Miracle-dz/UniFAR-FTUs huggingface dataset:
Compréhension des mécanismes moléculaires et des facteurs génétiques impliqués dans le paludisme sévère : analyse des profils transcriptomiques et processus biologiques caractéristiques du neuropaludisme et méta-analyse sur des gènes associés à la résistance au paludisme

Le paludisme est l'une des maladies infectieuses les plus devastatrices qui a affecte environ 214 millions de personnes dans le monde. Elle est causee par l'infection par le parasite plasmodium, dont P. falciparum et P. vivax sont les plus representes. Le developpement asexue du parasite dans le sang provoque la physiopathologie de la maladie dont l'evolution passe du paludisme simple au paludisme grave, notamment le neuropaludisme. Nos travaux ont d'abord porte sur l'analyse du transcriptome, par la technologie des microarrays, des cellules sanguines d'une cohorte constituee au Senegal. L'analyse des resultats a permis d'identifier un ensemble de genes dont l'expression permettait de distinguer le profil transcriptomique du neuropaludisme de ceux du paludisme simple et des autres formes de paludisme grave. Ces genes sont enrichis en voies biologiques impliquees dans l'activation des recepteurs des lymphocytes B et T mais aussi des TLR et des recepteurs Fcgamma. On y trouve aussi plusieurs genes candidats qui ont deja ete testes pour leur resistance au paludisme, dont RNASE3 et IL18R. Nous avons aussi realise, avec une partie de cette meme cohorte senegalaise, une etude d’association cas-controles qui n’a pas permis de detecter d’association entre le polymorphisme NCR3-412 et le paludisme severe. Enfin l’approche basee sur une metaanalyse a permis de confirmer son implication dans le paludisme simple, ainsi que celle du polymorphisme LTA+252 dans le paludisme severe, contrairement au LTA+80, au TNF-238 et au TNF-308. L’ensemble des travaux contribuent a une meilleure comprehension des facteurs genetiques et genomiques impliques dans la resistance de l’hote au paludisme.
RobNorm: Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform

Motivation In the analysis of proteomics data from mass spectrometry (MS), normalization is an important preprocessing step to correct sample-level variation and make abundance measurements for each specific protein comparable across different samples. Under heterogeneous samples such as in the Phase I study of the Enhancing Genotype-Tissue Expression (eGTEx) project (Jiang, et al., 2019), the samples coming from 32 different tissues, and without prior housekeeping protein information or spike-ins, how to robustly correct the bias but keep tissue internal variations becomes a challenging question. Majority of previous normalization methods cannot guarantee a robust and tissue adaptive correction. This motivates us to develop a data-driven robust normalization method in MS platform to adapt tissue sample heterogeneities. Methods To robustly estimate the sample effect, we take use of the density power weight to down weigh the outliers and extend the one-dimensional robust fitting in (Windham, 1995) and (Fujisawa and Eguchi, 2008) to our structured data. We construct our robust criterion and build the algorithm to get our robust normalization (RobNorm). Results We focus our comparison to the PQN a widely used normalization method in MS. In the simulation studies and real data application, we conclude that our robust normalization method to estimate the sample effect performs better than PQN especially when the regulation magnitude and proportion are large and strong. We also discuss some limitations in our method. Contact huatang@stanford.edu
Regulation of a muralytic resuscitation-promoting factor in Streptomyces coelicolor

iii ACKNOWLEDGEMENTS.iv LIST OF TABLES.ix LIST OF FIGURES.x LIST OF ABBREVIATIONS AND SYMBOLS.xiii PREFACE.xviii CHAPTER 1: GENERAL INTRODUCTION.1 1.1 STREPTOMYCES BACTERIA.1 1.2 STREPTOMYCES SPORES AND BACTERIAL DORMANCY.1 1.2. 1 Streptomyces spores are dormant cells. 1.2. 2 Streptomyces spores are resistant to abiotic stresses. 1.2. 3 Extensive cell wall remodeling occurs during spore maturation. 1.3 GERMINATION OF STREPTOMYCES SPORES.3 1.3. 1 Phase I: Spore darkening 1.3. 1.1 Germination initiation is marked by an increase in endogenous metabolism. 1.3. 1.2 Trehalose is rapidly mobilized during spore darkening. 1.3. 1.3 Carbon dioxide is used to replenish the tricarboxylic acid cycle by anaplerosis. 1.3. 1.4 Germicidins delay the initiation of spore germination by inhibiting ATPases. 1.3. 1.5 Ca triggers and sustains spore germination. 1.3. 2 Phase II: Spore swelling 1.3. 3 Phase III: Germ tube emergence 1.4 RESUSCITATION-PROMOTING FACTORS.8 1.4. 1 Rpfs modulate dormancy and resuscitation in the actinobacteria. 1.4. 2 Rpfs are muralytic enzymes. 1.4. 3 Muralytic activity is required for the resuscitative activities of Rpfs. 1.4. 4 Rpfs are expressed at specific growth stages. 1.5 REGULATION OF RPF GENES.12 1.5. 1 Transcriptional control by sigma factors
Epigenetic Roles of Microbiota and Aloe vera in Health and
Disease

Our healthspan is to a great extent epigenetically determined by diets, lifestyle, and various other environmental factors. Gut microbiota has been proven to be the major player in maintaining human health. Our previous report described health benefits of long-term ingestion of aloe vera gel through the modification of the intestinal microbiota. In the present review, we broadly cover the topics of microbiota and aloe vera gel ingestion related to attenuation of reactive oxygen species, prevention of cardiovascular disorders, effects of life-prolonging calorie restriction. Additional data are summarized on prophylactic actions of fermented butyrate, and aloe-emodin related components against obesity. Prophylactic actions of aloe vera gel on healthy aging, skin photo-aging, and the viability and lifespan in Drosophila melanogaster are discussed in relation to the properties of butyrate and its potential effects involved in health and disease.
Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV

Pattern recognition receptors (PRRs) protect against host invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. While microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation during viral infection remain overlooked. In this work, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by a positive-sense RNA virus, a negative-sense RNA virus or a retrovirus. We found that several endogenous RNAs transcribed by RNA polymerase 3 (Pol3) specifically engage RLRs, and in particular the family of small non-coding repeats Y-RNAs, which presents the highest affinity as RIG-I ligands. We show that this recognition is dependent on Y-RNA mimicking viral secondary structure and its 5’-triphosphate extremity. Further, we found that HIV-1 infection triggers a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, leading to an increase of Y-RNA 5’-triphosphorylation that enables their immunogenicity. Importantly, we show that altering DUSP11 expression is sufficient to induce a type-I interferon and T cell activation transcriptional program associated with HIV-1 infection. Overall, our work uncovers the critical contribution of endogenous repeat RNAs ligands to antiviral immunity and demonstrates the role of this pathway in HIV-1 infection.
A linked open data framework to enhance the discoverability and impact of culture heritage

Cultural heritage institutions have recently begun to consider the benefits of sharing their collections using linked open data to disseminate and enrich their metadata. As datasets become very large, challenges appear, such as ingestion, management, querying and enrichment. Furthermore, each institution has particular features related to important aspects such as vocabularies and interoperability, which make it difficult to generalise this process and provide one-for-all solutions. In order to improve the user experience as regards information retrieval systems, researchers have identified that further refinements are required for the recognition and extraction of implicit relationships expressed in natural language. We introduce a framework for the enrichment and disambiguation of locations in text using open knowledge bases such as Wikidata and GeoNames. The framework has been successfully used to publish a dataset based on information from the Biblioteca Virtual Miguel de Cervantes, thus illustrating how semantic enrichment can help information retrieval. The methods applied in order to automate the enrichment process, which build upon open source software components, are described herein.
Avaliação da produção de anticorpos contra a saliva de Lutzomyia longipalpis em crianças numa área endêmica de leishmaniose visceral

People living in endemic areas for Visceral Leishmaniasis present antibodies against the saliva of the vector, Lutzomyia longipalpis. We have quantified total as well as specific antibodies against salivary gland lysate of Lutzomyia longipalpis from the IgG, lgG1, lgG3, lgG4 and IgE subclasses in the serum of naturally exposed children (aged 0-5 years). Sera were obtained from a prospective study, in which ani\-Leishmania serologic assay (ELISA) and delayed- type hypersensitivity (DTH) were evaluated. Individuals who were negative for both ELISA and DTH in the first evaluation (phase 1) were followed and tested once more (phase 2) and classified into four groups (positive for both serology and DTH, positive serology and negative DTH, negative serology and positive DTH and negative for both serology and DTH). Fifteen sera from each group in each phase were assayed by ELISA and five from the same groups by Western blots using salivary gland extract as antigen. A significant increase of anti-saliva IgG, lgG1 and IgE were observed in the groups that became serology and DTH positive against Leishmania in the second phase. A significant increase of lgG4 titers was observed only in the group that became positive for ar\i\-Leishmania serology. An increase in total IgG was not observed in the ani\-Phlebotomus papatasi and anti-L. whitmani saliva response. Immmunoblot analysis showed an increase in the number of recognized bands in the group with positive DTH. There were 10 main antigens of which 2 (50 and 36 kDa) were commonly recognized by sera from children with positive DTH. Our results display an increase in anti-saliva IgG, lgG1 and IgE antibody titers in the group with positive ani\-Leistimania DTH. Antibodies against sandfly salivary proteins may be of relevance in studying leishmaniasis epidemiology and natural immunity.
The molecular epidemiology of Trypanosoma cruzi infection in wild and domestic transmission cycles, with special emphasis on multilocus microsatellite analysis

Trypanosoma cruzi is a zoonotic vector-bome unicellular parasite, with a highly complex silvatic ecology, and native to the Americas. Substantial genetic diversity has been identified in T. cruzi populations, with six phylogenetic groups or Discrete Typing Groups (DTUs) commonly recognised: TCI, TCIIa, TCIIb, TCIIc, TCIId, and TCIIe. The silvatic affinities of these groups are poorly defined, although broad associations between some lineages and distinct ecological niches are recognised. Additionally, a number of studies have demonstrated a degree of within-DTU diversity, and the current classification may be a poor reflection of the total diversity present. In this PhD thesis the genetic diversity of silvatic T. cruzi is examined, in conjunction with a limited number of domestic strains, to investigate the underlying ecological and epidemiological phenomena that dictate the population genetic structure of this parasite. >200 new T. cruzi and Trypanosoma rangeli isolates, including those from silvatic mammals, domestic and peridomestic triatomine bugs, were collected during fieldwork in Venezuela and Bolivia. Where possible, these isolates were genotyped to a DTU level, and the epidemiological significance of these data discussed. Original silvatic genotype data from this study were then compiled with >1000, historical records (1981-2007) for both mammals and triatomines. This dataset was subjected to basic statistical analysis, and strong support found for an association between parasite genotype, silvatic niche, and triatomine vector. Within-DTU genetic diversity was established for ~200 isolates from two widespread silvatic genotypes, TCI and TCIIc, using a genome-wide panel of 49 microsatellite markers, in tandem with sequence analysis. Substantial genetic diversity was identified in both lineages, coincident with weak spatial structuring. The possibility a population bottleneck was investigated within TCI derived from Andean rodent populations. Moreover, the possibility of a bottleneck was also examined in geographically dispersed human TCI isolates taken from lowland Venezuela. Associated epidemiological implications are discussed. Genetic diversity in TCI was additionally examined at a within-host level. A total of 211 clones were taken from eight mammals, and analysed using a subset of microsatellite markers. Again substantial genetic diversity was evident, with stable infection of the same mammal by a number of different stains. Limited evidence of genetic exchange was also observed, but could not be confirmed, and the implications of this are also discussed.
Rare Variants in the OTOG Gene Are a Frequent Cause of Familial Meniere’s Disease

Objectives Meniere’s disease (MD) is a rare inner ear disorder characterized by sensorineural hearing loss, episodic vertigo and tinnitus. Familial MD has been reported in 6-9% of sporadic cases, and few genes including FAM136A, DTNA, PRKCB, SEMA3D and DPT have been involved in single families, suggesting genetic heterogeneity. In this study, the authors recruited 46 families with MD to search for relevant candidate genes for hearing loss in familial MD. Design Exome sequencing data from MD patients were analyzed to search for rare variants in hearing loss genes in a case-control study. A total of 109 patients with MD (73 familial cases and 36 early-onset sporadic patients) diagnosed according to the diagnostic criteria defined by the Barany Society were recruited in 11 hospitals. The allelic frequencies of rare variants in hearing loss genes were calculated in individuals with familial MD. A single rare variant analysis (SRVA) and a gene burden analysis (GBA) were conducted in the dataset selecting one patient from each family. Allelic frequencies from European and Spanish reference datasets were used as controls. Results A total of 5136 single nucleotide variants in hearing loss genes were considered for SRVA in familial MD cases, but only one heterozygous variant in the OTOG gene (rs552304627) was found in two unrelated families. The GBA found an enrichment of rare missense variants in the OTOG gene in familial MD. So, 15/46 families (33%) showed at least one rare missense variant in the OTOG gene, suggesting a key role in familial MD. Conclusions The authors found an enrichment of multiplex rare missense variants in the OTOG gene in familial MD. This finding supports OTOG as a relevant gene in familial MD and set the groundwork for genetic testing in MD.
Alsidium oliveiranum sp. nov. (Rhodomelaceae, Rhodophyta), an overlooked species from the southwestern Atlantic based on morphology and DNA sequence data

Copyright © 2019 The Korean Society of Phycology 187 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 Alsidium oliveiranum sp. nov. (Rhodomelaceae, Rhodophyta), an overlooked species from the southwestern Atlantic based on morphology and DNA sequence data Silvia M. P. B. Guimarães, Luanda Pereira Soares, Mutue Toyota Fujii and Pilar Díaz-Tapia* Institute of Botany, Nucleus for Research in Phycology, Av. Miguel Estéfano 3687, 04301-012 São Paulo, Brazil Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, A Coruña 15071, Spain
Introductory Chapter: The Versatile Escherichia coli

There are not so many organisms that are so well studied and researched as the bacterium Escherichia coli (E. coli). Since its discovery in 1885, it was used in research, and by end of 2018, there are now already 368,071 publications in PubMed about E. coli [1]. Figure 1, presenting data about number of publications found in PubMed for the search term “Escherichia coli” in the time frame from 1932 to 2018, clearly demonstrates the high and still growing research interest in this microbe.
Cannibalism among same-aged nymphs of the omnivorous predator Dicyphus errans (Hemiptera: Miridae) is affected by food availability and nymphal density

Cannibalism, the act of eating an individual of the same species has been little studied in omnivorous insect predators. Dicyphus errans (Wolff) (Hemiptera: Miridae) is a generalist omnivorous predator that commonly occurs in tomato greenhouses and field crops in the Mediterranean basin. In this work cannibalism among same-aged neonate nymphs of D. errans was studied when 1, 2, 4, 8 or 16 individuals were placed in a Petri dish along with or without heterospecific prey. Although nymphs were unable to complete their development in the absence of prey they survived longer when there were initially 2 individuals per dish than in any other treatment including a single individual. This may indicate that cannibalism in this predator has positive effect on nymphal survival, which however was not the case at higher densities. The presence of heterospecific prey increased nymphal survival and individuals were as equally successful in completing their development as when kept singly. Developmental time in all the treatments was very similar. Adult weight of both females and males was significantly greater when a nymph was reared alone and similar in all the other treatments. The results indicate that cannibalism occurs among neonates of D. errans if heterospecific prey is scarce and has a negative effect on adult weight when heterospecific prey is abundant. This should be considered in studies on enhancing the biocontrol efficiency or mass rearing of this predator.
Twenty actions for a “good Anthropocene”—perspectives from early-career conservation professionals

Humans are now recognized as the main drivers of environmental change, leaving the future of our planet dependent on human action or inaction. Although the outlook of our planet is often depicted in a “doom and gloom” manner due to recent troubling environmental trends, we suggest that a “good Anthropocene” (in which human quality of life may be maintained or improved without cost to the environment) is attainable if we engage in adaptive, multi-disciplinary actions capable of addressing the socio-ecological issues of today and tomorrow. Early-career conservation scientists and practitioners have an unmatched understanding of novel technologies and social connectivity and, as those left with the ever-growing responsibility to be the problem solvers of the attributed increasing environmental consequences of living in the Anthropocene, their perspectives on steps towards a good Anthropocene are valuable. Here we present a list of 20 actions derived by early-career conservation scientists and practitioners for conservationists to help achieve a good Anthropocene that utilize the social connectivity and technology of today. Central to these actions are the notions that multi-, inter-, and trans-disciplinary collaboratives that embrace diverse world views need to be integrated into decision-making processes; training and outreach platforms need to communicate both environmental challenges and solutions broadly; and conservation successes need to be acknowledged and disseminated in a forward-looking, adaptive capacity. Together the 20 actions identified here reinforce the underlying paradigm shift that must accompany living in the Anthropocene, given that biodiversity and healthy ecosystems are requisite for sustained human life. By sharing this list of actions, we look to promote positive socio-environmental changes towards the collective goal of achieving a good Anthropocene.
Annual change in forest grouse in southern Norway: variation explained by temperatures, bilberry seed production and the lunar nodal phase cycle

Forage quality is rarely the focus of studies on grouse performance. The plant stress hypothesis predicts that the protein digestibility of a focal food plant for grouse in Norway, the bilberry Vaccinium myrtillus should be highest after a peak in seed production. Protein digestibility may also be affected positively by cosmic ray (muon) fluxes, which fluctuate with the 9.3-year lunar nodal phase cycle, and negatively by high temperatures in the preceding summers. The annual change (first difference) in ln-transformed black grouse Tetrao tetrix and capercaillie T. urogallus hunting statistic indices from southern Norway 1999–2017 was positively related to the mean June temperature, which is assumed to have a direct positive impact on chick survival. In multiple regression models, there was also a positive relationship with the seed production of bilberry in the preceding year, the lunar nodal phase index with a two-year time lag, and a negative relationship with the combined mean June–September temperature of the two preceding years. Small rodent numbers did not contribute significantly in these models. In further monitoring of grouse populations, the seed production of bilberry or other important food plants should also be recorded.
Multi-view Information-theoretic Co-clustering for Co-occurrence Data

Multi-view clustering has received much attention recently. Most of the existing multi-view clustering methods only focus on one-sided clustering. As the co-occurring data elements involve the counts of sample-feature co-occurrences, it is more efficient to conduct two-sided clustering along the samples and features simultaneously. To take advantage of two-sided clustering for the co-occurrences in the scene of multi-view clustering, a two-sided multi-view clustering method is proposed, i.e., multi-view information-theoretic co-clustering (MV-ITCC). The proposed method realizes two-sided clustering for co-occurring multi-view data under the formulation of information theory. More specifically, it exploits the agreement and disagreement among views by sharing a common clustering results along the sample dimension and keeping the clustering results of each view specific along the feature dimension. In addition, the mechanism of maximum entropy is also adopted to control the importance of different views, which can give a right balance in leveraging the agreement and disagreement. Extensive experiments are conducted on text and image multiview datasets. The results clearly demonstrate the superiority of the proposed method.