Miracle-dz/UniFAR-FTUs huggingface dataset:
Do the Moroccan SARS-CoV-2 genetic diversity hamper the use of the developed universal vaccines in Morocco?

The SARS-CoV-2 identified as coronavirus species associated with severe acute respiratory syndrome. At the time of writing, the genetic diversity of Moroccan strains of SARS-CoV-2 is poorly documented. The present study aims to analyze and identify the genetic variants of fortyeight Moroccan strains of SARS-CoV-2 collected from mid-March to the end of May and the prediction of their possible sources. Our results revealed 108 mutations in Moroccan SARS-CoV-2, 50% were non-synonymous were present in seven genes (S, M, N, E, ORF1ab, ORF3a, and ORF8) with variable frequencies. Remarkably, eight non-synonymous mutations were predicted to have a deleterious effect for (ORF1ab, ORF3a, and the N protein. The analysis of the haplotype network of Moroccan strains suggests different sources of SARS-CoV-2 infection in Morocco. Likewise, the phylogenetic analysis revealed that these Moroccan strains were closely related to those belonging to the five continents, indicating no specific strain dominating in Morocco. These findings have the potential to lead to new comprehensive investigations combining genomic data, epidemiological information, and clinical characteristics of SARS-CoV-2 patients in Morocco and could indicate that the developed vaccines are likely to be effective against Moroccan strains.
Sex makes them sleepy: change in host reproductive status induces diapause in parasitoids

When organisms coevolve, any change in one species can induce phenotypic changes in traits and ecology of the other species. The role such interactions play in ecosystems is central, but their mechanistic bases remain underexplored. Upper trophic level species have to synchronize their life-cycle to both abiotic conditions and to lower trophic level species’ phenology and phenotypic variations. We tested the effect of host seasonal strategy on parasitoid diapause induction by using a holocyclic clone of the pea aphid Acyrthosiphon pisum producing two morphs with either asexual (viviparous females) or sexual (oviparous females) reproduction, the latter being only present at the end of the growing season. Aphidius ervi parasitoids from contrasted climatic origin (harsh vs. mild winter areas) were allowed to parasitize each morph and developing parasitoids were next reared under either fall-like or summer-like temperature-photoperiod conditions. We next examined aspects of the host physiological state by comparing the relative proportion of forty-seven metabolites and lipid reserves in both morphs. We found that oviparous morphs are cues per se for diapause induction; parasitoids entered diapause at higher levels when developing in oviparous hosts (19.4 ± 3.0 %) than in viviparous ones (3.6 ± 1.3 %), under summer-like conditions (i.e. when oviparous aphids appear in the fields). This pattern was population-dependent, suggesting local adaptations to overwintering cues. Metabolomics analyses show parasitoids’ response to be mainly influenced by the host’s physiology, with higher proportion of polyols and sugars, and more fat reserves being found in oviparous morphs. Host quality thus varies across the seasons. Our results underline strong coevolutionary processes between hosts and parasitoids in their area of origin, leading to phenological synchronization, and we point out their importance for the provision of ecosystem service such as biological control in the context of climate change.
Relaxation times in diffusion processes

Relaxation time for diffusion between reflecting boundaries is defined and the theory for its evaluation using the backward‐equation approach is presented. A few simple examples are given and comparison with other results in the literature is made. We expect that relaxation time for nonreactive processes might assume the role of mean first passage times in reactive processes.
Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer

Background Ovarian cancer (OC) is a highly malignant disease with a poor prognosis and high recurrence rate. At present, there is no accurate strategy to predict the prognosis and recurrence of OC. The aim of this study was to identify gene-based signatures to predict OC prognosis and recurrence. Methods mRNA expression profiles and corresponding clinical information regarding OC were collected from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and LASSO analysis were performed, and Kaplan–Meier curves, time-dependent ROC curves, and nomograms were constructed using R software and GraphPad Prism7. Results We first identified several key signalling pathways that affected ovarian tumorigenesis by GSEA. We then established a nine-gene-based signature for overall survival (OS) and a five-gene-based-signature for relapse-free survival (RFS) using LASSO Cox regression analysis of the TCGA dataset and validated the prognostic value of these signatures in independent GEO datasets. We also confirmed that these signatures were independent risk factors for OS and RFS by multivariate Cox analysis. Time-dependent ROC analysis showed that the AUC values for OS and RFS were 0.640, 0.663, 0.758, and 0.891, and 0.638, 0.722, 0.813, and 0.972 at 1, 3, 5, and 10 years, respectively. The results of the nomogram analysis demonstrated that combining two signatures with the TNM staging system and tumour status yielded better predictive ability. Conclusion In conclusion, the two-gene-based signatures established in this study may serve as novel and independent prognostic indicators for OS and RFS.
Anticancer Effects and Mechanisms of Action of Plumbagin: Review of Research Advances

Plumbagin (PLB), a natural naphthoquinone constituent isolated from the roots of the medicinal plant Plumbago zeylanica L. , exhibited anticancer activity against a variety of cancer cell lines including breast cancer, hepatoma, leukemia, melanoma, prostate cancer, brain tumor, tongue squamous cell carcinoma, esophageal cancer, oral squamous cell carcinoma, lung cancer, kidney adenocarcinoma, cholangiocarcinoma, gastric cancer, lymphocyte carcinoma, osteosarcoma, and canine cancer. PLB played anticancer activity via many molecular mechanisms, such as targeting apoptosis, autophagy pathway, cell cycle arrest, antiangiogenesis pathway, anti-invasion, and antimetastasis pathway. Among these signaling pathways, the key regulatory genes regulated by PLB were NF-kβ, STAT3, and AKT. PLB also acted as a potent inducer of reactive oxygen species (ROS), suppressor of cellular glutathione, and novel proteasome inhibitor, causing DNA double-strand break by oxidative DNA base damage. This review comprehensively summarizes the anticancer activity and mechanism of PLB.
Clinical significance of pretreatment prognostic nutritional index and lymphocyte-to-monocyte ratio in patients with advanced p16-negative oropharyngeal cancer—a retrospective study

Background Systemic inflammation and nutritional status both play roles in the survival of cancer patients. Therefore, it is important to understand the effects of prognostic nutritional index (PNI) and lymphocyte-to-monocyte ratio (LMR) on the survival of patients with advanced p16-negative oropharyngeal cancer. Methods A total of 142 patients diagnosed with advanced p16-negative oropharyngeal cancer between 2008 and 2015 were enrolled in this study. All patients received primary treatment with definite concurrent chemoradiotherapy (CCRT). Optimal cutoff values for PNI and LMR were determined using receiver operating characteristic curves for survival prediction. Survival rates for different level of PNI and LMR were estimated and compared using Kaplan–Meier method and log-rank test to see if there were significant effects on these end points, including 5-year overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS) rates. The effects of PNI and LMR on survival were assessed using Cox regression model adjusted for other prognostic factors. Results The results showed the optimal cutoff values for PNI and LMR were 50.5 and 4.45, respectively. A high PNI (≧50.5) was significantly improved the 5-year OS. A low LMR (<4.45) was significantly associated with a poor 5-year DFS, DSS, and OS. In multivariate analysis, both PNI and LMR were independent prognosticators for 5-year OS. Conclusions Elevated pretreatment PNI and LMR are both favorable prognosticators in advanced p16-negative oropharyngeal cancer patients undergoing CCRT.
Genetic incompatibilities and reduced transmission in chickens may limit the evolution of reassortants between H9N2 and panzootic H5N8 clade 2.3.4.4 avian influenza virus showing high virulence for mammals

Abstract The unprecedented spread of H5N8- and H9N2-subtype avian influenza virus (AIV) in birds across Asia, Europe, Africa, and North America poses a serious public health threat with a permanent risk of reassortment and the possible emergence of novel virus variants with high virulence in mammals. To gain information on this risk, we studied the potential for reassortment between two contemporary H9N2 and H5N8 viruses. While the replacement of the PB2, PA, and NS genes of highly pathogenic H5N8 by homologous segments from H9N2 produced infectious H5N8 progeny, PB1 and NP of H9N2 were not able to replace the respective segments from H5N8 due to residues outside the packaging region. Furthermore, exchange of the PB2, PA, and NS segments of H5N8 by those of H9N2 increased replication, polymerase activity and interferon antagonism of the H5N8 reassortants in human cells. Notably, H5N8 reassortants carrying the H9N2-subtype PB2 segment and to lesser extent the PA or NS segments showed remarkably increased virulence in mice as indicated by rapid onset of mortality, reduced mean time to death and increased body weight loss. Simultaneously, we observed that in chickens the H5N8 reassortants, particularly with the H9N2 NS segment, demonstrated significantly reduced transmission to co-housed chickens. Together, while the limited capacity for reassortment between co-circulating H9N2 and H5N8 viruses and the reduced bird-to-bird transmission of possible H5N8 reassortants in chickens may limit the evolution of such reassortant viruses, they show a higher replication potential in human cells and increased virulence in mammals.
Defending subjective inflation: an inference to the best explanation

Abstract In a recent opinion piece, Abid (2019) criticizes the hypothesis that subjective inflation may partly account for apparent phenomenological richness across the visual field and outside the focus of attention. In response, we address three main issues. First, we maintain that inflation should be interpreted as an intraperceptual—and not post-perceptual—phenomenon. Second, we describe how inflation may differ from filling-in. Finally, we contend that, in general, there is sufficient evidence to tip the scales toward intraperceptual interpretations of visibility and confidence judgments.
Experimental evidence of transport of pesticides through field soils - a review

Much information is available in the literature about pesticide transport through soils at the field scale. The purpose of this study is to review the literature with a focus on pesticide leaching to groundwater. The literature was compiled and discussed with respect to different factors that influence pesticide leaching. Pesticide leaching below the root zone has been demonstrated in sandy as well as in loamy soils. Particularly in loamy soils, there is evidence that even strongly adsorbing chemicals can move along preferential flow pathways and that the travel times of pesticides are comparable to those of conservative solutes. The amounts of pesticides leached below the root zone by worst case rainfall events depend on the chemical properties and can reach up to 5% of the applied mass. When there is no heavy rainfall shortly following application of chemicals, the mass annually leached below the root zone is in the range of <0.1 to 1%, occasionally it can reach up to 4%. Although a direct comparison cannot be made, the mass lost by leaching seems generally to be smaller than that lost by runoff, depending of course on the slope of the fields. Several factors that affect pesticide leaching, such asmore » surface preparation, soil structure, soil water content, type of irrigation, pesticide formulation, time of application and rainfall events, are discussed with support of experimental evidence. While some factors showed inconsistent effects, others show promise in controlling leaching mechanisms. These latter factors include initial water content, surface preparation, and time of pesticide application. Based on the reviewed literature recommendations were made for future research activities. 172 refs., 1 fig., 7 tabs. « less
On an extended skew curved normal distribution and its application

summary In this paper we introduce a new class of asymmetric normal distributions, namely extended skew curved normal distribution, as a generalization of the skew curved normal distribution of Arellano-Valle et al. (Commun. Statist. Theor. Meth., 2004) and study some of its important aspects. A location scale extension of this family of distribution is also considered and the estimation of the parameters of the extended class is discussed.
Building a schizophrenia genetic network: Evidence that Transcription Factor 4 regulates schizophrenia risk genes

Background The transcription factor 4 (TCF4) locus is one of the most robust association findings with schizophrenia (SZ). However, little is known about the genes regulated by the encoded transcription factor. Methods We conduct chromatin immunoprecipitation sequencing (ChIP-seq) of TCF4 in neural-derived (SH-SY5Y) cells to identify genome-wide TCF4 binding sites, followed by data integration with functional experiments and SZ association findings. Results We identified 11,322 TCF4 binding sites present in two ChIP-seq experiments. These binding sites implicated a gene set that was significantly enriched in 1) Gene Ontology categories including axon/neuronal development and insulin signaling, 2) genes preferentially expressed in brain, in particular pyramidal neurons of the somatosensory cortex, 3) genes down-regulated in TCF4 siRNA knockdown experiments, 4) genes down-regulated in post-mortem brain tissue from SZ patients (OR=2.8, permutation p<4×10−5). Considering genomic alignments, TCF4 binding sites significantly overlapped those for neural DNA binding proteins such as FOXP2 and the SZ-associated EP300. TCF4 binding sites were modestly enriched among SZ risk loci from the Psychiatric Genomic Consortium (OR=1.56, p=0.03). In total, 130 TCF4 binding sites occurred in 39 of the 108 regions published in 2014. Thirteen genes within the 108 loci had both a TCF4 binding site ±10kb and were differentially expressed in siRNA knockdown experiments of TCF4, suggesting direct TCF4 regulation. Conclusions These findings confirm TCF4 as an important regulator of neural genes and point towards functional interactions with potential relevance for SZ.
High aggregation sensitivity of mammalian mitochondrial elongation factor Tu (Tufm) as a sensor for organellar stress

As proteins in mammalian cells exhibit optimal stability at natural temperatures, small temperature variations may cause unfolding and subsequent non-specific aggregation. As this process leads to a loss of function of the affected polypeptides as well as to further cytotoxic stress, aggregate formation has been recognized as a major pathogenic factor in human diseases. In this study we determined the impact of physiological heat stress on mammalian mitochondria on a proteomic level. The overall solubility of endogenous mitochondrial proteins was only marginally affected by a treatment at elevated temperatures. However, we identified a small subset of polypeptides that exhibited an exceptionally high sensitivity to heat stress. The mitochondrial translation elongation factor Tu (Tufm), a essential for organellar protein biosynthesis, was highly aggregation-prone and lost its solubility already under mild heat stress conditions. In parallel, mitochondrial translation as well as the import of cytosolic proteins was defective in heat stressed mitochondria. We propose that a shutdown of endogenous protein synthesis concomitant with a reduced preprotein import has a protective function by attenuating the proteotoxic
Transparent zinc oxide films prepared by electrochemical reaction

Transparent zinc oxide (ZnO) films has been cathodically deposited on conductive glasses from a simple aqueous zinc nitrate electrolyte kept at 335 K. ZnO films prepared had a wurtzite structure and exhibited an optical band gap energy of 3.3 eV which is characteristic of ZnO. A 2‐μm‐thick ZnO film with an optical transmittance of 72% has been deposited by electrolysis only for approximately 20 minutes at the cathodic potential of −1.0 V compared with the Ag/AgCl reference electrode.
Gravitropic Movement in Wheat Coleoptile is Regulated by Ultradian Growth Oscillations

To stand straight and upright along their growth, plants needs to regulate actively their posture. Gravitropic movement, which occurs when plants modify their growth and curvature to orient their aerial organ against the force of gravity, is a major feature of this postural control. A recent model has shown that graviception and proprioception are sufficient to account for the gravitropic movement and subsequent organ posture demonstrated by a range of species. However, some plants, including wheat coleoptiles, exhibit a stronger regulation of posture than predicted by the model. Here, we performed an extensive kinematics study on wheat coleoptiles during a gravitropic perturbation experiment in order to better understand this unexpectedly strong regulation. Close temporal observation of the data revealed that both perturbed and unperturbed coleoptiles showed oscillatory pulses of elongation and curvature variation that propagated from the apex to the base of their aerial organs. In perturbed (tilted) coleoptiles, we discovered a non-trivial coupling between the oscillatory dynamics of curvature and elongation. This relationship appears to be critical to the postural control of the organ, and indicates the presence of a mechanism that is capable of affecting the relationship between elongation rate, differential growth, and curvature.
Redesigning chromosomes for optimized Hi-C assay provides insights on loop formation and homologs pairing during meiosis

In all chromosome conformation capture based experiments the accuracy with which contacts are detected varies considerably because of the uneven distribution of restriction sites along genomes. In addition, repeated sequences as well as homologous, large identical regions remain invisible to the assay because of the ambiguities they introduce during the alignment of the sequencing reads along the genome. As a result, the investigation of homologs during meiosis prophase through 3C studies has been limited. Here, we redesigned and reassembled in yeast a 145kb region with regularly spaced restriction sites for various enzymes. Thanks to this Syn-3C design, we enhanced the signal to noise ratio and improved the visibility of the entire region. We also improved our understanding of Hi-C data and definition of resolution. The redesigned sequence is now distinguishable from its native homologous counterpart in an isogenic diploid strain. As a proof of principle, we track the establishment of homolog pairing during meiotic prophase in a synchronized population. This provides new insights on the individualization and pairing of homologs, as well as on their internal restructuration into arrays of loops during meiosis prophase. Overall, we show the interest of redesigned genomic regions to explore complex biological questions otherwise difficult to address.
IDENTIFICATION OF DRUG-RELATED PROBLEMS ON BETA LACTAM ANTIBIOTICS USED FOR PEDIATRIC AT A SECONDARY-CARE HOSPITAL IN CIMAHI

WHO estimated that >50% of medicines are used inappropriately. One that posess highest risk due to inappropriate use is beta-lactam antibiotic, espescially in pediatric patient since the organ function in pediatric patient has not fully developed as in adult yet. This cross-sectional study was performed to identify drug-related problems (DRPs) occurred during beta-lactam therapy in pediatric hospitalized in a secondary-care hospital in Cimahi. A predetermined medication-use criteria based on the current literatures was created as an assessment standard tools. Furthermore, identification of DRPs based on PCNE v6.2 classification was carried out concurrently (January-March 2015) to 351 patients. As many as 458 DRPs were found including 22 cases inappropriate drugs (category C1.1), 127 cases no indication for drug (C1.2), 42 cases inappropriate combination of drugs, or drugs and food (C1.4), 1 case of too many drugs prescibed for indication (C1.6), 137 cases drug dose too low (C3.1), 89 cases drug dose too high (C3.2), 39 cases duration of treatment too short (C4.1), and 1 case of duration of treatment too long (C4.2). The potential DRPs was estimated to be occured for approximately 1-2 DRPs per patient.Keywords: drug-related problems; beta-lactam antibiotic; pediatric; pharmaceutical care
SOME IMMUNE FACTORS AND HORMONES DETERMINED IN FEMALE ALBINO RATS INDUCED WITH INFERTILITY AND ADMINISTERED WITH ANTHOCLIESTA VOGELII

Funding information Abstract: Introduction: A. vogelii has not been scientifically proven to have the potential, for which it has been medicinally useful in treating ailments. The seed and bark are used as purgative and fertility enhancer among other claims. Aims: Anthocleista vogelii Planch, phyto-constituents were evaluated and the plant leaf extracts effects on the hormonal and immune factors were investigated based on the claims of the traditional medicine practitioners of its usage as fertility enhancer in females. Materials and Methods: Ethanolic extract of Anthocleista vogelii were administered orally for 14 days to female albino rats placed in different groups. First, temporary infertility was induced with Micronor (norethisterone) or Nacetylcysteine (NAC) given orally to some rats, for seven (7) days prior to other treatment. The rats were sacrificed after the completion of extract administration. The absolute counts of clusters of differentiation CD4+ and CD8+ was performed on the blood samples using the Becton Dickinson’s (BD) FACS Count Automated technique. Hormonal analysis was performed on sera obtained from the experimental animals using commercial standard enzyme-linked immunosorbent assay kit. Results: The extract was found to possess anthraquinones, terpenoids, flavonoids, saponins, alkaloids, phenols and phytosterols. The obtained results of the test group compared with control showed a statistically significant decrease (P<0.05) in CD4+ and CD8+ counts cells, prolactin, testosterone respectively. The results showed a significant increase of estradiol and luteinizing hormone in the female rats in the control group compared to extract treated group. The result also suggests that Anthocleista vogelii may have a role in creating the environment required for enhancing pregnancy by decreasing ratio of CD4+ and CD8+. Conclusion: The findings therefore support the claims on the traditional use of Anthocliesta vogelii in that it enhances fertility in female.