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The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics ( MD ) simulations complemented with a variety of experimental techniques . Results strongly suggest that the intermediate is reached very early in the thermal unfolding process ...	A simplistic view of protein structure tends to emphasize the opposition between the native state and the denatured ensemble of unfolded conformations . In addition to these extreme conformations , proteins subjected to a variety of perturbations often populate alternative partly unfolded conformations , some of which ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "computer", "science", "chemistry", "biology" ]	2012	Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
Inappropriate recollections and responses in stressful conditions are hallmarks of post-traumatic stress disorder and other anxiety and mood disorders , but how stress contributes to the disorders is unclear . Here we show that stress itself reactivates memories even if the memory is unrelated to the stressful experien...	This work identifies a powerful effect of stressful experiences on memories . We report that a single intensely stressful experience can activate memories in a situation that has essentially no physical or motivational relationship to the stressful experience . Using a forced-swim test as a stressor in rats , we find t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/neurobiology", "of", "disease", "and", "regeneration", "neuroscience/animal", "cognition", "neuroscience/experimental", "psychology" ]	2010	Stress-Induced Out-of-Context Activation of Memory
The MglA protein is the only known regulator of virulence gene expression in Francisella tularensis , yet it is unclear how it functions . F . tularensis also contains an MglA-like protein called SspA . Here , we show that MglA and SspA cooperate with one another to control virulence gene expression in F . tularensis ....	The Gram-negative bacterium Francisella tularensis is an intracellular pathogen and the causative agent of tularemia . In F . tularensis , the MglA protein is the only known regulator of virulence genes that are important for intracellular survival , yet it is not known how MglA functions . F . tularensis also contains...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "microbiology", "molecular", "biology", "eubacteria" ]	2007	Twin RNA Polymerase–Associated Proteins Control Virulence Gene Expression in Francisella tularensis
There is a revolution in the ability to analyze gene expression of single cells in a tissue . To understand this data we must comprehend how cells are distributed in a high-dimensional gene expression space . One open question is whether cell types form discrete clusters or whether gene expression forms a continuum of ...	In the past , biological experiments usually pooled together millions of cells , masking the differences between individual cells . Current technology takes a big step forward by measuring gene expression from individual cells . Interpreting this data is challenging because we need to understand how cells are arranged ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Geometry of the Gene Expression Space of Individual Cells
Follicular T helper cells ( TFH ) are fundamental in orchestrating effective antibody-mediated responses critical for immunity against viral infections and effective vaccines . However , it is unclear how virus infection leads to TFH induction . We here show that dengue virus ( DENV ) infection of human dendritic cells...	Strong antibody production is critical for effective immune responses against viral infections and is a primary factor in the development of successful vaccines . However , it is unclear how virus infection leads to effective antibody responses . Dengue virus ( DENV ) is known to induce potent antibody production , alt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "immune", "physiology", "gene", "regulation", "immunology", "microbiology", "cell", "differentiation", "developmental", "biology", "antibodi...	2017	RIG-I-like receptor activation by dengue virus drives follicular T helper cell formation and antibody production
Infection of the genitourinary tract with Group B Streptococcus ( GBS ) , an opportunistic gram positive pathogen , is associated with premature rupture of amniotic membrane and preterm birth . In this work , we demonstrate that GBS produces membrane vesicles ( MVs ) in a serotype independent manner . These MVs are loa...	Preterm birth is a major health concern globally as it is not only a leading cause of neonatal death , but also has long term consequences including defective brain development . Infection of vagina and cervix of pregnant women with the bacteria , Group B Streptococcus ( GBS ) , causes chorio-amnionitis that significan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "uterus", "medicine", "and", "health", "sciences", "reproductive", "system", "vesicles", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "hela", "cells", "immunology", "biological", "cultures", "collagens", "preterm...	2016	Membrane Vesicles of Group B Streptococcus Disrupt Feto-Maternal Barrier Leading to Preterm Birth
Wolbachia is currently being developed as a novel tool to block the transmission of dengue viruses ( DENV ) by Aedes aegypti . A number of mechanisms have been proposed to explain the DENV-blocking phenotype in mosquitoes , including competition for fatty acids like cholesterol , manipulation of host miRNAs and upregul...	Dengue virus ( DENV ) is a human pathogen transmitted by Aedes mosquitoes . Infection with DENV causes dengue fever and may develop into life-threatening dengue hemorrhagic fever . Dengue disease is increasing globally and current control methods are proving ineffective in curtailing this growing problem . A novel stra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "biological", "cultures", "microbiology", "wolbachia", "viruses", "micrornas", "rna", "viruses", "cell", "cultures", "bacteria", ...	2018	Wolbachia-mediated virus blocking in mosquito cells is dependent on XRN1-mediated viral RNA degradation and influenced by viral replication rate
HIV-1 escape from the cytotoxic T-lymphocyte ( CTL ) response leads to a weakening of viral control and is likely to be detrimental to the patient . To date , the impact of escape on viral load and CD4+ T cell count has not been quantified , primarily because of sparse longitudinal data and the difficulty of separating...	HIV , like many viruses , has evolved multiple strategies to evade immune surveillance . One of these strategies is the evolution of escape mutations which reduce the ability of the immune response to kill HIV-infected cells . But does HIV escape matter ? Some believe that the accumulation of escape mutations leads to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "computational", "biology" ]	2010	Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes
The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal , with subpopulations of neoplastic cells harboring distinct mutations . A fine resolution view of this clonal architecture provides insight into tumor heterogeneity , evolution , and treatment response , all of which may h...	Sequencing the genomic DNA of cancers has revealed that tumors are not homogeneous . As a tumor grows , new mutations accumulate in individual cells , and as these cells replicate , the mutations are passed on to their offspring , which comprise only a portion of the tumor when it is sampled . We present a method for i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "cancer", "genetics", "breast", "tumors", "obstetrics", "and", "gynecology", "cancer", "treatment", "cancers", "and", "neoplasms", "hematologic", "cancers", "and", "related", "disorders", "oncology", ...	2014	SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
One of the most obvious phenotypes of a cell is its metabolic activity , which is defined by the fluxes in the metabolic network . Although experimental methods to determine intracellular fluxes are well established , only a limited number of fluxes can be resolved . Especially in eukaryotes such as yeast , compartment...	Fluxes in metabolic pathways are a highly informative aspect of an organism's phenotype . The experimental determination of such fluxes is well established and has proven very useful . To address some of the limitations of experimental flux analysis , such as when the cell is divided in multiple compartments , stoichio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "model", "organisms", "yeast", "and", "fungal", "models", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes
Interferon-γ inducible factor 16 ( IFI16 ) is a multifunctional nuclear protein involved in transcriptional regulation , induction of interferon-β ( IFN-β ) , and activation of the inflammasome response . It interacts with the sugar-phosphate backbone of dsDNA and modulates viral and cellular transcription through larg...	HSV-1 , a ubiquitous human pathogen that establishes a life-long infection , has evolved several mechanisms to evade host immune detection and responses . However , it is still subject to regulation by cellular factors . Recently , a host nuclear protein , IFI16 , was shown to be involved in the innate defense response...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "herpes", "simplex", "virus", "gene", "expression", "and", "vector", "techniques", "medical", "microbiology", "virology", "viral", "pathogens", "molecular", "biology", "microbial", "pathogens", "biology", "and", "life", "sciences", "molecular", "biology", "...	2014	IFI16 Restricts HSV-1 Replication by Accumulating on the HSV-1 Genome, Repressing HSV-1 Gene Expression, and Directly or Indirectly Modulating Histone Modifications
Campylobacter is one of the main causes of gastroenteritis worldwide . Most of the current knowledge about the epidemiology of this food-borne infection concerns two species , C . coli and C . jejuni . Recent studies conducted in developing countries and using novel diagnostic techniques have generated evidence of the ...	Campylobacter is a major public health concern in developed and developing countries . C . coli and C . jejuni have long been considered to be the major disease-causing species , and clinical microbiologic approaches target these two species . However , less selective diagnostic approaches have shown the increasing imp...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "dysentery", "pathogens", "tropical", "diseases", "microbiology", "shigella", "pediatrics", "diarrhea", "bacterial", "diseases", "signs", "and", "symptoms", "gastroe...	2018	The other Campylobacters: Not innocent bystanders in endemic diarrhea and dysentery in children in low-income settings
Few data on dengue epidemiology are available for Lao PDR . Here , we provide information on the complexity of dengue epidemiology in the country , demonstrating dynamic circulation that varies over space and time , according to serotype . We recruited 1 , 912 consenting patients presenting with WHO dengue criteria at ...	Dengue is a mosquito-borne disease that can be caused by 4 viruses . It is a flu-like disease but can sometime be more severe and cause hemorrhage or death . An estimated 390 million people are infected every year , mainly in the Western Pacific and in South-East Asia . In Laos , where our study was conducted from 2006...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "taxonomy", "dengue", "virus", "medicine", "and", "health", "sciences", "lao", "people", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "rna", "extraction", "...	2018	Molecular epidemiology of dengue viruses in three provinces of Lao PDR, 2006-2010
In natural systems , selection acts on both protein sequence and expression level , but it is unclear how selection integrates over these two dimensions . We recently developed the EMPIRIC approach to systematically determine the fitness effects of all possible point mutants for important regions of essential genes in ...	Changes in protein sequence or expression strength can both lead to adaptation in natural systems . While many studies have focused individually on either expression strength or protein sequence , in principle the fitness effects of these two protein properties are interdependent . We systematically investigated the fi...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "mutagenesis", "mutation", "model", "organisms", "genetic", "mutation", "gene", "expression", "genetics", "population", "genetics", "yeast", "and", "fungal", "models", "biology", "saccharomyces", "cerevisiae" ]	2013	Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels
Rural populations in low-income countries commonly suffer from the co-morbidity of neglected tropical diseases ( NTDs ) . Podoconiosis , trachomatous trichiasis ( both NTDs ) and cataract are common causes of morbidity among subsistence farmers in the highlands of northern Ethiopia . We explored whether podoconiosis wa...	Podoconiosis is an NTD causing chronic leg swelling in subsistence farming communities in the tropics . There is no research on the association between podoconiosis and two common causes of blindness and visual impairment; trachomatous trichiasis ( TT ) and cataract . TT is the blinding consequence of conjunctival scar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "lens", "disorders", "tropical", "diseases", "geographical", "locations", "ocular", "anatomy", "parasitic", "diseases", "surgical", "and", "invasive", "medical", "procedures", "bacterial", "diseases", "eye", "diseases", "neglecte...	2017	Podoconiosis, trachomatous trichiasis and cataract in northern Ethiopia: A comparative cross sectional study
Chikungunya virus is a mosquito-borne alphavirus which causes an acute febrile illness associated with polyarthralgia . Beginning in August 2013 , clinicians from the Yap State Department of Health in the Federated States of Micronesia ( FSM ) identified an unusual cluster of illness which was subsequently confirmed to...	Chikungunya virus can cause large outbreaks with substantial morbidity , especially in places with certain Aedes species of mosquitos and immunologically-naïve populations . In August 2013 , chikungunya virus disease was identified for the first time in the Federated States of Micronesia . The explosive outbreak that f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "federated", "states", "of", "micronesia", "pathogens", "immunolog...	2017	Chikungunya virus disease outbreak in Yap State, Federated States of Micronesia
Synaptic structure and activity are sensitive to environmental alterations . Modulation of synaptic morphology and function is often induced by signals from glia . However , the process by which glia mediate synaptic responses to environmental perturbations such as hypoxia remains unknown . Here , we report that , in t...	Oxygen is essential for animals to maintain their life such as growth , metabolism , responsiveness , and movement . It is therefore important to understand how animal cells trigger hypoxia response and adapt to hypoxia thereafter . Both mammalian vascular and insect tracheal branches are induced to enhance the oxygen ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "oxygen", "neuroscience", "biological", "locomotion", "pulmonology", "animals", "animal", "models", "organisms", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "hypoxia", "experimenta...	2019	Glial response to hypoxia in mutants of NPAS1/3 homolog Trachealess through Wg signaling to modulate synaptic bouton organization
Genomic Selection ( GS ) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population . GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species , and here we evaluate for the first time its efficacy for breed...	Genomic selection is a promising breeding technique that aims to improve the efficiency and speed of the breeding process . While it has been shown to be effective in crops such as wheat and corn , it has not yet been applied to rice breeding . Genome-wide association studies ( GWAS ) , by contrast , are used to identi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines
Calmodulin ( CaM ) is a calcium sensing protein that regulates the function of a large number of proteins , thus playing a crucial part in many cell signaling pathways . CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner , mainly through the exposure of hydrophobic residues ....	Calmodulin is a protein involved in the regulation of a variety of cell signaling pathways . It acts by making usually calcium-insensitive proteins sensitive to changes in the calcium concentration inside the cell . Its two lobes bind calcium and allow the energetically unfavorable exposure of hydrophobic residues to t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "chemical", "characterization", "medicine", "and", "health", "sciences", "molecular", "dynamics", "protein", "interactions", "electrophysiology", "neuroscience", "ion", "channels", "molecular", "motors", "actin", "motors", "protein", "structure", "thermodynamics", "motor", ...	2018	Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
In 2005 , there were outbreaks of febrile polyarthritis due to Chikungunya virus ( CHIKV ) in the Comoros Islands . CHIKV then spread to other islands in the Indian Ocean: La Réunion , Mauritius , Seychelles and Madagascar . These outbreaks revealed the lack of surveillance and preparedness of Madagascar and other coun...	Chikungunya is a mosquito-transmitted viral disease . No treatment is currently available . The only way to prevent infection is to avoid mosquito bites . Surveillance of circulation by early diagnosis is useful to prevent or limit outbreak . CHIKV , like all RNA viruses , is heat-labile . Consequently , confirmatory d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "survey", "methods", "diagnostic", "medicine", "emerging", "infectious", "diseases", "infectious", "disease", "epidemiology", "virology", "epidemiology", "emerging", "viral", "diseases", "neglected", "tropical", ...	2013	Dried-Blood Spots: A Cost-Effective Field Method for the Detection of Chikungunya Virus Circulation in Remote Areas
The bank vole is a rodent susceptible to different prion strains from humans and various animal species . We analyzed the transmission features of different prions in a panel of seven rodent species which showed various degrees of phylogenetic affinity and specific prion protein ( PrP ) sequence divergences in order to...	Prions are unconventional infectious agents that cause fatal neurodegenerative diseases in animals and humans . A pathological form of the cellular prion protein ( PrPC ) , named PrPSc , appears to be the major or the sole component of prions . These agents are transmitted by inducing the conversion of host PrPC into P...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/prion", "diseases", "pathology/histopathology", "genetics", "and", "genomics/genetics", "of", "disease", "neuroscience/neurobiology", "of", "disease", "and", "regenerati...	2008	Prion Protein Amino Acid Determinants of Differential Susceptibility and Molecular Feature of Prion Strains in Mice and Voles
The adaptation of Chikungunya virus ( CHIKV ) to a new vector , the Aedes albopictus mosquito , is a major factor contributing to its ongoing re-emergence in a series of large-scale epidemics of arthritic disease in many parts of the world since 2004 . Although the initial step of CHIKV adaptation to A . albopictus was...	Since 2004 , chikungunya virus ( CHIKV ) has caused a series of devastating outbreaks in Asia , Africa and Europe that resulted in up to 6 . 5 million cases of arthritic disease and have been associated with several thousand human deaths . Although the initial step of CHIKV adaptation to A . albopictus mosquitoes , whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "organismal", "evolution", "infectious", "diseases", "forms", "of", "evolution", "microevolution", "microbial", "evolution", "virology", "biology", "evolutionary", "biology", "microbiology", "evolutionary", "genetics", "viral", "evolution" ]	2011	Sequential Adaptive Mutations Enhance Efficient Vector Switching by Chikungunya Virus and Its Epidemic Emergence
During lytic replication of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell . Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and , consequently , reduction of...	Herpesviruses produce noncoding RNAs , some of which are essential to the viral life cycle . One such noncoding RNA from Kaposi’s sarcoma-associated herpesvirus is the polyadenylated , nuclear ( PAN ) RNA , which is required for production and release of progeny virions from infected cells . In this study , we demonstr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "infographics", "medicine", "and", "health", "sciences", "non-coding", "rna", "sequences", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "nucleotides", "charts", "viruses", "dna", "viruses", "rna", "isolation", "epigeneti...	2018	Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci
Successive division events in the spherically shaped bacterium Staphylococcus aureus are oriented in three alternating perpendicular planes . The mechanisms that underlie this relatively unique pattern of division and coordinate it with chromosome segregation remain largely unknown . Thus far , the only known spatial r...	The mechanisms by which bacteria coordinate cell division with chromosome replication and segregation remain poorly understood . This coordination is particularly challenging in the spherical bacterium Staphylococcus aureus , which unlike rod-shaped bacteria , divides in three consecutive perpendicular division planes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "cycle", "and", "cell", "division", "cell", "processes", "bacillus", "microbiology", "light", "microscopy", "staphylococcus", "aureus", "prokaryotic", "models", ...	2017	The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus
Pleiotropy refers to the phenomenon in which a single gene controls several distinct , and seemingly unrelated , phenotypic effects . We use C . elegans early embryogenesis as a model to conduct systematic studies of pleiotropy . We analyze high-throughput RNA interference ( RNAi ) data from C . elegans and identify “p...	In a biological system , some genes play single roles while others perform multiple functions . How can we determine which genes are multi-functional ? An informative way for probing gene functions is to eliminate the expression of a given gene and observe the phenotypic consequences . RNAi techniques have enabled the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "computational", "biology/systems", "biology" ]	2008	Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis
Melioidosis is a neglected tropical disease endemic across South East Asia and Northern Australia . The etiological agent , Burkholderia pseudomallei ( B . pseudomallei ) , is a Gram-negative , rod-shaped , motile bacterium residing in the soil and muddy water across endemic regions of the tropical world . The bacteriu...	B . pseudomallei is a bacterium that causes melioidosis , a disease endemic in Southeastern Asia and Northern Australia . It is estimated that melioidosis leads to 89 , 000 deaths worldwide each year . Nevertheless , melioidosis continues to remain a neglected tropical disease that is not even on the list of neglected ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "spleen", "melioidosis", "immunology", "bacterial", "diseases", "signs", "and", "symptoms", "abscesses", "infectious", "...	2017	Persistent infection due to a small-colony variant of Burkholderia pseudomallei leads to PD-1 upregulation on circulating immune cells and mononuclear infiltration in viscera of experimental BALB/c mice
A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains , and how that chromatin state is faithfully transmitted . Stable heterochromatin is necessary to silence transposable elements ( TEs ) and maintain genome integrity . Both the RNAi system and heterochromatin compon...	Most eukaryotes harbor a high proportion of transposable elements ( TEs ) in their genomes . Heterochromatin , a condensed chromatin state found at domains enriched for TEs and other repetitious elements , is important for silencing TEs and maintaining the integrity of the genome . The RNAi system has been shown to be ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in Drosophila
Praziquantel-based mass treatment is the main approach to controlling schistosomiasis mansoni in endemic areas . Interventions such as provision and use of safe water , minimising contact with infested water , disposal of stool in latrines and snail control provide key avenues to break the transmission cycle and can su...	Schistosomiasis , a neglected tropical disease caused by the blood fluke Schistosoma , is still a huge burden in sub-Saharan Africa . The modalities for its control are mass treatment of the population with praziquantel , minimising contact with infested water , provision and use of safe water , intermediate host snail...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "surface", "water", "water", "resources", "landforms", "helminths", "topography", "tropical", "diseases", "parasitic", "diseases", "ani...	2017	Perceptions about interventions to control schistosomiasis among the Lake Victoria island communities of Koome, Uganda
Protein signaling networks are static views of dynamic processes where proteins go through many biochemical modifications such as ubiquitination and phosphorylation to propagate signals that regulate cells and can act as feed-back systems . Understanding the precise mechanisms underlying protein interactions can elucid...	Traditional canonical signaling pathways help to understand overall signaling processes inside the cell . Large scale phosphoproteomic data provide insight into alterations among different proteins under different experimental settings . Our goal is to combine the traditional signaling networks with complex phosphoprot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "learning", "medicine", "and", "health", "sciences", "breast", "tumors", "ontologies", "protein", "interaction", "networks", "signaling", "networks", "social", "sciences", "cancers", "and", "neoplasms", "neuroscience", "learning", "and", "memory", "on...	2018	Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data
Monocytes are innate immune cells that play a pivotal role in antifungal immunity , but little is known regarding the cellular metabolic events that regulate their function during infection . Using complementary transcriptomic and immunological studies in human primary monocytes , we show that activation of monocytes b...	Fungal infections are a major health concern for immunocompromised individuals due to the lack of success of the currently available antifungal therapies . Unveiling the metabolic processes involved in the immune function offers a promising opportunity for the development of new therapeutic approaches against these inf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "physiology", "carbohydrate", "metabolism", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "yeast", "infections", "p...	2017	Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis
The yellow fever vaccines ( YF-17D-204 and 17DD ) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection , although other immune effector mechanisms are known to be involved . T-cell responses are known to play an important role modulating antibody produ...	T-cell responses are considered to be very important; however , the role of T-cell responses in vaccine mediated immunity is still controversial . One reason may be that most studies of human T-cell responses are focused on a few epitopes . We still lack a systematic view of the repertoire of peptides presented by the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "immune", "cells", "clinical", "research", "design", "jungle", "yellow", "fever", "flavivirus", "immunity", "to", "infections", "dengue", "immunology", "vaccines", "adaptive", "immunity", "cohort", "studies", "neglected", "tropical", "diseases", "immunizatio...	2013	T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs
Anatomic connections between brain areas affect information flow between neuronal circuits and the synchronization of neuronal activity . However , such structural connectivity does not coincide with effective connectivity ( or , more precisely , causal connectivity ) , related to the elusive question “Which areas caus...	The circuits of the brain must perform a daunting amount of functions . But how can “brain states” be flexibly controlled , given that anatomic inter-areal connections can be considered as fixed , on timescales relevant for behavior ? We hypothesize that , thanks to the nonlinear interaction between brain rhythms , eve...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "medicine", "condensed-matter", "physics", "mathematics", "neuroanatomy", "computational", "neuroscience", "neurology", "interdisciplinary", "physics", "neurological", "disorders", "biology", "neuroscience", "nonlinear", "dynamics" ]	2012	Dynamic Effective Connectivity of Inter-Areal Brain Circuits
Resistance ( R ) protein–associated pathways are well known to participate in defense against a variety of microbial pathogens . Salicylic acid ( SA ) and its associated proteinaceous signaling components , including enhanced disease susceptibility 1 ( EDS1 ) , non–race-specific disease resistance 1 ( NDR1 ) , phytoale...	Salicylic acid and enhanced disease susceptibility 1 are important components of resistance gene-mediated defense signaling against diverse pathogens in a variety of plants . Present understanding of plant defense signaling pathways places salicylic acid and enhanced disease susceptibility 1 downstream of resistant pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology" ]	2009	Enhanced Disease Susceptibility 1 and Salicylic Acid Act Redundantly to Regulate Resistance Gene-Mediated Signaling
Escherichia coli translation initiation factor 2 ( IF2 ) performs the unexpected function of promoting transition from recombination to replication during bacteriophage Mu transposition in vitro , leading to initiation by replication restart proteins . This function has suggested a role of IF2 in engaging cellular rest...	Translation Initiation Factor 2 ( IF2 ) is a bacterial protein that plays an essential role in the initiation of protein synthesis . As such , it not only has an important influence on cellular growth but also is subject to regulation in response to physiological conditions such as nutritional deprivation . Biochemical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genetic", "mutation", "enzymes", "microbiology", "escherichia", "coli", "prokaryotic", "models", "model", "organisms", "dna", "replication", "microbial", "evolution", "cell", "growth", "dna", "molecular", "genetics", "dna", "synthesis", "microbial", "ph...	2012	A New Role for Translation Initiation Factor 2 in Maintaining Genome Integrity
Dengue virus ( DENV ) infections are preferentially diagnosed by detection of specific IgM antibodies , DENV NS1 antigen assays or by amplification of viral RNA in serum samples of the patients . The type-specific immunity to the four worldwide circulating DENV serotypes can be determined by neutralization assays . An ...	Infections with four different dengue viruses are threatening 2 . 5 billion people in tropical countries . Since most antibodies to these four viruses are cross-reacting , a type-specific ELISA would be valuable to study the immune response to the circulating viruses in patients but also in healthy subjects in endemic ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Detection of Serotype-Specific Antibodies to the Four Dengue Viruses Using an Immune Complex Binding (ICB) ELISA
Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites . Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression . Previous structural studies of riboswitches largely focused on apt...	Folding dynamics is crucial for RNA function . Riboswitches are a classic example . A typical riboswitch senses the cellular concentration of a small molecule . By refolding itself into a new structure , the riboswitch converts that information into changes in rates for synthesis of related metabolites . Understanding ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "rna", "structure", "prediction", "rna", "structure", "genomics", "computational", "chemistry", "molecular", "dynamics", "nucleic", "acids", "protein", "folding", "gene", "expression", "molecular", "genetics", "rna", "synthesis", "biology", "computational"...	2013	The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Microbial pathogens have developed efficient strategies to compromise host immune responses . Cryptococcus neoformans is a facultative intracellular pathogen , recognised as the most common cause of systemic fungal infections leading to severe meningoencephalitis , mainly in immunocompromised patients . This yeast is c...	Cryptococcus neoformans , the only encapsulated pathogenic yeast , is responsible for severe opportunistic meningoencephalitis mostly in immunocompromised patients . It is a facultative intracellular pathogen and , as such , has the ability to survive intra- and extracellularly . Whereas interactions of C . neoformans ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "molecular", "cell", "biology", "cell", "biology", "chromosome", "biology", "immunity", "biology", "microbiology" ]	2012	Fungal-Induced Cell Cycle Impairment, Chromosome Instability and Apoptosis via Differential Activation of NF-κB
Cereal storage proteins are major nitrogen sources for humans and livestock . Prolamins are the most abundant storage protein in most cereals . They are deposited into protein bodies ( PBs ) in seed endosperm . The inner structure and the storage mechanism for prolamin PBs is poorly understood . Maize opaque10 ( o10 ) ...	Through the positional cloning of the maize classic endosperm mutant opaque10 ( o10 ) , we identified a novel protein critical for PB morphology . O10 is a fast-evolving cereal-specific gene with recent origin . A thorough characterization of its three functional domains revealed its important functions for storage pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "luciferase", "chemical", "compounds", "molecular", "probe", "techniques", "enzymes", "immunoblotting", "enzymology", "cloning", "carbohydrates", "organic", "compounds", "endosperm", "cereal", "crops", "plant", "science", "model", "organisms", "crops",...	2016	Maize opaque10 Encodes a Cereal-Specific Protein That Is Essential for the Proper Distribution of Zeins in Endosperm Protein Bodies
Somatic mutations contribute to the development of age-associated disease . In earlier work , we found that , at high frequency , aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA , leading to loss of respiration competence and increased loss of heterozygosity ( LOH ) in the nucle...	There is a striking correlation between age and the onset of many diseases , such as cancer , suggesting that the aging process itself can contribute to their development . Cancer is a genetic disease caused by the accumulation of a series of deleterious somatic mutations leading to unchecked proliferation . In humans ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "metabolism", "cancer", "genetics", "genetic", "mutation", "chromosome", "structure", "and", "function", "developmental", "biology", "organism", "development", "mutation", "types", "dna", "chromosome", "biology", "biology", "molecular", "biology", "aging", "bioch...	2011	Replicative Age Induces Mitotic Recombination in the Ribosomal RNA Gene Cluster of Saccharomyces cerevisiae
Phlebotomine sand flies are insects that are highly relevant in medicine , particularly as the sole proven vectors of leishmaniasis . Accurate identification of sand fly species is an essential prerequisite for eco-epidemiological studies aiming to better understand the disease . Traditional morphological identificatio...	Phlebotomine sand flies are small insects , mostly known for their role in the transmission of Leishmania parasites to humans and other mammals . In French Guiana , the main clinical form of the disease manifests as cutaneous lesions also called American cutaneous leishmaniasis . The transmission of Leishmania from wil...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "tropical", "diseases", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "organisms", "protozoans", "leishmania", "neglected", "tropical", "diseases", "insect", "...	2019	Identification of French Guiana sand flies using MALDI-TOF mass spectrometry with a new mass spectra library
Hookworm disease is a major global health problem and principal among a number of soil-transmitted helminthiases ( STHs ) for the chronic disability inflicted that impacts both personal and societal productivity . Mass drug administration most often employs single-dose therapy with just two drugs of the same chemical c...	In spite of the enormous prevalence of hookworm disease , just two drugs , albendazole and mebendazole , are most commonly employed for treatment and control , and both belong to the same benzimidazole chemical class . There exists , therefore , a pressing need to develop new , safe and inexpensive agents for the treat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "parasitology" ]	2012	Cure of Hookworm Infection with a Cysteine Protease Inhibitor
Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing . We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast Bact spliceosomes formed on site-specifically labeled pre-mRNA , ...	The spliceosome is a highly dynamic RNP machine that during the catalytic cycle undergoes many changes in composition and conformation . The pre-catalytic Bact spliceosome contains the U2 , U6 and U5 snRNAs and ~40 proteins , which are evolutionarily conserved between budding yeast and metazoans . The Bact spliceosome ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes
HTLV-1/2 are transmitted sexually , by whole cell blood products and from mother-to-child ( MTC ) , mainly through breastfeeding . HTLV-1/2 prevalence in pregnant women is high in Rio de Janeiro , however there were no local studies addressing the rate of adverse pregnancy outcomes ( APO ) and MTC transmission . The ai...	HTLV-1/2 are retroviruses transmitted by sex , blood products and from mother to child ( MTC ) , mainly through breastfeeding . There is currently no vaccine , treatment or cure . Although it’s mostly asymptomatic it can cause disabling and even lethal diseases in carriers . The prevalence of HTLV-1/2 in pregnant women...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neonatology", "urology", "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "geographical", "locations", "tropical", "diseases", "pediatrics", "treponematoses", "bacterial", "diseases", "women's", "health", "sexually", "tran...	2019	Pregnancy outcomes and mother-to-child transmission rate in HTLV-1/2 infected women attending two public hospitals in the metropolitan area of Rio de Janeiro
The most widespread measures of human brain activity are the blood-oxygen-level dependent ( BOLD ) signal and surface field potential . Prior studies report a variety of relationships between these signals . To develop an understanding of how to interpret these signals and the relationship between them , we developed a...	There are several methods for measuring activity in the living human brain . Here , we studied functional magnetic resonance imaging ( fMRI ) , which depends on the vascular response to neuronal activity , and surface field potentials , which measure electrical activity from many neurons . These two widely used measure...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "magnetic", "resonance", "imaging", "simulation", "and", "m...	2017	Neuronal synchrony and the relation between the blood-oxygen-level dependent response and the local field potential
The lymphatic system is responsible for transporting interstitial fluid back to the bloodstream , but unlike the cardiovascular system , lacks a centralized pump-the heart–to drive flow . Instead , each collecting lymphatic vessel can individually contract and dilate producing unidirectional flow enforced by intralumin...	For decades , cardiovascular physiology has been an area of intense research , and we have a fundamental understanding of the mechanisms the heart uses to drive blood flow through the distributed network of vessels in the body . The lymphatic system is now receiving similar attention as more is learned about its functi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "acoustics", "medicine", "and", "health", "sciences", "neurochemistry", "body", "fluids", "classical", "mechanics", "fluid", "mechanics", "radii", "mechanical", "stress", "geometry", "neuroscience", "muscle", "contraction", "mathematics", "algebra", "sound", "pressure", ...	2016	Synchronization and Random Triggering of Lymphatic Vessel Contractions
Many nematodes form dauer larvae when exposed to unfavorable conditions , representing an example of phenotypic plasticity and a major survival and dispersal strategy . In Caenorhabditis elegans , the regulation of dauer induction is a model for pheromone , insulin , and steroid-hormone signaling . Recent studies in Pr...	The nematode dauer stage represents the major survival and dispersal strategy , and had a remarkable impact in the evolutionary and ecological success of nematodes . Our recent work in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development , i . e . pheromone production an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation
Trypanosoma cruzi has been subdivided into seven Discrete Typing Units ( DTUs ) , TcI-TcVI and Tcbat . Two major evolutionary models have been proposed to explain the origin of hybrid lineages , but while it is widely accepted that TcV and TcVI are the result of genetic exchange between TcII and TcIII strains , the ori...	Trypanosoma cruzi , the causative agent of Chagas disease , is a genetically complex protozoan parasite . T . cruzi strains have been classified into seven Discrete Typing Units ( DTUs ) , TcI-TcVI and Tcbat , which have been associated with different geographic distribution and transmission cycles . Two major evolutio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "parasite", "evolution", "population", "genetics", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "protozoans", "forms", "of", "dna", "dna", "pop...	2017	New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis
This study investigated the transmission and prevalence of Leishmania parasite infection of humans in two foci of Visceral Leishmaniasis ( VL ) in Georgia , the well known focus in Tbilisi in the East , and in Kutaisi , a new focus in the West of the country . The seroprevalence of canine leishmaniasis was investigated...	Leishmaniasis is a disease complex of various clinical manifestations caused by infection with protozoan parasites ( Leishmania spp ) . It is transmitted through the bite of infected sand flies ( Phlebotomus or Lutzomyia spp ) and dogs are the main reservoir host for the Leishmania infantum species described previously...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "disease", "epidemiology", "epidemiology" ]	2014	Epidemiology of Visceral Leishmaniasis in Georgia
Single genome sequencing of early HIV-1 genomes provides a sensitive , dynamic assessment of virus evolution and insight into the earliest anti-viral immune responses in vivo . By using this approach , together with deep sequencing , site-directed mutagenesis , antibody adsorptions and virus-entry assays , we found evi...	Characterizing early adaptive immune responses to HIV-1 can inform studies of virus persistence , pathogenesis and natural history and can guide rational vaccine design . Previous studies examined the role of neutralizing antibodies ( Nab ) in acute and chronic HIV-1 infection but not against the precise envelope ( Env...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "immune", "evasion", "virology", "biology", "microbiology" ]	2012	Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape
Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement . One of the most prominent theoretical models of neural sequence generation is the synfire chain , in which pulses of synchronized spiking activity propagate robust...	Sequences of stereotyped actions are central to the everyday lives of humans and animals . It was hypothesized over half a century ago that these behaviors were enabled by linking together groups of neurons ( or “cell assemblies” ) into a feedforward chain using correlation-based learning rules . These chains could the...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[]	2015	Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition
Identification of early mechanisms that may lead from obesity towards complications such as metabolic syndrome is of great interest . Here we performed lipidomic analyses of adipose tissue in twin pairs discordant for obesity but still metabolically compensated . In parallel we studied more evolved states of obesity by...	Obesity is characterized by excess body fat , which is predominantly stored in the adipose tissue . When adipose tissue expands too much it stops storing lipid appropriately . The excess lipid accumulates in organs such as muscle , liver , and pancreas , causing metabolic disease . In this study , we aim to identify fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "cell", "biology/membranes", "and", "sorting", "diabetes", "and", "endocrinology/obesity", "computational", "biology/metabolic", "networks", "computational", "biology/molecular", "dynamics", "computational", "biology/systems", "biology" ]	2011	Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in Humans
Pseudomonas aeruginosa strain PA14 is an opportunistic human pathogen capable of infecting a wide range of organisms including the nematode Caenorhabditis elegans . We used a non-redundant transposon mutant library consisting of 5 , 850 clones corresponding to 75% of the total and approximately 80% of the non-essential...	Pseudomonas aeruginosa is an opportunistic human pathogen that can also infect a wide range of model organisms , including the nematode Caenorhabditis elegans . To identify P . aeruginosa genes that play key roles in the pathogenic process , we performed a screen for mutants that exhibited reduced ability to kill C . e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbiology", "host-pathogen", "interaction", "animal", "models", "caenorhabditis", "elegans", "prokaryotic", "models", "model", "organisms", "microbial", "evolution", "bacterial", "pathogens", "microbial", "pathogens", "biology", "pathogenesis", "gram", "...	2012	Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model
Depending on the environmental conditions , the pathogenic yeast Candida albicans can undergo different developmental programs , which are controlled by dedicated transcription factors and upstream signaling pathways . C . albicans strains that are homozygous at the mating type locus can switch from the normal yeast fo...	The pathogenic yeast Candida albicans can switch from the white yeast form to the mating-competent opaque form . Opaque cells are less virulent than white cells , but they can avoid recognition by phagocytes , indicating that white-opaque switching has evolved as an adaptation mechanism of C . albicans to specific host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Activation of the Cph1-Dependent MAP Kinase Signaling Pathway Induces White-Opaque Switching in Candida albicans
We present a novel regularization scheme called The Generalized Elastic Net ( GELnet ) that incorporates gene pathway information into feature selection . The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired...	The low costs of sequencing and other high-throughput technologies have made available large amounts of data to address molecular biology problems . However , often this means thousands of measurements , for example on gene expression , are assayed for a much smaller number of samples . The imbalance complicates the id...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "medicine", "and", "health", "sciences", "genetic", "networks", "breast", "tumors", "cancers", "and", "neoplasms", "random", "variables", "covariance", "oncology", "mathematics", "pharmaceutics", "network", "analysis", "genome", "analysis", "pharmacology",...	2016	Pathway-Based Genomics Prediction using Generalized Elastic Net
Host encounters with viruses lead to an innate immune response that must be rapid and broadly targeted but also tightly regulated to avoid the detrimental effects of unregulated interferon expression . Viral stimulation of host negative regulatory mechanisms is an alternate method of suppressing the host innate immune ...	The response of cells to an invading pathogen must be swift and well controlled because of the detrimental effects of chronic inflammation . However , viruses often hijack host control mechanisms . HCV and flaviviruses are known to suppress the innate immune response in cells by a variety of mechanisms . This study cla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "light", "microscopy", "viruses", "rna", "viruses", "immunoprecipitation", "microscopy", "confocal", "microscopy", "sta...	2019	HCV and flaviviruses hijack cellular mechanisms for nuclear STAT2 degradation: Up-regulation of PDLIM2 suppresses the innate immune response
Variation in gene expression is a fundamental aspect of human phenotypic variation . Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes . However , these differences could largely be due to non-genet...	Variation in gene expression is a fundamental aspect of human phenotypic variation , and understanding how this variation is apportioned among human populations is an important aim . Previous studies have compared gene expression levels between distinct populations , but it is unclear whether the differences that were ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/population", "genetics", "genetics", "and", "genomics/gene", "expression" ]	2008	Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans
In the juvenile brain , the synaptic architecture of the visual cortex remains in a state of flux for months after the natural onset of vision and the initial emergence of feature selectivity in visual cortical neurons . It is an attractive hypothesis that visual cortical architecture is shaped during this extended per...	Neurons in the visual cortex of carnivores , primates and their close relatives form spatial representations or maps of multiple stimulus features . In part ( I ) of this study we theoretically predicted maps that are optima of a variety of optimization principles . When analyzing the joint optimization of two interact...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "general", "physics", "computational", "neuroscience", "interdisciplinary", "physics", "biology", "computational", "biology", "sensory", "systems" ]	2012	Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies
Intestinal Listeria monocytogenes infection is not efficient in mice and this has been attributed to a low affinity interaction between the bacterial surface protein InlA and E-cadherin on murine intestinal epithelial cells . Previous studies using either transgenic mice expressing human E-cadherin or mouse-adapted L ....	Ingestion of Listeria monocytogenes-contaminated food can be life-threatening for immune compromised individuals , can cause severe gastroenteritis in otherwise healthy people , and is also thought to occur frequently with little consequence . The factors that determine susceptibility to this infection are unknown , du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "model", "organisms", "biology", "microbiology", "bacterial", "pathogens", "pathogenesis" ]	2012	InlA Promotes Dissemination of Listeria monocytogenes to the Mesenteric Lymph Nodes during Food Borne Infection of Mice
From Darwin's study of the Galapagos and Wallace's study of Indonesia , islands have played an important role in evolutionary investigations , and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation . Even during the ongoing paradigm shift towards other mo...	Over the last 150 years , since Darwin's study of islands and his “Origin of Species , ” island archipelagos have played a central role in the understanding of evolution and how species multiply ( speciation ) . Islands epitomise the conventional view of geographic ( allopatric ) speciation , where genomes diverge in i...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics/population", "genetics", "evolutionary", "biology/animal", "genetics", "evolutionary", "biology/evolutionary", "ecology" ]	2010	Genetic Tests for Ecological and Allopatric Speciation in Anoles on an Island Archipelago
The central event underlying prion diseases involves conformational change of the cellular form of the prion protein ( PrPC ) into the disease-associated , transmissible form ( PrPSc ) . PrPC is a sialoglycoprotein that contains two conserved N-glycosylation sites . Among the key parameters that control prion replicati...	The central event underlying prion diseases involves conformational change of the cellular form of the prion protein ( PrPC ) into disease-associated , transmissible form ( PrPSc ) . The amino acid sequence of PrPC and strain-specific structure of PrPSc are among the key parameters that control prion replication and tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "neurology", "neurodegenerative", "diseases", "biology", "and", "life", "sciences", "veterinary", "science", "prion", "diseases" ]	2014	Sialylation of Prion Protein Controls the Rate of Prion Amplification, the Cross-Species Barrier, the Ratio of PrPSc Glycoform and Prion Infectivity
The cohesion of sister chromatids in the interval between chromosome replication and anaphase is important for preventing the precocious separation , and hence nondisjunction , of chromatids . Cohesion is accomplished by a ring-shaped protein complex , cohesin; and its release at anaphase occurs when separase cleaves t...	During cell division , identical DNA molecules , packaged in the sister chromatids of a chromosome , must be distributed to daughter cells . The cohesion of sister chromatids in the interval between DNA replication and mitotic anaphase is important for preventing the precocious separation , and hence nondisjunction , o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "chromosome", "structure", "and", "function", "microbiology", "mitosis", "model", "organisms", "cell", "division", "tetrahymena", "thermophila", "chromosome", "biology", "protozoan", "models", "biology", "cell", "biology", "cytogenetic", "techniques", "genetics...	2013	A Single Cohesin Complex Performs Mitotic and Meiotic Functions in the Protist Tetrahymena
Measures of allele and haplotype diversity , which are fundamental properties in population genetics , often follow heavy tailed distributions . These measures are of particular interest in the field of hematopoietic stem cell transplant ( HSCT ) . Donor/Recipient suitability for HSCT is determined by Human Leukocyte A...	The distribution of haplotypes and species tend to be heavy tailed . The heavy tail is expected from theoretical considerations and is observed in most populations . Accurate measures of diversity are difficult to achieve given that a limited number of common haplotypes represent the majority of the population , wherea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program
Mycobacterium ulcerans disease ( Buruli ulcer ) is the most widespread mycobacterial disease in the world after leprosy and tuberculosis . How M . ulcerans is introduced into the skin of humans remains unclear , but it appears that individuals living in the same environment may have different susceptibilities . This st...	Mycobacterium ulcerans disease ( Buruli ulcer ) is the most widespread mycobacterial disease in the world after leprosy and tuberculosis . How M . ulcerans is introduced into the skin of humans remains unclear , but it appears that individuals living in the same environment may have different susceptibilities . This ca...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/environmental", "health" ]	2010	Family Relationship, Water Contact and Occurrence of Buruli Ulcer in Benin
Clostridium difficile is a global health burden and the leading cause of antibiotic-associated diarrhoea worldwide , causing severe gastrointestinal disease and death . Three well characterised toxins are encoded by this bacterium in two genetic loci , specifically , TcdB ( toxin B ) and TcdA ( toxin A ) in the Pathoge...	Clostridium difficile is the leading cause of antibiotic-associated diarrhoea . The TcdB , TcdA and binary toxins produced by C . difficile are encoded in two genomically distinct loci: TcdB and TcdA in the Pathogenicity Locus ( PaLoc ) and binary toxin ( CDT ) in the CDT locus ( CdtLoc ) . Toxin production is primaril...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complement", "system", "medicine", "and", "health", "sciences", "gut", "bacteria", "toxins", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "gene", "regulation", "pathogens", "immunology", "toxicology", "toxic", "agents", "regulator", "genes", ...	2016	CdtR Regulates TcdA and TcdB Production in Clostridium difficile
Polycomb group ( PcG ) proteins are essential for the repression of key factors during early development . In Drosophila , the polycomb repressive complexes ( PRC ) associate with defined polycomb response DNA elements ( PREs ) . In mammals , however , the mechanisms underlying polycomb recruitment at targeted loci are...	Hox genes are essential for the proper organization of structures along the developing vertebrate body axis . These genes must be activated at a precise time and their premature transcription is deleterious to the organism . Early on , Hox gene clusters are covered by Polycomb Repressive protein Complexes ( PRCs ) , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Genetic Approach to the Recruitment of PRC2 at the HoxD Locus
Salmonella Typhimurium has evolved a complex functional interface with its host cell largely determined by two type III secretion systems ( T3SS ) , which through the delivery of bacterial effector proteins modulate a variety of cellular processes . We show here that Salmonella Typhimurium infection of epithelial cells...	Essential for the ability of Salmonella Typhimurium to cause disease is the function of a type III secretion system ( T3SS ) encoded within its pathogenicity island 1 ( SPI-1 ) , which through the delivery of bacterial effector proteins modulates a variety of cellular functions . This study reports that the infection o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Salmonella Modulation of Host Cell Gene Expression Promotes Its Intracellular Growth
Modularity analysis offers a route to better understand the organization of cellular biochemical networks as well as to derive practically useful , simplified models of these complex systems . While there is general agreement regarding the qualitative properties of a biochemical module , there is no clear consensus on ...	Mathematical models are powerful tools to understand and predict the behavior of complex systems . However , the complexity presents many challenges in developing such models . In the case of a biological cell , a fully detailed and comprehensive model of a major function such as signaling and metabolism remains out of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "computational", "biology", "metabolic", "networks" ]	2011	Identification of Biochemical Network Modules Based on Shortest Retroactive Distances
RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus . However , the molecular players and mechanisms involved in these processes are poorly understood . Here , we explored the functions of S . aureus endoribonuclease III ( RNase III )...	Control of mRNA stability is crucial for bacteria to survive and rapidly adapt to environmental changes and stress conditions . The molecular players and the degradation pathways involved in these adaptive processes are poorly understood in Staphylococcus aureus . The universally conserved double-strand-specific endori...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "prokaryotic", "models", "model", "organisms", "rna", "processing", "gene", "expression", "genetics", "bacillus", "subtilis", "biology", "microbiology", "microbial", "growth", "and", "development", "genetics", "and", "genomics", "rna", "stability" ]	2012	Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression
Endoplasmic reticulum ( ER ) stress generated unfolded stress response ( UPR ) is a basic survival mechanism which protects cell under unfavourable conditions . Leishmania parasite modulates host macrophages in various ways to ensure its survival . Modulation of PI3K-Akt pathway in delayed apoptotic induction of host; ...	Visceral Leishmaniasis or Kala-azar is one of the severe tropical neglected parasitic diseases caused by Leishmania donovani in Indian subcontinent . Modulation of host in terms of delayed apoptotic induction is one of the aspects which favours disease establishment; however the mechanism is not clearly understood yet ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "phosphorylation", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cell", "processes", "microbiology", "messenger", "rna", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", ...	2018	Leishmania donovani induced Unfolded Protein Response delays host cell apoptosis in PERK dependent manner
DNA repair mechanisms are essential for preservation of genome integrity . However , it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways . Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents a...	DNA repair relies on various enzymes , including exonucleases that bind and trim DNA at broken ends . However , we know little about how an exonuclease precisely selects and trims a DNA broken end in specific repair pathways . In this study , the enzyme RNase T , previously known for its involvement in processing RNA s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biochemistry", "biology" ]	2014	Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways
Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown . Here , we functionally characterize a member of one such family , the macoilins . Macoilins are characterized by several highly conserved predicted transmembrane domain...	The human genome project has given us a catalog of the genes that make a human; however , the function of about 40% of these genes remains elusive . Many of these mysterious genes have relatives in simpler organisms like worms and flies , where their function can be studied much more easily than in a mammal . Here , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "neuroscience/neuronal", "signaling", "mechanisms" ]	2011	Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability
The molecular determinants that render specific populations of normal cells susceptible to oncogenic reprogramming into self-renewing cancer stem cells are poorly understood . Here , we exploit T-cell acute lymphoblastic leukemia ( T-ALL ) as a model to define the critical initiating events in this disease . First , th...	Deciphering the initiating events in lymphoid leukemia is important for the development of new therapeutic strategies . In this manuscript , we define oncogenic reprogramming as the process through which non-self-renewing progenitors are converted into pre-leukemic stem cells with sustained self-renewal capacities . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hematologic", "cancers", "and", "related", "disorders", "developmental", "biology", "leukemias", "medicine", "and", "health", "sciences", "cancer", "genetics", "hematopoietic", "stem", "cells", "lymphoblastic", "leukemia", "stem", "cells", "animal", "cells", "cell", ...	2014	SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells
Double-stranded ( ds ) RNA fungal viruses are currently assigned to six different families . Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids , 300–450 Å in diameter . Helminthosporium victoriae virus 190S ( HvV190S ) , prototype of recently recognized genus Victorivi...	Of the known dsRNA fungal viruses , the best characterized is Saccharomyces cerevisiae virus L-A ( ScV-L-A ) , prototype of the genus Totivirus , family Totiviridae . Until the current study , there have been no subnanometer structures of dsRNA fungal viruses from the genus Victorivirus , which is the largest in family...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "nucleocapsid", "viral", "classification", "plant", "biology", "macromolecular", "assemblies", "microbiology", "viral", "structure", "chemical", "biology", "plant", "science", "rna", "viruses", "viruslike", "particles", "crops", "protein", "structure", "v...	2013	Three-dimensional Structure of Victorivirus HvV190S Suggests Coat Proteins in Most Totiviruses Share a Conserved Core
Phylogenetic networks represent the evolution of organisms that have undergone reticulate events , such as recombination , hybrid speciation or lateral gene transfer . An important way to interpret a phylogenetic network is in terms of the trees it displays , which represent all the possible histories of the characters...	We consider here an elementary question for the inference of phylogenetic networks: what networks can be reconstructed . Indeed , whereas in theory it is always possible to reconstruct a phylogenetic tree , given sufficient data for this task , the same does not hold for phylogenetic networks: most notably , the relati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
In the present paper , we quantify , with a rigorous approach , the nature of motor activity in response to Deep Brain Stimulation ( DBS ) , in the mouse . DBS is currently being used in the treatment of a broad range of diseases , but its underlying principles are still unclear . Because mouse movement involves rapidl...	Brainstem and thalamic regulation of arousal has been studied experimentally since the mid 20-th century . Today , Deep Brain Stimulation ( DBS ) is used in the treatment of movement disorders , chronic pain , clinical depression , amongst others . At present , the proper choice of DBS parameters ( frequency and streng...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information
A variety of adverse conditions including drought stress severely affect rice production . Root system plays a critical role in drought avoidance , which is one of the major mechanisms of drought resistance . In this study , we adopted genome-wide association study ( GWAS ) to dissect the genetic basis controlling vari...	Drought stress is a key environmental factor that severely reduces crop yield all over the world . The root system plays a critical role in the drought avoidance of crops , but the genetic basis of the root system in soil conditions has seldom been investigated in rice . We analyzed the genetic control of 21 root trait...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "genome-wide", "association", "studies", "ecology", "and", "environmental", "sciences", "quantitative", "trait", "loci", "plant", "physiology", "plant", "science", "rice", "genetically", "modified", "plants", "materials", "science", "experimental", "organ...	2017	Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study
Leaf angle is an important agronomic trait and influences crop architecture and yield . Studies have demonstrated the roles of phytohormones , particularly auxin and brassinosteroids , and various factors in controlling leaf inclination . However , the underlying mechanism especially the upstream regulatory networks st...	Leaf angle is a major trait of ideal architecture of crops that associates with photosynthetic efficiency and yields . Studies of the underlying mechanism will greatly help to improve the crop yield . Phytohormones especially auxin and brassinosteroids play crucial roles in regulating the leaf inclination , however , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "engineering", "and", "technology", "gene", "regulation", "hormones", "plant", "science", "rice", "plant", "hormones", "genetically", "modified", "plants", "experimental", "organism", "systems", "plants", "genetic", "engineering", "r...	2018	SPOC domain-containing protein Leaf inclination3 interacts with LIP1 to regulate rice leaf inclination through auxin signaling
Histone deacetylase 8 from Schistosoma mansoni ( SmHDAC8 ) is essential to parasite growth and development within the mammalian host and is under investigation as a target for the development of selective inhibitors as novel schistosomicidal drugs . Although some protein substrates and protein partners of human HDAC8 h...	Using a target-based strategy to develop new drugs for the treatment of schistosomiasis we had earlier identified Schistosoma mansoni histone deacetylase 8 ( SmHDAC8 ) as essential for parasite development and survival in the mammalian host . Selective inhibitors of this enzyme show promise as lead compounds for drug d...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "protein", "interactions", "helminths", "dna-binding", "proteins", "animals", "fungi", "model", "organisms", "immunoprecipitation", "experimental", "organism", "systems", "molecular", "biology", "techniques", "co-immun...	2017	Analysis of the interactome of Schistosoma mansoni histone deacetylase 8
Human papillomaviruses ( HPVs ) are epithelial tropic viruses that link their productive life cycles to the differentiation of infected host keratinocytes . A subset of the over 200 HPV types , referred to as high-risk , are the causative agents of most anogenital malignancies . HPVs infect cells in the basal layer , b...	Viruses that induce persistent infections often alter the expression and activities of cellular transcription factors to regulate their productive life cycles . Human papillomaviruses ( HPVs ) are epithelial tropic viruses that link their productive life cycles to the differentiation of infected host keratinocytes . Ou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "urology", "keratinocytes", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "cell", "differentiation", "epithelial", "cells", "viruses", "developmental", "biology", "immunoprecipitation", ...	2016	Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle
Ebola Virus Disease ( EVD ) is a condition with high fatality . Though the disease is deadly , taking precautions to reduce contact with infected people and their secretions can prevent cross- infection . In the 2014 EVD outbreak , socio-cultural factors were identified to be responsible for the spread of the disease i...	The 2014 Ebola Virus Disease outbreak emerged as the most devastating outbreaks in recent history . This outbreak spread across continents with West Africa remaining the epicenter . Although , the three most affected countries have been declared Ebola free , the recent re-emergence of cases in Sierra Leone require that...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "amorphous", "solids", "medicine", "and", "health", "sciences", "health", "services", "research", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "ebola", "hemorrhagic", "fever", "anthropology", "neuroscience", "glass", "herbs", "...	2016	Preparing towards Preventing and Containing an Ebola Virus Disease Outbreak: What Socio-cultural Practices May Affect Containment Efforts in Ghana?
Microglia are resident immune cells that play critical roles in maintaining the normal physiology of the central nervous system ( CNS ) . Remarkably , microglia have an intrinsic capacity to repopulate themselves after acute ablation . However , the underlying mechanisms that drive such restoration remain elusive . Her...	Microglia are the brain’s primary immune sentinels . After being seeded in the central nervous system ( CNS ) during embryonic development , microglia form an evenly distributed grid-like population in the adult brain . In the adult , microglia have the remarkable ability to regenerate and restore their population foll...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "nervous", "system", "cell", "processes", "diet", "microglial", "cells", "physiological", "processes", "developmental", "biology", "nutrition", "homeostasis", "microscopy", "research", "and", "analysis", "methods...	2019	Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain
Theoretical methods for predicting CD8+ T-cell epitopes are an important tool in vaccine design and for enhancing our understanding of the cellular immune system . The most popular methods currently available produce binding affinity predictions across a range of MHC molecules . In comparing results between these MHC m...	The use of prediction software has become an important tool in increasing our knowledge of infectious disease . It allows us to predict the interaction of molecules involved in an immune response , thereby significantly shortening the lengthy process of experimental elucidation . A high proportion of this software has ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/antigen", "processing", "and", "recognition", "immunology/immunity", "to", "infections", "computational", "biology" ]	2009	T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
The homeostasis of meristems in flowering plants is maintained by cell-to-cell communication via CLE ( CLAVATA3/EMBRYO SURROUNDING REGION-related ) peptide hormones . In contrast , cell signals that regulate meristem activity remains elusive in bryophytes that maintain apical meristems in the gametophyte ( haploid ) bo...	Land plants undergo an alternation of generations where both haploid and diploid phases develop multicellular bodies . Their growth relies on the activity of meristems at the growing tips of their bodies . Here we show a CLE peptide hormone acts as an intercellular signal controlling proliferative activity in the apica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "brassica", "bryology", "plant", "physiology", "notch", "signaling", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "plants", "nonvascular", "plants", "arabidopsis", "th...	2019	Control of proliferation in the haploid meristem by CLE peptide signaling in Marchantia polymorpha
Rift Valley fever virus ( RVFV ) causes outbreaks of severe disease in livestock and humans throughout Africa and the Arabian Peninsula . In people , RVFV generally causes a self-limiting febrile illness but in a subset of individuals , it progresses to more serious disease . One manifestation is a delayed-onset enceph...	Rift Valley fever virus ( RVFV ) is a mosquito-borne virus that causes severe disease in people and livestock throughout Africa and the Arabian Peninsula . Human disease is usually self-limiting , but a small proportion of individuals develop fatal encephalitis . The role of the host immune response in determining dise...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "microbiology", "animal", "models", "model", "organisms", "research", "and", "analysis", "methods", "animal", "models", "of", "infection", "infl...	2014	Rift Valley Fever Virus Encephalitis Is Associated with an Ineffective Systemic Immune Response and Activated T Cell Infiltration into the CNS in an Immunocompetent Mouse Model
The peregrine falcon Falco peregrinus is renowned for attacking its prey from high altitude in a fast controlled dive called a stoop . Many other raptors employ a similar mode of attack , but the functional benefits of stooping remain obscure . Here we investigate whether , when , and why stooping promotes catch succes...	Peregrine falcons are famed for their high-speed , high-altitude stoops . Hunting prey at perhaps the highest speed of any animal places a stooping falcon under extraordinary physical , physiological , and cognitive demands , yet it remains unknown how this behavioural strategy promotes catch success . Because the beha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "acceleration", "ornithology", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "dynamics", "classical", "mechanics", "bird", "flight", "vertebrates", "starlings", "biological", "locomotion", "animals", "flight", "(biology)", "animal...	2018	Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey
Human African Trypanosomiasis ( HAT ) is a neglected disease targeted for elimination as a public health problem by 2020 . Elimination requires a better understanding of the epidemiology and clinical evolution of HAT . In addition to the classical clinical evolution of HAT , asymptomatic carriers and spontaneous cure h...	Human African trypanosomiasis ( HAT ) or sleeping sickness is a neglected tropical disease targeted for elimination by 2020 . This elimination requires a better understanding of the epidemiology and clinical evolution of this disease . Beside the classical clinical evolution , asymptomatic carriers , seropositive and s...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "variant", "genotypes", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "genetic", "mapping", "protozoans", "neglected", "tropical", "diseases", ...	2017	A polymorphism in the haptoglobin, haptoglobin related protein locus is associated with risk of human sleeping sickness within Cameroonian populations
Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a γ-herpesvirus associated with KS and two lymphoproliferative diseases . Recent studies characterized epigenetic modification of KSHV episomes during latency and determined that latency-associated genes are associated with H3K4me3 while most lytic genes are associate...	KSHV is a DNA tumor virus which is associated with Kaposi's sarcoma and some lymphoproliferative diseases . During latent infection , the viral genome persists as circular extrachromosomal DNA in the nucleus and expresses a very limited number of viral proteins , including LANA , a multi-functional protein . KSHV viral...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "cell", "biology", "chromosome", "biology", "viral", "persistence", "and", "latency", "virology", "viruses", "and", "cancer", "genetics", "biology", "and", "life", "sciences", "microbiology", "genomics" ]	2014	LANA Binds to Multiple Active Viral and Cellular Promoters and Associates with the H3K4Methyltransferase hSET1 Complex
Chemokines have been shown to be effective bactericidal molecules against a variety of bacteria and fungi in vitro . These direct antimicrobial effects are independent of their chemotactic activities involving immunological receptors . However , the direct biological role that these proteins may play in host defense , ...	Host defense peptides are an essential part of the innate immune response to pathogens , particularly at mucosal surfaces . Some chemokines , previously known for their ability to recruit immune cells to a site of inflammation , have been identified to have direct antimicrobial activity in vitro against a variety of pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	CXCL9 Contributes to Antimicrobial Protection of the Gut during Citrobacter rodentium Infection Independent of Chemokine-Receptor Signaling
Tolerance to drugs that affect neural activity is mediated , in part , by adaptive mechanisms that attempt to restore normal neural excitability . Changes in the expression of ion channel genes are thought to play an important role in these neural adaptations . The slo gene encodes the pore-forming subunit of BK-type C...	A startlingly large number of adolescents abuse organic solvent inhalants , common components of glues , paints , and cleaning solutions . Our focus is on the molecular basis of tolerance—reduced response to a drug over time—which promotes increased drug consumption and accelerates the process of addiction . We use the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mental", "health", "pharmacology", "drosophila", "neuroscience", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Drug-Induced Epigenetic Changes Produce Drug Tolerance
Early mammalian development is both highly regulative and self-organizing . It involves the interplay of cell position , predetermined gene regulatory networks , and environmental interactions to generate the physical arrangement of the blastocyst with precise timing . However , this process occurs in the absence of ma...	The first 4 . 5 days of mammalian embryo development proceeds without maternal information and is remarkably robust to perturbations . For example , if an early embryo is cut in half , it produces 2 perfectly patterned , smaller embryos . Where does the information guiding this development come from ? Here , we explore...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blastocysts", "cell", "physiology", "cell", "death", "medicine", "and", "health", "sciences", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "regulatory", "proteins", "cell", "processes", "dna-binding", "proteins", "endocrine", "physiology", "cell"...	2017	Four simple rules that are sufficient to generate the mammalian blastocyst
Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi ( AMF ) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells . In model legumes such as Lotus japonicus and Medicago truncatula , rhizobia enter into roots through an intracellular inva...	Symbiosis between plants and beneficial microbes such as nitrogen-fixing bacteria and arbuscular mycorrhizal fungi has enabled plant colonization of new environments . Root nodule symbiosis with nitrogen-fixing rhizobia enables sessile plants to survive in a nitrogen-deficient environment . To establish the symbiosis ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "reverse", "transcriptase-polymerase", "chain", "reaction", "plant", "anatomy", "engineering", "and", "technology", "symbiosis", "root", "nodules", "cell", "signaling", "root", "hairs", "plant", "science", "genetically", "modified", "plants", "molecular",...	2019	LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus
Sulphur is an essential element that all pathogens have to absorb from their surroundings in order to grow inside their infected host . Despite its importance , the relevance of sulphur assimilation in fungal virulence is largely unexplored . Here we report a role of the bZIP transcription factor MetR in sulphur assimi...	Invasive pulmonary aspergillosis ( IPA ) is a life-threatening disease that affects primarily immunosuppressed patients . During the last decades the incidence of this disease that is accompanied by high mortality rates has increased . Since opportunistic pathogenic fungi , unlike other pathogens , do not express speci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "metabolism", "mycology", "medical", "microbiology", "biology", "microbiology", "pathogenesis", "fungal", "physiology" ]	2013	Regulation of Sulphur Assimilation Is Essential for Virulence and Affects Iron Homeostasis of the Human-Pathogenic Mould Aspergillus fumigatus
Iron is an essential nutrient for most bacterial pathogens , but is restricted by the host immune system . Mycobacterium tuberculosis ( Mtb ) utilizes two classes of small molecules , mycobactins and carboxymycobactins , to capture iron from the human host . Here , we show that an Mtb mutant lacking the mmpS4 and mmpS5...	In the late 19th century the French physician Armand Trousseau recognized that treating anemic tuberculosis patients with iron salts exacerbated the disease . In 1911 Twort postulated that mycobacteria produce an essential growth factor which was identified in 1953 as mycobactin . The hydrophobic mycobactin and its mor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "lipids", "microbial", "physiology", "proteins", "protein", "structure", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2013	Discovery of a Siderophore Export System Essential for Virulence of Mycobacterium tuberculosis
Dengue is becoming an increasing threat to non-endemic countries . In Japan , the reported number of imported cases has been rising , and the first domestic dengue outbreak in nearly 70 years was confirmed in 2014 , highlighting the need for greater situational awareness and better-informed risk assessment . Using nati...	With increasing globalization , the threat of dengue is rising in areas that were previously unaffected . Japan has been experiencing a rise in notifications of imported cases , and in 2014 confirmed the first domestic outbreak in nearly 70 years . Such events prompted the country to more actively utilize existing impo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "japan", "geographical", "locations", "india", "neuroscience", "indonesia", "cognition", "infectious", "disease", "control", "infectious", "diseases", "epidemiology", "people", "and", "places", "infectious", ...	2016	Dengue Sentinel Traveler Surveillance: Monthly and Yearly Notification Trends among Japanese Travelers, 2006–2014
Disease progression in response to infection can be strongly influenced by both pathogen burden and infection-induced immunopathology . While current therapeutics focus on augmenting protective immune responses , identifying therapeutics that reduce infection-induced immunopathology are clearly warranted . Despite the ...	Leishmaniasis is a parasitic disease where the host immune response plays an essential role in pathogenesis . However , the mechanisms promoting immunopathology in patients are still unclear . We performed gene expression profiling of skin lesions from cutaneous leishmaniasis patients and normal skin and the results de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "skin", "infections", "leishmaniasis", "neglected", "tropical", "diseases" ]	2013	Cytotoxic T Cells Mediate Pathology and Metastasis in Cutaneous Leishmaniasis
Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer . The toxin has a broad spectrum of biological effects within the host organism , stemming from its interaction with at least two molecular targets and the inhibition of protein ...	Mycolactone is a macrolide exotoxin secreted by Mycobacterium ulcerans , which causes a skin disease called Buruli ulcer , a neglected emerging disease . It is the third most common mycobacterial disease after tuberculosis and leprosy . Studies have shown how mycolactone plays a pivotal role in Buruli ulcer pathogenesi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "membrane", "potential", "tropical", "diseases", "electrophysiology", "toxic", "agents", "toxicology", "bacterial", "diseases", "neglected", "tropical", "diseases", "cellular"...	2018	Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans
Structural inhomogeneities in synaptic efficacies have a strong impact on population response dynamics of cortical networks and are believed to play an important role in their functioning . However , little is known about how such inhomogeneities could evolve by means of synaptic plasticity . Here we present an adaptiv...	It is widely believed that the structure of neuronal circuits plays a major role in brain functioning . Although the full synaptic connectivity for larger populations is not yet assessable even by current experimental techniques , available data show that neither synaptic strengths nor the number of synapses per neuron...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity
Leishmaniasis is an antropozoonosis caused by Leishmania parasites that affects around 12 million people in 98 different countries . The disease has different clinical forms , which depend mainly on the parasite genetics and on the immunologic status of the host . The promastigote form of the parasite is transmitted by...	Leishmaniasis is an antropozoonosis caused by Leishmania parasites that affects around 12 million people in 98 different countries . Cutaneous leishmaniasis caused by Leishmania amazonensis can have different clinical forms and severities depending on the parasite strain . We have here shown that two Leishmania amazone...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoa...	2017	Quantitative proteomic analysis of amastigotes from Leishmania (L.) amazonensis LV79 and PH8 strains reveals molecular traits associated with the virulence phenotype
Successful host defense against pathogens requires innate immune recognition of the correct pathogen associated molecular patterns ( PAMPs ) by pathogen recognition receptors ( PRRs ) to trigger the appropriate gene program tailored to the pathogen . While many PRR pathways contribute to the innate immune response to s...	Individual pathogen associated molecular patterns ( PAMPs ) induce gene expression in immune cells through distinct signaling pathways to protect cells from infection . However , pathogens typically possess many PAMPs , and the precise contribution of each PAMP to the gene expression program elicited by a live pathogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "staphylococcus", "aureus", "immune", "receptor", "signaling", "membrane", "receptor", "signaling", "hy...	2017	Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense
Cancer is a disease of cellular regulation , often initiated by genetic mutation within cells , and leading to a heterogeneous cell population within tissues . In the competition for nutrients and growth space within the tumors the phenotype of each cell determines its success . Selection in this process is imposed by ...	Multicellular organisms control their cells to facilitate higher level function of the whole organism . In tumors , this control is lost and cells are allowed to enhance their fitness by , for example , increased proliferation . Tumor cells continue to change their behavior through accumulating mutations , leading to a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "cell", "motility", "medicine", "and", "health", "sciences", "chemical", "compounds", "cardiovascular", "anatomy", "oxygen", "cell", "cycle", "and", "cell", "division", "cell", "processes", "carbohydrates", "cell", "...	2017	Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach

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