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Predicting function from sequence is an important goal in current biological research , and although , broad functional assignment is possible when a protein is assigned to a family , predicting functional specificity with accuracy is not straightforward . If function is provided by key structural properties and the re...	Globins are a superfamily of widely studied and diverse globular proteins whose function is tightly related to their oxygen affinity and reactivity . Two prominent members are the well-known tetrameric hemoglobin and the monomeric myoglobin , both involved in reversible oxygen storage and transport in mammals . Truncat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "sequencing", "techniques", "heme", "taxonomy", "oxygen", "split-decomposition", "method", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "phylogenetic", "analysis", "molecular", "biology", "techniques", "chemical", "dissociation", "research", ...	2016	Evolutionary and Functional Relationships in the Truncated Hemoglobin Family
Human T-cell leukemia virus type 1 ( HTLV-1 ) causes both a neoplastic disease and inflammatory diseases , including HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . The HTLV-1 basic leucine zipper factor ( HBZ ) gene is encoded in the minus strand of the proviral DNA and is constitutively expres...	Viral infection frequently induces tissue inflammation in the host . HTLV-1 infection is associated with chronic inflammation in the CNS , skin , and lung , but the inflammatory mechanism is not fully understood yet . Since HTLV-1 directly infects CD4+ T cells , central player of the host immune regulation , HTLV-1 sho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	HTLV-1 bZIP Factor Induces Inflammation through Labile Foxp3 Expression
Reciprocating exchange with other humans requires individuals to infer the intentions of their partners . Despite the importance of this ability in healthy cognition and its impact in disease , the dimensions employed and computations involved in such inferences are not clear . We used a computational theory-of-mind mo...	Human social interactions are extraordinarily rich and complex . The ability to infer the intentions of others is essential for successful social interactions . Although most of our inferences about others are silent and subtle , traces of their effects can be found in the behavior we exhibit in various tasks , notably...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "neuroscience" ]	2012	Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data . Applications of phylogeography are broad , and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks . Phylogeographic inference based on bot...	When studying infectious diseases it is often important to understand how germs spread from location-to-location , person-to-person , or even one part of the body to another . Using phylogeographic methods , it is possible to recover the history of spread of pathogens ( or other organisms ) by studying their genetic ma...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
Artificial Intelligence is exponentially increasing its impact on healthcare . As deep learning is mastering computer vision tasks , its application to digital pathology is natural , with the promise of aiding in routine reporting and standardizing results across trials . Deep learning features inferred from digital pa...	In this study , we examine the issue of evaluating accuracy of predictive models from deep learning features in digital pathology , as an hallmark of reproducibility . It is indeed a top priority that reproducibility-by-design gets adopted as standard practice in building and validating AI methods in the healthcare dom...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "medical", "doctors", "medical", "personnel", "biomarkers", "health", "care", "histology", "health", "care", "providers", "artificial", "intelligence", "research", "and", "analysis", "methods", "computer", "and", "information", ...	2019	Evaluating reproducibility of AI algorithms in digital pathology with DAPPER
Humans and animals face decision tasks in an uncertain multi-agent environment where an agent's strategy may change in time due to the co-adaptation of others strategies . The neuronal substrate and the computational algorithms underlying such adaptive decision making , however , is largely unknown . We propose a popul...	Socio-economic interactions are captured in a game theoretic framework by multiple agents acting on a pool of goods to maximize their own reward . Neuroeconomics tries to explain the agent's behavior in neuronal terms . Classical models in neuroeconomics use temporal-difference ( TD ) -learning . This algorithm increme...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "biology", "neuroscience" ]	2012	Spike-based Decision Learning of Nash Equilibria in Two-Player Games
Two-component signal transduction systems , where the phosphorylation state of a regulator protein is modulated by a sensor kinase , are common in bacteria and other microbes . In many of these systems , the sensor kinase is bifunctional catalyzing both , the phosphorylation and the dephosphorylation of the regulator p...	Bacteria often use two-component systems to sense and respond to environmental changes , which involves autophosphorylation of a sensor kinase and phosphotransfer to a cognate response regulator . However , despite conservation of this ‘classical’ scheme there exist substantial variations in the mechanism of phosphotra...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "and", "information", "sciences", "systems", "science", "mathematics", "network", "analysis", "regulatory", "networks", "biology", "and", "life", "sciences", "signaling", "networks", "computational", "biology", "nonlinear", "dynamics", "physical", "sciences" ]	2014	Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase
Although acetylated α-tubulin is known to be a marker of stable microtubules in neurons , precise factors that regulate α-tubulin acetylation are , to date , largely unknown . Therefore , a genetic screen was employed in the nematode Caenorhabditis elegans that identified the Elongator complex as a possible regulator o...	We were able to demonstrate how a screen , that utilized the nematode model organism Caenorhabditis elegans , yielded the novel discovery that the Elongator protein complex is critical for neuronal development and microtubule acetylation . Other scientists have previously shown that the Elongator is important for trans...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics" ]	2010	The Caenorhabditis elegans Elongator Complex Regulates Neuronal α-tubulin Acetylation
Mutations in sorting nexin 10 ( Snx10 ) have recently been found to account for roughly 4% of all human malignant osteopetrosis , some of them fatal . To study the disease pathogenesis , we investigated the expression of Snx10 and created mouse models in which Snx10 was knocked down globally or knocked out in osteoclas...	We found that Snx10 , a molecule expressed in osteoclasts , was also expressed in the stomach . Studies in tissue specific or global knock-down mice showed that Snx10 deficiency resulted in a phenotype that was a consequence of deficiencies in both osteoclasts and gastric zymogenic cells . Our studies add to a growing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Osteopetrorickets due to Snx10 Deficiency in Mice Results from Both Failed Osteoclast Activity and Loss of Gastric Acid-Dependent Calcium Absorption
IRF8 ( Interferon Regulatory Factor 8 ) plays an important role in defenses against intracellular pathogens , including several aspects of myeloid cells function . It is required for ontogeny and maturation of macrophages and dendritic cells , for activation of anti-microbial defenses , and for production of the Th1-po...	IRF8 is a member of the Interferon Regulatory Factor family that is expressed in myeloid cells such as macrophages and dendritic cells and that activates or represses gene transcription upon stimulation with interferon gamma ( IFNγ ) , lipopolysaccharide ( LPS ) , and other microbial stimuli . IRF8 plays an important r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "expression", "analysis", "animal", "genetics", "genetic", "mutation", "immune", "cells", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "bacterial", "diseases", "genome", ...	2011	Interferon Regulatory Factor 8 Regulates Pathways for Antigen Presentation in Myeloid Cells and during Tuberculosis
Genome-wide association studies ( GWASs ) have discovered numerous single nucleotide polymorphisms ( SNPs ) associated with human complex disorders . However , functional characterization of the disease-associated SNPs remains a formidable challenge . Here we explored regulatory mechanism of a SNP on chromosome 9p21 as...	A large number of variants associated with human complex diseases have been discovered by genome-wide association studies ( GWASs ) . These discoveries have been anticipated to be translated into the definitive understanding of disease pathogeneses; however , functional characterization of the disease-associated SNPs r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "population", "genetics", "carcinomas", "cancers", "and", "neoplasms", "endometrial", "carcinoma", "alleles", "oncology", "genome", "analysis", "sequence", "motif...	2016	Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus
In insects , precisely timed periodic pulses of the molting hormone ecdysone control major developmental transitions such as molts and metamorphosis . The synthesis and release of ecdysone , a steroid hormone , is itself controlled by PTTH ( prothoracicotopic hormone ) . PTTH transcript levels oscillate with an 8 h rhy...	Steroid hormones play fundamental roles in development and disease . They are often released as pulses , thereby orchestrating multiple physiological and developmental changes throughout the body . Hormone pulses must be regulated in a way so that they have a defined beginning , peak , and end . In Drosophila , pulses ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurochemistry", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "molecular", "development", "neuropeptides", "erk", "signaling", "cascade", "neurochemicals", "nuclear", "receptor", "signaling", "biology", "molecular", "b...	2011	Nuclear Receptor DHR4 Controls the Timing of Steroid Hormone Pulses During Drosophila Development
Targeting key regulators of the cancer stem cell phenotype to overcome their critical influence on tumor growth is a promising new strategy for cancer treatment . Here we present a modeling framework that operates at both the cellular and molecular levels , for investigating IL-6 mediated , cancer stem cell driven tumo...	A small population of cancer stem cells that share many of the biological characteristics of normal adult stem cells are believed to initiate and sustain tumor growth for a wide variety of malignancies . Growth and survival of these cancer stem cells is highly influenced by tumor micro-environmental factors and molecul...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "cell", "physiology", "cell", "death", "tumor", "stem", "cells", "medicine", "and", "health", "sciences", "endothelial", "cells", "cancer", "treatment", "cell", "processes", "cancer", "stem", "cells", "cell", "differentiation", "epithelial", "cell...	2018	A mathematical model for IL-6-mediated, stem cell driven tumor growth and targeted treatment
Accurate temporal control of gene expression is essential for normal development and must be robust to natural genetic and environmental variation . Studying gene expression variation within and between related species can delineate the level of expression variability that development can tolerate . Here we exploit the...	Embryonic development necessitates a delicate balancing act . On one hand , precise regulation of the expression of developmental genes is crucial for the maintenance of morphology and function . On the other hand , these same regulatory networks must allow normal development to proceed through genetic variation and en...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics
Buruli ulcer , caused by infection with Mycobacterium ulcerans , is a necrotizing disease of the skin and subcutaneous tissue , which is most prevalent in rural regions of West African countries . The majority of clinical presentations seen in patients are ulcers on limbs that can be treated by eight weeks of antibioti...	Infection with Mycobacterium ulcerans can lead to a slow progressing , ulcerative disease of the skin and underlying soft tissue called Buruli ulcer . The disease is most prevalent in rural African communities with limited access to health care facilities . The most efficient means to prevent the disease , a vaccine ag...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Use of Recombinant Virus Replicon Particles for Vaccination against Mycobacterium ulcerans Disease
Chikungunya is a mosquito-borne viral infection of humans that previously was confined to regions in central Africa . However , during this century , the virus has shown surprising potential for geographic expansion as it invaded other countries including more temperate regions . With no vaccine and no specific treatme...	Chikungunya fever is a mosquito-borne viral infection showing a surprising potential for geographic expansion . Similar to other tropical infectious diseases having no vaccine and no specific treatment , the main control strategy for Chikungunya remains reduction of mosquito population size . We developed a model for d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "theoretical", "ecology", "population", "biology", "infectious", "disease", "control", "infectious", "diseases", "environmental", "epidemiology", "epidemiology", "biology", "vect...	2012	Modeling Dynamic Introduction of Chikungunya Virus in the United States
Individual susceptibility to HIV is heterogeneous , but the biological mechanisms explaining differences are incompletely understood . We hypothesized that penile inflammation may increase HIV susceptibility in men by recruiting permissive CD4 T cells , and that male circumcision may decrease HIV susceptibility in part...	The per-contact risk of infection with HIV through sexual exposure is low and highly variable . Understanding the biological basis for this variability could help in the development of new methods to prevent infection . There is some evidence that penile inflammation , even in the absence of any clinical symptoms , may...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "antigen-presenting", "cells", "immunolo...	2016	Chemokine Levels in the Penile Coronal Sulcus Correlate with HIV-1 Acquisition and Are Reduced by Male Circumcision in Rakai, Uganda
The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire . One of these mechanisms , the affinity maturation process , works in an evolutionary-like fashion: after binding to a foreign molecule , the antibody-producing B-cells exhibit a high-frequency mutation...	Affinity maturation is a very complex biological process which enables activated B-cells to produce antibodies with increased affinity for a given antigen . Once B-cells begin to proliferate , each of the progeny cells introduces mutations in the antigen binding region in order to explore different affinities for the a...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "markov", "models", "evolutionary", "biology", "split-decomposition", "method", "pathogens", "immunology", "microbiology", "retroviruse...	2016	Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity
Nipah virus is a broadly tropic and highly pathogenic zoonotic paramyxovirus in the genus Henipavirus whose natural reservoirs are several species of Pteropus fruit bats . Nipah virus has repeatedly caused outbreaks over the past decade associated with a severe and often fatal disease in humans and animals . Here , a n...	Nipah virus and Hendra virus are closely related and highly pathogenic zoonoses whose primary natural reservoirs are several species of Pteropus fruit bats . Both Nipah and Hendra viruses can cause severe and often fatal disease in a variety of mammalian hosts , including humans . The henipaviruses are categorized as b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/animal", "models", "of", "infection", "virology/emerging", "viral", "diseases" ]	2009	A Neutralizing Human Monoclonal Antibody Protects against Lethal Disease in a New Ferret Model of Acute Nipah Virus Infection
The human herpes virus Epstein-Barr virus ( EBV ) latently infects and drives the proliferation of B lymphocytes in vitro and is associated with several forms of lymphoma and carcinoma in vivo . The virus encodes ~30 miRNAs in the BART region , the function of most of which remains elusive . Here we have used a new mou...	Epstein-Barr virus is a herpes virus that persistently infects essentially every human being for life . It also has the ability to latently infect B lymphocytes and cause them to proliferate indefinitely in culture , and is associated with several forms of carcinoma and lymphoma . The virus contains genes for ~30 miRNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Epstein-Barr Virus Encoded BART miRNAs Potentiate Tumor Growth In Vivo
The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins . How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown . We present a new method based on molec...	Many biological processes such as cell proliferation and signaling are guided by mechanical stress . Proteins as the molecular machinery behind these processes are reacting to or withstanding mechanical forces in specific ways . How mechanical stress propagates through proteins to induce a certain mechanical response i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/comparative", "sequence", "analysis", "biophysics/protein", "chemistry", "and", "proteomics" ]	2009	Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
Bartonella quintana , the etiologic agent of trench fever and other human diseases , is transmitted by the feces of body lice . Recently , this bacterium has been detected in other arthropod families such as bed bugs , which begs the question of their involvement in B . quintana transmission . Although several infectio...	Bartonella quintana , the etiologic agent of trench fever and other human diseases , is known to be transmitted by the feces of body lice . Recently , the DNA of this bacterium has been detected in bed bugs . Several pathogens have been associated and suggested to be transmitted by bed bugs , despite the insufficient e...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Competence of Cimex lectularius Bed Bugs for the Transmission of Bartonella quintana, the Agent of Trench Fever
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens . As with other ecosystems , its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically . Antibiotic cessation does not necessaril...	Recent applications of metagenomics have led to a flood of novel studies and a renewed interest in the role of the gut microbiota in human health . We can now envision a time in the near future where analysis of microbiota composition can be used for diagnostics and the rational design of new therapeutics . However , m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecosystem", "modeling", "ecology", "biology", "computational", "biology", "microbiology", "microbial", "ecology" ]	2012	Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota
Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in cancers . The tumor suppressors APC and Axin form the core of the multiprotein destruction complex , which targets the Wnt-effector beta-catenin for phosphorylation ...	Cell-cell communication is critical for cells to choose fates during embryonic development and often goes wrong in diseases like cancer . The Wnt cell signaling pathway provides a superb example . Loss of negative regulatory proteins like APC and Axin takes the brakes off cell proliferation and thus contributes to colo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "molecular", "probe", "techniques", "antigen-presenting", "cells", "immunology", "immunoblotting", "vertebrates", "animals", "mammals", "animal", "models", "developmental", "biol...	2018	Supramolecular assembly of the beta-catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo
Polyphenism is a successful strategy adopted by organisms to adapt to environmental changes . Brown planthoppers ( BPH , Nilaparvata lugens ) develop two wing phenotypes , including long-winged ( LW ) and short-winged ( SW ) morphs . Though insulin receptor ( InR ) and juvenile hormone ( JH ) have been known to regulat...	Polyphenism is a fascinating phenomenon which significantly improves the ability of a species to explore various environmental resources . Brown planthopper ( Nilaparvata lugens , BPH ) is a notorious insect pest which causes huge damages to rice . BPH has two wing phenotypes , long-winged ( LW ) and short-winged ( SW ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "molecular", "probe", "techniques", "natural", "antisense", "transcripts", "gene", "regulation", "enzymes", "enzymology", "hormones", "developmental", "biology", "regulator", "genes", "micrornas", "animal", "anatomy",...	2019	miR-34 modulates wing polyphenism in planthopper
The mechanism for cortical folding pattern formation is not fully understood . Current models represent scenarios that describe pattern formation through local interactions , and one recent model is the intermediate progenitor model . The intermediate progenitor ( IP ) model describes a local chemically driven scenario...	The size and shape of the cerebral cortex varies across species . The cortical folding pattern also varies from a smooth surface where no pattern is visible , as observed in the common treeshrew ( Tupaia glis ) and Eastern mole ( Scalopus aquaticus ) , to an intricate labyrinthine pattern , as observed in humans . One ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "developmental", "biology/morphogenesis", "and", "cell", "biology", "mathematics", "developmental", "biology/developmental", "evolution", "developmental", "biology/pattern", "formation", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "evolutionary", "bi...	2009	Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns
Massively parallel RNA sequencing ( RNA-seq ) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription , processing or decay . Regardless of advances in the experimental protocols and techniques , every experimentalist needs to specify the key aspects of...	Massively parallel RNA sequencing ( RNA-seq ) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription , processing or decay . In our manuscript , we address several key aspects of experimental design: 1 ) The optimal labeling time , 2 ) the number of re...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "nucleic", "acid", "synthesis", "experimental", "design", "rna", "extraction", "nucleotides", "research", "design", "molecular", "biology", "techniques", "rna", "synthesis", "rna", "sequencing", "extraction", "techniques", "rna", "transcription...	2019	On the optimal design of metabolic RNA labeling experiments
Continued exposure to malaria-causing parasites in endemic regions of malaria induces significant levels of acquired immunity in adult individuals . A better understanding of the transcriptional basis for this acquired immunological response may provide insight into how the immune system can be boosted during vaccinati...	Plasmodium vivax malaria is a debilitating , occasionally life-threatening , and economically burdensome disease in Central Latin America , where 70%- 80% of the population lives with the risk of infection . We performed a gene expression profiling experiment taking advantage of a previously described sporozoite challe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge
In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses . To investigate the origins of this behavior and to understand its functional relevance , we quantitatively analyzed this variability using new mathematical too...	Timing of biological processes such as gene transcription is crucial to ensure that cells and tissues respond appropriately to their environment . Until recently it was assumed that most cells in a tissue responded in a similar way , and that changes in cellular activity were relatively stable . However , studies of me...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "cell", "biology/gene", "expression", "computational", "biology/transcriptional", "regulation" ]	2011	Dynamic Analysis of Stochastic Transcription Cycles
Cell differentiation status is defined by the gene expression profile , which is coordinately controlled by epigenetic mechanisms . Cell type-specific DNA methylation patterns are established by chromatin modifiers including de novo DNA methyltransferases , such as Dnmt3a and Dnmt3b . Since the discovery of the myogeni...	How muscle homeostasis is maintained is not completely elucidated yet . Epigenetic disorders such as Beckwith-Wiedemann syndrome , which causes hypergrowth of skeletal muscles and rhabdomyosarcoma , indicate that epigenetic regulations such as DNA methylation , contribute to this homeostasis control . DNA methylation i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "muscle", "tissue", "skeletal", "muscles", "cell", "differentiation", "muscle", "regeneration", "developmental", "biology", "organism", "development", "epigenetics", "dna", "morphogenesis", "dna", "methylation", "chromatin", "muscu...	2016	Dnmt3a Regulates Proliferation of Muscle Satellite Cells via p57Kip2
Human lymphatic filariasis is a mosquito-vectored disease caused by the nematode parasites Wuchereria bancrofti , Brugia malayi and Brugia timori . These are relatively large roundworms that can cause considerable damage in compatible mosquito vectors . In order to assess how mosquitoes respond to infection in compatib...	Filarial worms that cause human lymphatic filariasis ( LF ) are transmitted by many species of mosquitoes . Within susceptible mosquitoes , Brugia malayi develop from microfilariae ( mf ) to infective-stage larvae ( L3s ) , in approximately eight days . These nematodes develop as intracellular parasites within mosquito...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity", "cell", "biology/microbial", "growth...	2009	Mosquito Infection Responses to Developing Filarial Worms
Sustained and coordinated vaccination efforts have brought polio eradication within reach . Anticipating the eradication of wild poliovirus ( WPV ) and the subsequent challenges in preventing its re-emergence , we look to the past to identify why polio rose to epidemic levels in the mid-20th century , and how WPV persi...	Thanks to global vaccination efforts , poliovirus is on the brink of worldwide eradication . However , achieving eradication and preventing re-emergence requires intimate knowledge of how the virus persists . In order to understand a system that is complicated by heavy human intervention , such as vaccination , it is i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Unraveling the Transmission Ecology of Polio
Mucins are heavily glycosylated proteins that give mucus its gel-like properties . Moreover , the glycans decorating the mucin protein core can alter the protective properties of the mucus barrier . To investigate whether these alterations could be parasite-induced we utilized the Trichuris muris ( T . muris ) infectio...	Approximately 2 billion people are infected with worms every year , causing physical , nutritional and cognitive impairment particularly in children . Mucins are large sugar-coated ( glycosylated ) proteins that form the intestinal mucus layer . This mucus layer protects our ‘insides’ from external insults and plays an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "helminths", "salts", "parasitic", "diseases", "animals", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "glycosylation", "digestive", ...	2017	Immune-driven alterations in mucin sulphation is an important mediator of Trichuris muris helminth expulsion
The Huntington's disease gene ( HTT ) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis . Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying mutation , an approach that is likely applicable to other trinucleotide repeat diseases . Huntingto...	The expansion of a CAG repeat underlies Huntington's disease ( HD ) , with longer CAG tracts giving rise to earlier onset and more severe disease . In individuals harboring a CAG expansion the repeat undergoes further somatic expansion over time , particularly in brain cells most susceptible to disease pathogenesis . P...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice: Genome-Wide and Candidate Approaches
The autonomous parvovirus Minute Virus of Mice ( MVM ) induces specific changes in the cytoskeleton filaments of infected permissive cells , causing in particular the degradation of actin fibers and the generation of “actin patches . ” This is attributed to a virus-induced imbalance between the polymerization factor N-...	Rodent parvoviruses are non-enveloped lytic viruses that are thought excellent tools for a virotherapy of cancer because of their strong natural oncolytic potential and low pathogenicity in humans . Egress of non-enveloped lytic viruses is commonly thought to occur as a virus burst after cell disintegration . Indeed , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "virology/virion", "structure,", "assembly,", "and", "egress", "cell", "biology/membranes", "and", "sorting", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "virology/viruses", "and", "cancer", "cell", "biology/cyt...	2008	Vesicular Egress of Non-Enveloped Lytic Parvoviruses Depends on Gelsolin Functioning
Dogs are the predominant domestic reservoir for human L . infantum infection . Zoonotic visceral leishmaniasis ( ZVL ) is an emerging problem in some U . S . dog breeds , with an annual quantitative PCR prevalence of greater than 20% within an at-risk Foxhound population . Although classically Leishmania is transmitted...	Dogs are a favored feeding source for sand flies that transmit human L . infantum infection . Zoonotic visceral leishmaniasis ( ZVL ) is an emerging problem in some U . S . dog breeds , with over 20% of at-risk Foxhounds infected . Although classically Leishmania is transmitted by infected sand flies which exist in the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "diagnostic", "medicine", "women's", "health", "clinical", "immunology", "global", "health", "immunology", "public", "health", "veterinary", "science" ]	2011	Transplacental Transmission of Leishmania infantum as a Means for Continued Disease Incidence in North America
Endosymbiotic bacteria from different species can live inside cells of the same eukaryotic organism . Metabolic exchanges occur between host and bacteria but also between different endocytobionts . Since a complete genome annotation is available for both , we built the metabolic network of two endosymbiotic bacteria , ...	Some bacteria , called endocytobionts , permanently live inside the cells of a pluricellular organism and often bring an adaptative advantage to their host by providing compounds that the latter cannot produce or find in its diet . The association may involve several species of bacteria within the same host . The sap-f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/metabolic", "networks" ]	2010	Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata
Accumulating evidence suggests that many tumors have a hierarchical organization , with the bulk of the tumor composed of relatively differentiated short-lived progenitor cells that are maintained by a small population of undifferentiated long-lived cancer stem cells . It is unclear , however , whether cancer stem cell...	Recent evidence suggests that , like many normal tissues , many cancers are maintained by a small population of immortal stem cells that divide indefinitely to produce many differentiated cells . Cancer stem cells may come directly from mutation of normal stem cells , but this route demands high mutation rates , becaus...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "mathematics", "theoretical", "biology", "applied", "mathematics", "biology", "evolutionary", "biology" ]	2014	Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers
Precise patterns of spatial and temporal gene expression are central to metazoan complexity and act as a driving force for embryonic development . While there has been substantial progress in dissecting and predicting cis-regulatory activity , our understanding of how information from multiple enhancer elements converg...	Development is a complex process in which a single cell gives rise to a multi-cellular organism comprised of diverse cell types and well-organized tissues . This transformation requires tightly coordinated expression , both spatially and temporally , of hundreds to thousands of genes specific to any given tissue . To o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "genome", "expression", "analysis", "developmental", "biology", "genomics", "functional", "genomics", "biology", "computational", "biology", "genetics", "and", "genomics", "cell", "fate", "determination" ]	2012	Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State
The use of high quality disease surveillance data has become increasingly important for public health action against new threats . In response , countries have developed a wide range of disease surveillance systems enabled by technological advancements . The heterogeneity and complexity of country data systems have cau...	The use of high quality data and information has become essential for public health agencies to monitor and protect population health . Technological advancement has enabled the development of sophisticated disease surveillance systems by many countries . Increasingly , countries are making surveillance data publicly a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Availability and Consistency of Dengue Surveillance Data Provided Online by the World Health Organization
HIV-1 is internalized into mature dendritic cells ( mDCs ) via an as yet undefined mechanism with subsequent transfer of stored , infectious virus to CD4+ T lymphocytes . Thus , HIV-1 subverts a DC antigen capture mechanism to promote viral spread . Here , we show that gangliosides in the HIV-1 membrane are the key mol...	Antigen-presenting cells such as dendritic cells ( DCs ) are required to combat infections , but viruses including HIV have evolved strategies to evade their anti-viral activity . HIV can enter DCs via a non-infectious endocytic mechanism and trick them into passing infectious virus on to bystander CD4+ T cells . Immat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "flow", "cytometry", "immune", "cells", "viral", "transmission", "and", "infection", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "immunodeficiency", "viruses", "viruslike", "particles", "immune...	2012	Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1
The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations . The rate constants found using this method agreed well with experimentally and theo...	We estimated the kon rate constant of four biochemically relevant ligand-receptor systems using milestoning theory . All results closely resemble experimentally and theoretically determined results , indicating that this technique may be applied toward accurate estimation of binding rate constants for additional ligand...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Mutations in GDAP1 , which encodes protein located in the mitochondrial outer membrane , cause axonal recessive ( AR-CMT2 ) , axonal dominant ( CMT2K ) and demyelinating recessive ( CMT4A ) forms of Charcot-Marie-Tooth ( CMT ) neuropathy . Loss of function recessive mutations in GDAP1 are associated with decreased mito...	Charcot-Marie-Tooth ( CMT ) disease is an inherited motor and sensory peripheral neuropathy . Mutations in the GDAP1 gene cause either an axonapathy or an myelinopathy that can be transmitted recessively or dominantly to offspring . GDAP1 is located in the mitochondrial outer membrane and seems to participate in the mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Lack of GDAP1 Induces Neuronal Calcium and Mitochondrial Defects in a Knockout Mouse Model of Charcot-Marie-Tooth Neuropathy
Neurotransmitter release depends on the fusion of secretory vesicles with the plasma membrane and the release of their contents . The final fusion step displays higher-order Ca2+ dependence , but also upstream steps depend on Ca2+ . After deletion of the Ca2+ sensor for fast release – synaptotagmin-1 – slower Ca2+-depe...	The release of neurotransmitter involves the rapid Ca2+-dependent fusion of vesicles with the plasma membrane . Kinetic heterogeneity is ubiquitous in secretory systems , with fast phases of release on the millisecond time scale being followed by slower phases . In the absence of synaptotagmin-1 – the Ca2+sensor for fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca2+-Dependent Priming Catalyst Effectively Explains Ca2+-Dependent Properties of Neurosecretion
Bacterial genomes typically consist of a single chromosome and , optionally , one or more plasmids . But whole-genome sequencing reveals about ten per-cent of them to be multipartite , with additional replicons which by size and indispensability are considered secondary chromosomes . This raises the questions of how th...	Unlike higher organisms , bacteria typically carry their genetic information on a single chromosome . But in a few bacterial families the genome includes one to three additional chromosome-like DNA molecules . Because these families are rich in pathogenic and environmentally versatile species , it is important to under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cell", "cycle", "and", "cell", "division", "plasmids", "cell", "processes", "pathogens", "microbiology", "vibrio", "plasmid", "construction", "vibrio", "cholerae", ...	2016	Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315
Kaposi’s sarcoma ( KS ) , a highly disseminated tumor of hyperproliferative spindle endothelial cells , is the most common AIDS-associated malignancy caused by infection of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) . KSHV-encoded viral interferon regulatory factor 1 ( vIRF1 ) is a viral oncogene but its role in ...	Kaposi's sarcoma-associated herpesvirus ( KSHV ) infection caused Kaposi’s sarcoma ( KS ) , a highly disseminated tumor that frequently occurs in patients with AIDS . KSHV-encoded viral interferon regulatory factor 1 ( vIRF1 ) is an oncogenic protein , which has been shown to be vital in KSHV evasion of innate antivira...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "motility", "luciferase", "gene", "regulation", "natural", "antisense", "transcripts", "enzymes", "enzymology", "long", "non-coding", "rnas", "developmental", "biology", "micrornas", "epigenetics", "dna", "molecular", "biology", "techniques", "dna", "methylation",...	2019	Oncogenic KSHV-encoded interferon regulatory factor upregulates HMGB2 and CMPK1 expression to promote cell invasion by disrupting a complex lncRNA-OIP5-AS1/miR-218-5p network
Most intracellular pathogens that reside in a vacuole prevent transit of their compartment to lysosomal organelles . Effector mechanisms induced by the pro-inflammatory cytokine Interferon-gamma ( IFNγ ) can promote the delivery of pathogen-occupied vacuoles to lysosomes for proteolytic degradation and are therefore im...	Coxiella burnetii is a mammalian pathogen that can cause a predominantly zoonotic disease called Q-fever . In humans , Q-fever manifests as an acute or chronic illness especially in immunocompromised individuals . C . burnetii is uniquely adapted to live in a lysosome-derived vacuole that degrades proteins and provides...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "lysosomes", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "intracellular", "pathogens", "hela", "cells", "gene", "regulation", "pathogens", "biological", "cultures", "microbiology", "organic", "compounds",...	2019	Host cell depletion of tryptophan by IFNγ-induced Indoleamine 2,3-dioxygenase 1 (IDO1) inhibits lysosomal replication of Coxiella burnetii
Genome-wide association studies have identified a wealth of genetic variants involved in complex traits and multifactorial diseases . There is now considerable interest in testing variants for association with multiple phenotypes ( pleiotropy ) and for testing multiple variants for association with a single phenotype (...	Pleiotropy appears when a variation in one gene affects to several non-related phenotypes . The study of this phenomenon can be useful in gene function discovery , but also in the study of the evolution of a gene . In this paper , we present a methodology , based on Canonical Correlation Analysis , which studies gene-c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "applied", "mathematics", "algorithms", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "trait", "locus", "analysis", "population", "biology", "biostatistics", "genetic", ...	2014	Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery
Planar cell polarity ( PCP ) instructs tissue patterning in a wide range of organisms from fruit flies to humans . PCP signaling coordinates cell behavior across tissues and is integrated by cells to couple cell fate identity with position in a developing tissue . In the fly eye , PCP signaling is required for the spec...	For functional tissues to form , individual cells must correctly orient themselves and function appropriately for their particular location in the body . The Planar Cell Polarity ( PCP ) complexes transmit one set of spatial cues by acting as signposts to mark direction across an epithelial layer . PCP signals can dire...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "rna", "interference", "social", "sciences", "cloning", "neuroscience", "pigments", "materials", "science", "molecular", "biology", "techniques", "epigenetics", "eyes", "research", "and", "analysis", "methods", ...	2018	Prickle is phosphorylated by Nemo and targeted for degradation to maintain Prickle/Spiny-legs isoform balance during planar cell polarity establishment
Copy number variants ( CNVs ) are a pervasive source of genetic variation and evolutionary potential , but the dynamics and diversity of CNVs within evolving populations remain unclear . Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation a...	Duplications and deletions of genomic sequence , known as copy number variants , are a common source of genetic diversity across all domains of life . Copy number variants play a crucial role in driving evolutionary processes but can also cause genetic disease and cancer . Although copy number variants are important dr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "and", "environmental", "sciences", "computational", "biology", "cloning", "fluorescence-activated", "cell", "sorting", "fungal", "evolution", "copy", "number", "variation", "molecular", "biology", "techniques", "evolutionary", "adaptation", "research", "and", ...	2018	Single-cell copy number variant detection reveals the dynamics and diversity of adaptation
The Dot/Icm type IVB secretion system ( T4BSS ) is a pivotal determinant of Legionella pneumophila pathogenesis . L . pneumophila translocate more than 100 effector proteins into host cytoplasm using Dot/Icm T4BSS , modulating host cellular functions to establish a replicative niche within host cells . The T4BSS core c...	Bacterial pathogens deliver virulence factors such as exotoxins and effector proteins to host cells . To accomplish this bacteria utilize specialized secretion systems such as type III and type IV secretion systems . The type IV secretion systems ( T4SS ) play a central role in pathogenesis by many important pathogens ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections" ]	2010	Crystal Structure of Legionella DotD: Insights into the Relationship between Type IVB and Type II/III Secretion Systems
The Long interspersed nuclear element 1 ( LINE-1 ) is a primary source of genetic variation in humans and other mammals . Despite its importance , LINE-1 activity remains difficult to study because of its highly repetitive nature . Here , we developed and validated a method called TeXP to gauge LINE-1 activity accurate...	Repetitive sequences , such as LINEs , comprise more than half of the human genome . Due to their repetitive nature , LINEs are hard to grasp . In particular , we find that pervasive transcription is a major confounding factor in transcriptome data . We observe that , on average , more than 90% of LINE signal derives f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "genetic", "fingerprinting", "cultured", "fibroblasts", "biological", "cultures", "human", "genomics", "dna", "transcription", "genetic", "elements", "molecular", "biology", "techniques", "rna", "sequencing", "research", "and", "analysis", "met...	2019	TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
In contrast to pathogenic HIV/SIV infections of humans and rhesus macaques ( RMs ) , natural SIV infection of sooty mangabeys ( SMs ) is typically non-pathogenic despite high viremia . Several studies suggested that low immune activation and relative resistance of CD4+ central memory T-cells from virus infection are me...	Sooty mangabey ( SM ) monkeys are an important model for studying HIV disease processes because they do not develop AIDS when infected with SIV , a primate version of HIV . The reasons why SIV-infected SMs remain healthy are not completely understood , but are related to reduced activation of the immune system , and to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "medicine", "infectious", "diseases", "inflammation", "cytokines", "immunity", "hiv", "innate", "immunity", "retrovirology", "and", "hiv", "immunopathogenesis", "immunology", "biology", "viral", "diseases", "immune", "system" ]	2013	Intact Type I Interferon Production and IRF7 Function in Sooty Mangabeys
Genotype I ( GI ) Japanese encephalitis virus ( JEV ) that replaced GIII virus has become the dominant circulating virus in Asia . Currently , all registered live and inactivated JEV vaccines are derived from genotype III viruses . In Taiwan , the compulsory JEV vaccination policy recommends that children receives four...	Genotype I ( GI ) Japanese encephalitis virus ( JEV ) that replaced GIII virus has become the dominant circulating virus in Asia; however , all available JEV vaccines are derived from genotype III viruses , and no study has been conducted on the cross-neutralization and protection elicited by GIII JEV vaccines against ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "viral", "vaccines", "clinical", "immunology", "immunity", "virology", "immunology", "biology", "microbiology" ]	2012	Partially Neutralizing Potency against Emerging Genotype I Virus among Children Received Formalin-Inactivated Japanese Encephalitis Virus Vaccine
MicroRNAs are short , noncoding RNAs that play important roles in post-transcriptional gene regulation . Although many functions of microRNAs in plants and animals have been revealed in recent years , the transcriptional mechanism of microRNA genes is not well-understood . To elucidate the transcriptional regulation of...	MicroRNAs are a class of short RNA sequences that have many regulatory functions in complex organisms such as plants and animals . However , our knowledge of the transcriptional mechanisms of microRNA genes is limited . Here , we analyze the upstream sequences of known microRNA genes in four model species , i . e . , C...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "oryza", "caenorhabditis", "arabidopsis", "computational", "biology", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Characterization and Identification of MicroRNA Core Promoters in Four Model Species
The transduction of sound in the auditory periphery , the cochlea , is inhibited by efferent cholinergic neurons projecting from the brainstem and synapsing directly on mechanosensory hair cells . One fundamental question in auditory neuroscience is what role ( s ) this feedback plays in our ability to hear . In the pr...	Nicotinic cholinergic receptors are essential to higher order brain function . Structurally , these operate through a myriad of ligand-gated pentameric arrangements of different homologous subunits . Here , we report progress in understanding the structural properties of a neuronal nicotinic receptor at the synapse . R...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "physiology" ]	2009	A Point Mutation in the Hair Cell Nicotinic Cholinergic Receptor Prolongs Cochlear Inhibition and Enhances Noise Protection
The cellular response elicited by an environmental cue typically varies with the strength of the stimulus . For example , in the yeast Saccharomyces cerevisiae , the concentration of mating pheromone determines whether cells undergo vegetative growth , chemotropic growth , or mating . This implies that the signaling pa...	Cells must be able to detect and respond to changes in their surroundings . Often environmental cues , such as hormones or growth factors , are received by membrane receptors that in turn activate intracellular signaling pathways . These pathways then transmit information about the stimulus to the cellular components r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "signaling", "physiology/cell", "signaling", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "pharmacology", "biotechnology/bioengineering", "computational", "biology", "computational", "biology/signaling", "networks", "biophysics/cell"...	2008	Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks
Human and animal African trypanosomiasis ( HAT & AAT , respectively ) remain a significant health and economic issue across much of sub-Saharan Africa . Effective control of AAT and potential eradication of HAT requires affordable , sensitive and specific diagnostic tests that can be used in the field . Small RNAs in t...	African trypanosomes cause significant disease in humans and animals across sub-Saharan Africa . For both human and animal infections diagnostics that can accurately identify an active infection are lacking–this is particularly the case in animal disease where most diagnosis is based upon clinical signs , which is not ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ruminants", "trypanosoma", "congolense", "rna", "extraction", "vertebrates", "parasitic", "diseases", "parasitic", "protozoans", "mammals", "animals", "parasitology", "trypanosoma", "brucei", "protozoans", "extraction", "techniques"...	2019	Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection
Excitatory synapses on mammalian principal neurons are typically formed onto dendritic spines , which consist of a bulbous head separated from the parent dendrite by a thin neck . Although activation of voltage-gated channels in the spine and stimulus-evoked constriction of the spine neck can influence synaptic signals...	The vast majority of excitatory synapses in the mammalian central nervous system are made onto dendritic spines , small ( < 1 fL ) membranous structures stippled along the dendrite . The head of each spine is separated from its parent dendrite by a thin neck – a morphological feature that intuitively suggests it might ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms" ]	2009	Biphasic Synaptic Ca Influx Arising from Compartmentalized Electrical Signals in Dendritic Spines
The common pathogen Epstein-Barr virus ( EBV ) transforms normal human B cells and can cause cancer . Latent membrane protein 2A ( LMP2A ) of EBV supports activation and proliferation of infected B cells and is expressed in many types of EBV-associated cancer . It is not clear how latent EBV infection and cancer escape...	Epstein-Barr virus ( EBV ) is carried by most humans . It can cause several types of cancer . In healthy infected people , EBV persists for life in a "latent" state in white blood cells called B cells . For infected persons to remain healthy , it is crucial that they harbor CD8-positive "killer" T cells that recognize ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Latent Membrane Protein LMP2A Impairs Recognition of EBV-Infected Cells by CD8+ T Cells
Under normal conditions the immune system has limited access to the brain; however , during toxoplasmic encephalitis ( TE ) , large numbers of T cells and APCs accumulate within this site . A combination of real time imaging , transgenic reporter mice , and recombinant parasites allowed a comprehensive analysis of CD11...	Toxoplasmic encephalitis ( TE ) , caused by the protozoan parasite Toxoplasma gondii , can be potentially life threatening especially in immuno-compromised individuals . Immune cells including dendritic cells have been shown to accumulate in the brain during chronic toxoplasmosis; however , little is known about their ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Analysis of Behavior and Trafficking of Dendritic Cells within the Brain during Toxoplasmic Encephalitis
Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations . Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change . However , attempts to assess the prevalence of stable epigenetic variation in natu...	DNA methylation is defined as an epigenetic modification because it can be inherited across cell division . Since variations in DNA methylation can affect gene expression and be inherited across generations , they can provide a source of heritable phenotypic variation that is not caused by changes in the DNA sequence ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "plant", "biology/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/complex", "traits", "plant", "biology/agricultural", "biotechnology", "evolutionary", "biology/genomics", "plant", "biology", "molecular", ...	2009	Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits
Although the genome contains all the information necessary for maintenance and perpetuation of life , it is the proteome that repairs , duplicates and expresses the genome and actually performs most cellular functions . Here we reveal strong phenotypes of physiological oxidative proteome damage at the functional and ge...	Cellular life is maintained by the activities of proteins that , together , prevent molecular damage from occurring in the first place and repair damaged DNA , proteins and other damaged cellular components . Cellular fitness decreases due to the fact that these proteins are themselves subject to damage , leading to th...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Phenotypic and Genetic Consequences of Protein Damage
The circuit organization within the mammalian brainstem respiratory network , specifically within and between the pre-Bötzinger ( pre-BötC ) and Bötzinger ( BötC ) complexes , and the roles of these circuits in respiratory pattern generation are continuously debated . We address these issues with a combination of optog...	We investigated the organization of key circuits within the brainstem respiratory central pattern generator ( CPG ) responsible for generating the basic breathing pattern in mammals . Our study focused on the organization and interactions of two core components of this CPG: the pre-Bötzinger ( pre-BötC ) and Bötzinger ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "optogenetics", "chemical", "compounds", "neural", "networks", "engineering", "and", "technology", "aliphatic", "amino", "acids", "lasers", "brain", "light", "neuroscience", "organic", "compounds", "electromagneti...	2018	Organization of the core respiratory network: Insights from optogenetic and modeling studies
Invariant Natural Killer T cells ( iNKT ) are a versatile lymphocyte subset with important roles in both host defense and immunological tolerance . They express a highly conserved TCR which mediates recognition of the non-polymorphic , lipid-binding molecule CD1d . The structure of human iNKT TCRs is unique in that onl...	Our immune system uses randomly modified T-cell receptors ( TCRs ) to adapt its discriminative capacity to rapidly changing pathogens . The T-cell receptor ( TCR ) has six flexible , variable peptide loops that make contact with antigens presented to them on the surface of other cells . Invariant Natural Killer T-cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "immunology/antigen", "processing", "and", "recognition", "immunology/autoimmunity", "immunology/innate", "immunity" ]	2010	Innate-Like Control of Human iNKT Cell Autoreactivity via the Hypervariable CDR3β Loop
European population genetic substructure was examined in a diverse set of >1 , 000 individuals of European descent , each genotyped with >300 K SNPs . Both STRUCTURE and principal component analyses ( PCA ) showed the largest division/principal component ( PC ) differentiated northern from southern European ancestry . ...	Ancestry differences corresponding to ethnic groups may be important in determining disease risk factors and optimizing treatment . Our study further defines ancestry relationship among different European ethnic groups by examining over 300 thousand variations in DNA , in over 2 , 000 individuals . This study allowed a...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2008	Analysis and Application of European Genetic Substructure Using 300 K SNP Information
In response to DNA damage , the eukaryotic genome surveillance system activates a checkpoint kinase cascade . In the fission yeast Schizosaccharomyces pombe , checkpoint protein Crb2 is essential for DNA damage-induced activation of downstream effector kinase Chk1 . The mechanism by which Crb2 mediates Chk1 activation ...	To preserve the integrity of genomic DNA , eukaryotic cells use a genome surveillance system to detect DNA damage and send a signal to prevent cell division before DNA repair has been completed . This signal transduction mechanism is called checkpoint signaling and is conserved from yeasts to humans . A key checkpoint ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "signaling", "in", "cellular", "processes", "biology", "molecular", "cell", "biology", "molecular", "biology" ]	2012	Phosphorylation-Dependent Interactions between Crb2 and Chk1 Are Essential for DNA Damage Checkpoint
Genomic disorders are often caused by recurrent copy number variations ( CNVs ) , with nonallelic homologous recombination ( NAHR ) as the underlying mechanism . Recently , several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining ( MMEJ ) , fork stalling and template switching ( FoSTe...	Genomic disorder is a general term describing conditions caused by genomic aberrations leading to a copy number change of one or more genes . Copy number changes with the same length and clustered breakpoints for a group of patients with the same disorder are named recurrent rearrangements . These originate mostly from...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "molecular", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2013	Microhomology-Mediated Mechanisms Underlie Non-Recurrent Disease-Causing Microdeletions of the FOXL2 Gene or Its Regulatory Domain
Plexins are cell surface receptors for the semaphorin family of cell guidance cues . The cytoplasmic region comprises a Ras GTPase-activating protein ( GAP ) domain and a RhoGTPase binding domain . Concomitant binding of extracellular semaphorin and intracellular RhoGTPase triggers GAP activity and signal transduction ...	Axon guidance is fundamental to the development of the central nervous system . The growing axon is guided to its correct location by a plethora of extracellular signals . One of the most important extracellular signals is semaphorin , which binds to plexin receptors on the axon . Usually , this kind of extracellular l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "protein", "interactions", "mechanisms", "of", "signal", "transduction", "signaling", "in", "selected", "disciplines", "neuroscience", "gtpase", "signaling", "developmental", "signaling", "cell", "movement", "signaling", "protein", "structure", ...	2011	A Dual Binding Mode for RhoGTPases in Plexin Signalling
The microRNA ( miRNA ) let-7 is an important miRNA identified in Caenorhabditis elegans and has been shown to be involved in the control of innate immunity . The underlying molecular mechanisms for let-7 regulation of innate immunity remain largely unclear . In this study , we investigated the molecular basis for intes...	Some microRNAs ( miRNAs ) have been identified recently to play important roles in the regulation of innate immunity in Caenorhabditis elegans . let-7 is one of important miRNAs identified to be involved in the control of innate immune response . However , the underlying molecular mechanism for let-7 in the regulation ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "rna", "interference", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "pseudomonas", "aeruginosa", "nematode", ...	2017	Molecular Control of Innate Immune Response to Pseudomonas aeruginosa Infection by Intestinal let-7 in Caenorhabditis elegans
Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes . Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity . We measur...	Different developmental environments change how genes are expressed and what phenotypes are produced . Here we examine how the responsiveness of gene expression to different environments ( “expression plasticity” ) evolves in populations adapted to constant environments or heterogeneous ones ( temporal or spatial heter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "sodium", "chloride", "salts", "diet", "developmental", "biology", "nutrition", "evolutionary", "adaptation", "cadmium", "gene", "expression", "life", "cycles", "chemistry", "evolutionary", "genetics", "g...	2016	Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes
Dengue virus ( DENV ) causes the most prevalent arthropod-borne viral disease in humans . Although Aedes mosquitoes transmit DENV when probing for blood in the skin , no information exists on DENV infection and immune response in the dermis , where the blood vessels are found . DENV suppresses the interferon response ,...	The skin and its immune cells are an important barrier against invading pathogens . Dengue is a major public health problem worldwide , with no specific therapeutic or vaccine available . Aedes mosquitoes transmit dengue virus ( DENV ) to humans via the skin when taking a blood meal . Previous studies have examined DEN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "blood", "cells", "langerhans", "cells", "dermatology", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "integumentary", "system", "antigen-presenting", "cells", "immunology", "animal", "models", "dendritic", "cells", "infectious...	2014	Monocyte Recruitment to the Dermis and Differentiation to Dendritic Cells Increases the Targets for Dengue Virus Replication
Cell division and development are regulated by networks of kinases and phosphatases . In early Drosophila embryogenesis , 13 rapid nuclear divisions take place in a syncytium , requiring fine coordination between cell cycle regulators . The Polo kinase is a conserved , crucial regulator of M-phase . We have recently re...	The development and survival of all living organisms relies on the fine regulation of cell division at the molecular level . This coordination depends on kinases and phosphatases , enzymes that catalyze the addition and removal of phosphate groups on specific target proteins . The genes encoding these enzymes have been...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "cellular", "structures", "gene", "function", "animal", "models", "mitosis", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "cell", "division", "molecular", "development", "molecular", "genetics", "cell", "nucleus", "cytoskeleto...	2011	PP2A-Twins Is Antagonized by Greatwall and Collaborates with Polo for Cell Cycle Progression and Centrosome Attachment to Nuclei in Drosophila Embryos
Next-generation sequencing of the exome and genome of prostate cancers has identified numerous genetic alternations . SPOP ( Speckle-type POZ Protein ) was one of the most frequently mutated genes in primary prostate cancer , suggesting SPOP is a potential driver of prostate cancer development and progression . However...	Prostate cancer is the leading cause of global cancer-related death . The development of improved diagnoses and novel therapies has been confounded by significant patient heterogeneity . During recent years , significant progress has been made in identifying the molecular alterations in prostate cancer using next-gener...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urology", "cell", "motility", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cancer", "cell", "migration", "293t", "cells", "pathogens", "biological", "cultures", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumor...	2017	Dysregulation of INF2-mediated mitochondrial fission in SPOP-mutated prostate cancer
Chronic infections are an increasing problem due to the aging population and the increase in antibiotic resistant organisms . Therefore , understanding the host-pathogen interactions that result in chronic infection is of great importance . Here , we investigate the molecular basis of chronic bacterial cystitis . We es...	The natural history of urinary tract infection ( UTI ) with uropathogenic E . coli in humans frequently includes persistent bacterial shedding in the urine for weeks after the initial infection , despite varying degrees of improvement of symptoms . Although antibiotic treatment has been very successful in treating UTI ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/urological", "infections", "infectious", "diseases", "microbiology/immunity", "to", "infections", "immunology/immune", "response", "microbiology/innate", "immunity", "immunology/innate", "immunity...	2010	Early Severe Inflammatory Responses to Uropathogenic E. coli Predispose to Chronic and Recurrent Urinary Tract Infection
Identification of novel cellular proteins as substrates to viral proteases would provide a new insight into the mechanism of cell–virus interplay . Eight nuclear proteins as potential targets for enterovirus 71 ( EV71 ) 3C protease ( 3Cpro ) cleavages were identified by 2D electrophoresis and MALDI-TOF analysis . Of th...	Many viruses contain specific proteases that are essential for processing their own viral proteins . For an efficient replication within their hosts , on the other hand , viruses also utilize these proteases to cleave a number of key host proteins and hijack cellular machineries . In this study , host proteins are iden...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology" ]	2009	Enterovirus 71 3C Protease Cleaves a Novel Target CstF-64 and Inhibits Cellular Polyadenylation
Gastropod-borne parasites may cause debilitating clinical conditions in animals and humans following the consumption of infected intermediate or paratenic hosts . However , the ingestion of fresh vegetables contaminated by snail mucus and/or water has also been proposed as a source of the infection for some zoonotic me...	Gastropod-borne parasites may cause debilitating clinical conditions in animals and humans . The infection occurs by consumption of intermediate hosts ( i . e . , snails ) . However , the ingestion of fresh vegetables contaminated by water and/or snail mucus has been proposed as a transmission source for some zoonotic ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Release of Lungworm Larvae from Snails in the Environment: Potential for Alternative Transmission Pathways
Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp . ( leishmaniasis ) , Trypanosoma brucei ( sleeping sickness ) , and Trypanosoma cruzi ( Chagas disease ) . Analysis of their recently completed genomes confirmed the presence of non–long-terminal repeat retrotransposons , also cal...	Transposable elements ( TEs ) are DNA sequences capable of moving from one chromosomal region to another . A considerable fraction of higher eukaryote genomes is comprised of TEs , as exemplified in human ( over 40% of the genome ) and maize ( over 50% of the genome ) . There is now a growing body of evidence to sugges...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "trypanosoma)", "microbiology", "computational", "biology", "evolutionary", "biology", "molecular", "biology", "kinetoplastid", "(leishmania" ]	2007	Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in Leishmania
Immunization vectors based on cytomegalovirus ( CMV ) have attracted a lot of interest in recent years because of their high efficacy in the simian immunodeficiency virus ( SIV ) macaque model , which has been attributed to their ability to induce strong , unusually broad , and unconventionally restricted CD8+ T cell r...	CMV-based vectors have attracted a lot of attention in the vaccine development field , since they were shown to induce unconventionally restricted CD8+ T cell responses and strong protection in the SIV rhesus macaque model . In a mouse retrovirus model , we show now that immunization with a mouse CMV-based vector encod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "animal", "models", "model", "organisms", "experimental", "organism", "systems", ...	2019	Immunization with a murine cytomegalovirus based vector encoding retrovirus envelope confers strong protection from Friend retrovirus challenge infection
The rhl quorum-sensing ( QS ) system plays critical roles in the pathogenesis of P . aeruginosa . However , the regulatory effects that occur directly upstream of the rhl QS system are poorly understood . Here , we show that deletion of gene encoding for the two-component sensor BfmS leads to the activation of its cogn...	The rhl quorum-sensing ( QS ) system allows P . aeruginosa to regulate diverse metabolic adaptations and virulence . However , how rhl QS system is regulated remains largely unknown . Here , we report that two-component sensor BfmS controls rhl QS system by repressing its cognate response regulator BfmR , which directl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biology", "and", "life", "sciences", "microbiology" ]	2014	A Novel Signal Transduction Pathway that Modulates rhl Quorum Sensing and Bacterial Virulence in Pseudomonas aeruginosa
With the approach of winter , many insects switch to an alternative protective developmental program called diapause . Drosophila melanogaster females overwinter as adults by inducing a reproductive arrest that is characterized by inhibition of ovarian development at previtellogenic stages . The insulin producing cells...	Diapause is a hormonally mediated process that allows insects to predict and respond to unfavourable conditions by altering their metabolism and behavior to resist the oncoming environmental challenges . In Drosophila melanogaster females a protective state of reproductive dormancy is induced by lower temperatures and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neurochemistry", "diabetic", "endocrinology", "neuroscience", "animals", "hormones", "animal", "models", "fluorophotometry", "physiological", "processes", "developmental", "biology", "drosophila", "melanogaster", "mod...	2019	Peptidergic signaling from clock neurons regulates reproductive dormancy in Drosophila melanogaster
In Caenorhabditis elegans the Toll-interleukin receptor domain adaptor protein TIR-1 via a conserved mitogen-activated protein kinase ( MAPK ) signaling cascade induces innate immunity and upregulates serotonin ( 5-HT ) biosynthesis gene tph-1 in a pair of ADF chemosensory neurons in response to infection . Here , we i...	Toll-interleukin receptor ( TIR ) –domain adaptor proteins are keys to activate signaling cascades inducing transcriptional responses to internal and external pathogenic signals in evolutionary disparate organisms . Despite lacking a homolog of the mammalian innate immunity transcriptional regulator nuclear factor-kapp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "genetic", "mutation", "gene", "regulation", "immunology", "neuroscience", "gene", "function", "molecular", "genetics", "neurotransmitters", "gene", "expression", "biology", "genetics", "of", "the", "immune", "system", "genetic", "screens", ...	2013	RFX Transcription Factor DAF-19 Regulates 5-HT and Innate Immune Responses to Pathogenic Bacteria in Caenorhabditis elegans
Hantaan virus ( HTNV ) infection in humans is a serious public health concern in Asia . A potent T cell activation peptide vaccine from HTNV structure protein represents a promising immunotherapy for disease control . However , the T cell epitopes of the HTNV restricted by the HLA alleles and the role of epitope-specif...	Hantaan virus ( HTNV ) , the prototype of the Hantavirus genus , is a rodent-borne pathogen that causes human hemorrhagic fever with renal syndrome ( HFRS ) with a mortality rate of approximately 15% in Asia . Since effective prevention is not available currently and the non-specific symptoms at the early stage of the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "viral", "hemorrhagic", "fevers", "infectious", "diseases", "hemorrhagic", "fever", "with", "renal", "syndrome", "adaptive", "immunity", "immunity", "virology", "neglected", "tropical", "diseases", "biology", "microbiology", "host-pathogen", "interaction", "vi...	2013	HLA-A2 and B35 Restricted Hantaan Virus Nucleoprotein CD8+ T-Cell Epitope-Specific Immune Response Correlates with Milder Disease in Hemorrhagic Fever with Renal Syndrome
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body . Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling exponents to quantify these changes . Prominent sca...	Vascular networks distribute resources and constrain metabolic rate . Founded on a few key principles , biological scaling theories predict characteristic patterns for vascular networks as they branch from large to small vessels . These theories also predict seemingly unrelated phenomena , such as size limits on mammal...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Methods", "and", "Materials" ]	[]	2015	Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
Migrating cells are guided in complex environments mainly by chemotaxis or structural cues presented by the surrounding tissue . During transmission of malaria , parasite motility in the skin is important for Plasmodium sporozoites to reach the blood circulation . Here we show that sporozoite migration varies in differ...	Guidance of motile cells plays an important role during the life of a multi-cellular organism from early embryogenesis to the intricate interactions of immune cells during an infection . These migrations , like those of pathogens , can be directed by both chemical and physical cues . The malaria parasite needs to migra...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "medicine", "cell", "motility", "biological", "data", "management", "parasitic", "diseases", "parasitology", "zoology", "infectious", "diseases", "cell", "adhesion", "biology", "vectors", "and", "hosts", "biophysics", "physics", "cell", "biology", "malaria", "computatio...	2011	Environmental Constraints Guide Migration of Malaria Parasites during Transmission
Stoichiometric balance , or dosage balance , implies that proteins that are subunits of obligate complexes ( e . g . the ribosome ) should have copy numbers expressed to match their stoichiometry in that complex . Establishing balance ( or imbalance ) is an important tool for inferring subunit function and assembly bot...	Protein copy numbers are often found to be stoichiometrically balanced for subunits of multi-protein complexes . Imbalance is believed to be deleterious because it lowers complex yield ( the dosage balance hypothesis ) and increases the risk of misinteractions , but imbalance may also provide unexplored functional bene...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "characterization", "vesicles", "protein", "interactions", "protein", "interaction", "networks", "cell", "processes", "membrane", "proteins", "network", "analysis", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "cell"...	2018	Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world . The HrpL sigma factor drives expression of the major P . syringae virulence regulon . HrpL controls expression of the genes encoding the structural and functional compon...	Pseudomonas syringae are environmentally ubiquitous bacteria of wide phylogenetic distribution , which can cause disease on a broad range of plant species . Pathogenicity requires the master regulator HrpL . HrpL controls the activation of virulence factor genes , including those encoding the type III secretion system ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny
The discovery of the life-threatening zoonotic infection Plasmodium knowlesi has added to the challenges of prompt and accurate malaria diagnosis and surveillance . In this study from Aceh Province , Indonesia , a malaria elimination setting where P . knowlesi endemicity was not previously known , we report the laborat...	In Southeast Asia , Plasmodium knowlesi , a malaria parasite of macaques , was recently discovered to infect humans . This emerging disease is important because it has potential for causing severe disease and death , and it is a threat to malaria elimination efforts in the region . In this report from Aceh Province , I...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusions" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "tropical", "diseases", "geographical", "locations", "vertebrates", "parasitic", "diseases", "parasitic", "protozoans", "animals", "parasitology", "mammals", "indonesia", "primates", "apicomplexa",...	2018	Laboratory challenges of Plasmodium species identification in Aceh Province, Indonesia, a malaria elimination setting with newly discovered P. knowlesi
Duplications at 15q11 . 2-q13 . 3 overlapping the Prader-Willi/Angelman syndrome ( PWS/AS ) region have been associated with developmental delay ( DD ) , autism spectrum disorder ( ASD ) and schizophrenia ( SZ ) . Due to presence of imprinted genes within the region , the parental origin of these duplications may be ke...	The genetic interval 15q11 . 2-q13 . 3 on human chromosome 15 contains several so-called “imprinted genes” which are subject to epigenetic marking leading to activity from only one parental copy . This is in contrast to non-imprinted genes , whose activity is independent of their parent-of-origin . Deletions affecting ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuropsychiatric", "disorders", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "adhd", "prader-willi", "syndrome", "angelman", "syndrome", "social", "sciences", "developmental", "psychology", "neuroscience", "disorders", "of", "imp...	2016	Parental Origin of Interstitial Duplications at 15q11.2-q13.3 in Schizophrenia and Neurodevelopmental Disorders
Class switch recombination ( CSR ) requires activation-induced cytidine deaminase ( AID ) to trigger DNA double strand breaks ( DSBs ) at the immunoglobulin heavy chain ( IGH ) in B cells . Joining of AID-dependent DSBs within IGH facilitate CSR and effective humoral immunity , but ligation to DSBs in non-IGH chromosom...	The production of different classes of antibodies/immunoglobulins ( IgM , IgG , etc . ) is essential for protection against diverse pathogens and effective immunity . This cellular process is triggered by the enzyme activation-induced cytidine deaminase ( AID ) . AID mutates DNA predominantly in antibody genes , genera...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "surgical", "and", "invasive", "medical", "procedures", "sequence", "motif", "analysis", "dna", "mammalian", "genomics", "research", "and", "analysis", "methods", "sequence", ...	2019	DSB structure impacts DNA recombination leading to class switching and chromosomal translocations in human B cells
Mali has become increasingly interested in the evaluation of transmission of both Wuchereria bancrofti and Onchocerca volvulus as prevalences of both infections move toward their respective elimination targets . The SD Bioline Onchocerciasis/LF IgG4 Rapid Test was used in 2 evaluation units ( EU ) to assess its perform...	After years of mass drug administration for lymphatic filariasis and onchocerciasis , many co-endemic countries need to demonstrate the interruption of transmission of these parasitic infections . This interruption of transmission is the key to stopping mass drug administration . One of the major challenges facing nati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "mali", "onchocerca", "volvulus", "immune", "physiology", "helminths", "immunology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "onchocerca", "filariasis", "pharmaceutics...	2019	Integrated seroprevalence-based assessment of Wuchereria bancrofti and Onchocerca volvulus in two lymphatic filariasis evaluation units of Mali with the SD Bioline Onchocerciasis/LF IgG4 Rapid Test
Neutrophil extracellular traps ( NETs ) comprise an ejected lattice of chromatin enmeshed with granular and nuclear proteins that are capable of capturing and killing microbial invaders . Although widely employed to combat infection , the antimicrobial mechanism of NETs remains enigmatic . Efforts to elucidate the bact...	Comprising the first line of the innate immune response , neutrophils combat infectious microorganisms through the release of toxic molecules , phagocytosis of invaders and the production of the recently characterized neutrophil extracellular traps ( NETs ) . The antimicrobial activity of NETs has been attributed to pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	DNA Is an Antimicrobial Component of Neutrophil Extracellular Traps
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates . While the impact of localization and recruitment on kinase–substrate targeting can be readily assessed , evaluating the relative importance of direct phosphorylation site interac...	Protein kinases , which catalyze the transfer of phosphate from ATP to substrate proteins , are important enzymes in cellular signal transduction pathways mediating responses to extracellular cues . In order to function properly in signal transmission , each kinase must phosphorylate only a limited number of proteins a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "protein", "interactions", "molecular", "probe", "techniques", "enzymes", "enzymology", "immunoblotting", "plasmid", "construction", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "dna", "construction", "research", "and", "analysis...	2019	Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease that was recently identified in China , South Korea and Japan . The objective of the study was to evaluate the epidemiologic and clinical characteristics of SFTS in South Korea . SFTS is a reportable disease in South Korea . We inclu...	Severe fever with thrombocytopenia ( SFTS ) is an emerging infectious disease that was first discovered in China in 2009 . Subsequently , SFTS has also been found in South Korea and Japan . Here , we report the epidemiologic and clinical characteristics of 172 confirmed SFTS cases in South Korea that occurred since the...	[ "Abstract", "Introduction", "Patients", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "c-reactive", "proteins", "clinical", "laboratory", "sciences", "ixodes", "pathology", "and", "laboratory", "medicine", "china", "geographical", "locations", "animals", "signs", "and", "symptoms", "nosocomial", "...	2016	Severe Fever with Thrombocytopenia Syndrome in South Korea, 2013-2015
The sleep onset process ( SOP ) is a dynamic process correlated with a multitude of behavioral and physiological markers . A principled analysis of the SOP can serve as a foundation for answering questions of fundamental importance in basic neuroscience and sleep medicine . Unfortunately , current methods for analyzing...	How can we tell when someone has fallen asleep ? Understanding the way we fall asleep is an important problem in sleep medicine , since sleep disorders can disrupt the process of falling asleep . In the case of insomnia , subjects may fall asleep too slowly , whereas during sleep deprivation or narcolepsy , subjects fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physiological", "processes", "medicine", "and", "health", "sciences", "mathematics", "statistics", "(mathematics)", "computational", "neuroscience", "physiology", "sleep", "mathematical", "and", "statistical", "techniques", "biology", "and", "life", "sciences", "physical",...	2014	Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics
The effects of various dengue control measures have been investigated in previous studies . The aim of this review was to investigate the relative effectiveness ( RE ) of different educational messages embedded in a community-based approach on the incidence of Aedes aegypti larvae using entomological measures as outcom...	Dengue fever is a mosquito-borne viral infection that is widespread in the tropics . Each year there are an estimated 50 million infections worldwide . Preventing infection relies on controlling the mosquitoes that spread disease . Unfortunately it is still not clear what does and does not work in the control of the mo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "mosquitoes", "health", "screening", "disease", "ecology", "public", "health", "and", "epidemiology", "global", "health", "dengue", "fever", "neglected", "tropical", "diseases", "vectors", "and", "hosts", "public", "health" ]	2011	The Value of Educational Messages Embedded in a Community-Based Approach to Combat Dengue Fever: A Systematic Review and Meta Regression Analysis
Genome and exome sequencing in large cohorts enables characterization of the role of rare variation in complex diseases . Success in this endeavor , however , requires investigators to test a diverse array of genetic hypotheses which differ in the number , frequency and effect sizes of underlying causal variants . In t...	Re-sequencing technologies allow for a more complete interrogation of the role of human variation in complex disease . The inadequate power of single variant methods to assess the role of less common variation has led to the development of numerous statistical methods for testing aggregate groups of variants for associ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease
Hansen’s disease ( HD ) , or leprosy , is still considered a public health risk in much of Brazil . Understanding the dynamics of the infection at a regional level can aid in identification of targets to improve control . A compartmental continuous-time model for leprosy dynamics was designed based on understanding of ...	Control of Hansen’s disease , or leprosy , requires understanding how quickly the infection moves through the population and how long it takes to detect the disease . These rates vary regionally , resulting in differences in the number of people detected with disease each year . We have estimated the risk of infection ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "pharmacologic", "analysis", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "demography", "tropical", "diseases", "geographical", "locations", "factor", "analysis", "bacterial", "diseases", "compartment", "models", "mathematics", "st...	2016	Proposing a Compartmental Model for Leprosy and Parameterizing Using Regional Incidence in Brazil
The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem , considered by both cytogeneticists and bioinformaticians . A comparison of the two approaches was recently investigated and discussed in a series of papers , sometimes with diverging ...	No DNA molecule is preserved after a few hundred thousand years , so inferring the DNA sequence organization of ancient living organisms beyond several million years can only be achieved by computational estimations , using the similarities and differences between chromosomes of extant species . This is the scope of “p...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods", "Acknowledgments" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/bioinformatics", "computational", "biology/genomics" ]	2008	A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes
There are various factors which construct the perception of stigma in both leprosy affected persons and unaffected persons . The main purpose of this study was to determine the level of perceived stigma and the risk factors contributing to it among leprosy affected person attending the Green Pastures Hospital , Pokhara...	A total of 135 leprosy affected persons were interviewed with a questionnaire containing EMIC questions designed to assess the level of perceived stigma and the questionnaire containing variables for socio-demographic characteristics , knowledge about leprosy and the clinical presentations of the participants . Clinica...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "social", "sciences" ]	2014	Factors Affecting Perceived Stigma in Leprosy Affected Persons in Western Nepal

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