Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunosuppressive and antidiabetic activity of polyphenols from Musa paradisiaca

The objective of our study is to examine its immunosuppressive and antidiabetic potential of polyphenols extracted from the peels of Musa paradisiaca . In this study, indirect ELISA was performed in order to determine its immunogenicity against rubella vaccine antigen (Serum institute of India Limited, India) using variable doses of polyphenols (0.312 - 5 mg/ml; 100 µl). In addition, studies were also conducted on normal human whole blood samples in order to examine its proliferation against rubella vaccine antigen (1:500 dilution; 10 µl). Similarly, polyphenols of variable concentration were also tested in diabetic human whole blood samples and measured total cellular content. The results showed that polyphenols at higher doses (5 mg/ml; 100 µl) showed decline in antibody production (immunogenicity) and proliferation assay (rubella vaccine) in human whole blood samples. In contrast, polyphenols also showed reduction in total cellular content in diabetic human whole blood sample at a very low concentration (0.312 mg/ml; 100 µl). Overall, the results indicate that polyphenols extracted from the peels of Musa paradisiaca showed immunosuppressive and
Population density and structure of diurnal primates in Pandam wildlife park, Plateau State, Nigeria.

A survey of diurnal primate species in Pandam wildlife park, Nigeria was conducted to determine its population density and structure. Eight transect lines (2.0km length, 0.02km width) at interval of 1.0km were located as representative samples in the park within the three range stratum (riparian forest, savannah woodland and, swampy area) based on proportional to size in providing information on the primate’s species present in the park. These include (Cercopithecus mona, Erythrocebus pata, Papio anubis and, Chlorocebus tantalus). Direct method of animal sighting was employed. Data was collected and analyzed using descriptive statistics, ANOVA and diversity indices. The result showed that savannah woodland strata had more number of individual species encountered (132) and the lowest was the swampy area. Also the savannah woodland had the highest species diversity and richness while the riparian forest strata had the highest number of species evenness. More so, Cercopithecus tantalus was widespread throughout the park among other primates and Cercopithecus mona is most likely to decline even more rapidly than others since they inhabit the very tall trees. However, the variation in mean value of species sampled were not statistically significance (P>0.05). Generally, atleast one primate can be sighted in every km2 of range strata covered within the park. This census provides update information on the status of primate diversity and numbers within the park which can help to direct conservation efforts of the primates and other animals by the state government. This will further enhance the sustainability and elevation of the park to a National park.Keywords: Population status, Diurnal Primates, ecology, Pandam Wildlife Park,
Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias

The activity of neural populations in the brains of humans and animals can exhibit vastly different spatial patterns when faced with different tasks or environmental stimuli. The degree of similarity between these neural activity patterns in response to different events is used to characterize the representational structure of cognitive states in a neural population. The dominant methods of investigating this similarity structure first estimate neural activity patterns from noisy neural imaging data using linear regression, and then examine the similarity between the estimated patterns. Here, we show that this approach introduces spurious bias structure in the resulting similarity matrix, in particular when applied to fMRI data. This problem is especially severe when the signal-to-noise ratio is low and in cases where experimental conditions cannot be fully randomized in a task. We propose Bayesian Representational Similarity Analysis (BRSA), an alternative method for computing representational similarity, in which we treat the covariance structure of neural activity patterns as a hyper-parameter in a generative model of the neural data. By marginalizing over the unknown activity patterns, we can directly estimate this covariance structure from imaging data. This method offers significant reductions in bias and allows estimation of neural representational similarity with previously unattained levels of precision at low signal-to-noise ratio. The probabilistic framework allows for jointly analyzing data from a group of participants. The method can also simultaneously estimate a signal-to-noise ratio map that shows where the learned representational structure is supported more strongly. Both this map and the learned covariance matrix can be used as a structured prior for maximum a posteriori estimation of neural activity patterns, which can be further used for fMRI decoding. We make our tool freely available in Brain Imaging Analysis Kit (BrainIAK). Author summary We show the severity of the bias introduced when performing representational similarity analysis (RSA) based on neural activity pattern estimated within imaging runs. Our Bayesian RSA method significantly reduces the bias and can learn a shared representational structure across multiple participants. We also demonstrate its extension as a new multi-class decoding tool.
Bacterias del suelo y su capacidad para inhibir a hongos patógenos de las plantas

Introducción: La rizósfera, se ha definido como el volumen del suelo que se encuentra próximo a la raíz, sitio en donde tanto la cantidad como la actividad de microorganismos es mayor [1]. Es decir, que la rizósfera es un ambiente en donde los metabolitos liberados por la planta influencian la actividad tanto de los microorganismos patógenos como benéficos afectando la sanidad y el crecimiento de las plantas. Los microorganismos que habitan en la rizósfera incluyen bacterias, hongos, virus y nematodos, entre otros [2]. En el suelo se encuentran bacterias, especialmente de los géneros Pseudomonas y Bacillus, que inhiben a los patógenos, sobre todo hongos, para lo cual sintetizan compuestos con actividad antifúngica. Otras especies y/o cepas bacterianas sintetizan inhibidores como por ejemplo los antibióticos [3]. Toyoda y Utsimi (1991) [4] demostraron que cepas de Pseudomonas cepacia y Pseudomonas solanacearum hidrolizan el ácido fusárico, que es un agente causal del marchitamiento cuando las plantas son afectadas por Fusarium. Rhizoctonia solani es hongo fitopatógeno que ataca a un amplio rango de cultivos. Las semillas y las plántulas son particularmente susceptibles a este hongo, que persiste en el suelo en forma de esclerocios [5]. Si bien existen fungicidas que se utilizan para el control de R. solani, estos no siempre son eficientes. Adicionalmente, recientemente se ha puesto énfasis en el aislamiento de organismos del suelos que tienen potencial para el desarrollo de formulados para control biológico de organismos patógenos [6]. A partir de cultivos de diluciones de suelo realizados con fines de aislar ciertos hongos identificamos microorganismos que demostraron ser antagónicos de diversos hongos, por lo que hipotetizamos que los mismos puede ser también antagónicos de R. solani. El objetivo de este trabajo fue analizar las interacciones entre microorganismos con capacidad antagonista sobre organismos patógenos de los cultivos.
University students' knowledge and perceived adequate conduct in cases of acute stroke

The ability of the general population to recognize the initial symptoms of acute stroke is important for the prevention of neurological damage. The objective of this study was to investigate the knowledge held by university students in health fields and what they perceived was adequate conduct after recognizing that someone is having an acute stroke. The students took a semi-structured, two-part questionnaire, with the first part referring to social and demographic data and the second containing a description of stroke’s typical clinical presentation and open-ended questions about it. Of the participants, 86.24% were able to recognize stroke. When comparing the initial and final years, the students in their final years had approximately a 10% increase in stroke recognition. Regarding the perceived correct conduct, it was observed that 84.60% of the students in the initial years would have the right conduct compared to 89.32% of the students in the final years. Even though a high percentage of students demonstrated some knowledge about stroke it is important that we aspire to further educate them about the subject, enabling them to eventually contribute to the general population’s education and to promote health.
A Review on Biohydrogenation and Effects of Tannin on It

The process called biohydrogenation occurs mainly in ruminant animals and during it, unsaturated fatty acids, and particularly poly-unsaturated ones (linoleic and linolenic) coverts to a saturated form of stearic acid. For many years, the beneficial effects of biohydrogenation intermediate fatty acids like cis-9 trans-11 linoleic acid, the main natural isomer of conjugated linoleic acids (CLA), and the isomer of trans-9 trans-11 CLA, especially in preventing cancer, has been proved. Many researches tried to use different components to interference biohydrogenation and increase the mediator substrates of CLA (e.g. vaccenic acid (VA)). Recently, due to the effects on rumen microorganism population, so do on biohydrogenation, tannin, a poly phenolic compound, is in the center of considerations. It is well known that tannins, specially condensed tannins, affect the bacteria population involved in biohydrogenation. Consequently, reduction in biohydrogenation via dietary inclusion of tannin is a useful tool to change the milk fatty acid profile toward health promoting fatty acids.
An examination of the evolve-and-resequence method using Drosophila simulans

We develop a set of analytical and simulation tools for Evolve-and-Resequence (E&R) experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood based test statistics combined with permutation suggest parallel evolution of about 120 polymorphisms across the genome. Whole genome simulations calibrated from several Drosophila genetic datasets indicate this response could be generated by as few as 20 loci under strong directional selection, with a corresponding hitch-hiking effect. While this resolves the “excessive significance” paradox typical of E&R experiments, a rank-based correlation analysis of genomic windows that suggests that weaker selection might be acting at a much larger number of sites. Finally, the allele frequency spectrum at sites that experience strong selection in the novel laboratory environment suggests that loci responding to selection may be balanced polymorphisms in nature.
Irrigation water quality and microbial safety of leafy greens in different vegetable production systems: A review

ABSTRACT Access to large sources of quality water for irrigation is fundamental to the hygienic cultivation of fresh produce. However, due to factors such as contamination of water bodies, access to clean uncontaminated water is fast becoming an ever increasing global challenge. The unavailability of quality source water increases the risk of contamination of fresh produce with human pathogenic microorganisms, which may compromise public health. Over the past few years, there has been a decline in the microbiological quality of surface water and other sources used for irrigation. This is mainly due to upstream fecal contamination. Therefore, the assessment and subsequent suitability of alternative water sources for irrigation such as roof-harvested rainwater should be considered. Contrasting views regarding the quality of roof-harvested rainwater (RHRW) have been published. Pathogens such as Salmonella and Campylobacter species and Listeria monocytogenes have been reported in RHRW. Leafy green vegetables such as cabbage, spinach, and lettuce are produced across a wide range of farming systems from regulated formal (commercial farms) to informal (small-scale and homestead gardens) setups. This review will discuss global water challenges associated with irrigation water, microbial quality of source water for irrigation, crop contamination, and pathogen detection and characterization methodologies.
Effect of Saline Water Irrigation on Sour Orange and Volkamer Lemon Seedling Rootstocks

This study was carried out during the two consecutive seasons of 2012 and 2013 in shade house for Plant Production Dept. Fac. Environ. Agri. Sci. Suez Canal Univ. Egypt. Two citrus six-month-old uniform seedling citrus rootstocks namely: Sour orange and Volkamer lemon transferred into black plastic tube PVC (15 cm diameter x 40 cm depth) filled with 2kg growth media mixture of sand soil and peat moss (4:1 by volume) and irrigated using the tap water at 14 days before run treatments. These seedlings were subjected to three different irrigation saline water levels (tap water 700 "control", 2000, and 3000 ppm) to determine the effects of water salt level on growth parameters, chemical compositions, leaf total pigments and proline. The results obtained showed that Volkamer lemon seedlings had the greatest leaf and root biomass, photosynthetic pigments, proline, leaf k content and area of root vascular bundle and had the lowest values leaf N, Cl and Na content, thickness of root cortex, thickness of mesophyll tissue and leaf blade, while Sour orange seedlings were on the contrary. On the other hand, irrigation with the saline water caused decrease the all vegetative growth parameters, plant photosynthetic pigments and area of root vascular cylinder, while increased the leaf N, Cl and Na content, leaf proline concentration and thickness of root cortex, thickness of mesophyll tissue and leaf blade. Finally, vegetative growth parameters, leaf mineral and leaf total pigments analysis and anatomy features for root and leaf blade indicated that Volkamer lemon rootstock is more tolerant to salinity of irrigation water.
Caractérisation fonctionnelle de la voie des microARNs chez le nématode caenorhabditis elegans

MicroRNAs are small non-coding RNA conserved from plants to animals that negatively affect gene expression at the post-transcriptional level. They play an important role in the gene regulation of several biological processes and their misregulations lead to many human diseases including cancers. The production of microRNAs involved two sequential maturation steps by RNAse Type III enzymes Drosha and Dicer to produce 21-23 nucleotides long RNA species. These tiny molecules form a ribonucleoprotein complex containing one Argonaute protein able to specifically target mRNA and repress translation. In order to better understand how microRNAs regulate gene expression, the main objective of my thesis was to investigate the role of the microRNA-specific Argonaute ALG-1, using the nematode Caenorhabditis elegans as animal model. We first focused our work in the identification of molecular cues important for the selection of specific Argonautes essential for the microRNA pathway among the several ones found in C. elegans. Using powerful genetic tools, we discovered that the selection of Argonaute proteins is affected by the structure of the Dicer-produced duplex and by characteristics specific to each protein. To next better understand the functions of the Argonaute protein ALG-1 in the microRNA pathway, we conducted a two-hybrid screen to identify new protein interactors. Among them, we characterized the new role of the ribosomal protein RACK1 in the microRNA pathway in both nematodes and human cells. We demonstrated that the alteration of RACK1 affects the association of the miRNA complex to the translating ribosome suggesting that RACK1 could contribute to recruit the miRISC to the active site of translation. Finally, we also developed a systematic genetic approach to analyze the implication of identified ALG-1 interactors in the microRNA pathway in animals. Collectively, my thesis work, help us to gain new insights about the roles of the microRNA-specific Argonaute complex in gene regulation by microRNAs in animals.
Amino Acid Metabolism Is Regulated by Glucagon Receptor Signaling in Mice

The pancreatic hormone glucagon contributes to diabetic hyperglycemia and glucagon receptor antagonists lower blood glucose in patients with type 2 diabetes. A liver-alpha cell axis has recently been identified which when disrupted leads to hypersecretion of glucagon and may contribute to the development of diabetes. Here, we investigated the hepatic effects of glucagon receptor signaling in rodents and hypothesized that intact glucagon receptor signaling is necessary for amino acid metabolism via non-transcriptional changes leading to increased ureagenesis. Female C57BL/6JRj mice (n=64) were given a glucagon receptor antagonist (GRA) or vehicle orally three hours prior to an intraperitoneal injection with amino acids (Vamin, 3.6 µmol/g body weight), glucagon (200 ng/g body weight), or both, and blood samples were obtained at 0, 4, 12, and 20 minutes after injection. GRA treated animals had a significant decrease in plasma urea (8.6±0.3 vs. 11.1±0.4 mmol/L, p Disclosure M. Winther-Soerensen: None. K.D. Galsgaard: None. R.E. Kuhre: None. J. Pedersen: None. N.J. Wewer Albrechtsen: Speaker9s Bureau; Self; Merck Sharp & Dohme Corp. Other Relationship; Self; Mercodia, Alpco. J.J. Holst: Advisory Panel; Self; Novo Nordisk A/S. Board Member; Self; Zealand Pharma A/S. Speaker9s Bureau; Self; Merck Sharp & Dohme Corp., AstraZeneca. Research Support; Self; Danish Diabetes Academy, Novo Nordisk Foundation. Other Relationship; Self; Antag Therapeutics. Other Relationship; Spouse/Partner; Antag Therapeutics.
Utilising embryonic and extra-embryonic stem cells to model early mammalian embryogenesis in vitro

xvii Chapter 1: Introduction 1 1.1 Early mouse embryonic development: from zygote to blastocyst 1 1.1.1 Cleavage divisions and zygotic genome activation, and early heterogeneity 1 1.1.2 The first cell fate decision and the formation of the blastocyst 2 1.1.3 The second cell fate decision and blastocyst maturation 4 1.2 Implantation of the embryo 7 1.3 Post implantation mouse embryo development 7 1.3. 1 Egg-cylinder morphogenesis 7 1.3. 2 Symmetry breaking and DVE migration 10 1.3. 3 Primitive streak formation and gastrulation 12 1.3. 4 Epithelial to mesenchymal transition 13 1.3. 5 Primordial Germ Cell specification 14 1.3. 6 Axis specification in non-mammalian vertebrates 16 1.4 In vitro models in mammalian developmental biology 18 1.4. 1 Stem cell derivation from the early embryo 18 1.4. 2 Use of ESCs to model development and organogenesis 22
Epigenetic Profiling of Primary DLBCLs Reveals Novel DNA Methylation-Based Clusters and New Underlying Mechanisms of Lymphomagenesis

Abstract 556 Epigenetic profiling of primary DLBCLs reveals novel DNA methylation-based clusters and new underlying mechanisms of lymphomagenesis. Nyasha Chambwe, Matthias Kormaksson, Subhajyoti De, Franziska Michor, Nathalie Johnson, David W. Scott, Randy D. Gascoyne, Ari Melnick, Fabien Campagne and Rita Shaknovich. Diffuse Large B Cell Lymphomas (DLBCLs) are a heterogeneous group of diseases from the clinical, molecular and genetic standpoints. While gene expression profiling has identified clinically and biologically relevant DLBCL subtypes, there is still considerable heterogeneity beyond what has been resolved through transcriptional and genetic profiling. It is increasingly clear that lesions in epigenetic regulatory proteins and transcription factors are a hallmark of DLBCL, which suggests that aberrant epigenetic programming is likely to be a significant factor in these tumors. Our recent preliminary data suggests that aberrant DNA methylation is also widespread in DLBCL and contributes to the abnormal expression patterns of GCB and ABC DLBCLs. Moreover recent data in the setting of AML show that DNA methylation profiles delineate disease subtypes not captured through transcriptional or genetic profiling. We hypothesized that DNA methylation profiles would allow us to identify new, biologically significant DLBCL subtypes. We therefore examined the DNA methylation of over 140 patients with DLBCL using the HELP assay covering multiple CpGs at over 14,000 gene loci. We next performed an unbiased (unsupervised) analysis of probesets that display significant variability (n=3,005), using K-means consensus clustering. This procedure identified four robust DLBCL subtypes based on epigenetic profiles. To identify the genes that define these four clusters we next performed supervised analysis of the DLBCL subtypes including the normal counterpart germinal center B-cells as a normal control, using three independent statistical methods. 46 genes defined cluster A, 236 genes defined cluster B, 376 genes defined cluster C and 1271 genes defined cluster D (selected genes displayed change in methylation of at least 30% at BH corrected p-value Disclosures: No relevant conflicts of interest to declare.
An Essential Erythroid-Specific Enhancer of ATP2B4 Associated with Red Blood Cell Traits and Malaria Susceptibility

Genome-wide association studies (GWASs) have identified thousands of common genetic variants associated with human traits and disease susceptibility. Given that the majority of GWAS-identified SNPs are located within non-coding regions of the genome, the mechanisms of these trait associations are frequently unknown. Here we investigate the biological underpinnings of common trait-associated genetic variation at ATP2B4 , a gene on chromosome 1q32 that encodes a major plasma membrane calcium ATPase (also known as PMCA4). Genetic variation within this locus is associated with several phenotypes including various red blood cell traits (mean corpuscular hemoglobin concentration and red cell distribution width) as well as susceptibility to severe malaria infection. We conducted an expression quantitative trait loci (eQTL) mapping analysis in human erythroblasts and identified a set of SNPs associated with ATP2B4 gene expression in cis. These included the same genetic variants found by GWAS to be associated with RBC traits and malaria susceptibility. Furthermore, these SNPs overlap an intronic erythroid DNase I hypersensitive site at ATP2B4 . An analysis of the ENCODE database showed that this element was erythroid specific in that it lacked DNase I hypersensitivity in >30 queried non-erythroid cell types. We used the CRISPR/Cas9 genome editing system to delete this element in HUDEP-2 immortalized human erythroid precursor cells. We observed that cells bearing a 927 bp biallelic deletion of this noncoding element displayed near complete loss of ATP2B4 expression (3% residual gene expression), while cells bearing heterozygous deletions showed an intermediate gene expression phenotype. We identified a core element that encompassed 3 of the highly trait associated SNPs and 5 GATA1-binding motifs. Biallelic deletion of this 98 bp core led to 83% reduction in ATP2B4 expression. Disruption of individual GATA1-binding motifs resulted in partial reduction of gene expression, suggesting the contribution of multiple binding sites to appropriate gene expression. Overall, this study suggests that variation within an essential erythroid-specific enhancer of ATP2B4 underlies the association of ATP2B4 with RBC traits and malaria susceptibility. Furthermore these results encourage combined analyses of gene expression, chromatin state, and prospective genetic perturbation as a means to explore the variants, elements and genes responsible for heritable blood phenotypes. Disclosures No relevant conflicts of interest to declare.