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Two-component signaling systems ( TCSs ) are major mechanisms by which bacteria adapt to environmental conditions . It follows then that TCSs would play important roles in the adaptation of pathogenic bacteria to host environments . However , no pathogen-associated TCS has been identified in uropathogenic Escherichia c...	Successful colonization requires bacterial pathogens to adapt their metabolism to the conditions encountered in particular infection sites . Two-component signaling systems ( TCSs ) enable bacterial pathogens to sense and respond to environmental cues , thus mediating their adaptation to environmental change . Though m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "genetics", "biology", "microbiology" ]	2013	A Novel Two-Component Signaling System Facilitates Uropathogenic Escherichia coli's Ability to Exploit Abundant Host Metabolites
Enterotoxigenic Escherichia coli ( ETEC ) is a major diarrheal pathogen in developing countries , where it accounts for millions of infections and hundreds of thousands of deaths annually . While vaccine development to prevent diarrheal illness due to ETEC is feasible , extensive effort is needed to identify conserved ...	Diarrheal diseases are responsible for more than 1 . 5 million deaths annually in developing countries . Enterotoxigenic E . coli ( ETEC ) are among the most common bacterial causes of diarrhea , accounting for an estimated 300 , 000–500 , 000 deaths each year , mostly in young children . There unfortunately is not yet...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunizations", "applied", "microbiology", "medicine", "infectious", "diseases", "emerging", "infectious", "diseases", "immunity", "global", "health", "immunology", "biology", "microbiology", "immune", "response" ]	2011	Directed Evaluation of Enterotoxigenic Escherichia coli Autotransporter Proteins as Putative Vaccine Candidates
Elimination of the proliferating germline extends lifespan in C . elegans . This phenomenon provides a unique platform to understand how complex metazoans retain metabolic homeostasis when challenged with major physiological perturbations . Here , we demonstrate that two conserved transcription regulators essential for...	The balance between production and breakdown of fats is critical for health , especially during reproduction-related changes such as onset of puberty or menopause . However , little is known about how animals retain a balanced metabolism when undergoing major life events . Here , we have used a C . elegans mutant that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "rna", "interference", "immunology", "germ", "cells", "age", "groups", "oocytes", "adults", "epigenetics", "antibodies", "immune", "system", "proteins", "lipids", "genetic", "interference", "proteins", "...	2016	DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans
Recent development of benzoxaborole-based chemistry gave rise to a collection of compounds with great potential in targeting diverse infectious diseases , including human African Trypanosomiasis ( HAT ) , a devastating neglected tropical disease . However , further medicinal development is largely restricted by a lack ...	Human African Trypanomiasis ( HAT ) is among a list of Neglected Tropical Diseases ( NTDs ) that impose devastating burdens on both public health and economy of some of the most unprivileged societies across the world . To secure the long-term global control of the disease , it is critical to understand the mechanisms ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "chemical", "compounds", "enzymology", "organic", "compounds", "parasitic", "protozoans", "trypanosoma", "brucei", "protozoans", "metabolites", "enzyme", "metabolism", "pharmacology", "epigenetics", "drug", "...	2018	Host-parasite co-metabolic activation of antitrypanosomal aminomethyl-benzoxaboroles
Cell migration in the absence of external cues is well described by a correlated random walk . Most single cells move by extending protrusions called pseudopodia . To deduce how cells walk , we have analyzed the formation of pseudopodia by Dictyostelium cells . We have observed that the formation of pseudopodia is high...	Even in the absence of external information , many organisms do not move in purely random directions . Usually , the current direction is correlated with the direction of prior movement . This persistent random walk is the typical way that simple cells or complex organisms move . Cells with poor persistence exhibit Bro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology/cytoskeleton", "biophysics/cell", "signaling", "and", "trafficking", "structures", "cell", "biology/cell", "signaling" ]	2010	A Model for a Correlated Random Walk Based on the Ordered Extension of Pseudopodia
Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception . However , little is known about the mechanisms that guide such a temporally structured replay in humans , because previous studies used either unsuitable methods or paradigms to addr...	A remarkable ability of the human brain is that it can mentally replay past episodes . For instance , if one remembers the last movie one has seen , one can vividly evoke parts of this event in a temporally highly structured manner . This implicates a neural mechanism that temporally guides the brain through memory ret...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Data", "Availability" ]	[ "learning", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "engineering", "and", "technology", "signal", "processing", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "magnetic", "r...	2016	The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans
Trafficking of human papillomaviruses to the Golgi apparatus during virus entry requires retromer , an endosomal coat protein complex that mediates the vesicular transport of cellular transmembrane proteins from the endosome to the Golgi apparatus or the plasma membrane . Here we show that the HPV16 L2 minor capsid pro...	The human papillomaviruses are important carcinogens , but little is known about how these non-enveloped viruses traffic to the nucleus , the site of genome replication . We use imaging , biochemical , and genetic techniques to show that a multi-subunit intracellular trafficking machine known as retromer binds directly...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Direct Binding of Retromer to Human Papillomavirus Type 16 Minor Capsid Protein L2 Mediates Endosome Exit during Viral Infection
Adult Clonorchis sinensis lives in the bile duct and causes endemic clonorchiasis in East Asian countries . Phosphagen kinases ( PK ) constitute a highly conserved family of enzymes , which play a role in ATP buffering in cells , and are potential targets for chemotherapeutic agents , since variants of PK are found onl...	The food-borne clonorchiasis imposes public health problems on inhabitants in endemic areas . Praziquantel has been employed as an efficacious anthelminthic in large-scale campaigns as well as for individual treatment of Clonorchis sinensis human infections . Although praziquantel continues to have good efficacy , new ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Molecular Cloning and Characterization of Taurocyamine Kinase from Clonorchis sinensis: A Candidate Chemotherapeutic Target
In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—which can be determined exactly in the model . Simulating the model on a computer , we consistently observe the “Bi...	Here , we address the question of how Darwinian evolution of organisms determines molecular evolution of their proteins and genomes . We developed a microscopic ab initio model of early biological evolution where the fitness ( essentially lifetime ) of an organism is explicitly related to the evolving sequences of its ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "viruses", "biophysics", "archaea", "computational", "biology" ]	2007	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold , shape , and transform the human genome . However , primate taxonomy is both complex and controversial , with marginal unifying consensus of the evolutionary hierarchy of extant primate species . Here...	Advances in human biomedicine , including those focused on changes in genes triggered or disrupted in development , resistance/susceptibility to infectious disease , cancers , mechanisms of recombination , and genome plasticity , cannot be adequately interpreted in the absence of a precise evolutionary context or hiera...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "evolutionary", "biology/animal", "genetics", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary...	2011	A Molecular Phylogeny of Living Primates
Australia is the only high-income country in which endemic trachoma persists . In response , the Australian Government has recently invested heavily towards the nationwide control of the disease . A novel simulation model was developed to reflect the trachoma epidemic in Australian Aboriginal communities . The model , ...	Australia is the only remaining high-income country reporting endemic levels of trachoma , with infections occurring predominantly within rural and remote Indigenous communities . Although the Australian government has recently invested large sums of money to combat the disease , it remains unclear whether the national...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Control of Trachoma in Australia: A Model Based Evaluation of Current Interventions
Cutaneous leishmaniasis ( CL ) is a skin disease caused by the protozoan parasite Leishmania . Few studies have assessed the influence of the sample collection site within the ulcer and the sampling method on the sensitivity of parasitological and molecular diagnostic techniques for CL . Sensitivity of the technique ca...	Cutaneous leishmaniasis ( CL ) is a parasitic disease of the skin caused by obligate intra-macrophage protozoa of the genus Leishmania which usually presents as ulcerative lesions at the site of infection . Traditionally , histopathological and diagnostic studies on CL have employed samples collected from the border of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Quantification of Leishmania (Viannia) Kinetoplast DNA in Ulcers of Cutaneous Leishmaniasis Reveals Inter-site and Inter-sampling Variability in Parasite Load
Forkhead box O ( FOXO ) transcription factors have a conserved function in regulating metazoan lifespan . A key function in this process involves the regulation of the cell cycle and stress responses including free radical scavenging . We employed yeast chronological and replicative lifespan assays , as well as oxidati...	Throughout human evolution , one question has remained constant: can we live forever ? We are continuously bombarded with products , diets , and exercise regimens that supposedly add years to our life . Is there an alterable program , whether genetic or environmental , that can be tweaked to increase longevity ? Medica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "model", "organisms", "molecular", "cell", "biology", "global", "health", "genetics", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2012	The Yeast Forkhead Transcription Factors Fkh1 and Fkh2 Regulate Lifespan and Stress Response Together with the Anaphase-Promoting Complex
Many cell functions rely on the ability of microtubules to self-organize as complex networks . In plants , cortical microtubules are essential to determine cell shape as they guide the deposition of cellulose microfibrils , and thus control mechanical anisotropy of the cell wall . Here we analyze how , in turn , cell s...	Plants exhibit an astonishing diversity in architecture and morphology . A key to such diversity is the ability of their cells to coordinate and grow to reach a broad spectrum of sizes and shapes . Cell growth in plants is guided by the microtubule cytoskeleton . Here , we seek to understand how microtubules self-organ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microtubules", "chemical", "compounds", "cellulose", "microtubule", "dynamics", "cell", "processes", "condensed", "matter", "physics", "anisotropy", "organic", "compounds", "membrane", "proteins", "materials", "science", "microtubule", "polymerization", "tubulins", "cellul...	2018	The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues
The morphogenesis of organs necessarily involves mechanical interactions and changes in mechanical properties of a tissue . A long standing question is how such changes are directed on a cellular scale while being coordinated at a tissular scale . Growing evidence suggests that mechanical cues are participating in the ...	Development and morphogenesis of tissues are dependent on a coordination between cell differentiation , proliferation and growth . Plants , which lack cell migration , control directional growth of tissues by adjusting cellulose fiber directions so forming the organ shapes . It has recently been shown that mechanical c...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "physics", "tissue", "mechanics", "developmental", "biology", "growth", "control", "plant", "growth", "and", "development", "biophysics", "simulations", "biology", "computational", "biology", "morphogenesis", "biophysics", "biomechanics", "cell", "mechanics" ]	2014	Stress and Strain Provide Positional and Directional Cues in Development
Integrative approaches to studying the coupled dynamics of skeletal muscles with their loads while under neural control have focused largely on questions pertaining to the postural and dynamical stability of animals and humans . Prior studies have focused on how the central nervous system actively modulates muscle mech...	Movement in organisms is a result of the interplay between biomechanics , neural control , and the influence of external environmental loads . Understanding the interaction between these factors is important not only for scientific reasons but also for engineering robotic systems and prostheses that strive to match bio...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science/systems", "and", "control", "theory", "computer", "science/control", "technology", "biophysics/theory", "and", "simulation", "computational", "biology" ]	2010	Optimal Workloop Energetics of Muscle-Actuated Systems: An Impedance Matching View
We present CATHEDRAL , an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures . CATHEDRAL builds on the features of a fast secondary-structure–based method ( using graph theory ) to locate known folds within a multidomain context and a residue-bas...	Proteins comprise individual folding units known as domains , with a significant proportion containing two or more ( multidomain structures ) . Each domain is thought to represent a unit of evolution and adopts a specific fold . Detecting domains is often the first step in classifying proteins into evolutionary familie...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "none", "computational", "biology" ]	2007	CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
Focal degradation of extracellular matrix ( ECM ) is the first step in the invasion of cancer cells . MT1-MMP is a potent membrane proteinase employed by aggressive cancer cells . In our previous study , we reported that MT1-MMP was preferentially located at membrane protrusions called invadopodia , where MT1-MMP under...	Metastasis is the major cause of death in cancer patients . If metastasis is blocked , the survival rate will be greatly increased . Cancer cells are surrounded by ECM ( extracellular matrix ) , which prevents their free movement . MT1-MMP is a potent membrane proteinase that degrades ECM , which is the first step of c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "extracellular", "matrix", "biology", "computational", "biology", "molecular", "cell", "biology" ]	2013	Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia
The Y chromosome harbors nine multi-copy ampliconic gene families expressed exclusively in testis . The gene copies within each family are >99% identical to each other , which poses a major challenge in evaluating their copy number . Recent studies demonstrated high variation in Y ampliconic gene copy number among huma...	The human genome harbors two sex chromosomes—X and Y . Among them , the Y chromosome is present only in males . Deletions of portions of this chromosome have been linked to male infertility , however exactly why the loss of these genes leads to this condition is not well understood . Here we study a group of Y chromoso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "population", "genetics", "cell", "processes", "sociology", "social", "sciences", "reproductive", "physiology", "human", "families", "population", "bi...	2019	Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes
The development of neutralizing anti-drug-antibodies to the Factor VIII protein-therapeutic is currently the most significant impediment to the effective management of hemophilia A . Common non-synonymous single nucleotide polymorphisms ( ns-SNPs ) in the F8 gene occur as six haplotypes in the human population ( denote...	The development of anti-drug antibodies to therapeutic proteins is a significant impediment to development and licensure of therapeutic proteins and limits their clinical utility . The development of such antibodies requires CD4+ T-cell activation , which is mediated by the recognition of epitopes presented by MHC clas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "major", "histocompatibility", "complex", "drug", "licensing", "and", "regulation", "drug", "research", "and", "development", "clinical", "immunology", "drugs", "and", "devices", "pharmacogenetics", "adverse", "reactions", "immunology", "biology", "computation...	2013	Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
Covalently closed circular DNA ( cccDNA ) of hepadnaviruses exists as an episomal minichromosome in the nucleus of infected hepatocyte and serves as the transcriptional template for viral mRNA synthesis . Elimination of cccDNA is the prerequisite for either a therapeutic cure or immunological resolution of HBV infectio...	Hepatitis B virus ( HBV ) infection affects approximately one-third of the world population and more than 350 million people are chronically infected by the virus , for which the currently available antiviral therapies fail to provide a cure . This is because the HBV DNA polymerase inhibitors have no direct effect on t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	Alpha-Interferon Suppresses Hepadnavirus Transcription by Altering Epigenetic Modification of cccDNA Minichromosomes
Coevolution of viruses and their hosts represents a dynamic molecular battle between the immune system and viral factors that mediate immune evasion . After the abandonment of smallpox vaccination , cowpox virus infections are an emerging zoonotic health threat , especially for immunocompromised patients . Here we deli...	Virus-infected or malignant transformed cells are eliminated by cytotoxic T lymphocytes , which recognize antigenic peptide epitopes in complex with major histocompatibility complex class I ( MHC I ) molecules at the cell surface . The majority of such peptides are derived from proteasomal degradation in the cytosol an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "biology", "and", "life", "sciences", "immunology", "biophysics", "molecular", "biology", "veterinary", "science" ]	2014	A Negative Feedback Modulator of Antigen Processing Evolved from a Frameshift in the Cowpox Virus Genome
Senataxin , mutated in the human genetic disorder ataxia with oculomotor apraxia type 2 ( AOA2 ) , plays an important role in maintaining genome integrity by coordination of transcription , DNA replication , and the DNA damage response . We demonstrate that senataxin is essential for spermatogenesis and that it functio...	Ataxia with oculomotor apraxia type 2 ( AOA2 ) caused by a defect in the gene Setx ( coding for senataxin ) is part of a subgroup of autosomal recessive ataxias characterized by defects in genes responsible for the recognition and/or repair of damage in DNA . Cells from these patients are characterized by oxidative str...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology" ]	2013	Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing
Plants under pathogen attack produce high levels of ethylene , which plays important roles in plant immunity . Previously , we reported the involvement of ACS2 and ACS6 , two Type I ACS isoforms , in Botrytis cinerea–induced ethylene biosynthesis and their regulation at the protein stability level by MPK3 and MPK6 , tw...	Plant immunity , similar to that in animals , also involves mitogen-activated protein kinase ( MAPK ) cascades . However , plants use unique MAPK substrates and secondary signaling molecules in the process . Among them , ethylene , a gaseous plant hormone , plays critical roles . Ethylene-regulated responses begin with...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Dual-Level Regulation of ACC Synthase Activity by MPK3/MPK6 Cascade and Its Downstream WRKY Transcription Factor during Ethylene Induction in Arabidopsis
Scabies and head lice are ubiquitous ectoparasitic infestations that are common across the Pacific Islands . Ivermectin is an effective treatment for both conditions , although the doses used vary . At a community level , mass drug administration ( MDA ) with ivermectin is an effective strategy to decrease prevalence o...	Head lice and scabies are both caused by ectoparasites and lead to itchy skin conditions that are associated with secondary bacterial infections and social stigma . Both are common in developing countries . In the Solomon Islands , mass treatment of communities using ivermectin ( at dose of 200 micrograms per kilogram ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine", "and", "health", "sciences", "solomon", "islands", "education", "scalp", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "animals", "age", "groups", "ectoparasitic", ...	2018	Impact of ivermectin administered for scabies treatment on the prevalence of head lice in Atoifi, Solomon Islands
Phosphorylation at specific residues can activate a protein , lead to its localization to particular compartments , be a trigger for protein degradation and fulfill many other biological functions . Protein phosphorylation is increasingly being studied at a large scale and in a quantitative manner that includes a tempo...	Cells employ protein phosphorylation – the addition of a phosphate group to serine , threonine or tyrosine residues – as a key regulatory mechanism for modulating protein function . Proteomics technologies can now quantify thousands of phosphorylation sites to reveal the dynamics of phosphorylation at each site in resp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "systems", "biology", "spectrometric", "identification", "of", "proteins", "structure", "prediction", "biochemistry", "genomics", "protein", "structure", "biology", "computational", "biology", "proteomics", "structural", "genomics", "macromolecular", ...	2013	Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins
The recombination activity of Escherichia coli ( E . coli ) RecA protein reflects an evolutionary balance between the positive and potentially deleterious effects of recombination . We have perturbed that balance , generating RecA variants exhibiting improved recombination functionality via random mutagenesis followed ...	The genetic recombination systems of bacteria have not evolved for optimal enzymatic function . As recombination and recombination systems can have deleterious effects , these systems have evolved sufficient function to repair a level of DNA double strand breaks typically encountered during replication and cell divisio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination
The TAR DNA-binding protein 43 ( TDP-43 ) has been identified as the major disease protein in amyotrophic lateral sclerosis ( ALS ) and frontotemporal lobar degeneration with ubiquitin inclusions ( FTLD-U ) , defining a novel class of neurodegenerative conditions: the TDP-43 proteinopathies . The first pathogenic mutat...	The abnormal accumulation of disease proteins in neuronal cells of the brain is a characteristic feature of many neurodegenerative diseases . Rare mutations in the genes that encode the accumulating proteins have been identified in these disorders and are crucial for the development of cell and animal models used to st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/movement", "disorders", "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders/cognitive", "neurology", "and", "dementia", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2008	Novel Mutations in TARDBP (TDP-43) in Patients with Familial Amyotrophic Lateral Sclerosis
In the current era of malaria eradication , reducing transmission is critical . Assessment of transmissibility requires tools that can accurately identify the various developmental stages of the malaria parasite , particularly those required for transmission ( sexual stages ) . Here , we present a method for estimating...	The human malaria parasite Plasmodium falciparum is transmitted through a mosquito vector and causes over half a million deaths per year . The microorganism cycles through asexual and sexual life cycle stages , and its successful transmission relies on cells in the sexual stage . These stages are , however , present on...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Inferring Developmental Stage Composition from Gene Expression in Human Malaria
Chikungunya virus ( CHIKV ) is a re-emerging mosquito-borne Alphavirus that causes a clinical disease involving fever , myalgia , nausea and rash . The distinguishing feature of CHIKV infection is the severe debilitating poly-arthralgia that may persist for several months after viral clearance . Since its re-emergence ...	Chikungunya virus ( CHIKV ) is a re-emerging Alphavirus that has caused recent massive outbreaks in the Indian Ocean region . In addition , outbreaks have been documented in Europe and elsewhere in the world , initiated by infected travelers returning to their homelands . The recent outbreak strains possess extended ve...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology" ]	2013	Chikungunya Virus Infection Results in Higher and Persistent Viral Replication in Aged Rhesus Macaques Due to Defects in Anti-Viral Immunity
The NAD+-dependent histone deacetylase Sir2 was originally identified in Saccharomyces cerevisiae as a silencing factor for HML and HMR , the heterochromatic cassettes utilized as donor templates during mating-type switching . MATa cells preferentially switch to MATα using HML as the donor , which is driven by an adjac...	Sir2 is a highly conserved NAD+-dependent protein deacetylase and defining member of the sirtuin protein family . It was identified 40 years ago in the budding yeast , Saccharomyces cerevisiae , as a factor that silences the cryptic mating-type loci , HML and HMR . These heterochromatic cassettes are utilized as templa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chromosome", "structure", "and", "function", "gene", "regulation", "hormones", "organisms", "fungi", "plant", "science", "model", "organisms", "plant", "hormones", "experimental", "organism", "systems", "molecular", "biology", "techniques", "epigenetics", "chromatin", ...	2019	A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure
Leprosy has a global presence; more than 180 thousand new cases were registered in 2013 , 15% of which were found in the Americas . The elderly are a very susceptible demographic in terms of developing illnesses , mainly because of characteristics natural to the senescence of the human organism . This study’s goals wer...	Leprosy , despite being an ancient disease , still represents a challenge to public health systems today . There are still just a few studies about it , particularly among the elderly . It is known that they constitute a very heterogeneous group in terms of immune response to infections , alterations to the peripheral ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "elderly", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "age", "groups", "developmental", "biology", "physiological", "processes", "organism", "developm...	2019	Leprosy in elderly people and the profile of a retrospective cohort in an endemic region of the Brazilian Amazon
Seed-setting rate is a critical determinant of grain yield in rice ( Oryza sativa L . ) . Rapid and healthy pollen tube growth in the style is required for high seed-setting rate . The molecular mechanisms governing this process remain largely unknown . In this study , we isolate a dominant low seed-setting rate rice m...	Rice is not only the staple food for more than half of the world’s population , but also a model species for plant developmental and genetic studies . After pollination , rice pollen grains adhere and hydrate at the surface of stigmatic papilla cells . Then , the germinated pollen tubes invade the stigma and navigate t...	[ "Abstract", "Introduction", "Result", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "plant", "physiology", "pollen", "membrane", "proteins", "plant", "science", "rice", "genetically", "modified", "plants", "experimental", "organism", "systems", "plants", "cellular", "structures", "and", "organelles", "flower", "anat...	2017	OsCNGC13 promotes seed-setting rate by facilitating pollen tube growth in stylar tissues
Integration of multimodal sensory information is fundamental to many aspects of human behavior , but the neural mechanisms underlying these processes remain mysterious . For example , during face-to-face communication , we know that the brain integrates dynamic auditory and visual inputs , but we do not yet understand ...	Combining different sources of information is fundamental to many aspects of behavior , from our ability to pick up a ringing mobile phone to communicating with a friend in a busy environment . Here , we have studied the integration of auditory and visual speech information . Our work demonstrates that integration reli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "acoustics", "medicine", "and", "health", "sciences", "linguistics", "engineering", "and", "technology", "audio", "signal", "processing", "visual", "signals", "signal", "processing", "brain", "social", "sciences", "neuroscience", "brain", "mapping", "vision", "neuroimag...	2018	Representational interactions during audiovisual speech entrainment: Redundancy in left posterior superior temporal gyrus and synergy in left motor cortex
Infection by the simian malaria parasite , Plasmodium knowlesi , can lead to severe and fatal disease in humans , and is the most common cause of malaria in parts of Malaysia . Despite being a serious public health concern , the geographical distribution of P . knowlesi malaria risk is poorly understood because the par...	Plasmodium knowlesi is a malaria parasite found in wild monkey populations and transmitted from this animal reservoir to humans via infected mosquitoes . It causes severe and fatal disease in humans , and is the most common cause of malaria in parts of Malaysia . The geographical distribution of this disease is largely...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "population", "dynamics", "tropical", "diseases", "geographical", "locations", "vertebrates", "parasitic", "diseases", "animals", "mammals", "parasitology", "parasitic", "protozoans", "primates", ...	2016	Estimating Geographical Variation in the Risk of Zoonotic Plasmodium knowlesi Infection in Countries Eliminating Malaria
Lipid rafts in eukaryotic cells are sphingolipid and cholesterol-rich , ordered membrane regions that have been postulated to play roles in many membrane functions , including infection . We previously demonstrated the existence of cholesterol-lipid-rich domains in membranes of the prokaryote , B . burgdorferi , the ca...	Specialized domains ( “lipid rafts” ) rich in specific membrane lipids ( sphingolipids and cholesterol ) have been proposed to form in the cell membranes of higher organisms , and to be of functional importance . We recently found that domains can be detected in the membranes of the bacterium that causes Lyme disease ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biochemistry", "biology", "microbiology" ]	2013	Proving Lipid Rafts Exist: Membrane Domains in the Prokaryote Borrelia burgdorferi Have the Same Properties as Eukaryotic Lipid Rafts
Genetic information should be accurately transmitted from cell to cell; conversely , the adaptation in evolution and disease is fueled by mutations . In the case of cancer development , multiple genetic changes happen in somatic diploid cells . Most classic studies of the molecular mechanisms of mutagenesis have been p...	Evolution and carcinogenesis are driven by mutations . Cells maintain constant mutation rates and can afford only transient mutagenesis bursts for adaptation . The nature of the mutational avalanches is not very clear . We sequenced the whole genomes of mutants induced in haploid and diploid yeast by nucleobase analog ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome-Wide Mutation Avalanches Induced in Diploid Yeast Cells by a Base Analog or an APOBEC Deaminase
Intracellular pathogenic bacteria evade the immune response by replicating within host cells . Legionella pneumophila , the causative agent of Legionnaires’ Disease , makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells . The L . pneumophila effector SidK wa...	V-ATPase-driven acidification of lysosomes in phagocytic cells activates enzymes important for killing of phagocytized pathogens . Successful pathogens can subvert host defenses by secreting effectors that target V-ATPases to inhibit lysosomal acidification or lysosomal fusion with other cell compartments . This study ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "condensed", "matter", "physics", "microbiology", "enzymology", "electron", "cryo-microscopy", "phosph...	2017	Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein
Oviparous animals across many taxa have evolved diverse strategies that deter egg predation , providing valuable tests of how natural selection mitigates direct fitness loss . Communal egg laying in nonsocial species minimizes egg predation . However , in cannibalistic species , this very behavior facilitates egg preda...	Egg-laying species that lack parental care often protect their eggs from predators by laying them in communal groups or by fortifying them with toxins . However , these strategies may backfire when the predators are from the same species ( cannibals ) since a ) there are plenty of available eggs in these sites , b ) th...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "invertebrates", "chemical", "compounds", "hexanes", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "waxes", "materials", "science", "experimental", "organism", "systems", "zoology", "drosophila", "research", ...	2019	Drosophila melanogaster cloak their eggs with pheromones, which prevents cannibalism
Surgery , Antibiotics , Facial cleanliness and Environmental improvement ( SAFE ) are advocated by the World Health Organization ( WHO ) for trachoma control . However , few studies have evaluated the complete SAFE strategy , and of these , none have investigated the associations of Antibiotics , Facial cleanliness , a...	Trachoma is an infectious disease that is cased by a bacterium , Chlamydia trachomatis , and is the leading cause of preventable blindness estimated to be responsible for 3 . 6% of blindness globally . The World Health Organization ( WHO ) recommends a strategy for trachoma control known as SAFE—surgery , antibiotics ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "ophthalmology/eye", "infections" ]	2008	Associations between Active Trachoma and Community Intervention with Antibiotics, Facial Cleanliness, and Environmental Improvement (A,F,E)
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough , a serious respiratory infection causing hundreds of thousands of deaths annually worldwide . There are effective vaccines , but their production requires growing large quantities of B . pertussis . Unfortunately , B . pertussis ...	Metabolic flux models have been used to understand how organisms adapt their metabolism under different growth conditions , and are finding increasing application in synthetic biology and biotechnology . One barrier to progress in this field is the construction and curation of metabolic flux models for new organisms . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bordetella", "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "metabolic", "networks", "microbiology", "neuroscience", "vaccines", "metabolites", "network", "analysis", "neurotran...	2017	A curated genome-scale metabolic model of Bordetella pertussis metabolism
Rift Valley fever virus is an arbovirus that affects both livestock and humans throughout Africa and in the Middle East . Despite its endemicity throughout Africa , it is a rare event to identify an infected individual during the acute phase of the disease and an even rarer event to collect serial blood samples from th...	Rift Valley fever virus is an emerging virus of public health significance . In endemic areas up to 60% of the population are seropositive by adulthood . This implies that most of the individuals living in these endemic areas become infected with this virus at some point in their lifetime . This highly prevalent virus ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "micro...	2018	Rift valley fever viral load correlates with the human inflammatory response and coagulation pathway abnormalities in humans with hemorrhagic manifestations
Mutations in the LIM-homeodomain transcription factor LMX1B cause nail-patella syndrome , an autosomal dominant pleiotrophic human disorder in which nail , patella and elbow dysplasia is associated with other skeletal abnormalities and variably nephropathy and glaucoma . It is thought to be a haploinsufficient disorder...	Nail-patella syndrome is a human genetic disease caused by an inactivating mutation in one copy of a gene called LMX1B , with the amount of protein produced from the remaining copy of the gene not being enough for normal function . Patients with this disease have malformations of their nails , elbows and kneecaps . Som...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "mutagenesis", "developmental", "biology", "mutation", "model", "organisms", "animal", "genetics", "organism", "development", "cell", "biology", "genetic", "screens", "gene", "identification", "and", "analysis", "genetics", "morphogenesis", "biology", ...	2014	A Dominant-Negative Mutation of Mouse Lmx1b Causes Glaucoma and Is Semi-lethal via LBD1-Mediated Dimerisation
Specific interactions between host genotypes and pathogen genotypes ( G×G interactions ) are commonly observed in invertebrate systems . Such specificity challenges our current understanding of invertebrate defenses against pathogens because it contrasts the limited discriminatory power of known invertebrate immune res...	The outcome of invertebrate host-pathogen interactions often depends on the specific pairing of host and pathogen genotypes . This genetic specificity challenges our current understanding of invertebrate resistance to pathogens because it contrasts the limited discriminatory power of known invertebrate defense mechanis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "heredity", "vector", "biology", "virology", "genetics", "host-pathogen", "interaction", "quantitative", "traits", "biology", "evolutionary", "biology", "microbiology", "genetics", "of", "disease" ]	2013	Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses
Burkholderia pseudomallei is a soil saprophytic bacterium that causes melioidosis . The infection occurs through cutaneous inoculation , inhalation or ingestion . Bacteriophages ( phages ) in the same ecosystem may significantly impact the biology of this bacterium in the environment , and in their culturability in the...	Burkholderia pseudomallei is a motile , Gram-negative bacterium that causes melioidosis . The disease is endemic in Southeast Asia and Northern Australia and can be fatal . In the zones of endemicity , B . pseudomallei are commonly found in soils , and the bacteria can move to the surface during the rainy season . In T...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "bacteriophages", "melioidosis", "microbiology", "viruses", "bacterial", "diseases", "microscopy", "molecular", "biology", "techniques", "mammalian", "genomics", "microbial", "genomics", "research", "and",...	2016	Analyses of the Distribution Patterns of Burkholderia pseudomallei and Associated Phages in Soil Samples in Thailand Suggest That Phage Presence Reduces the Frequency of Bacterial Isolation
Bleeding tendency , coagulopathy and platelet disorders are recurrent manifestations in snakebites occurring worldwide . We reasoned that by damaging tissues and/or activating cells at the site of the bite and systemically , snake venom toxins might release or decrypt tissue factor ( TF ) , resulting in activation of b...	Although the abundance of reports about hemostatic disturbances in snakebites , few studies have addressed how crude snake venoms evoke blood coagulation disturbances in vivo . Snake venoms contain several components that disturb hemostasis , and the prevailing model claims that coagulation disturbances observed in pat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "coagulation", "disorders", "medicine", "and", "health", "sciences", "blood", "coagulation", "body", "fluids", "blood", "anatomy", "coagulation", "factors", "proteins", "plasma", "proteins", "thrombocytopenia", "platelets", "biology", "and", "life", "sci...	2014	Bothrops jararaca Venom Metalloproteinases Are Essential for Coagulopathy and Increase Plasma Tissue Factor Levels during Envenomation
Metabolomics studies use quantitative analyses of metabolites from body fluids or tissues in order to investigate a sequence of cellular processes and biological systems in response to genetic and environmental influences . This promises an immense potential for a better understanding of the pathogenesis of complex dis...	Biomedical research has entered a new era where a large number of molecules and different components in biological systems can be quantitatively examined to investigate the causes of common human diseases . However , given the complexity of biological systems , those causes may not contribute to diseases individually b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "rheumatology", "medicine", "and", "health", "sciences", "chemical", "compounds", "applied", "mathematics", "metabolic", "networks", "organic", "compounds", "simulation", "and", "modeling", "algorithms", "evolutionary", "computation", "metabolomics", "mathematics", "metabol...	2018	An evolutionary learning and network approach to identifying key metabolites for osteoarthritis
Rift Valley fever ( RVF ) is an emerging , vector-borne viral zoonosis that has significantly impacted public health , livestock health and production , and food security over the last three decades across large regions of the African continent and the Arabian Peninsula . The potential for expansion of RVF outbreaks wi...	Rift Valley fever ( RVF ) is a vector-borne zoonotic disease that imparts a substantial burden to the economy and public health of pastoralist communities across the African continent and Arabian Peninsula . Furthermore , RVF is also an emerging pathogen of growing global concern . Knowledge of the epidemiological and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "invertebrates", "livestock", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "rift", "valley", "fever", "virus", "surface", "water", "pathology", "and", "laboratory", "medicine", "landforms", "ruminants", "pathog...	2017	Wetlands, wild Bovidae species richness and sheep density delineate risk of Rift Valley fever outbreaks in the African continent and Arabian Peninsula
Mutualisms between species play an important role in ecosystem function and stability . However , in some environments , the competitive aspects of an interaction may dominate the mutualistic aspects . Although these transitions could have far-reaching implications , it has been difficult to study the causes and conseq...	Species often engage in mutualistic interactions that are beneficial for both partners . However , there is also a cost associated with cooperation , for example , in the form of energy required to make nutrients for a partner . When environments change , the costs and benefits of cooperating can change as well , and t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "compounds", "aliphatic", "amino", "acids", "population", "dynamics", "organic", "compounds", "leucine", "mathematics", "chemical", "equilibrium", "algebra", "amino", "acids", "population", "biology", "physical", "chemistry", "aromatic", "amino", "acids", "p...	2016	Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism
Zika virus ( ZIKV ) and chikungunya virus ( CHIKV ) are highly pathogenic arthropod-borne viruses that are currently a serious health burden in the Americas , and elsewhere in the world . ZIKV and CHIKV co-circulate in the same geographical regions and are mainly transmitted by Aedes aegypti mosquitoes . There is a gro...	Zika virus ( ZIKV ) and chikungunya virus ( CHIKV ) are highly pathogenic arthropod-borne viruses that present a serious health threat to humans . Since 2015 , both viruses circulate in the same geographical regions of the Americas and are predominantly transmitted by the Yellow Fever mosquito Ae . aegypti . There is a...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "vero", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "biological", "cultures", "tropical", "diseases", "microbiology", "saliva", ...	2017	Mosquito co-infection with Zika and chikungunya virus allows simultaneous transmission without affecting vector competence of Aedes aegypti
Peroxisomes are membrane-bound organelles within eukaryotic cells that post-translationally import folded proteins into their matrix . Matrix protein import requires a shuttle receptor protein , usually PEX5 , that cycles through docking with the peroxisomal membrane , ubiquitination , and export back into the cytosol ...	Peroxisomes are small organelles that must continually import matrix proteins to contribute to cholesterol and bile acid synthesis , among other important functions . Cargo matrix proteins are shuttled to the peroxisomal membrane , but the only source of energy that has been identified to translocate the cargo into the...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "eukaryotic", "cells", "cellular", "structures", "subcellular", "organelles", "biophysic", "al", "simulations", "cellular", "types", "biology", "computational", "biology", "molecular", "cell", "biology", "biophysics", "simulations", "biophysics" ]	2014	PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes
Meiosis is the cell division that halves the genetic component of diploid cells to form gametes or spores . To achieve this , meiotic cells undergo a radical spatial reorganisation of chromosomes . This reorganisation is a prerequisite for the pairing of parental homologous chromosomes and the reductional division , wh...	Organisms store their genetic material in the form of chromosomes that must be replicated and shared out during cell division . In sexual reproduction the cell division , called meiosis , halves the number of chromosomes to form gametes . This halving requires a complex reorganisation of chromosomes . Each gamete recei...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computer", "science", "computer", "modeling", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition
We used a multi-round , two-party exchange game in which a healthy subject played a subject diagnosed with a DSM-IV ( Diagnostic and Statistics Manual-IV ) disorder , and applied a Bayesian clustering approach to the behavior exhibited by the healthy subject . The goal was to characterize quantitatively the style of pl...	Human social interaction is exquisitely complex , and perturbed social interaction is a hallmark of psychological pathogy . When someone has a psychological disorder the focus is generally on their behavior , but this behavior is rarely something displayed in isolation and typically induces profound changes in the peop...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "neuroscience", "neurological", "disorders/neuroimaging", "neurological", "disorders/neuropsychiatric", "disorders" ]	2010	Biosensor Approach to Psychopathology Classification
Adult-onset hearing loss is very common , but we know little about the underlying molecular pathogenesis impeding the development of therapies . We took a genetic approach to identify new molecules involved in hearing loss by screening a large cohort of newly generated mouse mutants using a sensitive electrophysiologic...	Progressive hearing loss with age is extremely common in the population , leading to difficulties in understanding speech , increased social isolation , and associated depression . We know it has a significant heritability , but so far we know very little about the molecular pathways leading to hearing loss , hampering...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ears", "brain", "alleles", "middle", "ear", "otology", "inner", "ear", "genome", "analysis", "hearing", "disorders", "genomics", "head", "otorhinolaryngology", "brainstem", "gene", "ontologies", "genetic", "loci", "deafness", ...	2019	Mouse screen reveals multiple new genes underlying mouse and human hearing loss
Phylogenetic studies have largely contributed to better understand the emergence , spread and evolution of highly pathogenic avian influenza during epidemics , but sampling of genetic data has never been detailed enough to allow mapping of the spatiotemporal spread of avian influenza viruses during a single epidemic . ...	Outbreaks of highly pathogenic avian influenza ( HPAI ) viruses have affected poultry worldwide in the last decades , resulting in vast socioeconomic damages and many human infections . It is important to determine the route of transmission between poultry farms to be able to implement efficient control measures . Here...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "evolutionary", "ecology", "infectious", "disease", "epidemiology", "influenza", "infectious", "disease", "control", "veterinary", "science", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "veterinary",...	2011	Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic
Quiescent long-term somatic stem cells reside in plant and animal stem cell niches . Within the Arabidopsis root stem cell population , the Quiescent Centre ( QC ) , which contains slowly dividing cells , maintains surrounding short-term stem cells and may act as a long-term reservoir for stem cells . The RETINOBLASTOM...	In the plant Arabidposis thaliana , root meristems ( in the growing tip of the root ) contain slowly dividing cells that act as an organizing center for the root stem cells that surround them . This centre is called the quiescent centre ( QC ) . In this study , we show that the slow rate of division in the QC is regula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer
In order to identify genetic factors related to thyroid cancer susceptibility , we adopted a candidate gene approach . We studied tag- and putative functional SNPs in genes involved in thyroid cell differentiation and proliferation , and in genes found to be differentially expressed in thyroid carcinoma . A total of 76...	Although follicular cell-derived thyroid cancer has an important genetic component , efforts in identifying major susceptibility genes have not been successful . Probably this is due to the complex nature of this disease that involves both genetic and environmental factors , as well as the interaction between them , wh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/cancer", "genetics" ]	2009	The Variant rs1867277 in FOXE1 Gene Confers Thyroid Cancer Susceptibility through the Recruitment of USF1/USF2 Transcription Factors
Schistosoma blood flukes , which infect over 200 million people globally , co-opt CD4+ T cell-dependent mechanisms to facilitate parasite development and egg excretion . The latter requires Th2 responses , while the mechanism underpinning the former has remained obscure . Using mice that are either defective in T cell ...	Schistosomes , or blood flukes , cause a debilitating illness in millions of people worldwide , which manifests when inflammation develops in response to parasite eggs that become trapped in the liver and other organs . Paradoxically , schistosomes require signals from the host's immune system in order to develop fully...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "immunology/innate", "immunity", "developmental", "biology/microbial", "growth", "and", "development", "infectious", "diseases/helminth", "infections", "immunology/leukocyte", "signaling", ...	2010	Blood Fluke Exploitation of Non-Cognate CD4+ T Cell Help to Facilitate Parasite Development
Chlamydia trachomatis is globally the predominant infectious cause of blindness and one of the most common bacterial causes of sexually transmitted infection . Infections of the conjunctiva cause the blinding disease trachoma , an immuno-pathological disease that is characterised by chronic conjunctival inflammation an...	Chlamydia trachomatis is a pathogen that causes sexually transmitted infections ( STIs ) and the blinding disease trachoma . Natural Killer ( NK ) cells are part of the host immune system's first line of defence against infection . NK cell functions are genetically encoded and differences between individuals mean that ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "haplotypes", "immune", "cells", "genetics", "of", "the", "immune", "system", "major", "histocompatibility", "complex", "nk", "cells", "genetic", "association", "studies", "natural", "selection", "immunity", "innate", "immunity", "genetics", "immunity", "to", "infecti...	2014	Conjunctival Scarring in Trachoma Is Associated with the HLA-C Ligand of KIR and Is Exacerbated by Heterozygosity at KIR2DL2/KIR2DL3
cis-regulatory modules ( CRMs ) generate precise expression patterns by integrating numerous transcription factors ( TFs ) . Surprisingly , CRMs that control essential gene patterns can differ greatly in conservation , suggesting distinct constraints on TF binding sites . Here , we show that a highly conserved Distal-l...	Enhancers are regulatory elements that interact with transcription factor proteins to control cell-specific gene expression during development . Surprisingly , only a subset of enhancers are highly conserved at the sequence level , even though the expression patterns they control are often conserved and essential for p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "abdomen", "dna-binding", "proteins", "dna", "transcription", "developmental", "biology", "mutation", "embryos", "embryology", "proteins", "gene", "expression", "homeobox", "biochemistry", "point", "mutation", "anatomy", "thorax", ...	2016	A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes
Alpha-methylacyl-coenzyme A racemase ( AMACR ) regulates peroxisomal β-oxidation of phytol-derived , branched-chain fatty acids from red meat and dairy products — suspected risk factors for colon carcinoma ( CCa ) . AMACR was first found overexpressed in prostate cancer but not in benign glands and is now an establishe...	Men consuming high amounts of red meat and dairy products are at a higher risk of developing colon and prostate cancer . Alpha-methylacyl-coenzyme A racemase ( AMACR ) is an enzyme that helps to break down fat from these foods to produce energy . An increase in the utilization of energy from fat is a hallmark of many c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "genetics", "and", "genomics/gene", "expression", "pathology/immunology", "molecular", "biology", "cell", "biology/gene", "expression" ]	2009	Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon
Regulatory T ( Treg ) cells dampen an exaggerated immune response to viral infections in order to avoid immunopathology . Cytomegaloviruses ( CMVs ) are herpesviruses usually causing asymptomatic infection in immunocompetent hosts and induce strong cellular immunity which provides protection against CMV disease . It re...	Treg cells are crucial for immune homeostasis and for dampening immune response to several diseased conditions , including viral infections . Murine cytomegalovirus ( MCMV ) is a herpesvirus with pathogenic potential , so that early immune mechanisms are essential in controlling virus and protecting from virus-induced ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "liver", "immune", "cells", "immune", "physiology", "spleen", "immunology", "cytomegalovirus", "infection", "cloning", "cytotoxic", "t", "cells", "molecular", "biology", "techniques", "research", "and", "analy...	2017	IL-33/ST2 pathway drives regulatory T cell dependent suppression of liver damage upon cytomegalovirus infection
Selective brain responses to objects arise within a few hundreds of milliseconds of neural processing , suggesting that visual object recognition is mediated by rapid feed-forward activations . Yet disruption of neural responses in early visual cortex beyond feed-forward processing stages affects object recognition per...	How much neural processing is required to detect objects of interest in natural scenes ? The speed and efficiency of object recognition suggests that fast feed-forward buildup of perceptual activity is sufficient . However , there is also evidence that disruption of visual processing beyond feed-forward stages leads to...	[ "Abstract", "Introduction", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "reaction", "time", "visual", "object", "recognition", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "brain", "neuroscience", "...	2018	Scene complexity modulates degree of feedback activity during object detection in natural scenes
Genomics has posed the challenge of determination of protein function from sequence and/or 3-D structure . Functional assignment from sequence relationships can be misleading , and structural similarity does not necessarily imply functional similarity . Proteins in the DJ-1 family , many of which are of unknown functio...	Genome sequencing has led to the discovery of many new gene products , proteins . These discoveries hold tremendous potential for totally new approaches to the diagnosis and treatment of disease . To realize this potential , one important step is to understand the function of the thousands of proteins whose function is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "neuroscience", "neurological", "disorders", "computational", "biology" ]	2007	Identification of Functional Subclasses in the DJ-1 Superfamily Proteins
Gag , as the major structural protein of HIV-1 , is necessary for the assembly of the HIV-1 sphere shell . An in-depth understanding of its trafficking and polymerization is important for gaining further insights into the mechanisms of HIV-1 replication and the design of antiviral drugs . We developed a mathematical mo...	The human immunodeficiency virus ( HIV-1 ) is a retrovirus that causes acquired immunodeficiency syndrome ( AIDS ) , an infectious disease with high annual mortality . Gag protein is the major structural protein of HIV-1 and can self-assemble into the HIV-1 sphere shell . Therefore , an in-depth understanding of Gag pr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "molecular", "motors", "rna", "viruses", "materials", "science"...	2017	Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization
Maps of genetic interactions can dissect functional redundancies in cellular networks . Gene expression profiles as high-dimensional molecular readouts of combinatorial perturbations provide a detailed view of genetic interactions , but can be hard to interpret if different gene sets respond in different ways ( called ...	Genes do not act in isolation , but rather in tight interaction networks . Maps of genetic interactions between pairs of genes are a powerful way to dissect these relationships . Genetic interactions are mostly defined by quantifying individual phenotypes like growth or survival . However , when high-dimensional phenot...	[ "Abstract", "Introduction", "Model", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "genetic", "networks", "engineering", "and", "technology", "signaling", "networks", "logic", "circuits", "epistasis", "regulator", "genes", "fungi", "model", "organisms", "network", "analysis", "experimental", "organism", "systems", "gene", "types", "genetic", "interact...	2017	Inferring modulators of genetic interactions with epistatic nested effects models
Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities ( SGAs ) . Non-steroidal anti-inflammatory drugs ( NSAIDs ) have been shown to reduce cancer risk , including risk of progression from Barrett's esophagus ( BE ) to esophageal adenocarcinoma ( EA ) . ...	Cancer is a disease that develops over decades as result of accumulation of abnormalities in the genomes of otherwise normal cells . Cells in tumors compete for space and resources . Those cells able to survive the Darwinian struggle for existence within tissues progressively evolve uncontrolled growth and in some case...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cancer", "detection", "and", "diagnosis", "medicine", "genome", "evolution", "population", "genetics", "cancer", "risk", "factors", "cancers", "and", "neoplasms", "chemoprevention", "gastrointestinal", "tumors", "predisposing", "conditions", "and", "syndromes", "oncology...	2013	NSAIDs Modulate Clonal Evolution in Barrett's Esophagus
Chikungunya virus ( CHIKV ) is a re-emerging arthropod-borne ( arbo ) virus that causes chikungunya fever in humans and is predominantly transmitted by Aedes aegypti mosquitoes . The CHIKV replication machinery consists of four non-structural proteins ( nsP1-4 ) that additionally require the presence of a number of hos...	Chikungunya virus ( CHIKV ) is a re-emerging arthropod-borne virus that is transmitted predominantly by Aedes aegypti mosquitoes . In 2016 alone CHIKV caused over 100 . 000 infections in South-America , exemplifying the impact of CHIKV disease . Previous research has suggested that the CHIKV non-structural protein 3 ( ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "vero", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "biological", "cultures", "tropical", "diseases", "microbiology", "saliva", ...	2018	Conserved motifs in the hypervariable domain of chikungunya virus nsP3 required for transmission by Aedes aegypti mosquitoes
DNA sequence variation causes changes in gene expression , which in turn has profound effects on cellular states . These variations affect tissue development and may ultimately lead to pathological phenotypes . A genetic locus containing a sequence variation that affects gene expression is called an “expression quantit...	Complex physiological traits are affected through subtle changes of molecular traits like gene expression in the relevant tissues , which in turn are caused by genetic variation . A genetic locus containing a sequence variation affecting gene expression is called an expression quantitative trait locus ( eQTL ) . Unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "dna", "modification", "gene", "expression", "genetics", "population", "genetics", "biology", "computational", "biology", "gene", "networks", "dna", "transcription" ]	2013	Impact of Natural Genetic Variation on Gene Expression Dynamics
The malaria parasite Plasmodium falciparum invades , replicates within and destroys red blood cells in an asexual blood stage life cycle that is responsible for clinical disease and crucial for parasite propagation . Invasive malaria merozoites possess a characteristic apical complex of secretory organelles that are di...	Despite improved control measures over recent decades , malaria is still a considerable health burden across much of the globe . The disease is caused by a single-celled parasite that invades and replicates within host cells . During invasion , the parasite discharges a set of flask-shaped secretory organelles called r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "parasite", "replication", "plasmodium", "viral", "transmission", "and", "infection", "microbiology", "cloning", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "sequence", "motif", "analysis", "molecular", "biology", "technique...	2019	The Plasmodium falciparum rhoptry bulb protein RAMA plays an essential role in rhoptry neck morphogenesis and host red blood cell invasion
Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron’s probability of spiking . One popular method , known as maximally informative dimensions ( MID ) , uses an information-theoretic quantity known as “single-spike information” to i...	A popular approach to the neural coding problem is to identify a low-dimensional linear projection of the stimulus space that preserves the aspects of the stimulus that affect a neuron’s probability of spiking . Previous work has focused on both information-theoretic and likelihood-based estimators for finding such pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
IFN-γ activates cells to restrict intracellular pathogens by upregulating cellular effectors including the p65 family of guanylate-binding proteins ( GBPs ) . Here we test the role of Gbp1 in the IFN-γ-dependent control of T . gondii in the mouse model . Virulent strains of T . gondii avoided recruitment of Gbp1 to the...	Emerging evidence suggests that the p65 family of guanylate-binding proteins ( GBPs ) , which is upregulated by interferon gamma , play an important role in host defense against intracellular pathogens . We demonstrate that the ability of virulent strains of Toxoplasma gondii to avoid recruitment of mouse Gbp1 is media...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology" ]	2013	Guanylate-binding Protein 1 (Gbp1) Contributes to Cell-autonomous Immunity against Toxoplasma gondii
Schistosomiasis and STH are among the list of neglected tropical diseases considered for control by the WHO . Although both diseases are endemic in Zimbabwe , no nationwide control interventions have been implemented . For this reason in 2009 the Zimbabwe Ministry of Health and Child Care included the two diseases in t...	Schistosomiasis ( S . haematobium and S . mansoni ) and soil transmitted helminthiasis ( STH ) are endemic in Zimbabwe but there has not been any study conducted to systematically map out the disease for control . Due to the public health significance of schistosomiasis and STH in Zimbabwe , a nationwide cross-sectiona...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "research", "design", "infectious", "diseases", "medicine", "and", "health", "sciences", "clinical", "medicine", "diagnostic", "medicine", "primary", "care", "clinical", "research", "design", "global", "health", "biology", "a...	2014	Distribution of Schistosomiasis and Soil Transmitted Helminthiasis in Zimbabwe: Towards a National Plan of Action for Control and Elimination
Ticks ( Family Ixodidae ) transmit a variety of disease causing agents to humans and animals . The tick-borne flaviviruses ( TBFs; family Flaviviridae ) are a complex of viruses , many of which cause encephalitis and hemorrhagic fever , and represent global threats to human health and biosecurity . Pathogenesis has bee...	High-throughput proteomics offers an approach to evaluate changes in cell protein levels following arboviral infection . Research to understand the molecular basis of human-flavivirus interactions has advanced significantly over the past decade , but comparatively little is known regarding interactions between ticks an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "protein", "metabolism", "ixodes", "microbiology", "database", "searching", "cell", "metabolism", "animals", "protein", "expression", "molecular", "biology", "techniques", "ticks", "research",...	2016	Changes in the Proteome of Langat-Infected Ixodes scapularis ISE6 Cells: Metabolic Pathways Associated with Flavivirus Infection
Repair of programmed DNA double-strand breaks ( DSBs ) by meiotic recombination relies on the generation of flanking 3′ single-stranded DNA overhangs and their interaction with a homologous double-stranded DNA template . In various common model organisms , the ubiquitous strand exchange protein Rad51 and its meiosis-sp...	Sexual reproduction relies on meiosis , the specialized cell division that allows diploid organisms to halve their chromosome content , resulting in the production of gametes containing one copy of each chromosome . In humans , defects in meiosis cause infertility , stillbirths , and congenital diseases . Homologous re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/nuclear", "structure", "and", "function", "molecular", "biology/recombination", "cell", "biology/cell", "growth", "and", "division", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "molecular", "biology/dna...	2011	The Recombinases Rad51 and Dmc1 Play Distinct Roles in DNA Break Repair and Recombination Partner Choice in the Meiosis of Tetrahymena
In molecular recognition , it is often the case that ligand binding is coupled to conformational change in one or both of the binding partners . Two hypotheses describe the limiting cases involved; the first is the induced fit and the second is the conformational selection model . The conformational selection model req...	Proteins that are capable of binding to many different ligands are said to have broad specificity . This is sometimes also referred to as promiscuity . Whether a protein is promiscuous or not can sometimes be readily explained by the structure of the protein and the ligand in terms of electrostatic and steric effects ....	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "protein", "interactions", "molecular", "dynamics", "chemical", "biology", "protein", "structure", "biophysics", "simulations", "biochemistry", "simulations", "proteins", "chemistry", "biology", "biophysics", "drug", "discovery", "bi...	2012	The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains
Pattern formation in developing tissues is driven by the interaction of extrinsic signals with intrinsic transcriptional networks that together establish spatially and temporally restricted profiles of gene expression . How this process is orchestrated at the molecular level by genomic cis-regulatory modules is one of ...	The complex organization of tissues is established precisely and reproducibly during development . In the vertebrate neural tube , as in many other tissues , the interplay between extrinsic morphogens and intrinsic transcription factors produces spatial patterns of gene expression that delineate precursors for specific...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Distinct Regulatory Mechanisms Act to Establish and Maintain Pax3 Expression in the Developing Neural Tube
Morbidity and mortality from acute diarrheal disease remains high , particularly in developing countries and in cases of natural or man-made disasters . Previous work has shown that the small molecule clotrimazole inhibits intestinal Cl- secretion by blocking both cyclic nucleotide- and Ca2+-gated K+ channels , implica...	In acute infectious diarrhea , the active secretion of Cl- ions contributes to the secondary loss of Na+ and water from the intestine . Apical Cl- secretion from intestinal epithelial cells is dependent upon cyclic nucleotide- and Ca2+-dependent intracellular signals and requires the concomitant transport of K+ through...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Electrophysiological Studies into the Safety of the Anti-diarrheal Drug Clotrimazole during Oral Rehydration Therapy
Nutritional immunity describes the host-driven manipulation of essential micronutrients , including iron , zinc and manganese . To withstand nutritional immunity and proliferate within their hosts , pathogenic microbes must express efficient micronutrient uptake and homeostatic systems . Here we have elucidated the pat...	All living organisms must secure certain trace metals such as iron and zinc in their diets . For the microbes that infect us , the source of these micronutrients is the tissues of their host . However , mammals have developed sophisticated mechanisms to manipulate microbial access to trace metals–a process called nutri...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "zinc", "transporters", "manganese", "pathogens", "microbiology", "fungi", "model", "organisms", "experimental", "organism", "systems", "biological", "transport", "kidneys", "fungal", ...	2018	Biphasic zinc compartmentalisation in a human fungal pathogen
Epidemic severe leptospirosis was recognized in Nicaragua in 1995 , but unrecognized epidemic and endemic disease remains unstudied . To determine the burden of and risk factors associated with symptomatic leptospirosis in Nicaragua , we prospectively studied patients presenting with fever at a large teaching hospital ...	Leptospirosis , transmitted by pathogenic species of the bacterium Leptospira , is distributed worldwide but infections due to unrecognized epidemic or endemic disease are under-appreciated . We prospectively studied patients ≥2 years of age who presented with acute febrile illness in Nicaragua and systematically colle...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "medicine", "and", "health", "sciences", "global", "health" ]	2014	Unsuspected Leptospirosis Is a Cause of Acute Febrile Illness in Nicaragua
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription . Yet , this link remains poorly investigated . Here , we introduce a simple biophysical model where interphase chromosomes are described in terms of the...	A key determining factor in many important cellular processes as DNA transcription , for instance , the specific composition of the chromatin fiber sequence has a major influence on chromosome folding during interphase . Yet , how this is achieved in detail remains largely elusive . In this work , we explore this link ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "dynamics", "chromosome", "structure", "and", "function", "materials", "science", "epigenetics", "macromolecules", "chromatin", "fibers", "materials", "by", "structure", "polymers", "polymer", "chemistry", "physical", "properties", "chromosome", "biology", "g...	2016	Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
Malaria transmission-blocking ( T-B ) interventions are essential for malaria elimination . Small molecules that inhibit the Plasmodium ookinete-to-oocyst transition in the midgut of Anopheles mosquitoes , thereby blocking sporogony , represent one approach to achieving this goal . Chondroitin sulfate glycosaminoglycan...	To achieve malaria elimination , the consensus expert opinion is that new approaches to drug and vaccine design are desperately needed . We have undertaken a novel , comprehensive approach towards the development of a malaria transmission-blocking drug based on the strategy of inhibiting Plasmodium development in the m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	A Small Molecule Glycosaminoglycan Mimetic Blocks Plasmodium Invasion of the Mosquito Midgut
Mild mutations in BRCA2 ( FANCD1 ) cause Fanconi anemia ( FA ) when homozygous , while severe mutations cause common cancers including breast , ovarian , and prostate cancers when heterozygous . Here we report a zebrafish brca2 insertional mutant that shares phenotypes with human patients and identifies a novel brca2 f...	Women with one strong BRCA2 ( FANCD1 ) mutation have high risks of breast and ovarian cancer . People with two mild BRCA2 ( FANCD1 ) mutations develop Fanconi Anemia , which reduces DNA repair leading to genome instability , small gonads , infertility , and cancer . Humans and mice lacking BRCA2 activity die before bir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology/germ", "cells", "genetics", "and", "genomics/animal", "genetics", "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/nuclear", "structure", "and", "function", "cell", "biology/cell", "signaling", "genetics", "and"...	2011	Roles of brca2 (fancd1) in Oocyte Nuclear Architecture, Gametogenesis, Gonad Tumors, and Genome Stability in Zebrafish
The Gcm/Glide transcription factor is transiently expressed and required in the Drosophila nervous system . Threshold Gcm/Glide levels control the glial versus neuronal fate choice , and its perdurance triggers excessive gliogenesis , showing that its tight and dynamic regulation ensures the proper balance between neur...	Epigenetic mechanisms are essential to define cell identity , and the Polycomb and the Trithorax Group proteins ( PcG and TrxG , respectively ) control the body plan by maintaining the epigenetic state of homeotic genes . PcG and TrxG act by triggering stable chromatin modifications that are “remembered” after cell div...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "neuroscience", "molecular", "development", "genetics", "gene", "expression", "biology", "neuroscience", "genetics", "and", "genomics", "cell", "fate", "determination" ]	2012	Polycomb Controls Gliogenesis by Regulating the Transient Expression of the Gcm/Glide Fate Determinant
The Serum and Glucocorticoid-regulated Kinase1 ( SGK1 ) gene is a target of the glucocorticoid receptor ( GR ) and is central to the stress response in many human tissues . Because environmental stress varies across habitats , we hypothesized that natural selection shaped the geographic distribution of genetic variants...	Susceptibility to many common human diseases including hypertension , heart disease , and the metabolic syndrome is associated with increased neuroendocrine signaling in response to environmental stressors . A key component of the human stress response involves increased systemic glucocorticoid secretion that in turn l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "diabetes", "and", "endocrinology/endocrinology", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/physiogenomics", "evolutionary", "biology/genomics", "genetics", "and", "genomics/genetics", "of", "dis...	2009	Adaptive Variation Regulates the Expression of the Human SGK1 Gene in Response to Stress
Dietary restriction extends lifespan in evolutionarily diverse animals . A role for the sensory nervous system in dietary restriction has been established in Drosophila and Caenorhabditis elegans , but little is known about how neuroendocrine signals influence the effects of dietary restriction on longevity . Here , we...	Reductions in food intake have long been observed to improve longevity , extending lifespan in many evolutionarily divergent organisms . While great progress has been made in identifying the mechanisms by which nutritional interventions act to delay the aging process , much remains unclear . Particularly , while work i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "molecular", "probe", "techniques", "caenorhabditis", "neuroscience", "animals", "animal", "models", "physiological", "processes", "developmental", "biology", "caenorhabditis", "elegans", "...	2017	Age-Dependent Neuroendocrine Signaling from Sensory Neurons Modulates the Effect of Dietary Restriction on Longevity of Caenorhabditis elegans
Thrombocytopenia , bleeding and plasma leakage are cardinal features of severe dengue . Endothelial cell activation with exocytosis of Weibel-Palade bodies ( WPBs ) may play an etiological role in this condition . In a cohort of 73 Indonesian children with dengue hemorrhagic fever ( DHF ) , of which 30 with dengue shoc...	Severe dengue infections are characterized by thrombocytopenia , clinical bleeding and plasma leakage . Activation of the endothelium , the inner lining of blood vessels , leads to the secretion of storage granules called Weibel Palade bodies ( WPBs ) . We demonstrated that severe dengue in Indonesian children is assoc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "coagulation", "disorders", "infectious", "diseases", "von", "willebrand", "disease", "thrombocytopenia", "tropical", "diseases", "(non-neglected)", "dengue", "fever", "flavivirus", "platelets", "neglected", "tropical", "diseases", "travel-associated", "diseases",...	2012	Severe Dengue Is Associated with Consumption of von Willebrand Factor and Its Cleaving Enzyme ADAMTS-13
Mechanosensing at focal adhesions regulates vital cellular processes . Here , we present results from molecular dynamics ( MD ) and mechano-biochemical network simulations that suggest a direct role of Focal Adhesion Kinase ( FAK ) as a mechano-sensor . Tensile forces , propagating from the membrane through the PIP2 bi...	Focal adhesions integrate external mechanical signals into biochemical circuits allowing cellular mechanosensing . Although the zoo of mechanosensing proteins at focal adhesions is steadily growing , force-induced enzymatic mechanisms , as those uncovered for autoinhibited kinases in muscle , remain to be identified fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Mechanism of Focal Adhesion Kinase Mechanosensing
Mitochondrial neurogastrointestinal encephalomyopathy ( MNGIE ) is a severe human disease caused by mutations in TYMP , the gene encoding thymidine phosphorylase ( TP ) . It belongs to a broader group of disorders characterized by a pronounced reduction in mitochondrial DNA ( mtDNA ) copy number in one or more tissues ...	Mitochondria are subcellular organelles that constitute the main energy supply within the cell . They contain their own DNA , which should be continuously replicated to ensure the correct mitochondrial function . Several mitochondrial diseases are caused by genetic defects that compromise this replication and result in...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "nucleotides", "mitochondrial", "myopathy", "dna", "replication", "dna", "myoneurogenic", "gastrointestinal", "encephalopathy", "mitochondrial", "diseases", "biology", "biochemistry", "nucleic", "acids", "neurological", "disorders", "neurology", "neuromuscular", "...	2011	Limited dCTP Availability Accounts for Mitochondrial DNA Depletion in Mitochondrial Neurogastrointestinal Encephalomyopathy (MNGIE)
The protease-resistant prion protein ( PrPres ) of a few natural scrapie isolates identified in sheep , reminiscent of the experimental isolate CH1641 derived from a British natural scrapie case , showed partial molecular similarities to ovine bovine spongiform encephalopathy ( BSE ) . Recent discovery of an atypical f...	The origin of the transmissible agent involved in the food-borne epidemic of bovine spongiform encephalopathy ( BSE ) remains a mystery . It has recently been proposed that this could have been the result of the recycling of an atypical , more probably sporadic , form of BSE ( called bovine amyloidotic spongiform encep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/prion", "diseases" ]	2008	A C-Terminal Protease-Resistant Prion Fragment Distinguishes Ovine “CH1641-Like” Scrapie from Bovine Classical and L-Type BSE in Ovine Transgenic Mice
Visceral leishmaniasis is a neglected parasitic disease with no vaccine available and its pharmacological treatment is reduced to a limited number of unsafe drugs . The scarce readiness of new antileishmanial drugs is even more alarming when relapses appear or the occurrence of hard-to-treat resistant strains is detect...	Visceral leishmaniasis is a neglected disease that poses a significant threat to impoverished human populations of low-income countries . Due to the unavailability of vaccines , pharmacological treatment is the only approach to control the disease that otherwise can be lethal . To date , drug management in endemic regi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "liver", "immune", "physiology", "spleen", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "animal", "models", "developmental", "biology", "model", "organisms", "protozoans", "le...	2019	A chronic bioluminescent model of experimental visceral leishmaniasis for accelerating drug discovery
Diverse plasticity mechanisms are orchestrated to shape the spatiotemporal dynamics underlying brain functions . However , why these plasticity rules emerge and how their dynamics interact with neural activity to give rise to complex neural circuit dynamics remains largely unknown . Here we show that both Hebbian and h...	Many experiments have documented a variety of ways in which the connectivity strengths between neurons change in response to the activity of neurons . These changes are an important part of learning . However , it is not understood how such a diverse range of observations can be understood as consequences of an underly...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "synaptic", "plasticity", "neuronal", "plasticity", "developmental", "neuroscience", "computer", "and", ...	2018	Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena
The microbiome shapes diverse facets of human biology and disease , with the importance of fungi only beginning to be appreciated . Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis , where chronic colonization and i...	Microbial cells vastly outnumber human cells in our bodies , yet we are only beginning to understand how these microbes influence human health and disease . One disease for which microbial communities are especially important is cystic fibrosis , where persistent lung infections can be lethal . Fungi are associated wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation
Chagas disease affects around 18 million people in the American continent . Unfortunately , there is no satisfactory treatment for the disease . The drugs currently used are not specific and exert serious toxic effects . Thus , there is an urgent need for drugs that are effective . Looking for molecules to eliminate th...	Most of the enzymes of parasites have their counterpart in the host . Throughout evolution , the three-dimensional architecture of enzymes and their catalytic sites are highly conserved . Thus , identifying molecules that act exclusively on the active sites of the enzymes from parasites is a difficult task . However , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/biocatalysis", "biochemistry/experimental", "biophysical", "methods", "infectious", "diseases/neglected", "tropical", "diseases", "biochemistry/protein", "chemistry", "biochemistry/biomacromolecule-ligand", "interactions", "microbiology/parasitology", "infectious", "disease...	2007	Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi
The performance of information processing systems , from artificial neural networks to natural neuronal ensembles , depends heavily on the underlying system architecture . In this study , we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and r...	Information processing systems , such as natural biological networks and artificial computational networks , exhibit a strong interdependence between structural organization and functional performance . However , the extent to which variations in structure impact performance is not well understood , particularly in sys...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "statistical", "mechanics", "neural", "networks", "statistics", "applied", "mathematics", "computerized", "simulations", "neuroscience", "learning", "and", "memory", "mathematics", "computational", "neuroscience", "distribution", "curves", "biophysics", "simulations", "circui...	2011	Learning, Memory, and the Role of Neural Network Architecture
The self-assembly of proteins into protein quaternary structures is of fundamental importance to many biological processes , and protein misassembly is responsible for a wide range of proteopathic diseases . In recent years , abstract lattice models of protein self-assembly have been used to simulate the evolution and ...	Protein complexes assemble by joining individual proteins together through interacting binding sites . Because of the long time scales of biological evolution , it can be difficult to reconstruct how these interactions change over time . We use simplified representations of proteins to simulate the evolution of these c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "engineering", "and", "technology", "statistics", "markov", "processes", "decision", "analysis", "mathematics", "management", "engineering", "protein", "structure", "research", "and", "analysis", "methods", "decision", "trees", "proteins", "stru...	2019	Evolution of interface binding strengths in simplified model of protein quaternary structure
Hemophagocytic lymphohistiocytosis ( HLH ) is a rare , potentially fatal disorder characterized by fever , pancytopenia , hepatosplenomegaly , and increased serum ferritin . HLH is being increasingly reported as a complication of dengue , a common tropical acute febrile illness . After a cluster of pediatric dengue-ass...	Hemophagocytic lymphohistiocytosis ( HLH ) is a rare , potentially fatal medical condition that can occur after a patient has an infection . While HLH is most commonly associated with Epstein-Barr virus infections , it has been reported as a complication of dengue , a common mosquito-borne , acute febrile illness . Aft...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "pediatrics", "north", "america", "signs", "and", "symptoms", "ferritin", "neglected", "tropical", ...	2016	Incidence and Risk Factors for Developing Dengue-Associated Hemophagocytic Lymphohistiocytosis in Puerto Rico, 2008 - 2013
Many fibroblast-secreted proteins promote tumorigenicity , and several factors secreted by cancer cells have in turn been proposed to induce these proteins . It is not clear whether there are single dominant pathways underlying these interactions or whether they involve multiple pathways acting in parallel . Here , we ...	There is increasing interest in developing methods to treat cancer by targeting non-cancer cells that play supportive roles in the tumor microenvironment . One type of non-cancer cell that has received considerable attention along these lines is cancer-associated fibroblasts , which can promote tumor formation and tumo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	System-Wide Analysis Reveals a Complex Network of Tumor-Fibroblast Interactions Involved in Tumorigenicity
Polycomb group ( PcG ) and trithorax group ( trxG ) proteins are conserved chromatin factors that regulate key developmental genes throughout development . In Drosophila , PcG and trxG factors bind to regulatory DNA elements called PcG and trxG response elements ( PREs and TREs ) . Several DNA binding proteins have bee...	Although all cells of a developing organism have the same DNA , they express different genes and transmit these gene expression patterns to daughter cells through multiple rounds of cell division . This cellular memory for gene expression states is maintained by two groups of proteins: Polycomb-group proteins ( PcG ) ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2009	Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos
The use of consumer-grade wearables for purposes beyond fitness tracking has not been comprehensively explored . We generated and analyzed multidimensional data from 233 normal volunteers , integrating wearable data , lifestyle questionnaires , cardiac imaging , sphingolipid profiling , and multiple clinical-grade card...	Little is known about how data from wearable sensors can be used apart from fitness tracking . We comprehensively studied 233 normal volunteers , integrating data from wearable sensors with lifestyle questionnaires , cardiac imaging , sphingolipid profiling , and clinical measurements of various heart and metabolic dis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "sphingolipids", "sports", "and", "exercise", "medicine", "physical", "activity", "research", "design", "questionnaires", "research", "and", "analysis", "methods", "cardiology", "public", "and", "occupational", "health", "exercis...	2018	Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research

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