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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Development of high-throughput monitoring technologies enables interrogation of cancer samples at various levels of cellular activity . Capitalizing on these developments , various public efforts such as The Cancer Genome Atlas ( TCGA ) generate disparate omic data for large patient cohorts . As demonstrated by recent ...	Identification of cancer-related genes is an important task , made more difficult by heterogeneity between samples and even within individual patients . Methods for identifying disease-related genes typically focus on individual data sets such as mutational and differential expression data , and therefore are limited t...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2015	Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer
Approximately 14 million persons living in areas endemic for lymphatic filariasis have lymphedema of the leg . Clinical studies indicate that repeated episodes of bacterial acute dermatolymphangioadenitis ( ADLA ) lead to progression of lymphedema and that basic lymphedema management , which emphasizes hygiene , skin c...	Lymphatic filariasis is a parasitic disease that is spread by mosquitoes . In tropical countries where lymphatic filariasis occurs , approximately 14 million people suffer from chronic swelling of the leg , known as lymphedema . Repeated episodes of bacterial skin infection ( acute attacks ) cause lymphedema to progres...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology/health", "policy", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/preventive", "medicine", "infectious", "...	2010	Feasibility and Effectiveness of Basic Lymphedema Management in Leogane, Haiti, an Area Endemic for Bancroftian Filariasis
Dengue virus ( DENV ) is the leading cause of arboviral diseases in humans worldwide . The envelope ( E ) protein of DENV is the major target of neutralizing antibodies ( Abs ) . Previous studies have shown that a significant proportion of anti-E Abs in human serum after DENV infection recognize the highly conserved fu...	The four serotypes of dengue virus ( DENV ) are the leading cause of mosquito-borne viral diseases in humans . Whereas infection with one DENV serotype is thought to confer protection against re-infection with that serotype , it can be either protective or enhance disease severity upon subsequent ( “secondary” ) infect...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Analysis of Cross-Reactive Antibodies Recognizing the Fusion Loop of Envelope Protein and Correlation with Neutralizing Antibody Titers in Nicaraguan Dengue Cases
Plasmodium vivax is a widely distributed , neglected parasite that can cause malaria and death in tropical areas . It is associated with an estimated 80–300 million cases of malaria worldwide . Brazilian tropical rain forests encompass host- and vector-rich communities , in which two hypothetical mechanisms could play ...	Plasmodium vivax malaria is a neglected infectious disease that can cause severe symptoms and death in tropical regions . It is associated with an estimated 80–300 million cases of malaria worldwide . Brazilian tropical rain forests are home to a rich community of animals that can participate in the dynamics of malaria...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "ecology", "epidemiology", "biology" ]	2013	Biodiversity Can Help Prevent Malaria Outbreaks in Tropical Forests
Alarm communication is a key adaptation that helps social groups resist predation and rally defenses . In Asia , the world’s largest hornet , Vespa mandarinia , and the smaller hornet , Vespa velutina , prey upon foragers and nests of the Asian honey bee , Apis cerana . We attacked foragers and colony nest entrances wi...	Asian honey bees are attacked by formidable predators , giant hornets , at food sources and at their nests . We show that one species of honey bee , Apis cerana , has evolved an alarm signal , the stop signal , which warns nestmates of this danger . The stop signal consists of a brief vibrational pulse that encodes inf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "acoustics", "waggle-dancing", "classical", "mechanics", "honey", "bees", "vibration", "animals", "animal", "signaling", "and", "communication", "signal", "inhibition", "animal", "behavior", "zoology", "bees", "hymenoptera", "behavior", "alarm", "pheromon...	2016	Honey Bee Inhibitory Signaling Is Tuned to Threat Severity and Can Act as a Colony Alarm Signal
There is a considerable contrast between the various functions assigned to Broca's region and its relatively simple subdivision into two cytoarchitectonic areas ( 44 and 45 ) . Since the regional distribution of transmitter receptors in the cerebral cortex has been proven a powerful indicator of functional diversity , ...	Broca's region is involved in many aspects of language processing in the brain . Such detailed functional diversity , however , is in contrast to its classical anatomical subdivision into only two cortical areas . Since the regional distribution of neurotransmitter receptors has been proven to be a powerful indicator o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "radiology", "and", "medical", "imaging/magnetic", "resonance", "imaging", "neuroscience/motor", "systems", "neurological", "disorders/neuroimaging", "neuroscience/neuronal", "signaling", "mechanisms", "radiology", "and", "medical", "imag...	2010	Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping
HTLV-1 infection is endemic in Brazil . About 1 to 2% of the Brazilian population is estimated to be infected , but most infected HTLV-1 individuals do not know about their own infection , which favors the continuity of sexual and vertical virus transmission . In addition , HTLV-1 associated central nervous system dise...	For the past 30 years , human T-cell lymphotropic virus type-1 ( HTLV-1 ) has been isolated and associated with neoplastic , inflammatory , and infectious diseases . It is known that the neurological disorder associated with HTLV-1 comprises HTLV-1-associated myelopathy ( HAM/TSP ) or any other isolated signals and sym...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "nervous", "system", "pathogens", "immunology", "microbiology", "neuroscience"...	2018	Spinal cord hypometabolism associated with infection by human T-cell lymphotropic virus type 1(HTLV-1)
At the early stage of infection , human immunodeficiency virus ( HIV ) -1 predominantly uses the CCR5 coreceptor for host cell entry . The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progressio...	At the start of infection , human immunodeficiency virus ( HIV ) generally requires a specific protein receptor ( CCR5 ) on the cell surface to bind and enter the cell . In roughly half of all HIV infections , the virus population eventually switches to using a different receptor ( CXCR4 ) . This ‘HIV coreceptor switch...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequence", "analysis", "medicine", "infectious", "diseases", "hiv", "evolutionary", "modeling", "population", "genetics", "biology", "computational", "biology", "viral", "diseases" ]	2012	Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
Mycobacterium ulcerans , a slow-growing environmental bacterium , is the etiologic agent of Buruli ulcer , a necrotic skin disease . Skin lesions are caused by mycolactone , the main virulence factor of M . ulcerans , with dermonecrotic ( destruction of the skin and soft tissues ) and immunosuppressive activities . Thi...	Mycolactone , a polyketide cytotoxic toxin , is the key virulence factor responsible for large skin ulcers in Buruli ulcer . This disease , mainly occurring in humid tropical zones , especially in West African countries , is due to infection by Mycobacterium ulcerans , a slow-growing environmental mycobacterium . The t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Regulation of Mycolactone, the Mycobacterium ulcerans Toxin, Depends on Nutrient Source
Delivery of microbial products into the mammalian cell cytosol by bacterial secretion systems is a strong stimulus for triggering pro-inflammatory host responses . Here we show that Salmonella enterica serovar Typhi ( S . Typhi ) , the causative agent of typhoid fever , tightly regulates expression of the invasion-asso...	Bacterial pathogens translocate effector proteins into the cytoplasm of host cells to manipulate the mammalian host . These processes , e . g . the stimulation of small regulatory GTPases , activate the innate immune system and induce pro-inflammatory responses aimed at clearing invading microbes from the infected tiss...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "medical", "microbiology", "gastroenterology", "and", "hepatology", "microbial", "pathogens", "biology"...	2014	Salmonella enterica Serovar Typhi Conceals the Invasion-Associated Type Three Secretion System from the Innate Immune System by Gene Regulation
Cell signaling dynamics and transcriptional regulatory activities are variable within specific cell types responding to an identical stimulus . In addition to studying the network interactions , there is much interest in utilizing single cell scale data to elucidate the non-random aspects of the variability involved in...	Single cell studies have shown that differential patterns in the dynamics of signaling proteins , transcription factor activity , gene expression , etc . produce distinct downstream outcomes . The opposite also holds true where particular cellular outcomes have been found to be associated with the dynamical pattern of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features
Tsetse flies use olfactory and gustatory responses , through odorant and gustatory receptors ( ORs and GRs ) , to interact with their environment . Glossina morsitans morsitans genome ORs and GRs were annotated using homologs of these genes in Drosophila melanogaster and an ab initio approach based on OR and GR specifi...	Tsetse flies navigate their environments using chemosensory receptors , which permit them to locate hosts , mating partners , and resting and larviposition sites . The genome of G . m . morsitans was interrogated for coding genes of odorant receptors ( ORs ) and gustatory receptors ( GRs ) that express in antennae and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genomics", "genome", "evolution", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "computational", "biology", "evolutionary", "biology" ]	2014	Odorant and Gustatory Receptors in the Tsetse Fly Glossina morsitans morsitans
Malaria burden in Brazil has reached its lowest levels in 35 years and Plasmodium vivax now accounts for 84% of cases countrywide . Targeting residual malaria transmission entrenched in the Amazon is the next major challenge for ongoing elimination efforts . Better strategies are urgently needed to address the vast res...	Addressing the vast reservoir of asymptomatic Plasmodium vivax carriers clustered in hard-to-reach rural communities is a major challenge faced by countries approaching malaria elimination across Latin America and Asia . Routine surveillance targets subjects presenting with fever or reporting recent fever , but overloo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "plasmodium", "vivax", "protozoans", "inf...	2016	Reactive Case Detection for Plasmodium vivax Malaria Elimination in Rural Amazonia
Most empirical studies support a decline in speciation rates through time , although evidence for constant speciation rates also exists . Declining rates have been explained by invoking pre-existing niches , whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation . Tr...	Ecological opportunity , or filling a pre-existing unoccupied adaptive zone , is considered the dominant mechanism explaining the initial explosion of diversity . Although this type of niche filling can explain rates of diversification in some lineages , it is not sufficient for a radiation to occur . Instead of attrib...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "ecology/community", "ecology", "and", "biodiversity", "evolutionary", "biology", "ecology/theoretical", "ecology" ]	2010	Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity
Masculinization of the external genitalia in humans is dependent on formation of 5α-dihydrotestosterone ( DHT ) through both the canonical androgenic pathway and an alternative ( backdoor ) pathway . The fetal testes are essential for canonical androgen production , but little is known about the synthesis of backdoor a...	The human penis starts to develop before birth from a structure called the genital tubercle . This process is dependent on the secretion of testosterone from the fetal testes and subsequent conversion of testosterone into dihydrotestosterone ( DHT ) by enzymes in the genital tubercle . Recently , an alternative "backdo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "body", "fluids", "chemical", "compounds", "organic", "compounds", "hormones", "developmental", "biology", "testosterone", "steroids", "androgens", "embryology", "placenta", "chemistry", "blood", "plasma",...	2019	Alternative (backdoor) androgen production and masculinization in the human fetus
The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply , as both livestock and plants are affected . Two principal factors contribute to this problem . First , nematode resistance to anthelmintic drugs is increasing worldwide and second , many effective nematicides...	With over two billion people infected and many billions of dollars of lost crops annually , nematode infections are a serious problem for human health and for agricultural production . While there are drugs to treat infections , many pockets of parasites have been identified worldwide that are developing immunity to th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "mitochondrial", "dna", "caenorhabditis", "parasitic", "diseases", "animals", "organic", "compounds", "nematode", "infections", "animal", "models", "caenorhabditis", "elegans", "model", "or...	2016	Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity
Spatial context in images induces perceptual phenomena associated with salience and modulates the responses of neurons in primary visual cortex ( V1 ) . However , the computational and ecological principles underlying contextual effects are incompletely understood . We introduce a model of natural images that includes ...	One of the most important and enduring hypotheses about the way that mammalian brains process sensory information is that they are exquisitely attuned to the statistical structure of the natural world . This allows them to come , over the course of development , to represent inputs in a way that reflects the facets of ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science", "computational", "neuroscience", "synthetic", "vision", "systems", "biology", "sensory", "systems", "neuroscience" ]	2012	Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics
In all animals managing the size of individual meals and frequency of feeding is crucial for metabolic homeostasis . In the current study we demonstrate that the noradrenalin analogue octopamine and the cholecystokinin ( CCK ) homologue Drosulfakinin ( Dsk ) function downstream of TfAP-2 and Tiwaz ( Twz ) to control th...	The size of individual meals and feeding frequency are important for homeostatic control . Due to the complex neuroendocrine system regulating human food intake it is difficult to uncover the mechanisms underlying eating disorders . The genetically tractable model system Drosophila melanogaster has a comparatively simp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "arthropoda", "animal", "models", "invertebrates", "behavioral", "neuroscience", "drosophila", "melanogaster", "model", "organisms", "research", "and", "analysis", "methods", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", ...	2014	Obesity-Linked Homologues TfAP-2 and Twz Establish Meal Frequency in Drosophila melanogaster
Two-component systems ( TCSs ) are important for the adaptation and survival of bacteria and fungi under stress conditions . A TCS is often composed of a membrane-bound sensor histidine kinase ( SK ) and a response regulator ( RR ) , which are relayed through sequential phosphorylation steps . However , the mechanism f...	Two-component signal transduction systems ( TCSs ) are promising targets for new antimicrobial research because they help bacteria and fungi adapt and survive . One of the main components of TCSs is a sensor histidine kinase ( SK ) , which relays extracellular signals to intracellular pathways . Despite intensive resea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "enzyme", "structure", "enzymes", "enzyme", "regulation", "macromolecular", "assemblies", "biology", "enzyme", "kinetics", "biophysics" ]	2013	Mechanistic Insights Revealed by the Crystal Structure of a Histidine Kinase with Signal Transducer and Sensor Domains
The position of genes in the interphase nucleus and their association with functional landmarks correlate with active and/or silent states of expression . Gene activation can induce chromatin looping from chromosome territories ( CTs ) and is thought to require de novo association with transcription factories . We iden...	The spatial organization of the genome inside the cell nucleus is important in regulating gene expression and in the response to external stimuli . Examples of changing spatial organization are the repositioning of genes outside chromosome territories during the induction of gene expression , and the gathering of activ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/chromatin", "structure", "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/gene", "expression", ...	2010	Poised Transcription Factories Prime Silent uPA Gene Prior to Activation
One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron . In the nematode Caenorhabditis elegans , the progression from egg to terminally differentiated neuron has been v...	The generation of a neuron from a fertilized egg requires a multi-step cascade of molecules acting from within and outside that cell to direct it towards a neuronal fate , rather than , say , a muscle cell . These cascades are not fully understood . In this study we systematically eliminate the function of almost all g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "neuroscience", "animal", "genetics", "model", "organisms", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2011	A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans
Bone morphogenetic protein ( BMP ) pathways control an array of developmental and homeostatic events , and must themselves be exquisitely controlled . Here , we identify Caenorhabditis elegans SMA-10 as a positive extracellular regulator of BMP–like receptor signaling . SMA-10 acts genetically in a BMP–like ( Sma/Mab )...	Bone morphogenetic protein ( BMP ) family members , small secreted signaling molecules , play diverse roles in development and homeostasis . Uncontrolled BMP signaling results in a variety of disorders and diseases . BMPs signal to receiving cells through two receptor types , which act together to propagate the BMP sig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/molecular", "development", "developmental", "biology/developmental", "molecular", "mechanisms", "cell", "biology/cell", "signaling" ]	2010	Caenorhabditis elegans SMA-10/LRIG Is a Conserved Transmembrane Protein that Enhances Bone Morphogenetic Protein Signaling
HEY bHLH transcription factors have been shown to regulate multiple key steps in cardiovascular development . They can be induced by activated NOTCH receptors , but other upstream stimuli mediated by TGFß and BMP receptors may elicit a similar response . While the basic and helix-loop-helix domains exhibit strong simil...	NOTCH signaling is a central developmental pathway that influences a multitude of cell fate decisions and differentiation steps as well as later tissue homeostasis and regeneration . The three HEY genes encode basic helix-loop-helix transcription factors that are critical effectors to convey signaling by NOTCH receptor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "expression", "analysis", "functional", "genomics", "gene", "regulation", "dna", "transcription", "gene", "function", "cardiovascular", "genome", "sequencing", "developmental", "biology", "organism", "development", "molecular", "development", "molecula...	2012	Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Male and female tsetse flies feed exclusively on vertebrate blood . While doing so they can transmit the diseases of sleeping sickness in humans and nagana in domestic stock . Knowledge of the host-orientated behavior of tsetse is important in designing bait methods of sampling and controlling the flies , and in unders...	Tsetse flies and other blood-sucking insects spread devastating diseases of humans and livestock . We must understand the host-finding behavior of these vectors to assess their epidemiological importance and to design optimal bait methods for controlling or sampling them . Unfortunately , mysteries abound in the host-f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "epidemiology" ]	2014	Explaining the Host-Finding Behavior of Blood-Sucking Insects: Computerized Simulation of the Effects of Habitat Geometry on Tsetse Fly Movement
Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins . While some circuits act to reduce this noise , others appear to exploit it . A striking example is the competence circuit in Bacillus subtilis , which exhibits much larger noise in the duration of its competence e...	Fluctuations , or “noise” , in the response of a system is usually thought to be harmful . However , it is becoming increasingly clear that in single-celled organisms , noise can sometimes help cells survive . This is because noise can enhance the diversity of responses within a cell population . In this study , we ide...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "signal", "processing", "cell", "processes", "bacillus", "microbiology", ...	2016	Noise Expands the Response Range of the Bacillus subtilis Competence Circuit
Emerging pathogens undermine initiatives to control the global health impact of infectious diseases . Zoonotic malaria is no exception . Plasmodium knowlesi , a malaria parasite of Southeast Asian macaques , has entered the human population . P . knowlesi , like Plasmodium falciparum , can reach high parasitaemia in hu...	Plasmodium knowlesi , a parasite of Southeast Asian macaques , has entered the human population . Approximately 10% of P . knowlesi infections are severe , 1–2% are fatal , in Sarawak , Malaysian Borneo . Increase in parasitaemia is associated with disease severity , but little is known about parasite virulence in this...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "veterinary", "diseases", "zoonoses", "biology", "and", "life", "sciences", "parasitic", "diseases", "veterinary", "science" ]	2014	Disease Progression in Plasmodium knowlesi Malaria Is Linked to Variation in Invasion Gene Family Members
Inflammation is a physiological response to tissue trauma or infection , but leukocytes , which are the effector cells of the inflammatory process , have powerful tissue remodelling capabilities . Thus , to ensure their precise localisation , passage of leukocytes from the blood into inflamed tissue is tightly regulate...	Inflammation is a physiological response to tissue trauma or infection . Neutrophils , which circulate in the blood stream , are the first inflammatory cells to be recruited to a site of tissue inflammation . In response to recruitment signals provided by chemotactic peptides called chemokines , neutrophils traverse th...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "physiology/immune", "response", "physiology/cardiovascular", "physiology", "and", "circulation", "nutrition", "immunology/innate", "immunity", "cell", "biology/cell", "adhesion", "immunology/leukocyte", "activation" ]	2009	Omega-3 Fatty Acids and Inflammation: Novel Interactions Reveal a New Step in Neutrophil Recruitment
Apicomplexan parasites are dependent on an F-actin and myosin-based motility system for their invasion into and escape from animal host cells , as well as for their general motility . In Toxoplasma gondii and Plasmodium species , the actin filaments and myosin motor required for this process are located in a narrow spa...	Protozoan parasites of humans are important causes of disease throughout the world . Amongst these , the apicomplexan parasites are an especially important group of pathogens , as they include Plasmodium species , the causative agents of malaria , and Toxoplasma gondii , an important cause of disease in people with AID...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/chemical", "biology", "of", "the", "cell", "infectious", "diseases/hiv", "infection", "and", "aids", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "microbiology/...	2008	Host Cell Egress and Invasion Induce Marked Relocations of Glycolytic Enzymes in Toxoplasma gondii Tachyzoites
The Vif protein of HIV-1 allows virus replication by degrading several members of the host-encoded APOBEC3 family of DNA cytosine deaminases . Polymorphisms in both host APOBEC3 genes and the viral vif gene have the potential to impact the extent of virus replication among individuals . The most genetically diverse of ...	The APOBEC3 enzymes protect cells by inhibiting the spread of retroelements , including HIV-1 , by blocking reverse transcription and mutating cytosines in single-stranded DNA replication intermediates . HIV-1 Vif counteracts restriction by marking APOBEC3 proteins for proteasomal degradation . APOBEC3H is the most div...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "innate", "immune", "system", "viral", "immune", "evasion", "viral", "genes", "microbial", "evolution", "virology", "biology", "and", "life", "sciences", "immunology", "microbiology", "evolutionary", "biology", "viral", "evolution", "immune", ...	2014	Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity
A typical Go/No-Go decision is suggested to be implemented in the brain via the activation of the direct or indirect pathway in the basal ganglia . Medium spiny neurons ( MSNs ) in the striatum , receiving input from cortex and projecting to the direct and indirect pathways express D1 and D2 type dopamine receptors , r...	The basal ganglia ( BG ) play a crucial role in a variety of cognitive and motor functions . BG dysfunction leads to brain disorders such as Parkinson’s disease . At the main input stage of the BG , the striatum , two competing pathways originate . Neurons projecting on these pathways either express D1 or D2 type dopam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum
While the importance of gene enhancers in transcriptional regulation is well established , the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled . Recent studies have shown that progesterone receptor ( PR ) binds regions that display typical features of gene ...	A lot of research has been devoted during the last decades to understand the mechanisms that control gene promoters activity , however , much less is known about enhancers . Only recently , the use of genome-wide chromatin immunoprecipitation techniques has revealed the existence of more than 400 , 000 enhancers in the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent Enhancers
Voluntary movements are widely considered to be planned before they are executed . Recent studies have hypothesized that neural activity in motor cortex during preparation acts as an ‘initial condition’ which seeds the proceeding neural dynamics . Here , we studied these initial conditions in detail by investigating 1 ...	Early studies of premotor cortex explored how individual neurons directly encode aspects of an upcoming movement during preparation . Recent developments have proposed that the dynamics of populations of neurons underlie motor control , and that neural activity during preparation serves to set up these dynamics . While...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "ellipses", "classical", "mechanics", "reaction", "time", "statistics", "social", "sciences", "vertebrates", "neuroscience", "animals", "mammals", "geometry", "primates", "multivariate", "analysis", "cognitive", "neuroscience", "mathematics", "artificial", "intelligence", "...	2019	Structure and variability of delay activity in premotor cortex
The prevalence of Wuchereria bancrofti , which causes lymphatic filariasis ( LF ) in The Gambia was among the highest in Africa in the 1950s . However , surveys conducted in 1975 and 1976 revealed a dramatic decline in LF endemicity in the absence of mass drug administration ( MDA ) . The decline in prevalence was part...	The prevalence of lymphatic filariasis ( LF ) , in The Gambia was among the highest in Africa in the 1950s when about 50% of the adult population was positive for microfilaraemia . However , surveys conducted in 1975 and 1976 revealed a dramatic decline in LF endemicity in the absence of systematic treatment with anti-...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Elimination of Lymphatic Filariasis in The Gambia
Toxocara canis and T . cati are parasites of dogs and cats , respectively , that infect humans and cause human toxocariasis . Infection may cause asthma-like symptoms but is often asymptomatic and is associated with a marked eosinophilia . Previous epidemiological studies indicate that T . canis infection may be associ...	Toxocara canis and T . cati are roundworms found in dogs and cats , respectively , that can also infect humans and cause several clinical features , including asthma-like symptoms . Human infections with T . canis have been associated with an increased prevalence of atopy and asthma . In the present study , we investig...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "immunology", "parasitic", "diseases", "pulmonology", "neglected", "tropical", "diseases", "asthma", "infectious", "diseases", "toxocariasis", "epidemiology", "biology", "child", "health", "public", "health", "pediatr...	2012	Toxocara Seropositivity, Atopy and Wheezing in Children Living in Poor Neighbourhoods in Urban Latin American
Recognition of peptidoglycan ( PGN ) is paramount for insect antibacterial defenses . In the fruit fly Drosophila melanogaster , the transmembrane PGN Recognition Protein LC ( PGRP-LC ) is a receptor of the Imd signaling pathway that is activated after infection with bacteria , mainly Gram-negative ( Gram− ) . Here we ...	Recognition of peptidoglycan on the bacteria cell wall triggers insect immune responses . The fruit fly PGRPLC receptor protein senses the presence of peptidoglycan and activates a pathway that mediates resistance to bacterial infections , mainly Gram-negative . We show that the PGRPLC receptor of the malaria vector mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "immunology/immune", "response", "microbiology/innate", "immunity", "immunology/innate", "immunity", "genetics", "and", "genomics/disease", "models", "microbi...	2009	Anopheles gambiae PGRPLC-Mediated Defense against Bacteria Modulates Infections with Malaria Parasites
The mechanistic target of rapamycin ( mTOR ) integrates both intracellular and extracellular signals to regulate cell growth and metabolism . However , the role of mTOR signaling in osteoblast differentiation and bone formation is undefined , and the underlying mechanisms have not been elucidated . Here , we report tha...	The coordinated activities of osteoblasts and osteoclasts in bone deposition and resorption form the internal structure of bone . Disruption of the balance between bone formation and resorption results in loss of bone mass and causes bone diseases such as osteoporosis . Current therapies for osteoporosis are limited to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	mTORC1 Prevents Preosteoblast Differentiation through the Notch Signaling Pathway
Lymphatic filariasis ( LF ) , a leading cause of permanent and long-term disability , affects 120 million people globally . Hydrocele , one of the chronic manifestations of LF among 27 million people worldwide , causes economic and psychological burdens on patients and their families . The present study explores and de...	Lymphatic filariasis , the second leading cause of permanent and long-term disability , affects 120 million people globally . Hydrocele , an accumulation of fluid in the scrotum that causes it to swell , is one of the chronic manifestations of LF among men and there are about 27 million men with hydrocele worldwide . W...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2009	Marriage, Sex, and Hydrocele: An Ethnographic Study on the Effect of Filarial Hydrocele on Conjugal Life and Marriageability from Orissa, India
The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation . However , it is currently not possible to interpret reliably the functional consequences of genetic variation within any given transcription factor recognition sequence . To address this , ...	A comprehensive understanding of the contribution of individual genome sequences to disease and quantitative traits will require the general ability to predict consequences of genetic variation in non-protein-coding regions , particularly those involved in gene regulation . Here we tested the power to predict such cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2012	Widespread Site-Dependent Buffering of Human Regulatory Polymorphism
The Type VI secretion system ( T6SS ) is a widespread weapon dedicated to the delivery of toxin proteins into eukaryotic and prokaryotic cells . The 13 T6SS subunits assemble a cytoplasmic contractile structure anchored to the cell envelope by a membrane-spanning complex . This structure is evolutionarily , structurall...	In the environment , bacteria compete for privileged access to nutrients or to a particular niche . Bacteria have therefore evolved mechanisms to eliminate competitors . Among them , the Type VI secretion system ( T6SS ) is a contractile machine functionally comparable to a crossbow: an inner tube is wrapped by a contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Type VI Secretion TssEFGK-VgrG Phage-Like Baseplate Is Recruited to the TssJLM Membrane Complex via Multiple Contacts and Serves As Assembly Platform for Tail Tube/Sheath Polymerization
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding . The study is carried out comparatively for two homologous carbamoyltransferases , a natively-knotted N-acetylornithine carbamoyltransferase ( AOTCase ) and an unknotted ornit...	Knotted proteins provide an ideal ground for examining how amino acid interactions ( which are local ) can favor their folding into a native state of non-trivial topology ( which is a global property ) . Some of the mechanisms that can aid knot formation are investigated here by comparing coarse-grained folding simulat...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "physics", "protein", "folding", "biophysics", "simulations", "biophysics" ]	2012	The Role of Non-Native Interactions in the Folding of Knotted Proteins
Spontaneous copy number variant ( CNV ) mutations are an important factor in genomic structural variation , genomic disorders , and cancer . A major class of CNVs , termed nonrecurrent CNVs , is thought to arise by nonhomologous DNA repair mechanisms due to the presence of short microhomologies , blunt ends , or short ...	Copy number variants ( CNVs ) are a major factor in genetic variation and are a common and important class of mutation in genomic disorders , yet there is limited understanding of how many CNVs arise and the risk factors involved . One DNA damage response pathway implicated in CNV formation is nonhomologous end joining...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutagenesis", "genetic", "mutation", "chromosome", "biology", "chromosome", "structure", "and", "function", "genetics", "biology", "genomics", "genetics", "and", "genomics", "mutational", "hypotheses" ]	2012	De Novo CNV Formation in Mouse Embryonic Stem Cells Occurs in the Absence of Xrcc4-Dependent Nonhomologous End Joining
High-throughput bisulfite sequencing technologies have provided a comprehensive and well-fitted way to investigate DNA methylation at single-base resolution . However , there are substantial bioinformatic challenges to distinguish precisely methylcytosines from unconverted cytosines based on bisulfite sequencing data ....	High-throughput bisulfite sequencing ( BS-seq ) has advanced tremendously the study of DNA methylation and the determination of methylcytosines at single-base resolution . In BS-seq data analysis , sequencing errors , incomplete bisulfite conversion , and cell heterozygosis affect the accuracy of methylcytosine detecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "bioinformatics", "database", "and", "informatics", "methods", "mathematical", "and", "statistical", "techniques", "genetics", "bayesian", "method", "biology", "and", "life", "sciences", "dna", "computational", "biology", "dna", "modification", "epigenetic...	2014	A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data
CD8+ T cells are essential for host defense to intracellular bacterial pathogens such as Mycobacterium tuberculosis ( Mtb ) , Salmonella species , and Listeria monocytogenes , yet the repertoire and dominance pattern of human CD8 antigens for these pathogens remains poorly characterized . Tuberculosis ( TB ) , the dise...	CD8+ T cells are essential for host defense to intracellular bacterial pathogens such as Mycobacterium tuberculosis ( Mtb ) , Salmonella species , and Listeria monocytogenes , yet little is known about the antigens recognized by human CD8+ T cells in response to tuberculosis ( TB ) . TB , the disease caused by Mtb infe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "immunology", "homo", "(human)", "eubacteria" ]	2007	Immunodominant Tuberculosis CD8 Antigens Preferentially Restricted by HLA-B
Locomotion is driven by shape changes coordinated by the nervous system through time; thus , enumerating an animal's complete repertoire of shape transitions would provide a basis for a comprehensive understanding of locomotor behaviour . Here we introduce a discrete representation of behaviour in the nematode C . eleg...	Technology for recording neural activity is advancing rapidly and whole-brain imaging with single neuron resolution has already been demonstrated for smaller animals . To interpret such complex neural recordings , we need comprehensive characterizations of behaviour , which is the principal output of the brain . Animal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion
Diagnosis of the neglected tropical disease , Buruli ulcer , can be made by acid-fast smear microscopy , specimen culture on mycobacterial growth media , polymerase chain reaction ( PCR ) , and/or histopathology . All have drawbacks , including non-specificity and requirements for prolonged culture at 32°C , relatively...	The diagnosis of Buruli ulcer , caused by infection with Mycobacterium ulcerans , is complicated by its resemblance to other diseases that may also cause ulcers in the skin . Clinical diagnosis can be supported by microscopic detection of acid-fast bacilli in the skin , by prolonged culture of at least 8 weeks , in a d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2014	Accelerated Detection of Mycolactone Production and Response to Antibiotic Treatment in a Mouse Model of Mycobacterium ulcerans Disease
Philadelphia chromosome-positive ( Ph+ ) acute lymphoblastic leukemia ( ALL ) is characterized by a very poor prognosis and a high likelihood of acquired chemo-resistance . Although tyrosine kinase inhibitor ( TKI ) therapy has improved clinical outcome , most ALL patients relapse following treatment with TKI due to th...	High likelihood of evolution of resistance to therapy is common in most forms of leukemia . This issue persists for tyrosine kinase inhibitor drug treatments as well as other forms of therapies . In the current work , we suggest a combination therapy where Ph+ acute lymphoblastic leukemic cells are treated with low-dos...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "death", "leukemias", "medicine", "and", "health", "sciences", "radiation", "therapy", "dose", "prediction", "methods", "cancer", "treatment", "clinical", "oncology", "cell", "processes", "cancers", "and", "neoplasms", "mathematical", "models", "oncology", "he...	2017	Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance
Establishing functional tissue-resident memory ( TRM ) cells at sites of infection is a newfound objective of T cell vaccine design . To directly assess the impact of antigen stimulation strength on memory CD8 T cell formation and function during a persistent viral infection , we created a library of mouse polyomavirus...	Tissue-resident memory ( TRM ) cells are a subset of memory T cells that primarily reside in non-lymphoid tissues and serve as sentinels and effectors against secondary infections . TRM cells have been extensively characterized in mucosal barriers , but much less is known about this population in non-barrier sites such...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "cloning", "neuroscience", "learning", "and", "memory", "cell", "differentiation", "developmental", "biology", "cognition", "memory", "cytotoxic...	2017	TCR stimulation strength is inversely associated with establishment of functional brain-resident memory CD8 T cells during persistent viral infection
Long term surveillance of vectors and arboviruses is an integral aspect of disease prevention and control systems in countries affected by increasing risk . Yet , little effort has been made to adjust space-time risk estimation by integrating disease case counts with vector surveillance data , which may result in inacc...	Dengue cases have increased in tropical regions worldwide owing to urbanization , globalization , and climate change facilitating the spread of Aedes mosquito vectors . National surveillance programs monitor trends in dengue fever and inform the public about epidemiological scenarios where outbreak preventive actions a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "panama", "animals", "north", "america", "mathematics", "algebra", "infectious", "disease", "control", "insect", "vectors", "central", "america", "public", "and", "occupational", "hea...	2019	Detecting space-time clusters of dengue fever in Panama after adjusting for vector surveillance data
Mozambique suffers recurrent annual cholera outbreaks especially during the rainy season between October to March . The African Cholera Surveillance Network ( Africhol ) was implemented in Mozambique in 2011 to generate accurate detailed surveillance data to support appropriate interventions for cholera control and pre...	Cholera is a major public health problem in many countries in sub-Saharan Africa . In Mozambique , annual outbreaks occur but the place and time may vary . Africhol was implemented in Mozambique in 2011 to generate more detailed information on disease burden and characteristics to support appropriate interventions for ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "geographical", "locations", "microbiology", "retroviruses", "viruses", "immuno...	2017	Multi-site cholera surveillance within the African Cholera Surveillance Network shows endemicity in Mozambique, 2011–2015
The evolution of multiple antibiotic resistance is an increasing global problem . Resistance mutations are known to impair fitness , and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact—epistasis . Information on the level of epistasis between antibiotic re...	Understanding the nature of genetic interactions , known as epistasis , is crucial in biology . The strength and type of epistasis is relevant for the evolution of sex , buffering of genetic variation , speciation , and the topography of fitness landscapes . While epistasis between gene deletions has been the recent fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "public", "health", "and", "epidemiology", "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "genetics", "and", "genomics/population", "genetics" ]	2009	Positive Epistasis Drives the Acquisition of Multidrug Resistance
Pseudomonas aeruginosa ( PA ) is an opportunistic pathogen that causes the relapse of illness in immunocompromised patients , leading to prolonged hospitalization , increased medical expense , and death . In this report , we show that PA invades natural killer ( NK ) cells and induces phagocytosis-induced cell death ( ...	Phagocytic leukocytes , including neutrophils and macrophages , are critical for innate immunity against invading bacteria . Binding and internalization of bacteria by these immune cells stimulates a variety of anti-microbial activities . Although the immune cells are specialized for elimination of bacteria , cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunity", "to", "infections", "immunology/innate", "immunity" ]	2009	Pseudomonas aeruginosa Eliminates Natural Killer Cells via Phagocytosis-Induced Apoptosis
The parasitic flatworm Schistosoma mansoni is a blood fluke that causes schistosomiasis . Current schistosomiasis control strategies are mainly based on chemotherapy , but many researchers believe that the best long-term strategy to control disease is a combination of drug treatment and immunization with an anti-schist...	Schistosomiasis mainly occurs in developing countries and is the most important human helminth infection in terms of global mortality . This parasitic disease affects more than 200 million people worldwide and causes more than 250 , 000 deaths per year . Current schistosomiasis control strategies are mainly based on ch...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology", "host-pathogen", "interaction", "biology", "microbiology", "parasitology" ]	2014	Sm10.3, a Member of the Micro-Exon Gene 4 (MEG-4) Family, Induces Erythrocyte Agglutination In Vitro and Partially Protects Vaccinated Mice against Schistosoma mansoni Infection
Mass drug administration ( MDA ) with antibiotics is a key component of the SAFE strategy for trachoma control . Guidelines recommend that where MDA is warranted the whole population be targeted with 80% considered the minimum acceptable coverage . In other countries , MDA is usually conducted by salaried Ministry of H...	The World Health Organization recommends that mass drug administration for trachoma control reach a minimum of 80% of the target population . Previous evaluations of MDA coverage have demonstrated that administrative reports can bias coverage estimates . A survey of participation in mass drug administration for trachom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "global", "health", "neglected", "tropical", "diseases", "trachoma", "public", "health" ]	2013	Monitoring of Mass Distribution Interventions for Trachoma in Plateau State, Nigeria
Environmental stresses increase genetic variation in bacteria , plants , and human cancer cells . The linkage between various environments and mutational outcomes has not been systematically investigated , however . Here , we established the influence of nutritional stresses commonly found in the biosphere ( carbon , p...	The importance of this study is in advancing our understanding of mutation supply—of the frequency that beneficial mutations arise in a population—in evolution and the contribution of stress-induced mutagenesis to this process . Evolutionary divergences , the emergence of antibiotic resistance in bacteria , and cancer ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mutagenesis", "mutation", "substitution", "mutation", "deletion", "mutation", "genomics", "point", "mutation", "microbial", "mutation", "genome", "evolution", "insertion", "mutation", "genetics", "biology", "and", "life", "sciences", "molecular", "evolution", "microbiolo...	2017	A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input–mutation output relationships
HIV-1 is extremely specialized since , even amongst CD4+ T lymphocytes ( its major natural reservoir in peripheral blood ) , the virus productively infects only a small proportion of cells under an activated state . As the percentage of HIV-1-infected cells is very low , most studies have so far failed to capture the p...	Some previous studies have monitored HIV-1-induced gene expression in various host cell targets and tissues but the discrimination between productively infected cells and uninfected bystander cells represents a technical challenge yet to be solved . Consequently , data interpretation has always been biased towards the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "expression", "analysis", "infectious", "diseases", "genome", "analysis", "tools", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "biology", "genomics", "viral", "diseases", "genetics", "and", "genomics", "transcriptomes" ]	2012	Exon Level Transcriptomic Profiling of HIV-1-Infected CD4+ T Cells Reveals Virus-Induced Genes and Host Environment Favorable for Viral Replication
There was a large dengue outbreak in Taiwan in 2015 , in which the ages of the affected individuals were higher than those in other countries . The aim of this study was to explore the characteristics and prognostic factors for adults with severe dengue in intensive care units ( ICUs ) . All adults admitted to ICUs wit...	Severe forms of dengue fever ( DF ) are usually considered as a pediatric disease in southern Asia and are graded from dengue hemorrhagic fever ( DHF ) to dengue with shock syndrome ( DSS ) . However , the age of affected individuals is increasing in Singapore , Thailand , Mainland China , Taiwan and many other countri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "elderly", "pathogens", "respiratory", "failure", "tropical", "diseases", "geographical", "locations", "microbiology", "pulmonology", "health", "care", "viruses", "...	2017	A Cohort Study of Adult Patients with Severe Dengue in Taiwanese Intensive Care Units: The Elderly and APTT Prolongation Matter for Prognosis
In the era of systems biology , multi-target pharmacological strategies hold promise for tackling disease-related networks . In this regard , drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites ac...	Traditionally , the fact that most drugs are promiscuous binders has been a major concern in pharmacology , due to the occurrence of undesired off-target clinical events . In the recent years , however , the realization that many diseases are the result of complex biological processes has encouraged rethinking of drug ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "protein", "metabolism", "protein", "interaction", "networks", "systems", "science", "mathematics", "network", "analysis", "protein", "structure", "pharmacology", "drug", "metabolism", "computer", "and", "i...	2017	Detecting similar binding pockets to enable systems polypharmacology
Inflammatory bowel diseases ( IBD ) are chronic inflammatory disorders of the gastrointestinal tract , strongly associated with an increased risk of colorectal cancer development . Parasitic infections caused by helminths have been shown to modulate the host’s immune response by releasing immunomodulatory molecules and...	Evidence from epidemiological studies indicates an inverse correlation between the incidence of certain immune-mediated diseases , including inflammatory bowel diseases , and exposure to helminths . As a consequence , helminth parasites were tested for treating IBD patients , resulting in clinical amelioration of the d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "parasitic", "diseases", "animal", "models", "colitis", "model", "organisms", "signs", "and", "symptoms", "gastroenterology", "and...	2017	Intestinal helminth infection drives carcinogenesis in colitis-associated colon cancer
Dominant mutations in the alpha-B crystallin ( CryAB ) gene are responsible for a number of inherited human disorders , including cardiomyopathy , skeletal muscle myopathy , and cataracts . The cellular mechanisms of disease pathology for these disorders are not well understood . Among recent advances is that the disea...	Cardiomyopathy is a specific form of heart disease that involves progressive restructuring of the heart muscle , resulting in reduced function and increased chance of sudden heart failure . Several mutations have been identified that cause inherited cardiomyopathy , including mutations in a gene called alpha B-crystall...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "drosophila", "melanogaster", "animal", "genetics", "congenital", "hereditary", "myopathies", "model", "organisms", "cellular", "stress", "responses", "genetic", "screens", "genetics", "biology", "human", "genetics", "molecular", "cell", "biology", "...	2013	The NADPH Metabolic Network Regulates Human αB-crystallin Cardiomyopathy and Reductive Stress in Drosophila melanogaster
Intraocular pressure ( IOP ) is a highly heritable risk factor for primary open-angle glaucoma and is the only target for current glaucoma therapy . The genetic factors which determine IOP are largely unknown . We performed a genome-wide association study for IOP in 11 , 972 participants from 4 independent population-b...	Glaucoma is a major eye disease in the elderly and is the second leading cause of blindness worldwide . The numerous familial glaucoma cases , as well as evidence from epidemiological and twin studies , strongly support a genetic component in developing glaucoma . However , it has proven difficult to identify the speci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "public", "health", "and", "epidemiology", "quantitative", "traits", "glaucoma", "genetic", "epidemiology", "disease", "mapping", "epidemiology", "gene", "expression", "biology", "heredity", "ophthalmology", "genetics", ...	2012	Common Genetic Determinants of Intraocular Pressure and Primary Open-Angle Glaucoma
Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology , yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations . Here we report a population genetic analysis of a two-locus α-globin pol...	A major goal in evolutionary biology is to identify the specific genetic mechanisms that have enabled organisms to adapt to their environments . Variation in deer mouse hemoglobin represents an especially promising system for examining the molecular underpinnings of adaptation because it has been possible to establish ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "genetics", "and", "genomics", "mammals" ]	2007	The Molecular Basis of High-Altitude Adaptation in Deer Mice
It has been shown that the same canonical cortical circuit model with mutual inhibition and a fatigue process can explain perceptual rivalry and other neurophysiological responses to a range of static stimuli . However , it has been proposed that this model cannot explain responses to dynamic inputs such as found in in...	When the brain is presented with an ambiguous stimulus like the Necker cube or what is known as the quartet illusion , the perception will alternate or rival between the possible interpretations . There are neurons in the brain whose activity is correlated with the perception and not the stimulus . Hence , perceptual r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "material", "fatigue", "medicine", "and", "health", "sciences", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "fatigue", "social", "sciences", "neuroscience", "learning", "and", "memory", "perception", "cognitive", "psychology", "signs", "and",...	2016	Canonical Cortical Circuit Model Explains Rivalry, Intermittent Rivalry, and Rivalry Memory
Gap junctions between fine unmyelinated axons can electrically couple groups of brain neurons to synchronise ﬁring and contribute to rhythmic activity . To explore the distribution and significance of electrical coupling , we modelled a well analysed , small population of brainstem neurons which drive swimming in young...	Some groups of nerve cells in the brain are connected to each other electrically where their processes make contact and form specialized “gap” junctions . The simplest function of electrical connections is to make activity propagate faster by avoiding the delays resulting from chemical messengers at synaptic connection...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity
The flagellar pocket ( FP ) of the pathogen Trypanosoma brucei is an important single copy structure that is formed by the invagination of the pellicular membrane . It is the unique site of endo- and exocytosis and is required for parasite pathogenicity . The FP consists of distinct structural sub-domains with the leas...	Trypanosoma brucei avoids destruction by , in part , changing its surface glycoprotein coat , which is trafficked onto the cell surface via an invagination of the cell surface called the flagellar pocket . The pocket is essential for pathogenicity . The distal membrane of the pocket is anchored to a cytoskeleton struct...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	BILBO1 Is a Scaffold Protein of the Flagellar Pocket Collar in the Pathogen Trypanosoma brucei
Ribosomal RNA synthesis is controlled by nutrient signaling through the mechanistic target of rapamycin complex 1 ( mTORC1 ) pathway . mTORC1 regulates ribosomal RNA expression by affecting RNA Polymerase I ( Pol I ) -dependent transcription of the ribosomal DNA ( rDNA ) but the mechanisms involved remain obscure . Thi...	All cells communicate their environmental nutrient status to the gene expression machinery so that transcription occurs in proportion to the nutrients available to support cell growth and proliferation . mTORC1 signaling , which is essential for this process , regulates Pol I-dependent rRNA expression . We provide evid...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis
Habitat destruction and land use change are making the world in which natural populations live increasingly fragmented , often leading to local extinctions . Although local populations might undergo extinction , a metapopulation may still be viable as long as patches of suitable habitat are connected by dispersal , so ...	Like the hundreds of paintings of water lilies by Monet , any two landscapes in which a metapopulation dwells are different , as the size , shape and location of the patches of suitable habitat ( the lilies ) , distributed over a inhospitable background ( the water ) vary among landscapes . Yet , as all the paintings d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Metapopulation Persistence in Random Fragmented Landscapes
Previous studies have shown that let-7 can repress the post-transcriptional translation of LIN28 , and LIN28 in turn could block the maturation of let-7 , forming a double-negative feedback loop . In this study , we investigated the effect of germline genetic variants on regulation of the homeostasis of the let-7/LIN28...	Genetic variants are the genetic basis of inter-individual differences in susceptibility to common diseases like cancer . Single nucleotide polymorphisms ( SNPs ) are the major type of genetic variation in human beings , and previous studies have linked many SNPs with the risk of suffering human malignancies . In this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "public", "health", "and", "epidemiology", "epidemiology", "genetics", "and", "genomics", "clinical", "genetics" ]	2011	Germline Genetic Variants Disturbing the Let-7/LIN28 Double-Negative Feedback Loop Alter Breast Cancer Susceptibility
Cys-loop receptors ( CLR ) are pentameric ligand-gated ion channels that mediate fast excitatory or inhibitory transmission in the nervous system . Strychnine and d-tubocurarine ( d-TC ) are neurotoxins that have been highly instrumental in decades of research on glycine receptors ( GlyR ) and nicotinic acetylcholine r...	Ligand-gated ion channels play an important role in fast electrochemical signaling in the brain . Cys-loop receptors are a class of pentameric ligand-gated ion channels that are activated by specific neurotransmitters , including acetylcholine ( ACh ) , serotonin ( 5-HT ) , glycine ( Gly ) , and γ-aminobutyric acid ( G...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "neuroscience" ]	2011	A Structural and Mutagenic Blueprint for Molecular Recognition of Strychnine and d-Tubocurarine by Different Cys-Loop Receptors
A survey of potential vector sand flies was conducted in the neighboring suburban communities of Vake and Mtatsminda districts in an active focus of visceral Leishmaniasis ( VL ) in Tbilisi , Georgia . Using light and sticky-paper traps , 1 , 266 male and 1 , 179 female sand flies were collected during 2006–2008 . Five...	Visceral Leishmaniasis ( VL ) is a public health problem in Tbilisi , capital of the Republic of Georgia . VL is caused by Leishmania parasites and dogs represent the main infection reservoirs . VL is transmitted among humans and dogs by sand fly bites . Here , we carried out a three-year survey to assess the sand fly ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "ecology", "biology", "parasitic", "diseases" ]	2012	Incrimination of Phlebotomus kandelakii and Phlebotomus balcanicus as Vectors of Leishmania infantum in Tbilisi, Georgia
The evolution of drug resistance in HIV occurs by the fixation of specific , well-known , drug-resistance mutations , but the underlying population genetic processes are not well understood . By analyzing within-patient longitudinal sequence data , we make four observations that shed a light on the underlying processes...	It is well known that HIV can evolve to become drug resistant if it acquires specific drug-resistance mutations , but the underlying population genetic processes are not well understood . We found that the evolution of drug resistance in HIV populations within infected patients occurs by one mutation at a time ( as opp...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "effective", "population", "size", "natural", "selection", "virology", "genetics", "population", "genetics", "biology", "evolutionary", "theory", "evolutionary", "biology", "genomic", "evolution", "genetics", "of", "disease", "evolutionary", "genetics", "microbiology" ]	2014	Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients , and infection represents an increased threat for human health worldwide . Because resistance of Pseudomonas aeruginosa to antibiotics is increasing , new inhibitors of pharmacologically validate...	Microbial resistance to antibiotics is a serious and growing threat to human health . Here , we used a novel approach that combines chemical and genetic perturbation of bakers yeast to find new targets that might be effective in controlling infections caused by the opportunistic human pathogen Pseudomonas aeruginosa . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/applied", "microbiology", "biochemistry/drug", "discovery", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2008	Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen
Many signaling proteins including G protein-coupled receptors localize to primary cilia , regulating cellular processes including differentiation , proliferation , organogenesis , and tumorigenesis . Bardet-Biedl Syndrome ( BBS ) proteins are involved in maintaining ciliary function by mediating protein trafficking to ...	Primary cilia are considered to be a signaling hub coordinating multiple signaling pathways . Impairment of ciliary function results in developmental defects in vertebrates and also underlies many human disorders including obesity , polycystic kidney disease , and retinopathy . BBS is a prototypical human genetic disor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "spectrometric", "identification", "of", "proteins", "protein", "interactions", "gene", "function", "proteins", "membranes", "and", "sorting", "biology", "proteomics", "molecular", "biology", "biochemistry", "signal", "transduction", "cell", "biology", "genetics", "human"...	2011	A Novel Protein LZTFL1 Regulates Ciliary Trafficking of the BBSome and Smoothened
In this work , a stochastic computational model of microscopic energy deposition events is used to study for the first time damage to irradiated neuronal cells of the mouse hippocampus . An extensive library of radiation tracks for different particle types is created to score energy deposition in small voxels and volum...	Changes to cognition and other central nervous system ( CNS ) effects following charged particle exposures are of concern for medical patients undergoing radiation treatment in cancer therapy and for cosmic ray exposures to astronauts during space travel . Neuronal cell injury initiated by ionizing energy deposition in...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Irradiation of Neurons with High-Energy Charged Particles: An In Silico Modeling Approach
Mucosal-associated invariant T ( MAIT ) cells contribute to protection against certain microorganism infections . However , little is known about the role of MAIT cells in Orientia tsutsugamushi infection . Hence , the aims of this study were to examine the level and function of MAIT cells in patients with scrub typhus...	Scrub typhus is a mite-borne bacterial infection in humans caused by Orientia tsutsugamushi , an obligate intracellular bacterium , prevalent in Asia , Northern Australia , and the Indian subcontinent . The pathogenesis of O . tsutsugamushi infection is known to be not only related to the virulence of O . tsutsugamushi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "typhus", "medicine", "and", "health", "sciences", "innate", "immune", "system", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "body", "fluids", "pathogens", "immunology", ...	2016	Activation, Impaired Tumor Necrosis Factor-α Production, and Deficiency of Circulating Mucosal-Associated Invariant T Cells in Patients with Scrub Typhus
Animal models are needed to better understand the pathogenic mechanisms of Zika virus ( ZIKV ) and to evaluate candidate medical countermeasures . Adult mice infected with ZIKV develop a transient viremia , but do not demonstrate signs of morbidity or mortality . Mice deficient in type I or a combination of type I and ...	Research addressing the severe clinical complications associated with ZIKV infection , including GBS and congenital ZIKV syndrome , are urgently needed . Key to this effort is development of well-characterized animal models that recapitulate human disease . Adult wild-type mice infected with ZIKV can develop viremia in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "group-specific", "staining", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hematoxylin", "staining", "nervous", "system", "pathogens", "skeletal", "muscles", "immunology", "microbiology", "neuroscience", "animal", "models", "viru...	2017	Neuropathogenesis of Zika Virus in a Highly Susceptible Immunocompetent Mouse Model after Antibody Blockade of Type I Interferon
Predicting the emergence of new pathogenic strains is a key goal of evolutionary epidemiology . However , the majority of existing studies have focussed on emergence at the population level , and not within a host . In particular , the coexistence of pre-existing and mutated strains triggers a heightened immune respons...	The ongoing evolution of infectious diseases provides a constant health threat . This evolution can either result in the production of new pathogens , or new strains of existing pathogens that escape prevailing drug treatments or immune responses . The latter process , also known as immune escape , is a predominant rea...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants
The published biomedical research literature encompasses most of our understanding of how drugs interact with gene products to produce physiological responses ( phenotypes ) . Unfortunately , this information is distributed throughout the unstructured text of over 23 million articles . The creation of structured resour...	Virtually all important biomedical knowledge is described in the published research literature , but Medline currently contains over 23 million articles and is growing at the rate of several hundred thousand new articles each year . In this environment , we need computational algorithms that can efficiently extract , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Learning the Structure of Biomedical Relationships from Unstructured Text
Recent studies have suggested that a sub-complex of RNA polymerase II composed of Rpb4 and Rpb7 couples the nuclear and cytoplasmic stages of gene expression by associating with newly made mRNAs in the nucleus , and contributing to their translation and degradation in the cytoplasm . Here we show by yeast two hybrid an...	In this work we show that , both in the nucleus and in the cytoplasm , Not5 plays a “bridging” role for RNA Polymerase II . In the cytoplasm , Not5 interacts with the mRNA encoding the largest subunit of RNA polymerase II Rpb1 and supports the association of a co-chaperone to newly produced protein , to keep it soluble...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "cell", "biology", "biology", "and", "life", "sciences" ]	2014	The Not5 Subunit of the Ccr4-Not Complex Connects Transcription and Translation
Human African trypanosomiasis ( HAT ) remains a major neglected tropical disease in Sub-Saharan Africa . As clinical symptoms are usually non-specific , new diagnostic and prognostic markers are urgently needed to enhance the number of identified cases and optimise treatment . This is particularly important for disease...	Metabolic profiling of biofluids and tissues in disease and healthy individuals is a powerful approach to discover new markers for diagnosis . We have applied these techniques to the protozoan infection human African trypanosomiasis ( HAT ) , otherwise known as sleeping sickness . The form of HAT endemic in East Africa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Discovery of Infection Associated Metabolic Markers in Human African Trypanosomiasis
Recognition of viral RNA structures by the intracytosolic RNA helicase RIG-I triggers induction of innate immunity . Efficient induction requires RIG-I ubiquitination by the E3 ligase TRIM25 , its interaction with the mitochondria-bound MAVS protein , recruitment of TRAF3 , IRF3- and NF-κB-kinases and transcription of ...	Hepatitis C Virus ( HCV ) is a poor interferon ( IFN ) inducer , despite recognition of its RNA by the cytosolic RNA helicase RIG-I . This is due in part through cleavage of MAVS , a downstream adapter of RIG-I , by the HCV NS3/4A protease and through activation of the eIF2α-kinase PKR to control IFN translation . Here...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immunology", "microbiology", "liver", "diseases", "infectious", "hepatitis", "gastroenterology", "and", "hepatology", "signaling", "pathways", "hepatitis", "c", "stress", "signaling", "cascade", "viral", "immune", "evasion", "biology", "molecular", "biology",...	2011	Hepatitis C Virus Reveals a Novel Early Control in Acute Immune Response
Aberrant DNA methylation is an important cancer hallmark , yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored . Moreover , the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers . Here we perform the most comprehensiv...	DNA methylation is an important chemical modification of DNA that can affect and regulate the activity of genes in human tissue . Abnormal DNA methylation and its subsequent effects on gene activity are a hallmark of cancer , yet when precisely these DNA methylation changes occur and how they contribute to the developm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "epigenetics", "biology", "genetics", "and", "genomics" ]	2012	The Dynamics and Prognostic Potential of DNA Methylation Changes at Stem Cell Gene Loci in Women's Cancer
Plant responses to low temperature are tightly associated with defense responses . We previously characterized the chilling-sensitive mutant chs3-1 resulting from the activation of the Toll and interleukin 1 receptor-nucleotide binding-leucine-rich repeat ( TIR-NB-LRR ) -type resistance ( R ) protein harboring a C-term...	Resistance ( R ) genes play central roles in recognizing pathogens and triggering plant defense responses . CHS3 encodes a TIR-NB-LRR-type R protein harboring a C-terminal LIM domain . A point mutation in CHS3 activates the defense response under chilling stress . Here we identified and characterized ibr5-7 , a mutant ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	IBR5 Modulates Temperature-Dependent, R Protein CHS3-Mediated Defense Responses in Arabidopsis
Severe outcomes have been described for both Plasmodium falciparum and P . vivax infections . The identification of sensitive and reliable markers of disease severity is fundamental to improving patient care . An intense pro-inflammatory response with oxidative stress and production of reactive oxygen species is presen...	Despite being considered a relatively benign disease , Plasmodium vivax infection has been associated with fatal outcomes due to treatment failure or inadequate health care . The identification of sensitive and reliable markers of disease severity is important to improve the quality of patient care . Although not imper...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "evidence-based", "healthcare/methods", "for", "diagnostic", "and", "therapeutic", "studies", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2010	Plasma Superoxide Dismutase-1 as a Surrogate Marker of Vivax Malaria Severity
Laboratory and epidemiological evidence indicate that ambient humidity modulates the survival and transmission of influenza . Here we explore whether the inclusion of humidity forcing in mathematical models describing influenza transmission improves the accuracy of forecasts generated with those models . We generate re...	Laboratory and epidemiological evidence indicate that atmospheric absolute humidity conditions modulate the survival , transmission , incidence and seasonality of influenza . Absolute humidity ( AH ) conditions are often incorporated as a forcing factor in mathematical models used to describe and forecast influenza inc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "influenza", "atmospheric", "science", "pathogens", "applied", "mathematics", "microbiology", "orthomyxoviruses", "simulation", "and", "modeling", "viruses", "algorithms", "optimization",...	2017	The use of ambient humidity conditions to improve influenza forecast
Sudden cardiac death ( SCD ) continues to be one of the leading causes of mortality worldwide , with an annual incidence estimated at 250 , 000–300 , 000 in the United States and with the vast majority occurring in the setting of coronary disease . We performed a genome-wide association meta-analysis in 1 , 283 SCD cas...	Family studies have clearly demonstrated a role for genes in modifying risk for sudden cardiac death ( SCD ) , however genetic studies have been limited by available samples . Here we have assembled over 4 , 400 SCD cases with >30 , 000 controls , all of European ancestry , and utilize a two-stage study design . In the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "acute", "cardiovascular", "problems", "genome-wide", "association", "studies", "medicine", "coronary", "artery", "disease", "arrhythmias", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "genetics", "and", "genomics", "cardiovascular" ]	2011	Identification of a Sudden Cardiac Death Susceptibility Locus at 2q24.2 through Genome-Wide Association in European Ancestry Individuals
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA . Here , we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast . Our results demonstrate , for the first time , that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kr...	Base-pairing of box C/D small nucleolar RNAs ( snoRNAs ) with the target RNA guides site-specific ribose methylation by fibrillarin ( Nop1 ) , a highly conserved methyltransferase . Some box C/D snoRNAs , like yeast U3 , U14 and U8 in higher eukaryotes are not involved in methylation but are essential for pre-rRNA proc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfer", "rna", "small", "nucleolar", "rnas", "chemical", "compounds", "gene", "regulation", "enzymes", "enzymology", "nucleotides", "organic", "compounds", "fungi", "pyrimidines", "sequence", "motif", "analysis", "cellular", "structures", "and", "organelles", "resea...	2017	Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation
Little is known about the role of viral genes in modulating host cytokine responses . Here we report a new functional role of the viral encoded IE1 protein of the murine cytomegalovirus in sculpting the inflammatory response in an acute infection . In time course experiments of infected primary macrophages ( MΦs ) meas...	The suppression of the production rather than the blockage of action of the potent inflammatory mediator TNFα is a particular hallmark of anti-TNFα mechanisms associated with microbial and parasitic infections . Whether this mode of counter-regulation is an important feature of infection by viruses is not clear . Also ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "viral", "diseases", "cytomegalovirus", "infection" ]	2012	Ablation of the Regulatory IE1 Protein of Murine Cytomegalovirus Alters In Vivo Pro-inflammatory TNF-alpha Production during Acute Infection
Spatiotemporal regulation of cell migration is crucial for animal development and organogenesis . Compared to spatial signals , little is known about temporal signals and the mechanisms integrating the two . In the Caenorhabditis elegans hermaphrodite , the stereotyped migration pattern of two somatic distal tip cells ...	The migratory path of DTCs determines the shape of the C . elegans gonad . How the spatiotemporal migration pattern is regulated is not clear . We identified a conserved transcription factor BLMP-1 as a central component of a gene regulatory circuit required for the spatiotemporal control of DTC migration . BLMP-1 leve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	BLMP-1/Blimp-1 Regulates the Spatiotemporal Cell Migration Pattern in C. elegans
During meiotic recombination , induced double-strand breaks ( DSBs ) are processed into crossovers ( COs ) and non-COs ( NCO ) ; the former are required for proper chromosome segregation and fertility . DNA synthesis is essential in current models of meiotic recombination pathways and includes only leading strand DNA s...	Meiotic recombination is important for pairing and sustained association of homologous chromosomes ( homologs ) , thereby ensuring proper homolog segregation and normal fertility . DNA synthesis is thought to be required for meiotic recombination , but few genes coding for DNA synthesis factors have been studied for po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology", "plant", "cell", "biology", "gene", "function", "model", "organisms", "molecular", "genetics", "arabidopsis", "thaliana", "chromosome", "biology", "plant", "genetics", "biology", "plant", "and", "algal", "models", "cell", "biology", "genetics", "...	2012	The DNA Replication Factor RFC1 Is Required for Interference-Sensitive Meiotic Crossovers in Arabidopsis thaliana
Infectious prions contain a self-propagating , misfolded conformer of the prion protein termed PrPSc . A critical prediction of the protein-only hypothesis is that autocatalytic PrPSc molecules should be infectious . However , some autocatalytic recombinant PrPSc molecules have low or undetectable levels of specific in...	A key prediction of the prion hypothesis is that autocatalytic , misfolded PrPSc molecules should be highly infectious . Various recombinant PrPSc conformers are able to self-propagate in vitro , yet paradoxically only some of these conformers possess significant levels of specific infectivity in bioassays . Here we us...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers
Hepadnaviruses , including hepatitis B virus ( HBV ) , a highly relevant human pathogen , are small enveloped DNA viruses that replicate via reverse transcription . All hepadnaviruses display a narrow tissue and host tropism . For HBV , this restricts efficient experimental in vivo infection to chimpanzees . While the ...	Hepatitis B virus ( HBV ) associated liver disease is a leading cause of death worldwide . Host range restrictions limit experimental HBV infections largely to chimpanzees or isolated human hepatocytes . A narrow host range is shared by the animal hepadnaviruses , e . g . from ducks ( DHBV ) and herons ( HHBV ) ; HHBV ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/animal", "models", "of", "infection", "virology/host", "invasion", "and", "cell", "entry" ]	2008	Heterologous Replacement of the Supposed Host Determining Region of Avihepadnaviruses: High In Vivo Infectivity Despite Low Infectivity for Hepatocytes
Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse . The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation ,...	The modular features of a protein's architecture are regulated after transcription by the process of alternative pre-mRNA splicing . Conditions that excite or stress neurons can induce changes in some splicing patterns , suggesting that cellular pathways can take advantage of the flexibility of splicing to tune their p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "in", "vitro", "computational", "biology", "neuroscience", "molecular", "biology" ]	2007	Exon Silencing by UAGG Motifs in Response to Neuronal Excitation
Cysteine-rich intestinal protein 1 ( CRIP1 ) has been identified as a novel marker for early detection of cancers . Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ligand for CRIP1 . Panning experiments using a circularized C7C phage library yielded several ...	Breast cancer is one of the most frequently diagnosed malignancies in American females and is the second leading cause of cancer deaths in women . Several improvements in diagnostic protocols have enhanced our ability for earlier detection of breast cancer , resulting in improvement of therapeutic outcome and an increa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "biochemistry/experimental", "biophysical", "methods", "biophysics/protein", "folding", "biochemistry/protein", "folding", "biophysics/theory", "and", "simulation", "computational", "biology/protein", "structure", "prediction", "biochemistry/bioinformatics", "biotechnolog...	2008	Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers
The outcome of viral infections is dependent on the function of CD8+ T cells which are tightly regulated by costimulatory molecules . The NK cell receptor 2B4 ( CD244 ) is a transmembrane protein belonging to the Ig superfamily which can also be expressed by CD8+ T cells . The aim of this study was to analyze the role ...	Infection with the hepatitis C Virus ( HCV ) is a world-wide health burden , the infection becomes persistent in the majority of cases . In chronic patients HCV-specific immune responses are weak , HCV-specific CD8+ T cells were shown to be functionally exhausted and to be negatively controlled by costimulatory molecul...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immune", "cells", "immune", "activation", "immunity", "to", "infections", "immunology", "liver", "diseases", "adaptive", "immunity", "infectious", "hepatitis", "hepatitis", "gastroenterology", "and", "hepatology", "immunoregulation", "hepatitis", "c", "infect...	2011	Dual Function of the NK Cell Receptor 2B4 (CD244) in the Regulation of HCV-Specific CD8+ T Cells
Chk2 is an effector kinase important for the activation of cell cycle checkpoints , p53 , and apoptosis in response to DNA damage . Mus81 is required for the restart of stalled replication forks and for genomic integrity . Mus81Δex3-4/Δex3-4 mice have increased cancer susceptibility that is exacerbated by p53 inactivat...	Failure to repair DNA damage has been associated with a number of human syndromes , neurodegenerative diseases , immunodeficiency , and cancer . In addition , radiotherapy and many cancer chemotherapeutic drugs induce DNA damage , thus allowing the killing of tumors . Recent data indicated Mus81's role in maintaining g...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/cancer", "genetics", "molecular", "biology/dna", "repair", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2011	Inactivation of Chk2 and Mus81 Leads to Impaired Lymphocytes Development, Reduced Genomic Instability, and Suppression of Cancer
Bacteria often face complex environments . We asked how gene expression in complex conditions relates to expression in simpler conditions . To address this , we obtained accurate promoter activity dynamical measurements on 94 genes in E . coli in environments made up of all possible combinations of four nutrients and s...	Bacteria face complex conditions in important settings such as our body and in biotechnological applications such as biofuel production . Understanding how bacteria respond to complex conditions is a hard problem: the number of conditions that need to be tested grows exponentially with the number of nutrients , stresse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "cell", "biology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "molecular", "cell", "biology", "dna", "transcription" ]	2014	Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
Hemorrhagic fever with renal syndrome ( HFRS ) is highly endemic in mainland China , and has extended from rural areas to cities recently . Beijing metropolis is a novel affected region , where the HFRS incidence seems to be diverse from place to place . The spatial scan analysis based on geographical information syste...	Hemorrhagic fever with renal syndrome ( HFRS ) is caused by Hantaviruses , the enzootic viruses with a worldwide distribution . In China , HFRS is a significant public health problem with more than 10 , 000 human cases reported annually and the endemic areas of the disease have extended from rural to urban areas and ev...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/virus", "evolution", "and", "symbiosis", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases/viral", "infections", "microbiology/medical", "microbiology", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "disea...	2011	Geo-spatial Hotspots of Hemorrhagic Fever with Renal Syndrome and Genetic Characterization of Seoul Variants in Beijing, China
In fungi , mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors . The fission yeast Schizosaccharomyces pombe ( Sp ) has two mating types , Plus ( P ) and Minus ( M ) . The mating pheromones P-factor and M-factor , secreted by P and M cells , are r...	The emergence of a new species might occur when two groups can no longer mate . Although such reproductive isolation is considered a key evolutionary process , the mechanisms by which it actually occurs have been confined to conjecture . The two sexes ( Plus [P] and Minus [M] ) of S . pombe each secrete a pheromone ( P...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plasmid", "construction", "germ", "cells", "zygotes", "fungi", "model", "organisms", "sex", "pheromones", "experimental", "organism", "systems", "dna", "construction", "molecular", "biology", "techniques", "dna", "schizosaccharomyces", "research", "and", "analysis", "m...	2019	Asymmetric diversification of mating pheromones in fission yeast
Refinement of the nervous system depends on selective removal of excessive axons/dendrites , a process known as pruning . Drosophila ddaC sensory neurons prune their larval dendrites via endo-lysosomal degradation of the L1-type cell adhesion molecule ( L1-CAM ) , Neuroglian ( Nrg ) . Here , we have identified a novel ...	During the maturation of the nervous system , some neurons can selectively eliminate their unnecessary connections , including dendrites and axons , to retain specific connections . In Drosophila , a class of sensory neurons lose all their larval dendrites during metamorphosis , when they transition from larvae to adul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna", "interference", "vesicles", "cloning", "neuroscience", "molecular", "motors", "nerve", "fibers", "epigenetics", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "neuronal", "dendrites", "motor", "proteins", "endosomes", "research...	2018	Prd1 associates with the clathrin adaptor α-Adaptin and the kinesin-3 Imac/Unc-104 to govern dendrite pruning in Drosophila
Since Kaposi's sarcoma-associated herpesvirus ( KSHV or human herpesvirus 8 ) was first identified in Kaposi's sarcoma ( KS ) lesions of HIV-infected individuals with AIDS , the basic biological understanding of KSHV has progressed remarkably . However , the absence of a proper animal model for KSHV continues to impede...	Kaposi's sarcoma-associated herpesvirus ( KSHV or human herpesvirus 8 ) , the most recently identified human tumor-inducing virus , has been linked to Kaposi's sarcoma , pleural effusion lymphomas and multicentric Castleman's disease . In fact , KSHV accounts for a large proportion of the cancer deaths in Africa . Furt...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/animal", "models", "of", "infection", "virology/host", "antiviral", "responses" ]	2009	Non-Human Primate Model of Kaposi's Sarcoma-Associated Herpesvirus Infection

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