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Killer-cell immunoglobulin-like receptors ( KIRs ) are a group of regulatory molecules able to activate or inhibit natural killer cells upon interaction with human leukocyte antigen ( HLA ) class I molecules . Combinations of KIR and HLA may contribute to the occurrence of different immunological and clinical responses...	Leprosy is a neglected disease with the highest worldwide prevalence , and remains a public health problem in Brazil . The innate immune mechanisms are determinants in the management of leprosy and its different clinical manifestations . Accordingly , genetic association study provides information about the contributio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "tropical", "diseases", "geographical", "locations", "genetic", "mapping", "bacterial", "diseases", "neglected", "tropical", "diseases", "infectious", ...	2019	The impact of KIR/HLA genes on the risk of developing multibacillary leprosy
HIV-1 is restricted for infection of primary quiescent T-cells . After viral entry , reverse transcription is initiated but is not completed . Various hypotheses have been proposed for this cellular restriction including insufficient nucleotide pools and cellular factors , but none have been confirmed as the primary me...	In 1990 , we demonstrated that unstimulated quiescent T-lymphocytes are resistant to HIV-1 infection . Viruses can get into the cell , and reverse transcription is started , but it is not completed . Various hypotheses have been proposed for this blockage including insufficient free nucleotides and inhibiting cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "infectious", "diseases/hiv", "infection", "and", "aids" ]	2009	Reassessing the Role of APOBEC3G in Human Immunodeficiency Virus Type 1 Infection of Quiescent CD4+ T-Cells
Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence . There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences . Methylation of cytosine ...	Heritable variation within a species provides the basis for natural and artificial selection . A substantial portion of heritable variation is based on alterations in DNA sequence among individuals and is termed genetic variation . There is also evidence for epigenetic variation , which refers to heritable differences ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "plant", "genetics", "epigenetics", "biology", "dna", "modification", "crop", "genetics", "genetics", "and", "genomics" ]	2011	Heritable Epigenetic Variation among Maize Inbreds
Nodding Syndrome was first reported from Tanzania in the 1960s but appeared as an epidemic in Northern Uganda in the 1990s during the LRA civil war . It is characterized by repetitive head nodding , often followed by other types of seizures , developmental retardation and growth faltering with onset occurring in childr...	Nodding Syndrome , a form of epilepsy that occurs in onchocerciasis-endemic areas has affected about 3000 children in Northern Uganda where the epidemic emerged at the time of the civil war . Although an association with onchocerciasis has been established , the disease etiology has not yet been identified . In conjunc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Strengths", "and", "limitations", "of", "the", "study" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "tropical", "diseases", "uganda", "social", "sciences", "political", "aspects", "of", "health", "parasitic", "diseases", "political", "science...	2019	"Those who died are the ones that are cured". Walking the political tightrope of Nodding Syndrome in northern Uganda: Emerging challenges for research and policy
The translation initiation factor eIF3 is a multi-subunit protein complex that coordinates the assembly of the 43S pre-initiation complex in eukaryotes . Prior studies have demonstrated that not all subunits of eIF3 are essential for the initiation of translation , suggesting that some subunits may serve regulatory rol...	The translation initiation factor eIF3 is the largest and most complex of the eukaryotic initiation factors , comprising 13 subunits in metazoans , and this protein complex plays a critical role in scaffolding key interactions among multiple cofactors required for translation initiation . Both evolutionary and biochemi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "pathogens", "messenger", "rna", "endoplasmic", "reticulum", "microbiology", "cell", "processes", "animals", "pseudomonas", "ae...	2016	Mutations in Nonessential eIF3k and eIF3l Genes Confer Lifespan Extension and Enhanced Resistance to ER Stress in Caenorhabditis elegans
The article demonstrates that computational modeling has the capacity to convert metabolic snapshots , taken sequentially over time , into a description of cellular , dynamic strategies . The specific application is a detailed analysis of a set of actions with which Saccharomyces cerevisiae responds to heat stress . Us...	The heat stress response in yeast is a model system for elucidating how cells organize and execute complex tasks . While a genomic response to heat is necessary , it is by itself too slow for immediate means of protecting the cell against damage . However , one observes changes in the physiology of the cells within a f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast
Endemic to the Democratic Republic of the Congo ( DRC ) , monkeypox is a zoonotic disease that causes smallpox-like illness in humans . Observed fluctuations in reported cases over time raises questions about when it is appropriate to mount a public health response , and what specific actions should be taken . We evalu...	Most of the scientific literature about statistical thresholds for outbreak detection is biased toward large datasets that derive from wealthy countries . In the scientific community , it is acknowledged that even objectively determined statistical thresholds can produce varied results when applied to the same dataset ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "applied", "mathematics", "spatial", "epidemiology", "simulation", "and", "modeling", "algorithms", "endemic", "diseases", "mathematics", "research", "and", "analysis", ...	2018	Sounding the alarm: Defining thresholds to trigger a public health response to monkeypox
A lysosomal storage disease ( LSD ) results from deficient lysosomal enzyme activity , thus the substrate of the mutant enzyme accumulates in the lysosome , leading to pathology . In many but not all LSDs , the clinically most important mutations compromise the cellular folding of the enzyme , subjecting it to endoplas...	Lysosomes are organelles that contain more than 50 hydrolytic enzymes that break down macromolecules in a cell . A lysosomal storage disease results from deficient activity of one or more of these enzymes , leading to the accumulation of corresponding substrate ( s ) . Currently , lysosomal storage diseases are treated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "non-clinical", "medicine", "cell", "biology", "chemical", "biology" ]	2008	Partial Restoration of Mutant Enzyme Homeostasis in Three Distinct Lysosomal Storage Disease Cell Lines by Altering Calcium Homeostasis
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids . The family includes grass symbionts in the epichloae clade ( Epichloë and Neotyphodium species ) , which are extraordinarily diverse both in their host interactions and in their alkal...	The fungal family , Clavicipitaceae , includes “ergot” fungi that parasitize ears of cereals and have historically caused mass poisonings , as well as “epichloae , ” which are symbionts of grasses . Many epichloae are mutualistic symbionts , but some are pathogenic , and others have both mutualistic and pathogenic char...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "agroecology", "ecology", "biology", "genomics", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics", "agriculture" ]	2013	Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci
The success of passive immunization suggests that antibody-based therapies will be effective at controlling malaria . We describe the development of fully human antibodies specific for Plasmodium falciparum by antibody repertoire cloning from phage display libraries generated from immune Gambian adults . Although these...	Malaria rivals HIV and tuberculosis as the world's most deadly infection killing a child every 30 seconds . Antibodies and their receptors ( Fc-receptors ) have been shown to be vital for the development of protective immunity , and as such they act as correlates of protection in studies aimed at defining the best anti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "immunology", "plasmodium", "microbiology" ]	2007	The Importance of Human FcγRI in Mediating Protection to Malaria
Recent models of movement generation in motor cortex have sought to explain neural activity not as a function of movement parameters , known as representational models , but as a dynamical system acting at the level of the population . Despite evidence supporting this framework , the evaluation of representational mode...	The question of how the brain generates movement has been extensively studied , yet multiple competing models exist . Representational approaches relate the activity of single neurons to movement parameters such as velocity and position , approaches useful for the decoding of movement intentions , while the dynamical s...	[ "Abstract", "Introduction", "Results", "/", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "brain", "random", "variables", "neuroscience", "covariance", "systems", "science", "mathematics", "discrete", "mathematics", "combinatorics", "neuronal", "tuning", "computer", "and", "information", "sciences"...	2016	Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning
The origin of the germline–soma distinction is a fundamental unsolved question . Plants and basal metazoans do not have a germline but generate gametes from pluripotent stem cells in somatic tissues ( somatic gametogenesis ) . In contrast , most bilaterians sequester a dedicated germline early in development . We devel...	Mammalian germ cells ( eggs and sperm ) are immortal in the sense that they propagate successive generations . In contrast , somatic ( body ) cells do not persist to the next generation . Yet neither plants nor basal animals such as sponges and corals have a germline; they simply form gametes from stem cells in adult t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "reproductive", "physiology", "germ", "cells", "zygotes", "mutation", "oocytes", "mitochondria", "bioenergetics", "cellular", "structures...	2016	Selection for Mitochondrial Quality Drives Evolution of the Germline
Actin-related proteins are ubiquitous components of chromatin remodelers and are conserved from yeast to man . We have examined the role of the budding yeast actin-related protein Arp6 in gene expression , both as a component of the SWR1 complex ( SWR-C ) and in its absence . We mapped Arp6 binding sites along four yea...	Actin and the structurally similar actin-related proteins ( ARPs ) are major components of nucleosome remodeling complexes in the nucleus . Here we show that budding yeast Arp6 has functions independent of its catalytic chromatin remodeling partner , Swr1 . Arp6 binds to multiple promoters and subtelomeric zones at whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/nuclear", "structure", "and", "function" ]	2010	Actin-Related Protein Arp6 Influences H2A.Z-Dependent and -Independent Gene Expression and Links Ribosomal Protein Genes to Nuclear Pores
Microbes are subjected to selective pressures during chronic infections of host tissues . Pseudomonas aeruginosa isolates with inactivating mutations in the transcriptional regulator LasR are frequently selected within the airways of people with cystic fibrosis ( CF ) , and infection with these isolates has been associ...	Chronic infections are distinguished from many other infections in that they are difficult to eradicate with antibiotics . Thus , the microbes that cause chronic infections persist within host tissues for long periods despite our best treatment efforts . During the course of these chronic infections , the causative mic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "respiratory", "medicine/respiratory", "infections", "microbiology/microbial", "evolution", "and", "genomics", "microbiology", "infectious", "diseases/respiratory", "infections", "infectious", "diseases/bacterial", "infections", "microbiology/microbial", "physiology", "and", "metab...	2010	Nutrient Availability as a Mechanism for Selection of Antibiotic Tolerant Pseudomonas aeruginosa within the CF Airway
Highly pathogenic avian H5N1 influenza A viruses have spread throughout Asia , Europe , and Africa , raising serious worldwide concern about their pandemic potential . Although more than 250 people have been infected with these viruses , with a consequent high rate of mortality , the molecular mechanisms responsible fo...	Highly pathogenic avian H5N1 influenza A viruses have spread around the world since 2003 , raising serious worldwide concern about their pandemic potential . Although efficient human-to-human transmission of this virus has not yet occurred , the potential of these viruses to acquire the ability is evident . The recepto...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "viruses", "in", "vitro", "virology" ]	2007	Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
A critical role for intracellular TLR9 has been described in recognition and host resistance to Leishmania parasites . As TLR9 requires endolysosomal proteolytic cleavage to achieve signaling functionality , we investigated the contribution of different proteases like asparagine endopeptidase ( AEP ) or cysteine protea...	Cutaneous forms of leishmaniasis are characterized by lesions that progress over months or years and that often leave permanent scars . Toll like receptors play an important role in the recognition and initiation of immune responses , and the intracellular TLR9 , a sensor of pathogen double-stranded DNA , plays a cruci...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "spleen", "immunology", "microbiology", "parasitic", "diseases", "parasitic", ...	2016	Cathepsin B-Deficient Mice Resolve Leishmania major Inflammation Faster in a T Cell-Dependent Manner
Melioidosis , caused by infection with Burkholderia ( B . ) pseudomallei , is a severe illness that is endemic in Southeast Asia . Osteopontin ( OPN ) is a phosphorylated glycoprotein that is involved in several immune responses including induction of T-helper 1 cytokines and recruitment of inflammatory cells . OPN lev...	Melioidosis is a severe tropical disease caused by infection with the bacterium Burkholderia ( B . ) pseudomallei . In northeast Thailand infection with this bacterium is the major cause of community-acquired septicemia with a mortality rate up to 40% . Extending the knowledge on the mechanisms of host defense against ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections", "respiratory", "medicine/respiratory", "infections", "pathology/immunology" ]	2010	Osteopontin Impairs Host Defense during Established Gram-Negative Sepsis Caused by Burkholderia pseudomallei (Melioidosis)
While elucidating the peculiar epitope of the α-PrP mAb IPC2 , we found that PrPSc exhibits the sulfoxidation of residue M213 as a covalent signature . Subsequent computational analysis predicted that the presence of sulfoxide groups at both Met residues 206 and 213 destabilize the α-fold , suggesting oxidation may fac...	The protein only theory , a widely accepted model describing the prion agent , assumes that the mechanism underlying prion disease pathogenesis includes a conformational change of the α-helix rich , soluble and protease sensitive PrPC into an aggregated and protease resistant β-sheet rich PrPSc form . Until recently , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/prion", "diseases", "neurological", "disorders/cognitive", "neurology", "and", "dementia", "neurological", "disorders/prion", "diseases" ]	2010	Oxidation of Helix-3 Methionines Precedes the Formation of PK Resistant PrPSc
Recent experimental advances are producing an avalanche of data on both neural connectivity and neural activity . To take full advantage of these two emerging datasets we need a framework that links them , revealing how collective neural activity arises from the structure of neural connectivity and intrinsic neural dyn...	Neuronal networks , like many biological systems , exhibit variable activity . This activity is shaped by both the underlying biology of the component neurons and the structure of their interactions . How can we combine knowledge of these two things—that is , models of individual neurons and of their interactions—to pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "action", "potentials", "medicine", "and", "health", "sciences", "legs", "neural", "networks", "membrane", "potential", "limbs", "(anatomy)", "electrophysiology", "neuroscience", "systems", "science", "mathematics", "computational", "neuroscience", "research...	2017	Linking structure and activity in nonlinear spiking networks
Current rates of species loss triggered numerous attempts to protect and conserve biodiversity . Species conservation , however , requires species identification skills , a competence obtained through intensive training and experience . Field researchers , land managers , educators , civil servants , and the interested...	Plant identification is not exclusively the job of botanists and plant ecologists . It is required or useful for large parts of society , from professionals ( such as landscape architects , foresters , farmers , conservationists , and biologists ) to the general public ( like ecotourists , hikers , and nature lovers ) ...	[ "Abstract", "Introduction", "Machine", "learning", "for", "species", "identification", "Challenges", "in", "image-based", "taxa", "identification", "Status", "quo", "Open", "problems", "and", "future", "directions", "A", "vision", "of", "automated", "identification", ...	[ "plant", "anatomy", "flowers", "plant", "science", "review", "eukaryota", "computer", "and", "information", "sciences", "machine", "learning", "data", "acquisition", "artificial", "intelligence", "computer", "vision", "flowering", "plants", "biology", "and", "life", "...	2018	Automated plant species identification—Trends and future directions
During the West Africa Ebola outbreak , cultural practices have been described as hindering response efforts . The acceptance of control measures improved during the outbreak , but little is known about how and why this occurred . We conducted a qualitative study in two administrative districts of Sierra Leone to under...	The scale of the 2014–15 Ebola epidemic was unprecedented and led to over 11 , 000 deaths in Sierra Leone , Liberia and Guinea . What is distinct about the findings of this study is the knowledge gained from experiences and reflections of communities , health workers and Ebola survivors living in the midst of an outbre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "health", "promotion", "medicine", "and", "health", "sciences", "body", "fluids", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "ebola", "hemorrhagic", "fever", "quarantines", "human", "families", "neglected", "tropical", "disea...	2018	‘When Ebola enters a home, a family, a community’: A qualitative study of population perspectives on Ebola control measures in rural and urban areas of Sierra Leone
Outer membrane vesicles ( OMVs ) that are released from Gram-negative pathogenic bacteria can serve as vehicles for the translocation of effectors involved in infectious processes . In this study we have investigated the role of OMVs of the Vibrio cholerae O1 El Tor A1552 strain in resistance to antimicrobial peptides ...	Cholera is an epidemic disease that has killed millions of people and continues to be a major health problem worldwide . The bacterium V . cholerae , the causative agent of cholera , is highly resistant to antimicrobial peptides , which are important effectors of human innate immunity . Moreover , it is well-establishe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Role of the Vibrio cholerae Matrix Protein Bap1 in Cross-Resistance to Antimicrobial Peptides
Amhara Regional State of Ethiopia has a population of approximately 19 . 6 million , is prone to unstable and epidemic malaria , and is severely affected by trachoma . An integrated malaria and trachoma control program is being implemented by the Regional Health Bureau . To provide baseline data , a survey was conducte...	The “big three” killer diseases are malaria , HIV/AIDS , and tuberculosis; control programs for these diseases are usually well developed and financed . The neglected tropical diseases ( NTDs ) are a group of ancient afflictions that are frequently sidelined by planners and are under-resourced . Opportunities of integr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Integrating an NTD with One of “The Big Three”: Combined Malaria and Trachoma Survey in Amhara Region of Ethiopia
Dengue causes 50 million infections per year , posing a large disease and economic burden in tropical and subtropical regions . Only a proportion of dengue cases require hospitalization , and predictive tools to triage dengue patients at greater risk of complications may optimize usage of limited healthcare resources ....	Dengue is a mosquito-borne tropical disease that poses a large economic and health burden to 40% of the world's population . Some dengue patients can evolve into a more severe form of the illness ( severe dengue ) and ideally should be hospitalized when this occurs . However , while only a small proportion of patients ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "socioeconomic", "aspects", "of", "health", "medicine", "and", "health", "sciences", "epidemiology", "dengue", "fever", "neglected", "tropical", "diseases", "tropical", "diseases", "viral", "diseases",...	2014	Predictive Tools for Severe Dengue Conforming to World Health Organization 2009 Criteria
Melioidosis is a serious , and potentially fatal community-acquired infection endemic to northern Australia and Southeast Asia , including Sarawak , Malaysia . The disease , caused by the usually intrinsically aminoglycoside-resistant Burkholderia pseudomallei , most commonly affects adults with predisposing risk facto...	Melioidosis is a serious , and often fatal community-acquired infection endemic to Southeast Asia and northern Australia . It is caused by the environmental saprophyte Burkholderia pseudomallei , a bacterium that is intrinsically resistant to many commonly used antibiotics . Its presence in Sarawak , Malaysian Borneo ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "melioidosis", "drugs", "microbiology", "pediatrics", "bacterial", "diseases", "signs", "and", "symptoms", "antibiotics", "pediatric", "infections", ...	2017	Pediatric melioidosis in Sarawak, Malaysia: Epidemiological, clinical and microbiological characteristics
Many immune response genes are highly polymorphic , consistent with the selective pressure imposed by pathogens over evolutionary time , and the need to balance infection control with the risk of auto-immunity . Epidemiological and genomic studies have identified many genetic variants that confer susceptibility or resi...	Granzymes ( Gzm ) are serine proteases expressed by cytotoxic T cells and natural killer cells , and are important for the destruction of virally infected cells . To date , the function of these molecules has been assessed exclusively in common laboratory mouse strains that express identical granzyme proteins . In wild...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "serine", "proteases", "biochemistry", "cell", "death", "genetics", "of", "the", "immune", "system", "cell", "biology", "clinical", "immunology", "proteins", "immunity", "apoptosis", "enzymes", "biology", "and", "life", "sciences", "proteases", "enzymology", "cell", ...	2014	A Natural Genetic Variant of Granzyme B Confers Lethality to a Common Viral Infection
Worldwide , snakebite envenomations total ~2 . 7 million reported cases annually with ~100 , 000 fatalities . Since 2009 , snakebite envenomation has intermittently been classified as a very important ‘neglected tropical disease’ by the World Health Organisation . Despite this emerging awareness , limited efforts have ...	Snakebite envenomations cause tens of thousands of deaths and hundred thousands of injuries in many developing tropical countries annually , and sub-Saharan Africa represents an epitome example of this ‘neglected tropical disease’ . We here present data collected over a 10-year period applying different methodologies a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "grasslands", "tropical", "diseases", "geographical", "locations", "vertebrates", "plant", "communities", "animals", "age", "groups", "plant", "science", "reptiles", "neglected", "tr...	2019	Epidemiology, ecology and human perceptions of snakebites in a savanna community of northern Ghana
Sex determination mechanisms play a central role in life-history characteristics , affecting mating systems , sex ratios , inbreeding tolerance , etc . Downstream components of sex determination pathways are highly conserved , but upstream components evolve rapidly . Evolutionary dynamics of sex determination remain po...	Whether a developing embryo becomes male or female has significant downstream consequences . Depending on the species , sex can be determined by a wide variety of mechanisms . Sex determination systems can evolve rapidly , but how this occurs , and even how widespread the same mechanism is within a given taxonomic grou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees
Seizures in focal epilepsies are sustained by a highly synchronous neuronal discharge that arises at restricted brain sites and subsequently spreads to large portions of the brain . Despite intense experimental research in this field , the earlier cellular events that initiate and sustain a focal seizure are still not ...	In focal epilepsy , seizures are generated by a localized , synchronous neuronal electrical discharge that may spread to large portions of the brain . Despite intense experimental research in this field , a key question relevant to the human epilepsy condition remains completely unanswered: what are the cellular events...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neuronal", "and", "glial", "cell", "biology", "neurological", "disorders/epilepsy" ]	2010	An Excitatory Loop with Astrocytes Contributes to Drive Neurons to Seizure Threshold
Hantavirus pulmonary syndrome ( HPS ) is a life threatening disease transmitted by the rodent Oligoryzomys longicaudatus in Chile . Hantavirus outbreaks are typically small and geographically confined . Several studies have estimated risk based on spatial and temporal distribution of cases in relation to climate and en...	Hantavirus pulmonary syndrome ( HPS ) is a severe disease present in Chile , Argentina and other countries in the Americas . Mortality rates for HPS can be as high as 60% for some outbreaks . Although hantavirus outbreaks tend to be small , the high death rate , unavailability of a vaccine , and occurrence of infection...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "mathematics", "statistics", "(mathematics)", "population", "modeling", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "bi...	2014	Modeling to Predict Cases of Hantavirus Pulmonary Syndrome in Chile
Infection with intestinal helminths is common and may contribute to the decreased efficacy of Vibrio cholerae vaccines in endemic compared to non-endemic areas . However , the immunomodulatory effects of concomitant intestinal parasitic infection in cholera patients have not been systematically evaluated . We evaluated...	Vibrio cholerae causes cholera , a severe diarrhea that may lead to fatal dehydration if not treated . Cholera occurs mostly in impoverished areas where there is poor sanitation and intestinal parasites are also common . However , little is known about the relationship between intestinal parasites and cholera . To lear...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections" ]	2009	Immunologic Responses to Vibrio cholerae in Patients Co-Infected with Intestinal Parasites in Bangladesh
Multi-species interactions can often have non-intuitive consequences . However , the study of parasite interactions has rarely gone beyond the effects of pairwise combinations of species , and the outcomes of multi-parasite interactions are poorly understood . We investigated the effects of co-infection by four gastroi...	Over the last decade , an increasing number of studies have shown that co-infected individuals can show strikingly different disease symptoms than singly infected individuals . Among these studies , the potential protective effect of some helminth species on malaria severity has attracted considerable attention because...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", "protozoans", "infectious", "diseases", "malarial", "parasites", "cerebral", "malaria", "helminth", "infections", ...	2018	Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another
Benznidazole ( BZL ) is the only antichagasic drug available in most endemic countries . Its effect on the expression and activity of drug-metabolizing and transporter proteins has not been studied yet . Expression and activity of P-glycoprotein ( P-gp ) , Multidrug resistance-associated protein 2 ( MRP2 ) , Cytochrome...	Chagas disease is an endemic infection caused by Trypanosoma cruzi . Benznidazole ( BZL ) is the only antichagasic drug available in most endemic countries . The liver plays a major role in disposition of endogenous and exogenous compounds and their excretion is mainly mediated by transporter proteins ( such as P-gp an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "rna", "interference", "pharmacodynamics", "drugs", "and", "devices", "gene", "expression", "pharmacology", "biology", "molecular", "cell", "biology", "drug", "interactions", "drug", "metabolism", "molecular", "biology", "pharmacokinetics", "drug", "excretion"...	2012	Regulation of Biotransformation Systems and ABC Transporters by Benznidazole in HepG2 Cells: Involvement of Pregnane X-Receptor
Food-borne helminthiases ( FBHs ) have become increasingly important due to frequent occurrence and worldwide distribution . There is increasing demand for developing more sensitive , high-throughput techniques for the simultaneous detection of multiple parasitic diseases due to limitations in differential clinical dia...	Food-borne helminthiases ( FBHs ) have caused significant problems in public health and also posed socio-economic concerns . Common FBHs , such as cysticercosis , trichinellosis , paragonimiasis , sparganosis and angiostrongyliasis , have a worldwide distribution with high morbidity and even death . The objective of th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "taeniasis", "medicine", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "ectoparasitic", "infections", "cysticercosis", "trichinellosis", "neglected", "tropical", "diseases", "parasitic", "diseases", "paragonimiasis", "food-borne", "trematodes", "he...	2012	A Protein Microarray for the Rapid Screening of Patients Suspected of Infection with Various Food-Borne Helminthiases
The RNase P family is a diverse group of endonucleases responsible for the removal of 5′ extensions from tRNA precursors . The diversity of enzyme forms finds its extremes in the eukaryal nucleus where RNA-based catalysis by complex ribonucleoproteins in some organisms contrasts with single-polypeptide enzymes in other...	Many biocatalysts apparently evolved independently more than once , leading to structurally unrelated macromolecules catalyzing the same biochemical reaction . The RNase P enzyme family is an exceptional case of this phenomenon called convergent evolution . RNase P enzymes use not only unrelated , but chemically distin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfer", "rna", "molecular", "complexes", "nucleases", "enzymes", "synthetic", "biology", "enzymology", "convergent", "evolution", "proteins", "ribonucleases", "gene", "expression", "molecular", "biology", "biochemistry", "rna", "hydrolases", "rna", "processing", "ribo...	2014	Playing RNase P Evolution: Swapping the RNA Catalyst for a Protein Reveals Functional Uniformity of Highly Divergent Enzyme Forms
Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries . Because praziquantel is the only drug in therapeutic use , the risk of drug resistance is a concern . In the search for new schistosomicidal drugs , we performed a target-based chemogenomics screen of a datase...	Schistosomiasis is a neglected tropical disease caused by schistosome parasites that affects millions of people worldwide . The current reliance on a single drug ( Praziquantel ) for treatment and control of the disease calls for the urgent discovery of novel schistosomicidal agents . One approach that can expedite dru...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "computer-aided", "drug", "design", "medicine", "and", "health", "sciences", "drug", "design", "drug", "research", "and", "development", "helminths", "biology", "and", "life", "sciences", "pharmacology", "animals...	2015	In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni
Antisense oligonucleotides ( ASOs ) have demonstrated variation of efficacy in patient populations . This has prompted our investigation into the contribution of genetic architecture to ASO pharmacokinetics ( PK ) and pharmacodynamics ( PD ) . Genome wide association ( GWA ) and transcriptomic analysis in a hybrid mous...	Previous work in the clinic has clearly demonstrated differential patient response to antisense oligonucleotide ( ASO ) drugs . However , to date there has been no systematic evaluation of genes associated with this response in vivo . In this study , we utilized an advanced genetic methodology in mice to identify genes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "gene", "regulation", "animal", "models", "model", "organisms", "genome", "analysis", "experimental", "organism", "systems", "molecular", "genetics", "inbred", "strains", "research", "and", "analysis", "methods", "small", "interf...	2018	Mouse genome-wide association studies and systems genetics uncover the genetic architecture associated with hepatic pharmacokinetic and pharmacodynamic properties of a constrained ethyl antisense oligonucleotide targeting Malat1
Classical swine fever ( CSF ) caused by classical swine fever virus ( CSFV ) is one of the most detrimental diseases , and leads to significant economic losses in the swine industry . Despite efforts by many government authorities to stamp out the disease from national pig populations , the disease remains widespread ....	Classical swine fever ( CSF ) , caused by classical swine fever virus ( CSFV ) , and is a highly contagious , often fatal porcine disease that causes significant economic losses . Due to the economic importance of this virus to the pig industry , the biology and pathogenesis of CSFV have been investigated extensively ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "animal", "diseases", "rna", "interference", "gene", "regulation", "microbiology", "vertebrates", "cloning", "light", "microscopy", "animals", "mammals", "microscopy", "molecular", "biology", "techniques", "epigenetics", "zoology", "research", "and", "analysis", "methods"...	2018	Genetically modified pigs are protected from classical swine fever virus
As the Zika virus epidemic continues to spread internationally , countries such as the United States must determine how much to invest in prevention , control , and response . Fundamental to these decisions is quantifying the potential economic burden of Zika under different scenarios . To inform such decision making ,...	Our work forecasts the cost and economic burden of the Zika virus across six states in the US which are at the greatest risk of Zika ( Alabama , Florida , Georgia , Louisiana , Mississippi , and Texas ) . We evaluated the burden by varying attack rates , scenarios , and circumstances . All costs are reported in 2016 do...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "microcephaly", "pathology", "and", "laboratory", "medicine", "nervous", "system", "pathogens", "immunology", "geographical", "locations", "microbiology", "social", "sciences", "health", "care", "viruses", "no...	2017	The potential economic burden of Zika in the continental United States
In many animals the ability to navigate over long distances is an important prerequisite for foraging . For example , it is widely accepted that desert ants and honey bees , but also mammals , use path integration for finding the way back to their home site . It is however a matter of a long standing debate whether ani...	When desert ants search for food , they often have to travel over long distances , more then ten thousand times their body lengths and then turn back to find the nest entrance . It is known from many experiments that these animals employ a skylight compass including the sun , a pedometer , and a mechanism called path i...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "behavioral", "neuroscience", "animal", "behavior", "biology", "computational", "biology", "zoology", "neuroscience" ]	2011	No Need for a Cognitive Map: Decentralized Memory for Insect Navigation
Accurate chromosome segregation during meiosis relies on the presence of crossover events distributed among all chromosomes . MutSγ and MutLγ homologs ( Msh4/5 and Mlh1/3 ) facilitate the formation of a prominent group of meiotic crossovers that mature within the context of an elaborate chromosomal structure called the...	At the heart of reproductive cell formation is a nuclear division process ( meiosis ) whereby homologous chromosomes segregate from one another . Meiotic partner chromosomes establish exclusive associations via a patterned distribution of crossover recombination events . During the maturation of recombination intermedi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Separable Crossover-Promoting and Crossover-Constraining Aspects of Zip1 Activity during Budding Yeast Meiosis
Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors . To discover genes and processes in yeast that are required for growth when zinc is limiting , we used genome-wide functional profiling . Mixed pools of ∼4 , 600 deletion mutants were inoculated into zinc-replete...	Zinc is needed for the growth of all organisms because it acts as a required cofactor for many different proteins . Zinc deficiency is a common problem faced by free-living microbes , as well as plants and animals including humans . Among bacterial and fungal pathogens , zinc deficiency is also a key problem they can e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "functional", "genomics", "microbiology", "gene", "function", "model", "organisms", "cell", "growth", "microbial", "physiology", "biology", "cell", "biology", "genetic", "screens", "genetics", "yeast", "and", "fungal", "models", "sac...	2012	Genome-Wide Functional Profiling Identifies Genes and Processes Important for Zinc-Limited Growth of Saccharomyces cerevisiae
Carrion' disease , caused by Bartonella bacilliformis , remains truly neglected due to its focal geographical nature . A wide spectrum of clinical manifestations , including asymptomatic bacteremia , and lack of a sensitive diagnostic test can potentially lead to a spread of the disease into non-endemic regions where c...	Carrion's disease , caused by Bartonella bacilliformis remains truly neglected due to its focal geographical nature . A wide spectrum of clinical manifestations , including asymptomatic bacteremia can potentially lead to a spread of the disease into non-endemic regions . The PCR-based approach is sensitive for detectio...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bartonella", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "molecular", "biology", "techniques", "microbiology", "molecular", "biology", ...	2014	Rapid and Sensitive Detection of Bartonella bacilliformis in Experimentally Infected Sand Flies by Loop-Mediated Isothermal Amplification (LAMP) of the Pap31 Gene
Fishes of the genus Danio exhibit diverse pigment patterns that serve as useful models for understanding the genes and cell behaviors underlying the evolution of adult form . Among these species , zebrafish D . rerio exhibit several dark stripes of melanophores with sparse iridophores that alternate with light interstr...	Neural crest derived pigment cells generate the spectacular variation in skin pigment patterns among vertebrates . Mammals and birds have just a single skin pigment cell , the melanocyte , whereas ectothermic vertebrates have several pigment cells including melanophores , iridophores and xanthophores , that together or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "vertebrates", "pigments", "animals", "alleles", "epithelial", "cells", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "materials", "science", "experimental", "organism", "systems", ...	2018	Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes
Listeria monocytogenes ( Lm ) is a ubiquitous bacterium able to survive and thrive within the environment and readily colonizes a wide range of substrates , often as a biofilm . It is also a facultative intracellular pathogen , which actively invades diverse hosts and induces listeriosis . So far , these two complement...	Listeria monocytogenes ( Lm ) is a ubiquitous bacterium that survives and thrives within the environment , and a facultative intracellular pathogen that induces listeriosis . So far , these two complementary facets of Lm biology have been studied independently . Here we identify ActA , which is a major Lm virulence det...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "microbiology", "host-pathogen", "interaction", "animal", "models", "bacterial", "diseases", "model", "organisms", "gastroenterology", "and", "hepatology", "microbial", "growth", "and", "development", "bacterial", "pathogens", "infectious", "dise...	2013	ActA Promotes Listeria monocytogenes Aggregation, Intestinal Colonization and Carriage
DJ-1 , a Parkinson's disease ( PD ) –associated gene , has been shown to protect against oxidative stress in Drosophila . However , the molecular mechanism underlying oxidative stress-induced phenotypes , including apoptosis , locomotive defects , and lethality , in DJ-1-deficient flies is not fully understood . Here w...	DJ-1 is an antioxidant protein that has been implicated in autosomal recessive Parkinson's disease ( PD ) , although the mechanism by which DJ-1 deficiency causes PD remains elusive . Drosophila DJ-1 mutants are highly sensitive to oxidative stress and UV irradiation , and oxidative stress-induced cell death is signifi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "drosophila", "melanogaster", "model", "organisms", "biology" ]	2013	Drosophila DJ-1 Decreases Neural Sensitivity to Stress by Negatively Regulating Daxx-Like Protein through dFOXO
In the savannahs of East and Southern Africa , tsetse flies ( Glossina spp . ) transmit Trypanosoma brucei rhodesiense which causes Rhodesian sleeping sickness , the zoonotic form of human African trypanosomiasis . The flies feed mainly on wild and domestic animals and are usually repelled by humans . However , this in...	In savannah areas of Africa the incidence of sleeping sickness is commonly low because the species of tsetse fly that spread the disease there feed mainly on wild and domestic animals , and are strongly repelled by humans . Environmental stresses can make the flies less responsive to the repellence , so threatening to ...	[ "Abstract", "Introduction", "Study", "Area", "and", "General", "Methods", "Experiments", "and", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology" ]	2012	Towards an Early Warning System for Rhodesian Sleeping Sickness in Savannah Areas: Man-Like Traps for Tsetse Flies
Hybrid sterility ( HS ) belongs to reproductive isolation barriers that safeguard the integrity of species in statu nascendi . Although hybrid sterility occurs almost universally among animal and plant species , most of our current knowledge comes from the classical genetic studies on Drosophila interspecific crosses o...	Genomes of newly emerging species restrict their gene exchange with related taxa in order to secure integrity . Hybrid sterility is one of the reproductive isolation mechanisms restricting gene flow between closely related , sexually reproducing organisms . We showed that hybrid sterility between two closely related mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "germ", "cells", "meiosis", "genomics", "molecular", "cell", "biology", "cell", "division", "chromosome", "biology", "speciation", "cellular", "types", "hybridization", "biology", "evolutionary", "biology", "evolutionary", "processes" ]	2014	X Chromosome Control of Meiotic Chromosome Synapsis in Mouse Inter-Subspecific Hybrids
Cis-regulation plays an essential role in the control of gene expression , and is particularly complex and poorly understood for developmental genes , which are subject to multiple levels of modulation . In this study , we performed a global analysis of the cis-acting elements involved in the control of the zebrafish d...	Animal development relies on the early delimitation of specific embryonic territories that will later participate in the formation of tissues and organs . This process is governed by sets of so-called developmental genes . The activities of the genes are themselves controlled by associated DNA sequences called enhancer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "in", "situ", "hybridization", "molecular", "probe", "techniques", "gene", "regulation", "brain", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "hindbrain"...	2018	Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation
Testing potential drug treatments in animal disease models is a decisive step of all preclinical drug discovery programs . Yet , despite the importance of such experiments for translational medicine , there have been relatively few efforts to comprehensively and consistently analyze the data produced by in vivo bioassa...	Before exposing human populations to potential drug treatments , novel compounds are tested in living non-human animals—arguably the most physiologically relevant model system known to drug discovery . Yet , high failure rates for new therapies in the clinic demonstrate a growing need for better understanding of the re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ontologies", "animal", "models", "of", "disease", "vertebrates", "animals", "mammals", "drug", "screening", "animal", "models", "genetics", "of", "disease", "data", "management", "model", "organisms", "experimental", "organism...	2017	Classification and analysis of a large collection of in vivo bioassay descriptions
What proteins interacted in a long-extinct ancestor of yeast ? How have different members of a protein complex assembled together over time ? Our ability to answer such questions has been limited by the unavailability of ancestral protein-protein interaction ( PPI ) networks . To overcome this limitation , we propose s...	Many questions about present-day interaction networks could be answered by tracking how the network changed over time . We present a suite of algorithms to uncover an approximate node-by-node and edge-by-edge history of changes of a network when given only a present-day network and a plausible growth model by which it ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/bioinformatics", "computer", "science", "computational", "biology/systems", "biology" ]	2011	Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions
Mitochondria are highly dynamic subcellular organelles participating in many signaling pathways such as antiviral innate immunity and cell death cascades . Here we found that mitochondrial fusion was impaired in dengue virus ( DENV ) infected cells . Two mitofusins ( MFN1 and MFN2 ) , which mediate mitochondrial fusion...	Dengue virus ( DENV ) threatens billions of people worldwide but no licensed vaccine or therapeutics is currently available . Knowing more details of DENV pathogenesis , such as antagonism of host immunity and cell death induction , may provide important clues to fight against this thorny disease . Incoming studies sho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dengue Virus Impairs Mitochondrial Fusion by Cleaving Mitofusins
Substantial evidence in support of the formation of opioid receptor ( OR ) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions . In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs , we conducted extensive coars...	Opioid receptors associate with each other in the plasma membrane , following a mechanism that has been implicated in either beneficial or adverse effects , depending on the environment and the interacting partners . Whether or not the different opioid receptor subtypes share a similar propensity to form di-/oligomers ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association
The principal virulence determinant of Mycobacterium tuberculosis ( Mtb ) , the ESX-1 protein secretion system , is positively controlled at the transcriptional level by EspR . Depletion of EspR reportedly affects a small number of genes , both positively or negatively , including a key ESX-1 component , the espACD ope...	A major infection mechanism employed by the causative agent of tuberculosis , Mycobacterium tuberculosis ( Mtb ) , is the ESX-1 secretion system . It has been postulated that the DNA-binding protein EspR controls the virulence of Mtb by specifically regulating expression of the exported EspA protein , which is required...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein
Knowledge of the within-host frequencies of resistance-associated amino acid variants ( RAVs ) is important to the identification of optimal drug combinations for the treatment of hepatitis C virus ( HCV ) infection . Multiple RAVs may exist in infected individuals , often below detection limits , at any resistance loc...	The spectrum of viral mutants that exists in infected individuals defines the diversity of drug resistance pathways accessible to any virus . Drug combinations that block these pathways the most effectively are likely to elicit the best responses . The mutants may lie below detection , rendering treatment optimization ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "genome", "evolution", "hepacivirus", "pathogens", "cell", "processes", "microbiology", "viral", "structure", "viruses", "rna", "viruses", ...	2019	Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs
For many complex traits , genetic variants have been found associated . However , it is still mostly unclear through which downstream mechanism these variants cause these phenotypes . Knowledge of these intermediate steps is crucial to understand pathogenesis , while also providing leads for potential pharmacological i...	Many genetic variants have been found associated with diseases . However , for many of these genetic variants , it remains unclear how they exert their effect on the eventual phenotype . We investigated genetic variants that are known to be associated with diseases and complex phenotypes and assessed whether these vari...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "genome", "expression", "analysis", "genomics", "functional", "genomics", "gene", "expression", "genetics", "regulatory", "networks", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2011	Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA
The non-visual ß-arrestins are cytosolic proteins highly conserved across species that participate in a variety of signalling events , including plasma membrane receptor degradation , recycling , and signalling , and that can also act as scaffolding for kinases such as MAPK and Akt/PI3K . In Drosophila melanogaster , t...	Non-visual β-arrestins are key proteins involved in plasma membrane receptor internalization , recycling , and signalling . The activity of β-arrestins is generally linked to seven-transmembrane receptors , but in vertebrates they can also participate in many other signalling pathways . Consistently , β-arrestins play ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "developmental", "biology/pattern", "formation", "genetics", "and", "genomics/gene", "function", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "developmental", "biology/molecular", "development", "develop...	2011	Role of the Drosophila Non-Visual ß-Arrestin Kurtz in Hedgehog Signalling
Cytosine methylation of repetitive sequences is widespread in plant genomes , occurring in both symmetric ( CpG and CpNpG ) as well as asymmetric sequence contexts . We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ...	In plants and animals , many DNA sequences are modified by the addition of methyl groups , but the principles governing methylation patterns are not well understood . In Arabidopsis , we show that repetitive sequences , derived from mobile ( transposable ) elements , are densely methylated throughout their length , whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "plant", "biology", "arabidopsis", "plants", "genetics", "and", "genomics" ]	2007	Epigenetic Natural Variation in Arabidopsis thaliana
To elucidate the mechanisms involved in early events in Chlamydia trachomatis infection , we conducted a large scale unbiased RNA interference screen in Drosophila melanogaster S2 cells . This allowed identification of candidate host factors in a simple non-redundant , genetically tractable system . From a library of 7...	Chlamydia trachomatis infections are a worldwide problem; they are the leading cause of preventable blindness in developing nations and the most common cause of sexually transmitted disease in the Western world . Binding and entry into host cells are critical steps to the pathogenesis of this obligate intracellular par...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "infectious", "diseases/sexually", "transmitted", "diseases", "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", "biology/cytoskeleton" ]	2008	RNA Interference Screen Identifies Abl Kinase and PDGFR Signaling in Chlamydia trachomatis Entry
DNA methyltransferases are ubiquitous enzymes conserved in bacteria , plants and opisthokonta . These enzymes , which methylate cytosines , are involved in numerous biological processes , notably development . In mammals and higher plants , methylation patterns established and maintained by the cytosine DNA methyltrans...	Sexual reproduction is considered to be essential for long-term persistence of eukaryotic species . Sexual reproduction is controlled by strict mechanisms governing which haploids can fuse ( mating ) and which developmental paths the resulting zygote will follow . In mammals , differential genomic DNA methylation patte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fungal", "genetics", "fungal", "structure", "developmental", "biology", "fungi", "model", "organisms", "mycelium", "experimental", "organism", "systems", "epigenetics", "dna", "morphogenesis", "dna", "methylation", "chromatin", "research", "and", "analysis", "methods", ...	2019	A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina
Polydnaviruses are mutualists of their parasitoid wasps and express genes in immune cells of their Lepidopteran hosts . Polydnaviral genomes carry multiple copies of viral ankyrins or vankyrins . Vankyrin proteins are homologous to IκB proteins , but lack sequences for regulated degradation . We tested if Ichnoviral Va...	Parasitoid wasps are insects whose development takes place within the body of other insects . To survive , wasp larvae must overcome the immune defenses of their hosts . How parasitic wasps overcome host immunity is not fully understood even though we know that different strategies using venoms , virus-like particles ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "animal", "models", "signal", "transduction", "drosophila", "melanogaster", "inflammation", "model", "organisms", "immunity", "innate", "immunity", "immune", "defense", "immunology", "immune", "suppression", "biology", "molecular", "cell", "biology"...	2013	Polydnaviral Ankyrin Proteins Aid Parasitic Wasp Survival by Coordinate and Selective Inhibition of Hematopoietic and Immune NF-kappa B Signaling in Insect Hosts
The X chromosome often plays a central role in hybrid male sterility between species , but it is unclear if this reflects underlying regulatory incompatibilities . Here we combine phenotypic data with genome-wide expression data to directly associate aberrant expression patterns with hybrid male sterility between two s...	The X chromosome plays an important role in the development of reproductive isolation between species , but the basis for this has remained unclear . One possible explanation is that sperm development is sensitive to disruption of X-linked gene regulation . In mice , evidence linking abnormal gene expression on the X c...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary", "biology/animal", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/genomics" ]	2010	Widespread Over-Expression of the X Chromosome in Sterile F1 Hybrid Mice
The Type VI secretion system ( T6SS ) is widespread among bacterial pathogens and acts as an effective weapon against competitor bacteria and eukaryotic hosts by delivering toxic effector proteins directly into target cells . The T6SS utilises a bacteriophage-like contractile machinery to expel a puncturing device base...	Pathogenic bacteria use a biological nanomachine called the ‘Type VI secretion system’ ( T6SS ) to fire toxic proteins into other cells . These target cells can be rival bacterial cells , allowing the T6SS-wielding bacteria to outcompete other pathogens or harmless bacteria , or cells of a human , animal or plant , to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "drugs", "microbiology", "immunoblotting", "plasmid", "construction", "physiological", "proce...	2016	VgrG and PAAR Proteins Define Distinct Versions of a Functional Type VI Secretion System
Programmed cell death is characterized by a cascade of tightly controlled events that culminate in the orchestrated death of the cell . In multicellular organisms autophagy and apoptosis are recognized as two principal means by which these genetically determined cell deaths occur . During plant-microbe interactions cel...	During plant-microbe interactions , regulated cell death known as programmed cell death ( PCD ) can mediate both resistant and susceptible interactions . Sclerotinia sclerotiorum induces an apoptotic spreading cell death during infection , via the secreted virulence determinant oxalic acid . Oxalic acid deficient funga...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "plant", "science", "plant", "microbiology", "plant", "biology", "plant", "pathogens", "microbial", "control", "plant", "pathology", "biology", "microbiology", "pathogenesis" ]	2013	Cell Death Control: The Interplay of Apoptosis and Autophagy in the Pathogenicity of Sclerotinia sclerotiorum
To explore the role of p16INK4a as an intrinsic barrier to B cell transformation by EBV , we transformed primary B cells from an individual homozygous for a deletion in the CDKN2A locus encoding p16INK4a and p14ARF . Using recombinant EBV-BAC viruses expressing conditional EBNA3C ( 3CHT ) , we developed a system that a...	Epstein-Barr virus ( EBV ) is a causative agent of several types of B cell lymphoma . In human B cells , EBV reduces protein levels of at least two tumour suppressors that would otherwise be activated in response to over-expressed oncogenes . These proteins are BIM , which induces cell death and p16INK4a , which preven...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cellular", "stress", "responses", "immune", "cells", "viruses", "and", "cancer", "immunology", "microbiology", "host-pathogen", "interaction", "cancer", "risk", "factors", "hematologic", "cancers", "and", "related", "disorders", "oncology", "cell", "divisio...	2013	Induction of p16INK4a Is the Major Barrier to Proliferation when Epstein-Barr Virus (EBV) Transforms Primary B Cells into Lymphoblastoid Cell Lines
Production of the pro-inflammatory cytokine IL-12 by innate phagocytes drives the differentiation of IFN-γ-producing effector T cells during Toxoplasma gondii infection . However , the role of IL-12 in the regulation of memory CD8+ T cell differentiation and function during murine toxoplasmosis is unclear . To track me...	Toxoplasma gondii is a ubiquitous protozoan parasite that causes severe disease in people with compromised immune function . It is known that CD8+ T cells are essential for the establishment of protective immunity , primarily through the delivery of the effector cytokine interferon-γ ( IFN-γ ) to Toxoplasma-infected ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immune", "response", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections", "immunology/leukocyte", "activation" ]	2010	Differential Regulation of Effector- and Central-Memory Responses to Toxoplasma gondii Infection by IL-12 Revealed by Tracking of Tgd057-Specific CD8+ T Cells
During vertebrate neurulation , the embryonic ectoderm is patterned into lineage progenitors for neural plate , neural crest , placodes and epidermis . Here , we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation , during the establis...	Vertebrate embryo germ layers become progressively regionalized by evolutionarily conserved molecular processes . Catching the early steps of this dynamic spatial cell diversification at the scale of the transcriptome was challenging , even with the advent of efficient RNA sequencing . We have microdissected complement...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genetic", "networks", "methods", "and", "resources", "vertebrates", "wnt", "signaling", "cascade", "animals", "xenopus", "multivariate", "analysis", "animal", "models", "developmental", "biology", "model", "organisms", "amphibians", "mathematics", "statistics", "(mathema...	2017	A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
The Asian tiger mosquito , Aedes albopictus ( Skuse ) , is a vector of several arboviruses including dengue and chikungunya . This highly invasive species originating from Southeast Asia has travelled the world in the last 30 years and is now established in Europe , North and South America , Africa , the Middle East an...	The Asian tiger mosquito , Aedes albopictus , is a highly invasive mosquito and has spread from South East Asia to Europe , the United States and northern areas of Asia in the past 30 years . Aedes mosquitoes transmit a range of viral diseases , including dengue and chikungunya . Aedes albopictus is generally considere...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "biotechnology/bioengineering" ]	2010	piggybac- and PhiC31-Mediated Genetic Transformation of the Asian Tiger Mosquito, Aedes albopictus (Skuse)
Antibiotics are a major tool in the WHO's trachoma control program . Even a single mass distribution reduces the prevalence of the ocular chlamydia that causes trachoma . Unfortunately , infection returns after a single treatment , at least in severely affected areas . Here , we test whether additional scheduled treatm...	Trachoma is one of the leading causes of blindness in the developing world . The World Health Organization has a multi-pronged approach to controlling the ocular chlamydial infection that causes the disease , including distributing antibiotics to entire communities . Even a single community treatment dramatically reduc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ophthalmology/pediatric", "ophthalmology", "ophthalmology/eye", "infections", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/bacterial", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	Reduction and Return of Infectious Trachoma in Severely Affected Communities in Ethiopia
Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells ( iPSCs ) . Here , we determined the DNA methylation profiles of 22 human iPSC lines derived from five different cell types ( human endometrium , placental artery endothelium , amnion , fetal lung fibroblast , and menstrual...	iPSCs change to resemble ESCs via two phases: the transgene-dependent phase , in which the transcription factors act to transform somatic cells into pluripotent stem cells , and the transgene-independent phase , in which the transcription factors are silenced . In this study , we established human iPSCs derived from 5 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "developmental", "biology", "stem", "cells", "induced", "pluripotent", "stem", "cells", "epigenetics", "epigenomics", "cell", "potency", "embryonic", "stem", "cells", "comparative", "genomics", ...	2011	DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time
Plant developmental dynamics can be heritable , genetically correlated with fitness and yield , and undergo selection . Therefore , characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically imp...	We estimate the developmental dynamics of plant growth using mathematical functions to fit continuous functions to discrete plant height data collected throughout growth , and we use the parameters defining these mathematical functions as data . We identify genomic regions controlling plant growth and filter a novel tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "computer", "and", "information", "sciences", "plant", "science", "genetic", "networks", "gene", "mapping", "quantitative", "trait", "loci", "phenotypes", "network", "analysis", "gene", "identification", "and", "analysis", "gene", "expression", "genetics", "gene", "re...	2019	Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
The transmission dynamics of mosquito-vectored pathogens are , in part , mediated by mosquito host-feeding patterns . These patterns are elucidated using blood meal analysis , a collection of serological and molecular techniques that determine the taxonomic identities of the host animals from which blood meals are deri...	Female mosquitoes take blood meals from diverse vertebrate hosts , including amphibians , birds , mammals , reptiles , and fishes . Mosquito species vary in their host-use patterns . Identifying which mosquitoes feed from which hosts is critical to understanding how mosquitoes transmit disease-causing pathogens between...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "vertebrates", "animals", "organisms", "molecular", "biology", "techniques", "dna", "insect", "vectors", "extraction", "techniques", "research", "and", "analysis", "methods", "sequence", "analys...	2018	Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals
The clinical outcome to Leishmania-infection is determined by the individual adaptive immune T helper cell responses and their interactions with parasitized host cells . An early development of a proinflammatory immune response ( Th1 response ) is necessary for Leishmania-infection resolution . The Toll-interacting pro...	Leishmaniasis is an infectious disease caused by the protozoan parasite of the Leishmania genus . It is transmitted by infected sandfly ( the phlebotomines ) and caused either visceral or tegumentary leishmaniasis depending on the species . In areas of endemicity for leishmaniasis , not all individuals exposed to the s...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Polymorphisms in the TOLLIP Gene Influence Susceptibility to Cutaneous Leishmaniasis Caused by Leishmania guyanensis in the Amazonas State of Brazil
Drug-induced toxicity is a significant problem in clinical care . A key problem here is a general understanding of the molecular mechanisms accompanying the transition from desired drug effects to adverse events following administration of either therapeutic or toxic doses , in particular within a patient context . Her...	Liver toxicity may occur at drug levels above the therapeutic range and is thus a crucial problem in clinical care . However , the cellular changes induced by drug administration of therapeutic and toxic doses in humans are still not well understood . We here coupled patient-specific drug concentration-time profiles fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "dose", "prediction", "methods", "cell", "processes", "biomarkers", "toxicology", "toxicity", "pharmaceutics", "drug", "administration", "pharmacology", "drug", "metabolism", "pharmacok...	2017	A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations
Visceral Leishmaniasis ( VL ) is a neglected tropical disease that afflicts some of the poorest populations in the world including people living in the Bihar state of India . Due to efforts from local governments , NGOs and international organizations , the number of VL cases has declined in recent years . Despite this...	Visceral leishmaniasis ( also known as kala-azar ) caused by infection with L . donovani is a deadly parasitic disease that afflicts some of world’s poorest populations , including the people of the northern Bihar State of India . Once transmitted to a human by an infected sandfly , the L . donovani parasite migrates f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "india", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "research", "design", "protozoans", "leishmania", "neglected", "tropical", "diseases", ...	2016	Longitudinal Study of Transmission in Households with Visceral Leishmaniasis, Asymptomatic Infections and PKDL in Highly Endemic Villages in Bihar, India
The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate . An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract . For this reason , it is thought the observed differences in nose shape among...	The study of human adaptation is essential to our understanding of disease etiology . Evolutionary investigations into why certain disease phenotypes such as sickle-cell anemia and lactose intolerance occur at different rates in different populations have led to a better understanding of the genetic and environmental r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nose", "face", "atmospheric", "science", "population", "genetics", "pigments", "respiratory", "system", "materials", "science", "population", "biology", "humidity", "genetic", "polymorphism", "materials", "by", "attribute", "hea...	2017	Investigating the case of human nose shape and climate adaptation
The parasitic protozoan Trypanosoma brucei utilizes glycolysis exclusively for ATP production during infection of the mammalian host . The first step in this metabolic pathway is mediated by hexokinase ( TbHK ) , an enzyme essential to the parasite that transfers the γ-phospho of ATP to a hexose . Here we describe the ...	African sleeping sickness is a disease found in sub-Saharan Africa that is caused by the single-celled parasite Trypanosoma brucei . The drugs used widely now to treat infections are 50 years old and notable for their toxicity , emphasizing the need for development of new therapeutics . In the search for potential drug...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "biochemistry/drug", "discovery" ]	2010	A Target-Based High Throughput Screen Yields Trypanosoma brucei Hexokinase Small Molecule Inhibitors with Antiparasitic Activity
The mouse has become the most popular organism for investigating molecular mechanisms of body weight regulation . But understanding the physiological context by which a molecule exerts its effect on body weight requires knowledge of energy intake , energy expenditure , and fuel selection . Furthermore , measurements of...	The unrelenting obesity epidemic has resulted in intensive basic scientific investigation into the molecular mechanisms of body weight regulation—with the mouse being the organism of choice for such studies . We know that any mechanism of body weight regulation must exert its effect by influencing food intake , energy ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "diabetes", "and", "endocrinology/obesity", "nutrition/obesity", "physiology/integrative", "physiology", "biochemistry/theory", "and", "simulation" ]	2009	Estimating the Continuous-Time Dynamics of Energy and Fat Metabolism in Mice
Fasciola spp . liver fluke cause pernicious disease in humans and animals . Whilst current control is unsustainable due to anthelmintic resistance , gene silencing ( RNA interference , RNAi ) has the potential to contribute to functional validation of new therapeutic targets . The susceptibility of juvenile Fasciola he...	RNA interference ( RNAi ) is a method for selectively silencing ( or reducing expression of ) mRNA transcripts , an approach which can be used to interrogate the function of genes and proteins , and enables the validation of potential targets for anthelmintic drugs or vaccines , by investigating the impact of silencing...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular", "biology", "biology", "and", "life", "sciences", "parasitology" ]	2014	RNAi Dynamics in Juvenile Fasciola spp. Liver Flukes Reveals the Persistence of Gene Silencing In Vitro
Dengue , a mosquito-borne viral illness , is a major public health problem worldwide , and its incidence continues to increase . In 2009 , the World Health Organization published guidelines that included a revision of the dengue case definition . Compared to the traditional definition , the revised case definition reli...	Dengue , a mosquito-borne viral infectious disease , is a major health problem worldwide . Its incidence has dramatically increased in the last 3 decades , particularly in the Americas . The traditional World Health Organization dengue case definition was in use for over 30 years , but in 2009 a revised dengue case def...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "pathology", "global", "health", "clinical", "pathology", "dengue", "fever", "neglected", "tropical", "diseases" ]	2013	Evaluation of the Diagnostic Utility of the Traditional and Revised WHO Dengue Case Definitions
The recognition of cryptic small-molecular binding sites in protein structures is important for understanding off-target side effects and for recognizing potential new indications for existing drugs . Current methods focus on the geometry and detailed chemical interactions within putative binding pockets , but may not ...	Small molecule drugs may interact with many proteins . Some of these interactions may cause unexpected effects , including side effects or potentially useful therapeutic effects . One way to predict these effects is to analyze the three-dimensional structure of target proteins , and identify new binding sites for small...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "chemistry", "chemistry", "biology", "computational", "biology" ]	2011	Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
The mechanisms of cell cycle exit by neurons remain poorly understood . Through genetic and developmental analysis of Drosophila eye development , we found that the cyclin-dependent kinase-inhibitor Roughex maintains G1 cell cycle exit during differentiation of the R8 class of photoreceptor neurons . The roughex mutant...	Neurons generally differentiate and never divide again . One barrier to understanding the mechanisms has been the paucity of genetic mutations that result in neuronal cell cycles . Here we show that mutation in three genes lead to cell cycle re-entry by a particular class of developing photoreceptor neurons in the fly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	Mitosis in Neurons: Roughex and APC/C Maintain Cell Cycle Exit to Prevent Cytokinetic and Axonal Defects in Drosophila Photoreceptor Neurons
Group 2 Innate lymphoid cells ( ILC2s ) are innate cells that produce the TH2 cytokines IL-5 and IL-13 . The importance of these cells has recently been demonstrated in experimental models of parasitic diseases but there is a paucity of data on ILC2s in the context of human parasitic infections and in particular of the...	Understanding how immune responses are generated is critical for vaccine development . There are comparatively few studies on the interface between the innate and adaptive immune system in generating protective immune responses . Infections with helminth parasites , a cause of neglected tropical diseases , have a huge ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Group 2 Innate Lymphoid Cell Proportions Are Diminished in Young Helminth Infected Children and Restored by Curative Anti-helminthic Treatment
Crimean-Congo hemorrhagic fever ( CCHF ) is an acute , often fatal viral disease characterized by rapid onset of febrile symptoms followed by hemorrhagic manifestations . The etiologic agent , CCHF orthonairovirus ( CCHFV ) , can infect several mammals in nature but only seems to cause clinical disease in humans . Over...	Crimean-Congo hemorrhagic fever ( CCHF ) is a tick-borne disease that can manifest as a viral hemorrhagic fever syndrome . The CCHF virus is widely spread throughout the African continent , the Balkans , the Middle East , Southern Russia and Western Asia where it remains a serious public health concern . Currently , th...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "spleen", "crimean-congo", "hemorrhagic", "fever", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vaccines", "preventive", "medicine", "anim...	2018	Nucleocapsid protein-based vaccine provides protection in mice against lethal Crimean-Congo hemorrhagic fever virus challenge
The RNA recognition motif ( RRM ) is the most common RNA binding domain across eukaryotic proteins . It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence . This was recently achieved for the RRM in Rbfox protein , where four mutations R118D , E147R , N151S , and E152T were des...	RNA is an outstanding target for oncological intervention . Engineering the most common RNA binding motif in human proteins ( called RRM ) so as to bind to a specific RNA has an enormous pharmacological potential . Yet , it is highly non trivial to design RRM-bearing protein variants with RNA selectivity and affinity s...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusions", "Methods" ]	[ "rna-binding", "proteins", "chemical", "bonding", "rna", "stem-loop", "structure", "simulation", "and", "modeling", "protein", "structure", "rna", "isolation", "molecular", "biology", "techniques", "hydrogen", "bonding", "physical", "chemistry", "research", "and", "anal...	2018	Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
Species expand their geographical ranges following an environmental change , long range dispersal , or a new adaptation . Range expansions not only bring an ecological change , but also affect the evolution of the expanding species . Although the dynamics of deleterious , neutral , and beneficial mutations have been ex...	Cooperation is beneficial for the species as a whole , but , at the level of an individual , defection pays off . Natural selection is then expected to favor defectors and eliminate cooperation . This prediction is in stark contrast with the abundance of cooperation at all levels of biological systems: from bacterial b...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "evolutionary", "ecology", "statistical", "mechanics", "applied", "mathematics", "population", "genetics", "mathematics", "population", "modeling", "theoretical", "ecology", "biophysics", "simulations", "evolutionary", "modeling", "biophysics", "theory", "biology", "evolution...	2013	The Fate of Cooperation during Range Expansions
In photosynthetic organisms , feedback dissipation of excess absorbed light energy balances harvesting of light with metabolic energy consumption . This mechanism prevents photodamage caused by reactive oxygen species produced by the reaction of chlorophyll ( Chl ) triplet states with O2 . Plants have been found to per...	Reactive oxygen species are formed during photosynthesis , particularly when electron transport is saturated in high light . The process of non-photochemical quenching ( NPQ ) helps protect plants against excess light by dissipating the excited states of chlorophyll into heat . By doing so , it prevents the formation o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biochemistry", "plant", "biology" ]	2011	Analysis of LhcSR3, a Protein Essential for Feedback De-Excitation in the Green Alga Chlamydomonas reinhardtii
While most sensory neurons will adapt to prolonged stimulation by down-regulating their responsiveness to the signal , it is not clear which events initiate long-lasting sensory adaptation . Likewise , we are just beginning to understand how the physiology of the adapted cell is altered . Caenorhabditis elegans is inhe...	Caenorhabditis elegans is capable of sensing a variety of attractive volatile compounds . These odors are the worm's “best guesses” as to how to track down food . Employing calculated approximations underlies a foraging strategy that is open to failure . When C . elegans track an odor which proves unrewarding , they mu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/animal", "genetics", "neuroscience/sensory", "systems", "cell", "biology/cell", "signaling", "cell", "biology/neuronal", "signaling", "mechanisms" ]	2009	Regulators of AWC-Mediated Olfactory Plasticity in Caenorhabditis elegans
Limited information is available regarding the modulation of genes involved in the innate host response to Paracoccidioides brasiliensis , the etiologic agent of paracoccidioidomycosis . Therefore , we sought to characterize , for the first time , the transcriptional profile of murine bone marrow-derived dendritic cell...	Paracoccidioidomycosis is a systemic disease that has an important mortality and morbidity impact in Latin America , mainly affecting rural workers of Argentina , Colombia , Venezuela and Brazil . Upon host infection , one of the most important aspects contributing to disease outcome is the initial encounter of the Par...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genome", "analysis", "tools", "mycology", "fungi", "immunity", "innate", "immunity", "immunology", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "transcriptomes" ]	2012	Murine Dendritic Cells Transcriptional Modulation upon Paracoccidioides brasiliensis Infection
Plasmodium vivax is one of the major species of malaria infecting humans . Although emphasis on P . falciparum is appropriate , the burden of vivax malaria should be given due attention . This study aimed to synthesize the evidence on severe malaria in P . vivax infection compared with that in P . falciparum infection ...	Until recently , vivax malaria has received less attention than falciparum malaria and was deemed neglected . There has been a surge in studies that documented the contribution of Plasmodium vivax to severe malaria in some endemic countries such as Thailand , Brazil , Indonesia , Papua New Guinea and India . We aimed t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "tropical", "diseases", "medicine", "and", "health", "sciences" ]	2014	Is Plasmodium vivax Malaria a Severe Malaria?: A Systematic Review and Meta-Analysis
The potential existence of a wild bird reservoir for highly pathogenic avian influenza ( HPAI ) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses , responsible for concurrent outbreaks in migratory and domestic birds over Asia , Europe , and Africa . During a large-scale sur...	Until recently , the highly pathogenic avian influenza ( HPAI ) viruses responsible for high mortality in some domestic poultry were considered not to have a wild bird reservoir , but to emerge in domestic poultry populations from low pathogenic viruses perpetuated in wild waterbirds . The rapid spread of H5N1 HPAI vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "virology", "infectious", "diseases/viral", "infections", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Evidence of Infection by H5N2 Highly Pathogenic Avian Influenza Viruses in Healthy Wild Waterfowl
Spontaneous retinal activity ( known as “waves” ) remodels synaptic connectivity to the lateral geniculate nucleus ( LGN ) during development . Analysis of retinal waves recorded with multielectrode arrays in mouse suggested that a cue for the segregation of functionally distinct ( ON and OFF ) retinal ganglion cells (...	Many central targets in the brain are involved in the processing of information from the outside world . Before information about the visual scene reaches the visual cortex , it is preprocessed in the retina and the lateral geniculate nucleus . Connections which relay this information between the different brain target...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "neuroscience/neurodevelopment", "computational", "biology/systems", "biology", "computational", "biology/computational", "neuroscience" ]	2009	Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus
The leishmaniases are a complex of neglected tropical diseases caused by more than 20 Leishmania parasite species , for which available therapeutic arsenal is scarce and unsatisfactory . Pentavalent antimonials ( SbV ) are currently the first-line pharmacologic therapy for leishmaniasis worldwide , but resistance to th...	Leishmaniasis represents a major international health problem , has a high morbidity and mortality rate , and is classified as an emerging and uncontrolled disease by the World Health Organization . The migration of population from endemic to nonendemic areas , and tourist activities in endemic regions are spreading th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "medicinal", "chemistry", "chemistry", "biology" ]	2012	In Vitro and In Vivo Efficacy of Ether Lipid Edelfosine against Leishmania spp. and SbV-Resistant Parasites
A large number of rare sequence variants of unknown clinical significance have been identified in the breast cancer susceptibility genes , BRCA1 and BRCA2 . Laboratory-based methods that can distinguish between carriers of pathogenic mutations and non-carriers are likely to have utility for the classification of these ...	A large number of rare sequence variants of unknown clinical significance have been identified in the breast cancer susceptibility genes , BRCA1 and BRCA2 . Laboratory methods to identify which of these variants are mutations would have utility for counseling and clinical decision making when identified in patients wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "genetics", "and", "genomics/gene", "discovery", "oncology/breast", "cancer", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/genetics", "of", "disease", "molecular", "biology", "genetics", "and", "genomics", "cell", "biology/gen...	2010	Use of DNA–Damaging Agents and RNA Pooling to Assess Expression Profiles Associated with BRCA1 and BRCA2 Mutation Status in Familial Breast Cancer Patients
Like several other intracellular pathogens , Mycobacterium marinum ( Mm ) escapes from phagosomes into the host cytosol where it can polymerize actin , leading to motility that promotes spread to neighboring cells . However , only ∼25% of internalized Mm form actin tails , and the fate of the remaining bacteria has bee...	M . tuberculosis is one of the world's most prevalent pathogens , infecting one third of humans and contributing to 2 million deaths each year . M . marinum ( Mm ) has been increasingly studied as a model of M . tuberculosis due to its relative safety and its shared mechanisms of pathogenesis; for example , previous st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "immunology/innate", "immunity", "cell", "biology/membranes", "and", "sorting", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "microbiology/cellular", "microbi...	2009	Atg5-Independent Sequestration of Ubiquitinated Mycobacteria
Serine proteases are important virulence factors for many pathogens . Recently , we discovered a group of trypsin-like serine proteases with domain organization unique to flatworm parasites and containing a thrombospondin type 1 repeat ( TSR-1 ) . These proteases are recognized as antigens during host infection and may...	Schistosomiasis ( bilharziasis ) is a global parasitic infection with more than 240 million people infected . It is caused by Schistosoma flatworms that live in the bloodstream . Current treatment relies on one drug , and no effective vaccine has yet been developed . Proteolytic enzymes ( proteases ) help the parasite ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Homology", "model", "of", "SmSP2", "reveals", "the", "trypsin-like", "active", "site", "pocket", "shielded", "by", "additional", "loops", "Substrate", "and", "inhibitor", "specificity", "classifies...	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "enzymes", "enzymology", "parasitic", "diseases", "animals", "serine", "proteases", "plasmins", "research", "and", "analysis", "methods", "s...	2018	SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties
Reproduction is inherently risky , in part because genomic replication can introduce new mutations that are usually deleterious toward fitness . This risk is especially severe for organisms whose genomes replicate “semi-conservatively , ” e . g . viruses and bacteria , where no master copy of the genome is preserved . ...	Most spontaneous mutations hurt organismal fitness , e . g . by destabilizing proteins . In many species , the normal mutation rate is strikingly high: on the order of one per genome per replication . In the face of these mutations , how can proteins maintain their native structure , and how can populations of organism...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology", "protein", "folding", "biology", "evolutionary", "theory", "biophysics" ]	2012	Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation
Identification of responsive genes to an extra-cellular cue enables characterization of pathophysiologically crucial biological processes . Deep sequencing technologies provide a powerful means to identify responsive genes , which creates a need for computational methods able to analyze dynamic and multi-level deep seq...	Cellular processes in mammalian cells are tightly regulated to ensure that the cells function properly as a part of an organism . Dysregulation of some of these processes , such as apoptosis , cell proliferation and growth , can lead to cancer . One of the most important regulation mechanisms for cellular processes is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "algorithms", "medicine", "oncology", "computer", "science", "software", "engineering", "software", "tools" ]	2013	Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
Zika virus ( ZIKV ) , an emerging arbovirus belonging to the genus Flavivirus , is transmitted by Aedes mosquitoes . ZIKV infection can cause microcephaly of newborn babies and Guillain–Barré syndrome in adults . Because no licensed vaccine or specific antiviral treatment is available for ZIKV infection , the most comm...	Zika virus ( ZIKV ) is a human threat with a global health burden . As many as 86 countries and territories have reported evidence of mosquito-transmitted Zika infection , and there is no effective means of control . Recently , several studies have identified FDA-approved drugs exerting anti-ZIKV activity in mammalian ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "toxicology", "drug", "screening", "viruses", "toxicity", "rna", "viruses", "pharmacology", "insect", "vecto...	2019	Identification of anti-flaviviral drugs with mosquitocidal and anti-Zika virus activity in Aedes aegypti
Reverse genetics systems have been established for all major groups of plant DNA and positive-strand RNA viruses , and our understanding of their infection cycles and pathogenesis has benefitted enormously from use of these approaches . However , technical difficulties have heretofore hampered applications of reverse g...	Reverse genetics is a powerful tool for fundamental studies of virus biology , pathology and biotechnology applications . Although plant negative-strand RNA ( NSR ) viruses consist of members in the Rhabdoviridae , Bunyaviridae , Ophioviridae families and several unassigned genera that collectively account for many eco...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Rescue of a Plant Negative-Strand RNA Virus from Cloned cDNA: Insights into Enveloped Plant Virus Movement and Morphogenesis

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