", "soil", "science", "biology", "genomics", "agriculture" ]	2014	Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus
Genes directly involved in male/female and host/parasite interactions are believed to be under positive selection . The flowering plant Arabidopsis thaliana has more than 300 defensin-like ( DEFL ) genes , which are likely to be involved in both natural immunity and cell-to-cell communication including pollen–pistil in...	Defensin-like ( DEFL ) peptides commonly function as effector peptides and are involved in male-female and host-parasite interactions in eukaryotes . In higher plants , DEFL genes belong to a large multigene family and are highly variable between species . However , little is known about the relationship between the mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "biology", "plant", "physiology" ]	2012	A Species-Specific Cluster of Defensin-Like Genes Encodes Diffusible Pollen Tube Attractants in Arabidopsis
Arabidopsis TSO1 encodes a protein with conserved CXC domains known to bind DNA and is homologous to animal proteins that function in chromatin complexes . tso1 mutants fall into two classes due to their distinct phenotypes . Class I , represented by two different missense mutations in the CXC domain , leads to failure...	Much of our current genetic concepts and terms came from early pioneering work in Drosophila melanogaster , which has a relatively simple genome with reduced gene sets . One noted example is the term antimorph or dominant-negative , which describes mutant proteins that antagonize the corresponding wild-type proteins in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "model", "organisms", "plant", "biology", "crops", "genetics", "genetics", "and", "genomics", "biology", "genomics", "molecular", "cell", "biology", "agricultural", "production", "agriculture" ]	2011	Recessive Antimorphic Alleles Overcome Functionally Redundant Loci to Reveal TSO1 Function in Arabidopsis Flowers and Meristems
Little is known about how changes in DNA methylation mediate risk for human diseases including dementia . Analysis of genome-wide methylation patterns in patients with two forms of tau-related dementia – progressive supranuclear palsy ( PSP ) and frontotemporal dementia ( FTD ) – revealed significant differentially met...	Progressive supranuclear palsy ( PSP ) and frontotemporal dementia ( FTD ) are two neurodegenerative diseases linked , at the pathologic and genetic level , to the microtubule associated protein tau . We studied epigenetic changes ( DNA methylation levels ) in peripheral blood from patients with PSP , FTD , and unaffec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurology", "genetics", "epigenetics", "biology", "dementia" ]	2014	An Epigenetic Signature in Peripheral Blood Associated with the Haplotype on 17q21.31, a Risk Factor for Neurodegenerative Tauopathy
The interaction between Plasmodium vivax Duffy binding protein ( PvDBP ) and Duffy antigen receptor for chemokines ( DARC ) has been described as critical for the invasion of human reticulocytes , although increasing reports of P . vivax infections in Duffy-negative individuals questions its unique role . To investigat...	Until recently , P . vivax was thought to infect only Duffy positive individuals , due to its dependence on binding the Duffy blood group antigen as a receptor for reticulocyte invasion and to be absent from parts of Africa where the Duffy-negative phenotype is highly frequent . However , a number of recent studies fro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "reticulocytes", "parasitology", "bone", "marrow", "cells", "apicomplexa", "red", "blood", "cells...	2018	Genetic diversity in two Plasmodium vivax protein ligands for reticulocyte invasion
We examined an eye-hand coordination task where optimal visual search and hand movement strategies were inter-related . Observers were asked to find and touch a target among five distractors on a touch screen . Their reward for touching the target was reduced by an amount proportional to how long they took to locate an...	A variety of human daily activities , such as cooking , drawing , and driving , involve coordination of eye and hand . Typically your hand moves towards whatever you have just looked at . But is this coupling compulsory ? To test whether human observers can adopt appropriate eye-hand coordination strategies to maximize...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "psychology", "social", "and", "behavioral", "sciences", "human", "performance", "behavior", "psychophysics" ]	2012	Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task
Salmonella is a principal health concern because of its endemic prevalence in food and water supplies , the rise in incidence of multi-drug resistant strains , and the emergence of new strains associated with increased disease severity . Insights into pathogen emergence have come from animal-passage studies wherein vir...	Salmonellosis continues to compromise human health , animal welfare , and modern agriculture . Developing a comprehensive control plan requires an understanding of how pathogens emerge and express traits that confer increased incidence and severity of disease . It is well-established that animal passage often results i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "emerging", "infectious", "diseases", "biology", "microbiology", "salmonella", "bacterial", "pathogens" ]	2012	Intraspecies Variation in the Emergence of Hyperinfectious Bacterial Strains in Nature
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration ( SCNA ) in human cancer . Our study employs Whole Genome DNA Sequence ( WGS ) data from tumor samples ( n = 103 ) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate ...	Cancer is a genetic disease where changes in DNA cause alterations in the control of cellular systems leading to unchecked growth . Copy number changes , including duplications , amplifications , and deletions , are a common type of DNA change observed in cancer cells but it is not always clear which of the changes are...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cancer", "genomics", "urology", "deletion", "mutation", "medicine", "and", "health", "sciences", "genitourinary", "tract", "tumors", "cancers", "and", "neoplasms", "basic", "cancer", "research", "alleles", "long", "non-coding", "rnas", "surgical", "and", "invasive", ...	2017	Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data
Human cytomegalovirus ( HCMV ) is a widely prevalent human herpesvirus , which , after primary infection , persists in the host for life . In healthy individuals , the virus is well controlled by the HCMV-specific T cell response . A key feature of this persistence , in the face of a normally robust host immune respons...	Human cytomegalovirus ( HCMV ) is a widely prevalent virus , which is normally carried without clinical symptoms , but often causes severe clinical disease in individuals with compromised immune responses . In healthy HCMV carriers , the immune response to HCMV is robust and includes large numbers of virus-specific T-c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Human Cytomegalovirus Latency-Associated Proteins Elicit Immune-Suppressive IL-10 Producing CD4+ T Cells
The phytohormone auxin is a key regulator of plant growth and development . Molecular studies in Arabidopsis have shown that auxin perception and signaling is mediated via TIR1/AFB–Aux/IAA co-receptors that assemble as part of the SCFTIR1/AFB E3 ubiquitin-ligase complex and direct the auxin-regulated degradation of Aux...	The phytohormone auxin plays a diverse and critical role in plant growth and development . In Arabidopsis , the F-box protein TIR1 is a component of an E3 SCF ubiquitin-ligase complex that serves as the auxin receptor and directs the ubiquitin-dependent degradation of repressors of auxin signaling known as the Aux/IAA ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "protein", "interactions", "enzymes", "brassica", "enzymology", "hormones", "plant", "science", "model", "organisms", "plant", "hormones", "genetically", "modified", "plants", "plants", "flowering", "plants", "extraction", "techniques", "ligases", "geneti...	2016	Oligomerization of SCFTIR1 Is Essential for Aux/IAA Degradation and Auxin Signaling in Arabidopsis
Zika virus ( ZIKV ) is a mosquito-borne flavivirus of significant public health concern . In the summer of 2016 , ZIKV was first detected in the contiguous United States . Here we present one of the first cases of a locally acquired ZIKV infection in a dengue-naïve individual . We collected blood from a female with a m...	Zika virus ( ZIKV ) is an emerging viral disease that has the potential to negatively impact future generations by causing birth defects in infected pregnant mothers . While there have been many studies performed in animal models of ZIKV infection , there have only been a limited number of reports studying the immune r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "body", "fluids", "enzyme-linked", "immunoassays", "pathogens", "immunology", "microbiology", "viruses", "developmental", ...	2017	Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL
HIV Nef acts as an anti-autophagic maturation factor through interaction with beclin-1 ( BECN1 ) . We report that exposure of macrophages to infectious or non-infectious purified HIV induces toll-like receptor 8 ( TLR8 ) and BECN1 dependent dephosphorylation and nuclear translocation of TFEB and that this correlates wi...	Under basal conditions , the mammalian target of rapamycin ( MTOR ) phosphorylates transcription factor EB ( TFEB ) resulting in its cytoplasmic retention . When MTOR is inhibited , TFEB is dephosphorylated and translocated to the nucleus where it increases autophagy and lysosomal gene expression . As human immunodefic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human Immunodeficiency Virus Type 1 Nef Inhibits Autophagy through Transcription Factor EB Sequestration
The emergence of drug resistant pathogens is a serious public health problem . It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly . To this end , it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics l...	When bacteria acquire drug resistance through mutation of their genomes , it renders once-powerful treatments useless . For some antibiotics , bacteria develop resistance rapidly , while for other antibiotics this process can be very slow . The causes of such differences in evolutionary dynamics between drugs remain po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance
Computer generated trajectories can , in principle , reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence . While such reversible folding trajectories can only be determined ab initio using all-atom transferab...	The process of protein folding is a complex transition from a disordered to an ordered state . Here , we simulate a specific fast-folding protein at the point at which the native and denatured states are at equilibrium and show that obtaining an accurate description of the mechanisms of folding and unfolding is far fro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/theory", "and", "simulation", "biophysics/protein", "folding" ]	2009	Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations
Aedes aegypti , the primary vector of dengue , yellow fever and Zika flaviviruses , consists of at least two subspecies . Aedes aegypti ( Aaa ) is light in color , has pale scales on the first abdominal tergite , oviposits in artificial containers , and preferentially feeds on humans . Aedes aegypti formosus ( Aaf ) , ...	Aedes aegypti is one of the best studied mosquito species and it is the principal vector of dengue , Zika , and yellow fever flaviviruses and the Chikungunya alphavirus . Aedes aegypti occurs throughout all tropical and subtropical regions of the world , and previous population genetic studies have shown that the highe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "urology", "chromosome", "staining", "medicine", "and", "health", "sciences", "nuclear", "staining", "chromosome", "1", "animals", "reproductive", "physiology", "population", "biology", "insect", "vectors", "fecundity", "research", "and", "analysis", "m...	2016	Reproductive Incompatibility Involving Senegalese Aedes aegypti (L) Is Associated with Chromosome Rearrangements
After more than 40 years of use , Praziquantel ( PZQ ) still remains the drug of choice for the treatment of intestinal and urogenital schistosomiasis . Its anti-parasitic activity resides primarily in the ( R ) -enantiomer . Hitherto neither the molecular target nor the pharmacokinetic-pharmacodynamic relationship hav...	After more than 40 years of use , Praziquantel ( PZQ ) still remains the drug of choice for the treatment of intestinal and urogenital schistosomiasis . However the relationship between pharmacokinetics and efficacy is not elucidated . For adults infected with intestinal schistosomiasis , a single oral dose of PZQ at 4...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "cardiovascular", "anatomy", "veins", "animals", "pediatrics", "animal", "models", "routes", "of", "administration", "model", "organisms", "...	2017	Evaluation of the pharmacokinetic-pharmacodynamic relationship of praziquantel in the Schistosoma mansoni mouse model
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions . Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes . We set out to determine which properties cause such differences in immunog...	T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions . Some peptide-MHC-I complexes ( pMHCs ) are better recognized by T-cells; we call such pMHCs more immunogenic . For other pMHCs , no recognizing T-cells seem to exist; we call such pMHCs non-immunogenic . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks , but their roles in stem cell pluripotency remain poorly understood . Here , we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in ste...	Although transcriptional regulation in stem cells is a very active subject , much less is known about how post-transcriptional mechanisms of gene expression affect stem cells . Here , we use freshwater planarians in order to address this question . Planarians have a striking regenerative capacity driven by a population...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation
The polymerase chain reaction ( PCR ) has been proposed for diagnosis , staging and post-treatment follow-up of sleeping sickness but no large-scale clinical evaluations of its diagnostic accuracy have taken place yet . An 18S ribosomal RNA gene targeting PCR was performed on blood and cerebrospinal fluid ( CSF ) of 36...	Post-treatment follow-up is crucial for sleeping sickness patient management and still relies on microscopic examination of the cerebrospinal fluid ( CSF ) . Detection of the parasites DNA with the polymerase chain reaction ( PCR ) is proposed as a promising and possibly non-invasive alternative for monitoring treatmen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2011	Diagnostic Accuracy of PCR in gambiense Sleeping Sickness Diagnosis, Staging and Post-Treatment Follow-Up: A 2-year Longitudinal Study
The present study analyzed whether or not the in vitro cultivation for long periods of time of pre-isolated Leishmania amazonensis from lesions of chronically infected BALB/c mice was able to interfere in the parasites' infectivity using in vivo and in vitro experiments . In addition , the proteins that presented a sig...	Leishmania amazonensis can induce a diversity of clinical manifestations in mammal hosts , including tegumentary and visceral leishmaniasis . The present study evaluated the variation of infectivity of L . amazonensis , which was pre-isolated from lesions of chronically infected mice and in vitro cultured for 150 days ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "spectrometric", "identification", "of", "proteins", "organismal", "evolution", "medicine", "and", "health", "sciences", "immunology", "protein", "abundance", "genomic", "databases", "developmental", "biology", "genome", "analysis", "veterinary", "science", "infectious", ...	2014	Identification of Differentially Expressed Proteins from Leishmania amazonensis Associated with the Loss of Virulence of the Parasites
The family Picornaviridae contains well-known human pathogens ( e . g . , poliovirus , coxsackievirus , rhinovirus , and parechovirus ) . In addition , this family contains a number of viruses that infect animals , including members of the genus Cardiovirus such as Encephalomyocarditis virus ( EMCV ) and Theiler's muri...	Recently , a new picornavirus was isolated from humans , named Saffold virus ( SAFV ) . Picornaviruses are small RNA viruses with poliovirus as prototype . Saffold virus is genetically related to Theiler's virus , a member of the Cardiovirus genus , which until this recent discovery did not contain human viruses . Thei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/emerging", "viral", "diseases" ]	2009	Saffold Virus, a Human Theiler's-Like Cardiovirus, Is Ubiquitous and Causes Infection Early in Life
S . aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics . Despite growing knowledge of S . aureus metabolic capabilities , our understanding of its systems-level responses to different media types remains incomplete . Here , we develop a manua...	Environmental perturbations ( e . g . , antibiotic stress , nutrient starvation , oxidative stress ) induce systems-level perturbations of bacterial cells that vary depending on the growth environment . The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "protein", "metabolism", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "metabolic", "processes", "microbiology", "carbohydrates", "glucose", "metabolism", "staphyloc...	2019	A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Dengue viruses are mosquito-borne flaviviruses that circulate in nature as four distinct serotypes ( DENV1-4 ) . These emerging pathogens are responsible for more than 100 million human infections annually . Severe clinical manifestations of disease are predominantly associated with a secondary infection by a heterotyp...	Despite decades of research , there remains a critical need for a dengue virus ( DENV ) vaccine . Vaccine development efforts are complicated by a requirement to protect against four DENV serotypes ( DENV1-4 ) , and incomplete immunity as a risk factor for severe disease . Antibodies play a major protective role agains...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Type-Specific Neutralizing Antibody Response Elicited by a Dengue Vaccine Candidate Is Focused on Two Amino Acids of the Envelope Protein
Productive herpesvirus infection requires a profound , time-controlled remodeling of the viral transcriptome and proteome . To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus ( KSHV ) , we performed a systematic genome-wide survey of viral transcription...	Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a cancer-causing agent in immunocompromised patients that establishes long-lasting infections in its hosts . Initially described in 1994 and extensively studied ever since , KSHV molecular biology is understood in broad outline , but many detailed questions are still ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genome", "expression", "analysis", "sequence", "analysis", "functional", "genomics", "molecular", "cell", "biology", "rna", "processing", "dna", "viruses", "virology", "viral", "classification", "gene", "expression", "protein", "translation", "b...	2014	KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features
Filoviruses , amongst the most lethal of primate pathogens , have only been reported as natural infections in sub-Saharan Africa and the Philippines . Infections of bats with the ebolaviruses and marburgviruses do not appear to be associated with disease . Here we report identification in dead insectivorous bats of a g...	A novel filovirus , provisionally named Lloviu virus ( LLOV ) , was detected during the investigation of Miniopterus schreibersii die-offs in Cueva del Lloviu in southern Europe . LLOV is genetically distinct from other marburgviruses and ebolaviruses and is the first filovirus detected in Europe that was not imported ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "classification", "emerging", "viral", "diseases", "microbiology", "host-pathogen", "interaction", "ebola", "hemorrhagic", "fever", "emerging", "infectious", "diseases", "infectious", "diseases", "medical", "microbiology", "microbial", "pathogens", "bio...	2011	Discovery of an Ebolavirus-Like Filovirus in Europe
Inclusions in the brain containing α-synuclein are the pathological hallmark of Parkinson's disease , but how these inclusions are formed and how this links to disease is poorly understood . We have developed a C . elegans model that makes it possible to monitor , in living animals , the formation of α-synuclein inclus...	Parkinson's disease is the second most common brain disorder of the elderly . It is thought to be caused by environmental and genetic factors . However , little is known about the genes and processes involved . Pathologically , Parkinson's disease is recognized by inclusions in the brain that contain a disease-specific...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/gene", "discovery" ]	2008	C. elegans Model Identifies Genetic Modifiers of α-Synuclein Inclusion Formation During Aging
Extraintestinal pathogenic E . coli ( ExPEC ) cause an array of diseases , including sepsis , neonatal meningitis , and urinary tract infections . Many putative virulence factors that might modulate ExPEC pathogenesis have been identified through sequencing efforts , epidemiology , and gene expression profiling , but f...	Escherichia coli can exist among the normal intestinal microbiota without causing any overt problems for the human host . However , humans as well as other animals can often acquire less-mild mannered variants of E . coli strains known as extraintestinal pathogenic E . coli ( ExPEC ) that can colonize sites outside of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/urological", "infections", "infectious", "diseases", "urology/urological", "infections", "microbiology/microbial", "evolution", "and", "genomics", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infect...	2009	Use of Zebrafish to Probe the Divergent Virulence Potentials and Toxin Requirements of Extraintestinal Pathogenic Escherichia coli
The basic reproduction number ( R0 ) is an important quantity summarising the dynamics of an infectious disease , as it quantifies how much effort is needed to control transmission . The relative change in R0 due to an intervention is referred to as the effect size . However malaria and other diseases are often highly ...	Mathematical models of the transmission of malaria and other infectious diseases are helpful for understanding and predicting the impact of interventions . An important summary of the dynamics of these models is the basic reproduction number , defined as the average number of secondary infections resulting from each in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Interaction between Seasonality and Pulsed Interventions against Malaria in Their Effects on the Reproduction Number
Sterol regulatory element binding proteins ( SREBPs ) are a class of basic helix-loop-helix transcription factors that regulate diverse cellular responses in eukaryotes . Adding to the recognized importance of SREBPs in human health , SREBPs in the human fungal pathogens Cryptococcus neoformans and Aspergillus fumigatu...	Advances in medical technologies over the past several years have led to an increasing population of patients susceptible to fungal infections . Despite the immunocompromised condition of most patients that acquire these infections , the majority are caused by three fungi: Candida albicans , Cryptococcus neoformans , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "metabolism", "mycology", "gene", "identification", "and", "analysis", "genetics", "gene", "regulation", "molecular", "genetics", "biology", "gene", "expression", "microbiology", "microbial", "pathogens", "genetics", "and", "genomics", "gene", "function" ]	2011	SREBP Coordinates Iron and Ergosterol Homeostasis to Mediate Triazole Drug and Hypoxia Responses in the Human Fungal Pathogen Aspergillus fumigatus
Spironucleus salmonicida causes systemic infections in salmonid fish . It belongs to the group diplomonads , binucleated heterotrophic flagellates adapted to micro-aerobic environments . Recently we identified energy-producing hydrogenosomes in S . salmonicida . Here we present a genome analysis of the fish parasite wi...	Studies of model organisms are very powerful . However , to appreciate the enormous diversity of genetic and cell biological processes we need to extend the number of available model organisms . For example , there are very few model organisms for diverse microbial eukaryotes , a group of organisms which indeed represe...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "giardia", "lamblia", "genome", "sequencing", "genome", "analysis", "tools", "genome", "evolution", "parasite", "evolution", "protozoology", "comparative", "genomics", "biology", "genomics", "gene", "prediction", "microbiology", "computational", ...	2014	The Genome of Spironucleus salmonicida Highlights a Fish Pathogen Adapted to Fluctuating Environments
Visceral Leishmaniasis , commonly known as kala-azar , is widely prevalent in Bihar . The National Kala-azar Control Program has applied house-to-house survey approach several times for estimating Kala-azar incidence in the past . However , this approach includes huge logistics and operational cost , as occurrence of k...	Visceral Leishmaniasis , commonly known as kala-azar , is one of the major health concerns for Bihar state in India . Time to time estimation of kala-azar incidence plays a pivotal role in defining and evaluating control strategies under National Kala-azar Elimination programme . The house-to-house survey approach , ad...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "india", "teachers", "parasitic", "diseases", "data", "management", "signs", "and", "symptoms", "neglected", "tropica...	2016	Snowball Vs. House-to-House Technique for Measuring Annual Incidence of Kala-azar in the Higher Endemic Blocks of Bihar, India: A Comparison
American Cutaneous Leishmaniasis ( ACL ) , a vector borne disease , is caused by various species of Leishmania and in the Amazonas , Leishmania guyanensis is predominant . The recommended drugs for treatment of cutaneous leishmaniasis ( CL ) in Brazil are pentavalent antimonials , pentamidine isethionate ( PI ) and amp...	Ninety percent of all cases of CL are concentrated in five countries , including Brazil . Brazil is among the most endemic countries in the Americas . According to the Brazilian Ministry of Health , 30 , 000 new cases are diagnosed every year and the prevalent species are L . braziliensis and L . guyanensis . In the re...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "diabetes", "mellitus", "research", "design", ...	2018	An open label randomized clinical trial comparing the safety and effectiveness of one, two or three weekly pentamidine isethionate doses (seven milligrams per kilogram) in the treatment of cutaneous leishmaniasis in the Amazon Region
The dynamic behaviors of signaling pathways can provide clues to pathway mechanisms . In cancer cells , excessive phosphorylation and activation of the Akt pathway is responsible for cell survival advantages . In normal cells , serum stimulation causes brief peaks of extremely high Akt phosphorylation before reaching a...	Influential pathways of cell signalling ( such as PI3K/Akt ) are routinely communicated using simple textbook-like diagrams that show only the most widely-accepted steps of the pathway . At the same time , there are countless other molecular influences relevant to each pathway , documented in the published literature ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics
The increasing rate of antibiotic resistance and slowing discovery of novel antibiotic treatments presents a growing threat to public health . Here , we consider a simple model of evolution in asexually reproducing populations which considers adaptation as a biased random walk on a fitness landscape . This model associ...	Increasing antibiotic resistance , coupled with the slowing rate of discovery of novel antibiotic agents , is a public health threat which could soon reach crisis point . Indeed , the last decade has seen the emergence of deadly , highly resistant forms of pathogens , such as Escherichia coli , Acenitobacter baumanii ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
CFTR is a dynamically regulated anion channel . Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms . Two severe CFTR mutations ( CFTRsev ) cause complete loss of CFTR function and r...	Genetic disorders of ion channels can affect the body's ability to function properly in many ways . CFTR , an ion channel regulating movement of chloride and bicarbonate across cell membranes , is important for absorbing and secreting fluids . If the gene responsible for the CFTR channel is mutated severely , the resul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "urology", "medicine", "and", "health", "sciences", "genetic", "dominance", "respiratory", "infections", "fibrosis", "electrophysiology", "pulmonology", "developmental", "biology", "cystic", "fibrosis", "gastroenterology", "and", "hepatology", "autosomal", "recessive", "tra...	2014	Mechanisms of CFTR Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis
Human microbiome research is rife with studies attempting to deduce microbial correlation networks from sequencing data . Standard correlation and/or network analyses may be misleading when taken as an indication of taxon interactions because “correlation is neither necessary nor sufficient to establish causation”; env...	The human microbiome comprises thousands of microbial taxa , each of them potentially having interactions with many other taxa . Elucidating these interactions can be helpful for human health and beyond . The most conclusive approach for understanding microbial interactions would be myriads of controlled experiments in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "interaction", "networks", "microbiome", "community", "structure", "microbiology", "charts", "tongue", "microbial", "genomics", "digestive", "system", "computer", "and"...	2019	Detecting interaction networks in the human microbiome with conditional Granger causality
In the Lao PDR ( Laos ) , urban dengue is an increasingly recognised public health problem . We describe a dengue-1 virus outbreak in a rural northwestern Lao forest village during the cool season of 2008 . The isolated strain was genotypically “endemic” and not “sylvatic , ” belonging to the genotype 1 , Asia 3 clade ...	Dengue disease is caused by a virus transmitted by mosquitoes . In Southeast Asia , where it is endemic , it represents a very important public health problem . Major outbreaks , including severe cases and death , occur every year . Two distinct transmission cycles have been described . Most common is the human-mosquit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genome", "sequencing", "medicine", "infectious", "diseases", "molecular", "epidemiology", "epidemiology", "dengue", "fever", "neglected", "tropical", "diseases", "dengue", "biology", "genomics", "viral", "diseases" ]	2013	An Epidemic of Dengue-1 in a Remote Village in Rural Laos
Cellular Ephrin receptor tyrosine kinases ( Ephrin receptors , Ephs ) were found to interact efficiently with the gH/gL glycoprotein complex of the rhesus monkey rhadinovirus ( RRV ) . Since EphA2 was recently identified as a receptor for the Kaposi's sarcoma-associated herpesvirus ( KSHV ) ( Hahn et al . , Nature Medi...	Here we show that the gH/gL glycoprotein complex of rhesus monkey rhadinovirus binds to and mediates entry of virus into target cells via cellular Ephrin receptor tyrosine kinase proteins . Rhesus monkey rhadinovirus is a gamma-2 herpesvirus that is a close homolog of the human Kaposi's sarcoma-associated herpesvirus (...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "diseases" ]	2013	Rhesus Monkey Rhadinovirus Uses Eph Family Receptors for Entry into B Cells and Endothelial Cells but Not Fibroblasts
Major Histocompatibility Complex ( MHC ) genes code for proteins involved in the incitation of the adaptive immune response in vertebrates , which is achieved through binding oligopeptides ( antigens ) of pathogenic origin . Across vertebrate species , substitutions of amino acids at sites responsible for the specifici...	Major Histocompatibility Complex ( MHC ) proteins , responsible for presenting antigens to lymphocytes and thus fundamental to immune response are highly diverse . This diversity , is due to extremely high polymorphism of genes that encode MHC . MHC genes are the paradigm for the positive selection whereby novel MHC al...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes
Formation of cytoplasmic inclusion bodies ( IBs ) is a hallmark of infections with non-segmented negative-strand RNA viruses ( order Mononegavirales ) . We show here that Nipah virus ( NiV ) , a bat-derived highly pathogenic member of the Paramyxoviridae family , differs from mononegaviruses of the Rhabdo- , Filo- and ...	Inclusion bodies ( IBs ) induced by non-segmented negative-strand RNA viruses ( Mononegavirales ) are described as mobile cytosolic compartments that concentrate viral proteins and represent the main viral replication sites in infected cells . This general concept is mainly based on studies with mononegaviruses from th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Nipah virus induces two inclusion body populations: Identification of novel inclusions at the plasma membrane
Striking individual differences in severity of group A streptococcal ( GAS ) sepsis have been noted , even among patients infected with the same bacterial strain . We had provided evidence that HLA class II allelic variation contributes significantly to differences in systemic disease severity by modulating host respon...	Group A streptococci ( GAS ) cause a wide variety of human diseases ranging from mild pharyngitis to streptococcal toxic shock syndrome and necrotizing faciitis . Our previous studies have shown that host immunogenetic variation can dictate the clinical outcome of GAS sepsis . As in most human disease , GAS sepsis is l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "microbiology/immunity", "to", "infections", "pathology/immunology" ]	2008	An Unbiased Systems Genetics Approach to Mapping Genetic Loci Modulating Susceptibility to Severe Streptococcal Sepsis
We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North , Central , and South America . These data were analyzed jointly with similar data available in 54 other ...	Studies of genetic variation have the potential to provide information about the initial peopling of the Americas and the more recent history of Native American populations . To investigate genetic diversity and population relationships in the Americas , we analyzed genetic variation at 678 genome-wide markers genotype...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Genetic Variation and Population Structure in Native Americans
Defects of atrial and ventricular septation are the most frequent form of congenital heart disease , accounting for almost 50% of all cases . We previously reported that a heterozygous G296S missense mutation of GATA4 caused atrial and ventricular septal defects and pulmonary valve stenosis in humans . GATA4 encodes a ...	Cardiac malformations occur due to abnormal heart development and are the most prevalent human birth defect . Defects of atrial and ventricular septation are the most common type of congenital heart defect and are the result of incomplete closure of the atrial and ventricular septa , a process required for formation of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "model", "organisms", "pediatric", "cardiology", "pediatrics", "and", "child", "health", "genetics", "biology", "genetics", "and", "genomics", "pediatrics" ]	2012	Congenital Heart Disease–Causing Gata4 Mutation Displays Functional Deficits In Vivo
L5 pyramidal neurons are the only neocortical cell type with dendrites reaching all six layers of cortex , casting them as one of the main integrators in the cortical column . What is the nature and mode of computation performed in mouse primary visual cortex ( V1 ) given the physiology of L5 pyramidal neurons ? First ...	Neurons in the brain have elaborate dendritic morphologies , hosting a variety of nonlinear channels that give way to single cell computation . In this study , we perform patch clamp recordings in the apical dendrites to establish the spatial distribution of nonlinear channels and the signals they support in the dendri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting
Asymptomatic Leishmania donovani infections outnumber clinical presentations , however the predictors for development of active disease are not well known . We aimed to identify serological , immunological and genetic markers for progression from L . donovani infection to clinical Visceral Leishmaniasis ( VL ) . We enr...	Visceral Leishmaniasis ( VL ) or Kala-azar is a vector born disease , deadly if not treated . On the Indian subcontinent VL is caused by the protozoan parasite Leismania donovani , transmitted by an insect vector , sand fly of the Phlebotomus argentipes species , and considered an anthroponotic disease . Not every L . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "immunology", "tropical", "diseases", "geographical", "locations", "india", "parasitic", "diseases", "neglected", "tropical", "diseases", "molecular", "genetics", ...	2019	Determinants for progression from asymptomatic infection to symptomatic visceral leishmaniasis: A cohort study
Reverse transcription is the central defining feature of HIV-1 replication . We previously reported that the cellular eukaryotic elongation factor 1 ( eEF1 ) complex associates with the HIV-1 reverse transcription complex ( RTC ) and the association is important for late steps of reverse transcription . Here we show th...	After infecting a target cell , HIV-1 like all retroviruses converts the viral single strand RNA genome into double strand DNA by the process called reverse transcription . Host proteins are known to be important for reverse transcription yet a direct role for any host protein has not been demonstrated . In this paper ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Specific Interaction between eEF1A and HIV RT Is Critical for HIV-1 Reverse Transcription and a Potential Anti-HIV Target
Lipids and lipid metabolites play important roles in plant-microbe interactions . Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis , the involvement of lipases in plant immunity remains largely unknown . In particular , GDSL esterases/lipases , characterized by the conserved GDSL ...	Lipases are a large family of enzymes conferring lipid metabolism . Lipids and their metabolites play diverse roles in plant growth as well as response to environmental stimuli . Accumulating evidence implicates lipids as signaling molecules mediating plant immunity . Therefore , lipases are presumed to be actively inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "enzymology", "plant", "physiology", "plant", "science", "rice", "genetically", "modified", "plants", "experimental", "org...	2017	GDSL lipases modulate immunity through lipid homeostasis in rice
Infections with helminth parasites are controlled by a concerted action of innate and adaptive effector cells in the frame of a type 2 immune response . Basophils are innate effector cells that may also contribute to the initiation and amplification of adaptive immune responses . Here , we use constitutively basophil-d...	Helminths are large multicellular parasites that infect approximately every third person . Infections are controlled by a concerted action of innate and adaptive immune responses . Basophils and mast cells are innate effector cells with overlapping functions that have recently been implicated in the initiation and prom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "mast", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "parasitic", "diseases", "parasitology", "connective", "tissue", "cells", "gastroenterology", "and", "hepatology", "white", "blood", "cells", "parasitic", "int...	2018	Basophils are dispensable for the establishment of protective adaptive immunity against primary and challenge infection with the intestinal helminth parasite Strongyloides ratti
Horizontal gene transfer mediated by plasmid conjugation plays a significant role in the evolution of bacterial species , as well as in the dissemination of antibiotic resistance and pathogenicity determinants . Characterization of their regulation is important for gaining insights into these features . Relatively litt...	Bacteria evolve rapidly due to their short generation time and their ability to exchange genetic material , which can occur via different processes , collectively named Horizontal Gene Transfer ( HGT ) . Most bacteria contain , besides a single chromosome , autonomously replicating units called plasmids . Many plasmids...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Mobility of the Native Bacillus subtilis Conjugative Plasmid pLS20 Is Regulated by Intercellular Signaling
Many fields face an increasing prevalence of multi-authorship , and this poses challenges in assessing citation metrics . Here , we explore multiple citation indicators that address total impact ( number of citations , Hirsch H index [H] ) , co-authorship adjustment ( Schreiber Hm index [Hm] ) , and author order ( tota...	Multiple citation indicators are used in science and scientific evaluation . With an increasing proportion of papers co-authored by many researchers , it is important to account for the relative contributions of different co-authors . We explored multiple citation indicators that address total impact , co-authorship ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "people", "and", "places", "physics", "computer", "engineering", "meta-research", "article", "professions", "medicine", "and", "health", "sciences", "scientists", "mathematical", "physics", "computer", "and", "information", "sciences", "infectious", "diseases", "engineeri...	2016	Multiple Citation Indicators and Their Composite across Scientific Disciplines
Certain theories suggest that it should be difficult or impossible to eradicate a vaccine-preventable disease under voluntary vaccination: Herd immunity implies that the individual incentive to vaccinate disappears at high coverage levels . Historically , there have been examples of declining coverage for vaccines , su...	Interest in infectious disease models that incorporate the effects of human behavior has been growing in recent years . However , most of these models predict that it should never be possible to eradicate a disease under voluntary vaccination , due to nonvaccinating “free riders” that emerge when vaccine coverage is hi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics", "infectious", "diseases", "public", "health", "and", "epidemiology", "computational", "biology" ]	2009	Social Contact Networks and Disease Eradicability under Voluntary Vaccination
SATB2 is associated with schizophrenia and is an important transcription factor regulating neocortical organization and circuitry . Rare mutations in SATB2 cause a syndrome that includes developmental delay , and mouse studies identify an important role for SATB2 in learning and memory . Interacting partners BCL11B and...	Schizophrenia is a complex disorder caused by many genes . Using new gene discoveries to understand pathobiology is a foundation for development of new treatments . Current drugs for schizophrenia are only partially effective and do not treat cognitive deficits , which are key factors for explaining disability , leadin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "cognitive", "neurology", "medicine", "and", "health", "sciences", "gene", "regulation", "brain", "neuroscience", "animal", "models", "cognitive", "neuroscience", "model", "organisms", "genome", "analysis", "experimental", "organis...	2018	Genes regulated by SATB2 during neurodevelopment contribute to schizophrenia and educational attainment
Gain control is essential for the proper function of any sensory system . However , the precise mechanisms for achieving effective gain control in the brain are unknown . Based on our understanding of the existence and strength of connections in the insect olfactory system , we analyze the conditions that lead to contr...	Neural networks in the brain can classify objects as being the same thing regardless of the stimulus intensity , which is referred to as gain control . This intensity invariance occurs during pattern recognition in any sensory modality . We evaluate whether it is possible to design stable neural circuits made of excita...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "circuit", "models", "mathematics", "neural", "networks", "population", "modeling", "computational", "neuroscience", "olfactory", "system", "sensory", "systems", "biology", "computational", "biology", "nonlinear", "dynamics", "neuroscience", "coding", "mechanisms" ]	2013	Gain Control Network Conditions in Early Sensory Coding
Neurocysticercosis ( NCC ) is an infection of the central nervous system ( CNS ) by the metacestode of the helminth Taenia solium . The severity of the symptoms is associated with the intensity of the immune response . First , there is a long asymptomatic period where host immunity seems incapable of resolving the infe...	Neurocysticercosis ( NCC ) is a disease caused by the larval form of a tapeworm parasite that preferentially migrates to the brain . It is characterized by a long asymptomatic period thought to result from the parasite's ability to evade host immunity . To date , the mechanisms of host–parasite interaction before sympt...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "infectious", "diseases/helminth", "infections", "pathology/histopathology", "pathology/neuropathology" ]	2008	Differential Release and Phagocytosis of Tegument Glycoconjugates in Neurocysticercosis: Implications for Immune Evasion Strategies
Cleft palate is a common congenital disorder that affects up to 1 in 2500 live births and results in considerable morbidity to affected individuals and their families . The aetiology of cleft palate is complex with both genetic and environmental factors implicated . Mutations in the transcription factor p63 are one of ...	Cleft palate is a serious congenital condition which affects approximately 1 in every 2500 births . Cleft palate occurs when the palatal shelves fail to grow , adhere or fuse during development . Mutations in the gene encoding the transcription factor p63 result in cleft palate in humans and mice . However , the role o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "palate", "epithelial", "cells", "developmental", "biology", "cleft", "palate", "bioassays", "and", "physiological", "analysis", "keratins", "embryos", "morphogenesis", "digestive", "system", "research", "an...	2017	p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Hemorrhagic fever with renal syndrome ( HFRS ) is a zoonosis caused by hantavirus ( belongs to Hantaviridae family ) . A large amount of HFRS cases occur in China , especially in the Heilongjiang Province , raising great concerns regarding public health . The distribution of these cases across space-time often exhibits...	Heilongjiang Province reported the largest number of HFRS cases in China . Previous studies focused on identifying the severe HFRS outbreak regions , exploring the relative impact of environmental factors , forecasting HFRS cases etc . However , the study of the spatiotemporal spread dynamics and patterns of HFRS is st...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "china", "geographical", "locations", "vertebrates", "random", "variables", "covariance", "animals", "mammals", "hemorrhagic", "fever", "with", "renal", "syndrome", "mathematics", "public", "and", "occupational", "health", "infec...	2019	Probabilistic logic analysis of the highly heterogeneous spatiotemporal HFRS incidence distribution in Heilongjiang province (China) during 2005-2013
Post kala-azar dermal leishmaniasis ( PKDL ) , a dermal sequel of visceral leishmaniasis , caused by Leishmania donovani , constitutes an important reservoir for the parasite . Parallel functioning of counter acting immune responses ( Th1/Th2 ) reflects a complex immunological scenario , suggesting the involvement of a...	Post kala azar dermal leishamniasis ( PKDL ) , an unusual dermatosis , develops in 5–15% of apparently cured visceral leishmaniasis cases in India and in about 60% of cases in Sudan . PKDL cases assume importance since they constitute an important human reservoir for the parasite . Host immunological responses , consid...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "infectious", "diseases", "global", "health", "leishmaniasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Evidence for Involvement of Th17 Type Responses in Post Kala Azar Dermal Leishmaniasis (PKDL)
Electrical synaptic transmission through gap junctions is a vital mode of intercellular communication in the nervous system . The mechanism by which reciprocal target cells find each other during the formation of gap junctions , however , is poorly understood . Here we show that gap junctions are formed between BDU int...	The establishment of functional neuronal circuits requires that different neurons respond selectively to guidance molecules at particular times and in specific locations . In the target region , where cells connect , the same guidance molecules steer the growth of neurites from both the neuron and its target cell . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "axon", "guidance", "developmental", "neuroscience", "biology" ]	2013	Neuronal Target Identification Requires AHA-1-Mediated Fine-Tuning of Wnt Signaling in C. elegans
Protein aggregation underlies a wide range of human disorders . The polypeptides involved in these pathologies might be intrinsically unstructured or display a defined 3D-structure . Little is known about how globular proteins aggregate into toxic assemblies under physiological conditions , where they display an initia...	The aggregation of proteins in tissues is associated with the pathogenesis of more than 40 human diseases . The polypeptides underlying disorders such as Alzheimer's and Parkinson's are devoid of any regular structure , whereas the polypeptides causing familial amyotrophic lateral sclerosis or nonneuropathic systemic a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/macromolecular", "assemblies", "and", "machines", "biophysics/protein", "folding", "biochemistry/protein", "folding", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/macromol...	2009	Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases
Macroautophagy is a conserved mechanism for the bulk degradation of proteins and organelles . Pathological studies have implicated defective macroautophagy in neurodegeneration , but physiological functions of macroautophagy in adult neurons remain unclear . Here we show that Atg7 , an essential macroautophagy componen...	Macroautophagy is a major recycling pathway in cells , and its dysfunction is associated with neurological disorders including Alzheimer's disease , Parkinson's disease , and frontotemporal dementia . Here we show that Atg7 , an essential component of macroautophagy , regulates mature dopaminergic axon terminal morphol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Coordinate Regulation of Mature Dopaminergic Axon Morphology by Macroautophagy and the PTEN Signaling Pathway
By modelling the average activity of large neuronal populations , continuum mean field models ( MFMs ) have become an increasingly important theoretical tool for understanding the emergent activity of cortical tissue . In order to be computationally tractable , long-range propagation of activity in MFMs is often approx...	Due to the sheer number of neurons and the complexity of their interactions , the modelling of brain activity is particularly challenging . How can computationally tractable models of brain function be developed that are nevertheless biologically plausible ? The “mean field” approach , borrowed from statistical physics...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "mathematics", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "computational", "biology/signaling", "networks", "radiology", "and", "medical", "i...	2010	Axonal Velocity Distributions in Neural Field Equations
The myeloid-related proteins ( MRPs ) 8/14 are small proteins mainly produced by neutrophils , which have been reported to induce NO production in macrophages . On the other hand , Leishmania survives and multiplies within phagocytes by inactivating several of their microbicidal functions . Whereas MRPs are rapidly rel...	Parasites of the Leishmania genus have developed multiple mechanisms to subvert the immune response . Among these mechanisms are the activation of host phosphatases and inactivation of cell signaling pathways , which in turn activate the immune response . On the other hand , it has been observed that the Myeloid Relate...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2013	Impact of Neutrophil-Secreted Myeloid Related Proteins 8 and 14 (MRP 8/14) on Leishmaniasis Progression
Access to “safe” water and “adequate” sanitation are emphasized as important measures for schistosomiasis control . Indeed , the schistosomes' lifecycles suggest that their transmission may be reduced through safe water and adequate sanitation . However , the evidence has not previously been compiled in a systematic re...	Schistosomiasis is a serious disease in many developing countries , and the control of schistosomiasis relies on the large-scale administration of praziquantel . However , this strategy fails to address the root causes of schistosomiasis , which people acquire during contact with freshwater bodies that contain infected...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "sanitary", "engineering", "infectious", "diseases", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "engineering", "and", "technology", "epidemiology", "environmental", "management" ]	2014	The Relationship between Water, Sanitation and Schistosomiasis: A Systematic Review and Meta-analysis
Nipah virus ( NiV ) infection can lead to severe respiratory or neurological disease in humans . Transmission of NiV has been shown to occur through contact with virus contaminated fomites or consumption of contaminated food . Previous results using the African green monkey ( AGM ) model of NiV infection identified asp...	The development of effective therapeutic approaches to the treatment of human diseases requires an understanding of the disease process induced by an infectious agent . Historically the development of medical countermeasures for highly pathogenic viruses required the use of a uniformly lethal animal model . While this ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "diagnostic", "radiology", "immunology", "magnetic", "resonance", "imaging", "developmental", "biology", "materials", "scienc...	2018	Aerosol exposure to intermediate size Nipah virus particles induces neurological disease in African green monkeys
From an evolutionary point of view a pathogen might benefit from regulating the inflammatory response , both in order to facilitate establishment of colonization and to avoid life-threatening host manifestations , such as septic shock . In agreement with this notion Streptococcus pyogenes exploits type I IFN-signaling ...	The biological role of type I IFN in bacterial infection may differ dependent on etiological agent . With regard to S . pyogenes infection the type I IFN response has been shown to protect the host by limiting detrimental inflammation without impacting on bacterial load , suggesting a selective pressure on S . pyogenes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "protein", "transport", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "fibrinogen", "pathogens", "immunology", "cell", "pro...	2018	Streptococcal M protein promotes IL-10 production by cGAS-independent activation of the STING signaling pathway
Silencing of T cell activation and function is a highly efficient strategy of immunosuppression induced by pathogens . By promoting formation of membrane microdomains essential for clustering of receptors and signalling platforms in the plasma membrane , ceramides accumulating as a result of membrane sphingomyelin brea...	The ability of measles virus ( MV ) to impair T cell–dependent immune responses noted more than 100 years ago continues to be central to the severe generalised immunosuppression by this virus . Much has been learned about receptors and mechanisms , which determine the predilection of MV for hematopoetic cells . In cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cytoskeleton", "immunology/immunomodulation", "virology/immunodeficiency", "viruses", "cell", "biology", "cell", "biology/membranes", "and", "sorting", "virology/immune", "evasion", "immunology/leukocyte", "activation" ]	2009	Induction of Membrane Ceramides: A Novel Strategy to Interfere with T Lymphocyte Cytoskeletal Reorganisation in Viral Immunosuppression
Schistosomiasis is an infectious disease infecting mammals as the definitive host and fresh water snails as the intermediate host . Understanding the molecular and biochemical relationship between the causative schistosome parasite and its hosts will be key to understanding and ultimately treating and/or eradicating th...	Bilharzia is a parasitic disease endemic in many parts of the world . The schistosoma parasite that causes Bilharzia infects humans but uses a fresh water snail as a secondary host . These two organisms have co-evolved together , and as such the parasite will have mechanisms to overcome the host defences . Understandin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "chromosome", "biology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "species", "interactions", "cellular", "structures", "and", "organelles", "parasitology", "gene", "function" ]	2014	Differential Spatial Repositioning of Activated Genes in Biomphalaria glabrata Snails Infected with Schistosoma mansoni
A cross-sectional study of intestinal parasitic infections amongst migrant workers in Malaysia was conducted . A total of 388 workers were recruited from five sectors including manufacturing , construction , plantation , domestic and food services . The majority were recruited from Indonesia ( n = 167 , 43 . 3% ) , fol...	Neglected intestinal parasitic infections ( IPIs ) such as soil-transmitted helminthes ( STH ) have been recognized as one of the main causes of illnesses especially among disadvantaged communities . The last survey of parasitic infections among migrant workers in Malaysia was conducted more than a decade ago . Althoug...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "labor", "mobility", "helminths", "geographical", "locations", "hookworms", "social", "sciences", "parasitic", "diseases", "animals", "nematode", "infections", "ascaris", "ascaris", "lumbricoides", "labor", "econom...	2016	Migrant Workers in Malaysia: Current Implications of Sociodemographic and Environmental Characteristics in the Transmission of Intestinal Parasitic Infections
Hepatitis C virus ( HCV ) and the malaria parasite Plasmodium use the membrane protein CD81 to invade human liver cells . Here we mapped 33 host protein interactions of CD81 in primary human liver and hepatoma cells using high-resolution quantitative proteomics . In the CD81 protein network , we identified five protein...	CD81 is a cell membrane protein , which functions as entry factor for hepatitis C virus ( HCV ) and malaria sporozoites in the human liver . Currently , it remains enigmatic how CD81 guides the entry process of both pathogens and whether it functions in a similar way during liver cell invasion of HCV and malaria parasi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "luciferase", "liver", "pathology", "and", "laboratory", "medicine", "plasmodium", "cd", "coreceptors", "hepacivirus", "pathogens", "protein", "interaction", "networks", "biological", "cultures", "enzymes", ...	2018	Hepatitis C virus enters liver cells using the CD81 receptor complex proteins calpain-5 and CBLB
Cell membranes have a complex lateral organization featuring domains with distinct composition , also known as rafts , which play an essential role in cellular processes such as signal transduction and protein trafficking . In vivo , perturbations of membrane domains ( e . g . , by drugs or lipophilic compounds ) have ...	Cell membranes consist of a variety of lipids and proteins with inhomogeneous lateral distribution , forming domains with distinct composition and properties . These domains play a fundamental role in a number of biological processes , and perturbing them can have important effects on cellular functions . Some chemical...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "biochemistry", "lipids", "computational", "chemistry", "membrane", "characteristics", "molecular", "dynamics", "cell", "biology", "lipid", "bilayer", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "computational", "biology", "cellul...	2014	Hydrophobic Compounds Reshape Membrane Domains
Protein binding often involves conformational changes . Important questions are whether a conformational change occurs prior to a binding event ( ‘conformational selection’ ) or after a binding event ( ‘induced fit’ ) , and how conformational transition rates can be obtained from experiments . In this article , we pres...	The function of proteins is affected by their conformational dynamics , i . e . by transitions between lower-energy ground-state conformations and higher-energy excited-state conformations of the proteins . Advanced NMR and single-molecule experiments indicate that higher-energy conformations in the unbound state of pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "characterization", "statistical", "noise", "quantum", "chemistry", "nmr", "spectroscopy", "nmr", "relaxation", "mathematics", "statistics", "(mathematics)", "ground", "state", "chemical", "dissociation", "research", "and", "analysis", "methods", "gaussian", "...	2016	How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates
Cyanobacteria are a monophyletic phylogenetic group of global importance and have received considerable attention as potential host organisms for the renewable synthesis of chemical bulk products from atmospheric CO2 . The cyanobacterial phylum exhibits enormous metabolic diversity with respect to morphology , lifestyl...	Cyanobacteria are photoautotrophic prokaryotes of global importance and offer great potential as host organisms for the renewable synthesis of chemical bulk products , including biofuels , from atmospheric CO2 . As yet , however , research has mostly focussed on a small number of model strains and the genetic inventory...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "genomic", "databases", "phylogenetics", "data", "management", "genome", "analysis", "bacteria", "research", "and", "analysis", "methods", "sequence", "analysis", "computer", "and", "information", "sciences", "bioinformatics", "proteins", "biological", "databa...	2018	Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes
Nuclear myosin 1c ( NM1 ) mediates RNA polymerase I ( pol I ) transcription activation and cell cycle progression by facilitating PCAF-mediated H3K9 acetylation , but the molecular mechanism by which NM1 is regulated remains unclear . Here , we report that at early G1 the glycogen synthase kinase ( GSK ) 3β phosphoryla...	Nuclear actin and myosin are essential regulators of gene expression . At the exit of mitosis , nuclear myosin 1c ( NM1 ) mediates RNA polymerase I ( pol I ) transcription activation and cell cycle progression by modulating assembly of the chromatin remodeling complex WICH with the subunits WSTF and SNF2h and , crucial...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "genomics", "molecular", "cell", "biology" ]	2014	Glycogen Synthase Kinase (GSK) 3β Phosphorylates and Protects Nuclear Myosin 1c from Proteasome-Mediated Degradation to Activate rDNA Transcription in Early G1 Cells
Chromatin structure can control gene expression and can define specific transcription states . For example , bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells ( ESC ) . It allows them to rapidly engage specific developmental pathways . We reasoned that n...	The blood fluke Schistosoma mansoni causes intestinal bilharzia . The parasite has a complex life cycle in which a freshwater snail serves as intermediate host from which the human infecting larvae hatch . These larvae will actively seek skin contact , penetrate through the epithelium and start developing straight away...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection
Human Ebola infection is characterized by a paralysis of the immune system . A signature of αβ T cells in fatal Ebola infection has been recently proposed , while the involvement of innate immune cells in the protection/pathogenesis of Ebola infection is unknown . Aim of this study was to analyze γδ T and NK cells in p...	Human Ebola infection presents a high lethality rate and is characterized by a paralysis of the immune response . The definition of the protective immune profile during Ebola infection represents a main challenge useful in vaccine and therapy design . In particular , the protective/pathogenetic involvement of innate im...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology", "ebola", "hemorrhagic", "fever", ...	2017	Different features of Vδ2 T and NK cells in fatal and non-fatal human Ebola infections
The fundamental process of ribosome biogenesis requires hundreds of factors and takes place in the nucleolus . This process has been most thoroughly characterized in baker's yeast and is generally well conserved from yeast to humans . However , some of the required proteins in yeast are not found in humans , raising th...	Ribosomes are the cellular factories that produce proteins . Making a ribosome is a complex and energy intensive process that requires hundreds of different factors . Ribosome biogenesis is an essential process , and therefore mutations that partially disrupt this process lead to disease . One such disease is North Ame...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "protein", "interactions", "macromolecular", "assemblies", "rna", "synthesis", "proteins", "biology", "clinical", "genetics", "biochemistry", "rna", "autosomal", "recessive", "rna", "processing", "nucleic", "acids", "genetics", "and", "genomics" ]	2012	NOL11, Implicated in the Pathogenesis of North American Indian Childhood Cirrhosis, Is Required for Pre-rRNA Transcription and Processing
Visceral Leishmaniasis ( VL; also known as kala-azar ) is an ultimately fatal disease endemic in the Indian state of Bihar , while HIV/AIDS is an emerging disease in this region . A 2011 observational cohort study conducted in Bihar involving 55 VL/HIV co-infected patients treated with 20–25 mg/kg intravenous liposomal...	Fifty percent of all visceral leishmaniasis ( VL ) cases globally occur in India , where up to 90% of cases occur in the state of Bihar . There are also an estimated 300 , 000 people in Bihar living with HIV/AIDS . Patients with HIV who are treated for VL typically have much worse outcomes than VL patients who are HIV-...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "medical", "microbiology", "hiv", "viral", "pathogens", "leishmaniasis", "microbial", "pathogens", "neglected", "tropical", "diseases", ...	2014	Visceral Leishmaniasis and HIV Co-infection in Bihar, India: Long-term Effectiveness and Treatment Outcomes with Liposomal Amphotericin B (AmBisome)
Gap junction channels are intercellular conduits that allow diffusional exchange of ions , second messengers , and metabolites . Human oligodendrocytes express the gap junction protein connexin47 ( Cx47 ) , which is encoded by the GJC2 gene . The autosomal recessive mutation hCx47M283T causes Pelizaeus-Merzbacher–like ...	Oligodendrocytes are the myelinating cells of the central nervous system . Together with astrocytes , oligodendrocytes form networks of coupled glial cells—so-called panglial networks—which are built by gap junctions , i . e . intercellular channels composed of connexin proteins . Pelizaeus-Merzbacher–like disease is a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "pediatrics", "and", "child", "health", "neurology", "genetics", "physiology", "neurological", "disorders", "biology", "anatomy", "and", "physiology", "neuroscience", "genetics", "and", "genomics", "pediatrics", "clinical", "genetics" ]	2011	Pathologic and Phenotypic Alterations in a Mouse Expressing a Connexin47 Missense Mutation That Causes Pelizaeus-Merzbacher–Like Disease in Humans
Long noncoding RNAs ( lncRNAs ) are a class of molecules that impinge on the expression of protein-coding genes . Previous studies have suggested that the GAL cluster-associated lncRNAs of Saccharomyces cerevisiae repress expression of the protein-coding GAL genes . Herein , we demonstrate a previously unrecognized rol...	Long noncoding RNAs ( lncRNAs ) are a recently identified class of molecules that regulate the expression of protein-coding genes through a number of mechanisms , some of them poorly characterized . The GAL gene cluster of the yeast Saccharomyces cerevisiae encodes a series of three inducible genes that are turned on o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Long Noncoding RNAs Promote Transcriptional Poising of Inducible Genes
The malaria parasite replicates within an intraerythrocytic parasitophorous vacuole ( PV ) . Eventually , in a tightly regulated process called egress , proteins of the PV and intracellular merozoite surface are modified by an essential parasite serine protease called PfSUB1 , whilst the enclosing PV and erythrocyte me...	Malaria is a scourge of the developing world and many researchers are seeking new ways to treat and control the disease . Malaria is caused by a single-celled parasite that grows within red blood cells , eventually rupturing them to release invasive merozoites in a process known as egress . In earlier work we found tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "enzyme", "regulation", "enzymes", "biochemistry", "biology" ]	2013	Malaria Parasite cGMP-dependent Protein Kinase Regulates Blood Stage Merozoite Secretory Organelle Discharge and Egress
Vertebrate mesendoderm specification requires the Nodal signaling pathway and its transcriptional effector FoxH1 . However , loss of FoxH1 in several species does not reliably cause the full range of loss-of-Nodal phenotypes , indicating that Nodal signals through additional transcription factors during early developme...	Multiple signaling pathways function combinatorially to form and pattern the primary tissue layers of almost all organisms , by interacting with each other and by utilizing different pathway components to perform specific roles . Here we investigated the combinatorial aspects of the Nodal signaling pathway , which is e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "gene", "function", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "pattern", "formation", "signaling", "in", "cellular", "processes", "smad", "signaling", "biology", "molecular", "biology", "zebra...	2011	Nodal-Dependent Mesendoderm Specification Requires the Combinatorial Activities of FoxH1 and Eomesodermin
Cytoadherance of Plasmodium falciparum-infected erythrocytes in the brain , organs and peripheral microvasculature is linked to morbidity and mortality associated with severe malaria . Parasite-derived P . falciparum Erythrocyte Membrane Protein 1 ( PfEMP1 ) molecules displayed on the erythrocyte surface are responsibl...	The unicellular parasite Plasmodium falciparum is the cause of the most severe form of malaria and is responsible for 300 million infections and ∼2 million deaths a year . Infected erythrocytes clump and block capillaries in the peripheral circulation , the brain , and placenta and are a major contributor to the pathol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "microbiology", "molecular", "biology", "genetics", "and", "genomics" ]	2009	Sir2 Paralogues Cooperate to Regulate Virulence Genes and Antigenic Variation in Plasmodium falciparum
The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals , although previous work in plants and yeast suggest a surprisingly modest correlation . We have examined this issue using a genetic approach in which natural variations were ...	An old dogma in biology states that , in every cell , the flow of biological information is from DNA to RNA to proteins and that the latter act as a working force to determine the organism's phenotype . This model predicts that changes in DNA that affect the clinical phenotype should also similarly change the cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/p...	2011	Comparative Analysis of Proteome and Transcriptome Variation in Mouse
Mammalian prion structures and replication mechanisms are poorly understood . Most synthetic recombinant prion protein ( rPrP ) amyloids prepared without cofactors are non-infectious or much less infectious than bona fide tissue-derived PrPSc . This effect has been associated with differences in folding of the aggregat...	Differences in the folding and packing of the prion protein into aggregates are thought to be the molecular basis for variability in prion transmissibility . Recombinant prion protein aggregates prepared without non-protein cofactors typically are less tightly packed within residues ~90–160 and are much less infectious...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "group-specific", "staining", "anatomical", "pathology", "animal", "diseases", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "hematoxylin", "staining", "enzymology", "vertebrates", "animals", "mammals", "or...	2017	Role of the central lysine cluster and scrapie templating in the transmissibility of synthetic prion protein aggregates
The dynamics of Plasmodium vivax infection is characterized by reactivation of hypnozoites at varying time intervals . The relative contribution of new P . vivax infection and reactivation of dormant liver stage hypnozoites to initiation of blood stage infection is unclear . In this study , we investigate the contribut...	Plasmodium vivax is one of two major parasite species causing human disease . This parasite can lie dormant in the liver as a hypnozoite , before later reactivating to cause blood-stage infection . Treatment to eliminate the dormant hypnozoite stage relies mostly on a single drug—primaquine . Understanding the rate of ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Modeling the Dynamics of Plasmodium vivax Infection and Hypnozoite Reactivation In Vivo
Human gene regulatory networks ( GRN ) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes . We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases . In a subnetwork of this GRN that is active during estrogen s...	A gene regulatory network ( GRN ) represents how some genes encoding regulatory molecules such as transcription factors or microRNAs regulate the expression of other genes . Researchers commonly study GRNs involved in a specific biological process with the aim of identifying a few important regulatory genes . In higher...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks
Candida albicans is an opportunistic fungal pathogen that can infect oral mucosal surfaces while being under continuous flow from saliva . Under specific conditions , C . albicans will form microcolonies that more closely resemble the biofilms formed in vivo than standard in vitro biofilm models . However , very little...	Candida albicans is an opportunistic fungal pathogen that can infect many parts of the body , including the oral cavity , where saliva continuously flows across exposed surfaces . However , only a handful of studies have looked at growth under flow , and many questions about how C . albicans grows in these conditions r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "population", "genetics", "microbiology", "epithelial", "cells", "fungi", "regulator", "genes", "experimental", "organism", "systems", "...	2018	Candida albicans Sfl1/Sfl2 regulatory network drives the formation of pathogenic microcolonies
The perceptual representation of individual faces is often explained with reference to a norm-based face space . In such spaces , individuals are encoded as vectors where identity is primarily conveyed by direction and distinctiveness by eccentricity . Here we measured human fMRI responses and psychophysical similarity...	Humans recognize conspecifics by their faces . Understanding how faces are recognized is an open computational problem with relevance to theories of perception , social cognition , and the engineering of computer vision systems . Here we measured brain activity with functional MRI while human participants viewed indivi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "face", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "magnetic", "resonance", "imaging", "face", "recognition", "percepti...	2017	Adjudicating between face-coding models with individual-face fMRI responses
There is widespread interest in the relationship between the neurobiological systems supporting human cognition and emerging computational systems capable of emulating these capacities . Human speech comprehension , poorly understood as a neurobiological process , is an important case in point . Automatic Speech Recogn...	The ability to understand spoken language is a defining human capacity . But despite decades of research , there is still no well-specified account of how sound entering the ear is neurally interpreted as a sequence of meaningful words . At the same time , modern computer-based Automatic Speech Recognition ( ASR ) syst...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "acoustics", "linguistics", "medicine", "and", "health", "sciences", "markov", "models", "magnetoencephalography", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "mathematics", "brain", "mapping", "bioassays", "and", "physiological", ...	2017	Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life . Here , we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swa...	Organisms vary in the number of chromosome sets contained within the nucleus of each cell , but neither the reasons nor the consequences of this variation are well understood . We designed yeasts that differed in the number of chromosome sets but were otherwise identical and mapped the consequences of such ploidy varia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "population", "genetics", "ploidy", "quantitative", "traits", "microbiology", "model", "organisms", "eukaryotic", "evolution", "biology", "trait", "locus", "phenotypes", "heredity", "genetic", "screens", "genetics", "yeast", "and", "fungal", "...	2013	Ancient Evolutionary Trade-Offs between Yeast Ploidy States
Over recent decades , Salmonella infection research has predominantly relied on murine infection models . However , in many cases the infection phenotypes of Salmonella pathovars in mice do not recapitulate human disease . For example , Salmonella Typhimurium ST313 is associated with enhanced invasive infection of immu...	Salmonella Typhimurium ST313 is associated with systemic infection in human populations in sub-Saharan Africa , and contrasts with the related pathovariant ST19 which causes gastrointestinal disease worldwide . Although the systemic pathology associated with ST313 infection in humans has been comprehensively documented...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "microbiology", "vertebrates", "salmonellosis", "animals", "animal", "models", "bacterial", "diseases", "developmental", "biology", "...	2019	The use of chicken and insect infection models to assess the virulence of African Salmonella Typhimurium ST313
Genome-wide association studies ( GWAS ) have now identified at least 2 , 000 common variants that appear associated with common diseases or related traits ( http://www . genome . gov/gwastudies ) , hundreds of which have been convincingly replicated . It is generally thought that the associated markers reflect the eff...	It has long been assumed that common genetic variants of modest effect make an important contribution to common human diseases , such as most forms of cardiovascular disease , asthma , and neuropsychiatric disease . Genome-wide scans evaluating the role of common variation have now been completed for all common disease...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "computational", "biology" ]	2010	Rare Variants Create Synthetic Genome-Wide Associations

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