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Ascaris suum and Ascaris lumbricoides are two closely related geo-helminth parasites that ubiquitously infect pigs and humans , respectively . Ascaris suum infection in pigs is considered a good model for A . lumbricoides infection in humans because of a similar biology and tissue migration to the intestines . Ascaris ...	Ascaris suum is an intestinal parasitic nematode of pigs that is very closely related to Ascaris lumbricoides , a major intestinal parasitic nematode of humans that infects more than one billion people worldwide . Because of reduced efficacy and the threat of resistance to the current small set of approved drugs to tre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "applied", "microbiology", "medicine", "small", "intestine", "infectious", "diseases", "soil-transmitted", "helminths", "drug", "research", "and", "development", "gastroenterology", "and", "hepatology", "drugs", "and", "devices", "global", "health", "microbial", "control"...	2013	Bacillus thuringiensis-derived Cry5B Has Potent Anthelmintic Activity against Ascaris suum
Ras proteins regulate signaling cascades crucial for cell proliferation and differentiation by switching between GTP- and GDP-bound conformations . Distinct Ras isoforms have unique physiological functions with individual isoforms associated with different cancers and developmental diseases . Given the small structural...	The proto-oncogene Ras mediates signaling pathways controlling cell proliferation and development by cycling between active and inactive conformational states . Mutations that affect the ability to switch between states are associated with over 25% of human tumors . However , despite much effort , details of how these ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/bioinformatics", "biochemistry/theory", "and", "simulation", "computational", "biology/molecular", "dynamics" ]	2010	The Distinct Conformational Dynamics of K-Ras and H-Ras A59G
Effective immunotherapies for HIV are needed . Drug therapies are life-long with significant toxicities . Dendritic-cell based immunotherapy approaches are promising but impractical for widespread use . A simple immunotherapy , reinfusing fresh autologous blood cells exposed to overlapping SIV peptides for 1 hour ex vi...	Effective immunotherapies for HIV are needed . We assessed a simple technique , reinfusion of fresh blood cells incubating with overlapping SIV peptides ( Overlapping Peptide-pulsed Autologous ceLls , OPAL ) , in 36 randomly allocated SIV-infected monkeys . We analyzed this therapy for the stimulation of immunity , con...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "virology/immunodeficiency", "viruses", "immunology/immunity", "to", "infections", "virology/vaccines" ]	2008	Control of Viremia and Prevention of AIDS following Immunotherapy of SIV-Infected Macaques with Peptide-Pulsed Blood
In Drosophila , ubiquitous expression of a short Cyclin G isoform generates extreme developmental noise estimated by fluctuating asymmetry ( FA ) , providing a model to tackle developmental stability . This transcriptional cyclin interacts with chromatin regulators of the Enhancer of Trithorax and Polycomb ( ETP ) and ...	During development , the part of stochasticity inherent to biological processes induces noise . In animals with bilateral symmetry , developmental noise can be estimated by the variance in a population of the difference between the left and the right sides of individuals , the so-called fluctuating asymmetry ( FA ) . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "invertebrate", "genomics", "dna", "transcription", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism",...	2018	Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability
The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize . The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conf...	The relationship between enzymatic activity and protein stability has long been a difficult problem in the study of protein biochemistry . Enzymes may undergo structural changes in order to bind substrates , catalyze chemical reactions , and release products , but flexibility often is inversely correlated with thermody...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Thermal Adaptation of Conformational Dynamics in Ribonuclease H
The hippocampus is known to store cognitive representations , or maps , that encode both positional and contextual information , critical for episodic memories and functional behavior . How path integration and contextual cues are dynamically combined and processed by the hippocampus to maintain these representations a...	As an animal moves in space and receives external sensory inputs , it must dynamically maintain the representations of its position and environment at all times . How the hippocampus , the brain area crucial for spatial representations , achieves this task , and manages possible conflicts between different inputs remai...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "brain", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "learning", "and", "memory", "cognition", "memory", "vision", "zoology", "animal", "cognition", "computer", "and", "infor...	2018	Integration and multiplexing of positional and contextual information by the hippocampal network
Understanding host defense against microbes is key to developing new and more effective therapies for infection and inflammatory disease . However , how animals integrate multiple environmental signals and discriminate between different pathogens to mount specific and tailored responses remains poorly understood . Usin...	Understanding how animals detect infection and mount appropriate responses is key to treating infection and inflammatory disease . We use the tractable model Caenorhabditis elegans to study mechanisms of host defense against pathogenic bacteria . Here we show that hypoxia-inducible factor ( HIF ) is important for ensur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "microbiology", "host-pathogen", "interaction", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "staphylococci", "bacterial", "pathogens", "inflammation", "biology", "immune", "response", "genetics", "of", "the", "immune", "system", "i...	2012	EGL-9 Controls C. elegans Host Defense Specificity through Prolyl Hydroxylation-Dependent and -Independent HIF-1 Pathways
Visceral leishmaniasis caused by the protozoan Leishmania infantum is a zoonotic , life threatening parasitic disease . Domestic dogs are the main peridomestic reservoir , and allopurinol is the most frequently used drug for the control of infection , alone or in combination with other drugs . Resistance of Leishmania ...	Visceral leishmaniasis caused by Leishmania infantum is a widespread , devastating zoonotic disease . Domestic dogs are considered the major reservoir for human L . infantum infection in an area stretching from Portugal to China , and across South America . Dogs not only carry infection and transfer it to humans via sa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Allopurinol Resistance in Leishmania infantum from Dogs with Disease Relapse
Retroviruses have been infecting mammals for at least 100 million years , leaving descendants in host genomes known as endogenous retroviruses ( ERVs ) . The abundance of ERVs is partly determined by their mode of replication , but it has also been suggested that host life history traits could enhance or suppress their...	Retroviruses have been invading mammalian genomes for over 100 million years , leaving traces known as endogenous retroviruses ( ERVs ) . Early genome sequencing studies revealed a marked difference in the activity of retroviruses among species , with humans largely containing inactive lineages of ERVs , while the mous...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "microbial", "evolution", "virology", "viruses", "and", "cancer", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "theory", "evolutionary", "biology", "evolutionary", "genetics", "viral", "evolution" ]	2014	Larger Mammalian Body Size Leads to Lower Retroviral Activity
Merkel cell polyomavirus ( MCPyV ) accounts for 80% of all Merkel cell carcinoma ( MCC ) cases through expression of two viral oncoproteins: the truncated large T antigen ( LT-t ) and small T antigen ( ST ) . MCPyV ST is thought to be the main driver of cellular transformation and has also been shown to increase LT pro...	Merkel cell carcinoma ( MCC ) is a very aggressive and deadly neuroendocrine skin cancer . Merkel cell polyomavirus ( MCPyV ) contributes to the development and maintenance of 80% of MCCs through the expression of its truncated large tumor antigen ( LT-t ) and small tumor antigen ( ST ) . MCPyV ST is thought to be prim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sv40", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "aliphatic", "amino", "acids", "molecular", "probe", "techniques", "enzymes", "pathogens", "microbiology", "enzymology", "immunoblotting", "ubiquitin", ...	2019	Merkel cell polyomavirus Tumor antigens expressed in Merkel cell carcinoma function independently of the ubiquitin ligases Fbw7 and β-TrCP
Genetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps , where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away . The positions close to a genotype make up its “mutational landscape” and , in aggr...	Cyclic environmental change can occur in many different timescales; from slow changes such as glacial cycles , to faster seasonal change , to the day-night cycle . All populations and organisms are exposed to changing environments , and understanding their effect on evolutionary trajectories is crucial to predicting th...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[]	2019	Fluctuating environments select for short-term phenotypic variation leading to long-term exploration
While novel picornaviruses are being discovered in rodents , their host range and pathogenicity are largely unknown . We identified two novel picornaviruses , rosavirus B from the street rat , Norway rat , and rosavirus C from five different wild rat species ( chestnut spiny rat , greater bandicoot rat , Indochinese fo...	We identified two novel picornaviruses , rosavirus B and C , infecting street and wild rats respectively in China . While rosavirus B was detected from Norway rats , rosavirus C was detected from five different wild rat species ( chestnut spiny rat , greater bandicoot rat , Indochinese forest rat , roof rat and Coxing'...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "sequencing", "techniques", "biological", "cultures", "vertebrates", "animals", "mammals", "animal", "models", "viruses", "organisms", "model", "organisms", "rna", "viruses", "sequence", "motif", "analysis", "mol...	2016	Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements . Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules , whose dynamic pattern of confor...	We have developed a new algorithm to better decode single molecule data with dynamic disorder . Our new algorithm , which represents a substantial improvement over other methodologies , can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy landscape...	[ "Abstract", "Introduction", "Algorithm", "Results", "and", "Discussion", "Methods" ]	[ "markov", "models", "applied", "mathematics", "simulation", "and", "modeling", "fluorophotometry", "algorithms", "probability", "distribution", "mathematics", "systems", "science", "clustering", "algorithms", "statistics", "(mathematics)", "research", "and", "analysis", "me...	2016	Decoding Single Molecule Time Traces with Dynamic Disorder
Worldwide , more than 40% of the population is at risk from dengue and recent estimates suggest that up to 390 million dengue infections are acquired every year . The Eliminate Dengue ( ED ) Program is investigating the use of Wolbachia-infected , transmission-compromised , mosquitoes to reduce dengue transmission . Pr...	Community Engagement ( CE ) is gaining increasing recognition as an important dimension of biomedical , public health and global health research , including neglected tropical disease research . Yet , there has been little agreement about the specific goals of CE and about the best ways to design , conduct , and evalua...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	What Makes Community Engagement Effective?: Lessons from the Eliminate Dengue Program in Queensland Australia
Histological evidence of Plasmodium in the placenta is indicative of placental malaria , a condition associated with severe outcomes for mother and child . Histological lesions found in placentas from Plasmodium-exposed women include syncytial knotting , syncytial rupture , thickening of the placental barrier , necrosi...	Malaria during pregnancy remains a risk for approximately 125 million women each year . Adverse outcomes of malaria during pregnancy include maternal anemia and low infant birth weight . Additionally , the presence of malaria parasites , namely Plasmodium falciparum , has been associated with the occurrence of placenta...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "obstetrics", "and", "gynecology", "pregnancy", "obstetrics", "biology", "microbiology", "malaria", "parasitic", "diseases", "parasitology" ]	2013	Placental Histopathological Changes Associated with Plasmodium vivax Infection during Pregnancy
Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding . Limited data on frequencies of genetic disease variants across breeds exists , and the disease heritage of mixed breed dogs remains poorly explored to date . Advances in gene...	Like any human , dogs may suffer from or pass on a variety of inherited disorders . Knowledge of how likely a typical dog is to carry an inherited disorder in its genome , and which disorders are the most common and relevant ones across dog breeds , is valuable for both veterinary care and breeding of healthy dogs . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", "mammals", "alleles", "telecommunications", "amniotes", "zoology", "veterinary", "science", "genetic"...	2018	Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs
The H3ABioNet pan-African bioinformatics network , which is funded to support the Human Heredity and Health in Africa ( H3Africa ) program , has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa r...	Many programs have been developed to boost the technical and computational skills of scientists working in low to medium income countries ( LMIC ) , who often struggle to remain competitive with their peers in more developed parts of the world . Typically , these programs rely on intensive workshops where students acqu...	[ "Abstract", "Introduction", "The", "node-assessment", "exercise", "Experiences", "from", "the", "nodes", "Lessons", "learned", "Conclusions" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "education", "health", "services", "research", "sociology", "sports", "and", "exercise", "medicine", "social", "sciences", "physical", "activity", "health", "care", "scientists", "genome",...	2017	Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
Insecticide spraying efficiently controls house infestation by triatomine bugs , the vectors of Trypanosoma cruzi . The strategy , however , is ineffective against sylvatic triatomines , which can transmit Chagas disease by invading ( without colonizing ) man-made structures . Despite growing awareness of the relevance...	Triatomine bugs are the vectors of Chagas disease , still a key public health concern in the Americas . Insecticide spraying efficiently controls house infestation by triatomines , but is useless against sylvatic bugs–which can transmit the disease by simply invading human residences . Although this behavior is common ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "species", "colonization", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "invasive", "species", "binomials", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "parasitic", "p...	2017	Drivers of house invasion by sylvatic Chagas disease vectors in the Amazon-Cerrado transition: A multi-year, state-wide assessment of municipality-aggregated surveillance data
Plasmodium vivax is the most prevalent human malaria parasite , causing serious public health problems in malaria-endemic countries . Until recently the Duffy-negative blood group phenotype was considered to confer resistance to vivax malaria for most African ethnicities . We and others have reported that P . vivax str...	Malaria results from infection of human red blood cells ( RBC ) by Plasmodium parasite's merozoite . For Plasmodium vivax the process of RBC invasion has been hypothesized to depend on interactions between the parasite's Duffy binding protein ( PvDBP ) and human Duffy blood group antigen because Duffy-negative people (...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2013	Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains
Infections with Strongyloides stercoralis and other helminths represent important , yet often neglected issues in developing countries . Indeed , strongyloidiasis can be fatal , but only a few studies provide information regarding its health relevance in Africa . Moreover , clinical data on symptomatology and typical r...	Infections with parasitic worms such as hookworm and threadworm ( Strongyloides stercoralis ) are widespread throughout the developing world . However , the symptoms caused by parasitic worms are unspecific and little is known about clinical presentations in endemic countries , and hence doctors' awareness of these dis...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "diagnostic", "medicine", "primary", "care", "epidemiology", "public", "health" ]	2011	Diagnosis, Clinical Features, and Self-Reported Morbidity of Strongyloides stercoralis and Hookworm Infection in a Co-Endemic Setting
FoxO transcription factors and sirtuin family deacetylases regulate diverse biological processes , including stress responses and longevity . Here we show that the Caenorhabditis elegans sirtuin SIR-2 . 4—homolog of mammalian SIRT6 and SIRT7 proteins—promotes DAF-16–dependent transcription and stress-induced DAF-16 nuc...	Sensing and responding appropriately to environmental insults is a challenge facing all organisms . In the roundworm C . elegans , the FoxO protein DAF-16 moves to the nucleus in response to stress , where it regulates gene expression and plays a key role in ensuring organismal survival . In this manuscript , we charac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "model", "organisms", "genetic", "mutation", "gene", "expression", "genetics", "molecular", "genetics", "biology", "genetics", "and", "genomics" ]	2012	C. elegans SIRT6/7 Homolog SIR-2.4 Promotes DAF-16 Relocalization and Function during Stress
Chromosome rearrangements can form when incorrect ends are matched during end joining ( EJ ) repair of multiple chromosomal double-strand breaks ( DSBs ) . We tested whether the ATM kinase limits chromosome rearrangements via suppressing incorrect end utilization during EJ repair of multiple DSBs . For this , we develo...	When a chromosome is fragmented by multiple double-strand breaks ( DSBs ) , each set of DSB ends needs to be matched correctly during repair to avoid chromosomal rearrangements . Considering the case of two tandem DSBs , if the ends of different breaks ( incorrect ends ) are used for repair , loss of the intervening DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "genetics", "and", "genomics/chromosome", "biology" ]	2010	ATM Limits Incorrect End Utilization during Non-Homologous End Joining of Multiple Chromosome Breaks
Clathrin is the scaffold of a conserved molecular machinery that has evolved to capture membrane patches , which then pinch off to become traffic carriers . These carriers are the principal vehicles of receptor-mediated endocytosis and are the major route of traffic from plasma membrane to endosomes . We report here th...	Here , we identify and characterize two distinct modes of clathrin-mediated uptake at the plasma membrane . The “canonical” coated pit is where assembly of a curved clathrin lattice , linked to deformation of the underlying membrane , gives rise to coated vesicles . Clathrin coated “plaques” are extended clathrin latti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting" ]	2009	Distinct Dynamics of Endocytic Clathrin-Coated Pits and Coated Plaques
House mice ( Mus musculus ) arrived in the Americas only recently in association with European colonization ( ~400–600 generations ) , but have spread rapidly and show evidence of local adaptation . Here , we take advantage of this genetic model system to investigate the genomic basis of environmental adaptation in hou...	The recent introduction of house mice into North America from Europe provides an opportunity to investigate environmental adaptation in an important genetic model system . We found that mice from different latitudes differed in body size and aspects of blood chemistry and behavior , and that those differences have a ge...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "population", "genetics", "vertebrates", "mice", "animals", "mammals", "cell", "signaling", "genome", "analysis", "mammalian", "genomics", "population", "biology", "genomic", "libraries", "geography", "genomic", "signal", "processing", "gene", "expression", "cartography",...	2018	The genomic basis of environmental adaptation in house mice
Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation . Knowledge of the genetic diversity of toxigenic V . cholerae isolates , particularly in Africa , remains scarce . The constraints in improving this understanding...	Cholera , caused by the bacterium Vibrio cholerae , causes an estimated 3–5 million cases every year and more than 100 , 000 deaths . The highest disease burden is reported from Africa , however , the epidemic potential and transmission patterns among circulating strains is scarcely understood . The challenges of disea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings
DNA double-strand breaks impact genome stability by triggering many of the large-scale genome rearrangements associated with evolution and cancer . One of the first steps in repairing this damage is 5′→3′ resection beginning at the break site . Recently , tools have become available to study the consequences of not ext...	Chromosomes encode most of the genetic information necessary for cells to function . When large changes in chromosome structure occur , these changes can lead to a variety of diseases , including cancer . One type of DNA damage that triggers chromosomal changes is a DNA double-strand break . These breaks are often heal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nucleic", "acids", "genetics", "dna", "biology", "genomics", "molecular", "cell", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	DNA Resection at Chromosome Breaks Promotes Genome Stability by Constraining Non-Allelic Homologous Recombination
Paracoccidioidomycosis ( PCM ) , caused by Paracoccidioides brasiliensis , is the most prevalent invasive fungal disease in South America . Systemic mycoses are the 10th most common cause of death among infectious diseases in Brazil and PCM is responsible for more than 50% of deaths due to fungal infections . PCM is ty...	Paracoccidioidomycosis ( PCM ) is the predominant systemic mycosis in Latin America causing half of the total deaths among systemic fungal infectious diseases in Brazil . Chemotherapy is the standard treatment , but the long time required , severe cases of immunosuppression and frequent relapses indicate that additiona...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mycology", "biology", "microbiology" ]	2012	Therapeutic DNA Vaccine Encoding Peptide P10 against Experimental Paracoccidioidomycosis
Previous studies have shown that neurons within the vestibular nuclei ( VN ) can faithfully encode the time course of sensory input through changes in firing rate in vivo . However , studies performed in vitro have shown that these same VN neurons often display nonlinear synchronization ( i . e . phase locking ) in the...	The vestibular system senses the motion of the head in space and is vital for gaze stability , posture control , and the computation of spatial orientation during everyday life . The activities of single vestibular neurons recorded in the brains of awake behaving animals show that they can accurately transmit informati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "single", "neuron", "function", "biology", "sensory", "systems", "neuroscience", "coding", "mechanisms" ]	2011	In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons
Leptospirosis , caused by pathogenic species of Leptospira , is the most widespread zoonosis and has emerged as a major public health problem worldwide . The adhesion of pathogenic Leptospira to host cells , and to extracellular matrix ( ECM ) components , is likely to be necessary for the ability of leptospires to pen...	Leptospirosis is a globally widespread bacterial infection caused by pathogenic species of the genus Leptospira . The disease manifestations of leptospirosis range from mild , non-specific illness to a severe disease that includes multi-organ failure , widespread damage to blood vessels , and hemorrhage . Attachment to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "veterinary", "diseases", "veterinary", "bacteriology", "veterinary", "science", "leptospirosis" ]	2014	Leptospira interrogans Binds to Cadherins
Despite evidence for avian influenza A virus ( AIV ) transmission between wild and domestic ecosystems , the roles of bird migration and poultry trade in the spread of viruses remain enigmatic . In this study , we integrate ecosystem interactions into a phylogeographic model to assess the contribution of wild and domes...	It is assumed that AIV outbreaks in poultry are introduced from wild birds . To test this , we incorporated ecosystem and location of isolation into a comparative genetic analysis . We show high rates of viral transmission from domestic to wild birds within a region and , that wild birds could transmit AIV to poultry b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biogeography", "livestock", "ecology", "and", "environmental", "sciences", "animal", "genetics", "china", "population", "genetics", "geographical", "locations", "vertebrates", "animals", "animal", "behavior", "bird", "genetics", "population", "biology", "zoology", "geogr...	2016	Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential
Little is known about porcine cysticercosis in Burkina Faso . We conducted a pilot study to estimate the prevalence of antigens of Taenia solium cysticercosis and to identify associated factors in pigs of three villages in Burkina Faso , selected to represent different pig management practices: one village where pigs a...	Taenia solium cysticercosis is a neglected tropical infection transmitted between humans and pigs . This infection is particularly common in areas where sanitation , hygiene and pig management practices are poor , and can sometimes lead to epilepsy in humans . There is very little information about the importance of th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "immunology" ]	2011	Factors Associated with the Prevalence of Circulating Antigens to Porcine Cysticercosis in Three Villages of Burkina Faso
In RNA interference , a guide strand derived from a short dsRNA such as a microRNA ( miRNA ) is loaded into Argonaute , the central protein in the RNA Induced Silencing Complex ( RISC ) that silences messenger RNAs on a sequence-specific basis . The positions of any mismatched base pairs in an miRNA determine which Arg...	Cells use the process of RNA interference ( RNAi ) to help orchestrate the production of the specific set of proteins needed at a given time . A given messenger RNA ( mRNA ) is produced using a gene in the cell's genomic DNA as a template . Each mRNA molecule is a blueprint for a particular protein and can then be “tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "rna", "interference", "molecular", "dynamics", "nucleic", "acids", "chemistry", "biology", "computational", "chemistry", "biophysics" ]	2012	Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network
Infection with the Epstein-Barr virus ( EBV ) can lead to a number of human diseases including Hodgkin's and Burkitt's lymphomas . The development of these EBV-linked diseases is associated with the presence of nine viral latent proteins , including the nuclear antigen 2 ( EBNA2 ) . The EBNA2 protein plays a crucial ro...	Infection with the Epstein-Barr virus ( EBV ) is linked to a number of human diseases and the nuclear antigen EBNA2 is one of nine viral latent proteins that plays a key role in EBV-linked diseases . EBNA2 activates expression of both viral and host gene in part through interaction between its C-terminal acidic transac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "protein", "chemistry", "molecular", "complexes", "proteins", "protein", "structure", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "chemical", "biology", "biophysics", "molecular", "bio...	2014	Structural and Functional Characterization of a Complex between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 Subunit of TFIIH
Relapsing C . difficile disease in humans is linked to a pathological imbalance within the intestinal microbiota , termed dysbiosis , which remains poorly understood . We show that mice infected with epidemic C . difficile ( genotype 027/BI ) develop highly contagious , chronic intestinal disease and persistent dysbios...	Pathological imbalances within the intestinal microbiota , termed dysbiosis , are often associated with chronic Clostridium difficile infections in humans . We show that infection of mice with the healthcare pathogen C . difficile leads to persistent intestinal dysbiosis that is associated with chronic disease and a hi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice
Planarians display remarkable plasticity in maintenance of their germline , with the ability to develop or dismantle reproductive tissues in response to systemic and environmental cues . Here , we investigated the role of G protein-coupled receptors ( GPCRs ) in this dynamic germline regulation . By genome-enabled rece...	G protein-coupled receptors ( GPCRs ) are the largest and most versatile family of cell-surface receptors . They play critical roles in various cellular and physiological systems and have emerged as a leading group of therapeutic targets . Due to their structural and functional conservation across animals , much has be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "animals", "cell", "differentiation", "germ", "cells", "developmental", "biology", "g", "protein", "coupled", "receptors", "planarians", "animal", "cells", "proteins", "flatwor...	2016	GPCRs Direct Germline Development and Somatic Gonad Function in Planarians
Intense selective pressures applied over short evolutionary time have resulted in homogeneity within , but substantial variation among , horse breeds . Utilizing this population structure , 744 individuals from 33 breeds , and a 54 , 000 SNP genotyping array , breed-specific targets of selection were identified using a...	A breed of the horse typically consists of individuals sharing very similar aesthetic and performance traits . However , a great deal of variation in traits exists between breeds . The range of variation observed among breeds can be illustrated by the size difference between the Miniature horse ( 0 . 74 m and 100 kg ) ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "genetic", "mutation", "genome", "evolution", "population", "genetics", "mutational", "hypotheses", "gene", "function", "mutation", "genetic", "polymorphism", "biology", "evolutionary", "genetics", "genetic", "drift", "haplotypes", "natural", "select...	2013	Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds
Drosophila female germline stem cells ( GSCs ) reside adjacent to a cellular niche that secretes Bone Morphogenetic Protein ( BMP ) ligands and anchors the GSCs through adherens junctions . The GSCs divide asymmetrically such that one daughter remains in the niche as a GSC , while the other is born away from the niche ...	Adult stem cells are undifferentiated cells within an organism that undergo continual asymmetric division to produce two daughter cells that have different cell fates: one daughter remains a stem cell like its parent , while the other daughter differentiates . Thus the stock of stem cells is renewed while new cells are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "cell", "fate", "determination", "drosophila", "melanogaster", "model", "organisms", "stem", "cells", "molecular", "development", "genetics", "biology", "genetics", "and", "genomics", "cell", "differentiation", "gene", "fu...	2012	Niche-Associated Activation of Rac Promotes the Asymmetric Division of Drosophila Female Germline Stem Cells
Familial Alzheimer’s disease ( FAD ) -causing mutant presenilins ( PS ) interact with inositol 1 , 4 , 5-trisphosphate ( IP3 ) receptor ( IP3R ) Ca2+ release channels resulting in enhanced IP3R channel gating in an amyloid beta ( Aβ ) production-independent manner . This gain-of-function enhancement of IP3R activity is...	Aberrant Ca2+ signaling caused by IP3R gating dysregulation is implicated in many neurodegenerative diseases such as Alzheimer’s , Huntington’s , Spinocerebellar ataxias , and endoplasmic reticulum stress-induced brain damage . Thus understanding IP3R dysfunction is important for the etiology of these diseases . It was...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins
Progressive retinal degeneration is the underlying feature of many human retinal dystrophies . Previous work using Drosophila as a model system and analysis of specific mutations in human rhodopsin have uncovered a connection between rhodopsin endocytosis and retinal degeneration . In these mutants , rhodopsin and its ...	Irreversible loss of photoreceptor cells has been attributed as a cause of blindness in many retinal degenerative disorders . One such group of disorders is retinitis pigmentosa , which affects 1 in 3 , 000 individuals . Over 100 mutations in the light-sensing molecule rhodopsin have been identified in patients with au...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ophthalmology/retinal", "disorders", "cell", "biology/cellular", "death", "and", "stress", "responses", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "ophthalmology/inherited", "eye", "disorders" ]	2009	Accumulation of Rhodopsin in Late Endosomes Triggers Photoreceptor Cell Degeneration
The presenilin/γ-secretase complex , an unusual intramembrane aspartyl protease , plays an essential role in cellular signaling and membrane protein turnover . Its ability to liberate numerous intracellular signaling proteins from the membrane and also mediate the secretion of amyloid-β protein ( Aβ ) has made modulati...	All cells face the challenge of removing transmembrane proteins from the lipid bilayer for the purpose of signaling or degradation . One molecular solution to this problem is the multiprotein enzyme complex γ-secretase , which is able to hydrolyze several known transmembrane proteins within the hydrophobic lipid enviro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "cell", "biology", "neurological", "disorders", "molecular", "biology" ]	2008	Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements
Protein AMPylation by Fic domain-containing proteins ( Fic proteins ) is an ancient and conserved post-translational modification of mostly unexplored significance . Here we characterize the Caenorhabditis elegans Fic protein FIC-1 in vitro and in vivo . FIC-1 is an AMPylase that localizes to the nuclear surface and mo...	Eukaryotic Fic domain containing proteins ( Fic proteins ) AMPylate target proteins at the expense of a single ATP molecule . Previous studies have established a first link between target protein AMPylation and the unfolded protein response ( UPR ) in the endoplasmic reticulum . Yet , the consequences of target AMPylat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "gene", "regulation", "pathogens", "regulatory", "proteins", "cell", "processes", "dna-b...	2016	The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones
Regulation of cell proliferation has been extensively studied in cultured cell systems that are characterized by coordinated growth and cell-cycle progression and relatively uniform cell size distribution . During the development of multicellular organisms , however , growth and division can be temporally uncoupled , a...	A fundamental issue in biology is the question of how the rate of cell division is coupled to cell growth . Coordination of these processes has been studied extensively in cultured cell systems but to a much lesser extent in intact organisms . To study this phenomenon in a physiological setting , we developed a methodo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "developmental", "biology" ]	2009	Dynamic Control of Cell Cycle and Growth Coupling by Ecdysone, EGFR, and PI3K Signaling in Drosophila Histoblasts
There is marked variation in the human response to Toxoplasma gondii infection . Epidemiological studies indicate associations between strain virulence and severity of toxoplasmosis . Animal studies on the pathogenic effect of chronic infection focused on relatively avirulent strains ( e . g . type II ) because they ca...	Chronic infection with Toxoplasma gondii , a common neurotropic pathogen , affects approximately 1 billion people worldwide . There is marked variation in the human response to infection . Epidemiological studies indicate that virulent strains of T . gondii are associated with increased frequency and severity of human ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "toxoplasma", "gondii", "immunology", "vertebrates", "mice", "parasitic", "diseases", "parasitic", "protozoans", "animals", "mammals", "biomechanics", "biological",...	2016	Behavioral Abnormalities in a Mouse Model of Chronic Toxoplasmosis Are Associated with MAG1 Antibody Levels and Cyst Burden
Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria . Using cryo-electron tomography ( cryo-ET ) , we characterized native environments within axons and presynaptic varicosit...	Neurons are complex cells that communicate with each other via axons that can extend over distances of a meter or longer . Axons place enormous demands on neuronal energy production , and to maintain connections with local and distal targets , neurons have efficient systems that transport mitochondria to areas of high ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "microtubules", "cell", "processes", "endoplasmic", "reticulum", "neuroscience", "nerve", "fibers", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "cytoskeleton", "animal", "cells", "axons", "short", "reports", "axonal", "transport", "cell...	2018	Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography
The whipworm , Trichuris trichiura , causes trichuriasis in ∼600 million people worldwide , mainly in developing countries . Whipworms also infect other animal hosts , including pigs ( T . suis ) , dogs ( T . vulpis ) and non-human primates , and cause disease in these hosts , which is similar to trichuriasis of humans...	Trichuriasis is a neglected tropical disease ( NTD ) caused by parasitic nematodes of the genus Trichuris ( Nematoda ) , causing significant human and animal health problems as well as considerable socio-economic consequences world-wide . Although Trichuris species are considered to be relatively host specific , there ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "biology", "zoology", "veterinary", "science" ]	2012	Clear Genetic Distinctiveness between Human- and Pig-Derived Trichuris Based on Analyses of Mitochondrial Datasets
An alarming number of fatal accidents involving snakes are annually reported in Africa and most of the victims suffer from permanent local tissue damage and chronic disabilities . Envenomation by snakes belonging to the genus Bitis , Viperidae family , are common in Sub-Saharan Africa . The accidents are severe and the...	In this report we have characterized the venoms from three species of Bitis snakes involved in accidents with humans in the Sub-Saharan Africa , i . e . , Bitis arietans , Bitis gabonica rhinoceros and Bitis nasicornis . These venoms possess a combination of proteases that can directly affect the coagulation system and...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	African Adders: Partial Characterization of Snake Venoms from Three Bitis Species of Medical Importance and Their Neutralization by Experimental Equine Antivenoms
There is debate over the effectiveness of deworming children against soil-transmitted helminthiasis ( STH ) to improve health outcomes , and current evidence may be limited in study design and generalizability . However , programmatic deworming continues throughout low and middle-income countries . We performed an empi...	Soil-transmitted helminths are parasitic worms that affect 1 . 5 billion people . The global public health strategy is regular deworming of children in endemic settings . In this study , we bring an independent dataset with over 320 , 000 pre-school age children across 45 STH-endemic countries to investigate the relati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "geographical", "locations", "anemia", "pediatrics", "age", "groups", "mathematics", "statistics", "(mathematics)", "global", "health", "africa", "families", "research", "and", "analysis", "methods", "public", "and", ...	2018	Deworming in pre-school age children: A global empirical analysis of health outcomes
Helminths immunomodulate their hosts and induce a regulatory , anti-inflammatory milieu that prevents allergies and autoimmune diseases . Helminth immunomodulation may benefit sepsis outcome by preventing exacerbated inflammation and severe pathology , but the influence on bacterial clearance remains unclear . To addre...	As the human immune system evolved in the presence of helminth infections , it is postulated that improved hygiene and subsequent loss of helminth infections and their immunomodulatory functions contributed to the sharp increase of autoimmune diseases and allergies over the last decades . Accordingly , helminth-induced...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Chronic Filarial Infection Provides Protection against Bacterial Sepsis by Functionally Reprogramming Macrophages
Plasmodium relies on numerous agonists during its journey through the mosquito vector , and these agonists represent potent targets for transmission-blocking by either inhibiting or interfering with them pre- or post-transcriptionally . The recently developed CRISPR/Cas9-based genome editing tools for Anopheles mosquit...	The causative agent of malaria , Plasmodium , has to complete a complex infection cycle in the Anopheles gambiae mosquito vector in order to reach the salivary gland from where it can be transmitted to a human host . The parasite’s development in the mosquito relies on numerous host factors ( agonists ) , and their inh...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome", "engineering", "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "engineering", "and", "technology", "synthetic", "biology", "tropical", "diseases", "gene", "knockout", "parasitic", ...	2018	CRISPR/Cas9 -mediated gene knockout of Anopheles gambiae FREP1 suppresses malaria parasite infection
Podoconiosis is one of the few diseases that could potentially be eliminated within one generation . Nonetheless , the global distribution of the disease remains largely unknown . The global atlas of podoconiosis was conceived to define the epidemiology and distribution of podoconiosis through dedicated surveys and ass...	Podoconiosis is one of the Neglected Tropical Diseases , and causes painful and massive swelling of the lower legs . Despite the importance of the disease , its global distribution and epidemiology are poorly understood . We conducted a systematic review to assess the global epidemiology of podoconiosis . We found that...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "uganda", "parasitic", "diseases", "parasitology", "neglected", "tropical", "diseases", "ethiopia", "africa", "research", "and", "analysis", "methods", "cameroon", "elephantiasis...	2018	Global epidemiology of podoconiosis: A systematic review
We observed a severe autosomal recessive movement disorder in mice used within our laboratory . We pursued a series of experiments to define the genetic lesion underlying this disorder and to identify a cognate disease in humans with mutation at the same locus . Through linkage and sequence analysis we show here that t...	We have identified a spontaneous in-frame deletion mutation in the gene Itpr1 that causes a recessive movement disorder in mice . In an attempt to define whether any similar disease occurs in humans we performed a literature search for diseases linked to the human chromosomal region containing ITPR1 . We identified the...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "homo", "(human)", "genetics", "and", "genomics", "neurological", "disorders" ]	2007	Deletion at ITPR1 Underlies Ataxia in Mice and Spinocerebellar Ataxia 15 in Humans
Chikungunya virus ( CHIKV ) is a worldwide emerging pathogen . In humans it causes a syndrome characterized by high fever , polyarthritis , and in some cases lethal encephalitis . Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection . We show here that CHIKV induces maj...	Chikungunya virus ( CHIKV ) infection , which is responsible for devastating human illness , is rapidly becoming a global concern . The spread of this disease throughout tropical areas , where it now affects nearly 40 countries , underlines the need to improve our understanding of this infection . In 2008 , CHIKV was l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "white", "cells", "infectious", "disease", "control", "hematology" ]	2011	Unconventional Repertoire Profile Is Imprinted during Acute Chikungunya Infection for Natural Killer Cells Polarization toward Cytotoxicity
The intrinsic stochasticity of gene expression leads to cell-to-cell variations , noise , in protein abundance . Several processes , including transcription , translation , and degradation of mRNA and proteins , can contribute to these variations . Recent single cell analyses of gene expression in yeast have uncovered ...	The stochastic nature of gene expression leads to cell-to-cell differences in protein level referred to as noise . Expression noise can be disadvantageous , by affecting the precision of biological functions , but it may also be advantageous by enabling heterogeneous stress-response programs to environmental changes . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genome", "expression", "analysis", "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression
The prokaryotic tubulin homolog , FtsZ , forms a ring-like structure ( FtsZ-ring ) at midcell . The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery ( divisome ) . Although many molecular components of the divisome have been identified and their interactions ext...	Bacterial cell division is a highly regulated process that must be coordinated with other cellular processes ( i . e . DNA replication and chromosome segregation ) to promote faithful reproduction . In Escherichia coli , this regulation is most often mediated through the polymerization of the prokaryotic tubulin homolo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Multi-layered Protein Network Stabilizes the Escherichia coli FtsZ-ring and Modulates Constriction Dynamics
Enterohemorrhagic Escherichia coli ( EHEC ) is a common cause of severe hemorrhagic colitis . EHEC's virulence is dependent upon a type III secretion system ( TTSS ) encoded by 41 genes . These genes are organized in several operons clustered in the locus of enterocyte effacement . Most of the locus of enterocyte effac...	Attaching and effacing pathogens are a group of enteric pathogens that includes the closely related enterohemorrhagic Escherichia coli ( EHEC ) and enteropathogenic E . coli ( EPEC ) . EPEC causes severe diarrhea in young children in developing countries , while EHEC is a causative agent of hemorrhagic colitis . A majo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "none", "in", "vitro", "microbiology", "computational", "biology", "biophysics", "eubacteria" ]	2007	Structure of GrlR and the Implication of Its EDED Motif in Mediating the Regulation of Type III Secretion System in EHEC
Huntington’s Disease ( HD ) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat , which continues to expand in somatic tissues with age . The inherited disease allele expresses a toxic protein , and whether further somatic expansion adds to toxicity is unknown . We have created a...	Huntington’s Disease ( HD ) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat , which continues to expand in somatic tissues with age . There is no correction for the inherited mutation , but if somatic expansion contributes to disease , then a therapeutic approach is possible ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Suppression of Somatic Expansion Delays the Onset of Pathophysiology in a Mouse Model of Huntington’s Disease
Leishmania parasites are transmitted to vertebrate hosts by female phlebotomine sand flies as they bloodfeed by lacerating the upper capillaries of the dermis with their barbed mouthparts . In the sand fly midgut secreted proteophosphoglycans from Leishmania form a biological plug known as the promastigote secretory ge...	Female phlebotomine sand flies efficiently transmit Leishmania parasites , yet the underlying mechanisms remain poorly understood . During transmission , promastigote secretory gel ( PSG ) regurgitated from the blocked sand fly gut promote Leishmania infection and exacerbates disease . Here we investigate mouse ear-ski...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "immunology", "microbiology", "sand", "flies", "parasitic", "diseases", "para...	2018	Leishmania proteophosphoglycans regurgitated from infected sand flies accelerate dermal wound repair and exacerbate leishmaniasis via insulin-like growth factor 1-dependent signalling
In the present study , we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection , and examined whether multifunctionality is required for selection of virus escape mutations . Seven anti-retroviral therapy-naïve subjects ...	An important role for the polyfunctional T-cell fraction of anti-HIV CD8 responses during chronic HIV infection has previously been suggested . This study characterized the role of polyfunctional T-cells directed against the transmitted/founder virus in the selection of viral escape mutants during acute HIV-1 infection...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids" ]	2011	Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection
AMP-activated kinase ( AMPK ) is a key regulator of many cellular mechanisms required for adjustment to various stresses induced by the changing environment . In C . elegans dauer larvae AMPK-null mutants expire prematurely due to hyperactive Adipose Triglyceride Lipase ( ATGL-1 ) followed by rapid depletion of triglyc...	Chanarin-Dorfman Syndrome ( CDS ) is a rare metabolic disease characterized by an abnormal accumulation of lipids in various tissues and organs due to a failure in lipid breakdown . Characteristic clinical features exhibited by affected patients include scaly skin ( ichthyosis ) , enlarged liver , blurred vision among ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Causative Gene in Chanarian Dorfman Syndrome Regulates Lipid Droplet Homeostasis in C. elegans
Eukaryotic genomes encode hundreds of RNA-binding proteins , yet the functions of most of these proteins are unknown . In a genetic study of stress signal transduction in Arabidopsis , we identified a K homology ( KH ) -domain RNA-binding protein , HOS5 ( High Osmotic Stress Gene Expression 5 ) , as required for stress...	Pre-mRNA processing , including 5′ capping , splicing , and 3′ polyadenylation , is critical for gene expression and is closely coupled with transcription . Phosphorylated carboxyl terminal domain ( CTD ) of RNA Polymerase II ( RNAP II ) serves as a platform for the recruitment of pre-mRNA processing factors , yet othe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis
The invasion of erythrocytes by Plasmodium merozoites requires specific interactions between host receptors and parasite ligands . Parasite proteins that bind erythrocyte receptors during invasion are localized in apical organelles called micronemes and rhoptries . The regulated secretion of microneme and rhoptry prote...	Malaria remains a major public health problem in many parts of the tropical world . All the clinical symptoms of malaria are attributed to the blood stage of the parasite life cycle during which Plasmodium merozoites invade and multiply within host erythrocytes . Invasion by Plasmodium merozoites is a complex process t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "microbiology/parasitology", "cell", "biology/cell", "signaling" ]	2010	Distinct External Signals Trigger Sequential Release of Apical Organelles during Erythrocyte Invasion by Malaria Parasites
The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes , diseases and cellular processes . A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence . Apart from its use in knowledge ret...	The biomedical literature is an important source of knowledge on the function of genes and on the mechanisms by which these genes regulate cellular processes . Several text mining approaches have been developed to leverage this rich source of information by automatically extracting associations between concepts such as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/literature", "analysis", "pharmacology/drug", "development", "molecular", "biology/bioinformatics" ]	2010	Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
Reduced tissue perfusion leading to tissue ischemia is a central component of the pathogenesis of myonecrosis caused by Clostridium perfringens . The C . perfringens α-toxin has been shown capable of inducing these changes , but its potential synergy with perfringolysin O ( θ-toxin ) is less well understood . Similarly...	Clostridial myonecrosis is a life-threatening process induced by infection with species such as C . perfringens and C . septicum . The associated pathology includes muscle death and a characteristic disruption in tissue perfusion . Exotoxins produced by these species have been implicated in the reduction in perfusion ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "physiology/cardiovascular", "physiology", "and", "circulation", "immunology/immune", "response", "immunology/innate", "immunity", "pathology/immunology" ]	2008	Molecular and Cellular Basis of Microvascular Perfusion Deficits Induced by Clostridium perfringens and Clostridium septicum
Molecular epidemiological assessments , drug treatment optimization , and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation , which differ for specific pathogens . Mycobacterium tuberculosis is an exceptionally successful human pathogen , yet beyond knowled...	Mycobacterium tuberculosis is amongst the most successful and enigmatic pathogens that has burdened humanity for thousands of years . The success of this pathogen depends on unique strategies employed to adapt during infection . Understanding these strategies is key to decipher the complexity of M . tuberculosis and cr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "protein", "metabolism", "immunology", "population", "genetics", "cell", "metabolism", "mammalian", "genomics", "population", "biology", "bacteria", "white", "blood", "...	2016	Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity
Kaposi's sarcoma associated herpesvirus ( KSHV ) , an etiologic agent of Kaposi's sarcoma , Body Cavity Based Lymphoma and Multicentric Castleman's Disease , establishes lifelong latency in infected cells . The KSHV genome tethers to the host chromosome with the help of a latency associated nuclear antigen ( LANA ) . A...	Kaposi's sarcoma associated herpesvirus ( KSHV ) establishes lifelong infection in the infected host and induces lymphoproliferative diseases , body cavity based lymphomas and sarcomas in immune compromised individuals . Herpesviruses including KSHV uses host cellular replication machinery for the replication of their ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology", "biology", "microbiology", "host-pathogen", "interaction" ]	2011	Single Molecule Analysis of Replicated DNA Reveals the Usage of Multiple KSHV Genome Regions for Latent Replication
The release of Wolbachia infected mosquitoes is likely to form a key component of disease control strategies in the near future . We investigated the potential of using near-infrared spectroscopy ( NIRS ) to simultaneously detect and identify two strains of Wolbachia pipientis ( wMelPop and wMel ) in male and female la...	Near infrared spectroscopy ( NIRS ) is a technique that measures specific frequencies of light absorbed by C-H , O-H , S-H and N-H functional groups . Mosquito samples are grouped based upon absorption differences between their chemical properties . In this study , we used NIRS to differentiate 1 ) Aedes aegypti infect...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "animals", "wolbachia", "alphaviruses", "organisms", ...	2016	Rapid and Non-destructive Detection and Identification of Two Strains of Wolbachia in Aedes aegypti by Near-Infrared Spectroscopy
Ovarian cancer is the fifth leading cause of cancer death in women . Almost 70% of ovarian cancer deaths are due to the high-grade serous subtype , which is typically detected only after it has metastasized . Characterization of high-grade serous cancer is further complicated by the significant heterogeneity and genome...	High-grade serous carcinoma ( HG-SC ) is the most common subtype of ovarian cancer observed in women . This subtype of ovarian cancer is typically detected at advanced stages due to lack of effective early screening tools . Recurrent cancer-specific gene fusions resulting from chromosomal translocations have the potent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "and", "health", "sciences", "cancer", "genetics", "genetics", "biology", "and", "life", "sciences", "cancers", "and", "neoplasms", "gynecological", "tumors" ]	2014	CDKN2D-WDFY2 Is a Cancer-Specific Fusion Gene Recurrent in High-Grade Serous Ovarian Carcinoma
Natural killer ( NK ) cells provide the first line of defense against malaria parasite infection . However , the molecular mechanisms through which NK cells are activated by parasites are largely unknown , so is the molecular basis underlying the variation in NK cell responses to malaria infection in the human populati...	Malaria is an important parasitic disease with a major public health concern . Malaria pathogenesis involves a complex interplay between parasitic and host factors . A better understanding of early host response and the determinants of immunity are essential to developing innovative therapeutic approaches . Natural kil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "cells", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "apicomplexa", ...	2018	Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway
The recent Middle East respiratory syndrome coronavirus ( MERS-CoV ) , Ebola and Zika virus outbreaks exemplify the continued threat of ( re- ) emerging viruses to human health , and our inability to rapidly develop effective therapeutic countermeasures . Many viruses , including MERS-CoV and the Crimean-Congo hemorrha...	Emerging viruses pose a tremendous challenge to human health . While vaccine-based approaches are desirable in terms of infection prevention in the longer term , alternative antiviral strategies are needed , especially when providing treatment options for infected patients during acute outbreaks . Here we applied prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "coronaviruses", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "enzymes", "pathogens", "sars", "coronavirus", "microbiology", "enzymology", "pulmonology", "viruses", "rna", "viruses", "m...	2017	Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
Many diverse biological systems are described by randomly moving particles that can be captured by traps in their environment . Examples include neurotransmitters diffusing in the synaptic cleft before binding to receptors and prey roaming an environment before capture by predators . In most cases , the traps cannot ca...	Consider particles that are released into an environment ( think diffusing molecules or plankton ) , and suppose that there are traps in the environment . How many particles will be captured by the traps before they escape ? In a standard model , the number of captured particles is proportional to the initial number re...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "astroparticle", "physics", "neurochemistry", "particle", "physics", "nervous", "system", "astronomical", "sciences", "electrophysiology", "neuroscience", "mathematics", "algebra", "neur...	2018	Receptor recharge time drastically reduces the number of captured particles
Virus-like particles ( VLPs ) have not been observed in Caenorhabditis germ cells , although nematode genomes contain low numbers of retrotransposon and retroviral sequences . We used electron microscopy to search for VLPs in various wild strains of Caenorhabditis , and observed very rare candidate VLPs in some strains...	Retrotransposons and retroviruses pose enormous threats to animal and plants because of their ability to insert into host genes . Retroelements that replicate in germ cells can , if left unchecked , expand exponentially in the host genome . C . elegans has proven to be an exceptional model system for studying many face...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "biology", "evolutionary", "biology" ]	2012	C. elegans Germ Cells Show Temperature and Age-Dependent Expression of Cer1, a Gypsy/Ty3-Related Retrotransposon
Various optimality principles have been proposed to explain the characteristics of coordinated eye and head movements during visual orienting behavior . At the same time , researchers have suggested several neural models to underly the generation of saccades , but these do not include online learning as a mechanism of ...	Human beings and many other species redirect their gaze towards targets of interest through rapid gaze shifts known as saccades . These are made approximately three to four times every second , and larger saccades result from fast and concurrent movement of the animal's eyes and head . Experimental studies have reveale...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "control", "engineering", "computer", "science", "control", "systems", "computational", "neuroscience", "biology", "computational", "biology" ]	2011	Learning the Optimal Control of Coordinated Eye and Head Movements
The soil dwelling Gram-negative pathogen Burkholderia pseudomallei is the cause of melioidosis . The diversity and population structure of this organism in the environment is poorly defined . We undertook a study of B . pseudomallei in soil sampled from 100 equally spaced points within 237 . 5 m2 of disused land in nor...	The soil dwelling Gram-negative bacterium Burkholderia pseudomallei is the cause of melioidosis , a serious human infection that occurs in Southeast Asia and northern Australia . The purpose of this study was to evaluate the population genetic structure of B . pseudomallei in the environment . To achieve this , we unde...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Genetic Diversity and Microevolution of Burkholderia pseudomallei in the Environment
Although recombination is essential to the successful completion of human meiosis , it remains unclear how tightly the process is regulated and over what scale . To assess the nature and stringency of constraints on human recombination , we examined crossover patterns in transmissions to viable , non-trisomic offspring...	In humans , as in most sexually reproducing organisms , recombination plays a fundamental role in meiosis , helping to align chromosomes and to ensure their proper segregation . Recombination events are tightly regulated both in terms of their minimum number ( the rule of “crossover assurance” ) and placement ( due to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/population", "genetics", "evolutionary", "biology/animal", "genetics", "computational", "biology/molecular", "genetics", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/plant", "...	2009	Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans
Accumulating infections of highly pathogenic H5N1 avian influenza in humans underlines the need to track the ability of these viruses to spread among humans . A human-transmissible avian influenza virus is expected to cause clusters of infections in humans living in close contact . Therefore , epidemiological analysis ...	Recent outbreaks of emerging diseases such as SARS and H5N1 avian influenza have underlined the fact that animal pathogens may acquire the ability to spread efficiently in humans . Monitoring the transmissibility of pathogens from the animal reservoir in humans is key for early detection of epidemic spread , and for ef...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "viruses", "infectious", "diseases", "public", "health", "and", "epidemiology", "virology" ]	2007	Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households
Variations in gene expression level might lead to phenotypic diversity across individuals or populations . Although many human genes are found to have differential mRNA levels between populations , the extent of gene expression that could vary within and between populations largely remains elusive . To investigate the ...	Many human genes have population-specific expression levels , which are linked to population-specific polymorphisms and copy-number variations . However , it is unclear whether human genes show similar dynamic range of expression between populations . In this work we analyzed HapMap gene expression compendium , and qua...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "computational", "biology/molecular", "genetics", "computational", "biology/genomics" ]	2010	Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility
Previous studies have reported the production of malformed virus-like-particles ( VLP ) in recombinant host systems . Here we computationally investigate the case of a large triple-layered rotavirus VLP ( RLP ) . In vitro assembly , disassembly and reassembly data provides strong evidence of microscopic reversibility o...	Virus-like particles ( VLP ) are multi-protein structures with potential to be used in biomedicine as therapeutic or prophylactic vaccines against many worldwide diseases . However , due to their complex process of assembly , production yields are commonly low hindering a fast transition from lab- to industrial-scale a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "immunology", "physical", "laws", "and", "principles", "physical", "chemistry", "vaccination", "infectious", "diseases", "proteins", "chemistry", "biology", "physics", "biochemistry", "computer", "science", "computer", "modeling", "clinical", "immunology", "im...	2012	On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP
We showed previously that eiger , the Drosophila tumor necrosis factor homolog , contributes to the pathology induced by infection with Salmonella typhimurium . We were curious whether eiger is always detrimental in the context of infection or if it plays a role in fighting some types of microbes . We challenged wild-t...	We show that the gene eiger , which is the sole tumor necrosis factor homolog in the fruit fly , can play opposing roles in the fly's response to infections . Sometimes eiger contributes to the disease induced by an infection , while at other times it is required to fight an infection . Commonly , the fly's immune resp...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "burholderia", "infectious", "diseases", "mycobacterium", "listeria", "immunology", "salmonella", "drosophila", "genetics", "and", "genomics" ]	2007	Drosophila eiger Mutants Are Sensitive to Extracellular Pathogens
When the error signals that guide human motor learning are withheld following training , recently-learned motor memories systematically regress toward untrained performance . It has previously been hypothesized that this regression results from an intrinsic volatility in these memories , resulting in an inevitable deca...	Suppose you are asked to shoot free throws with a basketball . If you’re an unskilled shooter , you may at first miss in a consistent way for consecutive shots—perhaps a bit to the right—but you will soon learn to correct that error . However , an often-repeated finding is that if error information is withheld , such a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Decay of Motor Memories Is Independent of Context Change Detection
We used phase resetting methods to predict firing patterns of rat subthalamic nucleus ( STN ) neurons when their rhythmic firing was densely perturbed by noise . We applied sequences of contiguous brief ( 0 . 5–2 ms ) current pulses with amplitudes drawn from a Gaussian distribution ( 10–100 pA standard deviation ) to ...	Most neurons receive thousands of synaptic inputs per second . Each of these may be individually weak but collectively they shape the temporal pattern of firing by the postsynaptic neuron . If the postsynaptic neuron fires repetitively , its synaptic inputs need not directly trigger action potentials , but may instead ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "anatomy", "computational", "neuroscience", "nervous", "system", "single", "neuron", "function", "biology", "and", "life", "sciences", "computational", "biology", "motor", "system", "neuroscience", "coding", "mechanisms" ]	2014	Predicting the Responses of Repetitively Firing Neurons to Current Noise
The idea that cognitive activity can be understood using nonlinear dynamics has been intensively discussed at length for the last 15 years . One of the popular points of view is that metastable states play a key role in the execution of cognitive functions . Experimental and modeling studies suggest that most of these ...	The modeling of the temporal structure of cognitive processes is a key step for understanding cognition . Cognitive functions such as sequential learning , short-term memory , and decision making in a changing environment cannot be understood using only the traditional view based on classical concepts of nonlinear dyna...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/cognitive", "neuroscience", "computational", "biology/computational", "neuroscience", "computational", "biology" ]	2008	Transient Cognitive Dynamics, Metastability, and Decision Making
Gaining and sustaining control of schistosomiasis and , whenever feasible , achieving local elimination are the year 2020 targets set by the World Health Organization . In Zanzibar , various institutions and stakeholders have joined forces to eliminate urogenital schistosomiasis within 5 years . We report baseline find...	Schistosomiasis is a chronic and debilitating disease caused by parasitic worms . It negatively impacts on the health and wellbeing of mainly rural dwellers in tropical and sub-tropical countries . The World Health Organization recently put forward an ambitious goal for the year 2020: to control schistosomiasis globall...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Elimination of Schistosomiasis Transmission in Zanzibar: Baseline Findings before the Onset of a Randomized Intervention Trial
High-throughput sequencing of transposon ( Tn ) libraries created within entire genomes identifies and quantifies the contribution of individual genes and operons to the fitness of organisms in different environments . We used insertion-sequencing ( INSeq ) to analyze the contribution to fitness of all non-essential ge...	To determine the contribution of all non-essential genes of Pseudomonas aeruginosa to overall fitness in laboratory and infectious settings , we used a high throughput sequencing method that quantitatively identifies the bacterial genes interrupted by random insertion of transposons ( Tn ) into the genome of strain PA1...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "medicine", "infectious", "diseases", "genetics", "immunology", "biology", "microbiology", "critical", "care", "and", "emergency", "medicine" ]	2013	A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries
Population geneticists often study small numbers of carefully chosen loci , but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences . Here , we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees , three ...	Studies of population history traditionally examine a small number of genetic regions in many individuals; however , with genome sequencing technologies it is possible to assemble data sets with thousands more aligned sequences albeit in fewer individuals . To explore whether such data can provide useful insights about...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/genomics", "evolutionary", "biology/evolutionary", "ecology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Analysis of Chimpanzee History Based on Genome Sequence Alignments
Many variant proteins encoded by Plasmodium-specific multigene families are exported into red blood cells ( RBC ) . P . falciparum-specific variant proteins encoded by the var , stevor and rifin multigene families are exported onto the surface of infected red blood cells ( iRBC ) and mediate interactions between iRBC a...	Malaria-parasites invade and multiply in hepatocytes and erythrocytes . The human parasite P . falciparum transports proteins encoded by multigene families onto the surface of erythrocytes , mediating interactions between infected red blood cells ( iRBCs ) and other host-cells and are thought to play a key role in para...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "body", "fluids", "plasmodium", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "membrane", "proteins", "apicomplexa", "protozoans", "phylogenetic", "analysis", "molecular", "biology", "tec...	2016	Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole
E-type cyclins ( cyclins E1 and E2 ) are components of the cell cycle machinery that has been conserved from yeast to humans . The major function of E-type cyclins is to drive cell division . It is unknown whether in addition to their ‘core’ cell cycle functions , E-type cyclins also perform unique tissue-specific role...	The proliferation of mammalian cells is driven by proteins called cyclins , which bind and activate their catalytic partners , the cyclin-dependent kinases ( Cdks ) . Cyclin-Cdk complexes drive cell proliferation by phosphorylating several cellular proteins . This study focuses on the E-type cyclins ( cyclins E1 and E2...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "physiology", "protein", "interactions", "spleen", "cell", "cycle", "and", "cell", "division", "cell", "processes", "reproductive", "physiology", "immunoprecipitatio...	2016	Proteomic Landscape of Tissue-Specific Cyclin E Functions in Vivo
Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection . There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations du...	Phenotypic variation within a grapevine cultivar arises from an accumulation of mutations from serial vegetative propagation . Old cultivars such as Chardonnay have been propagated for centuries resulting in hundreds of available ‘clones’ containing unique genetic mutations and a range of various phenotypic peculiariti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cloning", "sequence", "assembly", "tools", "genetic", "mapping", "genome", "analysis", "molecular", "biology", "techniques", "molecular", "genetics", "plants", "flowering", "plants", "research", "and", "analysis", "methods", "sequence", "analysis", "grapevine", "genomi...	2018	Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay
Structural and biochemical constraints force some segments of proteins to evolve more slowly than others , often allowing identification of conserved structural or sequence motifs that can be associated with substrate binding properties , chemical mechanisms , and molecular functions . We have assessed the functional a...	The sequencing of genomes from different species has provided a unique opportunity for comparative analysis and opened the door to a higher level of understanding of living organisms . However , identifying the biochemical functions of the protein products coded by these genes has proved to be a major challenge . Compu...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "none", "biochemistry" ]	2007	Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins
There is an urgent need to develop rapid and accurate point-of-care ( POC ) technologies for acute scrub typhus diagnosis in low-resource , primary health care settings to guide clinical therapy . In this study we present the clinical evaluation of loop-mediated isothermal PCR assay ( LAMP ) in the context of a prospec...	There is an urgent need for alternative diagnostic methods for scrub typhus , but evaluation of these is hampered because the current serological gold standard ( IFA ) is imperfect . In a study from Thailand , 3 of 20 ( 15% ) patients with fever had a positive Orientia tsutsugamushi PCR result despite negative serology...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "neglected", "tropical", "diseases" ]	2011	Diagnostic Accuracy of a Loop-Mediated Isothermal PCR Assay for Detection of Orientia tsutsugamushi during Acute Scrub Typhus Infection
MicroRNAs play an important role in the interplay between bacterial pathogens and host cells , participating as host defense mechanisms , as well as exploited by bacteria to subvert host cellular functions . Here , we show that microRNAs modulate infection by Shigella flexneri , a major causative agent of bacillary dys...	MicroRNAs are genome-encoded small non-coding RNAs that play a pivotal role in post-transcriptional regulation of gene expression . In addition to other biological functions , microRNAs are increasingly recognized as important players in the complex interaction between host and bacterial pathogens . In this work we sho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "hela", "cells", "gene", "regulation", "pathogens", "biological", "cultures", "tropical", "dise...	2017	Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia
Variation in human skin and eye color is substantial and especially apparent in admixed populations , yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry . We study pigmentary variation in 699 individuals from Cape Verde , where ext...	Differences in skin and eye color are some of the most obvious traits that underlie human diversity , yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry . We have studied a unique population in Cape Verde , an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "heredity", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetics", "and", "genomics", "human", "genetics" ]	2013	Genetic Architecture of Skin and Eye Color in an African-European Admixed Population
An integrative cell migration model incorporating focal adhesion ( FA ) dynamics , cytoskeleton and nucleus remodeling , actin motor activity , and lamellipodia protrusion is developed for predicting cell spreading and migration behaviors . This work is motivated by two experimental works: ( 1 ) cell migration on 2-D s...	Cell migration is a complex , multifaceted process , triggered by chemotaxis and haptotatic responses from the extracellular matrix ( ECM ) . It is triggered by a thin lamellipodium protrusion at the leading edge , followed by the assembly of a number of focal adhesions between the lamellipodium base and the ECM . Afte...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "systems", "biology", "biophysic", "al", "simulations", "biology", "computational", "biology", "biophysics", "simulations", "biophysics", "biomechanics" ]	2013	Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries
SUMO modification of transcription factors is linked to repression of transcription . The physiological significance of SUMO attachment to a particular transcriptional regulator , however , is largely unknown . We have employed the ubiquitously expressed murine transcription factor Sp3 to analyze the role of SUMOylatio...	Cell type–specific gene expression patterns are largely regulated by positively or negatively acting transcription factors binding to promoter and enhancer elements . The ubiquitous transcription factor Sp3 represents a paradigm for a dual function transcription factor as it can activate and repress transcription . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "biochemistry", "genetics", "and", "genomics/gene", "expression", "cell", "biology", "genetics", "and", "genomics/gene", "function", "biochemistry/transcription", "and", "translation", "genetics", "and", "genomics/epigenetics"...	2010	Epigenetic Silencing of Spermatocyte-Specific and Neuronal Genes by SUMO Modification of the Transcription Factor Sp3
Accuracy Maximization Analysis ( AMA ) is a recently developed Bayesian ideal observer method for task-specific dimensionality reduction . Given a training set of proximal stimuli ( e . g . retinal images ) , a response noise model , and a cost function , AMA returns the filters ( i . e . receptive fields ) that extrac...	In psychophysics and neurophysiology , the stimulus features that are manipulated in experiments are often selected based on intuition , trial-and-error , and historical precedence . Accuracy Maximization Analysis ( AMA ) is a Bayesian ideal observer method for determining the task-relevant features ( i . e . filters )...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "tangents", "ellipses", "social", "sciences", "geometry", "learning", "and", "memory", "neuroscience", "probability", "distribution", "mathematics", "cognitive", "psychology", "computational", "neuroscience", "vision", "coding", "mechanisms", "animal", "cells", ...	2017	Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
Antigenic variation in the globular domain of influenza A virus ( IAV ) hemagglutinin ( HA ) precludes effective immunity to this major human pathogen . Although the HA stem is highly conserved between influenza virus strains , HA stem-reactive antibodies ( StRAbs ) were long considered biologically inert . It is now c...	Extensive variation in the IAV HA globular domain severely impedes influenza vaccination . Recent findings demonstrate that StRAbs , specific Abs to the highly conserved stem region of HA , can protect hosts against a broad variety of influenza virus strains . In investigating the binding of StRAbs to HA during its bio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "biology", "and", "life", "sciences", "immunology", "microbiology", "molecular", "cell", "biology" ]	2014	Biogenesis of Influenza A Virus Hemagglutinin Cross-Protective Stem Epitopes
In many vertebrates and invertebrates , offspring whose mothers have been exposed to pathogens can exhibit increased levels of immune activity and/or increased survival to infection . Such phenomena , called “Trans-generational immune priming” ( TGIP ) are expected to provide immune protection to the offspring . As the...	In some insects , the immunological experience of mothers is transferred to their otherwise naïve offspring , protecting them against infection . Such a maternal effect has likely evolved from selective pressure imposed by the persistence of some microbial pathogens in the environment between insect generations . If mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Trans-generational Immune Priming Protects the Eggs Only against Gram-Positive Bacteria in the Mealworm Beetle
Alternative pre-mRNA splicing adjusts the transcriptional output of the genome by generating related mRNAs from a single primary transcript , thereby expanding protein diversity . A fundamental unanswered question is how splicing factors achieve specificity in the selection of target substrates despite the recognition ...	Alternative splicing is a precisely controlled process that determines whether an exon will be included or skipped in the mature mRNA transcript . Factors that control alternative splicing bind to RNA sequence motifs in the exon or flanking introns and guide tissue and developmental specific splicing events . CUGBP2 is...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "molecular", "biology/rna-protein", "interactions", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/rna", "splicing", "biochemistry/bioinformatics" ]	2009	The CUGBP2 Splicing Factor Regulates an Ensemble of Branchpoints from Perimeter Binding Sites with Implications for Autoregulation
Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself . Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer . To address the questions as to what a...	Living systems possess an endogenous time-generating system – the circadian clock - accountable for a 24 hours oscillation in the expression of about 10% of all genes . In mammals , disruption of oscillations is associated to several diseases including cancer . In this manuscript , we address the following question: wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "systems", "biology", "text", "mining", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "computer", "modeling", "theoretical", "biology", "basic", "cancer", "research", "genetics", "biology", "and", "life", "sciences"...	2014	Ras-Mediated Deregulation of the Circadian Clock in Cancer
Transduction of graded synaptic input into trains of all-or-none action potentials ( spikes ) is a crucial step in neural coding . Hodgkin identified three classes of neurons with qualitatively different analog-to-digital transduction properties . Despite widespread use of this classification scheme , a generalizable e...	Information is transmitted through the nervous system in the form of action potentials or spikes . Contrary to popular belief , a spike is not generated instantaneously when membrane potential crosses some preordained threshold . In fact , different neurons employ different rules to determine when and why they spike . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/neuronal", "signaling", "mechanisms", "biophysics/theory", "and", "simulation", "neuroscience/theoretical", "neuroscience" ]	2008	Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation
A critical accomplishment in the rapidly developing field of regenerative medicine will be the ability to foster repair of neurons severed by injury , disease , or microsurgery . In C . elegans , individual visualized axons can be laser-cut in vivo and neuronal responses to damage can be monitored to decipher genetic r...	Clinical success in reconnecting neurons damaged by injury will require detailed molecular understanding of how mature axons respond to being severed . To decipher intrinsic molecular pathways that stimulate axon regeneration , we use the small transparent model , Caenorhabditis elegans , in which individual labeled ax...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "cell", "death", "neurobiology", "of", "disease", "and", "regeneration", "caenorhabditis", "elegans", "model", "organisms", "molecular", "cell", "biology", "cell", "biology", "biology", "neuroscience" ]	2012	The Core Apoptotic Executioner Proteins CED-3 and CED-4 Promote Initiation of Neuronal Regeneration in Caenorhabditis elegans

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