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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
We present the results of a model inversion algorithm for electrocorticography ( ECoG ) data recorded during epileptic seizures . The states and parameters of neural mass models were tracked during a total of over 3000 seizures from twelve patients with focal epilepsy . These models provide an estimate of the effective...	A fundamental question in clinical neuroscience is how and why the brain generates epileptic seizures . To address this problem it is important to unify theoretical models of seizure mechanisms with clinical data . This study investigated a large database of human epileptic seizure recordings . Model inversion was used...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "mechanisms", "of", "signal", "transduction", "applied", "mathematics", "membrane", "potential", "brain", "electrophysiology", "electrophysiology", "random", "variables", "neuroscience", "covariance", "epileptic", "seizures", "algori...	2018	Seizure pathways: A model-based investigation
Sleep is critical for hippocampus-dependent memory consolidation . However , the underlying mechanisms of synaptic plasticity are poorly understood . The central controversy is on whether long-term potentiation ( LTP ) takes a role during sleep and which would be its specific effect on memory . To address this question...	Sleep is important for long lasting memories . There exists , however , a controversy regarding the mechanisms by which sleep modifies synapses to consolidate enduring memories . One theory posits that sleep weakens synapses , leading to the forgetting of all but the strongest memories . The alternative theory proposes...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle
Expression from the HIV-1 LTR can be repressed in a small population of cells , which contributes to the latent reservoir . The factors mediating this repression have not been clearly elucidated . We have identified a network of nuclear RNA surveillance factors that act as effectors of HIV-1 silencing . RRP6 , MTR4 , Z...	Following integration into the host genome , HIV-1 expression is silenced in a small population of cells , largely via epigenetic mechanisms that repress LTR-mediated transcription . This repression creates a reservoir of cells that prevent an effective cure . It is unclear how and why integrated HIV-1 becomes transcri...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "microbiology", "immunoblotting", "dna", "transcription", "retroviruses", "viruse...	2018	Nuclear RNA surveillance complexes silence HIV-1 transcription
Vertebrate limb outgrowth is driven by a positive feedback loop that involves Sonic hedgehog ( Shh ) and Gremlin1 ( Grem1 ) in the posterior limb bud mesenchyme and Fibroblast growth factors ( Fgfs ) in the overlying epithelium . Proper spatio-temporal control of these signaling activities is required to avoid limb mal...	Developmental defects of the limb skeleton , such as variations from the normal number of digits , can result from an abnormal size of the early limb bud . The mechanisms that restrict limb bud growth to avoid polydactyly , i . e . the formation of extra digits , are unclear . Gremlin 1 ( Grem1 ) has been identified as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "musculoskeletal", "system", "bone", "birth", "defects", "molecular", "development", "gene", "regulation", "genetics", "gene", "expression", "molecular", "genetics", "musculoskeletal", "anatomy", "biology", "anatomy", "and", "physiology", "cart...	2013	Tbx2 Terminates Shh/Fgf Signaling in the Developing Mouse Limb Bud by Direct Repression of Gremlin1
Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions . Conjugation allows the broadest range and the highest gene transfer input per transfer event . While conjugative plasmids have been studied for decades , the number and diversity of integrative conjuga...	Some mobile genetic elements spread genetic information horizontally between prokaryotes by conjugation , a mechanism by which DNA is transferred directly from one cell to the other . Among the processes allowing genetic transfer between cells , conjugation is the one allowing the simultaneous transfer of larger amount...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genomics", "genome", "evolution", "heredity", "genetics", "molecular", "genetics", "biology", "gene", "flow", "microbiology", "bacterial", "evolution", "genetics", "and", "genomics" ]	2011	The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation
A three-stage genome-wide association study recently identified single nucleotide polymorphisms ( SNPs ) in five loci ( fibroblast growth receptor 2 ( FGFR2 ) , trinucleotide repeat containing 9 ( TNRC9 ) , mitogen-activated protein kinase 3 K1 ( MAP3K1 ) , 8q24 , and lymphocyte-specific protein 1 ( LSP1 ) ) associated...	This report from the Breast Cancer Association Consortium evaluates whether common variants in five recently identified breast cancer susceptibility loci ( FGFR2 , TNRC9 , MAP3K1 , 8q24 , and LSP1 ) influence the clinical presentation of breast cancer and survival after diagnosis . We studied these susceptibility loci ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "oncology/breast", "cancer" ]	2008	Heterogeneity of Breast Cancer Associations with Five Susceptibility Loci by Clinical and Pathological Characteristics
The WHO yaws eradication strategy consists of one round of total community treatment ( TCT ) of single-dose azithromycin with coverage of > 90% . The efficacy of the strategy to reduce the levels on infection has been demonstrated previously in isolated island communities in the Pacific region . We aimed to determine t...	In this study , we provided a single round of total community treatment ( TCT ) with azithromycin to the population of a sub-district in Ghana ( 16 , 287 people ) that is endemic for yaws and surrounded by other yaws-endemic communities to determine whether a sustained decrease in yaws prevalence could be achieved up t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schoolchildren", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "pathogens", "sociology", "tropical", "diseases", "microbiology", "social", "sciences", "geographical", "locations", "treponematoses", "bacterial", "disease...	2018	Community-based mass treatment with azithromycin for the elimination of yaws in Ghana—Results of a pilot study
Bushmeat represents an important source of animal protein for humans in tropical Africa . Unsustainable bushmeat hunting is a major threat to wildlife and its consumption is associated with an increased risk of acquiring zoonotic diseases , such as Ebola virus disease ( EVD ) . During the recent EVD outbreak in West Af...	The consumption of wild animal meat , commonly known as bushmeat , is widespread throughout tropical regions . Bushmeat provides an essential source of protein and income for human livelihoods . However , its consumption is linked to the transmission of zoonotic diseases , such as Ebola , and its over-harvest is a majo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "domestic", "animals", "tropical", "diseases", "diet", "social", "sciences", "ebola", "hemorrhagic", "fever", "neuroscience", "animals", "habits", "animal", "products", "physiological", "processes", "research",...	2017	The socio-economic drivers of bushmeat consumption during the West African Ebola crisis
Many mRNAs specifically localize within the cytoplasm and are present in RNA-protein complexes . It is generally assumed that localization and complex formation of these RNAs are controlled by trans-acting proteins encoded by genes different than the RNAs themselves . Here , we analyze slow as molasses ( slam ) mRNA th...	While proteins and their encoding messenger RNAs share the same intracellular space during the translation process , thereafter they are usually spatially and biochemically separated . RNA localization follows a specific subcellular pattern—such as apical or basal—and is thought to have important physiological implicat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nucleic", "acid", "synthesis", "non-coding", "rna", "sequences", "messenger", "rna", "rna", "extraction", "green", "fluorescent", "protein", "membrane", "proteins", "developmental", "biology", "luminescent", "proteins", "rna", "synthesis", "embryos", "cellular", "struc...	2017	Slam protein dictates subcellular localization and translation of its own mRNA
Within sub-Saharan Africa , helminth and malaria infections cause considerable morbidity in HIV-positive pregnant women and their offspring . Helminth infections are also associated with a higher risk of mother-to-child HIV transmission . The aim of this study was to determine the prevalence of , and the protective and...	There is an overlap in the worldwide distribution of intestinal worms ( helminths ) , malaria and HIV . Co-infections with helminth and malaria parasites cause a significant problem in the host , particularly in the presence of HIV infection . The aim of this study was to assess the prevalence of intestinal worm and ma...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2013	Helminthic Infections Rates and Malaria in HIV-Infected Pregnant Women on Anti-Retroviral Therapy in Rwanda
Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile . But how progenitor cells overcome the stability of their gene expression configuration ( attractor ) to exit the attractor in one direction remains elusive . Here we show...	A certain type of multipotent progenitor cell of the blood can commit to either the white ( myeloid ) or the red ( erythroid ) blood cell lineage , thus making a discrete binary cell fate decision . To test a theory on fundamental principles of cell fate dynamics ( as opposed to the usually studied molecular mechanisms...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "immunology", "cell", "differentiation", "developmental", "biology", "systems", "science", "mathematics", "stem", "cells", "genome", "analysi...	2016	Cell Fate Decision as High-Dimensional Critical State Transition
“Use it and improve it , or lose it” is one of the axioms of motor therapy after stroke . There is , however , little understanding of the interactions between arm function and use in humans post-stroke . Here , we explored putative non-linear interactions between upper extremity function and use by developing a first-...	Although , there is now definitive evidence that intensive task-specific practice is effective for improving upper extremity function and use after stroke , it is unclear how individual patients recover from stroke , and how they respond to therapy . Here , we propose a novel computational model of stroke recovery to s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "computer", "science", "computer", "modeling", "biology", "neuroscience", "physiotherapy", "and", "rehabilitation" ]	2012	Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke
Interferon-γ ( IFN-γ ) represents one of the most important innate immunity responses in a host to combat infections of many human viruses including human herpesviruses . Human N-myc interactor ( Nmi ) protein , which has been shown to interact with signal transducer and activator of transcription ( STAT ) proteins inc...	Interferon-γ ( IFN-γ ) responses are vital for a host to combat infections of many human viruses including human herpesviruses . Upon treatment of IFN-γ , transcription of many genes responsible for IFN-γ immune responses is activated primarily by the signal transducer and activator of transcription ( STAT ) proteins s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "dna", "transcription", "viruses", "dna", "viruses", "molecular", "biology",...	2018	Human cytomegalovirus UL23 inhibits transcription of interferon-γ stimulated genes and blocks antiviral interferon-γ responses by interacting with human N-myc interactor protein
BREVIPEDICELLUS ( BP or KNAT1 ) , a class-I KNOTTED1-like homeobox ( KNOX ) transcription factor in Arabidopsis thaliana , contributes to shaping the normal inflorescence architecture through negatively regulating other two class-I KNOX genes , KNAT2 and KNAT6 . However , the molecular mechanism of BP-mediated transcri...	BP is a class-I KNOX transcription factor that controls normal inflorescence architecture development by repressing the expression of two KNOX genes , KNAT2 and KNAT6 . In this study , we showed that Arabidopsis BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRM . brm and bp mutants displayed simi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Arabidopsis BREVIPEDICELLUS Interacts with the SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA to Regulate KNAT2 and KNAT6 Expression in Control of Inflorescence Architecture
The phytochrome ( phy ) family of photoreceptors is of crucial importance throughout the life cycle of higher plants . Light-induced nuclear import is required for most phytochrome responses . Nuclear accumulation of phyA is dependent on two related proteins called FHY1 ( Far-red elongated HYpocotyl 1 ) and FHL ( FHY1 ...	In response to changes in the environment , animals can take shelter while the sessile plants must adapt to the prevalent conditions . Great plasticity in growth and development are striking examples of how plants cope with a changing environment . In plants , light is both a source of energy and an essential informati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "developmental", "biology/plant", "growth", "and", "development", "cell", "biology/developmental", "molecular", "mechanisms", "plant", "biology/plant-environment", "interactions", "cell", "biology/plant", "cell", "biology", "genetics", "an...	2008	FHY1 Mediates Nuclear Import of the Light-Activated Phytochrome A Photoreceptor
The incidence of zoonotic cutaneous leishmaniasis ( ZCL ) makes it the most widespread parasitic disease in Tunisia and the Arab world . Yet , few studies have addressed its psychological and psychosocial effects . The purpose of this study was to examine the psychosocial impact of ZCL scars among Tunisian women . We c...	Zoonotic cutaneous leishmaniasis ( ZCL ) is the most common form of leishmaniasis in Tunisia . The disease is not severe and heal spontaneously with a definitive scar causing a social impact mainly when the lesion occurs in the face . Yet , few studies have addressed these psychological and psychosocial effects . To ex...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "tropical", "diseases", "social", "sciences", "sand", "flies", "parasitic", "diseases", "neuroscience", "psychological", "and", "psychosocial", "issues", "health", "care", "neglected", "tropical", "diseases", "inse...	2016	Psychological and Psychosocial Consequences of Zoonotic Cutaneous Leishmaniasis among Women in Tunisia: Preliminary Findings from an Exploratory Study
Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds . Therefore , ovule specification is a critical developmental program . In Arabidopsis thaliana , ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 ( SHP1 ) , SHP2 and SEEDSTICK ( STK ) , p...	Plant ovules are crucial reproductive structures in which the female gametophyte develops , giving rise to seeds after fertilization . Global food supply depends mainly on seed production , thus understanding the underlying regulatory mechanisms that orchestrate ovule development is vitally important . The establishmen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "gene", "regulation", "ovules", "brassica", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "plants", "flowering", "plants", "research", "and", "analysis", "methods", "arabidopsis", "thaliana", "genome", "complexity",...	2018	Ovule identity mediated by pre-mRNA processing in Arabidopsis
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks ( GRNs ) . In this view , different phenotypes are associated with alternative states of complex nonlinear systems: stable attractors in deterministic models or mo...	Regulatory mechanisms of slow gene activation and deactivation play a role in triggering and sustaining phenotypically heterogeneous , yet genetically identical ( clonal ) , cellular populations in a wide variety of biological processes . These range from embryonic development and hematopoietic cell differentiation to ...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "synthetic", "genetic", "systems", "genetic", "networks", "engineering", "and", "technology", "synthetic", "biology", "cell", "differentiation", "dna", "transcription", "developmental", "biology", "protein", "expression", "network", "analysis", "molecular", "biology", "te...	2019	Multi-modality in gene regulatory networks with slow promoter kinetics
Parkinson's disease ( PD ) is the most common neurodegenerative movement disorder characterized by the progressive loss of dopaminergic ( DA ) neurons . Both environmental and genetic factors are thought to contribute to the pathogenesis of PD . Although several genes linked to rare familial PD have been identified , e...	Parkinson's disease is a common movement disorder with no known cure . Its characteristic motor symptoms are primarily caused by the progressive loss of midbrain dopaminergic neurons . Although studies have shown that various environmental and genetic factors both contribute to the development of the disease , the unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "animal", "genetics", "nervous", "system", "neuronal", "differentiation", "neuroscience", "cell", "differentiation", "gene", "function", "developmental", "biology", "behavioral", "neuroscience", "genetic", "predisposition", "animal", "cells", "g...	2014	A Conserved Role for p48 Homologs in Protecting Dopaminergic Neurons from Oxidative Stress
Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge . Most current approaches rely on likelihood functions , which raise specific issues that range from computing these functions to finding their maxima numerically . Here , we present a new regression-based Approximate...	Given the rapid evolution of many pathogens , analysing their genomes by means of phylogenies can inform us about how they spread . This is the focus of the field known as “phylodynamics” . Most existing methods inferring epidemiological parameters from virus phylogenies are limited by the difficulty of handling comple...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "plant", "anatomy", "medicine", "and", "health", "sciences", "applied", "mathematics", "epidemiological", "methods", "and", "statistics", "simulation", "and", "modeling", "algorithms", "phylogenetics", "data", "management", "plant", "science", "mathematics", ...	2017	Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer . Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54 . We show that LIN-54 DNA-bin...	X chromosomes differ in number between the sexes and differ from autosomes in their associated proteins and gene regulatory properties . In C . elegans both X chromosomes are partially silenced in hermaphrodite germlines . Germline-expressed and essential genes are autosome-enriched and are thought to have fled the X c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "x", "chromosome", "inactivation", "genome", "evolution", "gene", "regulation", "dna", "transcription", "gene", "function", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "molecular", "genetics", "chromosome", ...	2011	Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex
The Spumaretrovirinae , or foamy viruses ( FVs ) are complex retroviruses that infect many species of monkey and ape . Despite little sequence homology , FV and orthoretroviral Gag proteins perform equivalent functions , including genome packaging , virion assembly , trafficking and membrane targeting . However , there...	Foamyviruses ( FVs ) or Spuma-retroviruses derive their name from the cytopathic effects they cause in cell culture . However , infection in humans is benign and FVs have entered the human population through zoonosis from apes resulting in the emergence of Prototype FV ( PFV ) . Like all retroviruses , FVs contain gag ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "viral", "structure", "retroviruses", "viruses", "immunodeficiency", "viruses", "rna", "viruses", "materials", "science", "mater...	2016	Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid
It is widely accepted that the growth and regeneration of tissues and organs is tightly controlled . Although experimental studies are beginning to reveal molecular mechanisms underlying such control , there is still very little known about the control strategies themselves . Here , we consider how secreted negative fe...	Many tissues and organs grow to precise sizes and , when injured , regenerate accurately and rapidly . Here , we ask whether the organization of cells into lineages , and the feedback interactions that occur within lineages , are necessary elements of control strategies that make such behavior possible . Drawing on mat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "neuroscience" ]	2009	Cell Lineages and the Logic of Proliferative Control
Latency reversal agents ( LRAs ) have proven to induce HIV-1 transcription in vivo but are ineffective at decreasing the size of the latent reservoir in antiretroviral treated patients . The capacity of the LRAs to perturb the viral reservoir present in distinct subpopulations of cells is currently unknown . Here , usi...	HIV infection is an incurable disease . Despite antiretroviral therapy , a pool of cells with HIV in a latent state persists and precludes fully eradication of the viral infection . The cells that contain this latent viral reservoir are very diverse , and therefore different therapeutic strategies would be necessary to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "microbiology", "toxicology", "retroviruses", "viruses", "immunodeficiency", "vir...	2019	Latency reversal agents affect differently the latent reservoir present in distinct CD4+ T subpopulations
Maturation of vertebrate oocytes into haploid gametes relies on two consecutive meioses without intervening DNA replication . The temporal sequence of cellular transitions driving eggs from G2 arrest to meiosis I ( MI ) and then to meiosis II ( MII ) is controlled by the interplay between cyclin-dependent and mitogen-a...	In the life cycle of sexual organisms , a specialized cell division -meiosis- reduces the number of chromosomes in gametes or spores while fertilization or mating restores the original number . The essential feature that distinguishes meiosis from mitosis ( the usual division ) is the succession of two rounds of divisi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	2012	A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions
The unique avian vocal organ , the syrinx , is located at the caudal end of the trachea . Although a larynx is also present at the opposite end , birds phonate only with the syrinx . Why only birds evolved a novel sound source at this location remains unknown , and hypotheses about its origin are largely untested . Her...	The larynx is an important valve in the respiratory system of all air-breathing vertebrates that is located at the upper end of the trachea . In some amphibians , in nonavian reptiles , and in mammals , it has also assumed the function of a vocal organ . In contrast , birds have evolved a new and unique vocal organ , t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "acoustics", "medicine", "and", "health", "sciences", "resonance", "frequency", "classical", "mechanics", "vibration", "larynx", "vertebrates", "animals", "mammals", "throat", "respiratory", "system", "sound", "pressure", "amniotes", "trachea", "birds", "resonance", "ph...	2019	The evolution of the syrinx: An acoustic theory
Repeated exposure to a novel physical environment eventually leads to a mature adaptive response whereby feedforward changes in motor output mirror both the amplitude and temporal structure of the environmental perturbations . However , adaptive responses at the earliest stages of learning have been found to be not onl...	With repeated exposure to a perturbation , the sensorimotor system learns to develop an adaptive response that is highly specific to both the amplitude and temporal structure of that perturbation in order to effectively counteract it . It is widely known that the amplitude of the adaptive response starts small and grad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "velocity", "learning", "medicine", "and", "health", "sciences", "classical", "mechanics", "education", "adaptive", "training", "sociology", "experimental", "design", "social", "sciences", "neuroscience", "learning", "and", "memory", "training", "(education)", "research",...	2017	Temporal specificity of the initial adaptive response in motor adaptation
For persistent infections of the mammalian host , African trypanosomes limit their population size by quorum sensing of the parasite-excreted stumpy induction factor ( SIF ) , which induces development to the tsetse-infective stumpy stage . We found that besides this cell density-dependent mechanism , there exists a se...	African trypanosomes escape the mammalian host’s immune system by antigenic variation of their variant surface glycoprotein ( VSG ) coat . VSGs are expressed from a specialized region in the genome , the expression site ( ES ) , that contains essential expression site associated genes ( ESAGs ) . So far , it was assume...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "invertebrates", "medicine", "and", "health", "sciences", "nuclear", "staining", "parasitic", "cell", "cycles", "cell", "cycle", "and", "cell", "division", "drugs", "cell", "processes", "microbiology", "cloning", "parasitic", "diseases", "animals", "...	2017	A quorum sensing-independent path to stumpy development in Trypanosoma brucei
During Coxsackievirus B3 ( CVB3 ) infection hepatitis is a potentially life threatening complication , particularly in newborns . Studies with type I interferon ( IFN-I ) receptor ( IFNAR ) -deficient mice revealed a key role of the IFN-I axis in the protection against CVB3 infection , whereas the source of IFN-I and c...	CVB3 belongs to human enteroviruses and is transmitted through the fecal-oral route . Infections with CVB3 are mostly unnoticed or cause flu-like symptoms , however , they can also cause severe disease , such as myocarditis , pancreatitis , and hepatitis . Although CVB3 does not efficiently trigger plasmacytoid dendrit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "liver", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "in", "vivo", "imaging", "epithelial", "cells", "bone", "marrow", "cells", "signs", "and", "symptoms", "immunologic", "techniques", "resear...	2018	Interferon-beta expression and type I interferon receptor signaling of hepatocytes prevent hepatic necrosis and virus dissemination in Coxsackievirus B3-infected mice
Recent studies suggest that motor adaptation is the result of multiple , perhaps linear processes each with distinct time scales . While these models are consistent with some motor phenomena , they can neither explain the relatively fast re-adaptation after a long washout period , nor savings on a subsequent day . Here...	Trying to explain how humans adapt to new motor behaviors and retain them over time is a central focus in motor control . Many aspects of adaptation , including savings and interference , have proven difficult to explain in a coherent manner . Linear dynamical models have been successful at describing the observed incr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "motor", "systems", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience", "learning", "and", "memory" ]	2011	Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects
Cellular fusion is required in the development of several tissues , including skeletal muscle . In vertebrates , this process is poorly understood and lacks an in vivo-validated cell surface heterophilic receptor pair that is necessary for fusion . Identification of essential cell surface interactions between fusing ce...	The fusion of precursor cells is a crucial step in many biological processes , one of which is the development of skeletal muscle . The molecular and cell biology of fusion of muscle precursors has been well described in Drosophila melanogaster larvae , leading to insights into the process in vertebrates . However , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "protein", "interactions", "animal", "models", "model", "organisms", "membrane", "receptor", "signaling", "proteins", "muscle", "fibers", "biology", "molecular", "biology", "biochemistry", "zebrafish", "signal", "transduction", "tr...	2011	Jamb and Jamc Are Essential for Vertebrate Myocyte Fusion
Haplotype maps ( HapMaps ) reveal underlying sequence variation and facilitate the study of recombination and genetic diversity . In general , HapMaps are produced by analysis of Single-Nucleotide Polymorphism ( SNP ) segregation in large numbers of meiotic progeny . Candida albicans , the most common human fungal path...	Candida albicans , a heterozygous diploid yeast , is the most prevalent fungal pathogen . It often acquires resistance to anti-fungal drugs via genome-altering recombination events . In many organisms , recombination events are analyzed using Haplotype Maps ( HapMaps ) , which show the location of different alleles on ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "yeast", "and", "fungi", "infectious", "diseases", "genetics", "and", "genomics", "eukaryotes" ]	2008	Haplotype Mapping of a Diploid Non-Meiotic Organism Using Existing and Induced Aneuploidies
The structure of BG505 gp140 SOSIP , a soluble mimic of the native HIV-1 envelope glycoprotein ( Env ) , marks the beginning of new era in Env structure-based immunogen design . Displaying a well-ordered quaternary structure , these subtype A-derived trimers display an excellent antigenic profile , discriminating recog...	The HIV envelope glycoprotein ( Env ) is the sole virally encoded gene product on the surface of the virus and , as such , is the only target of neutralizing antibodies . A broadly efficacious HIV vaccine will likely need to generate a robust neutralizing antibody response directed at conserved elements of the variable...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "envelope", "virology", "biology", "and", "life", "sciences", "microbiology", "viral", "structure" ]	2015	Well-Ordered Trimeric HIV-1 Subtype B and C Soluble Spike Mimetics Generated by Negative Selection Display Native-like Properties
Evidence for minimally symptomatic Ebola virus ( EBOV ) infection is limited . During the 2013–16 outbreak in West Africa , it was not considered epidemiologically relevant to published models or projections of intervention effects . In order to improve our understanding of the transmission dynamics of EBOV in humans ,...	With over 28 , 000 reported cases , the 2013–16 West African Ebola virus disease epidemic is the largest and longest on record . This study provides further evidence that Ebola , like other viruses , causes a spectrum of clinical manifestations that may include minimally symptomatic infection . The findings also sugges...	[ "Abstract", "Introduction", "Methods", "and", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "ge...	2016	Minimally Symptomatic Infection in an Ebola ‘Hotspot’: A Cross-Sectional Serosurvey
FGF signaling is a potent inducer of lacrimal gland development in the eye , capable of transforming the corneal epithelium into glandular tissues . Here , we show that genetic ablation of the Pea3 family of transcription factors not only disrupted the ductal elongation and branching of the lacrimal gland , but also bi...	FGF signaling regulates cell fate decision by inducing genome-wide changes in gene expression . We identified Pea3 family transcription factors as the key effectors of FGF signaling in reprograming the epithelia transcriptome . Pea3 factors control both the feedback and feedforward circuities of FGF signaling in lacrim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "notch", "signaling", "dna", "transcription", "endocrine", "physiology", "developmental", "biology", "organism", "development", "gland", "development", "tra...	2018	FGF-induced Pea3 transcription factors program the genetic landscape for cell fate determination
CHTF18 ( chromosome transmission fidelity factor 18 ) is an evolutionarily conserved subunit of the Replication Factor C-like complex , CTF18-RLC . CHTF18 is necessary for the faithful passage of chromosomes from one daughter cell to the next during mitosis in yeast , and it is crucial for germline development in the f...	Meiosis is the specialized process of cell division during germ cell development that results in formation of eggs and sperm . Genetic exchange between maternal and paternal chromosomes occurs during meiosis in a process called homologous recombination , in which DNA double- strand breaks are made and then repaired to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "genetics", "and", "genomics" ]	2012	Disruption of Chtf18 Causes Defective Meiotic Recombination in Male Mice
Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae infection . In 2016 , more than 200 , 000 new cases of leprosy were detected around the world , representing the most frequent cause of infectious irreversible deformities and disabilities . In the present work , we demonstrate a consisten...	Hemostatic illnesses are frequently associated with acute and chronic infections . In the present work we demonstrated that leprosy patients developed hemostatic abnormalities , like the formation of an atypical lipid clot mass during sera harvesting , a phenomenon previously observed and never unraveled . We character...	[ "Abstract", "Introduction", "Materials,", "subjects", "and", "methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "body", "fluids", "fibrinogen", "tropical", "diseases", "neutral", "lipids", "fibrin", "bacterial", "diseases", "neglected", "tropical", "diseases", "glycoproteins", "bacteria", "infectious", "diseases", ...	2018	Blood coagulation abnormalities in multibacillary leprosy patients
Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics . We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data . The procedure , called Genome Order Optimizati...	Genome sequences are an essential resource for genetic research in many species . However , most species exhibit considerable variation in genomic organization , making a single reference sequence inadequate . This variation complicates quantitative trait mapping and population genomics . We introduce a new statistical...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "markov", "models", "chromosomal", "inversions", "invertebrate", "genomics", "chromosome", "mapping", "mathematics", "dna", "recombination", "molecular", "biology", "techniques", "dna", "genotyping", "research", "and", "analysis", "methods", "gene", "mapping", "chromosome...	2019	GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity
Hepatitis C virus ( HCV ) nonstructural protein 2 ( NS2 ) is a hydrophobic , transmembrane protein that is required not only for NS2-NS3 cleavage , but also for infectious virus production . To identify cellular factors that interact with NS2 and are important for HCV propagation , we screened a human liver cDNA librar...	Viruses hijack host cells and utilize host-derived proteins for viral propagation . In the case of hepatitis C virus ( HCV ) , many host factors have been identified that are required for genome replication; however , only a little is known about cellular proteins that interact with HCV proteins and are important for t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	Signal Peptidase Complex Subunit 1 Participates in the Assembly of Hepatitis C Virus through an Interaction with E2 and NS2
In the visual system , large ensembles of neurons collectively sample visual space with receptive fields ( RFs ) . A puzzling problem is how neural ensembles provide a uniform , high-resolution visual representation in spite of irregularities in the RFs of individual cells . This problem was approached by simultaneousl...	All visual information reaching the brain is transmitted by retinal ganglion cells , each of which is sensitive to a small region of space known as its receptive field . Each of the 20 or so distinct ganglion cell types is thought to transmit a complete visual image to the brain , because the receptive fields of each t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2009	Receptive Fields in Primate Retina Are Coordinated to Sample Visual Space More Uniformly
Malaria , caused by Plasmodium parasite infection , continues to be one of the leading causes of worldwide morbidity and mortality . Development of an effective vaccine has been encumbered by the complex life cycle of the parasite that has distinct pre-erythrocytic and erythrocytic stages of infection in the mammalian ...	Malaria is arguably one of the deadliest infectious diseases in human history . Today , it infects nearly 300 million people each year and kills up to 1 million of those—mostly women and children under the age of 5—and no effective malaria vaccine has been developed . Traditional subunit vaccines for pathogens work by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Mechanisms of Stage-Transcending Protection Following Immunization of Mice with Late Liver Stage-Arresting Genetically Attenuated Malaria Parasites
Entamoeba histolytica is a protist parasite that is the causative agent of amoebiasis , and is a highly motile organism . The motility is essential for its survival and pathogenesis , and a dynamic actin cytoskeleton is required for this process . EhCoactosin , an actin-binding protein of the ADF/cofilin family , parti...	E . histolytica is an important pathogen and a major cause of morbidity and mortality in developing nations . High level of motility and phagocytosis is responsible for the parasite invading different tissues of the host . Phagocytosis and motility depend on highly dynamic actin cytoskeleton of this organism . The mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cytoskeletal", "proteins", "cell", "motility", "actin", "filaments", "cell", "biology", "proteins", "protein", "structure", "structural", "proteins", "biology", "and", "life", "sciences", "dynamic", "actin", "filaments" ]	2014	EhCoactosin Stabilizes Actin Filaments in the Protist Parasite Entamoeba histolytica
This study aimed to evaluate the risk factors associated with developing leprosy among the contacts of newly-diagnosed leprosy patients . A total of 6 , 158 contacts and 1 , 201 leprosy patients of the cohort who were diagnosed and treated at the Leprosy Laboratory of Fiocruz from 1987 to 2007 were included . The conta...	Leprosy is an infectious disease that can lead to physical disabilities , social stigma , and great hardship . Transmitted from person to person , it is still endemic in developing countries , like Brazil and India . Effective treatment has been available since 1960 , but early diagnosis of the disease remains the most...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "leprosy" ]	2011	Leprosy among Patient Contacts: A Multilevel Study of Risk Factors
Identifying etiologies of acute febrile illnesses ( AFI ) is challenging due to non-specific presentation and limited availability of diagnostics . Prospective AFI studies provide a methodology to describe the syndrome by age and etiology , findings that can be used to develop case definitions and multiplexed diagnosti...	We conducted a prospective study of acute febrile illness ( AFI ) in Puerto Rico to better understand the etiology of AFI among all age groups in the tropics . Such findings could assist clinicians to identify disease-specific characteristics , which can then be used to initiate proper patient management . We enrolled ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "influenza", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "orthomyxoviruses", "alphaviru...	2017	Clinical and epidemiologic characteristics of dengue and other etiologic agents among patients with acute febrile illness, Puerto Rico, 2012–2015
It has been demonstrated that Terminal Flowering 1 ( TFL1 ) in Arabidopsis and its functional orthologs in other plants specify indeterminate stem growth through their specific expression that represses floral identity genes in shoot apical meristems ( SAMs ) , and that the loss-of-function mutations at these functiona...	Similar to the “green revolution” semi-dwarf cereals , semi-determinate soybean varieties are lodging-resistant and particularly suitable for planting in high fertility and irrigated environments . Nevertheless , molecular mechanisms underlying semi-determinate stem growth have not been deciphered in any flowering plan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "dna-binding", "proteins", "cloning", "plant", "physiology", "habits", "plant", "science", "crops", "molecular", "biology", "techniques", "dna", "plants", "flowering", "plants", "promoter", "regions", "research", "and", "analysis", "methods", "cr...	2016	Innovation of a Regulatory Mechanism Modulating Semi-determinate Stem Growth through Artificial Selection in Soybean
Innate immunity is the first line of defense against invading microorganisms . Trypanosome Lytic Factor ( TLF ) is a minor sub-fraction of human high-density lipoprotein that provides innate immunity by completely protecting humans from infection by most species of African trypanosomes , which belong to the Kinetoplast...	Innate immunity ( present from birth ) is the first line of defense against microorganisms and provides an initial barrier against disease . Here we show that a minor sub-fraction of human high-density lipoprotein ( the good cholesterol ) , known as Trypanosome Lytic Factor ( TLF ) , not only kills the parasite Trypano...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity", "cell", "biology/microbial", "growth", "and", "development", "biochemistry/biomacromolecule-ligand", "interactions", "microbiology/parasitology", "infectious", "diseases/protozoal", "infectio...	2009	Trypanosome Lytic Factor, an Antimicrobial High-Density Lipoprotein, Ameliorates Leishmania Infection
Uncontrolled trachoma is a leading cause of blindness . Current global trachoma burden summary measures are presented as disability adjusted life years but have limitations due to inconsistent methods and inadequate population-based data on trachomatous low vision and blindness . We aimed to describe more completely th...	Summary measures of population health attempt to express disease burden in terms of a common “currency” and are useful in establishing public health priorities . Disability adjusted life years ( DALYs ) , a health gap measure , have previously been used to estimate burden due to trachoma; however , their methods and re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/neglected", "tropical", "diseases", "ophthalmology/eye", "infections" ]	2009	What Will Happen If We Do Nothing To Control Trachoma: Health Expectancies for Blinding Trachoma in Southern Sudan
Neurons process and convey information by transforming barrages of synaptic inputs into spiking activity . Synaptic inhibition typically suppresses the output firing activity of a neuron , and is commonly classified as having a subtractive or divisive effect on a neuron’s output firing activity . Subtractive inhibition...	Neurons process information by generating spikes in response to two types of synaptic inputs . Excitatory inputs increase spike rates and inhibitory inputs decrease spike rates ( typically ) . The interaction between these two input types and the transformation of these inputs into spike outputs is not , however , a si...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "pharmacologic", "analysis", "knees", "action", "potentials", "medicine", "and", "health", "sciences", "legs", "membrane", "potential", "limbs", "(anatomy)", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "compartment", "models", "one-compartment", ...	2018	Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition
The mechanism of rapid energy supply to the brain , especially to accommodate the heightened metabolic activity of excited states , is not well-understood . We explored the role of glycogen as a fuel source for neuromodulation using the noradrenergic stimulation of glia in a computational model of the neural-glial-vasc...	Although efficient compared to computers , the human brain utilizes energy at 10-fold the rate of other organs by mass . How the brain is supplied with sufficient on-demand energy to support its activity in the absence of neuronal storage capacity remains unknown . Neurons are not capable of meeting their own energy re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "carbohydrate", "metabolism", "neurochemistry", "chemical", "compounds", "astrocytes", "carbohydrates", "neuroscience", "organic", "compounds", "macroglial", "cells", "glucose", "glucose", "metabolism", "camp", "signaling", "cascade", "cell", "signaling", "protein", "kinase...	2018	Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate
Lens induction is a classical developmental model allowing investigation of cell specification , spatiotemporal control of gene expression , as well as how transcription factors are integrated into highly complex gene regulatory networks ( GRNs ) . Pax6 represents a key node in the gene regulatory network governing mam...	While significant insights into the functional role of some transcription factors during lens formation have been accomplished , much less is known about the intricate wiring of the gene regulatory network ( GRN ) that controls the earliest stages of lens development . Our genetic experiments presented here demonstrate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "regulatory", "proteins", "ocular", "anatomy", "dna-binding", "proteins", "vertebrates", "reporter", "genes", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", ...	2016	The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6
The transmission of mosquito-borne diseases is strongly linked to the abundance of the host vector . Identifying the environmental and biological precursors which herald the onset of peaks in mosquito abundance would give health and land-use managers the capacity to predict the timing and distribution of the most effic...	Mosquitoes carry several diseases that are potentially fatal to people . The risk of disease transmission is high when mosquitoes are abundant in an area , and it is therefore the job of health professionals to control or prevent mosquito outbreaks in certain areas , especially those close to human habitation . Biologi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "ecology/population", "ecology", "public", "health", "and", "epidemiology" ]	2009	Predicting the Timing and Magnitude of Tropical Mosquito Population Peaks for Maximizing Control Efficiency
The clinical use of the anthracycline doxorubicin is limited by its cardiotoxicity which is associated with mitochondrial dysfunction . Redox cycling , mitochondrial DNA damage and electron transport chain inhibition have been identified as potential mechanisms of toxicity . However , the relative roles of each of thes...	Doxorubicin is a potent anticancer drug , but its efficacy is limited by a cumulative dose-dependent cardiotoxicity . Multiple pathways are involved in the drug cardiotoxicity , however , the underlying mechanisms are still not fully elucidated . Here we developed a computational model to study doxorubicin mitochondria...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "mitochondrial", "dna", "dose", "prediction", "methods", "toxicology", "dna", "damage", "toxicity", "pharmaceutics", "forms", "of", "dna", "mitochondria", "dna", "bioenergetics", "p...	2016	A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity
Messenger RNA splicing is an essential and complex process for the removal of intron sequences . Whereas the composition of the splicing machinery is mostly known , the kinetics of splicing , the catalytic activity of splicing factors and the interdependency of transcription , splicing and mRNA 3′ end formation are les...	The coding information for the synthesis of proteins in mammalian cells is first transcribed from DNA to messenger RNA ( mRNA ) , before being translated from mRNA to protein . Each step is complex , and subject to regulation . Certain sequences of DNA must be skipped in order to generate a functional protein , and the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "rna", "processing", "biophysic", "al", "simulations", "gene", "expression", "genetics", "molecular", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2011	Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing
TDP-43 proteinopathies have been observed in a wide range of neurodegenerative diseases . Mutations in the gene encoding TDP-43 ( i . e . , TDP ) have been identified in amyotrophic lateral sclerosis ( ALS ) and in frontotemporal lobe degeneration associated with motor neuron disease . To study the consequences of TDP ...	Amyotrophic lateral sclerosis , a condition also known as Lou Gehrig's disease , is characterized by progressive degeneration of motor neurons , denervation atrophy of skeletal muscles , and eventual paralysis of affected limbs . The signature pathology of Lou Gehrig's disease is the formation of intracellular inclusio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "neurological", "disorders/movement", "disorders" ]	2010	Transgenic Rat Model of Neurodegeneration Caused by Mutation in the TDP Gene
One of the hallmarks of neocortical circuits is the predominance of recurrent excitation between pyramidal neurons , which is balanced by recurrent inhibition from smooth GABAergic neurons . It has been previously described that in layer 2/3 of primary visual cortex ( V1 ) of cat and monkey , pyramidal cells filled wit...	The mammalian visual cortex , which is part of the cerebral cortex , contains 50 to 100 thousands of neurons per cubic millimetre , most of which are excitatory ( 85% ) and the minority , inhibitory ( 15% ) . Unlike neurons in the retina , neurons in the visual cortex are preferentially activated by lines or edges of a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "connectomics", "calcium", "imaging", "visual", "system", "cellular", "neuroscience", "neuroanatomy", "anatomy", "neuronal", "morphology", "neural", "networks", "nervous", "system", "biology", "and", "life", "sciences", "sensory", "systems", "neuroscience", "neuroimaging"...	2014	Pyramidal Cells Make Specific Connections onto Smooth (GABAergic) Neurons in Mouse Visual Cortex
Encoding properties of sensory neurons are commonly modeled using linear finite impulse response ( FIR ) filters . For the auditory system , the FIR filter is instantiated in the spectro-temporal receptive field ( STRF ) , often in the framework of the generalized linear model . Despite widespread use of the FIR STRF ,...	Understanding how the brain solves sensory problems can provide useful insight for the development of automated systems such as speech recognizers and image classifiers . Recent developments in nonlinear regression and machine learning have produced powerful algorithms for characterizing the input-output relationship o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Essential Complexity of Auditory Receptive Fields
Synonymous mutations do not alter the specified amino acid but may alter the structure or function of an mRNA in ways that impact fitness . There are few examples in the literature , however , in which the effects of synonymous mutations on microbial growth rates have been measured , and even fewer for which the underl...	When a new enzyme is needed , microbes often recruit a pre-existing enzyme with a promiscuous activity corresponding to the newly needed activity . Such enzymes are often the “weak-link” in metabolism because they have not evolved to efficiently catalyze the new reaction . Under these circumstances , increasing the lev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "operons", "bacterial", "diseases", "mutation", "enterobacteriaceae", "dna", "cellular", "structures", "and", "organelles", "bacteria", ...	2018	Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme
Leishmaniasis is increasingly reported among travellers . Leishmania species vary in sensitivity to available therapies . Fast and reliable molecular techniques have made species-directed treatment feasible . Many treatment trials have been designed poorly , thus developing evidence-based guidelines for species-directe...	Human leishmaniasis is caused by unicellular parasites that are injected into the skin by sand-flies , small , flying insects . Many different Leishmania species cause various manifestations of disease , both of the skin and internal organs . Leishmaniasis is a curable disease but clear guidelines on the best available...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "dermatology", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "skin", "infections", "travel-associated", "diseases", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "trop...	2014	Species-Directed Therapy for Leishmaniasis in Returning Travellers: A Comprehensive Guide
Bone is a common site for cancer metastasis . To create space for their growth , cancer cells stimulate bone resorbing osteoclasts . Cytokine RANKL is a key osteoclast activator , while osteoprotegerin ( OPG ) is a RANKL decoy receptor and an inhibitor of osteoclastogenesis . Consistently , systemic application of OPG ...	Breast and prostate cancers commonly metastasize to bone . To create more space for their expansion , metastatic tumors activate osteoclasts , the only cells capable of bone destruction . The main osteoclast stimulator is the cytokine RANKL , while osteoprotegerin ( OPG ) acts as a RANKL inhibitor . Systemic applicatio...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "theoretical", "biology", "physiology", "biology", "anatomy", "and", "physiology", "molecular", "cell", "biology" ]	2012	Osteoprotegerin in Bone Metastases: Mathematical Solution to the Puzzle
Leishmania donovani is known to induce myelopoiesis and to dramatically increase extramedullary myelopoiesis . This results in splenomegaly , which is then accompanied by disruption of the splenic microarchitecture , a chronic inflammatory environment , and immunosuppression . Chronically inflamed tissues are typically...	The protozoan parasite Leishmania donovani causes chronic infection in the spleen , which is accompanied by a chronic inflammatory environment , an enlargement of the organ , and immunosuppression . The environment of chronically inflamed tissues is characterized by low oxygen levels and tissue disruption , which induc...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "bone", "marrow", "cells", "developmental", ...	2017	HIF-1α is a key regulator in potentiating suppressor activity and limiting the microbicidal capacity of MDSC-like cells during visceral leishmaniasis
The activation of phase-specific cyclin-dependent kinases ( Cdks ) is associated with ordered cell cycle transitions . Among the mammalian Cdks , only Cdk1 is essential for somatic cell proliferation . Cdk1 can apparently substitute for Cdk2 , Cdk4 , and Cdk6 , which are individually dispensable in mice . It is unclear...	Metazoan cells contain multiple Cdks that regulate cell cycle progression . Recent studies have shown that mouse cells can grow normally with just Cdk1 . The roles of the non-essential Cdks remain a fundamental question . In this study , we describe the generation and detailed characterization of CDK2-knockout human so...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	Cdk2 Is Required for p53-Independent G2/M Checkpoint Control
One of the major breakthroughs in oncogenesis research in recent years is the discovery that , in most patients , oncogenic mutations are concentrated in a few core biological functional pathways . This discovery indicates that oncogenic mechanisms are highly related to the dynamics of biologic regulatory networks , wh...	Among complex genetic diseases affecting humans , cancer is a major cause of death . In 2008 , a genome-wide analysis of hundreds of tumour samples showed that oncogenic mutations are concentrated in a few core functional pathways , revealing a new conceptual framework for cancer biology research , where the role of on...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology" ]	2014	Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model
The basic metabolic cytochrome P450 ( CYP ) system is essential for biotransformation of sterols and xenobiotics including drugs , for synthesis and degradation of signaling molecules in all living organisms . Most eukaryotes including free-living flatworms have numerous paralogues of the CYP gene encoding heme monooxy...	The basic metabolic system CYP ( cytochrome P450 ) is essential for biotransformation of sterols and xenobiotics , for synthesis and degradation of signaling molecules in all living organisms . Most eukaryotes including free-living flatworms evolved numerous paralogues of the CYP gene . Notably , by contrast , flukes a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Functional Analysis of the Unique Cytochrome P450 of the Liver Fluke Opisthorchis felineus
In every motor task , our brain must handle external forces acting on the body . For example , riding a bike on cobblestones or skating on irregular surface requires us to appropriately respond to external perturbations . In these situations , motor predictions cannot help anticipate the motion of the body induced by e...	It is commonly assumed that the brain uses internal estimates of the state of the body to adjust motor commands and perform successful movements . A problem arises when external disturbances deviate the limb from the ongoing task . In such cases , the estimated state of the body must be corrected based on sensory feedb...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "motor", "systems", "computational", "neuroscience", "biology", "neuroscience", "neurophysiology" ]	2013	Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
NSMCE2 is an E3 SUMO ligase and a subunit of the SMC5/6 complex that associates with the replication fork and protects against genomic instability . Here , we study the fate of collapsed replication forks generated by prolonged hydroxyurea treatment in human NSMCE2-deficient cells . Double strand breaks accumulate duri...	DNA damage encountered by the replication fork causes fork stalling and is a major source of mutations when not adequately repaired . Fork stalling can lead to fork collapse , that is , a state of the fork in which normal DNA synthesis cannot be resumed at the site of stalling . Collapsed forks must be rescued by repli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "hela", "cells", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "biological", "cultures", "immunology", "cell", "processes", "dna", "damage", "mitosis", "dna", "replic...	2019	Rescue of collapsed replication forks is dependent on NSMCE2 to prevent mitotic DNA damage
Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible . In silico evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Dipterian sp...	The last common ancestor of the fruit fly ( Drosophila ) and mosquito ( Anopheles ) lived more than 200 Million years ago . Can we use available data on insects alive today to infer what their ancestor looked like ? In this manuscript , we focus on early embryonic development , when stripes of genetic expression appear...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "morphogenic", "segmentation", "gene", "regulation", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "insect", "vectors", "morphogenesis", "drosophila", ...	2016	Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution
Mms21 , a subunit of the Smc5/6 complex , possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier ( SUMO ) . Here we show that the mms21-CH mutation , which inactivates Mms21 ligase activity , causes increased accumulation of gross chromosomal rearrangements ( GCRs ) selected in the dGCR assay . These dGC...	Chromosomal rearrangement is a hallmark of cancer . Saccharomyces cerevisiae Mms21 is an E3 ligase for Small Ubiquitin like MOdifer ( SUMO ) , which has been shown to have a major role in preventing chromosomal rearrangement . Despite extensive studies about the function of Mms21 in regulating the repair of exogenously...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chromosome", "structure", "and", "function", "dna", "damage", "telomeres", "mutation", "sumoylation", "dna", "replication", "dna", "research", "and", "analysis", "methods", "sequence", "analysis", "sequence", "alignment", "bioinformatics", "proteins", "chromosome", "bi...	2018	SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements
Growing cells are subject to cycles of nutrient depletion and repletion . A shortage of nutrients activates a starvation program that promotes growth in limiting conditions . To examine whether nutrient-deprived cells prepare also for their subsequent recovery , we followed the transcription program activated in buddin...	Cells must have sufficient nutrients in order to perform their different functions . This becomes particularly critical when the nutrient composition in their environment changes . To accommodate such changes , cells have evolved specialized adaptation pathways that sense the nutrients available in their surrounding an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "chemical", "compounds", "phosphates", "cell", "processes", "mutation", "fungi", "substitution", "mutation", "model", "organisms", "cell", "growth", "experimental", "organism", "systems", "molecular", "biology", "techniques", "research", "and", "ana...	2017	Dual role of starvation signaling in promoting growth and recovery
Dengue fever is a ubiquitous arboviral infection in tropical and sub-tropical regions , whose incidence has increased over recent decades . In the absence of a rapid point of care test , the clinical diagnosis of dengue is complex . The World Health Organisation has outlined diagnostic criteria for making the diagnosis...	Dengue is an infectious disease transmitted by mosquitoes in the Tropics . There are 2 . 5 billion people around the world at risk . Dengue presents as an acute febrile illness with symptoms including headache , bone or joint and muscular pains and rash . The objective of this study is to perform a diagnostic accuracy ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "database", "searching", "research", "design", "age", "groups", "mathematics", "signs", "and", "symptoms", "statis...	2016	Tourniquet Test for Dengue Diagnosis: Systematic Review and Meta-analysis of Diagnostic Test Accuracy
Checkpoint pathways regulate genomic integrity in part by blocking anaphase until all chromosomes have been completely replicated , repaired , and correctly aligned on the spindle . In Saccharomyces cerevisiae , DNA damage and mono-oriented or unattached kinetochores trigger checkpoint pathways that bifurcate to regula...	Previous studies showed that phosphorylation of a subset of regulatory ( R ) subunits of the cAMP-dependent protein kinase ( PKA ) occurred under conditions that down-regulate global PKA activity , including growth on non-fermentable carbon sources . However , the role of the phosphorylation sites has not been elucidat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "mitosis", "model", "organisms", "cell", "division", "chromosome", "biology", "biology", "molecular", "biology", "signal", "transduction", "pka", "signaling", "cascade", "cell", "biology", "yeast", "and", "fungal", "models", "molecular", "cell", "biolo...	2011	Proteins in the Nutrient-Sensing and DNA Damage Checkpoint Pathways Cooperate to Restrain Mitotic Progression following DNA Damage
Real-time tracking of vigilance states related to both sleep or anaesthesia has been a goal for over a century . However , sleep scoring cannot currently be performed with brain signals alone , despite the deep neuromodulatory transformations that accompany sleep state changes . Therefore , at heart , the operational d...	Real-time tracking of vigilance states related to wake , sleep , and anaesthesia has been a goal for over a century . However identification of wakefulness and different sleep states cannot currently be performed routinely with brain signals and instead relies on motor activity . Here we demonstrate that 50–70 Hz elect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "methods", "and", "resources", "sleep", "anesthesiology", "brain", "electrophysiology", "brain", "electrophysiology", "neuroscience", "physiological", "processes", "clinical", "medicine", "pharmaceutics", "anesthesia", "gamma", "spec...	2018	Harnessing olfactory bulb oscillations to perform fully brain-based sleep-scoring and real-time monitoring of anaesthesia depth
Ectomycorrhizal fungi ( EMF ) represent one of the major guilds of symbiotic fungi associated with roots of forest trees , where they function to improve plant nutrition and fitness in exchange for plant carbon . Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the...	Ectomycorrhizal fungi ( EMF ) comprise the dominant group of symbiotic fungi associated with plant roots in temperate and boreal forests . We examined host-specificity and gene-expression of five EMF Suillus species that exhibited strong patterns of mycorrhizal compatibility/incompatibility with either white pines ( Pi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "symbiosis", "trees", "fungi", "plant", "science", "genome", "analysis", "plant", "pathology", "plants", "mycology", "genomics", "pines", "gene", "expression",...	2016	Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus
Allantoin is the end product of purine catabolism in all mammals except humans , great apes , and one breed of dog , the Dalmatian . Humans and Dalmatian dogs produce uric acid during purine degradation , which leads to elevated levels of uric acid in blood and urine and can result in significant diseases in both speci...	Animals excrete waste products in their urine . When most mammals metabolize compounds , called purines , they produce allantoin as one waste product in their urine . Humans , great apes , and Dalmatian dogs produce a different breakdown product , uric acid . This leads to high levels of uric acid in the urine and bloo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/animal", "genetics", "biochemistry", "genetics", "and", "genomics/animal", "genetics", "physiology/renal,", "fluid,", "and", "electrolyte", "physiology", "physiology/gastroenterology", "and", "hepatology" ]	2008	Mutations in the SLC2A9 Gene Cause Hyperuricosuria and Hyperuricemia in the Dog
The current antibody detection tests for the diagnosis of gambiense human African trypanosomiasis ( HAT ) are based on native variant surface glycoproteins ( VSGs ) of Trypanosoma brucei ( T . b . ) gambiense . These native VSGs are difficult to produce , and contain non-specific epitopes that may cause cross-reactions...	The control of human African trypanosomiasis or sleeping sickness , a deadly disease in sub-Saharan Africa , mainly depends on a correct diagnosis and treatment . The aim of our study was to identify mimotopic peptides ( mimotopes ) that may replace the native proteins in antibody detection tests for sleeping sickness ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "sequencing", "medicine", "clinical", "laboratory", "sciences", "protein", "interactions", "immunology", "microbiology", "parastic", "protozoans", "glycoproteins", "sequence", "analysis", "synthetic", "peptide", "biology", "proteomics", "biochemistry", ...	2011	Identification of Peptide Mimotopes of Trypanosoma brucei gambiense Variant Surface Glycoproteins
Despite many advances in AIDS research , a cure for HIV infection remains elusive . Here , we performed autologous hematopoietic stem cell transplantation ( HSCT ) in three Simian/Human Immunodeficiency Virus ( SHIV ) -infected , antiretroviral therapy ( ART ) -treated rhesus macaques ( RMs ) using HSCs collected prior...	While antiretroviral therapy ( ART ) can reduce HIV replication , it does not eradicate the virus from an infected individual . Replication-competent viruses persist on ART and our incomplete understanding of these viral reservoirs greatly complicates the generation of a cure for HIV . In this study we performed , for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "antiviral", "therapeutics", "viral", "persistence", "and", "latency", "virology", "biology", "and", "life", "sciences", "microbiology" ]	2014	Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus Macaques after Autologous Hematopoietic Stem Cell Transplant
Leptospirosis is a bacterial zoonosis of major concern on tropical islands . Human populations on western Indian Ocean islands are strongly affected by the disease although each archipelago shows contrasting epidemiology . For instance , Mayotte , part of the Comoros Archipelago , differs from the other neighbouring is...	Islands are exceptionally prone to species introduction , including pathogens with detrimental public health consequences for which the invasive alien species could act as reservoirs . Our study shows how the local non-native mammal fauna of Mayotte Island is associated with the introduction and epidemiology of human l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "leptospira", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "dogs", "urine", "molecular...	2016	Identification of Tenrec ecaudatus, a Wild Mammal Introduced to Mayotte Island, as a Reservoir of the Newly Identified Human Pathogenic Leptospira mayottensis
Visceral leishmaniasis ( VL ) , caused by protozoa of the Leishmania donovani complex , is a widespread parasitic disease of great public health importance; without effective chemotherapy symptomatic VL is usually fatal . Distinction of asymptomatic carriage from progressive disease and the prediction of relapse follow...	Visceral leishmaniasis ( VL ) is a systemic disease with highest prevalence in South Asia , East Africa , and Brazil . VL is caused by protozoan ( unicellular ) parasites of the Leishmania donovani complex , transmitted to humans when an infected sandfly takes a bloodmeal . Within the human host , the parasites replica...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "biochemistry", "immune", "system", "proteins", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "antibody", "isotypes", "proteins", "leishmaniasis", "protozoan", "infections", "biology", "and", "life", "sciences", "immunology", ...	2014	IgG1 as a Potential Biomarker of Post-chemotherapeutic Relapse in Visceral Leishmaniasis, and Adaptation to a Rapid Diagnostic Test
The information processing capacity of the human mind is limited , as is evidenced by the so-called “attentional-blink” deficit: When two targets ( T1 and T2 ) embedded in a rapid stream of events are presented in close temporal proximity , the second target is often not seen . This deficit is believed to result from c...	Meditation includes the mental training of attention , which involves the selection of goal-relevant information from the array of inputs that bombard our sensory systems . One of the major limitations of the attentional system concerns the ability to process two temporally close , task-relevant stimuli . When the seco...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "homo", "(human)" ]	2007	Mental Training Affects Distribution of Limited Brain Resources
All Yersinia species target and bind to phagocytic cells , but uptake and destruction of bacteria are prevented by injection of anti-phagocytic Yop proteins into the host cell . Here we provide evidence that CD8+ T cells , which canonically eliminate intracellular pathogens , are important for restricting Yersinia , ev...	Pathogenic Yersinia are bacteria that cause diverse diseases such as gastroenteritis and plague . Yersinia binds to specialized immune cells called macrophages , which attempt to engulf and destroy the bacteria . The bacteria resist destruction by injecting proteins called Yops into macrophages , which stops the engulf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections" ]	2009	CD8+ T Cells Restrict Yersinia pseudotuberculosis Infection: Bypass of Anti-Phagocytosis by Targeting Antigen-Presenting Cells
The microtubule-based motor dynein generates pulling forces for centrosome centration and mitotic spindle positioning in animal cells . How the essential dynein activator dynactin regulates these functions of the motor is incompletely understood . Here , we dissect the role of dynactin's microtubule binding activity , ...	Animal cells rely on molecular motor proteins to distribute intracellular components and organize their cytoplasmic content . The motor cytoplasmic dynein 1 ( dynein ) uses microtubule filaments as tracks to transport cargo from the cell periphery to the cell center , where the microtubule minus ends are embedded at th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "centrosomes", "vesicles", "caenorhabditis", "animals", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "dyneins", "molecular", "motors", "model", "organisms", "mathematics", "statistics", "(mathematics)", "experimental", "organis...	2017	Dynactin binding to tyrosinated microtubules promotes centrosome centration in C. elegans by enhancing dynein-mediated organelle transport
In recent years , two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations . However , the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators ....	Two-photon calcium imaging is one of the major tools to study the activity of large populations of neurons in the brain . In this technique , a fluorescent calcium indicator changes its brightness when a neuron fires an action potential due to an associated increase in intracellular calcium . However , while a number o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "machine", "learning", "algorithms", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "applied", "mathematics", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "algorithms", "mathematics", ...	2018	Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
For many bacteria with sequenced genomes , we do not understand how they synthesize some amino acids . This makes it challenging to reconstruct their metabolism , and has led to speculation that bacteria might be cross-feeding amino acids . We studied heterotrophic bacteria from 10 different genera that grow without ad...	For a few bacteria , it is well known how they can make all 20 of the standard amino acids ( the building blocks of proteins ) . For many other bacteria , their genome sequence implies that there are gaps in these biosynthetic pathways , so that the bacteria cannot make all of the amino acids and would need to take up ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "b", "vitamins", "chemical", "compounds", "enzymes", "enzymology", "organic", "compounds", "phosphatases", "serine", "genetic", "elements", "basic", "amino", "acids", "amino", "acids", "cobalamins", "genomics", "proteins", "chemistry", "vitamins", "methionine", "sulfur"...	2018	Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
The intrinsic oncotropism and oncosuppressive activities of rodent protoparvoviruses ( PVs ) are opening new prospects for cancer virotherapy . Virus propagation , cytolytic activity , and spread are tightly connected to activation of the PDK1 signaling cascade , which delays stress-induced cell death and sustains func...	The H-1 protoparvovirus ( H-1PV ) is the first replication-competent member of the Parvoviridae family to undergo a phase I/IIa clinical trial in patients suffering from glioblastoma multiforme . Although the intrinsic oncotropism and oncolytic activity of protoparvoviruses are well known , the underlying molecular mec...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	PKCη/Rdx-driven Phosphorylation of PDK1: A Novel Mechanism Promoting Cancer Cell Survival and Permissiveness for Parvovirus-induced Lysis
The activation of interferon ( IFN ) -regulatory factor-3 ( IRF3 ) , characterized by phosphorylation and nuclear translocation of the latent transcription factor , is central to initiating innate antiviral responses . Whereas much has been learned about the upstream pathways and signaling mechanisms leading to IRF3 ac...	The induction of IFN antiviral response is a hallmark of immediate host immune responses to viral infections . In a majority of cell types , eliciting this intrinsic defense mechanism depends on activation of IRF3 , characterized by C-terminal phosphorylation , dimerization and subsequent nuclear translocation of the l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "immunology", "immunoblotting", "microbiology", "immune", "...	2017	Pivotal role for the ESCRT-II complex subunit EAP30/SNF8 in IRF3-dependent innate antiviral defense
Leprosy is a persistent infectious disease caused by Mycobacterium leprae that still affects over 200 , 000 new patients annually . The host genetic background is an important risk factor for leprosy susceptibility and the PARK2 gene is a replicated leprosy susceptibility candidate gene . The protein product of PARK2 ,...	Leprosy is an infectious disease with a strong host genetic component . The identification of host genetic lesions predisposing to disease is a powerful approach for mapping key junctions in the host pathogen interplay . Genetic variants located in the promoter region of the PARK2 gene are replicated leprosy susceptibi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "leprosy" ]	2013	PARK2 Mediates Interleukin 6 and Monocyte Chemoattractant Protein 1 Production by Human Macrophages
Establishment of left-right ( LR ) asymmetry occurs after gastrulation commences and utilizes a conserved cascade of events . In the mouse , LR symmetry is broken at a midline structure , the node , and involves signal relay to the lateral plate , where it results in asymmetric organ morphogenesis . How information tra...	Superficially , humans , like other vertebrates , are bilaterally symmetrical . Nonetheless , the internal configuration of visceral organs reveals a stereotypical asymmetry . For example , human hearts are generally located on the left and the liver on the right side within the body cavity . How this left-right asymme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "histology", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Role of the Gut Endoderm in Relaying Left-Right Patterning in Mice
Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera , a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care . Like most pathogenic bacteria , V . cholerae secretes virulence factors to assist colonization of human hosts , several of whi...	Bacterial pathogens secrete multiple virulence factors to aid in infection including adhesion molecules , effector proteins , enzymes , toxins and biofilm proteins . To increase the potency and specificity of these molecules , many factors contain binding sites for host cell-surface receptors . This study involves two ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "bacteriology", "medicine", "and", "health", "sciences", "toxins", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "vibrio", "condensed", "matter", "physics", "microbiology", "carbohydrates", "organic...	2018	Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins
Meiotic recombination , which is necessary to ensure that homologous chromosomes segregate properly , begins with the induction of meiotic DNA double-strand breaks ( DSBs ) and ends with the repair of a subset of those breaks into crossovers . Here we investigate the roles of two paralogous genes , CG12200 and CG31053 ...	Errors in chromosome segregation during meiosis are the leading cause of miscarriages and can result in genetic abnormalities like Down syndrome or Turner syndrome . For chromosomes to segregate faithfully , they must recombine with their homolog during the early steps of meiosis . An essential component of the process...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "meiosis", "yeast", "two-hybrid", "assays", "rna", "interference", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "animal", "models", "germ", "cells", "oocytes", "drosophila", "melanogaster", "model", "organisms", "protein...	2019	Narya, a RING finger domain-containing protein, is required for meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster
MicroRNAs ( miRNAs ) , single-stranded non-coding RNAs , influence myriad biological processes that can contribute to cancer . Although tumor-suppressive and oncogenic functions have been characterized for some miRNAs , the majority of microRNAs have not been investigated for their ability to promote and modulate tumor...	MicroRNAs are small noncoding RNAs that act as posttranscriptional repressors of gene expression . A pivotal role for miRNAs in all the molecular processes driving initiation and progression of various malignancies , including breast cancer , has been described . Divergent miRNA expression between normal and neoplastic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "cancer", "genetics", "genetics", "biology", "basic", "cancer", "research", "genetics", "and", "genomics" ]	2013	Estrogen Mediated-Activation of miR-191/425 Cluster Modulates Tumorigenicity of Breast Cancer Cells Depending on Estrogen Receptor Status
Shiga toxin ( Stx ) is the main virulence factor of enterohemorrhagic Escherichia coli , which are non-invasive strains that can lead to hemolytic uremic syndrome ( HUS ) , associated with renal failure and death . Although bacteremia does not occur , bacterial virulence factors gain access to the circulation and are t...	Shiga toxin-producing enterohemorrhagic Escherichia coli are non-invasive bacteria that , after ingestion , cause disease by systemic release of toxins and other virulence factors . These infections cause high morbidity , including hemolytic uremic syndrome with severe anemia , low platelet counts , renal failure , and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Novel Mechanism of Bacterial Toxin Transfer within Host Blood Cell-Derived Microvesicles
The structural proteins of DNA viruses are generally encoded by late genes , whose expression relies on recruitment of the host transcriptional machinery only after the onset of viral genome replication . β and γ-herpesviruses encode a unique six-member viral pre-initiation complex ( vPIC ) for this purpose , although ...	Gene expression in DNA viruses often occurs in temporal waves , with expression of essential structural proteins occurring late in infection , after viral genome replication has begun . Strategies underlying expression of these viral late genes are often sophisticated; for example , the β- and γ-herpesviruses encode a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "gene", "regulation", "microbiology", "enzymology", "dna", "transcription", "viruses", "dna", "replication", "dna", "viruses", "sequence", "motif...	2019	An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking , identifying 4609 unique-mass crosslink ions at an effective FDR of 0 . 33% , covering 2534 unique pairs of crosslinked protein positions , 625 of which were inter-protein . The data were statisti...	Vaccinia is one of the most complex virions among the animal viruses , containing 70+ distinct gene products . Although virion ultrastructure has been apparent , at least in outline by electron microscopy since the year 1961 or earlier , its molecular architecture is largely unknown: Vaccinia is resistant to classical ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "chemical", "bonding", "urea", "protein", "interactions", "chemical", "compounds", "enzymes", "microbiology", "enzymology", "viral", "structure", "organic", "compounds", "tartrates", "membrane", "proteins", "serine", "proteases", "cellular", "structures", "and", "organell...	2019	The Vaccinia virion: Filling the gap between atomic and ultrastructure
Cells live in changing , dynamic environments . To understand cellular decision-making , we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks . Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represen...	Cells do not live in constant conditions , but in environments that change over time . To adapt to their surroundings , cells must therefore sense fluctuating concentrations and ‘interpret’ the state of their environment to see whether , for example , a change in the pattern of gene expression is needed . This task is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complex", "systems", "systems", "biology", "mathematics", "applied", "mathematics", "biology", "genetics", "and", "genomics" ]	2013	The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
Changes in histone acetylation occur during oocyte development and maturation , but the role of specific histone deacetylases in these processes is poorly defined . We report here that mice harboring Hdac1−/+/Hdac2−/− or Hdac2−/− oocytes are infertile or sub-fertile , respectively . Depleting maternal HDAC2 results in ...	Oocyte development is becoming of increasing interest not only in the broad research community but also within the general public due , in part , to the ever increasing demand for and use of assisted reproductive technologies ( ART ) to treat human infertility , and because the oocyte-to-embryo transition encompasses a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Histone Deacetylase 2 (HDAC2) Regulates Chromosome Segregation and Kinetochore Function via H4K16 Deacetylation during Oocyte Maturation in Mouse
Asparagine synthetase ( ASNS ) and CTP synthase ( CTPS ) are two metabolic enzymes crucial for glutamine homeostasis . A genome-wide screening in Saccharomyces cerevisiae reveal that both ASNS and CTPS form filamentous structures termed cytoophidia . Although CTPS cytoophidia were well documented in recent years , the ...	Asparagine synthetase ( ASNS ) is an essential enzyme for biosynthesis of asparagine . We have recently shown that ASNS , similar to CTP synthase ( CTPS ) , can assemble into snake-shaped structures termed cytoophidia . In this study , we reveal that the ASNS cytoophidium stays close with the CTPS cytoophidium in most ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "enzymes", "enzymology", "carbohydrates", "organic", "compounds", "glucose", "asparagine", "fungi", "model", "organisms", "materials", "science", "experimental", "organism", "systems", "enzyme", "metabolism", "acidic", "amino", "acids", "amino", ...	2018	Filamentation of asparagine synthetase in Saccharomyces cerevisiae
Brucellosis is a worldwide recognized bacterial zoonotic disease . There is currently no information on bovine brucellosis sero-prevalence in South Sudan regardless of the economic , social and public health impact on populations . Therefore , for the first time in 33 years , we report the sero-prevalence of brucellosi...	Enzootic brucellosis is a bacterial infectious disease , which represents millions of dollars in production losses in livestock , as well as Disability- Adjusted Life Years ( DALYS ) associated with health and treatment in the human populations for Low and Middle Income Countries ( LMICs ) . Despite these unequivocally...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "ruminants", "tropical", "diseases", "geographical", "locations", "vertebrates", "south", "sudan", "animals", "brucellosis", "mammals", "bacterial", "diseases", "neglected", "tropical", "diseases", "africa", "veterinar...	2018	The sero-prevalence of brucellosis in cattle and their herders in Bahr el Ghazal region, South Sudan
Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation . In contrast , less is known about the effects of large sequence or structure changes on the stability of a particular fold . Almost completely unknown is the degree to which stability of differ...	Protein structure and function are fundamentally determined by thermodynamics . However , for technical as well as historical reasons , current evolutionary classification schemes and bioinformatics tools do not fully utilize thermodynamic information to describe or analyze proteins . In this work , we address this def...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biophysics", "evolutionary", "biology/bioinformatics", "computational", "biology" ]	2010	Investigating Homology between Proteins using Energetic Profiles
Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom ( AA ) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein ( HA-Gō ) , the assoc...	Although experimentalists can now unfold single proteins in the lab by pulling them apart and measuring the force and extension , a clear idea of how the protein changes shape and loses structure during this process is currently missing . Molecular dynamics simulations can offer insight as to what is actually happening...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "enzymes", "condensed", "matter", "physics", "enzymology", "dismutases", "simulation", "and", "modeling", "protein", "structure", "prediction", "protein", "structure", "research", "and", "analysis", "methods", "relaxation", "(physics)", "proteins", "melting", "phase", "...	2016	As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy
Chlamydia trachomatis attachment to cells induces the secretion of the elementary body–associated protein TARP ( Translocated Actin Recruiting Protein ) . TARP crosses the plasma membrane where it is immediately phosphorylated at tyrosine residues by unknown host kinases . The Rac GTPase is also activated , resulting i...	The human pathogen Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted disease in industrialized nations , and of the preventable blinding condition trachoma in developing countries . Survival and replication of chlamydial species occur exclusively inside a host cell , and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", "biology/cell", "signaling" ]	2008	Chlamydial Entry Involves TARP Binding of Guanine Nucleotide Exchange Factors
After endocytic uptake , influenza viruses transit early endosomal compartments and eventually reach late endosomes . There , the viral glycoprotein hemagglutinin ( HA ) triggers fusion between endosomal and viral membrane , a critical step that leads to release of the viral segmented genome destined to reach the cell ...	Influenza A virus carries its segmented genome inside a lipid envelope . Since genome replication occurs inside the nucleus , the main goal of virus infection is to deliver all genome segments through the cytoplasm into the nucleus . After endocytic uptake , influenza viruses transit early endosomal compartments and ev...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "signaling", "networks", "orthomyxoviruses", "viruses", "wireless", "sensor", "networks", "membrane", "fusion", "rna", "...	2016	Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

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