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DEAD-box proteins are ubiquitous regulators of RNA biology . While commonly dubbed “helicases , ” their activities also include duplex annealing , adenosine triphosphate ( ATP ) -dependent RNA binding , and RNA-protein complex remodeling . Rok1 , an essential DEAD-box protein , and its cofactor Rrp5 are required for ri...	Assembly of the small and large ribosomal subunits requires two separate machineries . The assembly factor Rrp5 is unusual in being one of only three proteins required for assembly of both subunits . While it binds cotranscriptionally during early stages of small subunit assembly , it departs with large subunit interme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "characterization", "crystal", "structure", "condensed", "matter", "physics", "monomers", "(chemistry)", "dead-box", "crystallography", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "polymer", "chemistry", "solid", "s...	2016	The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation
Neutrophils play a central role in eliminating bacterial pathogens , but may also contribute to end-organ damage in sepsis . Interleukin-8 ( IL-8 ) , a key modulator of neutrophil function , signals through neutrophil specific surface receptors CXCR-1 and CXCR-2 . In this study a mechanistic computational model was use...	Sepsis occurs when a patient develops a whole body immune response due to infection . In this condition , white blood cells called neutrophils circulate in an active state , seeking and eliminating invading bacteria . However , when neutrophils are activated , healthy tissue is inadvertently targeted , leading to organ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis
Current Global Program to Eliminate Lymphatic Filariasis ( GPELF ) that prohibits pregnant mothers and children below two years of age from coverage targeted interruption of transmission after 5–6 rounds of annual mass drug administration ( MDA ) . However , after more than 10 rounds of MDA in India the target has not ...	Lymphatic filariasis ( LF ) has been targeted for elimination by 2020 through a major global initiative . The elimination strategy mainly aims to interrupt the transmission , or spread of infection , through annual mass drug administration ( MDA ) to entire at-risk population except the pregnant women and children belo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "children", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "cell", "cycle", "and", "cell", "division", "immunology", "cell", "processes", "parasitic", "diseases", "pediatrics", "age", "groups", "developmenta...	2018	Filarial infection during pregnancy has profound consequences on immune response and disease outcome in children: A birth cohort study
Both cholera and food insecurity tend to occur in impoverished communities where poor access to food , inadequate sanitation , and an unsafe water supply often coexist . The relationship between the two , however , has not been well-characterized . We performed a secondary analysis of household-level data from the 2012...	In this study , we identified an independent relationship between household food insecurity , defined as a persistent lack of access to food in adequate quantity or quality and measured using the Household Hunger Scale , and reported history of cholera and death from cholera in a general population . We performed a sec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "surface", "water", "behavioral", "and", "social", "aspects", "of", "health", "tropical", "diseases", "geographical", "locations", "diet", "health", "care", ...	2019	Food insecurity and self-reported cholera in Haitian households: An analysis of the 2012 Demographic and Health Survey
Over the last ten years , isogenic tagging ( IT ) has revolutionised the study of bacterial infection dynamics in laboratory animal models . However , quantitative analysis of IT data has been hindered by the piecemeal development of relevant statistical models . The most promising approach relies on stochastic Markovi...	Recent advancements in technology have meant that microbiologists are producing vast amounts of experimental data . However , statistical methods by which we can analyse that data , draw informative inference , and test relevant hypotheses , are much needed . Here , we present a new , efficient inference tool for estim...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "ellipses", "immune", "physiology", "body", "fluids", "spleen", "geometry", "simulation", "and", "modeling", "bacterial", "diseases", "mathematics", "population", "biology", "research", "and", "analysis", "met...	2017	An efficient moments-based inference method for within-host bacterial infection dynamics
Complex patterns of neural activity appear during up-states in the neocortex and sharp waves in the hippocampus , including sequences that resemble those during prior behavioral experience . The mechanisms underlying this replay are not well understood . How can small synaptic footprints engraved by experience control ...	Synaptic plasticity is the basis for learning and memory , and many experiments indicate that memories are imprinted in synaptic connections . However , basic mechanisms of how such memories are retrieved and consolidated remain unclear . In particular , how can one-shot learning of a sequence of events achieve a suffi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "learning", "and", "memory", "sequence", "assembly", "tools", "synaptic", "plasticity", "cognition", "genome", "analysis", "...	2017	Memory replay in balanced recurrent networks
Lethal mutagenesis is an antiviral strategy consisting of virus extinction associated with enhanced mutagenesis . The use of non-mutagenic antiviral inhibitors has faced the problem of selection of inhibitor-resistant virus mutants . Quasispecies dynamics predicts , and clinical results have confirmed , that combinatio...	RNA viruses are associated with many important human and animal diseases such as AIDS , influenza , hemorrhagic fevers and several forms of hepatitis . RNA viruses mutate at very high rates and , therefore , can adapt easily to environmental changes . Viral mutants resistant to antiviral inhibitors are readily selected...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "molecular", "biology/molecular", "evolution", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology", "infectious", "diseases/viral", "infections", "molecular", "biology", "infectious", "diseases/antimicrobials", "...	2009	Potential Benefits of Sequential Inhibitor-Mutagen Treatments of RNA Virus Infections
Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases . They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames . We previously reported the protein interaction networks of two herpesviruses , varicel...	Herpesvirus proteins interact with each other in a complex manner throughout the infectious cycle . This is probably best exemplified in the process where a large number of viral proteins come together to form new viral particles which are subsequently released from the infected cell . A more detailed understanding of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "virology/virion", "structure,", "assembly,", "and", "egress", "virology", "molecular", "biology/bioinformatics", "computational", "biology/systems", "biology" ]	2009	Evolutionarily Conserved Herpesviral Protein Interaction Networks
Bacterial biofilm is considered as a particular lifestyle helping cells to survive hostile environments triggered by a variety of signals sensed and integrated through adequate regulatory pathways . Pseudomonas aeruginosa , a Gram-negative bacterium causing severe infections in humans , forms biofilms and is a fantasti...	We unraveled that once the two-component system PprAB regulatory pathway is activated , Pseudomonas aeruginosa displays a unique hyper-biofilm phenotype due to a molecular signature combining a T1SS high molecular weight substrate , BapA , fimbriae of the chaperone-usher pathway , Type IVb pili and eDNA . Originally , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genetics", "genetics", "and", "genomics", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2012	Unique Biofilm Signature, Drug Susceptibility and Decreased Virulence in Drosophila through the Pseudomonas aeruginosa Two-Component System PprAB
In the developing world where parasitic worm infections are pervasive , preventive chemotherapy is the key strategy for morbidity control . However , local knowledge , attitudes , and practices ( KAP ) of parasitic worms are poorly understood , although such information is required for prevention and sustainable contro...	There is a need to better understand communities' knowledge , attitudes , and practices ( KAP ) of neglected tropical diseases to improve prevention and control efforts . We studied the socio-cultural aspects of parasitic worm infections in two villages ( Mélapleu and Zouatta II ) of western Côte d'Ivoire , where resea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health" ]	2010	Parasitic Worms: Knowledge, Attitudes, and Practices in Western Côte d’Ivoire with Implications for Integrated Control
Zika virus ( Flavivirus genus ) is the first mosquito-borne virus known to cause high rates of microcephaly and abortion in humans . Typically , Zika virus causes a self-limiting , systemic illness; however , the current outbreak of Zika virus in the Americas has been associated with increased rates of fetal malformati...	Zika virus ( ZIKV ) is a mosquito-transmitted virus that causes a febrile illness characterized by a pronounced rash and occasional arthralgia . Serious complications from ZIKV infections were rarely reported until 2015 , when Brazilian officials first reported an association between ZIKV infections and a dramatic incr...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "sequencing", "techniques", "dengue", "virus", "vero", "cells", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chikungunya", "infection", "pathogens", "biological", "cultures", "tropical", "diseases", "microbiology...	2016	Characterization of a Zika Virus Isolate from Colombia
Riverine species of tsetse are responsible for most human African trypanosomiasis ( HAT ) transmission and are also important vectors of animal trypanosomiasis . This study concerns the development of visual control devices for two such species , Glossina fuscipes fuscipes and Glossina tachinoides , at the eastern limi...	The riverine tsetse Glossina fuscipes fuscipes and Glossina tachinoides are among the principal vectors of African trypanosomiasis . Their range stretches from West across Central to East Africa , with isolated populations in Sudan and Ethiopia . Population suppression is one of the most effective methods to control di...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "vector-borne", "diseases", "tropical", "diseases", "parasitic", "diseases", "parasitology", "integrated", "control", "pest", "control", "neglected", "tropical", "diseases", "agricultural", ...	2014	Standardizing Visual Control Devices for Tsetse Flies: East African Species Glossina fuscipes fuscipes and Glossina tachinoides
Control of nuclear RNA stability is essential for proper gene expression , but the mechanisms governing RNA degradation in mammalian nuclei are poorly defined . In this study , we uncover a mammalian RNA decay pathway that depends on the nuclear poly ( A ) -binding protein ( PABPN1 ) , the poly ( A ) polymerases ( PAPs...	In eukaryotes , mRNAs include a stretch of adenosine nucleotides at their 3′ end termed the poly ( A ) tail . In the cytoplasm , the poly ( A ) tail stimulates translation of the mRNA into protein , and protects the transcript from degradation . Evidence suggests that poly ( A ) tails may play distinct roles in RNA met...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Human Nuclear Poly(A)-Binding Protein Promotes RNA Hyperadenylation and Decay
The histone demethylase LSD1 has been known as a key transcriptional coactivator for DNA viruses such as herpes virus . Inhibition of LSD1 was found to block viral genome transcription and lytic replication of DNA viruses . However , RNA virus genomes do not rely on chromatin structure and histone association , and the...	The viral genomes of DNA viruses but not RNA viruses form chromatin structure during infection . Thus , epigenetic modulators are not expected to have crucial roles in RNA viral infection . However , here , we identify for the first time , that , opposite to its role in enhancing DNA virus replication , LSD1 , a histon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "orthomyxoviruses", "viruses", "methylation", "rna", "viruses", "immunoprecipitation", "dna", "replication", "dna", "res...	2017	Histone demethylase LSD1 restricts influenza A virus infection by erasing IFITM3-K88 monomethylation
In South America , accidental contact with Lepidoptera larvae can produce a diversity of reactions that vary from dermatological problems to severe hemorrhagic syndromes , such as those caused by contact with caterpillars of the genus Lonomia ( Saturniidae ) . Lonomia venom can alter the hemostatic system and lead to r...	A specific antivenom therapy is recommended for treating envenomation caused by venomous animals , such as snakes , spiders , scorpions , and Lonomia caterpillars . Studies with snake bites have shown that antivenoms are effective for treating the envenomation caused by snakes of the same genus , even when the antigen ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "caterpillars", "body", "fluids", "toxins", "moths", "and", "butterflies", "fibrinogen", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "vertebrates", "animals", "tox...	2018	Effectiveness of Lonomia antivenom in recovery from the coagulopathy induced by Lonomia orientoandensis and Lonomia casanarensis caterpillars in rats
Only a few genes remain in the mitochondrial genome retained by every eukaryotic organism that carry out essential functions and are implicated in severe diseases . Experimentally relocating these few genes to the nucleus therefore has both therapeutic and evolutionary implications . Numerous unproductive attempts have...	The mitochondrion , centre of cellular energy production , is derived from an ancient alpha-proteobacterium . While the vast majority of its genes have been transferred to the nuclear genome during evolution , a handful of genes remain in all mitochondrial genomes for reasons that are not fully understood . To investig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "gene", "regulation", "synthetic", "biology", "microbiology", "model", "organisms", "molecular", "cell", "biology", "energy-producing", "organelles", "molecular", "genetics", "bioenergetics", "gene", "expression", "biology", "energy-produ...	2012	Experimental Relocation of the Mitochondrial ATP9 Gene to the Nucleus Reveals Forces Underlying Mitochondrial Genome Evolution
Protein transmembrane domains ( TMDs ) are generally hydrophobic , but our bioinformatics analysis shows that many TMDs contain basic residues at terminal regions . Physiological functions of these membrane-snorkeling basic residues are largely unclear . Here , we show that a membrane-snorkeling Lys residue in integrin...	Integrin αLβ2 is the major integrin in T cells and plays a vital role in regulating T-cell activation , adhesion , and migration . The transmembrane association of αL and β2 is crucial for maintaining the integrin at low-affinity conformation . Here , we find that the conserved basic residue ( K702 ) in the transmembra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "membrane", "proteins", "fluorophotometry", "integrins", "membrane", "receptor", "signaling", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "metho...	2018	Intramembrane ionic protein–lipid interaction regulates integrin structure and function
Leprosy is a chronic infectious disease caused by Mycobacterium Leprae , where the host genetic background plays an important role toward the disease pathogenesis . Various studies have identified a number of human genes in association with leprosy or its clinical forms . However , non-replication of results has hinted...	Leprosy is a chronic granulomatous infection caused by the intracellular organism Mycobacterium leprae . The disease affects the skin and the peripheral nerves and can cause irreversible impairment of the nerve function with consequent chronic disabilities . The prevalence of leprosy has declined dramatically after the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "genetic", "association", "studies", "biology", "human", "genetics" ]	2013	Mapping of PARK2 and PACRG Overlapping Regulatory Region Reveals LD Structure and Functional Variants in Association with Leprosy in Unrelated Indian Population Groups
Chromatin immunoprecipitation coupled with deep sequencing ( ChIP-seq ) has great potential for elucidating transcriptional networks , by measuring genome-wide binding of transcription factors ( TFs ) at high resolution . Despite the precision of these experiments , identification of genes directly regulated by a TF ( ...	Transcription factors ( TFs ) are the main regulators of gene transcription . Thus , knowing the genes that are targeted by a specific TF is of utmost importance for understanding developmental processes , cellular stress response , or disease etiology . Chromatin immunoprecipitation coupled with deep sequencing ( ChIP...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
Mycetoma is a chronic infectious disease of the subcutaneous tissue with a high morbidity . This disease has been reported from countries between 30°N and 15°S since 1840 but the exact burden of disease is not known . It is currently unknown what the incidence , prevalence and the number of reported cases per year per ...	Mycetoma is a chronic infection resulting in large masses of the subcutaneous tissue of mainly the foot . It can be caused by bacteria or fungi . Treatment for most mycetoma cases is poor and amputations are common . Although this disease was already described almost 200 years ago , it is currently not known how many p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Global Burden of Human Mycetoma: A Systematic Review and Meta-analysis
The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors , thus demonstrating that evolutionary changes can have profound implications for population dynamics . At the same time , the relative fitness of cooperative traits often depends upon population density ,...	The fact that rapid evolution within a species can cause dramatic ecological changes has only recently begun to be appreciated . In particular , it has often been assumed that population dynamics , controlled by ecological circumstances such as the presence of predators or disease , occur at such different timescales c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "ecology", "population", "biology", "biology", "evolutionary", "biology" ]	2013	Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations
Infectious diseases are one of the leading causes of morbidity and mortality around the world; thus , forecasting their impact is crucial for planning an effective response strategy . According to the Centers for Disease Control and Prevention ( CDC ) , seasonal influenza affects 5% to 20% of the U . S . population and...	We use modern methods for injecting current data into epidemiological models in order to offer a probabilistic evaluation of the future influenza state in the U . S . population . This type of disease forecasting is still in its infancy , but as these methods become more developed it will allow for increasingly robust ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Forecasting the 2013–2014 Influenza Season Using Wikipedia
Plasmodium malariae is a slow-growing parasite with a wide geographic distribution . Although generally regarded as a benign cause of malaria , it has been associated with nephrotic syndrome , particularly in young children , and can persist in the host for years . Morbidity associated with P . malariae infection has r...	Plasmodium malariae is a relatively rare , but widely distributed , cause of malaria . It can persist in the human host for years , often without causing significant symptoms . As a result , P . malariae will be a very difficult species to eradicate . Our study used data from a routine hospital-based surveillance syste...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Plasmodium malariae Infection Associated with a High Burden of Anemia: A Hospital-Based Surveillance Study
Influenza A ( H3N2 ) offers a well-studied , yet not fully understood , disease in terms of the interactions between pathogen population dynamics , epidemiology and genetics . A major open question is why the virus population is globally dominated by a single and very recently diverged ( 2–8 years ) lineage . Classical...	Influenza A ( H3N2 ) has circulated in the human population since 1968 causing considerable annual morbidity and mortality worldwide . Despite the rapid evolution of the hemagglutinin ( HA ) protein and strong diversifying selection , the global virus population is characterized by a low standing diversity , evident in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "health", "and", "epidemiology", "evolutionary", "ecology", "ecology", "evolutionary", "biology", "virology", "epidemiology", "infectious", "disease", "epidemiology", "biology", "computational", "biology", "microbiology", "population", "biology", "viral", "evoluti...	2013	The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza
Approximately 10 million people are infected with Trypanosoma cruzi , the causative agent of Chagas disease , which remains the most serious parasitic disease in the Americas . Most people are infected via triatomine vectors . Transmission has been largely halted in South America in areas with predominantly domestic ve...	The Chagas disease parasite , transmitted to humans by triatomine bugs , remains a leading cause of heart and digestive disease in Latin America . Pesticide spraying has effectively halted transmission in most of southern South America , especially where the bugs live exclusively inside houses . In Mesoamerica , bugs l...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2009	Two Distinct Triatoma dimidiata (Latreille, 1811) Taxa Are Found in Sympatry in Guatemala and Mexico
Endoplasmic reticulum ( ER ) stress is a condition in which the protein folding capacity of the ER becomes overwhelmed by an increased demand for secretion or by exposure to compounds that disrupt ER homeostasis . In yeast and other fungi , the accumulation of unfolded proteins is detected by the ER-transmembrane senso...	Aspergillus fumigatus is the predominant mold pathogen of humans , responsible for life-threatening infections in patients with depressed immunity . The fungus is highly adapted for secretion , a feature that it uses to extract nutrients from the host environment . High rates of protein secretion can overwhelm the prot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "fungi", "cellular", "stress", "responses", "molecular", "cell", "biology", "cell", "biology", "cell", "growth", "biology", "microbiology", "fungal", "physiology", "pathogenesis" ]	2011	HacA-Independent Functions of the ER Stress Sensor IreA Synergize with the Canonical UPR to Influence Virulence Traits in Aspergillus fumigatus
Zoonotic cutaneous leishmaniasis ( ZCL ) due to Leishmania major is highly prevalent in Tunisia and is transmitted by a hematophagous vector Phlebotomus papatasi ( P . papatasi ) . While probing for a blood meal , the sand fly injects saliva into the host's skin , which contains a variety of compounds that are highly i...	Leishmania is transmitted by female sand flies and deposited during a blood meal together with saliva . Saliva contains a vast repertoire of pharmacologically active molecules that facilitate the acquisition of the blood meal and contribute to the establishment of the infection . These molecules can induce the producti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology", "biology" ]	2012	Salivary Antigen SP32 Is the Immunodominant Target of the Antibody Response to Phlebotomus papatasi Bites in Humans
The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole , and thus its potential suitability as a drug target . Despite the importance of the network environment , it is neglected during target selection for drug discovery . Here ,...	The need for well-validated targets for drug discovery is more pressing than ever , especially in cancer in view of resistance to current therapeutics coupled with late stage drug failures . Target prioritization and selection methodologies have typically not taken the protein interaction environment into account . Her...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Distinctive Behaviors of Druggable Proteins in Cellular Networks
White-nose syndrome ( WNS ) in North American bats is caused by an invasive cutaneous infection by the psychrophilic fungus Pseudogymnoascus destructans ( Pd ) . We compared transcriptome-wide changes in gene expression using RNA-Seq on wing skin tissue from hibernating little brown myotis ( Myotis lucifugus ) with WNS...	White-nose syndrome is the most devastating epizootic wildlife disease of mammals in history , having killed millions of hibernating bats in North America since 2007 . We have used next-generation RNA sequencing to provide a survey of the gene expression changes that accompany this disease in the skin of bats infected ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The White-Nose Syndrome Transcriptome: Activation of Anti-fungal Host Responses in Wing Tissue of Hibernating Little Brown Myotis
Dipteran insects transmit serious diseases to humans , often in the form of trypanosomatid parasites . To accelerate research in more difficult contexts of dipteran-parasite relationships , we studied the interaction of the model dipteran Drosophila melanogaster and its natural trypanosomatid Herpetomonas muscarum . Pa...	Neglected Tropical Diseases are the most common diseases of the world’s poorest people . Many are caused by parasites called trypanosomatids that are transmitted to humans via insects belonging to the order of Diptera ( also known as true flies ) . These flies ( including tsetse , sand flies and black flies ) are diffi...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasitic", "diseases", "animals", "parasitic", "protozoans", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "protozoans", "stem", "cells", "experimental", "organism", "systems", "drosophi...	2019	Intestinal NF-κB and STAT signalling is important for uptake and clearance in a Drosophila-Herpetomonas interaction model
ATP-fuelled molecular motors are responsible for rapid and specific transfer of double-stranded DNA during several fundamental processes , such as cell division , sporulation , bacterial conjugation , and viral DNA transport . A dramatic example of intercompartmental DNA transfer occurs during sporulation in Bacillus s...	Molecular motors are implicated in myriad cellular processes , notably in the transcription , replication , and segregation of DNA . Segregation or packaging of DNA is essential for production of viable viral particles , proper division of bacterial cells , and production of spores . A dramatic example of this process ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "developmental", "biology", "prokaryotic", "models", "model", "organisms", "microbial", "physiology", "nucleic", "acids", "bacillus", "subtilis", "dna", "biology", "microbial", "growth", "and", "development", "microbiology", "biophysics" ]	2013	Recruitment, Assembly, and Molecular Architecture of the SpoIIIE DNA Pump Revealed by Superresolution Microscopy
More than 200 , 000 new cases of leprosy were reported by 105 countries in 2011 . The disease is a public health problem in Brazil , particularly within high-burden pockets in the Amazon region where leprosy is hyperendemic among children . We applied geographic information systems and spatial analysis to determine the...	Leprosy can lead to physical disabilities and deformities if not diagnosed and treated early . Even today , the disease affects more than 200 , 000 people per year , particularly the poorest people from developing countries , such as India , Brazil and Indonesia . Cases among children <15 years old have been used as an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "disease", "mapping", "infectious", "diseases", "infectious", "disease", "epidemiology", "epidemiology", "leprosy", "neglected", "tropical", "diseases", "spatial", "epidemiology" ]	2014	Spatial Analysis Spotlighting Early Childhood Leprosy Transmission in a Hyperendemic Municipality of the Brazilian Amazon Region
An ideal model system to study antiviral immunity and host-pathogen co-evolution would combine a genetically tractable small animal with a virus capable of naturally infecting the host organism . The use of C . elegans as a model to define host-viral interactions has been limited by the lack of viruses known to infect ...	The nematode C . elegans is a robust model organism that is broadly used in biology . It also has great potential for the study of host-microbe interactions , as it is possible to systematically knockout almost every gene in high-throughput fashion to examine the potential role of each gene in infection . While C . ele...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology/environmental", "microbiology", "virology", "virology/animal", "models", "of", "infection", "immunology/innate", "immunity" ]	2011	Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses
Verticillium dahliae is a phytopathogenic fungus obligate in root infection . A few hyphopodia differentiate from large numbers of hyphae after conidia germination on the root surface for further infection . However , the molecular features and role of hyphopodia in the pathogenicity of V . dahliae remain elusive . In ...	Beyond the harmful roles in pathological processes and aging , growing evidence indicates that reactive oxygen species ( ROS ) play a pivotal role in physiological processes , including cell differentiation and development in fungi . Verticillium dahliae Kleb . , a soil-born phytopathogenic fungus , germinates larger n...	[ "Abstract", "Introduction", "Result", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "redox", "signaling", "light", "microscopy", "plasmid", "construction", "membrane", "proteins", "mutation", "confocal", "laser", "microscopy", "microscopy", "confocal", "microscopy", ...	2016	Hyphopodium-Specific VdNoxB/VdPls1-Dependent ROS-Ca2+ Signaling Is Required for Plant Infection by Verticillium dahliae
Measles virus ( MeV ) is dual-tropic: it replicates first in lymphatic tissues and then in epithelial cells . This switch in tropism raises the question of whether , and how , intra-host evolution occurs . Towards addressing this question , we adapted MeV either to lymphocytic ( Granta-519 ) or epithelial ( H358 ) cell...	Key questions in infectious disease are how pathogens adapt to different cells of their hosts , and how the interplay between the virus and host factors controls the outcome of infection . Human measles virus ( MeV ) and related animal morbilliviruses provide important models of pathogenesis because they are dual-tropi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "biological", "cultures", "microbiology", "epithelial", "cells", "viruses", "raji", "cells", "protein", "expression", "rna", "viruses", "molecular", "biology", "techniques", "mammalian", "genomics", "r...	2019	Cyclical adaptation of measles virus quasispecies to epithelial and lymphocytic cells: To V, or not to V
Behavioral states marked by varying levels of arousal and attention modulate some properties of cortical responses ( e . g . average firing rates or pairwise correlations ) , yet it is not fully understood what drives these response changes and how they might affect downstream stimulus decoding . Here we show that chan...	The brain controls behavior fluidly in a wide variety of cognitive contexts that alter the precision of neural responses . We examine how neural variability changes versus the mean response as a function of the stimulus and the behavioral state . We show that this scaled variability can have qualitatively different sti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "anesthesiology", "drugs", "opioids", "social", "sciences", "vertebrates", "neuroscience", "animals", "mammals", "primates", "pharmaceutics", "anesthesia", "analgesics", "vision", "pharmacology", "neuronal", "tuning", "old", "world...	2018	State dependence of stimulus-induced variability tuning in macaque MT
Genes encoding ROOT HAIR DEFECTIVE SIX-LIKE ( RSL ) class I basic helix loop helix proteins are expressed in future root hair cells of the Arabidopsis thaliana root meristem where they positively regulate root hair cell development . Here we show that there are three RSL class I protein coding genes in the Brachypodium...	Root hairs are tubular extensions that extend from specialized cells in the root surface . They take up nutrients and water from the soil and tether the root to its substrate . The differentiation of root hair cells in the cress family is controlled by a group of regulators called RSL class I transcription factors . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "sequencing", "techniques", "plant", "anatomy", "medicine", "and", "health", "sciences", "integumentary", "system", "cell", "cycle", "and", "cell", "division", "cell", "processes", "brassica", "cell", "differentiation", "root", "hairs", "developmental", "biolo...	2016	ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon
Streptococcus agalactiae ( Group B streptococcus , GBS ) is a leading cause of infections in neonates and an emerging pathogen in adults . The Lancefield Group B carbohydrate ( GBC ) is a peptidoglycan-anchored antigen that defines this species as a Group B Streptococcus . Despite earlier immunological and biochemical ...	Streptococcus agalactiae ( Group B Streptococcus ) is a leading cause of sepsis ( blood infection ) and meningitis ( brain infection ) in newborns and in adults with underlying diseases . S . agalactiae is a Gram-positive coccus surrounded by a thick cell wall that acts as an exoskeleton to guarantee resistance to mech...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "streptococci", "biology", "microbiology", "microbial", "growth", "and", "development", "bacterial", "pathogens" ]	2012	Role of the Group B Antigen of Streptococcus agalactiae: A Peptidoglycan-Anchored Polysaccharide Involved in Cell Wall Biogenesis
The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development . Morphological traits result from gene regulatory networks ( GRNs ) that form a web of transcription factors , which regulate multiple cis-regulatory element ( CRE ) sequences to ...	The genomic content of regulatory genes such as transcription factors is surprisingly conserved between diverse animal species , raising the paradox of how new traits emerge , and are subsequently modified and lost . In this study we make a connection between the developmental basis for the formation of a fruit fly tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans
Many filamentous organisms , such as fungi , grow by tip-extension and by forming new branches behind the tips . A similar growth mode occurs in filamentous bacteria , including the genus Streptomyces , although here our mechanistic understanding has been very limited . The Streptomyces protein DivIVA is a critical det...	Amongst the great variety of shapes that organisms assume , many grow in a filamentous manner and develop at least partly into a network of branches . Examples include plant roots , fungi and some bacteria . Whereas the mechanisms of filamentous growth are partially understood in fungi , the same cannot be said in fila...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "theoretical", "biology", "biology", "microbiology", "molecular", "cell", "biology", "biophysics" ]	2012	Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria
Reverse transcriptase ( RT ) is the target for the majority of anti-HIV-1 drugs . As with all anti-AIDS treatments , continued success of RT inhibitors is persistently disrupted by the occurrence of resistance mutations . To explore latent resistance mechanisms potentially accessible to therapeutically challenged HIV-1...	The majority of anti-AIDS drugs target the reverse transcriptase ( RT ) enzyme of the HIV-1 virus . RT catalyzes the central step in the virus replication cycle converting the viral RNA genome into DNA for subsequent integration into the host genome . As with all anti-AIDS treatments , continued success of RT inhibitor...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "enzymology", "dna", "manipulations", "retroviruses", "viruses", "immunodeficiency", "viruses", "d...	2018	The structure of FIV reverse transcriptase and its implications for non-nucleoside inhibitor resistance
Single-neuron models are useful not only for studying the emergent properties of neural circuits in large-scale simulations , but also for extracting and summarizing in a principled way the information contained in electrophysiological recordings . Here we demonstrate that , using a convex optimization procedure we pre...	Large-scale , high-throughput data acquisition is revolutionizing the field of neuroscience . Single-neuron electrophysiology is moving from the situation where a highly skilled experimentalist can patch a few cells per day , to a situation where robots will collect large amounts of data . To take advantage of this qua...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models
The importance of wildlife as reservoirs of African trypanosomes pathogenic to man and livestock is well recognised . While new species of trypanosomes and their variants have been identified in tsetse populations , our knowledge of trypanosome species that are circulating in wildlife populations and their genetic dive...	The trypanosomes include a number of species that cause disease in livestock . In recent years , several trypanosomes have been identified which do not fit into the classic trypanosome classification system . However , previous work has focused on trypanosomes identified in the tsetse vector , with little information a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "protozoan", "classification", "trypanosoma", "genetics", "parasitology", "protozoology", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Trypanosome Diversity in Wildlife Species from the Serengeti and Luangwa Valley Ecosystems
Plant viruses have evolved multiple strategies to overcome host defense to establish an infection . Here , we identified two components of a host mitogen-activated protein kinase ( MAPK ) cascade , MKK2 and MPK4 , as bona fide targets of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China viru...	We identified a plant MAPK cascade that contributes to the defense against geminiviruses . Rapid activation of MAPKs was observed upon geminivirus infection . The βC1 protein of geminivirus betasatellite interacts with MKK2 and MPK4 and inhibits their kinase activity . Also , βC1 suppresses flagellin-induced MAPK activ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "phosphorylation", "plant", "anatomy", "engineering", "and", "technology", "molecular", "probe", "techniques", "brassica", "immunoblotting", "plant", "biotechnology", "plant", "science", "model", "organisms", "genetically", "modified", "plants", "experiment...	2019	βC1 protein encoded in geminivirus satellite concertedly targets MKK2 and MPK4 to counter host defense
Muscle spindle proprioceptive receptors play a primary role in encoding the effects of external mechanical perturbations to the body . During externally-imposed stretches of passive , i . e . electrically-quiescent , muscles , the instantaneous firing rates ( IFRs ) of muscle spindles are associated with characteristic...	Proprioceptive sensory information is essential to movement , particularly in sensorimotor responses to external perturbations to the body–such as a push or bump–whether maintaining the posture of a limb , or during standing balance control . Here we show that rapid increase in resistive force of a passive muscle when ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "velocity", "acceleration", "soleus", "muscles", "medicine", "and", "health", "sciences", "classical", "mechanics", "biomechanics", "bioassays", "and", "physiological", "analysis", "research", "and", "analysis", "methods", "muscle", "analysis", "musculoskeletal", "mechani...	2017	Force encoding in muscle spindles during stretch of passive muscle
Vinyl chloride ( VC ) is a human carcinogen and widespread priority pollutant . Here we report the first , to our knowledge , complete genome sequences of microorganisms able to respire VC , Dehalococcoides sp . strains VS and BAV1 . Notably , the respective VC reductase encoding genes , vcrAB and bvcAB , were found em...	Dehalococcoides are free-living sediment and subsurface bacteria with remarkably small , streamlined genomes and an unusual degree of niche specialization . These strictly anaerobic bacteria gain metabolic energy exclusively through a novel type of respiration that results in reductive elimination of chlorides from org...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "microbiology/microbial", "evolution", "and", "genomics" ]	2009	Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
The endothelial protein C receptor ( EPCR ) enhances anticoagulation by accelerating activation of protein C to activated protein C ( APC ) and mediates anti-inflammatory effects by facilitating APC-mediated signaling via protease activated receptor-1 . We studied the role of EPCR in the host response during pneumonia-...	During pneumonia and sepsis a procoagulant state is observed , with activation of coagulation and downregulation of anticoagulant pathways , both closely interrelated with inflammation . The protein C ( PC ) system is an important anticoagulant pathway implicated in the pathogenesis of sepsis . The rate of conversion o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "models", "medicine", "bacterial", "diseases", "infectious", "diseases", "gram", "negative", "model", "organisms", "burkholderia", "infection", "host-pathogen", "interaction", "biology", "microbiology", "mouse", "bacterial", "pathogens" ]	2013	Overexpression of the Endothelial Protein C Receptor Is Detrimental during Pneumonia-Derived Gram-negative Sepsis (Melioidosis)
To thrive in diverse environments , bacteria must shift their metabolic output in response to nutrient bioavailability . In many bacterial species , such changes in metabolic flux depend upon lipoic acid , a cofactor required for the activity of enzyme complexes involved in glycolysis , the citric acid cycle , glycine ...	Staphylococcus aureus is a predominant cause of infectious diseases ranging from superficial skin and soft tissue infections to necrotizing pneumonia and sepsis . A remarkable aspect of S . aureus pathobiology lies in the ability of the microorganism to infect a wide variety of host tissues . This infectious promiscuit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "lipoic", "acids", "lipoylation", "microbiology", "enzymology", "immunoblotting", "staphylococcus", ...	2016	Staphylococcus aureus Tissue Infection During Sepsis Is Supported by Differential Use of Bacterial or Host-Derived Lipoic Acid
Brucellosis is a world-wide extended zoonosis that causes a grave problem in developing economies . Animal vaccination and diagnosis are essential to control brucellosis , and the need for accurate but also simple and low-cost tests that can be implemented in low-infrastructure laboratories has been emphasized . We eva...	Brucellosis is an important zoonosis of worldwide distribution with a heavy impact wherever domestic livestock are bred , including extensive areas of developing economies . The diagnosis of brucellosis is hampered by the absence of pathognomonic symptoms , and thus accurate laboratory tests are essential . Many serolo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "brucellosis", "mammals", "bacterial", "diseases"...	2019	Comparative performance of lateral flow immunochromatography, iELISA and Rose Bengal tests for the diagnosis of cattle, sheep, goat and swine brucellosis
T cell receptor ( TCR ) recognition of peptide-MHC class I ( pMHC ) complexes is a crucial event in the adaptive immune response to pathogens . Peptide epitopes often display a strong dominance hierarchy , resulting in focusing of the response on a limited number of the most dominant epitopes . Such T cell responses ma...	CD8+ T cells are essential for host defense to many intracellular pathogens . The CD8+ T cell receptor ( TCR ) detects small peptide fragments presented at the surface of infected cells . These peptide epitopes are bound by major histocompatibility complex ( MHC ) molecules . Such T cell responses are often inexplicabl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition", "biochemistry/protein", "chemistry", "immunology/genetics", "of", "the", "immune", "system", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2010	MHC Class I Bound to an Immunodominant Theileria parva Epitope Demonstrates Unconventional Presentation to T Cell Receptors
Coordination of fetal maturation with birth timing is essential for mammalian reproduction . In humans , preterm birth is a disorder of profound global health significance . The signals initiating parturition in humans have remained elusive , due to divergence in physiological mechanisms between humans and model organi...	The control of birth timing in humans is the greatest unresolved question in reproductive biology , and preterm birth is the most important medical issue in maternal and child health . To begin to address this critical problem , we test the hypothesis that genes accelerated in their rate of evolution in humans , as com...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/comparative", "genomics" ]	2011	An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing
Apicomplexan parasites are auxotrophic for a range of amino acids which must be salvaged from their host cells , either through direct uptake or degradation of host proteins . Here , we describe a family of plasma membrane-localized amino acid transporters , termed the Apicomplexan Amino acid Transporters ( ApiATs ) , ...	The Apicomplexa comprise a large number of parasitic protozoa that have obligate intracellular lifestyles and cause significant human and animal diseases , including malaria , cryptosporidiosis , toxoplasmosis , coccidiosis in poultry , and various cattle fevers . Apicomplexans must scavenge essential nutrients from th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "toxoplasma", "gondii", "vertebrates", "parasitic", "diseases", "parasitic", "protozoans", "animals", "parasitology", "xenopus", "germ", "cells", "membrane", "proteins", "animal", "models", "developmental", ...	2019	The tyrosine transporter of Toxoplasma gondii is a member of the newly defined apicomplexan amino acid transporter (ApiAT) family
Trypanosomatid parasites represent a major health issue affecting hundreds of million people worldwide , with clinical treatments that are partially effective and/or very toxic . They are responsible for serious human and plant diseases including Trypanosoma cruzi ( Chagas disease ) , Trypanosoma brucei ( Sleeping sick...	In this work , we show that riboflavin plays a key role in the trypanosomatid life cycles and describe a novel family of riboflavin transporters ( RibJ ) with uptake function . Despite the vital importance of riboflavin for all living cells , RibJ are the first transporters described in protists . We functionally chara...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "b", "vitamins", "taxonomy", "medicine", "and", "health", "sciences", "chemical", "compounds", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "organic", "compounds", "protozoan", "life", "cycles", "developmental", "biology", "riboflavin", "flavin", ...	2017	The superfamily keeps growing: Identification in trypanosomatids of RibJ, the first riboflavin transporter family in protists
An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes , but rather in functional neighborhoods . Nevertheless , the driving force that originated and maintains such neighborhoods is still a matter of controversy . We present the first detailed multispecies cartogra...	We describe here the most extensive functional cartography of the genomes of multiple species carried out to date . Our study shows , for the first time , how neighborhoods of functionally related genes arise and how they are maintained through evolution following a pattern that is fully consistent with the evolutionar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/comparative", "sequence", "analysis", "evolutionary", "biology/bioinformatics", "evolutionary", "biology/genomics" ]	2010	Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes
Fanconi anemia ( FA ) is a devastating genetic disease , associated with genomic instability and defects in DNA interstrand cross-link ( ICL ) repair . The FA repair pathway is not thought to be conserved in budding yeast , and although the yeast Mph1 helicase is a putative homolog of human FANCM , yeast cells disrupte...	Individuals with Fanconi anemia ( FA ) suffer from bone marrow failure and from elevated rates of haematological and solid malignancy . Moreover , FA patients exhibit extreme sensitivity to DNA interstrand cross-links ( ICLs ) , but not other forms of DNA damage . Despite recent progress in identifying and characterisi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "nucleic", "acids", "basic", "cancer", "research", "dna", "recombination", "dna", "biology", "molecular", "cell", "biology", "dna", "repair", "molecular", "biology" ]	2012	Components of a Fanconi-Like Pathway Control Pso2-Independent DNA Interstrand Crosslink Repair in Yeast
Seasonal epidemics of bacterial meningitis in the African Meningitis Belt carry a high burden of disease and mortality . Reactive mass vaccination is used as a control measure during epidemics , but the time taken to gain immunity from the vaccine reduces the flexibility and effectiveness of these campaigns . Targeted ...	Until a low-cost polyvalent conjugate meningococcal vaccine becomes available in the African Meningitis Belt , reactive strategies to control meningitis epidemics should be considered and tested , and refined in order to maximise effectiveness . A recent cluster-randomised trial conducted in Niger showed promising evid...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "niger", "pathogens", "immunology", "geographical", "locations", "microbiology", "spatial", "epidemiology", "preventive", "medicine", "bacterial", "diseases", ...	2019	Analysis of a meningococcal meningitis outbreak in Niger – potential effectiveness of reactive prophylaxis
The residue composition of a ligand binding site determines the interactions available for diffusion-mediated ligand binding , and understanding general composition of these sites is of great importance if we are to gain insight into the functional diversity of the proteome . Many structure-based drug design methods ut...	Describing the general structure of protein binding sites is fundamentally important for guiding drug design and better understanding structure-function relationships . Here , we analyze small molecules bound to proteins within our large database , Binding MOAD ( Mother of All Databases , pronounced like “mode” as a pu...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale
Mitral cells ( MCs ) of the mammalian olfactory bulb have a single primary dendrite extending into a single glomerulus , where they receive odor information from olfactory sensory neurons ( OSNs ) . Molecular mechanisms for controlling dendritic arbors of MCs , which dynamically change during development , are largely ...	Olfactory circuits are critical for the survival of many animals . Odor information is transmitted from olfactory sensory neurons ( OSNs ) to relay neurons , the morphology of which is crucial for processing of the information and similar among species . The major relay neurons , mitral cells ( MCs ) in mammals and pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "brain", "vertebrates", "mice", "neuroscience", "animals", "notch", "signaling", "mammals", "developmental", "biology", "luminescent", "proteins", "yellow", "fluorescent", "protein", "amniotes", "nerve", "fibers", "embryos", "neu...	2016	Olfactory Sensory Neurons Control Dendritic Complexity of Mitral Cells via Notch Signaling
Enterovirus 71 ( EV71 ) is the most virulent pathogen among enteroviruses that cause hand , foot and mouth disease in children but rarely in adults . The mechanisms that determine the age-dependent susceptibility remain largely unclear . Here , we found that the paucity of invariant natural killer T ( iNKT ) cells toge...	Enterovirus 71 ( EV71 ) is a major causative pathogen of hand , foot and mouth disease . EV71 infection occurs mainly in children but rarely in adults . The factors that determine the susceptibility of children to EV71 infection remain elusive . Here , we found that the paucity of invariant natural killer T ( iNKT ) ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TLR3 Signaling in Macrophages Is Indispensable for the Protective Immunity of Invariant Natural Killer T Cells against Enterovirus 71 Infection
Chikungunya virus ( CHIKV ) entered Brazil in 2014 , causing a large outbreak in Feira de Santana , state of Bahia . Although cases have been recorded in Salvador , the capital of Bahia , located ~100 km of Feira de Santana , CHIKV transmission has not been perceived to occur epidemically , largely contrasting with the...	Since 2014 , Brazil has experienced simultaneous transmission of dengue ( DENV ) , chikungunya ( CHIKV ) and Zika virus ( ZIKV ) , hampering clinical differentiation of infections due to the close manifestations caused by these viruses . Salvador , Brazil’s third largest city , was one of the cities most affected by th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "a...	2017	Unrecognized Emergence of Chikungunya Virus during a Zika Virus Outbreak in Salvador, Brazil
Pinpointing the small number of causal variants among the abundant naturally occurring genetic variation is a difficult challenge , but a crucial one for understanding precise molecular mechanisms of disease and follow-up functional studies . We propose and investigate two complementary statistical approaches for ident...	Sequencing technologies allow identification of genetic variants down to single base resolution for a whole human genome . The vast majority of these variants ( over 90% ) are rare , with population frequencies less than 1% . Furthermore , in a specific study , many of the variants identified are not associated with th...	[ "Abstract", "Introduction", "Methods", "Results", "Effect", "size", "estimation", "for", "variants", "in", "the", "hierarchical", "model", "Application", "to", "the", "Dallas", "Heart", "Study", "and", "Application", "to", "the", "Cohen", "syndrome", "and", "Discu...	[ "mathematical", "and", "statistical", "techniques", "computational", "techniques", "research", "and", "analysis", "methods" ]	2014	Identification of Rare Causal Variants in Sequence-Based Studies: Methods and Applications to VPS13B, a Gene Involved in Cohen Syndrome and Autism
Networks of specific inhibitory interneurons regulate principal cell firing in several forms of neocortical activity . Fast-spiking ( FS ) interneurons are potently self-inhibited by GABAergic autaptic transmission , allowing them to precisely control their own firing dynamics and timing . Here we show that in FS inter...	In the cerebral cortex ( neocortex ) of the brain , fast-spiking ( FS ) inhibitory cells contact many principal pyramidal ( P ) neurons on their cell bodies , which allows the FS cells to control the generation of action potentials ( neuronal output ) . FS-cell-mediated rhythmic and synchronous inhibition drives cohere...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "neuroscience/neuronal", "and", "glial", "cell", "biology", "neuroscience/sensory", "systems", "neuroscience/neuronal", "signaling", "mechanisms" ]	2010	Desynchronization of Neocortical Networks by Asynchronous Release of GABA at Autaptic and Synaptic Contacts from Fast-Spiking Interneurons
Sleep fragmentation , particularly reduced and interrupted night sleep , impairs the quality of life of older people . Strikingly similar declines in sleep quality are seen during ageing in laboratory animals , including the fruit fly Drosophila . We investigated whether reduced activity of the nutrient- and stress-sen...	Sleep is essential for human health , but the quality of this fundamental physiological process declines with age and reduces quality of life . We therefore investigated the mechanisms by which ageing impairs sleep . We used the fruit fly Drosophila , whose sleep has many features in common with that of humans , includ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "behavioral", "neuroscience", "medicine", "and", "health", "sciences", "model", "organisms", "cell", "biology", "neurology", "biology", "and", "life", "sciences", "molecular", "cell", "biology", "neuroscience", "sleep", "disorders", "research", "an...	2014	Lowered Insulin Signalling Ameliorates Age-Related Sleep Fragmentation in Drosophila
Iron sulfur ( Fe/S ) proteins are ubiquitous and participate in multiple biological processes , from photosynthesis to DNA repair . Iron and sulfur are highly reactive chemical species , and the mechanisms allowing the multiprotein systems ISC and SUF to assist Fe/S cluster formation in vivo have attracted considerable...	Iron sulfur ( Fe/S ) proteins are found in all living organisms where they participate in a wide array of biological processes . Accordingly , genetic defects in Fe/S biogenesis yield pleiotropic phenotypes in bacteria and several syndromes in humans . Multiprotein systems that assist Fe/S cluster formation and inserti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "microbiology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/genomics", "chemical", "biology/bioinorganic", "chemistry", "microbiology/microbial", "physiology", "and", "metabolism", "molecular", "biology...	2009	Iron-Sulfur (Fe/S) Protein Biogenesis: Phylogenomic and Genetic Studies of A-Type Carriers
Development of antiviral drugs that have broad-spectrum activity against a number of viral infections would be of significant benefit . Due to the evolution of resistance to currently licensed antiviral drugs , development of novel anti-influenza drugs is in progress , including Favipiravir ( T-705 ) , which is current...	Broad-spectrum antiviral drugs are preferred because they have the capacity to treat a range of viral illnesses rather than just one . Food and Drug Administration ( FDA ) approval of antiviral drugs to treat neglected tropical diseases is difficult to obtain due to ethical and logistical considerations when conducting...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "viral", "hemorrhagic", "fevers", "rift", "valley", "fever", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "pathology", "and", "laboratory", "medicine", "virology", "neglect...	2014	Broad Spectrum Antiviral Activity of Favipiravir (T-705): Protection from Highly Lethal Inhalational Rift Valley Fever
Peroxiredoxins ( Prxs ) constitute a family of thiol-specific peroxidases that utilize cysteine ( Cys ) as the primary site of oxidation during the reduction of peroxides . To gain more insight into the physiological role of the five Prxs in budding yeast Saccharomyces cerevisiae , we performed a comparative study and ...	Aerobically growing cells are continuously challenged by potent oxidants produced during normal cellular metabolism . These oxidants , including hydrogen peroxide and organic peroxides , are important components mediating various cell functions . However , they can also cause cell damage when present at toxic levels . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2009	Peroxiredoxin Tsa1 Is the Key Peroxidase Suppressing Genome Instability and Protecting against Cell Death in Saccharomyces cerevisiae
With the increasing amount of data made available in the chemical field , there is a strong need for systems capable of comparing and classifying chemical compounds in an efficient and effective way . The best approaches existing today are based on the structure-activity relationship premise , which states that biologi...	Among the existing systems capable of computationally comparing chemical compounds , the majority use only structural and physicochemical properties . However , with the emergence of ChEBI and other chemical compound databases , it has become feasible to create a system that can use the relevance of compounds in a biol...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/bio-ontology", "biochemistry/bioinformatics" ]	2010	Semantic Similarity for Automatic Classification of Chemical Compounds
Mycobacterium ulcerans infection causes a neglected tropical disease known as Buruli ulcer that is now found in poor rural areas of West Africa in numbers that sometimes exceed those reported for another significant mycobacterial disease , leprosy , caused by M . leprae . Unique among mycobacterial diseases , M . ulcer...	Mycobacterium ulcerans infection causes Buruli ulcer ( BU ) , a disfiguring skin disease now found principally in poor rural areas of West Africa . M . ulcerans produces a toxin called mycolactone ( ML ) , which destroys fat cells in skin tissue . BU typically first shows as a nodule that eventually ulcerates . The les...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "cytokines", "immunology", "microbiology", "bacterial", "diseases", "histology", "model", "organisms", "skin", "infections", "global", "health", "neglected", "tropical", "diseases", "infectious", "diseases", "buruli", "ulcer", "mycobacterium", "biology", "immu...	2013	Microbiological, Histological, Immunological, and Toxin Response to Antibiotic Treatment in the Mouse Model of Mycobacterium ulcerans Disease
Huntington's disease ( HD ) is a progressive neurodegenerative disorder caused by expansion of an unstable CAG repeat in the coding sequence of the Huntingtin ( HTT ) gene . Instability affects both germline and somatic cells . Somatic instability increases with age and is tissue-specific . In particular , the CAG repe...	Huntington's disease ( HD ) is a neurodegenerative disorder that belongs to a family of genetic diseases caused by abnormal expansion of CAG/CTG repetitive sequences . The instability of trinucleotide repeat expansions in germline and somatic cells has deleterious clinical consequences in HD . For instance , transmissi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/animal", "genetics", "molecular", "biology/dna", "repair", "neurological", "disorders/movement", "disorders" ]	2009	Stoichiometry of Base Excision Repair Proteins Correlates with Increased Somatic CAG Instability in Striatum over Cerebellum in Huntington's Disease Transgenic Mice
Photoperiod is one of the most reliable environmental cues for plants to regulate flowering timing . In Arabidopsis thaliana , CONSTANS ( CO ) transcription factor plays a central role in regulating photoperiodic flowering . In contrast to posttranslational regulation of CO protein , still little was known about CO tra...	For plant adaptation to seasonal environments , a crucial developmental event is flowering , as proper timing of flowering affects reproductive success . Although plants monitor various environmental parameters to optimize this timing , photoperiod information is important for plants to regulate seasonal flowering time...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "gene", "regulation", "regulatory", "proteins", "brassica", "dna-binding", "proteins", "cloning", "vector", "cloning", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "transcription", "factors", "molecular", "biology", ...	2017	TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis
Several models have been employed to study human postural control during upright quiet stance . Most have adopted an inverted pendulum approximation to the standing human and theoretical models to account for the neural feedback necessary to keep balance . The present study adds to the previous efforts in focusing more...	The control of upright stance is a challenging task since the objective is to maintain the equilibrium of an intrinsically unstable biomechanical system . Somatosensory information is used by the central nervous system to modulate muscle contraction , which prevents the body from falling . While the visual and vestibul...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "bioengineering", "neuroscience", "somatosensory", "system", "reflexes", "anatomy", "engineering", "and", "technology", "computational", "neuroscience", "nervous", "system", "biology", "and", "life", "sciences", "sensory", "systems", "computational", "biolo...	2014	Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model
In recent years , the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically . However , it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels , due to...	Reciprocal crosstalk between metabolism and cellular signaling pathways plays a crucial role in cellular decision-making . In recent years , this premise has motivated several metabolomics studies that aimed to gain a mechanistic understanding of metabolic phenotypes . However , due to complex interactions within metab...	[ "Abstract", "Introduction", "Design", "and", "implementation", "of", "the", "MNS", "algorithm", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "enzymes", "metabolic", "networks", "enzymology", "metabolomics", "metabolites", "network", "analysis", "enzyme", "metabolism", "pharmacology", "molecular", "biology", "techniques", "drug", "metabolism", "enzyme", "chemistry", "res...	2017	Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data
Systemic dimorphic fungi cause more than one million new infections each year , ranking them among the significant public health challenges currently encountered . Penicillium marneffei is a systemic dimorphic fungus endemic to Southeast Asia . The temperature-dependent dimorphic phase transition between mycelium and y...	Penicillium marneffei is a significant dimorphic fungal pathogen capable of causing lethal systemic infections . It grows in a yeast-like form at mammalian body temperature and a mold-like form at ambient temperature . The thermal dimorphism of P . marneffei is closely related to its virulence . In the present study , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "next-generation", "sequencing", "genome", "expression", "analysis", "fungal", "genomics", "mycology", "genomics", "fungal", "genomes", "penicillium", "marneffei", "medical", "microbiology", "genome", "analysis", "fungal", "genetics", "transcriptome", "analysis", "genome", ...	2014	Signature Gene Expression Reveals Novel Clues to the Molecular Mechanisms of Dimorphic Transition in Penicillium marneffei
Hepatitis C virus ( HCV ) is transmitted between hepatocytes via classical cell entry but also uses direct cell-cell transfer to infect neighboring hepatocytes . Viral cell-cell transmission has been shown to play an important role in viral persistence allowing evasion from neutralizing antibodies . In contrast , the r...	In spite of the rapid development of antiviral agents , antiviral resistance remains a challenge for the treatment of viral infections including hepatitis B and C virus ( HBV , HCV ) , human immunodeficiency virus ( HIV ) and influenza . Virus spreads from infected cells to surrounding uninfected host cells to develop ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "hepatitis", "c", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "infectious", "hepatitis", "hepatitis", "rna", "viruses", "gastroenterology", "and", "hepatology", "viral", "classification", "virology", "biology", "and", "life", "sciences"...	2014	Hepatitis C Virus Cell-Cell Transmission and Resistance to Direct-Acting Antiviral Agents
During vertebrate axis extension , adjacent tissue layers undergo profound morphological changes: within the neuroepithelium , neural tube closure and neural crest formation are occurring , while within the paraxial mesoderm somites are segmenting from the presomitic mesoderm ( PSM ) . Little is known about the signals...	During embryological development , the vertebrate embryo undergoes profound growth in a head-to-tail direction . During this process , formation of different structures within adjacent tissue layers must occur in a coordinated fashion . Insights into how these adjacent tissues molecularly communicate with each other is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "neural", "tube", "defects", "cell", "processes", "neuroscience", "somites", "developmental", "biology", "animal", "anatomy", "organism", "development", "stem", "cells", "embryos", "zoology", "morphogenesis", "...	2016	An FGF3-BMP Signaling Axis Regulates Caudal Neural Tube Closure, Neural Crest Specification and Anterior-Posterior Axis Extension
The natural killer cell receptor NKG2D activates NK cells by engaging one of several ligands ( NKG2DLs ) belonging to either the MIC or ULBP families . Human cytomegalovirus ( HCMV ) UL16 and UL142 counteract this activation by retaining NKG2DLs and US18 and US20 act via lysomal degradation but the importance of NK cel...	Natural killer ( NK ) cells are an important subset of the innate immune system that rapidly responds to cellular transformation and infection . The importance of NK cell control of viral infection is dramatically illustrated by our results revealing that cytomegalovirus ( CMV ) is unable to establish infections in hea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cytomegalovirus", "infection", "fibroblasts", "immunoprecipitation", "connective", "tissue", "cells", "cytotoxic", "t", "cells", "research", "and", "analysi...	2016	Natural Killer Cell Evasion Is Essential for Infection by Rhesus Cytomegalovirus
HIV-1 variants resistant to small molecule CCR5 inhibitors recognize the inhibitor-CCR5 complex , while also interacting with free CCR5 . The most common genetic route to resistance involves sequence changes in the gp120 V3 region , a pathway followed when the primary isolate CC1/85 was cultured with the AD101 inhibito...	Human immunodeficiency virus type 1 ( HIV-1 ) is the causative agent of AIDS . HIV-1 entry into target cells is triggered by the interaction of the viral envelope glycoproteins with a cell-surface receptor ( CD4 ) and a co-receptor ( CCR5 ) , and culminates in fusion of the viral and cell membranes . Small molecule inh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance", "infectious", "diseases/hiv", "infection", "and", "aids", "microbiology/medical", "microbiology", "virology/host", "invasion", "and", "cell", "entry" ]	2009	Two HIV-1 Variants Resistant to Small Molecule CCR5 Inhibitors Differ in How They Use CCR5 for Entry
Drosophila Argonaute2 ( AGO2 ) has been shown to regulate expression of certain loci in an RNA interference ( RNAi ) -independent manner , but its genome-wide function on chromatin remains unknown . Here , we identified the nuclear scaffolding protein LaminB as a novel interactor of AGO2 . When either AGO2 or LaminB ar...	Argonaute proteins are an evolutionarily conserved protein family engaged in gene silencing . The key RNA interference ( RNAi ) pathway protein AGO2 interacts with small RNAs to regulate gene silencing in the cytoplasm . In addition , AGO2 has been shown to regulate gene expression by functioning in the nucleus . In th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "meiosis", "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "transcription", "reproductive", "physiology", "epigenetics", "molecular"...	2018	Argonaute2 and LaminB modulate gene expression by controlling chromatin topology
We show that the cyclin-dependent kinase inhibitor 1B ( CDKN1B ) /p27 , previously known as a cell cycle inhibitor , is also localized within mitochondria . The migratory capacity of endothelial cells , which need intact mitochondria , is completely dependent on mitochondrial p27 . Mitochondrial p27 improves mitochondr...	The protein p27 is a nuclear cell cycle inhibitor that can be shuttled to the cytoplasm to inactivate its inhibitory role , and this mechanism is thought to be used by cancer cells to unlock cell cycle arrest . Recent reports , however , have shown that p27 has other roles independent of cell cycle regulation , and it ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "caffeine", "cell", "motility", "alkaloids", "medicine", "and", "health", "sciences", "chemical", "compounds", "molecular", "probe", "techniques", "cardiovascular", "anatomy", "endothelial", "cells", "immunoblotting", "fibroblasts", "epithelial", "cells", "developmental", ...	2018	CDKN1B/p27 is localized in mitochondria and improves respiration-dependent processes in the cardiovascular system—New mode of action for caffeine
The filarial nematode Mansonella perstans is endemic throughout Africa , northern South America and the Caribbean . Interestingly , M . perstans-infected individuals present no distinct clinical picture associated with certain pathology . Due to its relatively silent nature , research on this tropical disease has been ...	Although there are approximately 114 million infected people with Mansonella perstans , there is a paucity of information about how this filarial nematode affects the host's immune system . M . perstans currently poses a potential risk to 581 million people throughout Africa and for many years infections were considere...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "cytokines", "immune", "cells", "onchocerca", "volvulus", "helminths", "immunology", "animals", "onchocerca", "development...	2018	Mansonella perstans microfilaremic individuals are characterized by enhanced type 2 helper T and regulatory T and B cell subsets and dampened systemic innate and adaptive immune responses
Cells must coordinate DNA replication with cell division , especially during episodes of DNA damage . The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the transcriptional repressor LexA induces a division inhibitor . However , in Caulobacter crescentus ...	Cells have evolved sophisticated mechanisms for repairing their DNA and maintaining genome integrity . A critical aspect of the repair process is an arrest of cell cycle progression , thereby ensuring that cell division is not attempted before the genome has been repaired and fully duplicated . Our paper explores the m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biology", "and", "life", "sciences", "microbiology" ]	2014	A DNA Damage-Induced, SOS-Independent Checkpoint Regulates Cell Division in Caulobacter crescentus
The availability of epidemiological data in the early stages of an outbreak of an infectious disease is vital for modelers to make accurate predictions regarding the likely spread of disease and preferred intervention strategies . However , in some countries , the necessary demographic data are only available at an agg...	Mathematical models of infectious diseases are increasingly used to inform policy decisions . The advantages of such models are that multiple control options can be rapidly tested and compared , without the risks and costs associated with field experiments . However , for such models to be practically useful tools deta...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science", "mathematical", "computing", "geography", "computer", "modeling", "mathematics", "social", "and", "behavioral", "sciences", "theoretical", "biology", "veterinary", "diseases", "veterinary", "epidemiology", "applied", "mathematics", "biology", "computa...	2012	Disease Prevention versus Data Privacy: Using Landcover Maps to Inform Spatial Epidemic Models
Deficits in prepulse inhibition ( PPI ) are a biological marker for schizophrenia . To unravel the mechanisms that control PPI , we performed quantitative trait loci ( QTL ) analysis on 1 , 010 F2 mice derived by crossing C57BL/6 ( B6 ) animals that show high PPI with C3H/He ( C3 ) animals that show low PPI . We detect...	A startle response to an unexpected , strong startling stimulus can be suppressed by an immediately preceding low-intensity stimulus , thereby eliciting little behavioral response . This phenomenon , called prepulse inhibition ( PPI ) , has been observed in all mammals tested and is thought to reflect sensory-motor gat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mental", "health", "neuroscience", "genetics", "and", "genomics" ]	2007	Fabp7 Maps to a Quantitative Trait Locus for a Schizophrenia Endophenotype
Following myonecrosis , muscle satellite cells proliferate , differentiate and fuse , creating new myofibers . The Runx1 transcription factor is not expressed in naïve developing muscle or in adult muscle tissue . However , it is highly expressed in muscles exposed to myopathic damage yet , the role of Runx1 in muscle ...	In response to muscle injury , the muscle initiates a repair process that calls for the proliferation of muscle stem cells , which differentiate and fuse to create the myofibers that regenerate the tissue . Maintaining the balance between myoblast proliferation and differentiation is crucial for proper regeneration , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites . Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing . We analyzed by NGS technology the mitochondrial g...	U-insertion/deletion RNA editing is a unique post-transcriptional mRNA modification process that occurs in trypanosomatid parasites and is required for viability . The participation of guide RNAs which are transcribed from the thousands of catenated minicircles in determining the precise sites and number of U’s inserte...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae
Infection of plants by bacterial leaf pathogens at wound sites is common in nature . Plants defend wound sites to prevent pathogen invasion , but several pathogens can overcome spatial restriction and enter leaf tissues . The molecular mechanisms used by pathogens to suppress containment at wound infection sites are po...	Bacterial plant pathogens are usually contained at wound infection sites by an effective immune response . The ways in which bacteria can overcome this spatial restriction is poorly understood . Here , we studied two Pseudomonas syringae pv . syringae strains that cause brown spot on bean and blossom blight on pear and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "science", "plant", "biology", "plant", "pathogens", "plant", "pathology", "biology" ]	2013	Pseudomonas syringae pv. syringae Uses Proteasome Inhibitor Syringolin A to Colonize from Wound Infection Sites
Cell-surface receptors are the most common target for therapeutic drugs . The design and optimization of next generation synthetic drugs require a detailed understanding of the interaction with their corresponding receptors . Mathematical approximations to study ligand-receptor systems based on reaction kinetics strong...	The current importance of cell surface receptors as primary targets for drug treatment explains the increasing interest in a mathematical and quantitative description of the process of ligand-receptor interaction . Recently , a new generation of synthetic chimeric ligands has been developed to selectively target unheal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
Leprosy remains an important public health problem in Brazil where 28 , 761 new cases were diagnosed in 2015 , the second highest number of new cases detected globally . The disease is caused by Mycobacterium leprae , a pathogen spread by patients with multibacillary ( MB ) leprosy . This study was designed to identify...	Leprosy is caused by Mycobacterium leprae , a bacillus transmitted by patients with multibacillary ( MB ) disease . Men and elderly are more likely to have MB leprosy , which has been attributed to an increased exposure to infection by male sex , decreased access of men to healthcare resulting in delayed diagnosis and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "disabilities", "elderly", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "age", "groups", "neglected", "tropical", "diseases", "infectious", "disease", "control", "bacteria...	2017	Multibacillary leprosy by population groups in Brazil: Lessons from an observational study
Optic cups are a structural feature of diverse eyes , from simple pit eyes to camera eyes of vertebrates and cephalopods . We used the planarian prototypic eye as a model to study the genetic control of optic cup formation and regeneration . We identified two genes encoding transcription factors , sp6-9 and dlx , that ...	Some invertebrates , such as planarians and Hydra , can regenerate fully after amputations that remove large parts of the body . We investigated how cells in the body of planarians provide new cells for eye regeneration after complete head removal . Planarians possess highly potent regenerative cells ( neoblasts ) in a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "biology", "evolutionary", "biology" ]	2011	dlx and sp6-9 Control Optic Cup Regeneration in a Prototypic Eye
Although it has recently been shown that A/J mice are highly susceptible to Staphylococcus aureus sepsis as compared to C57BL/6J , the specific genes responsible for this differential phenotype are unknown . Using chromosome substitution strains ( CSS ) , we found that loci on chromosomes 8 , 11 , and 18 influence susc...	Staphylococcus aureus has a wide spectrum of human infection , ranging from asymptomatic nasal carriage to overwhelming sepsis and death . Mouse models offer an attractive strategy for investigating complex diseases such as S . aureus infections . A/J mice are highly susceptible to S . aureus infection compared with C5...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/genetics", "of", "disease", "pathology/immunology", "genetics", "and", ...	2010	Two Genes on A/J Chromosome 18 Are Associated with Susceptibility to Staphylococcus aureus Infection by Combined Microarray and QTL Analyses
Wnt and Netrin signaling regulate diverse essential functions . Using a genetic approach combined with temporal gene expression analysis , we found a regulatory link between the Wnt receptor MOM-5/Frizzled and the UNC-6/Netrin receptor UNC-5 . These two receptors play key roles in guiding cell and axon migrations , inc...	Cells are exposed to a multitude of environmental cues that are often eliciting additive , overlapping , or even conflicting inputs . How the information from multiple extracellular cues is integrated within the cell to generate distinct patterning is largely unknown . Netrin and Wnt signaling pathways are critical to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Wnt Frizzled Receptor MOM-5 Regulates the UNC-5 Netrin Receptor through Small GTPase-Dependent Signaling to Determine the Polarity of Migrating Cells
Multiple Sclerosis ( MS ) is a chronic inflammatory demyelinating disease of the central nervous system . The risk of developing MS is strongly influenced by genetic predisposition , and over 100 loci have been established as associated with susceptibility . However , the biologically relevant variants underlying disea...	Multiple sclerosis ( MS ) is the most common neurological disease of young Caucasian adults . Oligodendrocytes are the key cell type damaged in MS , a process that is accompanied by loss of the myelin sheath that these cells produce , resulting in demyelination and ultimately in secondary damage to nerve cells . Suscep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "multiple", "sclerosis", "neurodegenerative", "diseases", "immunology", "population", "genetics", "variant", "genotypes", "alleles", "genetic", "mapping", "demyelinat...	2016	Common and Low Frequency Variants in MERTK Are Independently Associated with Multiple Sclerosis Susceptibility with Discordant Association Dependent upon HLA-DRB1*15:01 Status
Neurons in the brain are known to operate under a careful balance of excitation and inhibition , which maintains neural microcircuits within the proper operational range . How this balance is played out at the mesoscopic level of neuronal populations is , however , less clear . In order to address this issue , here we ...	One of the salient characteristics of neurons is their ability to either excite or inhibit other neurons , depending on the type of neurotransmitter they use to act upon them . In fact , a careful balance between excitation and inhibition is required for the brain to operate in a sustained state , away from both epilep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model
The HIV transactivator protein , Tat , enhances HIV transcription by recruiting P-TEFb from the inactive 7SK snRNP complex and directing it to proviral elongation complexes . To test the hypothesis that T-cell receptor ( TCR ) signaling induces critical post-translational modifications leading to enhanced interactions ...	The release of the transcription elongation factor P-TEFb from the 7SK RNP complex and its binding to the HIV Tat transactivator protein enables the efficient transcription of HIV proviruses . In resting memory T-cells , which carry the bulk of the latent HIV viral pool , limiting the cellular levels of P-TEFb ensures ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mitogenic", "signaling", "enzymes", "microbiology", "dna", "transcription", "immunodeficiency", "viruses", "rna", "synthesis", "signaling", "in", "cellular", "processes", "transcriptional", "signaling", "enzyme", "regulation", "gene", "expression", "nuclear", "signaling", ...	2013	Phosphorylation of CDK9 at Ser175 Enhances HIV Transcription and Is a Marker of Activated P-TEFb in CD4+ T Lymphocytes
Zhongshan City of Guangdong Province ( China ) is a key provincial and national level area for dengue fever prevention and control . The aim of this study is to analyze how the direct hospitalization costs and the length of stay of dengue hospitalization cases vary according to associated factors such as the demographi...	There is little literature estimating dengue disease burdens and treatment costs worldwide; however , still fewer studies focus on the hospitalization cost of Dengue . Using the quantile regression method to analyze the administrative data of 1 , 432 confirmed dengue inpatients in Zhongshan City ( Guangdong , China ) d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "hospitalizations", "medicine", "and", "health", "sciences", "demography", "china", "tropical", "diseases", "geographical", "locations", "pediatrics", "health", "care", "epidemiological", "methods", "and", "statistics", "neglected", "tropical", "diseases", "infectious", "...	2017	Direct cost of dengue hospitalization in Zhongshan, China: Associations with demographics, virus types and hospital accreditation
Feeding , a vital behavior in animals , is modulated depending on internal and external factors . In the nematode Caenorhabditis elegans , the feeding organ called the pharynx ingests food by pumping driven by the pharyngeal muscles . Here we report that optical silencing of the body wall muscles , which drive the loco...	Since feeding is an essential behavior for the survival of animals , it is modulated by a variety of neural and neuroendocrine signals that are generated depending on internal and external conditions . To elucidate the cellular and molecular mechanisms underlying the regulation of feeding , the nematode Caenorhabditis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "muscle", "tissue", "caenorhabditis", "pharyngeal", "muscles", "neuroscience", "biological", "locomotion", "animals", "animal", "models", "signal", "inhibition", "caenorhabditis", "elegans", "respiratory", "system", ...	2017	Optical silencing of body wall muscles induces pumping inhibition in Caenorhabditis elegans
Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution . In principle , mutation and evolutionary rates for neutral regions of the same species are expected to be equal . However , a number of recent studies have shown that mutation rates estimated from pedigree materi...	Molecular evolutionary theory suggests that for neutral DNA sequences , rates of mutation and evolution should be equal . However , there has been considerable variation in empirical estimates of rates of molecular change in vertebrate animals , even for the same regions of the mitochondrial genome . A difficulty is th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/animal", "genetics", "genetics", "and", "genomics/animal", "genetics", "molecular", "biology/molecular", "evolution", "evolutionary", "biology/genomics", "evolutionary", "biology", "genetics", "and", "genomics/population", "genetics" ]	2008	Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic
Newly synthesized envelope glycoproteins of neuroinvasive viruses can be sorted in a polarized manner to the somatodendritic and/or axonal domains of neurons . Although critical for transneuronal spread of viruses , the molecular determinants and interregulation of this process are largely unknown . We studied the pola...	Neurons are highly polarized cells exhibiting somatodendritic and axonal domains with distinct protein and lipid compositions . Some enveloped viruses target neurons by binding of the viral envelope glycoproteins to neuronal surface receptors . The ensuing fusion of the viral and neuronal membranes delivers the genetic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "molecular", "neuroscience", "cellular", "neuroscience", "medicine", "and", "health", "sciences", "cell", "biology", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "virology", "emerging", "viral", "diseases", "biology"...	2014	Co-assembly of Viral Envelope Glycoproteins Regulates Their Polarized Sorting in Neurons
Horizontal gene transfer ( HGT ) is a major force driving bacterial evolution . Because of their ability to cross inter-species barriers , bacterial plasmids are essential agents for HGT . This ability , however , poses specific requisites on plasmid physiology , in particular the need to overcome a multilevel selectio...	In the environment , bacteria often evolve by the acquisition of new genes from different species . Plasmids are small DNA molecules that mediate horizontal gene transfer in bacteria , thus they are fundamental agents for the spread of antibiotic resistances . Plasmids replicate inside the bacterial cytoplasm , and pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "systems", "biology", "genetics", "population", "dynamics", "synthetic", "biology", "population", "biology", "biology", "microbiology", "gene", "networks" ]	2014	Negative Feedback and Transcriptional Overshooting in a Regulatory Network for Horizontal Gene Transfer
Oocytes are stockpiled with proteins and mRNA that are required to drive the initial mitotic divisions of embryogenesis . But are there proteins specific to meiosis whose levels must be decreased to begin embryogenesis properly ? The Drosophila protein Cortex ( Cort ) is a female , meiosis-specific activator of the Ana...	Despite their many differences , the meiotic and mitotic divisions of the early embryo take place within the same cytoplasmic space . The oocyte-to-embryo transition is the process by which an oocyte , which initially undergoes meiosis , becomes “adapted” to support the rapid mitotic divisions of embryogenesis . This i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "mitosis", "meiosis", "embryology", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "cell", "division", "chromosome", "biology", "genetics", "biology", "cyclins", "molecular", "cell", "biology", "gene", "function" ]	2013	A Meiosis-Specific Form of the APC/C Promotes the Oocyte-to-Embryo Transition by Decreasing Levels of the Polo Kinase Inhibitor Matrimony

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