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Dorsal closure ( DC ) is a developmental process in which two contralateral epithelial sheets migrate to seal a large hole in the dorsal ectoderm of the Drosophila embryo . Two signaling pathways act sequentially to orchestrate this dynamic morphogenetic process . First , c-Jun N-terminal kinase ( JNK ) signaling activ...	The developmental process of dorsal closure ( DC ) in Drosophila embryogenesis has provided many fundamental insights into conserved mechanisms controlling epithelial dynamics and cell migration , and therefore serves as a model for studying tissue morphogenesis and wound repair . DC is known to require the coordinated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "skin", "invertebrates", "medicine", "and", "health", "sciences", "integumentary", "system", "egfr", "signaling", "animals", "animal", "models", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "developmental", "biology", "drosophila", "melanogaster", "model", "...	2017	Novel interplay between JNK and Egfr signaling in Drosophila dorsal closure
Phenotypic transitions play critical roles in host adaptation , virulence , and sexual reproduction in pathogenic fungi . A minority of natural isolates of Candida albicans , which are homozygous at the mating type locus ( MTL , a/a or α/α ) , are known to be able to switch between two distinct cell types: white and op...	Phenotypic transitions enable fungal pathogens to better adapt to their ever-changing environments . Approximately 10% of natural Candida albicans strains , which are homozygous at the mating type locus ( MTL , a/a and α/α ) , can switch between two distinguishable morphological forms: white and opaque . The two cell t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "medical", "microbiology", "microbial", "pathogens", "biology", "microbiology", "fungal", "physiology", "yeast" ]	2013	White-Opaque Switching in Natural MTLa/α Isolates of Candida albicans: Evolutionary Implications for Roles in Host Adaptation, Pathogenesis, and Sex
Cytomegalovirus ( CMV ) infection is a common infection in adults ( seropositive 60–99% globally ) , and is associated with cardiovascular diseases , in line with risk factors such as hypertension and atherosclerosis . Several viral infections are linked to hypertension , including human herpes virus 8 ( HHV-8 ) and HI...	Cytomegalovirus ( CMV ) infection is associated with cardiovascular diseases . The exact mechanisms , however , remain to be defined . Using both mouse model and cell culture analyses , we find that CMV infection alone causes an increase in blood pressure . Additionally , CMV infection augments the increased blood pres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "pathology/molecular", "pathology", "cardiovascular", "disorders/hypertension", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "microbiology/medical", "microbiology" ]	2009	Cytomegalovirus Infection Causes an Increase of Arterial Blood Pressure
The variable domains of antibodies and T-Cell receptors ( TCRs ) share similar structures . Both molecules act as sensors for the immune system but recognise their respective antigens in different ways . Antibodies bind to a diverse set of antigenic shapes whilst TCRs only recognise linear peptides presented by a major...	The immune system needs to be able to sense molecules that might be harmful to the organism . Such harmful molecules are known as antigens . Two classes of receptor proteins that mediate antigen recognition are antibodies and T-Cell receptors ( TCRs ) . Antibodies are able to bind a diverse range of antigen shapes whil...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "protein", "structure", "comparison", "biochemistry", "immune", "system", "proteins", "t", "cell", "receptors", "major", "histocompatibility", "complex", "antibody", "specificity", "clinical", "immunology", "proteins", "b", "cell", "receptors", "bioinformatics", "database...	2014	Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design
Zoonoses are common causes of human and livestock illness in Tanzania . Previous studies have shown that brucellosis , leptospirosis , and Q fever account for a large proportion of human febrile illness in northern Tanzania , yet they are infrequently diagnosed . We conducted this study to assess awareness and knowledg...	Zoonoses are diseases that are naturally transmitted between animals and humans . In Tanzania , research has shown that several zoonoses , including brucellosis , leptospirosis , and Q fever , are common , but under-diagnosed , causes of human illness . We conducted a mixed methods survey , combining quantitative and q...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "health", "care", "sector", "brucellosis", "health", "care", "bacterial", "diseases", "health", "care", "providers", "neglected", "tropical", "diseases", "v...	2016	Mixed Methods Survey of Zoonotic Disease Awareness and Practice among Animal and Human Healthcare Providers in Moshi, Tanzania
In dengue-endemic areas , transmission shows both a seasonal and interannual variability . To investigate how rainfall impacts dengue seasonality in Singapore , we carried out a longitudinal survey in the Geylang neighborhood from August 2014 to August 2015 . The survey comprised of twice-weekly random inspections to o...	Increasing concerns about the arboviral diseases transmitted by Aedes aegypti mosquito—which include dengue , Chikungunya , yellow fever and Zika virus—demand a better understanding for the breeding ecology of this mosquito . A common observation on mosquito-borne diseases in endemic countries is that they peak followi...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "insect", "metamorphosis", "monsoons", "atmospheric", "science", "geographical", "locations", "animals", "singapore", "seasons", "developmental", "biology", "animal", "behavior", "pupae", "infectious", "disease", "...	2016	A Sequence of Flushing and Drying of Breeding Habitats of Aedes aegypti (L.) Prior to the Low Dengue Season in Singapore
Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a “toxin” and its corresponding neutralizing “antitoxin” . Regulation of these modules involves a complex mechanism known as conditional cooperativity , which is supposed to prevent unwanted toxin activation ....	Bacterial persistence plays an important role in many chronic infections . Persisters are subpopulations of bacteria which are tolerant to biological stresses such as antibiotics because they are in a dormant , non-dividing state . Toxin-antitoxin ( TA ) modules play a pivotal role in persister generation and bacterial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli
There is ample empirical evidence revealing that fitness landscapes are often complex: the fitness effect of a newly arisen mutation can depend strongly on the allelic state at other loci . However , little is known about the effects of recombination on adaptation on such fitness landscapes . Here , we investigate how ...	The emergence and persistence of recombination is a long-standing open question in evolutionary biology . Most previous theoretical studies assumed relatively simple fitness landscapes , i . e . , simple relationships between allelic states at different loci and fitness . By contrast , empirically determined bacterial ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "population", "modeling", "population", "genetics", "biology", "population", "biology", "genetics", "and", "genomics" ]	2012	The Effect of Bacterial Recombination on Adaptation on Fitness Landscapes with Limited Peak Accessibility
The liver removes quickly the great bulk of virus circulating in blood , leaving only a small fraction to infect the host , in a manner characteristic of each virus . The scavenger cells of the liver sinusoids are implicated , but the mechanism is entirely unknown . Here we show , borrowing a mouse model of adenovirus ...	The liver has long been known as the garbage dump of the body , capable of rapidly removing hazardous pathogens and useless particles from the blood stream , thereby protecting the host . The only cell doing the removal has been thought to be the liver's macrophages . This is likely true for larger particles such as ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immune", "cells", "viral", "transmission", "and", "infection", "immunology", "microbiology", "viral", "vectors", "immunodeficiency", "viruses", "mechanisms", "of", "resistance", "and", "susceptibility", "immunologic", "techniques", "immunohistochemical", "analysis", "anima...	2011	Rapid and Efficient Clearance of Blood-borne Virus by Liver Sinusoidal Endothelium
Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism , which is coupled with the transcription of non-coding RNA from the repeats by RNA polymerase II . In addition , Rrp6 , a component of the nuclear exosome , also contributes to heterochromatin assembl...	DNA is packaged into chromatin structure , which is important for various genome functions such as gene expression and maintenance of genetic information . Heterochromatin is a condensed chromatin structure and involved in epigenetic regulation of gene expression through repression of transcription . Heterochromatin at...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "rna", "processing", "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "cell", "biology", "chromatin", "histone", "modification" ]	2013	Mediator Directs Co-transcriptional Heterochromatin Assembly by RNA Interference-Dependent and -Independent Pathways
Fungal biofilms are complex , structured communities that can form on surfaces such as catheters and other indwelling medical devices . Biofilms are of particular concern with Candida albicans , one of the leading opportunistic fungal pathogens of humans . C . albicans biofilms include yeast and filamentous cells that ...	Most microorganisms exist in surface-associated communities known as biofilms in their natural environment . These biofilms can pose a major threat to human health , as with those formed by the opportunistic fungal pathogen Candida albicans , which is capable of colonizing medical devices such catheters and pacemakers ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biofilms", "cell", "walls", "chitin", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "microbiology", "dna", "transcription", "fungi", "regulator", "genes", "model", "organ...	2016	Functional Genomic Analysis of Candida albicans Adherence Reveals a Key Role for the Arp2/3 Complex in Cell Wall Remodelling and Biofilm Formation
Reovirus is a nonenveloped mammalian virus that provides a useful model system for studies of viral infections in the young . Following internalization into host cells , the outermost capsid of reovirus virions is removed by endosomal cathepsin proteases . Determinants of capsid disassembly kinetics reside in the viral...	Following attachment and internalization , viruses disassemble to complete the entry process , establish infection , and cause disease . Viral capsid stability balances on a fulcrum , as viruses must be sufficiently stable in the environment to reach the host yet also uncoat efficiently once the target cell barrier has...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Diminished Reovirus Capsid Stability Alters Disease Pathogenesis and Littermate Transmission
Histone methylation is a prominent feature of eukaryotic chromatin that modulates multiple aspects of chromosome function . Methyl modification can occur on several different amino acid residues and in distinct mono- , di- , and tri-methyl states . However , the interplay among these distinct modification states is not...	Histone methylation is a widespread feature of eukaryotic chromatin and has been implicated in numerous aspects of chromosome function . Methyl marks have been noted to occur on numerous different amino acid residues and in distinct mono- , di- , and tri-methyl states . However , the interplay among these distinct modi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "molecular", "biology/histone", "modification", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromatin", "structure" ...	2010	Differential Localization and Independent Acquisition of the H3K9me2 and H3K9me3 Chromatin Modifications in the Caenorhabditis elegans Adult Germ Line
Accurate segregation of homologous chromosomes of different parental origin ( homologs ) during the first division of meiosis ( meiosis I ) requires inter-homolog crossovers ( COs ) . These are produced at the end of meiosis I prophase , when recombination intermediates that contain Holliday junctions ( joint molecules...	Cell proliferation involves DNA replication followed by a mitotic division , producing two cells with identical genomes . Diploid organisms , which contain two genome copies per cell , also undergo meiosis , where DNA replication followed by two divisions produces haploid gametes , the equivalent sperm and eggs , with ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "mitosis", "cell", "division", "dna", "recombination", "dna", "chromosomal", "inheritance", "chromosome", "biology", "biology", "biochemistry", "cell", "biology", "nucleic", "acids", "heredity", "genetics", "dna", "repair", "genomics", "molecular", "cell", ...	2011	Meiotic Recombination Intermediates Are Resolved with Minimal Crossover Formation during Return-to-Growth, an Analogue of the Mitotic Cell Cycle
Mutation of the DNA molecule is one of the most fundamental processes in biology . In this study , we use 283 parent-offspring trios to estimate the rate of mutation for both single nucleotide variants ( SNVs ) and short length variants ( indels ) in humans and examine the mutation process . We found 17812 SNVs , corre...	In each generation new genetic variants are introduced by mutations . In this study we use whole genome sequence data from Icelandic families to directly observe such new mutations . Our estimate of the mutation rate implies that a newborn with 30-year-old parents will on average carry 75 new SNV mutations and 6 new sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "compounds", "insertion", "mutation", "dna-binding", "proteins", "nucleotides", "organic", "compounds", "alleles", "mutation", "mathematics", "polymerases", "statistics", "(mathematics)", "pyrimidines", "dna", "discrete", "mathematics", "combinatorics", "proteins"...	2016	Multi-nucleotide de novo Mutations in Humans
The peritrophic matrix ( PM ) is an acellular chitin-containing envelope which in most blood sucking insects encloses the ingested blood meal and protects the midgut epithelium . Type I PM present in sand flies and other blood sucking batch feeders is secreted around the meal by the entire midgut in response to feeding...	Phlebotomine sand flies are the main vectors of Leishmania parasites . However , only about ten percent of the described sand fly species are proven or suspected vectors . Several factors controlling vector competence act during the early phase of infection preceding defecation of bloodmeal remnants . Sand flies of the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "microbiology", "light", "microscopy", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "physiological", "processes", "developmental", "biology", "protozoans", ...	2018	Refractoriness of Sergentomyia schwetzi to Leishmania spp. is mediated by the peritrophic matrix
Bis- ( 3′ , 5′ ) cyclic di-guanylate ( cyclic di-GMP ) is a key bacterial second messenger that is implicated in the regulation of many critical processes that include motility , biofilm formation and virulence . Cyclic di-GMP influences diverse functions through interaction with a range of effectors . Our knowledge of...	Cyclic di-GMP is a bacterial second messenger that acts to regulate a wide range of functions including those that contribute to the virulence of pathogens . Our knowledge of the different actions and receptors for this nucleotide is far from complete . An understanding of the action of these elements may be key to int...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "molecular", "biology", "biology", "and", "life", "sciences", "microbiology" ]	2014	Novel Cyclic di-GMP Effectors of the YajQ Protein Family Control Bacterial Virulence
In the last decade dendrites of cortical neurons have been shown to nonlinearly combine synaptic inputs by evoking local dendritic spikes . It has been suggested that these nonlinearities raise the computational power of a single neuron , making it comparable to a 2-layer network of point neurons . But how these nonlin...	Error-backpropagation is a successful algorithm for supervised learning in neural networks . Whether and how this technical algorithm is implemented in cortical structures , however , remains elusive . Here we show that this algorithm may be implemented within a single neuron equipped with nonlinear dendritic processin...	[ "Abstract", "Introduction", "Results" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "dendritic", "structure", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "synaptic", "plasticity", "neuronal", "dendrites", "neuronal", "plasticity", "developmental", "neuro...	2016	Somato-dendritic Synaptic Plasticity and Error-backpropagation in Active Dendrites
Learning rules , such as spike-timing-dependent plasticity ( STDP ) , change the structure of networks of neurons based on the firing activity . A network level understanding of these mechanisms can help infer how the brain learns patterns and processes information . Previous studies have shown that STDP selectively po...	Our brain's ability to perform cognitive processes , such as object identification , problem solving , and decision making , comes from the specific connections between neurons . The neurons carry information as spikes that are transmitted to other neurons via connections with different strengths and propagation delays...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "developmental", "neuroscience", "synaptic", "plasticity", "neural", "networks", "computational", "neuroscience", "biology", "neuroscience", "learning", "and", "memory", "coding", "mechanisms" ]	2013	Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
Filarial infections are tropical diseases caused by nematodes of the Onchocercidae family such as Mansonella perstans . The infective larvae ( L3 ) are transmitted into the skin of vertebrate hosts by blood-feeding vectors . Many filarial species settle in the serous cavities including M . perstans in humans and L . si...	Mansonella perstans is a widespread human filarial parasite in Africa responsible for pleural and peritoneal cavity filariasis . Compared to other filarial parasites such as Wuchereria bancrofti , Brugia malayi , and Loa loa , the biology of M . perstans is poorly known . The blood-feeding vectors inject infective larv...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "cardiovascular", "anatomy", "immunology", "parasitic", "diseases", "nematode",...	2017	Migratory phase of Litomosoides sigmodontis filarial infective larvae is associated with pathology and transient increase of S100A9 expressing neutrophils in the lung
Genetic instability plays a key role in the formation of naturally occurring cancer . The formation of long DNA palindromes is a rate-limiting step in gene amplification , a common form of tumor-associated genetic instability . Genome-wide analysis of palindrome formation ( GAPF ) has detected both extensive palindrome...	Genetic instability is a key process in the development of naturally occurring cancer . Gene amplification is one important consequence of underlying oncogenic instability . Long DNA palindrome formation is a rate-limiting early step in gene amplification . The development of a new functional genomic tool called genome...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "genetics", "and", "genomics/cancer", "genetics" ]	2008	Myc Oncogene-Induced Genomic Instability: DNA Palindromes in Bursal Lymphomagenesis
Schistosomiasis and HIV are both associated with kidney disease . Prevalence and factors associated with abnormal renal function among HIV-infected children in Africa compared to uninfected controls have not been well described in a schistosomiasis endemic area . This cross-sectional study was conducted at the Sekou To...	Ninety percent of schistosomiasis occurs in sub-Saharan Africa , where 91% of HIV-infected children reside . Both schistosomiasis and HIV affect the kidney , but their respective effects on kidney disease in children are not well described . Our prior work in HIV-infected adults demonstrated a high prevalence of kidney...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Influence of HIV and Schistosomiasis on Renal Function: A Cross-sectional Study among Children at a Hospital in Tanzania
In order to further our understanding of how gene expression contributes to key functional properties of neurons , we combined publicly accessible gene expression , electrophysiology , and morphology measurements to identify cross-cell type correlations between these data modalities . Building on our previous work usin...	The behavior of neurons is governed by their electrical properties , for example how readily they respond to a stimulus or at what rate they are able to send signals . Additionally , neurons come in different shapes and sizes , and their shape defines how they can form connections with specific partners and thus functi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "voltage-gated", "ion", "channels", "medicine", "and", "health", "sciences", "action", "potentials", "membrane", "potential", "brain", "electrophysiology", "electrophysiological", "properties", "electrophysiology", "neuroscience", "ion", "channels", "genome", "analysis", "b...	2019	Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
The primary role of cytoplasmic viral RNA-dependent RNA polymerase ( RdRp ) is viral genome replication in the cellular cytoplasm . However , picornaviral RdRp denoted 3D polymerase ( 3Dpol ) also enters the host nucleus , where its function remains unclear . In this study , we describe a novel mechanism of viral attac...	RNA-dependent RNA polymerase ( RdRp ) is an enzyme that catalyzes the replication from an RNA template and is encoded in the genomes of all RNA viruses . RNA viruses in general replicate in cytoplasm and interfere host cellular gene expression by utilizing proteolytic destruction of cellular targets as the primary mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "cell", "biology", "pathology", "and", "laboratory", "medicine", "cell", "adhesion", "host-pathogen", "interactions", "cell", "growth", "virology", "cell", "cycle", "and", "cell", "division", "biology", "and"...	2014	Cytoplasmic Viral RNA-Dependent RNA Polymerase Disrupts the Intracellular Splicing Machinery by Entering the Nucleus and Interfering with Prp8
DNA methylation is a fundamental epigenetic modification that regulates gene expression and represses endogenous transposons and invading DNA viruses . As a counter-defense , the geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing ( TGS ) . Some geminiviruses have acquired a betasa...	Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses , and geminiviruses respond by elaborating proteins that inhibit methylation and transcriptional gene silencing ( TGS ) . Some geminiviruses have acquired a satellite called DNA β ( betasatellite ) , which depends on the he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Suppression of Methylation-Mediated Transcriptional Gene Silencing by βC1-SAHH Protein Interaction during Geminivirus-Betasatellite Infection
The role of the immune response in influencing leptospirosis clinical outcomes is not yet well understood . We hypothesized that acute-phase serum cytokine responses may play a role in disease progression , risk for death , and severe pulmonary hemorrhage syndrome ( SPHS ) . We performed a case-control study design to ...	Leptospirosis is a tropical bacterial disease that is transmitted to humans from infected animals . Leptospirosis symptoms can range from mild fever to fatal disease forms , such as massive bleeding into the lungs , called Severe Pulmonary Hemorrhage Syndrome ( SPHS ) . It is not known what determines the severity of l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Cytokine Response Signatures in Disease Progression and Development of Severe Clinical Outcomes for Leptospirosis
The benzimidazole ( BZ ) anthelmintics , albendazole ( ABZ ) and mebendazole ( MBZ ) are the most common drugs used for treatment of soil-transmitted helminths ( STHs ) . Their intensive use increases the possibility that BZ resistance may develop . In veterinary nematodes , BZ resistance is caused by a single nucleoti...	The soil-transmitted helminths ( STHs ) Ascaris lumbricoides , Trichuris trichiura , and the hookworms Necator americanus and Ancylostoma duodenale , are the most prevalent intestinal helminths of humans , causing morbidity in developing countries . Large-scale preventive chemotherapy with albendazole or mebendazole is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "dna-binding", "proteins", "parasitic", "diseases", "animals", "optimization", "ascaris", "ascaris", "lumbricoides", "mathematics", "polymerases", "neglected", "tropical", "diseas...	2017	Rapid Genotyping of β-tubulin Polymorphisms in Trichuris trichiura and Ascaris lumbricoides
Highly connected recurrent neural networks often produce chaotic dynamics , meaning their precise activity is sensitive to small perturbations . What are the consequences of chaos for how such networks encode streams of temporal stimuli ? On the one hand , chaos is a strong source of randomness , suggesting that small ...	Recurrently connected populations of excitatory and inhibitory neurons found in cortex are known to produce rich and irregular spiking activity , with complex trial-to-trial variability in response to input stimuli . Many theoretical studies found this firing regime to be associated with chaos , where tiny perturbation...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "signaling", "networks", "electrophysiology", "neuroscience", "jitter", "systems", "science", "mathe...	2016	Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems
Double muscling is a trait previously described in several mammalian species including cattle and sheep and is caused by mutations in the myostatin ( MSTN ) gene ( previously referred to as GDF8 ) . Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known a...	An individual's genetic profile can play a role in defining their natural skills and talents . The canine species presents an excellent system in which to find such associative genes . The purebred dog has a long history of selective breeding , which has produced specific breeds of extraordinary strength , intelligence...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "genetics", "and", "genomics", "dog" ]	2007	A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs
An unprecedented epidemic of chikungunya virus ( CHIKV ) infection recently started in countries of the Indian Ocean area , causing an acute and painful syndrome with strong fever , asthenia , skin rash , polyarthritis , and lethal cases of encephalitis . The basis for chikungunya disease and the tropism of CHIKV remai...	Chikungunya virus ( CHIKV ) is a reemerging alphavirus responsible for an unprecedented epidemic in countries of the Indian Ocean region , causing an acute and painful syndrome with strong fever , asthenia , skin rash , polyarthritis , and lethal cases of encephalitis . The most recent epidemic reemergences were docume...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "infectious", "diseases" ]	2007	Characterization of Reemerging Chikungunya Virus
Spatial memory is often studied in the Morris Water Maze , where the animal's spatial orientation has been shown to be mainly shaped by distal visual cues . Cognition-related behavior has also been described along “well-trodden paths”—spatial habits established by animals in the wild and in captivity reflecting a form ...	Spatially guided behavior and spatial memory are central subjects in behavioral neuroscience . Many tasks have been developed for laboratory investigations of these subjects since no single task can reveal their full richness . Here we turn to the simplest and oldest “task” , which involves no task at all: introducing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/cognitive", "neuroscience", "computational", "biology/computational", "neuroscience", "computational", "biology", "neuroscience", "neuroscience/animal", "cognition" ]	2008	Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction
Plasmodium sporozoites , the infective stage of the malaria parasite , move by gliding motility , a unique form of locomotion required for tissue migration and host cell invasion . TRAP , a transmembrane protein with extracellular adhesive domains and a cytoplasmic tail linked to the actomyosin motor , is central to th...	Malaria infection begins with the bite of an infected mosquito which inoculates sporozoites into the skin . Sporozoites then go to the liver where they invade hepatocytes and replicate , ultimately leading to the blood stage of infection . Sporozoites are motile and actively invade hepatocytes using a unique form of mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cell", "motility", "infectious", "diseases", "biology", "parasitic", "diseases", "malaria", "biophysics" ]	2012	Shedding of TRAP by a Rhomboid Protease from the Malaria Sporozoite Surface Is Essential for Gliding Motility and Sporozoite Infectivity
Fatty acids ( FAs ) are involved in cellular processes important for normal body function , and perturbation of FA balance has been linked to metabolic disturbances , including type 2 diabetes . An individual’s level of FAs is affected by diet , lifestyle , and genetic variation . We aimed to improve the understanding ...	Disruption of fatty-acid balance has in several previous studies been linked to human health conditions , including the metabolic syndrome , type 2 diabetes , and insulin resistance . Composition of fatty acids in lipid membranes is influenced , not only by diet and lifestyle , but also by genetic variation . By identi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "inuit", "people", "linoleic", "acid", "oleic", "acid", "ethnicities", "endocrine", "physiology", "red", "blood", "cells", "insulin", "resistance", "membrane", "metabolism", "cellular", "structures", "and", ...	2016	Identification of Novel Genetic Determinants of Erythrocyte Membrane Fatty Acid Composition among Greenlanders
We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest . We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes . We summarize the number of genetic varian...	We report here the nearly complete genomic sequence of 20 different individuals , determined using “next-generation” sequencing technologies . We use these data to characterize the type of genetic variation carried by humans in a sample of this size , which is to our knowledge the largest set of unrelated genomic seque...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/genomics" ]	2010	The Characterization of Twenty Sequenced Human Genomes
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is a γ-herpesvirus closely associated with Kaposi’s sarcoma , primary effusion lymphoma and multicentric Castleman disease . Open reading frame 57 ( ORF57 ) , a viral early protein of KSHV promotes splicing , stability and translation of viral mRNA and is essential for v...	KSHV encoded multifunctional protein ORF57 plays a key role in promoting viral mRNA accumulation and translation . Previous biochemical studies showed that ORF57 is stabilized by dimerization , which is critical for its function . To better understand ORF57 dimerization , we resolved the structure of the C-terminal dom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "viruses", "mutation", "crystals", "dna", "viruses", "materia...	2018	The crystal structure of KSHV ORF57 reveals dimeric active sites important for protein stability and function
We show that existing RNA-seq , DNase-seq , and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions . To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count ...	High-throughput DNA sequencing has been adapted to measure diverse biological state information including RNA expression , chromatin accessibility , and transcription factor binding to the genome . The accurate inference of biological mechanism from sequence counts requires a model of how sequence counts are distribute...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "analysis", "tools", "mathematics", "statistics", "statistical", "methods", "biology", "genomics", "computational", "biology" ]	2014	Universal Count Correction for High-Throughput Sequencing
Eukaryotic cells commonly use protein kinases in signaling systems that relay information and control a wide range of processes . These enzymes have a fundamentally similar structure , but achieve functional diversity through variable regions that determine how the catalytic core is activated and recruited to phosphory...	The core organization of systems that relay information inside cells is preserved across vast evolutionary distances . Thus , detailed characterization of these systems’ crucial modules can provide insight into the emergence and adaptation of signaling pathways , and illuminate broadly relevant mechanisms that control ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism
Here , we discovered an endogenous dafachronic acid ( DA ) in the socioeconomically important parasitic nematode Haemonchus contortus . We demonstrate that DA promotes larval exsheathment and development in this nematode via a relatively conserved nuclear hormone receptor ( DAF-12 ) . This stimulatory effect is dose- a...	In the present study , using an integrative multi-omics approach , we show that dafachronic acid ( DA ) plays a critical functional role in the developmental transition in larvae of the parasitic nematode Haemonchus contortus ( barber’s pole worm ) by modulating the dauer-like signalling pathway and lipid metabolism . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "signal", "transduction", "lipids", "metabolism", "rna", "developmental", "signaling", "cell", "biology", "membrane", "receptor", "signaling", "nucleic", "acids", "hormone", "receptor", "signaling", "lipid", "signaling", "cgmp", "signaling", "biology", "...	2019	Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
Melanocyte stem cells ( McSCs ) and mouse models of hair graying serve as useful systems to uncover mechanisms involved in stem cell self-renewal and the maintenance of regenerating tissues . Interested in assessing genetic variants that influence McSC maintenance , we found previously that heterozygosity for the melan...	Hair pigmentation over the course of a lifetime depends on melanocyte stem cells that reside in the hair follicle . As old hairs fall out and new hairs grow in , melanocyte stem cells serve as a reservoir for the melanocytes that produce the pigment that gives hair its visible color . The loss of these stem cells leads...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "integumentary", "system", "gene", "regulation", "epithelial", "cells", "dna", "transcription", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "chromatophores", "research", "and", "analysis", "me...	2018	A direct link between MITF, innate immunity, and hair graying
Cell growth and proliferation depend upon many different aspects of lipid metabolism . One key signaling pathway that is utilized in many different anabolic contexts involves Phosphatidylinositide 3-kinase ( PI3K ) and its membrane lipid products , the Phosphatidylinositol ( 3 , 4 , 5 ) -trisphosphates . It remains unc...	Lipids play diverse roles in health and disease . Some types of lipids function as metabolic fuels for energy homeostasis , whereas others act as components of cell membranes or serve as signals regulating cell behaviors . Much , however , remains to be discovered about the molecular connections between different categ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "rna", "interference", "cloning", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "lipid", "signaling", "epigenetics", "molecular", "biology", "techniques", "drosophila", "lipid", "metabolism", ...	2016	Drosophila Spidey/Kar Regulates Oenocyte Growth via PI3-Kinase Signaling
High-density , strand-specific cDNA sequencing ( ssRNA–seq ) was used to analyze the transcriptome of Salmonella enterica serovar Typhi ( S . Typhi ) . By mapping sequence data to the entire S . Typhi genome , we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded with...	We have applied a novel , strand-specific variation of RNA–seq ( ssRNA–seq ) to an analysis of the prokaryotic enteric pathogen Salmonella enterica serovar Typhi , the causative agent of Typhoid fever . Strand-specific data facilitated a high-resolution analysis of RNA transcription at a whole genome level with base-pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "molecular", "biology", "genetics", "and", "genomics/gene", "expression" ]	2009	A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
In terrestrial vertebrates such as birds and mammals , neurotrophin receptor expression is considered fundamental for the specification of distinct somatosensory neuron types where TrkA , TrkB and TrkC specify nociceptors , mechanoceptors and proprioceptors/mechanoceptors , respectively . In turn , Runx transcription f...	Our perception of the external world comes from our senses . Often overlooked the skin is our largest sensory organ . Specialized neurons located in the dorsal root ganglion ( DRG ) , which innervate the body , and trigeminal ganglion ( TG ) , which innervate the face , sense the somatosensory perceptions: light touch ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "in", "situ", "hybridization", "molecular", "probe", "techniques", "vertebrates", "social", "sciences", "neuroscience", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "nociceptors",...	2017	An ancient neurotrophin receptor code; a single Runx/Cbfβ complex determines somatosensory neuron fate specification in zebrafish
Auditory information is processed in a fine-to-crude hierarchical scheme , from low-level acoustic information to high-level abstract representations , such as phonological labels . We now ask whether fine acoustic information , which is not retained at high levels , can still be used to extract speech from noise . Pre...	One of the central questions in sensory neuroscience is the determination of the maximal amount of task-relevant information that is encoded in our brain . It is often assumed that all of this information is available for making perceptual decisions . We now show that this assumption does not hold generally . We find t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Low-Level Information and High-Level Perception: The Case of Speech in Noise
Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides . They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores , whose detailed structure is still unclear . Here we report the results of 5–9 μs all-atom molecular dy...	The emergence of antibiotic resistance has created a compelling need for new potent antibiotics . Antimicrobial peptides , naturally produced by many organisms , have long been pursued as a means to fill this gap . However , they have not yet realized their practical potential , partly due to a lack of full understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family
Recent interest has focused on the importance of the nucleus and associated nucleoskeleton in regulating changes in cardiac gene expression in response to biomechanical load . Mutations in genes encoding proteins of the inner nuclear membrane and nucleoskeleton , which cause cardiomyopathy , also disrupt expression of ...	Cardiomyopathy is one of the major causes of heart failure , and the leading cause of mortality in the western world . A number of cardiomyopathies are caused by genetic mutations in structural proteins within the cardiomyocyte . Recent interest has turned to structural proteins that link the nucleoskeleton to the cyto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cellular", "structures", "cardiomyopathies", "cellular", "stress", "responses", "cell", "nucleus", "biology", "anatomy", "and", "physiology", "molecular", "cell", "biology", "cardiovascular", "system", "biophysics", "biomechanics", "cytoskeleton", "cell", "me...	2014	Targeted Ablation of Nesprin 1 and Nesprin 2 from Murine Myocardium Results in Cardiomyopathy, Altered Nuclear Morphology and Inhibition of the Biomechanical Gene Response
Cysticercosis is caused by Taenia solium , a parasitic disease that affects humans and rurally bred pigs in developing countries . The cysticercus may localize in the central nervous system of the human , causing neurocysticercosis , the most severe and frequent form of the disease . There appears to be an association ...	Taenia solium cysticercosis is a parasitic disease that severely affects human health in underdeveloped countries and has re-emerged in North America . The adult parasite lives in the intestines of humans , where it thrives and sheds packages ( proglottids ) loaded with thousands of eggs that are , in turn , expelled u...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2008	Spatial Distribution of Taenia solium Porcine Cysticercosis within a Rural Area of Mexico
Mutations in the glucosidase , beta , acid ( GBA1 ) gene cause Gaucher’s disease , and are the most common genetic risk factor for Parkinson’s disease ( PD ) and dementia with Lewy bodies ( DLB ) excluding variants of low penetrance . Because α-synuclein-containing neuronal aggregates are a defining feature of PD and D...	Mutations in the glucosidase , beta , acid ( GBA1 ) gene cause Gaucher’s disease ( GD ) , a lysosomal storage disease that includes neurodegenerative phenotypes . Recently , mutations in GBA1 were identified as the strongest genetic risk factor for Parkinson’s disease ( PD ) and dementia with Lewy bodies ( DLB ) , whic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "lysosomes", "neurochemistry", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "neurodegenerative", "diseases", "dopaminergics", "variant", "genotypes", "neuroscience", "animals", "genetic", "mapping", "toxicology", "a...	2016	Glucocerebrosidase Deficiency in Drosophila Results in α-Synuclein-Independent Protein Aggregation and Neurodegeneration
Intracellular pathogens including the apicomplexan and opportunistic parasite Toxoplasma gondii profoundly modify their host cells in order to establish infection . We have shown previously that intracellular T . gondii inhibit up-regulation of regulatory and effector functions in murine macrophages ( MΦ ) stimulated w...	Toxoplasma gondii is a common unicellular parasite of humans and other vertebrates and can lead to overt disease mostly in immune-suppressed patients or in fetuses . Since IFN-γ is the major mediator of resistance against T . gondii , inhibition of IFN-γ-mediated gene expression may be a crucial mechanism to allow para...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "immunology", "microbiology", "parasitic", "diseases", "infectious", "diseases", "signaling", "in", "cellular", "processes", "gene", "expression", "biology", "molecular", "biology", "signal", "transduction", "genetics", "molecular", "cell", ...	2012	Impaired Chromatin Remodelling at STAT1-Regulated Promoters Leads to Global Unresponsiveness of Toxoplasma gondii-Infected Macrophages to IFN-γ
Staphylococcus aureus USA300 strains cause a highly inflammatory necrotizing pneumonia . The virulence of this strain has been attributed to its expression of multiple toxins that have diverse targets including ADAM10 , NLRP3 and CD11b . We demonstrate that induction of necroptosis through RIP1/RIP3/MLKL signaling is a...	Staphylococcus aureus ( SA ) cause a highly inflammatory pneumonia associated with substantial morbidity and mortality . Much of this lung destruction is attributed to toxins that target specific receptors on human and murine cells . We demonstrate that the α-hemolysin ( Hla ) and other agr-regulated toxins activate RI...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Toxin-Induced Necroptosis Is a Major Mechanism of Staphylococcus aureus Lung Damage
The clinical manifestations of neurocysticercosis ( NCC ) are poorly understood . This systematic review aims to estimate the frequencies of different manifestations , complications and disabilities associated with NCC . A systematic search of the literature published from January 1 , 1990 , to June 1 , 2008 , in 24 di...	Neurocysticercosis is an infection of the brain with the flatworm Taenia solium which is normally transmitted between humans and pigs . Sometimes , humans can infect other humans and the larva of the parasite can go the brain , causing the disease neurocysticercosis . There has never been a systematic review of what cl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "neurocysticercosis", "infectious", "disease", "epidemiology", "headaches", "neglected", "tropical", "diseases", "infectious", "diseases", "epilepsy", "infectious", "diseases", "of", "the", "nervous", "system", "epide...	2011	Clinical Manifestations Associated with Neurocysticercosis: A Systematic Review
A key function of the brain is to provide a stable representation of an object’s location in the world . In hearing , sound azimuth and elevation are encoded by neurons throughout the auditory system , and auditory cortex is necessary for sound localization . However , the coordinate frame in which neurons represent so...	When we hear a sound , we can describe its location relative to ourselves ( e . g . , “the phone is on my right” ) or relative to the world ( e . g . , “the phone is in the corner” ) . These descriptions of space are known as egocentric and allocentric , respectively , and illustrate the representation of sound locatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory", "cortex", "medicine", "and", "health", "sciences", "action", "potentials", "membrane", "potential", "brain", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "animal", "behavior", "zoology", "neuronal", "tuning", "sensory", "physiology...	2017	Egocentric and allocentric representations in auditory cortex
Tsetse-transmitted human and animal trypanosomiasis are constraints to both human and animal health in sub-Saharan Africa , and although these diseases have been known for over a century , there is little recent evidence demonstrating how the parasites circulate in natural hosts and ecosystems . The spread of Rhodesian...	Rhodesian sleeping sickness is a deadly disease , which is spread by the bite of infected tsetse flies in sub Saharan Africa . Rhodesian sleeping sickness has been spreading into new areas of Uganda over the past 15 years; this has been linked to the movement of infected , untreated livestock ( which can carry the dise...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Dispersal Ecology of Rhodesian Sleeping Sickness Following Its Introduction to a New Area
Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions . In the current study , signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B ( PTP1B ) was investigated using frequency r...	Similar to a machine in which interactions between different parts determine its function , signaling between the residues of a protein may play an important role in determining its function . External perturbations , such as ligand binding to a local region , may trigger a global response of the protein , manifested a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Frequency Response of a Protein to Local Conformational Perturbations
Intrinsically disordered regions ( IDRs ) of proteins play significant biological functional roles despite lacking a well-defined 3D structure . For example , IDRs provide efficient housing for large numbers of post-translational modification ( PTM ) sites in eukaryotic proteins . Here , we study the distribution of mo...	Eukaryotic proteins can be parsed into sections that are ‘ordered’ ( having a fixed three-dimensional structure ) or ‘disordered’ . The latter do not take on a fixed structure during some of their functioning . Proteins are often chemically modified in cells after translation . Such modifications alter the functioning ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "organismal", "evolution", "chemical", "compounds", "dna-binding", "proteins", "organic", "compounds", "methylation", "basic", "amino", "acids", "amino", "acids", "eukaryotic", "evolution", "proteins", "chemistry", "ubiquitination", "histones", "biochemistry", "eukaryota", ...	2018	Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins
We present an approach for answering similarity queries about gene expression time series that is motivated by the task of characterizing the potential toxicity of various chemicals . Our approach involves two key aspects . First , our method employs a novel alignment algorithm based on time warping . Our time warping ...	We are developing an approach to characterize chemicals and environmental conditions by comparing their effects on gene expression with those of well characterized treatments . We evaluate our approach in the context of the Edge ( Environment , Drugs , and Gene Expression ) database , which contains microarray observat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science/applications", "computational", "biology/genomics" ]	2008	Similarity Queries for Temporal Toxicogenomic Expression Profiles
The innate immune response mediated by cells such as natural killer ( NK ) cells is critical for the rapid containment of virus replication and spread during acute infection . Here , we show that subtype 11 of the type I interferon ( IFN ) family greatly potentiates the antiviral activity of NK cells during retroviral ...	The innate immune response mediated by cells such as natural killer ( NK ) cells can contribute to immunity against viral infections . NK cells can kill virus-infected cells and thus inhibit virus replication and spread during acute infection . However , in infections with retroviruses , like HIV , these cells are not ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "viral", "diseases" ]	2012	Interferon-alpha Subtype 11 Activates NK Cells and Enables Control of Retroviral Infection
Persistent TH2 cytokine responses following chronic helminth infections can often lead to the development of tissue pathology and fibrotic scarring . Despite a good understanding of the cellular mechanisms involved in fibrogenesis , there are very few therapeutic options available , highlighting a significant medical n...	Chronic helminth infections can cause significant morbidity and organ damage in their definitive mammalian hosts . Managing this collateral damage can reduce morbidity and preserve vital tissues for normal organ function . One particular consequence of some chronic helminth infections is the deposition of fibrotic scar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "helminths", "immunology", "rna", "extraction", "fibrosis", "a...	2016	TPL-2 Regulates Macrophage Lipid Metabolism and M2 Differentiation to Control TH2-Mediated Immunopathology
Amino acid signaling mediated by the activation of mechanistic target of rapamycin complex 1 ( mTORC1 ) is fundamental to cell growth and metabolism . However , how cells negatively regulate amino acid signaling remains largely unknown . Here , we show that interaction between 4F2 heavy chain ( 4F2hc ) , a subunit of m...	The mechanistic target of rapamycin complex 1 ( mTORC1 ) protein kinase is a master regulator of cell growth , which senses several extracellular signals , such as growth factors and nutrient levels , to coordinate cell metabolism . The activation of mTORC1 by amino acids requires many proteins such as Rag GTPase , GAT...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cell", "motility", "lysosomes", "actin", "filaments", "hek", "293", "cells", "gene", "regulation", "biological", "cultures", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "protein", "kinase", "signaling", ...	2018	Negative regulation of amino acid signaling by MAPK-regulated 4F2hc/Girdin complex
Interactions between embryo and endometrium at implantation are critical for the progression of pregnancy . These reciprocal actions involve exchange of paracrine signals that govern implantation and placentation . However , it remains unknown how these interactions between the conceptus and the endometrium are coordin...	Implantation in mammals requires a complex crosstalk between the conceptus ( the embryo and associated membranes ) and the uterus . An imbalanced regulation of the factors contributing to these interactions has negative impacts on the attachment of the fetus , the progression of the pregnancy , and the progeny . Focusi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Fine-tuned adaptation of embryo–endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus
We investigated the pathological and diagnostic role of selected markers of inflammation , oxidant/antioxidant status , and cellular injury in human Chagas disease . Seropositive/chagasic subjects characterized as clinically-symptomatic or clinically-asymptomatic ( n = 116 ) , seronegative/cardiac subjects ( n = 102 ) ...	Chagas disease is a chronic disease of the heart , and caused by Trypanosoma cruzi infection . In this study , we have monitored the biomarkers of inflammation caused by innate immune cells , oxidative stress , and antioxidant status in seropositive/chagasic , seronegative/cardiac disease , and seronegative/healthy sub...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "chagas", "disease", "diagnostic", "medicine", "pathology", "neglected", "tropical", "diseases", "general", "pathology", "biomarkers", "parasitic", "diseases" ]	2013	Innate Immune Responses and Antioxidant/Oxidant Imbalance Are Major Determinants of Human Chagas Disease
Community-based randomized controlled trials are often complex pieces of research with significant challenges around the approach to the community , information provision , and decision-making , all of which are fundamental to the informed consent process . We conducted a rapid ethical assessment to guide the preparati...	Community-based randomised controlled trials in developing countries , especially in settings with no research experience , are faced with significant challenges around approaching the community and obtaining informed consent . We conducted a Rapid Ethical Assessment , a simple and quick qualitative technique involving...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "randomized", "controlled", "trials", "anthropology", "parasitic", "diseases", "neuroscience", "ethnicities", "clinical", ...	2016	Preparing for and Executing a Randomised Controlled Trial of Podoconiosis Treatment in Northern Ethiopia: The Utility of Rapid Ethical Assessment
Members of the LCCL/lectin adhesive-like protein ( LAP ) family , a family of six putative secreted proteins with predicted adhesive extracellular domains , have all been detected in the sexual and sporogonic stages of Plasmodium and have previously been predicted to play a role in parasite–mosquito interactions and/or...	Malaria parasites are transmitted between human hosts by female mosquitoes . Following fertilization between male and female gametes in the blood meal , zygotes develop into motile ookinetes that , 24 hours later , cross the mosquito midgut epithelium and encyst on the midgut wall . During this development , parasite n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "cell", "biology", "plasmodium", "anopheles", "microbiology", "mus", "(mouse)", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Female Inheritance of Malarial lap Genes Is Essential for Mosquito Transmission
Studies of coat color mutants have greatly contributed to the discovery of genes that regulate melanocyte development and function . Here , we generated Yy1 conditional knockout mice in the melanocyte-lineage and observed profound melanocyte deficiency and premature gray hair , similar to the loss of melanocytes in hum...	Skin and hair pigmentation is among the most identifiable human traits . Disorders of pigment cells , melanocytes , result in multiple hypopigmentation conditions . Here , we described the phenotype of loss of a ubiquitous transcription factor YY1 in mouse melanocytes , which is reminiscent of certain human hypopigment...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2012	YY1 Regulates Melanocyte Development and Function by Cooperating with MITF
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter ( NAT ) family of proteins , and is responsible for the proton-driven uptake of uracil . Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1 ) 1-palmitoyl 2-oleoyl-phos...	Symporters are proteins that are responsible for the co-transport of ions and small molecule solutes across cell membranes . UraA is an example of a symporter , and is responsible for the proton-driven uptake of uracil in bacteria like E . coli . Despite its importance as a member of a large family of nucleobase/ascorb...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin
Type VI secretion systems ( T6SS ) are trans-envelope machines dedicated to the secretion of virulence factors into eukaryotic or prokaryotic cells , therefore required for pathogenesis and/or for competition towards neighboring bacteria . The T6SS apparatus resembles the injection device of bacteriophage T4 , and is a...	Type VI secretion systems ( T6SS ) are specialized secretion machines responsible for the transport of virulence factors . T6SS are versatile as they are able to target both eukaryotic and prokaryotic cells . They therefore play an important role in pathogenesis by acting directly on the host , as well as eliminating c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "macromolecular", "assemblies", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "biophysics", "bacterial", "pathogens", "pathogenesis" ]	2011	Towards a Structural Comprehension of Bacterial Type VI Secretion Systems: Characterization of the TssJ-TssM Complex of an Escherichia coli Pathovar
Zika virus ( ZIKV ) is an emerging arbovirus of the Flaviviridae family . Although ZIKV infection is typically mild and self-limiting in healthy adults , infection has been associated with neurological symptoms such as Guillain-Barré syndrome , and a causal link has been established between fetal microcephaly and ZIKV ...	Zika virus ( ZIKV ) is a mosquito-borne human pathogen of the Flaviviridae family . Most notably , it is responsible for an ongoing epidemic in the Americas , and has been causally linked to birth defects such as fetal microcephaly . These factors have led to an urgent need for small animal models , which may be used t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "spleen", "pathogens", "immunology", "microbiology", "cloning", "viruses", "a...	2017	Analysis of the T Cell Response to Zika Virus and Identification of a Novel CD8+ T Cell Epitope in Immunocompetent Mice
Histopathological classification of human tumors relies in part on the degree of differentiation of the tumor sample . To date , there is no objective systematic method to categorize tumor subtypes by maturation . In this paper , we introduce a novel computational algorithm to rank tumor subtypes according to the dissi...	Gene expression profiling of malignancies is often held to demonstrate genes that are “up-regulated” or “down-regulated” , but the appropriate frame of reference against which observations should be compared has not been determined . Fully differentiated somatic cells arise from stem cells , with changes in gene expres...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "oncology/breast", "cancer", "oncology/sarcomas", "evolutionary", "biology/bioinformatics", "computational", "biology", "evolutionary", "biology", "oncology/hematological", "malignancies" ]	2010	A Differentiation-Based Phylogeny of Cancer Subtypes
Treatment and morbidity control of schistosomiasis relies on a single drug , praziquantel ( PZQ ) , and the selection of resistant worms under repeated treatment is a concern . Therefore , there is a pressing need to understand the molecular effects of PZQ on schistosomes and to investigate alternative or synergistic d...	Schistosomiasis causes severe health problems in endemic areas of Africa , Southeast Asia , and Central and South America . Praziquantel is the drug of choice for treatment of at-risk populations; however , evolution of resistant worms under repeated treatment is of great concern . Combining praziquantel with another d...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[]	2015	Synergy of Omeprazole and Praziquantel In Vitro Treatment against Schistosoma mansoni Adult Worms
The multispecies coalescent ( MSC ) is a statistical framework that models how gene genealogies grow within the branches of a species tree . The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC , owing mainly to the accumulating evidence ...	Trees have long formed in biology the basic structure with which to represent and understand evolutionary relationships . Mathematical models , computational methods , and software tools for inferring phylogenetic trees and studying their mathematical properties are currently the norm in biology . The availability of g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "taxonomy", "genetic", "networks", "genome", "evolution", "animal", "phylogenetics", "phylogenetics", "data", "management", "phylogenetic", "analysis", "network", "analysis", "genome", "analysis", "molecular", "biology", "techniques", "zoology", "research", "and", "analys...	2016	Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent
Cystic fibrosis ( CF ) lung infections caused by members of the Burkholderia cepacia complex , such as Burkholderia multivorans , are associated with high rates of mortality and morbidity . We performed a population genomics study of 111 B . multivorans sputum isolates from one CF patient through three stages of infect...	Cystic fibrosis ( CF ) is the most common lethal genetic disorder affecting individuals of European descent . Most CF patients die at a young age due to chronic lung infections . Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex ( BCC ) , which are strongly associated w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "population", "genetics", "microbiology", "antibiotic", "resistance", "mutation", "substitution", "mutation", "phylogenetics", "data", ...	2018	A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans
Dynamic activity of signaling pathways , such as Notch , is vital to achieve correct development and homeostasis . However , most studies assess output many hours or days after initiation of signaling , once the outcome has been consolidated . Here we analyze genome-wide changes in transcript levels , binding of the No...	Signaling via the Notch pathway conveys important information that helps to shape tissues and , when misused , contributes to diseases . Cells respond to the Notch signal by changing which genes are transcribed . Most previous studies have looked at changes in gene activity at a single time point , long after the start...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "developmental", "biology", "signal", "transduction", "molecular", "cell", "biology", "signaling", "molecular", "development", "genetics", "gene", "expression", "biology", "genomics", "genetics", "and", "genomics" ]	2013	Transcriptional Dynamics Elicited by a Short Pulse of Notch Activation Involves Feed-Forward Regulation by E(spl)/Hes Genes
Tsetse flies transmit trypanosomes that cause human and African animal trypanosomosis , a debilitating disease of humans ( sleeping sickness ) and livestock ( nagana ) . An area-wide integrated pest management campaign against Glossina palpalis gambiensis has been implemented in Senegal since 2010 that includes a steri...	An area-wide integrated pest management campaign against Glossina palpalis gambiensis has been implemented in Senegal since 2010 that includes a sterile insect technique component . The sterile males used for the releases emerged from pupae that were produced and irradiated in Burkina Faso and Slovakia ( irradiation do...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Quality of Sterile Male Tsetse after Long Distance Transport as Chilled, Irradiated Pupae
Chagas disease , caused by Trypanosoma cruzi , remains a serious public health concern in many areas of Latin America , including México . It is also endemic in Texas with an autochthonous canine cycle , abundant vectors ( Triatoma species ) in many counties , and established domestic and peridomestic cycles which make...	Chagas disease is endemic in Texas and spread through triatomine insect vectors known as kissing bugs , assassin bugs , or cone–nosed bugs , which transmit the protozoan parasite , Trypanosoma cruzi . We examined the threat of Chagas disease due to the three most prevalent vector species and from human case occurrences...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "infectious", "diseases/neglected", "tropical", "diseases", "ecology/spatial", "and", "landscape", "ecology", "infectious", "diseases/protozoal", "infections", "computational", "biology/ecosystem", "modeling" ]	2010	Chagas Disease Risk in Texas
The wide utilization of biocides poses a concern on the impact of these compounds on natural bacterial populations . Furthermore , it has been demonstrated that biocides can select , at least in laboratory experiments , antibiotic resistant bacteria . This situation has raised concerns , not just on scientists and clin...	The wide utilization of biocides for different purposes , including toothpastes , soaps , house-hold compounds surfaces' disinfectants and even their use as additives of different materials ( from textiles to concrete used in germ-free buildings ) to avoid their colonization by microorganisms , poses a concern on the i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biomacromolecule-ligand", "interactions", "medicine", "public", "health", "and", "epidemiology", "protein", "interactions", "drugs", "and", "devices", "microbiology", "emerging", "infectious", "diseases", "microbial", "evolution", "protein", "structure", "p...	2011	The Binding of Triclosan to SmeT, the Repressor of the Multidrug Efflux Pump SmeDEF, Induces Antibiotic Resistance in Stenotrophomonas maltophilia
In Bilateria , many axons cross the midline of the central nervous system , forming well-defined commissures . Whereas in mammals the functions of commissures in the forebrain and in the visual system are well established , functions at other axial levels are less clearly understood . Here , we have dissected the funct...	Coordination of the left and right sides of the body requires the action of neurons whose axons cross the nervous system midline . The precise contributions of “commissural” neurons to sensory and motor functions remain poorly understood . To probe these crossing circuits , we took advantage of the recent finding that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/animal", "genetics", "ophthalmology/inherited", "eye", "disorders", "neurological", "disorders", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "developmental", "biology/developmental...	2010	Genetic Dissection of the Function of Hindbrain Axonal Commissures
The burden of human leptospirosis in Uganda is unknown . We estimated the seroprevalence of Leptospira antibodies , probable acute/recent leptospirosis , and risk factors for seropositivity in humans in rural Western Uganda . 359 non-pregnant adults visiting the Kikuube and Kigorobya Health Centers were sequentially re...	Leptospirosis is an emerging zoonotic disease caused by bacteria of the genus Leptospira . Despite its relatively common frequency , mild/moderate leptospirosis often goes unrecognized , due to its usually non-specific symptoms of fever , vomiting , and malaise . Knowledge of leptospirosis in Uganda is limited , and th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "uganda", "vertebrates", "parasitic", "diseases", "animals", "m...	2016	Leptospira Seroprevalence and Risk Factors in Health Centre Patients in Hoima District, Western Uganda
Primate lentiviruses encode four “accessory proteins” including Vif , Vpu , Nef , and Vpr/Vpx . Vif and Vpu counteract the antiviral effects of cellular restrictions to early and late steps in the viral replication cycle . We present evidence that the Vpx proteins of HIV-2/SIVSM promote virus infection by antagonizing ...	Defense against infection by the primate lentiviruses HIV/SIV is mediated primarily by antibodies that can neutralize the virus and by cytotoxic cells that can recognize and kill other virus-infected cells . However , in the past several years , research has revealed the existence of an additional line of host defense ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/host", "antiviral", "responses" ]	2008	Primate Lentiviral Vpx Commandeers DDB1 to Counteract a Macrophage Restriction
Behavioural and neurophysiological studies in primates have increasingly shown the involvement of urgency signals during the temporal integration of sensory evidence in perceptual decision-making . Neuronal correlates of such signals have been found in the parietal cortex , and in separate studies , demonstrated attent...	Perceptual decision-making involves not only simple transformation of sensory information to a motor decision , but can also be modulated by high-level cognition . For example , the latter may include strategic allocation of limited attentional resources over time in a decision task to improve performance . At the neur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "decision", "theory", "decision", "making", "neural", "networks", "applied", "mathematics", "neuroscience", "cognitive", "neuroscience", "behavioral", "neuroscience", "mathematics", "cognition", "computational", "neuroscience", "biophysics", "simulations", "animal", "cognitio...	2013	Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making
Metabolite quantitative traits carry great promise for epidemiological studies , and their genetic background has been addressed using Genome-Wide Association Studies ( GWAS ) . Thus far , the role of less common variants has not been exhaustively studied . Here , we set out a GWAS for metabolite quantitative traits in...	Human metabolic individuality is under strict control of genetic and environmental factors . In our study , we aimed to find the genetic determinants of circulating molecules in sera of large set of individuals representing the general population . First , we performed a hypothesis-free genome wide screen in this popul...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "biomarker", "epidemiology", "molecular", "epidemiology", "epidemiology", "metabolic", "disorders", "genetic", "epidemiology" ]	2015	Insight in Genome-Wide Association of Metabolite Quantitative Traits by Exome Sequence Analyses
Long-chain n-3 polyunsaturated fatty acids ( PUFAs ) can derive from diet or from α-linolenic acid ( ALA ) by elongation and desaturation . We investigated the association of common genetic variation with plasma phospholipid levels of the four major n-3 PUFAs by performing genome-wide association studies in five popula...	Circulating long-chain n-3 polyunsaturated fatty acids ( PUFAs ) derive from fatty fish or from the conversion of the plant n-3 PUFA by elongation and desaturation . We looked for common genetic markers throughout the genome that might influence plasma phospholipid levels of the four major n-3 PUFAs in five large studi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "biochemistry", "lipids", "genetics", "biology", "fatty", "acids", "genetics", "and", "genomics", "human", "genetics" ]	2011	Genetic Loci Associated with Plasma Phospholipid n-3 Fatty Acids: A Meta-Analysis of Genome-Wide Association Studies from the CHARGE Consortium
The Pam/Highwire/RPM-1 ( PHR ) proteins are key regulators of neuronal development that function in axon extension and guidance , termination of axon outgrowth , and synapse formation . Outside of development , the PHR proteins also regulate axon regeneration and Wallerian degeneration . The PHR proteins function in pa...	The molecular mechanisms that govern formation of functional synaptic connections are central to brain development and function . We have used the nematode C . elegans to explore the mechanism of how the intracellular signaling protein RPM-1 regulates neuronal development . Using a combination of proteomic , genetic , ...	[ "Abstract" ]	[ "developmental", "biology", "model", "organisms", "biology", "and", "life", "sciences", "neuroscience", "research", "and", "analysis", "methods" ]	2014	RPM-1 Uses Both Ubiquitin Ligase and Phosphatase-Based Mechanisms to Regulate DLK-1 during Neuronal Development
The application of RNA interference ( RNAi ) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes . Although RNAi has revolutionized loss-of-function genetic experiments , it has been difficult to systematically assess the prevalence and consequences of off-target ...	The Connectivity Map ( CMAP ) is a large-scale resource of the gene expression changes caused by small-molecule and genetic perturbations in multiple cell types . Here , we analyze 2 types of genetic perturbations , RNAi and CRISPR , using CMAP data . RNAi and CRISPR are both used to generate loss-of-function mutants b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "genome", "engineering", "methods", "and", "resources", "rna", "interference", "engineering", "and", "technology", "gene", "regulation", "synthetic", "biology", "crispr", "synthetic", "bioengineering", "rna", "stem-loop", "structure", "micrornas", "mathem...	2017	Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map
Leprosy is caused by the bacterial pathogens Mycobacterium leprae and Mycobacterium lepromatosis . Apart from humans , animals such as nine-banded armadillos in the Americas and red squirrels in the British Isles are naturally infected with M . leprae . Natural leprosy has also been reported in certain nonhuman primate...	Mycobacterium leprae , which causes leprosy in humans , also infects nine-banded armadillos , red squirrels , and nonhuman primates . Genomic data for M . leprae strains from wild armadillos and red squirrels show that humans were responsible for the original introduction of M . leprae to these species . It is not know...	[ "Abstract", "Introduction", "Discussion" ]	[ "taxonomy", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "tropical", "diseases", "vertebrates", "animals", "mammals", "primates", "bacterial", "diseases", "phylogenetics", "data", "management", "phylogenetic", "analysis", "neglected", "tropical", "d...	2018	Mycobacterium leprae genomes from naturally infected nonhuman primates
Outbreaks of orally transmitted Trypanosoma cruzi continue to be reported in Brazil and are associated with a high mortality rate , mainly due to myocarditis . This study is a detailed report on the disease progression of acute Chagas disease in 13 patients who were infected during two micro-outbreaks in two northeaste...	Chagas disease is caused by a parasitic protozoan transmitted to humans by the contaminated feces of blood-feeding assassin bugs from the Triatominae subfamily . It may also be transmitted from mother to baby during pregnancy , by breastfeeding , blood transfusion or organ transplant . In rare cases , the disease can a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "cardiovascular", "disorders/myopathies" ]	2010	Clinical Outcomes of Thirteen Patients with Acute Chagas Disease Acquired through Oral Transmission from Two Urban Outbreaks in Northeastern Brazil
Hantaviruses can cause hantavirus pulmonary syndrome or hemorrhagic fever with renal syndrome in humans . To enter cells , hantaviruses fuse their envelope membrane with host cell membranes . Previously , we have shown that the Gc envelope glycoprotein is the viral fusion protein sharing characteristics with class II f...	The infection of cells by enveloped viruses involves the fusion of membranes between viruses and cells . This process is mediated by viral fusion proteins that have been grouped into at least three structural classes . Membrane-enveloped hantaviruses are worldwide spread pathogens that can cause human disease with mort...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "viruses", "membrane", "proteins", "membrane", "fusion", "hantavirus", "rna", "viruses", "andes", "virus", "glycoproteins", "cellula...	2016	Inhibition of the Hantavirus Fusion Process by Predicted Domain III and Stem Peptides from Glycoprotein Gc
During spermiogenesis , haploid round spermatids undergo dramatic cell differentiation and morphogenesis to give rise to mature spermatozoa for fertilization , including nuclear elongation , chromatin remodeling , acrosome formation , and development of flagella . The molecular mechanisms underlining these fundamental ...	Cilia are microtubule-based structures present in virtually all cells in vertebrates . Cilia have diverse functions in development , growth , signaling , and fertilization . Primary ciliary dyskinesia ( PCD ) affects one in 16 , 000 individuals . PCD is characterized by bronchiectasis and chronic sinusitis , and is oft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	MNS1 Is Essential for Spermiogenesis and Motile Ciliary Functions in Mice
A large variety of severe medical conditions involve alterations in microvascular circulation . Hence , measurements or simulation of circulation and perfusion has considerable clinical value and can be used for diagnostics , evaluation of treatment efficacy , and for surgical planning . However , the accuracy of tradi...	An accurate simulation of blood-flow in the human brain can be used for improved diagnostics and assignment of personalized treatment regimes . However , current algorithms are limited to simulation of blood flow within tumours only , and in terms of parameter estimation , traditional compartment models have limited ac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "fluid", "mechanics", "nervous", "system", "vertebrates", "animals", "simulation", "and", "modeling", "amphibians", "tongue", "materials", "science", "network", "analysis", "digestive", "system", "resear...	2019	A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model
RsaE is a conserved small regulatory RNA ( sRNA ) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis . Here we show that RsaE contributes to extracellular ( e ) DNA release and biofilm-matrix switching towards pol...	Bacterial biofilms are highly organized structures which functionally emulate multicellular organisms , last but not least through heterogeneous gene expression patterns displayed by biofilm subpopulations . Here we analyzed the functions of the non-coding RNA RsaE in Staphylococcus epidermidis biofilm communities . Rs...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "light", "microscopy", "staphylococcus", "aureus", "physiological", "processes", "confocal", "laser", "micro...	2019	The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities
Chemical and mechanical pattern formation is fundamental during embryogenesis and tissue development . Yet , the underlying molecular and cellular mechanisms are still elusive in many cases . Most current theories assume that tissue development is driven by chemical processes: either as a sequence of chemical patterns ...	During embryogenesis , biological tissues gradually increase their complexity by self-organised creation of diverse chemical and mechanical patterns . Detailed mechanisms driving and controlling these patterns are not well understood . Previous theories mostly assume that these patterns are driven by chemical processes...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "methods" ]	[ "tissue", "mechanics", "classical", "mechanics", "applied", "mathematics", "biomechanics", "finite", "element", "analysis", "developmental", "biology", "mathematics", "molecular", "development", "damage", "mechanics", "morphogenesis", "pattern", "formation", "embryonic", "p...	2018	Post-Turing tissue pattern formation: Advent of mechanochemistry
Podoconiosis is a non-filarial elephantiasis caused by long-term barefoot exposure to volcanic soils in endemic areas . Irritant silicate particles penetrate the skin , causing a progressive , debilitating lymphoedema of the lower leg , often starting in the second decade of life . A simple patient-led treatment approa...	Podoconiosis is a type of leg swelling that occurs in the tropics among subsistence farmers who spend long hours in contact with irritant soil derived from volcanic parent rock . People with this disease often live in very remote areas far from health facilities , and do not realize that the condition can be treated . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evidence-based", "healthcare/health", "services", "research", "and", "economics", "public", "health", "and", "epidemiology/health", "services", "research", "and", "economics" ]	2010	Effectiveness of a Simple Lymphoedema Treatment Regimen in Podoconiosis Management in Southern Ethiopia: One Year Follow-Up
Wolbachia pipientis from Drosophila melanogaster ( wMel ) is an endosymbiotic bacterium that restricts transmission of human pathogenic flaviviruses and alphaviruses , including dengue , Zika , and chikungunya viruses , when introduced into the mosquito vector Aedes aegypti . To date , wMel-infected Ae . aegypti have b...	Dengue viruses are transmitted by the Aedes aegypti mosquito , with an estimated 390 million human infections occurring per year worldwide . There is no approved antiviral therapeutic , and vaccines described so far have had limited efficacy . Recently , the endosymbiotic bacterium Wolbachia from Drosophila melanogaste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Ethics", "statement" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "rna", "extraction", "microbiology", "animals", "wolbachia", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "population", "biology",...	2017	Novel Wolbachia-transinfected Aedes aegypti mosquitoes possess diverse fitness and vector competence phenotypes
The merging of network theory and microarray data analysis techniques has spawned a new field: gene coexpression network analysis . While network methods are increasingly used in biology , the network vocabulary of computational biologists tends to be far more limited than that of , say , social network theorists . Her...	Similar to natural languages , network language is ever evolving . While some network terms ( concepts ) are widely used in gene coexpression network analysis , others still need to be developed to meet the ever increasing demand for describing the system of gene transcripts . There is a need to provide an intuitive ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/metabolic", "networks", "computational", "biology/signaling", "networks", "mathematics/statistics", "computational", "biology", "computational", "biology/systems", "biology" ]	2008	Geometric Interpretation of Gene Coexpression Network Analysis
The kinetics of label uptake and dilution in dividing stem cells , e . g . , using Bromodeoxyuridine ( BrdU ) as a labeling substance , are a common way to assess the cellular turnover of all hematopoietic stem cells ( HSCs ) in vivo . The assumption that HSCs form a homogeneous population of cells which regularly unde...	Hematopoietic stem cells ( HSCs ) are among the best-studied populations of adult stem cells . Commonly HSCs are considered to be in a so called quiescent state of reduced cellular turnover . However , it appears that even quiescent HSCs are activated into the cell cycle from time to time to support the continuous prod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "hematology/hematopoiesis", "computational", "biology/systems", "biology" ]	2009	Stem Cell Proliferation and Quiescence—Two Sides of the Same Coin
The conserved herpesvirus fusion complex consists of glycoproteins gB , gH , and gL which is critical for virion envelope fusion with the cell membrane during entry . For Varicella Zoster Virus ( VZV ) , the complex is necessary for cell-cell fusion and presumed to mediate entry . VZV causes syncytia formation via cell...	Varicella zoster virus ( VZV ) infects the human population globally , causing chickenpox in children and shingles in adults . While those afflicted with shingles experience severe pain that might last from weeks to months , the cause is not known . Biopsies of VZV infected skin and specimens of nerve ganglia collected...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Truncation", "of", "the", "gHcyt", "enhances", "VZV", "syncytia", "formation", "while", "reducing", "viral", "titers", "Viral", "particle", "formation", "and", "egress", "are", "unaffected", "by"...	[ "dermatology", "chickenpox", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "herpes", "simplex", "pathogens", "regulatory", "proteins", "microbiology", "membrane", "proteins", "skin", "infections", "sexually", "transmitted", "diseas...	2014	The Cytoplasmic Domain of Varicella-Zoster Virus Glycoprotein H Regulates Syncytia Formation and Skin Pathogenesis
The Plasmodium vivax Reticulocyte Binding Protein ( PvRBP ) family is involved in red blood cell recognition and members of this family are potential targets for antibodies that may block P . vivax invasion . To date , the acquisition of immunity against PvRBPs in low malaria transmission settings and in a broad age gr...	Plasmodium vivax preferentially invades young red blood cells called reticulocytes . Successful parasite invasion relies on the interaction between parasite ligands with human red blood cell receptors . The P . vivax reticulocyte binding protein family ( PvRBP ) plays a role in the invasion process . The role of PvRBP ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "parasite", "groups", "medicine", "and", "health", "sciences", "immune", "physiology", "plasmodium", "immunology", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "reticulocytes", "parasitology", "ethnicities", "bone", "marr...	2019	Antibodies to Plasmodium vivax reticulocyte binding protein 2b are associated with protection against P. vivax malaria in populations living in low malaria transmission regions of Brazil and Thailand
It is widely believed that learning is due , at least in part , to long-lasting modifications of the strengths of synapses in the brain . Theoretical studies have shown that a family of synaptic plasticity rules , in which synaptic changes are driven by covariance , is particularly useful for many forms of learning , i...	It is widely believed that learning is due , at least in part , to modifications of synapses in the brain . The ability of a synapse to change its strength is called “synaptic plasticity , ” and the rules governing these changes are a subject of intense research . Theoretical studies have shown that a particular family...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2008	Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity
Perturbation experiments , in which a certain gene is knocked out and the expression levels of other genes are observed , constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation . Here we present a novel framework...	Observing a complex biological system in steady state is often insufficient for a thorough understanding of its working . For such inference , perturbation experiments are necessary and are traditionally employed . In this work we focus on perturbations in which a gene is knocked out and as a result multiple genes chan...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation" ]	2010	Network-Free Inference of Knockout Effects in Yeast
Trypanosoma cruzi is the etiological agent of Chagas disease , a debilitating illness that affects millions of people in the Americas . A major finding of the T . cruzi genome project was the discovery of a novel multigene family composed of approximately 1 , 300 genes that encode mucin-associated surface proteins ( MA...	The parasite Trypanosoma cruzi is the etiologic agent of Chagas disease , a neglected tropical disease . A major finding of the T . cruzi genome project was the discovery of a multigene family that encodes mucin-associated surface proteins ( MASP ) , a highly polymorphic family expressed at the surface of infective for...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "zoology", "gene", "expression", "genetics", "parasitology", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "immune", "response" ]	2012	The MASP Family of Trypanosoma cruzi: Changes in Gene Expression and Antigenic Profile during the Acute Phase of Experimental Infection
The Mayaro virus ( MAYV ) is an endemic arbovirus in South American countries , where it is responsible for sporadic outbreaks of Mayaro fever . Clinical manifestations include fever , headache , ocular pain , rash , myalgia , and debilitating and persistent polyarthralgia . Understanding the mechanisms associated with...	The Mayaro virus , although restricted to some regions of Latin America , has great potential for emergence , which makes it of great medical-scientific interest . Therefore , pathogenesis study of the MAYV in an animal model has fundamental importance for the determination of viral and host factors that contribute to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "inflammatory", "diseases", "rheumatology", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "immunology", "microbiology", "alphaviruses", ...	2019	Animal model of arthritis and myositis induced by the Mayaro virus
Cutaneous leishmaniasis is one of the highly prevalent endemic diseases in the Middle East and North Africa . Many treatment modalities have been recommended for this condition but success rates remain limited . Herbal remedies have also been used for treatment but evidence-based clinical trials with these products are...	Many people are afflicted in the world by cutaneous leishmaniasis ( CL ) . The pathogen in this disease is an intracellular parasite . In 2007 , The World Health Organization , defined leishmaniasis as a neglected disease . Many treatment modalities have been recommended for cutaneous leishmaniasis , but success rates ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "tropical", "diseases", "randomized", "controlled", "trials", "parasitic", "diseases", "parasitic", "protozoans", "organisms", "plant", "s...	2017	Efficacy of cryotherapy plus topical Juniperus excelsa M. Bieb cream versus cryotherapy plus placebo in the treatment of Old World cutaneous leishmaniasis: A triple-blind randomized controlled clinical trial

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