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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Toll-like receptor signaling requires functional Toll/interleukin-1 ( IL-1 ) receptor ( TIR ) domains to activate innate immunity . By producing TIR homologous proteins , microbes inhibit host response induction and improve their own survival . The TIR homologous protein TcpC was recently identified as a virulence fact...	The clinical manifestations of infection range from beneficial , asymptomatic states to life threatening disease , depending on the arsenal of virulence factors carried by the bacteria and the host immune defence repertoire . Pathogenic bacteria have evolved many sophisticated ways of avoiding the host defence and espe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/innate", "immunity" ]	2010	Inhibition of TIR Domain Signaling by TcpC: MyD88-Dependent and Independent Effects on Escherichia coli Virulence
Pseudokinases lack essential residues for kinase activity , yet are emerging as important regulators of signal transduction networks . The pseudokinase STRAD activates the LKB1 tumour suppressor by forming a heterotrimeric complex with LKB1 and the scaffolding protein MO25 . Here , we describe the structure of STRADα i...	There are 518 human protein kinases that are responsible for orchestrating the phosphorylation-dependant signal transduction events that regulate almost all cellular processes . Curiously , approximately 10% of protein kinases lack one or more catalytic residues , and these kinases have been termed pseudokinases . It h...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/structural", "genomics", "molecular", "bi...	2009	ATP and MO25α Regulate the Conformational State of the STRADα Pseudokinase and Activation of the LKB1 Tumour Suppressor
Wolbachia endosymbionts carried by filarial nematodes give rise to the neglected diseases African river blindness and lymphatic filariasis afflicting millions worldwide . Here we identify new Wolbachia-disrupting compounds by conducting high-throughput cell-based chemical screens using a Wolbachia-infected , fluorescen...	Wolbachia-based neglected diseases currently threaten one sixth of the world population . Millions of people are infected with filarial nematodes that rely upon endosymbiotic Wolbachia bacteria for their survival . These Wolbachia ultimately induce an immune response that gives rise to African river blindness or lympha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "drugs", "and", "devices", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	A Cell-Based Screen Reveals that the Albendazole Metabolite, Albendazole Sulfone, Targets Wolbachia
In the sea urchin embryo , specification of the dorsal-ventral axis critically relies on the spatially restricted expression of nodal in the presumptive ventral ectoderm . The ventral restriction of nodal expression requires the activity of the maternal TGF-β ligand Panda but the mechanism by which Panda restricts noda...	Specification of the embryonic axes is an essential step during early development of metazoa . In the sea urchin embryo , specification of the dorsal-ventral axis critically relies on the spatial restriction of the expression of the TGF-ß family member Nodal in ventral cells , a process that requires the activity of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "invertebrates", "morpholino", "rna", "interference", "nucleotides", "animals", "blastulas", "animal", "models", "developmental", "biology", "experimental", "organism", "systems", "epigenetics", "molecular", "biology", "techniques", "embryos", "echinoderms"...	2018	MAPK and GSK3/ß-TRCP-mediated degradation of the maternal Ets domain transcriptional repressor Yan/Tel controls the spatial expression of nodal in the sea urchin embryo
The Drosophila larva executes a stereotypical exploratory routine that appears to consist of stochastic alternation between straight peristaltic crawling and reorientation events through lateral bending . We present a model of larval mechanics for axial and transverse motion over a planar substrate , and use it to deve...	We investigate the relationship between brain , body and environment in the exploratory behaviour of fruitfly larva . A larva crawls forward by propagating a wave of compression through its segmented body , and changes its crawling direction by bending to one side or the other . We show first that a purely mechanical m...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "neuroscience", "biological", "locomotion", "motor", "neurons", "developmental", "biology", "reflexes", "damage", "mechanics", "waves", "traveling", "waves", "bending", "animal", "cells", "deformation", ...	2019	Modelling the mechanics of exploration in larval Drosophila
Animal African trypanosomosis , a disease mainly caused by the protozoan parasite Trypanosoma congolense , is a major constraint to livestock productivity and has a significant impact in the developing countries of Africa . RNA interference ( RNAi ) has been used to study gene function and identify drug and vaccine tar...	Trypanosoma congolense is a parasite responsible for severe disease of African livestock . Its life cycle is complex and divided into two phases , one in the tsetse fly vector and one in the bloodstream of the mammalian host . Molecular tools for gene function analyses in parasitic organisms are essential . Previous st...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/microbial", "growth", "and", "development", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections" ]	2010	Complete In Vitro Life Cycle of Trypanosoma congolense: Development of Genetic Tools
PARP inhibition can induce anti-neoplastic effects when used as monotherapy or in combination with chemo- or radiotherapy in various tumor settings; however , the basis for the anti-metastasic activities resulting from PARP inhibition remains unknown . PARP inhibitors may also act as modulators of tumor angiogenesis . ...	Metastasis is the spread of malignant tumor cells from their original site to other parts of the body and is responsible for the vast majority of solid cancer-related mortality . PARP inhibitors are emerging as promising anticancer therapeutics and are currently undergoing clinical trials . It is therefore important to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "cancer", "genetics", "rna", "interference", "antiangiogenesis", "therapy", "gene", "expression", "genetics", "cancer", "treatment", "biology", "dna", "modification", "dna", "transcription" ]	2013	PARP-1 Regulates Metastatic Melanoma through Modulation of Vimentin-induced Malignant Transformation
Brucella melitensis is a facultative intracellular bacterium that causes brucellosis , the most prevalent zoonosis worldwide . The Brucella intracellular replicative niche in macrophages and dendritic cells thwarts immune surveillance and complicates both therapy and vaccine development . Currently , host-pathogen inte...	Brucella melitensis is an intracellular bacterium that invades and replicates within macrophages and dendritic cells . With over 500 , 000 new infections per year , brucellosis is the most prevalent zoonosis worldwide and incurs significant human morbidity and economic loss . The intracellular location of Brucella rend...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Brucella Induces an Unfolded Protein Response via TcpB That Supports Intracellular Replication in Macrophages
Nearly 45% of people living at risk for lymphatic filariasis ( LF ) worldwide live in India . India has faced challenges obtaining the needed levels of compliance with its mass drug administration ( MDA ) program to interrupt LF transmission , which utilizes diethylcarbamazine ( DEC ) or DEC plus albendazole . Previous...	Global elimination of lymphatic filariasis requires giving drugs at least annually to populations who live at risk of becoming infected with the parasite . At least 80% of people at risk need to take the drugs annually for 5 or more years to stop transmission of the infection . People suffering from the long-term effec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	Increasing Compliance with Mass Drug Administration Programs for Lymphatic Filariasis in India through Education and Lymphedema Management Programs
Cryptococcus neoformans is an opportunistic fungal pathogen that causes serious human disease in immunocompromised populations . Its polysaccharide capsule is a key virulence factor which is regulated in response to growth conditions , becoming enlarged in the context of infection . We used microarray analysis of cells...	Cryptococcus neoformans is a fungal pathogen that causes serious disease in immunocompromised individuals , killing over 600 , 000 people per year worldwide . A major factor in the ability of this microbe to cause disease is an extensive polysaccharide capsule that surrounds the cell and interferes with the host immune...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "cellular", "stress", "responses", "genetic", "networks", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "microbiology", "histone", "modification", "genome", "analysis", "tools", "molecular", "genetics", "chr...	2011	Toward an Integrated Model of Capsule Regulation in Cryptococcus neoformans
The continued northwards spread of Rhodesian sleeping sickness or Human African Trypanosomiasis ( HAT ) within Uganda is raising concerns of overlap with the Gambian form of the disease . Disease convergence would result in compromised diagnosis and treatment for HAT . Spatial determinants for HAT are poorly understood...	Human African Trypanosomiasis ( HAT ) or sleeping sickness is a parasitic disease of humans , transmitted by the tsetse fly . There are two different forms of HAT: Rhodesian ( in eastern sub-Saharan Africa ) , which also affects wild and domestic animals , and Gambian ( in western and central sub-Saharan Africa ) . Dia...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	Spatial Predictions of Rhodesian Human African Trypanosomiasis (Sleeping Sickness) Prevalence in Kaberamaido and Dokolo, Two Newly Affected Districts of Uganda
Linkage analysis is useful in investigating disease transmission dynamics and the effect of interventions on them , but estimates of probabilities of linkage between infected people from observed data can be biased downward when missingness is informative . We investigate variation in the rates at which subjects' viral...	The analysis of viral genomes has great potential for investigating transmission of disease , including the identification of risk factors and transmission clusters , and can thereby aid in targeting interventions . To make use of genetic data in this way , it is necessary to make inferences about population-level patt...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequence", "analysis", "epidemiological", "methods", "mathematics", "infectious", "disease", "epidemiology", "epidemiology", "statistics", "genetics", "population", "biology", "biology", "computational", "biology", "biostatistics", "genetics", "of", "disease", "statistical",...	2014	Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data
ESCRT-III proteins catalyze membrane fission during multi vesicular body biogenesis , budding of some enveloped viruses and cell division . We suggest and analyze a novel mechanism of membrane fission by the mammalian ESCRT-III subunits CHMP2 and CHMP3 . We propose that the CHMP2-CHMP3 complexes self-assemble into hemi...	Membrane fission is a key step of fundamental intracellular processes such as endocytosis , membrane trafficking , cytokinesis and virus budding . The fission reaction requires substantial energy inputs provided by specialized proteins . Recently , the ESCRT-III proteins have been implicated in membrane budding and fis...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "biophysics/cell", "signaling", "and", "trafficking", "structures", "biophysics/theory", "and", "simulation" ]	2009	Computational Model of Membrane Fission Catalyzed by ESCRT-III
Human bocavirus 1 ( HBoV1 ) belongs to the genus Bocaparvovirus of the Parvoviridae family , and is an emerging human pathogenic respiratory virus . In vitro , HBoV1 infects well-differentiated/polarized primary human airway epithelium ( HAE ) cultured at an air-liquid interface ( HAE-ALI ) . Although it is well known ...	Parvovirus is unique among DNA viruses . It has a single stranded DNA genome of ~5 . 5 kb in length . Autonomous parvoviruses , which replicate autonomously in cells , rely on the S phase cell cycle for genome amplification . In the current study , we demonstrated that human bocavirus 1 ( HBoV1 ) , an autonomous human ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Replication of an Autonomous Human Parvovirus in Non-dividing Human Airway Epithelium Is Facilitated through the DNA Damage and Repair Pathways
Cripto , the founding member of the EGF-CFC genes , plays an essential role in embryo development and is involved in cancer progression . Cripto is a GPI-anchored protein that can interact with various components of multiple signaling pathways , such as TGF-β , Wnt and MAPK , driving different processes , among them ep...	Cripto gene has a fundamental role in embryo development and is also involved in cancer . The protein is bound to the cell membrane through an anchor , that can be cleaved , causing the secretion of the protein , in a still active form . In the adult , CRIPTO is detected at very low levels in normal tissues and in the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Genetic Variants Modulating CRIPTO Serum Levels Identified by Genome-Wide Association Study in Cilento Isolates
The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes , called PIWI-interacting RNA ( piRNA ) , with similarities to microRNAs and repeat-associated small interfering RNAs ( rasiRNAs ) , has raised puzzling questions regarding their biogenesis and function . We report a comparative analysis...	The discovery of a new class of mammalian small regulatory RNAs termed PIWI-interacting RNA ( piRNA ) has extended the diverse family of small regulatory RNAs . PIWI proteins are a subclass of the larger Argonaute proteins family , of which the Ago members bind microRNAs and play a critical role in gene silencing . Des...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "mus", "(mouse)", "homo", "(human)", "genetics", "and", "genomics", "computational", "biology" ]	2007	Computational Analysis of Mouse piRNA Sequence and Biogenesis
Influenza is a major cause of morbidity and mortality in immunosuppressed persons , and vaccination often confers insufficient protection . IL-28B , a member of the interferon ( IFN ) -λ family , has variable expression due to single nucleotide polymorphisms ( SNPs ) . While type-I IFNs are well known to modulate adapt...	Infection with influenza viruses is associated with high morbidity and mortality . Therefore , vaccination is recommended in immunosuppressed patients , however often the post-vaccine induced protection is insufficient . Factors associated with reduced vaccine responses may guide preventive strategies and could offer n...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "vaccines", "clinical", "immunology", "virology", "immune", "deficiency", "biology", "and", "life", "sciences", "immunology", "vaccination", "and", "immunization", "microbiology", "immune", "response", "immunocompetence" ]	2014	IL-28B is a Key Regulator of B- and T-Cell Vaccine Responses against Influenza
Learning arises through the activity of large ensembles of cells , yet most of the data neuroscientists accumulate is at the level of individual neurons; we need models that can bridge this gap . We have taken spatial learning as our starting point , computationally modeling the activity of place cells using methods de...	One of the challenges in contemporary neuroscience is that we have few ways to connect data about the features of individual neurons with effects ( such as learning ) that emerge only at the scale of large cell ensembles . We are tackling this problem using spatial learning as a starting point . In previous work we cre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "learning", "and", "memory" ]	2014	The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map
To communicate effectively animals need to detect temporal vocalization cues that vary over several orders of magnitude in their amplitude and frequency content . This large range of temporal cues is evident in the power-law scale-invariant relationship between the power of temporal fluctuations in sounds and the sound...	The efficient coding hypothesis posits that the brain encodes sensory signals efficiently in order to reduce metabolic cost and preserve behaviorally relevant environment information . In audition , recognition and coding depends on the brain’s ability to accurately and efficiently encode statistical regularities that ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "acoustics", "vocalization", "linguistics", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "neuroscience", "animal", "signaling", "and", "communication", "animal", "behavior", "computational", "neuroscience", "bandwidth", "(signal", "proce...	2018	Origins of scale invariance in vocalization sequences and speech
Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression , protein synthesis , and viral . We report herein that high-throughput chemical experiments can isolate an RNA’s multiple alternative secondary structures as they are stabilized by systematic mutagenesis ( ...	RNA is a versatile macromolecule that underlies core natural processes throughout living systems and new strategies to re-engineer these systems . In several cases , this versatility is due to the ability of an RNA molecule to adopt multiple conformations: the full description of the molecule involves a ‘landscape’ of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Data", "set", "and", "software", "availability" ]	[]	2015	Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis
Feeding behavior is one of the most essential activities in animals , which is tightly regulated by neuroendocrine factors . Drosophila melanogaster short neuropeptide F ( sNPF ) and the mammalian functional homolog neuropeptide Y ( NPY ) regulate food intake . Understanding the molecular mechanism of sNPF and NPY sign...	Feeding behavior is one of the most essential activities in animals . Abnormal feeding behaviors cause metabolic syndromes including obesity and diabetes . Neuropeptides regulate feeding behavior in animals from nematode to human . Here , we presented molecular genetic evidences of how neuropeptides regulate food intak...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "gene", "regulation", "neuroscience", "gene", "function", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "molecular", "genetics", "biology", "mouse", "molecular", "biology", "signal", "transduction", "phenotypes", "heredity",...	2012	Minibrain/Dyrk1a Regulates Food Intake through the Sir2-FOXO-sNPF/NPY Pathway in Drosophila and Mammals
In order to be transmitted , a pathogen must first successfully colonize and multiply within a host . Ecological principles can be applied to study host-pathogen interactions to predict transmission dynamics . Little is known about the population biology of Salmonella during persistent infection . To define Salmonella ...	Salmonella enterica serovars infect various mammalian hosts , causing disease ranging from self-limiting diarrhea to persistent systemic infections such as typhoid fever . Here we investigated the impact of an established intestinal S . Typhimurium population on fecal shedding in the presence of another challenging str...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "ecological", "niches", "community", "structure", "microbiology", "bacterial", "diseases", "bacterial", "pathogens", "salmonella", "typhimurium", "animal", "models", "of", "infection", "infectious", "diseases", "medical", "microbio...	2014	Intraspecies Competition for Niches in the Distal Gut Dictate Transmission during Persistent Salmonella Infection
Prostate cancer ( PCa ) is the most commonly diagnosed malignancy and the second leading cause of cancer-related death in American men . Androgen deprivation therapy ( ADT ) has become a standard treatment strategy for advanced PCa . Although a majority of patients initially respond to ADT well , most of them will even...	Prostate cancer ( PCa ) is the second leading cause of cancer-related deaths in American men . Androgen deprivation therapy ( ADT ) is the first-line therapy for advanced PCa , yet a significant number of primary PCa patients treated with ADT eventually develop incurable castration-resistant prostate cancer ( CRPC ) . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "urology", "medicine", "and", "health", "sciences", "immune", "cells", "cardiovascular", "physiology", "cancer", "treatment", "immunology", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "basic", "cancer", "research", "surgical", ...	2019	Systematically understanding the immunity leading to CRPC progression
It has been suggested that genetic susceptibility plays an important role in the pathogenesis of diabetic nephropathy . A large-scale genotyping analysis of gene-based single nucleotide polymorphisms ( SNPs ) in Japanese patients with type 2 diabetes identified the gene encoding acetyl-coenzyme A carboxylase beta ( ACA...	Although cumulative epidemiological findings have suggested that genetic susceptibility plays an important role in the pathogenesis of diabetic nephropathy , no gene conferring susceptibility to diabetic nephropathy has been definitively identified . In a large-scale association study of 1 , 312 Japanese subjects with ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "nephrology", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2010	A Single Nucleotide Polymorphism within the Acetyl-Coenzyme A Carboxylase Beta Gene Is Associated with Proteinuria in Patients with Type 2 Diabetes
The removal of introns from eukaryotic RNA transcripts requires the activities of five multi-component ribonucleoprotein complexes and numerous associated proteins . The lack of mutations affecting splicing factors essential for animal survival has limited the study of the in vivo regulation of splicing . From a screen...	Eukaryotic genes contain intervening intronic sequences that must be removed from pre-mRNA transcripts by RNA splicing to generate functional messenger RNAs . While studying genes that encode and control a presumptive muscle potassium channel complex in the nematode Caenorhabditis elegans , we found that mutations in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/gene", "expression" ]	2009	Mutations in the Caenorhabditis elegans U2AF Large Subunit UAF-1 Alter the Choice of a 3′ Splice Site In Vivo
The elderly are particularly susceptible to influenza A virus infections , with increased occurrence , disease severity and reduced vaccine efficacy attributed to declining immunity . Experimentally , the age-dependent decline in influenza-specific CD8+ T cell responsiveness reflects both functional compromise and the ...	The elderly population is particularly susceptible to novel infections , especially the annual , seasonal epidemics caused by influenza viruses . Established T cell immunity directed at conserved viral regions provides some protection against influenza infection and promotes more rapid recovery , thus leading to better...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases" ]	2012	Early Priming Minimizes the Age-Related Immune Compromise of CD8+ T Cell Diversity and Function
Schistosomiasis japonica still remains of public health and economic significance in China , especially in the lake and marshland areas along the Yangtze River Basin , where the control of transmission has proven difficult . In the study , we investigated spatio-temporal variations of S . japonicum infection risk in An...	Schistosomiasis japonica is one of the most serious parasitic diseases in China . It is estimated that more than 50 million people are still at risk , especially those living in the lake and marshland areas along the Yangtze River Basin . The Chinese government has made great efforts to implement schistosomiasis contro...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Spatio-temporal Transmission and Environmental Determinants of Schistosomiasis Japonica in Anhui Province, China
Multifunctionality is a common trait of many natural proteins and peptides , yet the rules to generate such multifunctionality remain unclear . We propose that the rules defining some protein/peptide functions are compatible . To explore this hypothesis , we trained a computational method to predict cell-penetrating pe...	Most proteins and peptides in nature display multiple activities either by fusing different domains ( with different activities ) or by evolving multiple activities in a single domain . Understanding which activities may be combined to render multifunctional proteins remains an open question relevant to understanding t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "sequencing", "techniques", "medicine", "and", "health", "sciences", "drugs", "microbiology", "dna-binding", "proteins", "optimization", "mathematics", "antibacterials", "pharmacology", "molecular", "biology", "techniques", "chemical", "synthesis", "research...	2016	Effective Design of Multifunctional Peptides by Combining Compatible Functions
Sugars are important nutrients for many animals , but are also proposed to contribute to overnutrition-derived metabolic diseases in humans . Understanding the genetic factors governing dietary sugar tolerance therefore has profound biological and medical significance . Paralogous Mondo transcription factors ChREBP and...	Diet displays extreme natural variation between animal species , which range from highly specialized carnivores , herbivores , and nectarivores to flexible dietary generalists . Humans are not identical in this respect either , but the genetic background likely defines the framework for a healthy diet . However , we un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "genetic", "mutation", "molecular", "cell", "biology", "genetic", "screens", "gene", "expression", "genetics", "biology", "gene", "networks", "molecular", "biology", "genetics", "and", "genomics", "gene", "function" ]	2013	Mondo/ChREBP-Mlx-Regulated Transcriptional Network Is Essential for Dietary Sugar Tolerance in Drosophila
Dengue virus ( DENV ) is a pathogen with a high impact on human health . It replicates in a wide range of cells involved in the immune response . To efficiently infect humans , DENV must evade or inhibit fundamental elements of the innate immune system , namely the type I interferon response . DENV circumvents the host...	Dengue virus ( DENV ) is a pathogen with a high impact in human health that replicates in a wide range of cells of the immune system . To efficiently infect humans , DENV must evade or inhibit fundamental elements of the innate immune system , namely the type I interferon response ( IFN ) . Thus , DENV can inhibit type...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2012	DENV Inhibits Type I IFN Production in Infected Cells by Cleaving Human STING
Retroviral recombination is thought to play an important role in the generation of immune escape and multiple drug resistance by shuffling pre-existing mutations in the viral population . Current estimates of HIV-1 recombination rates are derived from measurements within reporter gene sequences or genetically divergent...	HIV's ability to generate and maintain high genetic diversity leads to multiple drug resistances and evasion from the immune system , eventually leading to immune failure and progression to AIDS . HIV maintains this diversity with a process of mutation ( incorrect copying of genetic information in viral replication ) a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "mathematics/statistics", "virology/viral", "replication", "and", "gene", "regulation", "computational", "biology" ]	2010	Accurately Measuring Recombination between Closely Related HIV-1 Genomes
Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations . Recent studies have shown that the summed activity of all neurons strongly shapes the population response . A separate recent finding has been that neural populations also exhibit criticality , an ...	Populations of sensory neurons represent information about the outside environment in a collective fashion . A salient property of this distributed neural code is criticality . Yet most models used to date to analyze recordings from large neural populations do not take this observation explicitly into account . Here we...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "linguistics", "social", "sciences", "random", "variables", "neuroscience", "covariance", "probability", "distribution", "mathematics", "statistics", "(mathematics)", "thermodynamics", "entropy", "animal", "cells", "probability", "density", "probability", "theory", "physics",...	2017	Probabilistic models for neural populations that naturally capture global coupling and criticality
Extracellular trypanosomes can cause a wide range of diseases and pathological complications in a broad range of mammalian hosts . One common feature of trypanosomosis is the occurrence of anemia , caused by an imbalance between erythropoiesis and red blood cell clearance of aging erythrocytes . In murine models for T ...	Extracellular trypanosomes , causative agents of sleeping sickness and Nagana , threaten human and animal health throughout the world . Anemia is a hallmark feature of virtually every type of trypanosome infection . During the early phase of experimental murine trypanosomosis , acute anemia occurs as witnessed by a 50%...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Development of a pHrodo-Based Assay for the Assessment of In Vitro and In Vivo Erythrophagocytosis during Experimental Trypanosomosis
A cross sectional serological survey of arboviral infections in humans was conducted on the three islands of the Union of Comoros , Indian Ocean , in order to test a previously suggested contrasted exposure of the three neighboring islands to arthropod-borne epidemics . Four hundred human sera were collected on Ngazidj...	Peculiarities of Island ecosystems make oceanic islands most suitable areas for analyzing how variations in local ecological conditions may impact on the intensity of arboviral transmission . The Comoros archipelago ( 2144 Km2 ) consists of four volcanic islands that are distant of 40–60 Km apart , located at the north...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "immunology", "geographical", "locations", "microbiology", "alph...	2016	Serological Evidence of Contrasted Exposure to Arboviral Infections between Islands of the Union of Comoros (Indian Ocean)
Phytoplankton are key components of aquatic ecosystems , fixing CO2 from the atmosphere through photosynthesis and supporting secondary production , yet relatively little is known about how future global warming might alter their biodiversity and associated ecosystem functioning . Here , we explore how the structure , ...	At the global scale , phytoplankton take up about as much carbon dioxide ( CO2 ) as the tropical rainforests . However , in spite of their importance in global carbon cycles , we understand very little about how phytoplankton communities and the critical functions they mediate , including CO2 sequestration , are likely...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Five Years of Experimental Warming Increases the Biodiversity and Productivity of Phytoplankton
Insect flight is regulated by various sensory inputs and neuromodulatory circuits which function in synchrony to control and fine-tune the final behavioral outcome . The cellular and molecular bases of flight neuromodulatory circuits are not well defined . In Drosophila melanogaster , it is known that neuronal IP3 rece...	A majority of behavioral patterns in flying insects depend upon their ability to modulate flight . In Drosophila melanogaster , mutations in the IP3 receptor gene lead to loss of voluntary flight in response to a natural stimulus like a gentle air-puff . From previous genetic and cellular studies it is known that the I...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Genetic RNAi Screen for IP3/Ca2+ Coupled GPCRs in Drosophila Identifies the PdfR as a Regulator of Insect Flight
Impaired mitochondrial oxidative phosphorylation ( OXPHOS ) has been proposed as an etiological mechanism underlying insulin resistance . However , the initiating organ of OXPHOS dysfunction during the development of systemic insulin resistance has yet to be identified . To determine whether adipose OXPHOS deficiency p...	Type 2 diabetes is one of the most challenging health problems in the 21st century . Although insulin resistance is regarded as a fundamental defect that precedes the development of type 2 diabetes , the nature and cause of insulin resistance remain unknown . Adipose tissue is an important organ that determines whole-b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	Crif1 Deficiency Reduces Adipose OXPHOS Capacity and Triggers Inflammation and Insulin Resistance in Mice
Plants are continually exposed to pathogen attack but usually remain healthy because they can activate defences upon perception of microbes . However , pathogens have evolved to overcome plant immunity by delivering effectors into the plant cell to attenuate defence , resulting in disease . Recent studies suggest that ...	The highly conserved Mediator complex plays an essential role in transcriptional regulation by providing a molecular bridge between transcription factors and RNA polymerase II . Recent studies in Arabidopsis have revealed that it also performs an essential role in plant defence . However , it remains unknown how pathog...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging tick-borne viral disease caused by the SFTS virus ( SFTSV ) from Bunyaviridae that is endemic in East Asia . However , the genetic and evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited . In this ...	Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging tick-borne viral disease caused by the SFTS virus ( SFTSV ) . During entomological surveillance of SFTSV infection in Korean ticks collected from SFTS outbreak areas , we isolated a single SFTSV strain which we designated KAGWT . In addition , we isola...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "taxonomy", "amino", "acid", "sequence", "analysis", "phylogenetics", "data", "management", "phylogenetic", "analysis", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "computer", "and", ...	2017	Molecular genomic characterization of tick- and human-derived severe fever with thrombocytopenia syndrome virus isolates from South Korea
New approaches and tools were needed to support the strategic planning , implementation and management of a Program launched by the Brazilian Government to fund research , development and capacity building on neglected tropical diseases with strong focus on the North , Northeast and Center-West regions of the country w...	The selection and prioritization of research proposals is always a challenge , particularly when addressing neglected tropical diseases , as the scientific communities are relatively small , funding is usually limited and the disparity between the science and technology capacity of different countries and regions is en...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "science", "policy" ]	2009	Co-authorship Network Analysis: A Powerful Tool for Strategic Planning of Research, Development and Capacity Building Programs on Neglected Diseases
Neurons must faithfully encode signals that can vary over many orders of magnitude despite having only limited dynamic ranges . For a correlated signal , this dynamic range constraint can be relieved by subtracting away components of the signal that can be predicted from the past , a strategy known as predictive coding...	An animal exploring a natural scene receives sensory inputs that vary , rapidly , over many orders of magnitude . Neurons must transmit these inputs faithfully despite both their limited dynamic range and relatively slow adaptation time scales . One well-accepted strategy for transmitting signals through limited dynami...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit
Typhoid is an important public health challenge for India , especially with the spread of antimicrobial resistance . The decision about whether to introduce a public vaccination programme needs to be based on an understanding of disease burden and the age-groups and geographic areas at risk . We searched Medline and We...	Typhoid fever is an important cause of avoidable mortality in regions without adequate access to safe water and sanitation . Highly immunogenic typhoid conjugate vaccines are now licensed and under consideration as a public health intervention in India . The decision about whether and how to introduce a public vaccinat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "geographical", "locations", "india", "vaccines", "preventive", "medicine", "bacterial", "diseases", "signs", "and", "symptoms", "vaccination", "and", "immunization", "r...	2016	The Burden of Typhoid and Paratyphoid in India: Systematic Review and Meta-analysis
Environmental signals induce diverse cellular differentiation programs . In certain systems , cells defer differentiation for extended time periods after the signal appears , proliferating through multiple rounds of cell division before committing to a new fate . How can cells set a deferral time much longer than the c...	How long should a cell wait to respond to an environmental change ? While many pathways such as those affecting chemotaxis respond to environmental signals quickly , in other contexts a cell may want to defer its response until long after the signal's onset—sometimes waiting multiple cell cycles . How can cells create ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "prokaryotic", "models", "model", "organisms", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Pulsed Feedback Defers Cellular Differentiation
Since the 1990s , Singapore has experienced periodic dengue epidemics of increasing frequency and magnitude . In the aftermath of the 2004–2005 dengue epidemic , hospitals refined their admission criteria for dengue cases to right-site dengue case management and reduce the burden of healthcare utilization and negative ...	Following the review of hospital admission criteria for dengue cases in the aftermath of the 2004–2005 dengue epidemic in Singapore , the proportion of dengue cases hospitalized plummeted from 72 . 6% in 2006 to the nadir of 25 . 6% in 2014 . There was no concomitant increase in adverse outcomes as a result of the more...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "hospitalizations", "medicine", "and", "health", "sciences", "elderly", "geographical", "locations", "tropical", "diseases", "health", "care", "singapore", "age", "groups", "neglected", "tropical", "diseases", "infectious", "diseases", "intensive", "care", "units", "pri...	2019	A 15-year review of dengue hospitalizations in Singapore: Reducing admissions without adverse consequences, 2003 to 2017
A fundamental problem in developmental biology concerns how multipotent precursors choose specific fates . Neural crest cells ( NCCs ) are multipotent , yet the mechanisms driving specific fate choices remain incompletely understood . Sox10 is required for specification of neural cells and melanocytes from NCCs . Like ...	Stem and other multipotent cells generate diverse cell-types , but our understanding of how they make these decisions , which is important for their therapeutic use , is incomplete . Neural crest cells are an important class of multipotent cells and generate multiple stem cell types . We have looked at how pigment cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/developmental", "molecular", "mechanisms", "developmental", "biology/stem", "cells" ]	2008	Leukocyte Tyrosine Kinase Functions in Pigment Cell Development
Sensitization to Anisakis spp . can produce allergic reactions after eating raw or undercooked parasitized fish . Specific IgE is detected long after the onset of symptoms , but the changes in specific IgE levels over a long follow-up period are unknown; furthermore , the influence of Anisakis spp . allergen exposure t...	The nematode Anisakis spp . is a parasite of marine mammals that can parasitize humans when a raw or undercooked fish containing live Anisakis spp . larvae is consumed . As a result , gastrointestinal and/or allergic symptoms are reported . The allergic reaction can be diagnosed by quantifying the serum specific IgE ag...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "molecular", "probe", "techniques", "immunology", "immunoblotting", "vertebrates", "diet", "marine", "biology", "animals", "marine", "fish", "physiological", "processes", "clinical", "medicine", "nutrition", "fishe...	2016	Changes over Time in IgE Sensitization to Allergens of the Fish Parasite Anisakis spp.
The secondary metabolome provides pathogenic fungi with a plethoric and versatile panel of molecules that can be deployed during host ingress . While powerful genetic and analytical chemistry methods have been developed to identify fungal secondary metabolites ( SMs ) , discovering the biological activity of SMs remain...	Several fungal pathogens produce bioactive small molecules , commonly known as secondary metabolites ( SMs ) that contribute towards disease development in susceptible hosts . Genome assessment of human pathogenic Aspergillus species indicates these fungi have the capabilities of producing hundreds of SMs , most of whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bioengineering", "biomedical", "engineering", "biotechnology", "mycology", "fungi", "immunology", "biology", "microbiology", "immune", "response", "engineering" ]	2013	Low-Volume Toolbox for the Discovery of Immunosuppressive Fungal Secondary Metabolites
Myosin VI has been studied in both a monomeric and a dimeric form in vitro . Because the functional characteristics of the motor are dramatically different for these two forms , it is important to understand whether myosin VI heavy chains are brought together on endocytic vesicles . We have used fluorescence anisotropy...	Myosin VI is a molecular motor implicated in diverse cell processes , including trafficking endocytic vesicles into the cell , transporting proteins to the leading edge of a migrating cell , and anchoring stereocilia to the hair cells of inner ear sensory epithelia . The motor has been studied in both a monomeric and d...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "in", "vitro", "biophysics" ]	2007	Precise Positioning of Myosin VI on Endocytic Vesicles In Vivo
Chemical and nutrient signaling are fundamental for all cellular processes , including interactions between the mammalian host and the microbiota , which have a significant impact on health and disease . Ethanolamine is an essential component of cell membranes and has profound signaling activity within mammalian cells ...	Chemical signaling underlies all cellular processes . Bacteria rely on chemical signaling to gain information about the local environment and precisely regulate gene expression . Ethanolamine is an abundant molecule within mammalian hosts that plays an important role in mammalian physiology and also serves as a carbon ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection
International seaports are hotspots for disease invasion and pathogens can persist in seaports even after ports are abandoned . Transmitted by fleas infected by Rickettsia typhi , murine typhus , a largely neglected and easily misdiagnosed disease , is known to occur primarily in large seaports . However , the signific...	Globalization has hastened the spread of infectious diseases , with seaports as hotspots for disease invasion . Transmitted by fleas infected with the rickettsia Rickettsia typhi , murine typhus occurs worldwide , but its significance as a common causative agent of illness in tropical regions remains largely neglected ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "typhus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "rickettsia", "bacterial", "diseases", "fleas", "murine", "typh...	2017	Significance of major international seaports in the distribution of murine typhus in Taiwan
Schistosomiasis is a parasitic flatworm disease that infects 200 million people worldwide . The drug praziquantel ( PZQ ) is the mainstay therapy but the target of this drug remains ambiguous . While PZQ paralyses and kills parasitic schistosomes , in free-living planarians PZQ caused an unusual axis duplication during...	Schistosomiasis ( Bilharzia ) is one of the most burdensome parasitic worm infections , encumbering third world economies with an annual loss of several million disability-adjusted life years . The key treatment for schistosome infections is the drug praziquantel but the mechanism of action of this drug remains controv...	[ "Abstract", "Introduction", "Results", "&", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "molecular", "neuroscience", "stem", "cells", "small", "molecules", "parasitology", "neurotransmitters", "biology", "cell", "differentiation", "zoology", "neuroscience", "pattern", "formation", "drug", "discovery", "evolutionary", ...	2014	‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-schistosomal Agents
The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen , Burkholderia pseudomallei . B . ubonensis has been reported in northern Australia and Thailand but not North America , suggesting similar geographic distribution to B . pseudomallei . Unlike m...	The pathogenic bacterium Burkholderia pseudomallei causes the disease melioidosis , which occurs in most tropical regions across the globe . The true burden of melioidosis is unknown but has been predicted to affect 165 , 000 people every year , resulting in 89 , 000 deaths . B . pseudomallei is easily confused with it...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion", "Conclusions" ]	[ "biogeography", "taxonomy", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "burkholderia", "pseudomallei", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "genetics", "microbiology", "ethnicities", "animal", ...	2017	Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis
Fungal biofilms are a major cause of human mortality and are recalcitrant to most treatments due to intrinsic drug resistance . These complex communities of multiple cell types form on indwelling medical devices and their eradication often requires surgical removal of infected devices . Here we implicate the molecular ...	Candida albicans and Aspergillus fumigatus are the most common causative agents of fungal infections worldwide . Both species can form biofilms on host tissues and indwelling medical devices that are highly resistant to antifungal treatment . Here we implicate the molecular chaperone Hsp90 as a key regulator of biofilm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology" ]	2011	Hsp90 Governs Dispersion and Drug Resistance of Fungal Biofilms
We have developed an efficient method to quantify cell-to-cell infection with single-cycle , replication dependent reporter vectors . This system was used to examine the mechanisms of infection with HTLV-1 and HIV-1 vectors in lymphocyte cell lines . Effector cells transfected with reporter vector , packaging vector , ...	Cell-free virus particles released from infected cells can be transmitted to target cells by diffusion or may be conveyed directly to target cells via specific intercellular contacts; the latter is referred to as cell-to-cell infection . Microscopic imaging has shown how viral proteins and virus particles move within a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/viral", "replication", "and", "gene", "regulation", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Quantitative Comparison of HTLV-1 and HIV-1 Cell-to-Cell Infection with New Replication Dependent Vectors
The functional networks of cultured neurons exhibit complex network properties similar to those found in vivo . Starting from random seeding , cultures undergo significant reorganization during the initial period in vitro , yet despite providing an ideal platform for observing developmental changes in neuronal connecti...	Many social , technological and biological networks exhibit properties that are neither completely random , nor fully regular . They are known as complex networks and statistics exist to characterize their structure . Until recently , such networks have primarily been analyzed as fixed structures , which enable interac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "neurobiology", "of", "disease", "and", "regeneration", "signaling", "networks", "geometry", "neuroscience", "biomedical", "engineering", "biological", "systems", "engineering", "mathematics", "bioengineering", "developmental", "neuroscience", "biology", "neu...	2012	Emergence of a Small-World Functional Network in Cultured Neurons
Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes . Many bacterial mRNAs adopt structures in their 5′ untranslated regions that modulate the accessibility of the 30S ribosomal subunit . Structured mRNAs interact with the 30S in a two-step proce...	Gene expression is regulated at multiple levels , including the decision of whether or not to translate a mRNA . This phenomenon , known as translational regulation , allows rapid changes in cellular concentrations of proteins and is well suited to the adjustment of cellular growth in response to stress and environment...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation
High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition . However , these methods are limited in number of peptides , sequence variation , and length of peptides that can be explored , and often produce solutions that are not found in the cell . Des...	Here we describe the first strategy for the exhaustive search of the linear information encoding protein-peptide recognition; an approach that has previously been physically unfeasible because the combinatorial space of polypeptide sequences is too vast . The search covers the entire space of sequences with no restrict...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "protein", "interactions", "chemical", "compounds", "organic", "compounds", "fungi", "model", "organisms", "amino", "acid", "substitution", "experimental", "organism", "systems", "amino", "acids", "sequence", "motif", "analysis", "research", "and", "analysis", "methods"...	2017	Exhaustive search of linear information encoding protein-peptide recognition
Glia are of vital importance for all complex nervous system . One of the many functions of glia is to insulate and provide trophic and metabolic support to axons . Here , using glial-specific RNAi knockdown in Drosophila , we silenced 6930 conserved genes in adult flies to identify essential genes and pathways . Among ...	Glia are essential for the function of any nervous system . The number of glia correlates with the complexity of the nervous system . Important functions of glia include maintaining ionic homeostasis , supporting neurotransmission , and insulating axons to speed up nerve conduction . The biomedical relevance of glia is...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Global In Vivo Drosophila RNAi Screen Identifies a Key Role of Ceramide Phosphoethanolamine for Glial Ensheathment of Axons
Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements , and its power should increase with the number of species compared . Here , we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding a...	Comparing the genomes of related species is a powerful approach to the discovery of functional elements such as protein-coding genes . Theoretically , using more species should lead to more discovery power . Many questions remain , however , surrounding the optimal choice of species to compare and how to best use multi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/genomics" ]	2008	Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes
Although there have been great advances in our understanding of the bacterial cytoskeleton , major gaps remain in our knowledge of its importance to virulence . In this study we have explored the contribution of the bacterial cytoskeleton to the ability of Salmonella to express and assemble virulence factors and cause ...	Salmonella are major global pathogens responsible for causing food-borne disease . In recent years the existence of a cytoskeleton in prokaryotes has received much attention . In this study the Salmonella cytoskeleton has been genetically disrupted , causing changes in morphology , motility and expression of key virule...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "cellular", "structures", "infectious", "diseases", "cell", "biology", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	The Bacterial Cytoskeleton Modulates Motility, Type 3 Secretion, and Colonization in Salmonella
Mammalian sex chromosomes stem from ancestral autosomes and have substantially differentiated . It was shown that X-linked genes have generated duplicate intronless gene copies ( retrogenes ) on autosomes due to this differentiation . However , the precise driving forces for this out-of-X gene “movement” and its evolut...	Our sex chromosomes have profoundly differentiated since evolving from an ancestral pair of non-sex chromosomes ( autosomes ) . In this study , we first show that X chromosome–derived retrogenes ( genes that arose as duplicates of “parental” X-linked genes ) are specifically expressed during the meiotic and postmeiotic...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "evolutionary", "biology" ]	2008	Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes
Spliceosomal SNRNP200 is a Ski2-like RNA helicase that is associated with retinitis pigmentosa 33 ( RP33 ) . Here we found that SNRNP200 promotes viral RNA sensing and IRF3 activation through the ability of its amino-terminal Sec63 domain ( Sec63-1 ) to bind RNA and to interact with TBK1 . We show that SNRNP200 relocal...	The innate immune system is the first line of defense against pathogens and relies on the recognition of molecular structures specific to pathogens by sensor receptors . These receptors activate a signaling cascade and induce a protective cellular innate immune response . In this study , we provide evidence for a role ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "293t", "cells", "enzymes", "biological", "cultures", "immunology", "enzymology", "plasmid", "construction", "rna", "helicases", "dna", "construction", "molecular", "biology", "techniques", "research", "and", "...	2016	Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response
More than 80% of schistosomiasis patients in China live in the lake and marshland regions . The purpose of our study is to assess the effect of a comprehensive strategy to control transmission of Schistosoma japonicum in marshland regions . In a cluster randomized controlled trial , we implemented an integrated control...	More than 80% of schistosomiasis patients in China live in the lake and marshland regions . Hence , how to control transmission of Schistosoma japonicum in these regions is especially important . From 2009 through 2011 , we implemented an integrated control strategy , designed to reduce the role of bovines and humans a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "preventive", "medicine", "infectious", "diseases", "schistosomiasis", "public", "health", "and", "epidemiology", "neglected", "tropical", "diseases", "infectious", "disease", "control", "public", "health" ]	2013	Assessing the Effect of an Integrated Control Strategy for Schistosomiasis Japonica Emphasizing Bovines in a Marshland Area of Hubei Province, China: A Cluster Randomized Trial
Clostridium botulinum produces botulinum neurotoxins ( BoNTs ) , highly potent substances responsible for botulism . Currently , mathematical models of C . botulinum growth and toxigenesis are largely aimed at risk assessment and do not include explicit genetic information beyond group level but integrate many componen...	Clostridium botulinum produces botulinum neurotoxins ( BoNTs ) , highly potent substances responsible for botulism . Currently , mathematical models of C . botulinum growth and toxigenesis are largely aimed at risk assessment and do not include explicit genetic information . In this paper we present modelling based on ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "and", "Conclusions" ]	[ "clostridium", "botulinum", "medicine", "and", "health", "sciences", "toxins", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "operons", "neurotoxins", "toxicology", "toxic", "agents", "neurotoxicology", "dna", "bacteria", "bacter...	2016	An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production
Neglected Tropical Diseases ( NTDs ) are important causes of morbidity , disability , and mortality among poor and vulnerable populations in several countries worldwide , including Brazil . We present the burden of NTDs in Brazil from 1990 to 2016 based on findings from the Global Burden of Diseases , Injuries , and Ri...	Neglected Tropical Diseases ( NTDs ) are a public health problem in Brazil . We used findings from the Global Burden of Disease Study 2016 ( GBD 2016 ) to explore the burden of NTDs in Brazil by sex , age group , specific causes , and Brazilian states from 1990 to 2016 . In 2016 , NTDs caused 475 , 410 disability-adjus...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "age", "groups", "global", "health", "neglected", "tropical", "diseases", "infectious", "disease", "control", "public", "and", "occupational", "health"...	2018	The burden of Neglected Tropical Diseases in Brazil, 1990-2016: A subnational analysis from the Global Burden of Disease Study 2016
Echinococcus granulosus is characterized by high intra-specific variability ( genotypes G1–G10 ) and according to the new molecular phylogeny of the genus Echinococcus , the E . granulosus complex has been divided into E . granulosus sensu stricto ( G1–G3 ) , E . equinus ( G4 ) , E . ortleppi ( G5 ) , and E . canadensi...	The dog tapeworm Echinococcus granulosus ( E . granulosus ) is a cosmopolitan parasite . The adult worms reside in the small intestine of their definitive hosts ( dogs ) . Infective eggs are shed with the feces into the environment and are orally ingested by intermediate hosts where they develop into the metacestode ( ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "veterinary", "parasitology", "veterinary", "diagnostics", "biology", "microbiology", "veterinary", "science", "parasitology", "veterinary", "medicine" ]	2013	A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex
Chronic atrial fibrillation ( AF ) is a complex disease with underlying changes in electrophysiology , calcium signaling and the structure of atrial myocytes . How these individual remodeling targets and their emergent interactions contribute to cell physiology in chronic AF is not well understood . To approach this pr...	Atrial fibrillation is a complex disease which , at the level of individual atrial muscle cells , is a result of changes in a number of ion channels and transporters , as well as in cellular structure . How these alterations , together and separately , affect electrical and contractile function of the atrial cells is n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "physical", "sciences" ]	2014	In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation
The protozoan parasite Entamoeba histolytica causes a wide spectrum of intestinal infections . In severe cases , the trophozoites can breach the mucosal barrier , invade the intestinal epithelium and travel via the portal circulation to the liver , where they cause hepatic abscesses , which can prove fatal if left untr...	Entamoeba histolytica is one of the major causes of morbidity and mortality in developing economies . Severe amoebic infection leads to metastatic spread of the pathogen to extra intestinal sites , especially the liver , causing hepatic abscess . The migratory ability of the pathogen contributes to the spread of the di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Small GTPase Rab21 Mediates Fibronectin Induced Actin Reorganization in Entamoeba histolytica: Implications in Pathogen Invasion
Learning in a stochastic environment consists of estimating a model from a limited amount of noisy data , and is therefore inherently uncertain . However , many classical models reduce the learning process to the updating of parameter estimates and neglect the fact that learning is also frequently accompanied by a vari...	Learning is often accompanied by a “feeling of knowing” , a growing sense of confidence in having acquired the relevant information . Here , we formalize this introspective ability , and we evaluate its accuracy and its flexibility in the face of environmental changes that impose a revision of one’s mental model . We e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Sense of Confidence during Probabilistic Learning: A Normative Account
Gibberellins ( GAs ) are a class of important phytohormones regulating a variety of physiological processes during normal plant growth and development . One of the major events during GA-mediated growth is the degradation of DELLA proteins , key negative regulators of GA signaling pathway . The stability of DELLA prote...	Gibberellins ( GAs ) are essential regulators of plant growth and development . They are tightly related to crop productivity in the first “green revolution . ” GA triggers its responses by targeting DELLA proteins , the important repressors , for degradation . This process is believed to be regulated by protein phosph...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "plant", "science", "plant", "hormones", "plant", "growth", "and", "development", "biology", "and", "life", "sciences", "hormones" ]	2014	Arabidopsis DELLA Protein Degradation Is Controlled by a Type-One Protein Phosphatase, TOPP4
Four sesquiterpene lactones , mikanolide , deoxymikanolide , dihydromikanolide and scandenolide , were isolated by a bioassay-guided fractionation of Mikania variifolia and Mikania micrantha dichloromethane extracts . Mikanolide and deoxymikanolide were the major compounds in both extracts ( 2 . 2% and 0 . 4% for Mikan...	Chagas' disease and Leishmaniasis are parasitic diseases that affect especially poor people in developing countries . They are caused by the protozoan parasites Trypanosoma cruzi and different Leishmania species , respectively . According to the World Health Organization they are considered , among others , Neglected T...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "chemical", "compounds", "immunology", "lactones", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "esters", "d...	2017	Assessment of sesquiterpene lactones isolated from Mikania plants species for their potential efficacy against Trypanosoma cruzi and Leishmania sp.
Leukocyte telomere length ( LTL ) is a complex genetic trait . It shortens with age and is associated with a host of aging-related disorders . Recent studies have observed that offspring of older fathers have longer LTLs . We explored the relation between paternal age and offspring's LTLs in 4 different cohorts . Moreo...	Leukocyte telomere length becomes shorter with age and is apparently a biomarker of aging and a forecaster of longevity in humans . Leukocyte telomere length is heritable , longer in women than in men , and is relatively shorter in persons who suffer from aging-related diseases , cardiovascular diseases in particular ....	[ "Abstract", "Introduction", "Discussion", "Methods" ]	[ "homo", "(human)", "genetics", "and", "genomics", "public", "health", "and", "epidemiology" ]	2008	Offspring's Leukocyte Telomere Length, Paternal Age, and Telomere Elongation in Sperm
Poxviruses have evolved multiple strategies to subvert signaling by Nuclear Factor κB ( NF-κB ) , a crucial regulator of host innate immune responses . Here , we describe an orf virus ( ORFV ) virion-associated protein , ORFV119 , which inhibits NF-κB signaling very early in infection ( ≤ 30 min post infection ) . ORFV...	Poxviruses have evolved multiple strategies to subvert signaling by NF-κB , a crucial regulator of host innate immune responses . Viruses often encode multiple inhibitory proteins , which largely target cytoplasmic activation events of NF-κB signaling . The retinoblastoma protein ( pRb ) , a multifunctional protein bes...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "phosphorylation", "transfection", "medicine", "and", "health", "sciences", "luciferase", "poxviruses", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "microbiology", "enzymology", "viral", "structure", "viruses", "signal", "inhibition", "immunoprecip...	2017	A parapoxviral virion protein targets the retinoblastoma protein to inhibit NF-κB signaling
Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis , Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi . Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia , with a s...	Strongyloidiasis is a neglected tropical disease caused by the human infective worms ( nematodes ) Strongyloides stercoralis , Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi . Little is known about the genetic diversity of these nematodes and the possibility of geographically isolated geneti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "vertebrates", "parasitic", "diseases", "dogs", "animals", "genetic", "mapping", "mammals", "nematode", "infections", "primates", "molecular", "biology", "techniques", "strongyloides", "stercoralis", "genotyping", ...	2019	A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing
Drosophila Little imaginal discs ( Lid ) is a recently described member of the JmjC domain class of histone demethylases that specifically targets trimethylated histone H3 lysine 4 ( H3K4me3 ) . To understand its biological function , we have utilized a series of Lid deletions and point mutations to assess the role tha...	Correct spatial and temporal control of gene expression is essential for development . One of the many ways that gene expression is regulated is by the addition , recognition , and removal of methyl groups from the histone proteins around which DNA is wrapped within the nucleus . Here we describe a systematic analysis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/chromatin", "structure", "cell", "biology/cell", "growth", "and", "division", "biochemistry/transcription", "and", "translation", "cell", "biology/gene", "expression" ]	2010	Essential Functions of the Histone Demethylase Lid
Promoters process signals through recruitment of transcription factors and RNA polymerase , and dynamic changes in promoter activity constitute a major noise source in gene expression . However , it is barely understood how complex promoter architectures determine key features of promoter dynamics . Here , we employ pr...	Combinatorial regulation of gene expression is an important mechanism for signal integration in prokaryotes and eukaryotes . Typically , this regulation is established by transcription factors that bind to DNA or to other regulatory proteins . Modifications of the DNA structure provide another layer of control , for in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/transcriptional", "regulation" ]	2009	Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures
Evolutionarily conserved mitogen activated protein kinase ( MAPK ) pathways regulate the response to stress as well as cell differentiation . In Saccharomyces cerevisiae , growth in non-preferred carbon sources ( like galactose ) induces differentiation to the filamentous cell type through an extracellular-signal regul...	In fungal species , differentiation to the filamentous/hyphal cell type is critical for entry into host cells and virulence . Comparative RNA sequencing was used to explore the pathways that regulate differentiation to the filamentous cell type in yeast . This approach uncovered a role for the stress-response MAPK path...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fungal", "genetics", "microbiology", "osmotic", "shock", "systems", "ecology", "fungi", "nutrition", "microbial", "genomics", "mycology", "medical", "microbiology", "yeast", "systems", "biology", "signal", "transduction", "cell", "biology", "ecology", "phenotypes", "ge...	2014	Metabolic Respiration Induces AMPK- and Ire1p-Dependent Activation of the p38-Type HOG MAPK Pathway
HIV-1 replicative capacity ( RC ) provides a measure of within-host fitness and is determined in the context of phenotypic drug resistance testing . However it is unclear how these in-vitro measurements relate to in-vivo processes . Here we assess RCs in a clinical setting by combining a previously published machine-le...	Determining how well different genotypes of HIV can replicate within a patient is central for our understanding of the evolution of HIV . Such in vivo fitness is often approximated by in vitro measurements of viral replicative capacities . Here we use a machine-learning algorithm to predict in vitro replicative capacit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "genetics", "biology", "microbiology", "evolutionary", "biology", "population", "biology", "genetics", "and", "genomics" ]	2011	Assessing Predicted HIV-1 Replicative Capacity in a Clinical Setting
In order to eliminate viral infections , hundreds of interferon-stimulated genes ( ISGs ) are induced via type I interferons ( IFNs ) . However , the functions and mechanisms of most ISGs are largely unclear . A tripartite motif ( TRIM ) protein encoding gene TRIM69 is induced by dengue virus ( DENV ) infection as an I...	Mosquito-borne viruses , such as Dengue virus ( DENV ) , have become global threats to human health in recent years . However , no antiviral drugs have been approved to treat DENV induced diseases , and the safe and effective vaccines are still under development . It is of great importance to explore the detail mechani...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "enzymes", "biological", "cultures", "microbiology", "enzymology", "ubiquitin", "ligases", "viruses", "rna", "viruses", "immunoprecipi...	2018	Interferon-stimulated TRIM69 interrupts dengue virus replication by ubiquitinating viral nonstructural protein 3
Members of the family of calcium dependent protein kinases ( CDPK’s ) are abundant in certain pathogenic parasites and absent in mammalian cells making them strong drug target candidates . In the obligate intracellular parasite Toxoplasma gondii TgCDPK3 is important for calcium dependent egress from the host cell . Non...	Toxoplasma gondii can cause severe disease and death in the immunocompromised and in those infected congenitally . Due to limitations of existing drugs there is a need for studying proteins that are unique and essential to the parasite . We recently established that TgCDPK3 , a member of a family of calcium dependent p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phosphorylation of a Myosin Motor by TgCDPK3 Facilitates Rapid Initiation of Motility during Toxoplasma gondii egress
Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem . Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas , Middle East and Africa . Adult female worms ( mated to males ) release eggs in the hepatic portal vasculature an...	Schistosomiasis is a public health problem caused by parasites of the genus Schistosoma , of which S . mansoni is the primary causative agent . The parasite has a complex life cycle; their sexual reproductive stage is dependent on female and male adult worms mating inside the mesenteric circulation of the human host , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq
While the majority of multiexonic human genes show some evidence of alternative splicing , it is unclear what fraction of observed splice forms is functionally relevant . In this study , we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions...	Most human genes are split into pieces , such that the protein-coding parts ( exons ) are separated in the genome by large tracts of non-coding DNA ( introns ) that must be transcribed and spliced out to create a functional transcript . Variation in splicing reactions can create multiple transcripts from the same gene ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics", "evolutionary", "biology/genomics" ]	2010	Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Control of tsetse flies using insecticide-treated targets is often hampered by vegetation re-growth and encroachment which obscures a target and renders it less effective . Potentially this is of particular concern for the newly developed small targets ( 0 . 25 high × 0 . 5 m wide ) which show promise for cost-efficien...	Sleeping Sickness ( Human African Trypanosomiasis ) is a serious threat to health and development in sub-Saharan Africa . Due to lack of vaccines and prophylactic drugs , vector control is the only method of disease prevention . Small ( 0 . 25×0 . 5 m ) insecticide-treated targets have been shown to be cost-efficient f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "african", "trypanosomiasis", "parasitic", "diseases" ]	2011	Vegetation and the Importance of Insecticide-Treated Target Siting for Control of Glossina fuscipes fuscipes
On a global scale scabies is one of the most common dermatological conditions , imposing a considerable economic burden on individuals , communities and health systems . There is substantial epidemiological evidence that in tropical regions scabies is often causing pyoderma and subsequently serious illness due to invas...	The molecular mechanisms that underpin the link between scabies and bacterial pathogens were unknown . We proposed that scabies mites play a role in the establishment , proliferation and transmission of opportunistic pathogens . We investigated here the synergy between mites and one of the most recognised mite associat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "p...	2017	Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes - An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions
Viral infection is a stimulus for apoptosis , and in order to sustain viral replication many viruses are known to carry genes encoding apoptosis inhibitors . F1L , encoded by the orthopoxvirus modified vaccinia virus Ankara ( MVA ) has a Bcl-2-like structure . An MVA mutant lacking F1L ( MVAΔF1L ) induces apoptosis , i...	Viruses have come up with a diverse set of mechanisms to stop infected cells from committing suicide and hence secure their own propagation . In this study we use the DNA virus Modified Vaccinia virus Ankara , a highly attenuated version Vaccinia Virus , to study how cells detect viral infection and induce apoptosis . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "signal", "transduction", "signaling", "in", "cellular", "processes", "molecular", "cell", "biology", "cell", "biology", "viral", "immune", "evasion", "virology", "biology", "microbiology", "apoptotic", "signaling", "molecular", "biology", "antiapoptoti...	2011	Induction of Noxa-Mediated Apoptosis by Modified Vaccinia Virus Ankara Depends on Viral Recognition by Cytosolic Helicases, Leading to IRF-3/IFN-β-Dependent Induction of Pro-Apoptotic Noxa
While a primary genital tract infection with C . trachomatis stimulates partial-protection against re-infection , it may also result in severe inflammation and tissue destruction . Here we have dissected whether functional compartments exist in the genital tract that restrict Th1-mediated protective immunity . Apart fr...	The immune response to the genital tract pathogen C . trachomatis can result in a number of pathological outcomes including tubal scarring and consequently , infertility . CD4+ T helper 1 ( Th1 ) cells are critical for host protection against infection , but may also contribute to immunopathology . Apart from the Th1 c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/sexually", "transmitted", "diseases", "immunology/reproductive", "immunology", "microbiology/immunity", "to", "infections", "immunology/immunomodulation", "immunology/immune", "response", "immunology", "infectious", "diseases/bacterial", "infections", "immunol...	2010	The Female Lower Genital Tract Is a Privileged Compartment with IL-10 Producing Dendritic Cells and Poor Th1 Immunity following Chlamydia trachomatis Infection
Pentameric ligand-gated ion channels ( pLGICs ) mediate intercellular communication at synapses through the opening of an ion pore in response to the binding of a neurotransmitter . Despite the increasing availability of high-resolution structures of pLGICs , a detailed understanding of the functional isomerization fro...	Pentameric ligand-gated ion channels ( pLGICs ) control membrane conductance in living systems from bacteria to humans . Here , we report on μs-long , atomistic Molecular Dynamics simulations of the glutamate-gated chloride channel ( GluCl ) with an explicit treatment of the solvent and the membrane environment . The c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "allosteric", "regulation", "medicine", "and", "health", "sciences", "chemical", "characterization", "molecular", "dynamics", "chemical", "compounds", "computational", "biology", "enzymology", "electrophysiology", "neuroscience", "organic", "compounds", "isomerism", "ion", ...	2017	Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
Following antifungal treatment , Candida albicans , and other human pathogenic fungi can undergo microevolution , which leads to the emergence of drug resistance . However , the capacity for microevolutionary adaptation of fungi goes beyond the development of resistance against antifungals . Here we used an experimenta...	Pathogenic microbes often evolve complex traits to adapt to their respective hosts , and this evolution is ongoing: for example , microorganisms are developing resistance to antimicrobial compounds in the clinical setting . The ability of the common human pathogenic fungus , Candida albicans , to switch from yeast to h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "microbiology", "mutation", "fungi", "model", "organisms", "fungal", "pathogens", "research", "and", "analysis", "methods", "mycology", "medical", "microbiology"...	2014	Microevolution of Candida albicans in Macrophages Restores Filamentation in a Nonfilamentous Mutant
The association between species richness and ecosystem energy availability is one of the major geographic trends in biodiversity . It is often explained in terms of energetic constraints , such that coexistence among competing species is limited in low productivity environments . However , it has proven challenging to ...	The increase in the number of species with the availability of energy in the environment is one of the most general but least understood patterns in global biodiversity . The finite amount of energy flowing through an ecosystem has long been suspected to place a fundamental constraint on the ability of species to subdi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "taxonomy", "biogeography", "ecology", "and", "environmental", "sciences", "population", "genetics", "vertebrates", "animals", "animal", "phylogenetics", "phylogenetics", "data", "management", "phylogenetic", "analysis", "speciation", "molecular", "biology", "techniques", "...	2016	Energetic Constraints on Species Coexistence in Birds
The lack of an effective diagnostic tool for Carrion’s disease leads to misdiagnosis , wrong treatments and perpetuation of asymptomatic carriers living in endemic areas . Conventional PCR approaches have been reported as a diagnostic technique . However , the detection limit of these techniques is not clear as well as...	Carrion’s disease is an endemic illness in the Andean valleys of Peru that achieves high mortality rates in the absence of antibiotic treatment . There are three clinical manifestations , febrile acute patients , chronic patients as well as asymptomatic carriers . No effective diagnostic tool exists nowadays leading to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "laboratory", "equipment", "engineering", "and", "technology", "pathogens", "microbiology", "organisms", "bacterial", "diseases", "non-coding", "rna", "filter", "pap...	2016	Evaluation of PCR Approaches for Detection of Bartonella bacilliformis in Blood Samples
A common biological pathway reconstruction approach—as implemented by many automatic biological pathway services ( such as the KAAS and RAST servers ) and the functional annotation of metagenomic sequences—starts with the identification of protein functions or families ( e . g . , KO families for the KEGG database and ...	Even though there is only a single large biological network within any cell and all pathways are to some extent connected , the partition of the entire cellular network into smaller units ( e . g . , KEGG pathways ) is extremely important for understanding biological processes . Biological pathway reconstruction , ther...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/metagenomics", "computational", "biology/metabolic", "networks", "computational", "biology/genomics" ]	2009	A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins , such as Neanderthals and Denisovans , interbred or admixed with the ancestors of present-day humans . Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day indivi...	Recent analyses of modern human genomes have shown that archaic hominins like Neanderthals and Denisovans contribute a few percentage of ancestry to many populations . These analyses rely on having accurate reference genomes from these archaic populations . Due to the difficulty in sequencing these genomes , we lack a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "population", "genetics", "social", "sciences", "anthropology", "human", "genomics", "genetic", "mapping", "simulation", "and", "modeling", "neanderthals", "archaic", "humans", "paleontology", "population", "biology", "paleoanthropology", "research", "and", "analysis", "m...	2019	A statistical model for reference-free inference of archaic local ancestry
MicroRNAs ( miRNAs ) play important roles in normal cellular differentiation and oncogenesis . microRNA93 ( mir-93 ) , a member of the mir106b-25 cluster , located in intron 13 of the MCM7 gene , although frequently overexpressed in human malignancies may also function as a tumor suppressor gene . Using a series of bre...	Recent evidence suggests that many cancers , including those of the breast , are maintained by a population of cancer cells that display stem cell properties . These “cancer stem cells” may also contribute to tumor metastasis , treatment resistance , and relapse . Recently , miRNAs ( small non-coding RNAs ) have been r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	MicroRNA93 Regulates Proliferation and Differentiation of Normal and Malignant Breast Stem Cells
Neuroblastoma is a cancer of the developing sympathetic nervous system that most commonly presents in young children and accounts for approximately 12% of pediatric oncology deaths . Here , we report on a genome-wide association study ( GWAS ) in a discovery cohort or 2 , 101 cases and 4 , 202 controls of European ance...	Neuroblastoma is an embryonal tumor of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths . Approximately 1–2% of cases are inherited in an autosomal dominant fashion . These familial cases often harbor germline mutations in ALK or PHOX2B . However , the vast majority of neurobla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Web", "resources" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "biological", "cultures", "blastomas", "cancers", "and", "neoplasms", "variant", "genotypes", "neuroblastoma", "cells", "african", "americans", "genetic", "mapping", "ethnicities", "oncology...	2017	Common variants upstream of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma
New architectures of multilayer artificial neural networks and new methods for training them are rapidly revolutionizing the application of machine learning in diverse fields , including business , social science , physical sciences , and biology . Interpreting deep neural networks , however , currently remains elusive...	Deep learning is a state-of-the-art reformulation of artificial neural networks that have a long history of development . It can perform superbly well in diverse automated classification and prediction problems , including handwriting recognition , image identification , and biological pattern recognition . Its modern ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "neural", "networks", "neuroscience", "artificial", "neural", "networks", "nucleosome", "mapping", "artificial", "intelligence", "network", "analysis", "computational", "neuroscience", "sequence", "motif", "analysis", "molecular", "biology", "tec...	2017	Maximum entropy methods for extracting the learned features of deep neural networks
Plasmacytoid dendritic cells ( pDC ) provide an important link between innate and acquired immunity , mediating their action mainly through IFN-α production . pDC suppress HIV-1 replication , but there is increasing evidence suggesting they may also contribute to the increased levels of cell apoptosis and pan-immune ac...	Infection by HIV-2 , the second AIDS-associated virus , is considered a unique natural model of attenuated HIV disease . HIV-2 infected individuals exhibit much lower levels of circulating virus ( viremia ) and progress to AIDS at slower rates than HIV-1 infected patients . In this study , we characterized for the firs...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "immunology/innate", "immunity", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/viral", "infections", "immunology", "immunology/immunity", "to", "infections", "virology/host", "antiviral", "responses" ]	2009	Major Depletion of Plasmacytoid Dendritic Cells in HIV-2 Infection, an Attenuated Form of HIV Disease
The HIV-1 accessory protein Vpu counteracts tetherin ( BST-2/CD317 ) by preventing its incorporation into virions , reducing its surface expression , and ultimately promoting its degradation . Here we characterize a putative trafficking motif , EXXXLV , in the second alpha helix of the subtype-B Vpu cytoplasmic tail as...	Tetherin inhibits the release of several diverse enveloped viruses from infected cells and is counteracted by the HIV-1 accessory gene Vpu . Vpu prevents tetherin's incorporation into nascent viral particles , promotes its downregulation from the cell surface and targets tetherin for degradation . Here we identify a de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "molecular", "cell", "biology" ]	2012	A Cytoplasmic Tail Determinant in HIV-1 Vpu Mediates Targeting of Tetherin for Endosomal Degradation and Counteracts Interferon-Induced Restriction
Protein misfolding and aggregation are typically perceived as inevitable and detrimental processes tied to a stress- or age-associated decline in cellular proteostasis . A careful reassessment of this paradigm in the E . coli model bacterium revealed that the emergence of intracellular protein aggregates ( PAs ) was no...	Since accurate protein folding is crucial for cellular viability , misfolded and aggregated proteins have typically been thought of as detrimental structures with potentially harmful physiological effects . In this report , we show that this general paradigm does not appear to hold in the model bacterium Escherichia co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "fluorescence", "imaging", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "manufacturing", "processes", "green", "fl...	2018	Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells
Insulin signaling has a profound effect on longevity and the oxidative stress resistance of animals . Inhibition of insulin signaling results in the activation of DAF-16/FOXO and SKN-1/Nrf transcription factors and increased animal fitness . By studying the biological functions of the endogenous RNA interference factor...	Reduced activity of the insulin-signaling pathway genes has been associated with a longer lifespan and increased resistance to oxidative stress in animals due to the activation of important transcription factors , which act as master regulators and affect large networks of genes . The ability to manipulate insulin sign...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "genomics", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	A Conserved PHD Finger Protein and Endogenous RNAi Modulate Insulin Signaling in Caenorhabditis elegans
Genome-wide association studies have revealed an association between coronary heart disease ( CHD ) and genetic variation on chromosome 13q34 , with the lead single nucleotide polymorphism rs4773144 residing in the COL4A2 gene in this genomic region . We investigated the functional effects of this genetic variant . Ana...	People who carry certain variants in their DNA are genetically predisposed to suffer from coronary heart disease ( CHD ) caused by abnormal tissue buildup ( known as atherosclerosis ) and blood clotting in the blood vessels of the heart . One of the DNA variants reported to increase CHD risk is named single nucleotide ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "luciferase", "molecular", "probe", "techniques", "enzymes", "gene", "regulation", "cell", "processes", "immunoblotting", "enzymology", "collagens", "coronary", "heart", "disease", "microscopy", "molecular", "bio...	2016	Coronary-Heart-Disease-Associated Genetic Variant at the COL4A1/COL4A2 Locus Affects COL4A1/COL4A2 Expression, Vascular Cell Survival, Atherosclerotic Plaque Stability and Risk of Myocardial Infarction

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