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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
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Dengue virus ( DENV ) infection is prevalent across tropical regions and may cause severe disease . Early diagnosis may improve supportive care . We prospectively assessed the Standard Diagnostics ( Korea ) BIOLINE Dengue Duo DENV rapid diagnostic test ( RDT ) to NS1 antigen and anti-DENV IgM ( NS1 and IgM ) in childre... | DENV infection first manifests as an undifferentiated fever before either settling without complications , or progressing to severe disease requiring inpatient admission and careful supportive intravenous fluid management . The ability to differentiate DENV infection from other febrile illnesses , and to predict those ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Rapid Diagnostic Tests for Dengue Virus Infection in Febrile Cambodian Children: Diagnostic Accuracy and Incorporation into Diagnostic Algorithms |
The fate of HIV-infected cells after reversal of proviral latency is not well characterized . Simonetti , et al . recently showed that CD4+ T-cells containing intact proviruses can clonally expand in vivo and produce low-level infectious viremia . We hypothesized that reversal of HIV latency by activation of CD4+ T-cel... | Stable latent reservoirs of HIV persist despite suppressive antiretroviral therapy ( ART ) and cause rebound viremia following interruption of ART . New HIV cure strategies aim to deplete the latent reservoir by reversing HIV latency and promoting the death of cells containing inducible proviruses . Multiple latency re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"biological",
"cultures",
"microbiology",
"viral",
"structure",
"retroviruses",
"viruses",
"immunodeficiency",
"viruses",... | 2017 | Ex vivo activation of CD4+ T-cells from donors on suppressive ART can lead to sustained production of infectious HIV-1 from a subset of infected cells |
Sporotrichosis associated with zoonotic transmission remains a relevant public health problem in Rio de Janeiro , Brazil , affecting a large at-risk population , which includes HIV-infected individuals . We assessed patients co-infected by Sporothrix spp . and HIV over time in the context of an unabated sporotrichosis ... | Sporotrichosis is a subcutaneous , worldwide-distributed mycosis , endemic in some areas and is caused by dimorphic fungi from the complex Sporothrix schenckii . Its association with zoonotic transmission remains a relevant public health problem in Rio de Janeiro , Brazil , affecting a large at-risk population , which ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"medicine",
"and",
"health",
"sciences",
"infectious",
"disease",
"epidemiology",
"immunology",
"tropical",
"diseases",
"microbiology",
"health",
"care",
"immunodeficiency",
"viruses",
"plant",
"science",
"skin",
"infections",
"sporotrichosis",
"clinical",
... | 2014 | Sporotrichosis: An Emerging Neglected Opportunistic Infection in HIV-Infected Patients in Rio de Janeiro, Brazil |
The extracellular matrix ( ECM ) supports vascular integrity during embryonic development . Proteolytic degradation of ECM components is required for angiogenesis , but excessive ECM proteolysis causes blood vessel fragility and hemorrhage . Little is understood about how ECM proteolysis is transcriptionally regulated ... | Blood vessels are surrounded by an extracellular matrix ( ECM ) , which provides structural support and helps vessels withstand the biomechanical pressure of flowing blood . As blood vessels grow during embryonic development , the ECM is locally degraded to allow new vessels to sprout from existing ones . This localize... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The NuRD Chromatin-Remodeling Enzyme CHD4 Promotes Embryonic Vascular Integrity by Transcriptionally Regulating Extracellular Matrix Proteolysis |
The Prader-Willi syndrome ( PWS [MIM 17620] ) and Angelman syndrome ( AS [MIM 105830] ) locus is controlled by a bipartite imprinting center ( IC ) consisting of the PWS-IC and the AS-IC . The most widely accepted model of IC function proposes that the PWS-IC activates gene expression from the paternal allele , while t... | Prader-Willi and Angelman syndromes are neurobehavioral disorders arising from dysregulation of a cluster of imprinted genes located at chromosome 15q11–q13 . PWS results from the absence of paternally expressed genes and AS from the absence of maternally expressed genes . Two elements , termed the PWS-IC and the AS-IC... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomic",
"imprinting",
"genetics",
"epigenetics",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Transcription Is Required to Establish Maternal Imprinting at the Prader-Willi Syndrome and Angelman Syndrome Locus |
Organisms that can learn about their environment and modify their behaviour appropriately during their lifetime are more likely to survive and reproduce than organisms that do not . While associative learning – the ability to detect correlated features of the environment – has been studied extensively in nervous system... | Whilst one may have believed that associative learning requires a nervous system , this paper shows that chemical networks can be evolved in silico to undertake a range of associative learning tasks with only a small number of reactions . The mechanisms are surprisingly simple . The networks can be analysed using Bayes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Evolution of Associative Learning in Chemical Networks |
Escherichia coli chemotactic motion in spatiotemporally varying environments is studied by using a computational model based on a coarse-grained description of the intracellular signaling pathway dynamics . We find that the cell's chemotaxis drift velocity vd is a constant in an exponential attractant concentration gra... | A computational model , based on a coarse-grained description of the cell's underlying chemotaxis signaling pathway dynamics , is used to study Escherichia coli chemotactic motion in realistic environments that change in both space and time . We find that in an exponential attractant gradient , E . coli cells swim ( ra... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/systems",
"biology",
"computational",
"biology/signaling",
"networks"
] | 2010 | Quantitative Modeling of Escherichia coli Chemotactic Motion in Environments Varying in Space and Time |
Previous studies have compared the physicochemical properties of allosteric compounds to non-allosteric compounds . Those studies have found that allosteric compounds tend to be smaller , more rigid , more hydrophobic , and more drug-like than non-allosteric compounds . However , previous studies have not properly corr... | We investigated the differences between allosteric and competitive ligands . Competitive ligands bind in the active site of a protein while allosteric ligands exhibit their effect from a remote location on the protein . Traditionally , drugs take advantage of competitive binding; however when this is not possible , an ... | [
"Abstract",
"Introduction",
"Result",
"and",
"discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"physicochemical",
"properties",
"probability",
"distribution",
"mathematics",
"statistics",
"(mathematics)",
"pharmacology",
"g",
"protein",
"coupled",
"receptors",
"physical",
"chemistry",
"chemical",
"properties",
"statistical",
"... | 2017 | Are there physicochemical differences between allosteric and competitive ligands? |
While a number of studies have identified host factors that influence endosymbiont titer , little is known concerning environmental influences on titer . Here we examined nutrient impact on maternally transmitted Wolbachia endosymbionts in Drosophila . We demonstrate that Drosophila reared on sucrose- and yeast-enriche... | Many invertebrate organisms carry bacterial endosymbionts within their cells . In many cases , this ensures host access to resources provided by the endosymbionts , and reciprocally , a rich source of host-supplied nutrients supports bacterial growth and reproduction . However if bacterial reproduction is uncontrolled ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Impact of Host Diet on Wolbachia Titer in Drosophila |
Guilt-by-association codifies the empirical observation that a gene’s function is informed by its neighborhood in a biological network . This would imply that when a gene’s network context is altered , for instance in disease condition , so could be the gene’s function . Although context-specific changes in biological ... | Proteins that cooperate to perform a specific cellular function often interact with each other and are clustered together in a protein-protein interaction network ( PIN ) . Thus , a protein’s function can be inferred from the prevailing functions of its network neighbors . However , the network neighborhood is highly d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"genetic",
"networks",
"cancer",
"genetics",
"gene",
"regulation",
"protein",
"interaction",
"networks",
"cancers",
"and",
"neoplasms",
"oncogenes",
"oncology",
"mutation",
"network",
"analysis",
"nonsense",
... | 2017 | A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer |
Trypanosomatid parasites are the causative agents of many neglected tropical diseases and there is currently considerable interest in targeting endogenous sterol biosynthesis in these organisms as a route to the development of novel anti-infective drugs . Here , we report the first x-ray crystallographic structures of ... | Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and affects eight million individuals , primarily in Latin America . Currently there is no cure for chronic T . cruzi infections . Unlike humans , this parasite use a variety of sterols ( e . g . ergosterol , 24-ethyl-cholesta-5 , 7 , 22-trien-3 beta ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"clinical",
"medicine",
"drug",
"research",
"and",
"development",
"proteins",
"protein",
"structure",
"neglected",
"tropical",
"diseases",
"biology",
"and",
"life",
"sciences",
"pharmacol... | 2014 | Squalene Synthase As a Target for Chagas Disease Therapeutics |
Molecular chaperones participate in the maintenance of cellular protein homeostasis , cell growth and differentiation , signal transduction , and development . Although a vast body of information is available regarding individual chaperones , few studies have attempted a systems level analysis of chaperone function . I... | Among the infectious diseases affecting humans , the malarial parasite is responsible for a very high number of deaths . About 2 million people die of malaria every year , of which more than a million are children in sub-Saharan Africa . Malaria is caused by a protozoan parasite belonging to the genus Plasmodium , and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"homo",
"(human)",
"plasmodium",
"microbiology",
"computational",
"biology"
] | 2007 | Systems Analysis of Chaperone Networks in the Malarial Parasite Plasmodium falciparum |
Leishmania parasites are transmitted to vertebrate hosts by phlebotomine sandflies and , in humans , may cause tegumentary or visceral leishmaniasis . The role of PKR ( dsRNA activated kinase ) and Toll-like receptor 3 ( TLR3 ) activation in the control of Leishmania infection highlights the importance of the engagemen... | Cutaneous Leishmaniasis is highly prevalent worldwide , affecting millions of people in undeveloped countries . Leishmania parasites are transmitted to humans by phlebotomine flies . The transmission occurs mainly in rural areas , although the urbanization of the disease is in process . Phlebotomine vectors may also tr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"tropical",
"diseases",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"developmental",
"biology",
"protozoans",
"leishmania",
... | 2019 | Amazonian Phlebovirus (Bunyaviridae) potentiates the infection of Leishmania (Leishmania) amazonensis: Role of the PKR/IFN1/IL-10 axis |
Development of an effective vaccine against human cytomegalovirus ( HCMV ) is a need of utmost medical importance . Generally , it is believed that a live attenuated vaccine would best provide protective immunity against this tenacious pathogen . Here , we propose a strategy for an HCMV vaccine that aims at the simulta... | Human cytomegalovirus ( CMV ) is a major cause of morbidity and mortality in congenitally infected newborns and immunocompromised individuals , indicating an utmost need for a vaccine to protect these vulnerable groups . Recent experimental studies in animal models , including non-human primates , have shown that atten... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"animal",
"models",
"viruses",
"vaccines",
"preventive",
"medicine",
"model",
... | 2016 | Activation of Innate and Adaptive Immunity by a Recombinant Human Cytomegalovirus Strain Expressing an NKG2D Ligand |
Transforming growth factor β ( TGF-β ) signaling acts through Smad proteins to play fundamental roles in cell proliferation , differentiation , apoptosis , and metabolism . The Receptor associated Smads ( R-Smads ) interact with DNA and other nuclear proteins to regulate target gene transcription . Here , we demonstrat... | All animals must ensure metabolic homeostasis; if they fail to do so , diseases such as obesity and diabetes can develop . To maintain glucose balance , insulin is secreted upon glucose intake in a highly regulated and coordinated process . Previous studies suggested that the transforming growth factor beta ( TGF-β ) s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"medicine",
"developmental",
"biology",
"model",
"organisms",
"organism",
"development",
"diabetic",
"endocrinology",
"molecular",
"development",
"genetics",
"gene",
"expression",
"molecular",
"genetics",
"biology",
"endocrinology",
"diabetes",
"and",
... | 2012 | Repression of a Potassium Channel by Nuclear Hormone Receptor and TGF-β Signaling Modulates Insulin Signaling in Caenorhabditis elegans |
The Binary State Speciation and Extinction ( BiSSE ) model is a branching process based model that allows the diversification rates to be controlled by a binary trait . We develop a general approach , based on the BiSSE model , for predicting pathogenicity in bacterial populations from microsatellites profiling data . ... | An important challenge in Computational Biology is the analysis of genetic molecular data through sophisticated computer science and mathematical methods that are implemented by interdisciplinary research groups . The resulting comprehensive approach , based on the BiSSE model and microsatellites profiling ( TRS-PCR ) ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"population",
"genetics",
"microbiology",
"urine",
"speciation",
"population",
"biology",
"bacterial",
"p... | 2018 | Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling |
We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus ( VEEV ) genome . We initially used a capi... | Venezuelan equine encephalitis virus ( VEEV ) is a New World Alphavirus that was first identified in Venezuela in 1938 . VEEV normally circulates in rodent populations , but during outbreaks it can jump to horses and humans where it can cause debilitating and potentially fatal disease . There are currently no vaccines ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"virology/vaccines",
"immunology/immunity",
"to",
"infections",
"infectious",
"diseases/viral",
"infections",
"genetics",
"and",
"genomics"
] | 2010 | High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing |
The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts . The RNA world hypothesis , however , posits that , at the earlier stages of evolution , RNA acted as both template and catalyst . Why would such di... | At the core of all biological systems lies the division of labor between the storage of genetic information and its phenotypic implementation , in other words , the functional differentiation between templates ( DNA ) and catalysts ( proteins ) . This fundamental property of life is believed to have been absent at the ... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"emergence",
"theoretical",
"biology",
"evolutionary",
"biology",
"population",
"modeling",
"evolutionary",
"modeling",
"population",
"dynamics",
"origin",
"of",
"life",
"biology",
"computational",
"biology",
"population",
"biology",
"evolutionary",
"processes",
"evolutiona... | 2011 | On the Origin of DNA Genomes: Evolution of the Division of Labor
between Template and Catalyst in Model Replicator Systems |
Arthropod-borne viruses are a major cause of emerging disease with significant public health and economic impacts . However , the factors that determine their activity and seasonality are not well understood . In Australia , a network of sentinel cattle herds is used to monitor the distribution of several such viruses ... | Arthropod-borne viruses ( arboviruses ) are a group of viruses that can have major impacts on public health , animal health and agricultural trade , and appear to be increasing in both number and prevalence worldwide . Despite their importance as emerging pathogens , the spatial patterns , long-term seasonal characteri... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"infectious",
"diseases",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"environmental",
"geography",
"epidemiology",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"tropical",
"diseases",
"computat... | 2014 | Seasonal Drivers of the Epidemiology of Arthropod-Borne Viruses in Australia |
Histone deacetylases ( HDACs ) execute biological regulation through post-translational modification of chromatin and other cellular substrates . In humans , there are eleven HDACs , organized into three distinct subfamilies . This large number of HDACs raises questions about functional overlap and division of labor am... | Histone deacetylases ( HDACs ) are enzymes that reverse acetylation of protein substrates inside the cell . Like phosphorylation , acetylation/deacetylation can alter the biochemical properties of a protein target and thereby regulate its functions . Histones are a major target of certain HDACs . When histones become d... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/histone",
"modification",
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/epigenetics",
"developmental",
"biology/developmental",
"molecular",
"mechanisms"
] | 2008 | Drosophila Histone Deacetylase-3 Controls Imaginal Disc Size through Suppression of Apoptosis |
Tandem repeats are common in eukaryotic genomes , but due to difficulties in assaying them remain poorly studied . Here , we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number , and apply this technology to genotyp... | Here we utilize Nanostring digital assays and show their utility for estimating copy number of 186 multicopy genes and tandem repeats . By analyzing patterns of single nucleotide variation around these variants , we show that copy number variation at the vast majority of tandem repeat variations is not effectively tagg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"genomics",
"cell",
"biology",
"chromosome",
"biology",
"chromosome",
"structure",
"and",
"function",
"genome",
"analysis",
"transcriptome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"st... | 2014 | Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats |
Coupling immunity and development is essential to ensure survival despite changing internal conditions in the organism . Drosophila metamorphosis represents a striking example of drastic and systemic physiological changes that need to be integrated with the innate immune system . However , nothing is known about the me... | Hormones orchestrate physiological processes such as metabolism , immunity and development , and allow the body to respond systemically to external stresses and resources . Steroid hormones , such as sex hormones and corticosteroids , affect the function of the immune system , but how they do so is not well understood ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Steroid Hormone Signaling Is Essential to Regulate Innate Immune Cells and Fight Bacterial Infection in Drosophila |
Scrub typhus is a rickettsiosis which is caused by Orientia tsutsugamushi and occurs throughout the Asia-Pacific region . Molecular diagnosis of rickettsioses using eschar swabs has recently emerged , and may be very useful for the diagnosis of these diseases in tropical settings . Quantitative polymerase chain reactio... | Orientia tsutsugamushi is the causative agent of scrub typhus , one of the most common of the rickettsioses in Pacific Asia . Although the disease is an important public health issue in Vietnam , there is a lack of diagnostic tools in almost all health facilities and very little clinical research has been done . In par... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"dermatology",
"typhus",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"geographical",
"locations",
"microbiology",
"rickettsia",
"bacterial",
"diseases",
"molecular",
"biology",
"techniques",
"bacter... | 2017 | Use of eschar swabbing for the molecular diagnosis and genotyping of Orientia tsutsugamushi causing scrub typhus in Quang Nam province, Vietnam |
Small drug molecules usually bind to multiple protein targets or even unintended off-targets . Such drug promiscuity has often led to unwanted or unexplained drug reactions , resulting in side effects or drug repositioning opportunities . So it is always an important issue in pharmacology to identify potential drug-tar... | Small drug molecules usually bind to unintended off-targets , leading to unexpected drug responses such as side effects or drug repositioning opportunities . Thus , identifying unintended drug-target interactions ( DTI ) is particularly required for understanding complicated drug actions . It remains expensive nowadays... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [] | 2013 | Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity |
It is believed that energy efficiency is an important constraint in brain evolution . As synaptic transmission dominates energy consumption , energy can be saved by ensuring that only a few synapses are active . It is therefore likely that the formation of sparse codes and sparse connectivity are fundamental objectives... | Recent estimates point out that a large part of the energetic budget of the mammalian cortex is spent in transmitting signals between neurons across synapses . Despite this , studies of learning and memory do not usually take energy efficiency into account . In this work we address the canonical computational problem o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules |
The presence in Morocco of Argasid ticks of the Ornithodoros erraticus complex , the vector of tick-borne relapsing fever ( TBRF ) in North Africa , has been known since 1919 , but the disease is rarely diagnosed and few epidemiological data are available . Between 2006 and 2011 , we investigated the presence of Ornith... | In North Africa , Argasid ticks of the Ornithodoros erraticus complex are the only known vector of Borrelia infections causing tick-borne relapsing fever ( TBRF ) in humans . There is limited data on vector distribution , the animal reservoir of the disease has never been investigated , and there is no published data o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"biology"
] | 2012 | Epidemiology of Tick-Borne Borreliosis in Morocco |
The increasing abundance of large-scale , high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species . These analyses require a reformulation of how to organize multi-species datasets and visualize compa... | Advancing high-throughput experimental technologies are providing access to genome-wide measurements for multiple related species on multiple information levels ( e . g . mRNA , protein , interactions , functional assays , etc . ) . We present a biclustering algorithm and an associated visualization system for generati... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results/Discussion"
] | [
"computer",
"applications",
"systems",
"biology",
"genome",
"analysis",
"tools",
"computer",
"science",
"genomics",
"genetic",
"networks",
"web-based",
"applications",
"microbial",
"evolution",
"biology",
"computational",
"biology",
"comparative",
"genomics",
"microbiology"... | 2011 | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
Typhoid fever , caused by the bacterium Salmonella Typhi , is an endemic cause of febrile disease in Cambodia . The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia . We accessed routine blood culture data from Angkor Hospital for Children ( AHC ) in Siem Reap province ... | Typhoid fever is an infectious disease caused by the bacterium Salmonella Typhi . The disease is generally restricted to those living in low-income settings with poor sanitation . Typhoid fever is a common cause of fever requiring hospital treatment in Cambodia , but limited data is available on the epidemiology of the... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"surface",
"water",
"body",
"fluids",
"water",
"resources",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"geographical",
"locations",
"microbiology",
"salmonella",
"typ... | 2016 | The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia |
Neuroimaging research has largely focused on the identification of associations between brain activation and specific mental functions . Here we show that data mining techniques applied to a large database of neuroimaging results can be used to identify the conceptual structure of mental functions and their mapping to ... | One of the major challenges of neuroscience research is to integrate the results of the large number of published research studies in order to better understand how psychological functions are mapped onto brain systems . In this research , we take advantage of a large database of neuroimaging studies , along with text ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computer",
"science",
"cognitive",
"neuroscience",
"natural",
"language",
"processing",
"biology",
"neuroscience",
"neuroimaging"
] | 2012 | Discovering Relations Between Mind, Brain, and Mental Disorders Using Topic Mapping |
Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation ( ChIP ) . ChIP-reported regions are typically investigated for enriched sequence-motifs , which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins .... | A high-throughput chromatin immunoprecipitation ( ChIP ) experiment identifies genomic regions bound by a protein in vivo . Current motif-discovery approaches seek an enriched motif signature in the reported regions , which they can attribute to the protein’s binding preferences . However , Diversity models the fact th... | [
"Abstract",
"Introduction",
"Design",
"and",
"implementation",
"Results",
"Discussion"
] | [
"gene",
"regulation",
"neuronal",
"differentiation",
"dna-binding",
"proteins",
"neuroscience",
"cell",
"differentiation",
"dna",
"transcription",
"developmental",
"biology",
"sequence",
"motif",
"analysis",
"epigenetics",
"chromatin",
"research",
"and",
"analysis",
"method... | 2018 | DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP |
Borrelia burgdorferi is remarkable for its ability to thrive in widely different environments due to its ability to infect various organisms . In comparison to enteric Gram-negative bacteria , these spirochetes have only a few transmembrane proteins some of which are thought to play a role in solute and nutrient uptake... | Lyme disease is caused by infection with the spirochete Borrelia burgdorferi . These spirochetes cycle between Ixodes ticks and vertebrate reservoirs , mainly rodents , but also birds . Previous studies have revealed major differences in the B . burgdorferi cell envelope structure and membrane composition compared to t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry/experimental",
"biophysical",
"methods",
"genetics",
"and",
"genomics/gene",
"function",
"biophysics/membrane",
"proteins",
"and",
"energy",
"transduction",
"infectious",
"diseases/bacterial",
"infections",
"molecular",
"biology",
"microbiology/cellular",
"microbiol... | 2008 | An RND-Type Efflux System in Borrelia burgdorferi Is Involved in Virulence and Resistance to Antimicrobial Compounds |
During tissue development , patterns of gene expression determine the spatial arrangement of cell types . In many cases , gradients of secreted signalling molecules—morphogens—guide this process by controlling downstream transcriptional networks . A mechanism commonly used in these networks to convert the continuous in... | The bistable switch , a common regulatory sub-network , is found in many biological processes . It consists of cross-repressing components that generate a switch-like transition between two possible states . In developing tissues , bistable switches , created by cross-repressing transcriptional determinants , are often... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"engineering",
"and",
"technology",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"dna",
"transcription",
"developmental",
"biology",
"systems",
"science",
"mathematics",
"molecular",
"development",
"transcription",
"factors",
"molecular",
"biol... | 2016 | Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches |
Prions are infectious proteins that possess multiple self-propagating structures . The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform , PrPSc . Many recent studies determined that de novo prion strains could be generated in vitro f... | Prions are infectious proteins capable of acquiring multiple self-propagating structures . The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform , designated as PrPSc . During propagation , disease-associated conformer PrPSc coerces t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Synthetic prions with novel strain-specified properties |
Introns are a prevalent feature of eukaryotic genomes , yet their origins and contributions to genome function and evolution remain mysterious . In budding yeast , repression of the highly transcribed intron-containing ribosomal protein genes ( RPGs ) globally increases splicing of non-RPG transcripts through reduced c... | The protein coding information in eukaryotic genes is broken by intervening sequences called introns that are removed from RNA during transcription by a large protein-RNA complex called the spliceosome . Where introns come from and how the spliceosome contributes to genome evolution are open questions . In this study ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"evolutionary",
"biology",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"genome",
"analysis",
"saccharomyces",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"genome",
"complexity",
"sequence",
"alignment",
"animal",
"studies",
... | 2019 | Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome |
Epigenetic regulation of the replication program during mammalian cell differentiation remains poorly understood . We performed an integrative analysis of eleven genome-wide epigenetic profiles at 100 kb resolution of Mean Replication Timing ( MRT ) data in six human cell lines . Compared to the organization in four ch... | During development , embryonic stem cell ( ESC ) enter a program of cell differentiation eventually leading to all the necessary differentiated cell types . Understanding the mechanisms responsible for the underlying modifications of the gene expression program is of fundamental importance , as it will likely have stro... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency |
The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations . Here , we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles ( Cuba , P... | Latinos are often regarded as a single heterogeneous group , whose complex variation is not fully appreciated in several social , demographic , and biomedical contexts . By making use of genomic data , we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale pattern... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Reconstructing the Population Genetic History of the Caribbean |
Selective attention is an important filter for complex environments where distractions compete with signals . Attention increases both the gamma-band power of cortical local field potentials and the spike-field coherence within the receptive field of an attended object . However , the mechanisms by which gamma-band act... | Rhythmic brain activity is observed in many neural structures and is an inferred critical component of neural processing . In particular , stimulus induced oscillations in the gamma-frequency band ( 30–80 Hz ) are common in several cortical networks . Many experimental and theoretical studies have established the neura... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"signal",
"discrimination",
"gamma",
"oscillation",
"neural",
"population",
"neuroscience",
"attention"
] | 2007 | Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination |
The brain tumour glioblastoma is characterised by diffuse and infiltrative growth into surrounding brain tissue . At the macroscopic level , the progression speed of a glioblastoma tumour is determined by two key factors: the cell proliferation rate and the cell migration speed . At the microscopic level , however , pr... | In this work , we develop a spatial mathematical model in order to analyse the growth behavior of the brain tumour glioblastoma . Tumours of this type have a diffuse boundary , with considerable local invasion of surrounding brain tissue , making surgery difficult . At the cellular level , the progression of a glioblas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"oncology",
"medicine",
"mathematics",
"applied",
"mathematics",
"biology",
"computational",
"biology"
] | 2012 | The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion |
Aedes aegypti ( Linnaeus ) and Aedes albopictus Skuse mosquitoes transmit serious human arboviral diseases including yellow fever , dengue and chikungunya in many tropical and sub-tropical countries . Females of the two species have adapted to undergo preimaginal development in natural or artificial collections of fres... | Aedes aegypti and Aedes albopictus mosquitoes transmit arboviral disease like dengue and chikungunya that are of international concern . Control of dengue and chikungunya presently focuses on eliminating freshwater larval development habitats of the two mosquitoes in urban surroundings . We investigated the ability of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"physiological",
"ecology",
"infectious",
"disease",
"epidemiology",
"neuroscience",
"animal",
"behavior",
"aquatic",
"environments",
"infectious",
"disease",
"control",
"marine",
"environments",
"zoology",
"infectious"... | 2011 | Larval Development of Aedes aegypti and Aedes albopictus in Peri-Urban Brackish Water and Its Implications for Transmission of Arboviral Diseases |
CD4 positive T helper cells control many aspects of specific immunity . These cells are specific for peptides derived from protein antigens and presented by molecules of the extremely polymorphic major histocompatibility complex ( MHC ) class II system . The identification of peptides that bind to MHC class II molecule... | CD4 positive T helper cells provide essential help for stimulation of both cellular and humoral immune reactions . T helper cells recognize peptides presented by molecules of the major histocompatibility complex ( MHC ) class II system . HLA-DR is a prominent example of a human MHC class II locus . The HLA molecules ar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/antigen",
"processing",
"and",
"recognition",
"immunology/immune",
"response",
"computational",
"biology/sequence",
"motif",
"analysis",
"virology/host",
"antiviral",
"responses"
] | 2008 | Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan |
Temperature is an important factor that influences the biology and ecology of intermediate host ( IH ) snails and the schistosome parasites they transmit . Although temperature shifts due to climate change has been predicted to affect the life history traits of IH snails and parasite production , the mechanisms of how ... | The implementation of schistosomiasis control/elimination strategies depend on accurate estimations and predictions of the changes in the snail and parasite population . This is essential especially in the allocation of limited resources . The simulation model and the results presented here provide useful information o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"helminths",
"atmospheric",
"science",
"population",
"dynamics",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"parasitology",
"simulation",
"and",
"modeling",
"developmental",
"biology",... | 2018 | Simulation of population dynamics of Bulinus globosus: Effects of environmental temperature on production of Schistosoma haematobium cercariae |
Hantavirus , the hemorrhagic causative agent of two clinical diseases , is found worldwide with variation in severity , incidence and mortality . The most lethal hantaviruses are found on the American continent where the most prevalent viruses like Andes virus and Sin Nombre virus are known to cause hantavirus pulmonar... | Hemorrhagic fever viruses have become of much greater importance in recent years . The more prominent presence of these viruses in a day-to-day setting and their impact on global health has had a positive impact on studying these viruses . Resolving their disease mechanisms and ways to intervene in their replication an... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"hantavirus",
"pulmonary",
"syndrome",
"pathogens",
"drugs",
"puumala",
"virus",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"viruse... | 2017 | A lethal disease model for New World hantaviruses using immunosuppressed Syrian hamsters |
Human influenza infections exhibit a strong seasonal cycle in temperate regions . Recent laboratory and epidemiological evidence suggests that low specific humidity conditions facilitate the airborne survival and transmission of the influenza virus in temperate regions , resulting in annual winter epidemics . However ,... | Human influenza infections have a pronounced seasonal cycle in temperate regions . Recent laboratory and epidemiological evidence suggests that low humidity conditions in the winter may increase virus survival and enable the virus to transmit efficiently between hosts . However , seasonal influenza activity in some tro... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"biogeography",
"medicine",
"public",
"health",
"and",
"epidemiology",
"environmental",
"sciences",
"infectious",
"disease",
"epidemiology",
"influenza",
"spatial",
"epidemiology",
"infectious",
"diseases",
"geography",
"environmental",
"epidemiology",
"environmental",
"geogr... | 2013 | Environmental Predictors of Seasonal Influenza Epidemics across Temperate and Tropical Climates |
Leishmania ( Leishmania ) mexicana causes cutaneous leishmaniasis , an endemic zoonosis affecting a growing number of patients in the southeastern states of Mexico . Some foci are found in shade-grown cocoa and coffee plantations , or near perennial forests that provide rich breeding grounds for the sand fly vectors , ... | Leishmaniasis is endemic in southeastern Mexico , where Leishmania ( L . ) mexicana is the principle parasite species causing disease in humans . Previous studies using methodology for inferring potential biotic interactions between species had shown a high prevalence of bat species as potential hosts for Leishmania , ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Leishmania (L.) mexicana Infected Bats in Mexico: Novel Potential Reservoirs |
Cell competition is a phenomenon originally described as the competition between cell populations with different genetic backgrounds; losing cells with lower fitness are eliminated . With the progress in identification of related molecules , some reports described the relevance of cell mechanics during elimination . Fu... | When genetically different cell populations are mixed , there is competition between cells such that losing cells are eliminated from a tissue . Such cell elimination is also observed during normal development in genetically-homogeneous tissues . In addition to the identification of key genes and molecular mechanisms r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"mechanisms",
"of",
"signal",
"transduction",
"demography",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"condensed",
"matter",
"physics",
"population",
"genetics"... | 2017 | Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis |
Fundamental response properties of neurons centrally underly the computational capabilities of both individual nerve cells and neural networks . Most studies on neuronal input-output relations have focused on continuous-time inputs such as constant or noisy sinusoidal currents . Yet , most neurons communicate via excha... | Brain function relies on robust communication between a huge number of nerve cells ( neurons ) that exchange short-lasting electrical pulses ( called action potentials or spikes ) at certain times . How nerve cells process their spiking inputs to generate spiking outputs thus is key not only to individual neurons’ comp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | When Less Is More: Non-monotonic Spike Sequence Processing in Neurons |
Trichinellosis is a serious food-borne parasitic zoonosis worldwide . In the effort to develop vaccine against Trichinella infection , we have identified Trichinella spiralis Heat shock protein 70 ( Ts-Hsp70 ) elicits partial protective immunity against T . spiralis infection via activating dendritic cells ( DCs ) in o... | Trichinellosis is a serious food-borne parasitic zoonosis caused by tissue-dwelling nematode Trichinella spiralis . Vaccine development is needed as an alternative approach to control the infection in domestic livestock or in humans . Ts-Hsp70 has been identified to elicit partial protective immunity against Trichinell... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"enzyme-linked",
"immunoassays",
"immunology",
"cell-mediated",
"immunity",
"developmental",
"biology",
"molecular",
"developme... | 2018 | Ts-Hsp70 induces protective immunity against Trichinella spiralis infection in mouse by activating dendritic cells through TLR2 and TLR4 |
Identifying the molecular genetic basis of traits contributing to speciation is of crucial importance for understanding the ecological and evolutionary mechanisms that generate biodiversity . Despite several examples describing putative “speciation genes , ” it is often uncertain to what extent these genetic changes ha... | A fundamental goal of evolutionary biology is to identify the genetic changes and evolutionary mechanisms involved in speciation . Knowledge of the genes allows us to address important unresolved questions about the genetics of speciation , such as what role does ecologically based natural selection play during the pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"organismal",
"evolution",
"adaptation",
"plant",
"evolution",
"natural",
"selection",
"speciation",
"population",
"genetics",
"biology",
"evolutionary",
"biology",
"hybridization",
"evolutionary",
"processes",
"evolutionary",
"genetics"
] | 2013 | Divergent Selection Drives Genetic Differentiation in an R2R3-MYB Transcription Factor That Contributes to Incipient Speciation in Mimulus aurantiacus |
The OAS/RNase L pathway is one of the best-characterized effector pathways of the IFN antiviral response . It inhibits the replication of many viruses and ultimately promotes apoptosis of infected cells , contributing to the control of virus spread . However , viruses have evolved a range of escape strategies that act ... | Oligoadenylate synthetases ( OAS ) are a family of enzymes that produce 2’-5’ oligoadenylates ( 2-5A ) from ATP . OAS accumulate as inactive enzymes in cells that have been exposed to interferon . When infection of these cells occurs , double-stranded RNA produced during virus replication activates OAS , which produce ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"rnase",
"inhibitors",
"rna-binding",
"proteins",
"rna",
"interference",
"nucleases",
"enzymes",
"rna",
"extraction",
"dna-binding",
"proteins",
"enzymology",
"plasmid",
"construction",
"viruses",
"rna",
"viruses",
"dna",
"construction",
"molecular",
"biology",
"technique... | 2018 | A novel mechanism of RNase L inhibition: Theiler's virus L* protein prevents 2-5A from binding to RNase L |
Recent clusters of outbreaks of mosquito-borne diseases ( Rift Valley fever and chikungunya ) in Africa and parts of the Indian Ocean islands illustrate how interannual climate variability influences the changing risk patterns of disease outbreaks . Although Rift Valley fever outbreaks have been known to follow periods... | Interannual climate variability associated with the El Niño/Southern Oscillation ( ENSO ) phenomenon and regional climatic circulation mechanisms in the equatorial Indian Ocean result in significant rainfall and ecological anomaly patterns that are major drivers of spatial and temporal patterns of mosquito-borne diseas... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"environmental",
"sciences",
"plant",
"biology",
"atmospheric",
"science",
"physical",
"geography",
"geoinformatics",
"plant",
"science",
"population",
"biology",
"atmospheric",
"dynamics",
"zoology",
"veterinary",
"science",
"geography",
"veterinary",
"epidemiology",
"biol... | 2012 | Climate Teleconnections and Recent Patterns of Human and Animal Disease Outbreaks |
The studies reported herein are the first to document the effect of the in vivo administration of a JAK3 inhibitor for defining the potential role of NK cells during acute SIV infection of a group of 15 rhesus macaques ( RM ) . An additional group of 16 MHC/KIR typed RM was included as controls . The previously optimiz... | In efforts to define the potential role of innate immune effector mechanisms in influencing the course of SIV infection during the acute infection period , our lab utilized the in vivo daily administration of 20 mg/kg orally of a compound called Tofacitinib ( a Janus kinase 3 inhibitor ) to a group of 15 rhesus macaque... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"hiv",
"medicine",
"infectious",
"diseases",
"viral",
"diseases"
] | 2014 | In Vivo Administration of a JAK3 Inhibitor during Acute SIV Infection Leads to Significant Increases in Viral Load during Chronic Infection |
Chikungunya virus ( CHIKV ) is an emerging mosquito-borne alphavirus indigenous to tropical Africa and Asia . Acute illness is characterized by fever , arthralgias , conjunctivitis , rash , and sometimes arthritis . Relatively little is known about the antigenic targets for immunity , and no licensed vaccines or therap... | Chikungunya fever epidemics are sustained by a cycle of human-mosquito-human transmission , with the epidemic cycle being similar to those of dengue and urban yellow fever . While the threat of a pandemic continues to engage the public's attention , the peculiar problems associated with the more immediate and very real... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"immunology/immune",
"response",
"virology/vaccines"
] | 2011 | A DNA Vaccine against Chikungunya Virus Is Protective in Mice and Induces Neutralizing Antibodies in Mice and Nonhuman Primates |
A fundamental issue in molecular evolution is how to identify the evolutionary forces that determine the fate of duplicated genes . The dosage balance hypothesis has been invoked to explain gene duplication patterns at the genomic level under the premise that a dosage imbalance among protein-complex subunits or interac... | A gene duplication provides an extra gene copy that can be free to accumulate mutations and gain a new function . Therefore , gene duplication plays a very important role in evolution . However , the presence of an additional gene copy can sometimes be deleterious because it can lead to an excessive dosage relative to ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"e.",
"coi",
"fly",
"worm",
"human",
"evolutionary",
"biology",
"biophysics",
"yeast"
] | 2008 | Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability |
While Escherichia coli has one of the most comprehensive datasets of experimentally verified transcriptional regulatory interactions of any organism , it is still far from complete . This presents a problem when trying to combine gene expression and regulatory interactions to model transcriptional regulatory networks .... | The proper functioning of transcriptional gene regulation is essential for all living organisms . Several diseases are associated with loss of appropriate transcriptional regulation . Even in relatively simple organisms , such as the bacterium E . coli , response to environmental stress is a complex and highly regulate... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology",
"computational",
"biology/systems",
"biology",
"computational",
"biology/sequence",
"motif",
"analysis",
"computational",
"biology/transcriptional",
"regulation"
] | 2008 | A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli |
Although host–parasitoid interactions are becoming well characterized at the organismal and cellular levels , much remains to be understood of the molecular bases for the host immune response and the parasitoids' ability to defeat this immune response . Leptopilina boulardi and L . heterotoma , two closely related , hi... | The fruitfly Drosophila melanogaster has become a model system for the study of innate immunity , and parasitic wasps are one of the most obvious natural pathogens of Drosophila , making this a great system for studying interactions between the host immune system and pathogen virulence proteins . We have focused on two... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"ecology",
"immunology",
"microbiology",
"evolutionary",
"biology",
"drosophila",
"genetics",
"and",
"genomics",
"insects"
] | 2007 | Contrasting Infection Strategies in Generalist and Specialist Wasp Parasitoids of Drosophila melanogaster |
We have recently observed that a fatty acid auxotrophic mutant ( fatty acid synthase , Fas2Δ/Δ ) of the emerging human pathogenic yeast Candida parapsilosis dies after incubation in various media including serum . In the present study we describe the mechanism for cell death induced by serum and glucose containing medi... | Candida parapsilosis is a human opportunistic pathogen associated with significant morbidity and mortality , especially in immunocompromised individuals such as premature , low-birthweight neonates . Our prior studies have indicated that C . parapsilosis effectively utilizes fatty acids/lipids for growth and virulence ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"fungal",
"biochemistry",
"biochemistry",
"cell",
"death",
"lipids",
"mycology",
"cellular",
"stress",
"responses",
"molecular",
"cell",
"biology",
"cell",
"biology",
"biology",
"fatty",
"acids",
"microbiology",
"lipid",
"metabolism"
] | 2012 | Inhibition of Candida parapsilosis Fatty Acid Synthase (Fas2) Induces Mitochondrial Cell Death in Serum |
Competing endogenous RNA ( ceRNA ) has emerged as an important post-transcriptional mechanism that simultaneously alters expressions of thousands genes in cancers . However , only a few ceRNA genes have been studied for their functions to date . To understand the major biological functions of thousands ceRNA genes as a... | Competing endogenous RNAs ( ceRNA ) are RNAs known to co-regulate each other’s expression levels by competing for the binding of shared microRNAs . In human cancer , thousands genes are known to be in the ceRNA relationship . To understand the major biological functions of the ceRNA genes as a whole , we offer Model-ba... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"cancer",
"genetics",
"gene",
"regulation",
"cancers",
"and",
"neoplasms",
"oncogenes",
"oncology",
"micrornas",
"dna",
"replication",
"gene",
"types",
"dna",
"tumor",
"suppressor",
"genes",
"gene",
"expre... | 2018 | Model-based analysis of competing-endogenous pathways (MACPath) in human cancers |
Acetylation of lysine residues in histone tails is associated with gene transcription . Because histone tails are structurally flexible and intrinsically disordered , it is difficult to experimentally determine the tail conformations and the impact of acetylation . In this work , we performed simulations to sample H3 t... | Post-translational modification ( PTM ) of histone tails is an important component of epigenetics . Acetylation of histone tails generally functions to activate gene expression , though the molecular mechanism is not well understood . We used enhanced sampling simulation to examine the impact of acetylation on the stru... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"chemical",
"compounds",
"dna-binding",
"proteins",
"organic",
"compounds",
"simulation",
"and",
"modeling",
"basic",
"amino",
"acids",
"amino",
"acids",
"epigenetics",
"chromatin",
"research",
"and",
"analysis",
"methods",
"chromosome",
"biology",
"proteins",
"gene",
... | 2016 | H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation |
Leishmania species are parasitic protozoa that have a tightly controlled cell cycle , regulated by cyclin-dependent kinases ( CDKs ) . Cdc2-related kinase 3 ( CRK3 ) , an essential CDK in Leishmania and functional orthologue of human CDK1 , can form an active protein kinase complex with Leishmania cyclins CYCA and CYC6... | CRK3 , a cdc2-related serine/threonine protein kinase of the CDK family , is essential for transition through the G2-M phase checkpoint of the Leishmania cell cycle . An expression and purification system has been developed to produce active L . major CRK3 in complex with a cyclin partner , CYC6 . CRK3:CYC6 was used to... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"pharmacology/drug",
"development",
"infectious",
"diseases/protozoal",
"infections",
"biochemistry/small",
"molecule",
"chemistry",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2011 | High Throughput Screens Yield Small Molecule Inhibitors of Leishmania CRK3:CYC6 Cyclin-Dependent Kinase |
Rare variants of major effect play an important role in human complex diseases and can be discovered by sequencing-based genome-wide association studies . Here , we introduce an integrated approach that combines the rare variant association test with gene network and phenotype information to identify risk genes implica... | Case-control sequencing studies are a promising design to uncover risk genes of human complex diseases implicated by rare variants . The recent development of different types of rare variant association tests has improved the statistical power to identify disease genes that harbor risk rare variants . However , none of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"signaling",
"networks",
"gene",
"sequencing",
"developmental",
"biology",
"organism",
"development",
"network",
"analysis",
"genome",
"ana... | 2017 | Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies |
The increase in the global land temperature , expected under predictions of climate change , can directly affect the transmission of some infectious diseases , including Chagas disease , an anthropozoonosis caused by Trypanosoma cruzi and transmitted by arthropod vectors of the subfamily Triatominae . This work seeks t... | Chagas disease is an anthropozoonosis caused by the flagellated protozoan Trypanosoma cruzi and mainly transmitted through the infected faeces of insects of the subfamily Triatominae . Because these insects are sensitive to climatic conditions , it is expected that disease transmission may be affected by the increase i... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"atmospheric",
"science",
"microbiology",
"parasitic",
"diseases",
"animals",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"parasitology",
"developmental",
"biology",
"trypomastigotes",
"protozoans",
"in... | 2018 | The effect of temperature increase on the development of Rhodnius prolixus and the course of Trypanosoma cruzi metacyclogenesis |
Respiratory syncytial virus ( RSV ) is a major human pathogen that infects the majority of children by two years of age . The RSV fusion ( F ) protein is a primary target of human antibodies , and it has several antigenic regions capable of inducing neutralizing antibodies . Antigenic site IV is preserved in both the p... | Respiratory syncytial virus ( RSV ) and human metapneumovirus ( hMPV ) are major causes of viral bronchiolitis and pneumonia in infants and children . A licensed vaccine is not currently available for either virus , therefore , the characterization of the human antibody response to these viruses is of the utmost import... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"binding",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"immunology",
"antibodies",
"immunologic",
"techniques",
"cross",
"reactivity",
"research",
"and",
"analysis",
"methods",
"immune",
... | 2018 | Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins |
ANTAR proteins are widespread bacterial regulatory proteins that have RNA–binding output domains and utilize antitermination to control gene expression at the post-initiation level . An ANTAR protein , EutV , regulates the ethanolamine-utilization genes ( eut ) in Enterococcus faecalis . Using this system , we present ... | In bacteria , two-component regulatory systems comprise the primary mechanisms for how microorganisms respond to changes in their environment . These signal transduction systems rely upon phosphotransfer between two conserved proteins , a histidine kinase and a response regulator , to propagate the signal and affect ce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"microbial",
"metabolism",
"gene",
"regulation",
"regulatory",
"proteins",
"microbiology",
"molecular",
"genetics",
"proteins",
"biology",
"biochemistry",
"rna",
"nitrogen",
"metabolism",
"nucleic",
"acids",
"genetics",
"metabolism",... | 2012 | The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression |
Multiple infections with diverse enterotoxigenic E . coli ( ETEC ) strains lead to broad spectrum protection against ETEC diarrhea . However , the precise mechanism of protection against ETEC infection is still unknown . Therefore , memory B cell responses and affinity maturation of antibodies to the specific ETEC anti... | Enterotoxigenic Escherichia coli ( ETEC ) is a non-invasive pathogen causing diarrhea in children as well as in adults and travelers in developing countries . After colonizing the intestine using colonization factors , the organisms secrete heat-stable ( ST ) and/or heat-labile ( LT ) enterotoxin to cause watery diarrh... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences"
] | 2014 | Antigen-Specific Memory B-cell Responses to Enterotoxigenic Escherichia coli Infection in Bangladeshi Adults |
The Hepatitis B Virus ( HBV ) double-stranded DNA genome is reverse transcribed from its RNA pregenome ( pgRNA ) within the virus core ( or capsid ) . Phosphorylation of the arginine-rich carboxy-terminal domain ( CTD ) of the HBV capsid protein ( Cp183 ) is essential for pgRNA encapsidation and reverse transcription .... | Many single stranded RNA virus encapsidate their genome through positively-charged domains of their capsid proteins . Hepatitis B virus ( HBV ) is a double stranded DNA virus which packages a single-stranded RNA pregenome ( pgRNA ) that is reverse transcribed within the capsid . RNA packaging requires a phosphorylated ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"virology",
"macromolecular",
"assemblies",
"biology",
"microbiology"
] | 2012 | Structural Organization of Pregenomic RNA and the Carboxy-Terminal Domain of the Capsid Protein of Hepatitis B Virus |
Molecular mechanisms employed by individual multipotent cells at the point of lineage commitment remain largely uncharacterized . Current paradigms span from instructive to noise-driven mechanisms . Of considerable interest is also whether commitment involves a limited set of genes or the entire transcriptional program... | Stem cells have the capacity to both self-renew and differentiate into specialized cell lineages , thus sustaining tissue formation during embryonic development and permitting tissue homeostasis throughout adult life . Previous studies have suggested that stem cell commitment to a specific lineage may constitute a disc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"developmental",
"biology",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology"
] | 2013 | Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions |
Neural oscillations occur within a wide frequency range with different brain regions exhibiting resonance-like characteristics at specific points in the spectrum . At the microscopic scale , single neurons possess intrinsic oscillatory properties , such that is not yet known whether cortical resonance is consequential ... | When entrained using repetitive stimulation , sensory cortices appear to respond maximally , or resonate , at different driving frequencies: 10Hz in visual cortex; 20Hz and 40Hz in somatosensory and auditory cortices , respectively . The resonance frequencies are inversely correlated to the cortical volume of the respe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"resonance",
"frequency",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"engineering",
"and",
"technology",
"signal",
"processing",
"brain",
"brain",
"electrophysiology",
"electrophysiology",
"neuroscience",
"analysis",
"of",
"variance",
"mathematics",
"s... | 2016 | Cortical Resonance Frequencies Emerge from Network Size and Connectivity |
Numerous Gram-negative pathogens use a Type III Secretion System ( T3SS ) to promote virulence by injecting effector proteins into targeted host cells , which subvert host cell processes . Expression of T3SS and the effectors is triggered upon host cell contact , but the underlying mechanism is poorly understood . Here... | Many bacterial pathogens sense contact to host cells and respond by inducing expression of crucial virulence factors . This includes the type III secretion systems ( T3SSs ) and their substrates , which manipulate different host cell functions to promote colonization and survival of the pathogen within its host . In th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"nucleic",
"acid",
"synthesis",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"nucleases",
"enzymes",
"pathogens",
"messenger",
"rna",
"microbiology",
"dna-binding",
"proteins",
"enzym... | 2019 | A bacterial secreted translocator hijacks riboregulators to control type III secretion in response to host cell contact |
Pseudorabies virus ( PRV ) belongs to the Herpesviridae family , and is an important veterinary pathogen . Highly pathogenic PRV variants have caused severe epidemics in China since 2011 , causing huge economic losses . To tackle the epidemics , we identified a panel of mouse monoclonal antibodies ( mAbs ) against PRV ... | Pseudorabies virus ( PRV ) is an emerging veterinary pathogen that infects many domestic animals . Since 2011 , highly pathogenic PRV variants have emerged in many farms in China and posed great economic burdens to the animal industry . However , the current marketed vaccines cannot provide effective protection against... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"flow",
"cytometry",
"complement",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"crystal",
"structure",
"enzyme-linked",
"immunoassays",
"respiratory",
"infections",
"immunology",
"condensed",
"matter",
"physics",
"vertebrates",
"animals",
"p... | 2017 | Two classes of protective antibodies against Pseudorabies virus variant glycoprotein B: Implications for vaccine design |
The contribution of pre-mRNA processing mechanisms to the regulation of immune responses remains poorly studied despite emerging examples of their role as regulators of immune defenses . We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections . He... | Changes in gene regulation have long been known to play important roles in both innate and adaptive immune responses . While transcriptional responses to infection have been well-characterized , much less is known about the extent to which co-transcriptional mechanisms of mRNA processing are involved in the regulation ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"3'",
"utr",
"gene",
"regulation",
"pathogens",
"messenger",
"rna",
"immunology",
"microbiology",
"salmonellosis",
"bacterial",
"diseases",
"micrornas",
"untranslated",
"regions",
"en... | 2016 | Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection |
Cortico-basal-ganglia-thalamic ( CBGT ) networks are critical for adaptive decision-making , yet how changes to circuit-level properties impact cognitive algorithms remains unclear . Here we explore how dopaminergic plasticity at corticostriatal synapses alters competition between striatal pathways , impacting the evid... | Cognitive process models such as reinforcement learning ( RL ) and the drift diffusion model ( DDM ) have helped to elucidate the basic algorithms underlying error-corrective learning and the evaluation of accumulating decision evidence leading up to a choice . While these relatively abstract models help to guide exper... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"chemical",
"compounds",
"decision",
"making",
"neural",
"networks",
"nervous",
"system",
"brain",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"organic",
"... | 2019 | Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making |
Mutations of WD repeat domain 62 ( WDR62 ) lead to autosomal recessive primary microcephaly ( MCPH ) , and down-regulation of WDR62 expression causes the loss of neural progenitor cells ( NPCs ) . However , how WDR62 is regulated and hence controls neurogenesis and brain size remains elusive . Here , we demonstrate tha... | Microcephaly is a neural developmental disorder characterized by significantly reduced brain size and variable intellectual disability . WD repeat domain 62 ( WDR62 ) was identified as the second most common gene for autosomal recessive primary microcephaly ( MCPH ) in human . Here , we studied the underlying regulator... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"brain",
"development",
"nuclear",
"staining",
"enzymes",
"enzymology",
"green",
"fluorescent",
"protein",
"c-jun",
"n-terminal",
"kinase",
"signaling",
"cascade",
"developmental",
"biology",
"luminescent",
"proteins",
"organism",
"development",
"immunopr... | 2018 | MEKK3 coordinates with FBW7 to regulate WDR62 stability and neurogenesis |
The glycosylphosphatidylinositol ( GPI ) moiety is one of the ways by which many cell surface proteins , such as Gal/GalNAc lectin and proteophosphoglycans ( PPGs ) attach to the surface of Entamoeba histolytica , the agent of human amoebiasis . It is believed that these GPI-anchored molecules are involved in parasite ... | The causative agent of the infectious disease , amoebiasis , is the parasite Entamoeba histolytica , which targets human intestine and liver . Once in the host , this parasite attaches to human cells and matrix components via factors at its surface such as the Gal/GalNAc lectin and proteophosphoglycans ( PPGs ) . These... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"biology/cell",
"growth",
"and",
"division",
"cell",
"biology/cell",
"adhesion",
"biochemistry/bioinformatics",
"biochemistry/protein",
"folding"
] | 2008 | Bioinformatics and Functional Analysis of an Entamoeba histolytica Mannosyltransferase Necessary for Parasite Complement Resistance and Hepatical Infection |
Current models of embryological development focus on intracellular processes such as gene expression and protein networks , rather than on the complex relationship between subcellular processes and the collective cellular organization these processes support . We have explored this collective behavior in the context of... | The proper operation of the brain depends on the correct developmental wiring of billions of neurons . Understanding this process of living self-construction is crucial not only for biological explanation and medical therapy , but could also provide an entirely new approach to industrial fabrication . We are approachin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biochemical",
"simulations",
"developmental",
"biology",
"developmental",
"neuroscience",
"computational",
"neuroscience",
"biology",
"computational",
"biology",
"neuroscience"
] | 2013 | Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects |
Leprosy is a chronic granulomatous infectious disease and is still endemic in many parts of the world . It causes disabilities which are the consequence of nerve damage . This damage is in most cases the result of immunological reactions . To investigate the differences between a type 1 leprosy ( reversal ) reaction an... | Leprosy is a serious infectious disease whose treatment still poses some challenges . Patients are usually treated with a combination of antimicrobial drugs called multidrug therapy . Although this treatment is effective against Mycobacterium leprae , the bacillus that causes leprosy , patients may develop severe infla... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"dermatology/dermatologic",
"pathology",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/bacterial",
"infections",
"immunology/immunity",
"to",
"infections"
] | 2010 | Granulomatous Reactivation during the Course of a Leprosy Infection: Reaction or Relapse |
Host factors play crucial roles in the replication of plus-strand RNA viruses . In this report , a heat shock protein 90 homologue of Nicotiana benthamiana , NbHsp90 , was identified in association with partially purified replicase complexes from BaMV-infected tissue , and shown to specifically interact with the 3′ unt... | Heat shock protein 90 ( Hsp90 ) is a highly conserved molecular chaperone in prokaryotes and eukaryotes , and regulates diverse cellular processes through ensuring the correct folding of numerous client proteins . However , there are no reports of direct interactions between Hsp90 with viral RNA . Here , we report that... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"rna",
"structure",
"rna",
"viruses",
"nucleic",
"acids",
"proteins",
"virology",
"chaperone",
"proteins",
"viral",
"classification",
"biology",
"rna",
"synthesis",
"microbiology"
] | 2012 | Hsp90 Interacts Specifically with Viral RNA and Differentially Regulates Replication Initiation of Bamboo mosaic virus and Associated Satellite RNA |
Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction . The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect of perturbations in metabolite concentrations and reaction fluxes in response to genetic and environmental perturbation that are beyo... | Microbial production hosts are used for production of a wide range of commodity chemicals . Improving the conversion efficiency of microbial strains is critical to the economic viability and the continued push towards the use of environmentally neutral bioprocesses as a means for producing the chemicals society depends... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"metabolic",
"networks",
"enzymology",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"mutation",
"metabolites",
"network",
"analysis",
"enzyme",
"metabolism",
"molecular",
"biology",
"tech... | 2019 | From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline |
Recent analyses indicate that differences in protein concentrations are only 20%–40% attributable to variable mRNA levels , underlining the importance of posttranscriptional regulation . Generally , protein concentrations depend on the translation rate ( which is proportional to the translational activity , TA ) and th... | Large-scale mRNA concentration measurements are a hallmark of our post-genomic era . Usually they are taken as a surrogate for the corresponding protein concentrations . For most genes , proteins are the actual cellular players , but up to now it has been much more difficult to measure protein concentrations than mRNA ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"cell",
"biology",
"yeast",
"and",
"fungi",
"eukaryotes",
"computational",
"biology",
"saccharomyces"
] | 2007 | Posttranscriptional Expression Regulation: What Determines Translation Rates? |
Parasitic helminth infections can be associated with lifelong morbidity such as immune-mediated organ failure . A better understanding of the host immune response to helminths could provide new avenues to promote parasite clearance and/or alleviate infection-associated morbidity . Murine resistin-like molecules ( RELM ... | Parasitic helminths , which infect an estimated two billion people worldwide , represent a significant global public health problem . Infection is associated with life-long morbidity including growth retardation and organ failure . Despite these debilitating conditions , there are currently no successful vaccines again... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"biology",
"and",
"life",
"sciences",
"immunology",
"parasitic",
"diseases"
] | 2015 | Macrophage-Derived Human Resistin Is Induced in Multiple Helminth Infections and Promotes Inflammatory Monocytes and Increased Parasite Burden |
All animals rely on their ability to sense and respond to their environment to survive . However , the suitability of a behavioral response is context-dependent , and must reflect both an animal’s life history and its present internal state . Based on the integration of these variables , an animal’s needs can be priori... | Studying the logic of small neural circuits is an essential step toward understanding more complex circuits and , ultimately , the computational and integrative properties of whole nervous systems . With a compact nervous system ( just 302 neurons ) and a well-characterized behavioral repertoire , the small roundworm C... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"cell",
"physiology",
"invertebrates",
"alkaloids",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"nervous",
"system",
"caenorhabditis",
"immunology",
"junctional",
"complexes",
"electrophysiology",
"neuroscience",
"animals",
"gap",
"jun... | 2016 | Aversive Behavior in the Nematode C. elegans Is Modulated by cGMP and a Neuronal Gap Junction Network |
Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge . Functional regions of DNA , RNA , and protein sequences often exhibit characteristic but subtle motifs; thus , computational discovery of motifs in sequences is a fundamental and much-studied problem . However , ... | In recent decades , scientists have extracted genetic sequences—DNA , RNA , and protein sequences—from numerous organisms . These sequences hold the information for the construction and functioning of these organisms , but as yet we are mostly unable to read them . It has long been known that these sequences contain ma... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/sequence",
"motif",
"analysis"
] | 2008 | Discovering Sequence Motifs with Arbitrary Insertions and Deletions |
Community drug distributors or neglected tropical disease ( NTD ) volunteers have played a crucial role in ensuring the success of mass drug administration ( MDA ) programs using preventive chemotherapy ( PC ) for lymphatic filariasis , onchocerciasis , schistosomiasis , trachoma and soil transmitted helminths . In rec... | Volunteer community drug distributors play an important role in preventing and treating many neglected tropical diseases ( NTD ) through their participation in mass drug administration ( MDA ) programs for lymphatic filariasis ( elephantiasis ) , onchocerciasis ( river blindness ) , soil transmitted helminths ( intesti... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine",
"and",
"health",
"sciences",
"sociology",
"tropical",
"diseases",
"social",
"sciences",
"database",
"searching",
"parasitic",
"diseases",
"neuroscience",
"social",
"systems",
"cognitive",
"psychology",
"pharmaceutics",
"neglected",
"tropical",
"diseases",
"onc... | 2017 | Review of the factors influencing the motivation of community drug distributors towards the control and elimination of neglected tropical diseases (NTDs) |
Probabilistic inference offers a principled framework for understanding both behaviour and cortical computation . However , two basic and ubiquitous properties of cortical responses seem difficult to reconcile with probabilistic inference: neural activity displays prominent oscillations in response to constant input , ... | Our brain operates in the face of substantial uncertainty due to ambiguity in the inputs , and inherent unpredictability in the environment . Behavioural and neural evidence indicates that the brain often uses a close approximation of the optimal strategy , probabilistic inference , to interpret sensory inputs and make... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"neural",
"networks",
"population",
"dynamics",
"membrane",
"potential",
"electrophysiology",
"random",
"variables",
"neuroscience",
"covariance",
"systems",
"science",
"mathematics",
"probability",
"distrib... | 2016 | The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics |
The multiple circulating human influenza A virus subtypes coupled with the perpetual genomic mutations and segment reassortment events challenge the development of effective therapeutics . The capacity to drug most RNAs motivates the investigation on viral RNA targets . 123 , 060 segment sequences from 35 , 938 strains... | An average of three influenza pandemics occurred in each century over the last 300 years . As occurrence of the next influenza pandemic is definite , developing new antivirals is imperative since resistance to the remaining class of antivirals has been reported occasionally , and vaccines are ineffective in the initial... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance |
The metabolic processes that enable the replication of intracellular Salmonella under nitrosative stress conditions engendered in the innate response of macrophages are poorly understood . A screen of Salmonella transposon mutants identified the ABC-type high-affinity zinc uptake system ZnuABC as a critical determinant... | Microbial pathogens are exposed to multiple antimicrobial defenses during their associations with host cells . Nitric oxide generated in the innate response exerts widespread antimicrobial activity against a variety of pathogenic microorganisms . Nitric oxide has high affinity for metal groups of terminal cytochromes o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"metabolic",
"processes",
"immunology",
"microbiology",
"carbohydrates",
"neuroscience",
"or... | 2018 | Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response |
The notion that sequence homology implies functional similarity underlies much of computational biology . In the case of protein-protein interactions , an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact . The use of transferred interactions is ... | It is widely assumed that knowledge gained in one species can be transferred to another species , even among species that are widely separated on the tree of life . This transfer is often done at the level of proteins under the assumption that if two proteins have similar sequences , they will share similar properties ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"protein",
"interactions",
"evolutionary",
"modeling",
"biology",
"computational",
"biology",
"proteomics"
] | 2012 | What Evidence Is There for the Homology of Protein-Protein Interactions? |
Extrathymic CD4+CD8+ double-positive ( DP ) T cells are increased in some pathophysiological conditions , including infectious diseases . In the murine model of Chagas disease , it has been shown that the protozoan parasite Trypanosoma cruzi is able to target the thymus and induce alterations of the thymic microenviron... | The thymus is a primary lymphoid organ that plays an important role on the development of the immune system and maturation of the T cell repertoire . During the normal life span , this organ undergoes involution during the aging and also in the presence of a wide variety of infectious diseases . It has been shown that ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"immunopathology",
"immunology",
"biology",
"lymphoid",
"organs",
"autoimmunity",
"immune",
"system"
] | 2011 | Chagasic Thymic Atrophy Does Not Affect Negative Selection but Results in the Export of Activated CD4+CD8+ T Cells in Severe Forms of Human Disease |
Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli . Methods for global network inference have been developed and applied to a variety of species . Most approaches consider the problem of network inference independently in each species , despite... | Gene regulatory networks describing related biological processes are thought to share conserved interaction structure . This assumption motivates a great deal of work in model systems–where discovery of gene regulation may be more experimentally tractable–but is difficult to directly evaluate using existing methods . T... | [
"Abstract",
"Introduction",
"Results",
"Methods",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"regulatory",
"proteins",
"bacillus",
"microbiology",
"dna-binding",
"proteins",
"operons",
"prokaryotic",
"models",
"model",
... | 2016 | Fused Regression for Multi-source Gene Regulatory Network Inference |
The formation and release of outer membrane vesicles ( OMVs ) is a phenomenon of Gram-negative bacteria . This includes Legionella pneumophila ( L . pneumophila ) , a causative agent of severe pneumonia . Upon its transmission into the lung , L . pneumophila primarily infects and replicates within macrophages . Here , ... | Of all intracellular pathogens , Legionella pneumophila show the highest genetic adaptation to the host . They are important human pathogens causing mainly pneumonia , but are also highly successful pathogens of water amoeba . To manipulate host cells for optimal intracellular replication , they express several hundred... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"vacuoles",
"cytokines",
"gene",
"regulation",
"pathogens",
"immunology",
"microbiology",
... | 2016 | Legionella pneumophila-Derived Outer Membrane Vesicles Promote Bacterial Replication in Macrophages |
Raccoon rabies is endemic in the eastern U . S . ; however , an epizootic had not been confirmed on Long Island , New York until 2004 . An oral rabies vaccination ( ORV ) program was initiated soon after the first rabies-positive raccoon was discovered , and continued until raccoon rabies was eliminated from the vaccin... | Raccoon rabies , a type of rabies found most frequently in raccoons , is common in the eastern U . S . Raccoon rabies is at times controlled through oral rabies vaccination ( ORV ) programs , in which baits containing rabies vaccine are distributed throughout the affected area to be consumed by wildlife , which then de... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"epizootics",
"united",
"states",
"medicine",
"and",
"health",
"sciences",
"animal",
"diseases",
"pathology",
"and",
"laboratory",
"medicine",
"economic",
"analysis",
"pathogens",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"microbiology",
"social"... | 2016 | The Economics of a Successful Raccoon Rabies Elimination Program on Long Island, New York |
The essential role of pathogens in host metabolism is widely recognized , yet the mechanisms by which they affect host physiology remain to be fully defined . Here , we found that NleB , an enteropathogenic Escherichia coli ( EPEC ) type III secretion system effector known to possess N-acetylglucosamine ( GlcNAc ) tran... | Accumulating evidence shows that pathogens can affect host metabolism , resulting in human diseases such as obesity and type 2 diabetes . However , how pathogens influence their hosts is still not clear , and this results in a lack of effective and specific clinical treatments . Further investigations into the causes o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"transfection",
"carbohydrate",
"metabolism",
"luciferase",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"enzymes",
"enzymology",
"glucose",
"metabolism",
"organic",
"compounds",
"mutation",
"hypoxia",
"basic",
"amino",
"acids",
"amino",
"acids",
"m... | 2018 | A pathogen-derived effector modulates host glucose metabolism by arginine GlcNAcylation of HIF-1α protein |
Arboviral disease transmission by Aedes mosquitoes poses a major challenge to public health systems in Ecuador , where constraints on health services and resource allocation call for spatially informed management decisions . Employing a unique dataset of larval occurrence records provided by the Ecuadorian Ministry of ... | The yellow fever mosquito ( Aedes aegypti ) is a medically important vector of arboviral diseases in Ecuador , such as dengue fever and chikungunya . Managing Ae . aegypti is a challenge to public health agencies in Latin America , where the use of limited resources must be planned in an efficient , targeted manner . T... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2019 | Geographic shifts in Aedes aegypti habitat suitability in Ecuador using larval surveillance data and ecological niche modeling: Implications of climate change for public health vector control |
Differentiation-dependent regulation of the Ifng cytokine gene locus in T helper ( Th ) cells has emerged as an excellent model for functional study of distal elements that control lineage-specific gene expression . We previously identified a cis-regulatory element located 22 kb upstream of the Ifng gene ( Conserved No... | Differentiation of multipotent naïve T cell precursors into functionally mature effector cells that control different types of immune responses is an excellent model to study lineage-specific regulation of gene expression . A number of cis-regulatory elements have been reported to control expression of the gene that en... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immune",
"cells",
"cytokines",
"immune",
"activation",
"immunology",
"dna",
"transcription",
"gene",
"function",
"histone",
"modification",
"animal",
"models",
"adaptive",
"immunity",
"model",
"organisms",
"epigenetics",
"immunomodulation",
"chromatin",
"chromosome",
"bi... | 2014 | Deletion of a Conserved cis-Element in the Ifng Locus Highlights the Role of Acute Histone Acetylation in Modulating Inducible Gene Transcription |
In meiosis I , homologous chromosomes become paired and then separate from one another to opposite poles of the spindle . In humans , errors in this process are a leading cause of birth defects , mental retardation , and infertility . In most organisms , crossing-over , or exchange , between the homologous partners pro... | Meiosis is a specialized cell division that halves the chromosome number and results in the production of gametes . In humans , meiosis normally produces gametes containing exactly one copy of each chromosome . Meiotic errors lead to gametes with incorrect chromosome numbers , a major cause of birth defects and inferti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"growth",
"and",
"division",
"molecular",
"biology/centromeres",
"genetics",
"and",
"genomics/chromosome",
"biology"
] | 2009 | The Synaptonemal Complex Protein Zip1 Promotes Bi-Orientation of Centromeres at Meiosis I |
Class-switch recombination ( CSR ) , induced by activation-induced cytidine deaminase ( AID ) , can be divided into two phases: DNA cleavage of the switch ( S ) regions and the joining of the cleaved ends of the different S regions . Here , we show that the DSIF complex ( Spt4 and Spt5 ) , a transcription elongation fa... | Class switch recombination ( CSR ) in B cells is required for interaction with different effector molecules while retaining the affinity for the same antigens . CSR mechanism involves the orchestrated steps of transcription , DNA break , and repair of the target loci . Within the cells , these processes occur at the ch... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunoglobulins",
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"immunology",
"chromatin",
"genetics",
"and",
"genomics",
"dna",
"transcription",
"histone",
"modification"
] | 2012 | The DSIF Subunits Spt4 and Spt5 Have Distinct Roles at Various Phases of Immunoglobulin Class Switch Recombination |
Renewable in vitro cell cultures , such as lymphoblastoid cell lines ( LCLs ) , have facilitated studies that contributed to our understanding of genetic influence on human traits . However , the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated . We have previousl... | For those studying the effect of genotype on human traits , a collection of genetically diverse renewable cell lines can be an indispensable resource . B-cells immortalized with Epstein-Barr virus , also known as lymphoblastoid cell lines or LCLs , have been particularly favored as such a model because they are easy to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature |
Schistosomiasis ( bilharzia ) , one of the most relevant parasitoses of humans , is confirmed by microscopic detection of eggs in stool , urine , or organ biopsies . The sensitivity of these procedures is variable due to fluctuation of egg shedding . Serological tests on the other hand do not distinguish between active... | Bilharzia ( schistosomiasis ) occurs in the tropics and subtropics and is one of the most important parasite diseases of humans . It is caused by flukes residing in the vessels of the gut or bladder , causing fever , pain , and bleeding . Bladder cancer or esophageal varices may follow . Diagnosis is difficult , requir... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"public",
"health",
"and",
"epidemiology/screening",
"microbiology/parasitology"
] | 2009 | Diagnosing Schistosomiasis by Detection of Cell-Free Parasite DNA in Human Plasma |
Current models of sensorimotor control posit that motor commands are generated by combining multiple modules which may consist of internal models , motor primitives or motor synergies . The mechanisms which select modules based on task requirements and modify their output during learning are therefore critical to our u... | Research in motor learning has focused on how we acquire new motor memories for novel situations . However , in many real world motor tasks , the challenge is to select appropriate memories for a given context . In such tasks , we are guided by two key types of information . First , contextual information from vision (... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"cognitive",
"psychology",
"cognition",
"computer",
"vision",
"memory",
"kinematics",
"n... | 2017 | An error-tuned model for sensorimotor learning |
Stem cell divisions are either asymmetric—in which one daughter cell remains a stem cell and one does not—or symmetric , in which both daughter cells adopt the same fate , either stem or non-stem . Recent studies show that in many tissues operating under homeostatic conditions stem cell division patterns are strongly b... | Recently , highly symmetric patterns of stem cell division have been observed in a variety of adult mammalian somatic tissues . Here we identify conditions under which this behavior serves as a strategy to protect the organism against mutation accumulation . First , we find that a sufficient number of lifetime stem cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"genetics",
"theoretical",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"computational",
"biology"
] | 2014 | The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage |
Melioidosis is an infection caused by Burkholderia pseudomallei , a Gram-negative bacillus found in soil and water . Diabetes mellitus is the most important risk factor for melioidosis . The recommendations for disease prevention include avoiding direct contact with soil and water , and drinking only boiled or bottled ... | Melioidosis is a serious infectious disease caused by the Gram-negative environmental bacterium , Burkholderia pseudomallei . Infection in humans occurs following skin inoculation , inhalation or ingestion . The recommendations for melioidosis prevention include using protective gear such as rubber boots when in direct... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"water",
"resources",
"rubber",
"elastomers",
"melioidosis",
"condensed",
"matter",
"physics",
"geographical",
"locations",
"diabetes",
"mellitus",
"bacterial",
"diseases",
"boiling",
... | 2018 | Feasibility and initial outcomes of a multifaceted prevention programme of melioidosis in diabetic patients in Ubon Ratchathani, northeast Thailand |
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