Miracle-dz/UniFAR-FTUs huggingface dataset:
Elysium: RNA-seq Alignment in the Cloud

Motivation RNA-sequencing (RNA-seq) is currently the leading technology for genome-wide transcript quantification. Mapping the raw reads to transcript and gene level counts can be achieved by a variety of aligners and pipelines. The diversity of processing options reduces interoperability. In addition, the alignment step requires significant computational resources and basic programming knowledge. Elysium enables users of all skill levels to perform a uniform and free RNA-seq alignment in the cloud. Results The Elysium infrastructure is comprised of four components: A file upload API that enables storage of FASTQ files on Amazon S3 without Amazon credentials; an API to handle the cloud alignment job scheduling for uploaded files; and a graphical user interface (GUI) to provide intuitive access to users that do not have command-line access skills. Availability The Elysium source code is available under the Apache Licence 2.0 on GitHub at: https://github.com/maayanlab/elysium The service of cloud based RNA-seq alignment is freely accessible through the Elysium GUI at: http://elysium.cloud
HIV-1-Syphilis Co-infection Associated with High Viral Load in Female Sex Workers in the Democratic Republic of the Congo

Background: Sexually transmitted infection (STI) and HIV co-infection are common in countries where resources are limited constituting a leading public health issue. The negative impact of HIV transmission and acquisition are known. The aim of this study was to determine whether HIV-1-syphilis co-infection is associated with high HIV-1 viral load (VL) in female sex workers (FSWs) in the Democratic Republic of the Congo (DRC). Methods: Sera from 411 FSWs tested HIV+ in a national, DRC HIV/STI Integrated Biological and Behavioral Surveillance Survey (IBBSS) conducted between December 2012 and January 2013. HIV and syphilis testing were performed according to validated DRC national testing algorithms used by the national HIV-AIDS and STI program (PNLS). VL was measured according to Abbot m2000sp and m2000rt protocols. HIV-1-syphilis co-infection proportion was determined and multivariate analyses were used to identify factors associated with higher VL in HIV-1-syphilis co-infected FSWs. Results: Of 411 HIV-infected FSWs, 19.2% (95% CI: 15.4 – 23.0) were co-infected with syphilis. The mean HIV-1 VL in HIV-1-positive FSWs co-infected with syphilis [2.9 log10 HIV RNA/mL (95% CI: 2.49 – 3.29)] was higher compared with those not co-infected with syphilis [2.2 log10 HIV RNA/mL (95% CI: 1.97 – 2.46)]. Multivariate analysis showed that syphilis co-infection was associated with high HIV-1 VL (aOR [95% CI] = 1.90 [1.03, 3.52]) but HIV-1 VL was not influenced by age, education level, duration in sex profession, abnormal fluid, and sore to sex. Conclusion and Implications for Translation: HIV-1 – Syphilis co-infection was associated with higher HIV-1 VL. Preventing FSWs from getting STIs and screening HIV infected individuals for STIs and providing them with appropriate treatment could impact the transmission of HIV from FSWs to their clients. Keywords: • HIV-1 • Syphilis • Co-infection • Viral load • Female sex workers • DRC Copyright © 2020 Musema et al. Published by Global Health and Education Projects, Inc. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in this journal, is properly cited.
Nutri-Epigenetics and Gut Microbiota: How Birth Care, Bonding and Breastfeeding Can Influence and Be Influenced?

Maternal lifestyle is an important factor in the programming of an infant’s epigenome, in particular when considered alongside the mode of birth and choice of feeding method (i.e., breastfeeding or formula feeding). Beginning in utero, and during the first two years of an infant’s life, cells acquire an epigenetic memory of the neonatal exposome which can be influential across the entire lifespan. Parental lifestyle (e.g., malnutrition, alcohol intake, smoke, stress, exposure to xenobiotics and/or drugs) can modify both the maternal and paternal epigenome, leading to epigenetic inheritance in their offspring. This review aims to outline the origin of early life modulation of the epigenome, and to share this fundamental concept with all the health care professionals involved in the development and provision of care during childbirth in order to inform future parents and clinicians of the importance of the this process and the key role it plays in the programming of a child’s health.
Source identification of atmospheric organic vapors in two European pine forests: Results from Vocus PTR-TOF observations

Abstract. Atmospheric organic vapors play essential roles in the formation of secondary organic aerosol. Source identification of these vapors is thus fundamental to understand their emission sources and chemical evolution in the atmosphere and their further impact on air quality and climate change. In this study, a Vocus proton-transfer-reaction time-of-flight mass spectrometer (PTR-TOF) was deployed in two forested environments, the Landes forest in southern France and the boreal forest in southern Finland, to measure atmospheric organic vapors, including both volatile organic compounds (VOCs) and their oxidation products. For the first time, we performed binned positive matrix factorization (binPMF) analysis on the complex mass spectra acquired with the Vocus PTR-TOF and identified various emission sources as well as oxidation processes in the atmosphere. Based on separate analysis of low- and high-mass ranges, fifteen PMF factors in the Landes forest and nine PMF factors in the Finnish boreal forest were resolved, showing a high similarity between the two sites. Factors representing monoterpenes dominate the biogenic VOCs in both forests, with less contributions from the isoprene factors and sesquiterpene factors. Particularly, various terpene reaction products were separated into individual PMF factors with varying oxidation degrees, such as lightly oxidized compounds from both monoterpene and sesquiterpene oxidations, monoterpene-derived organic nitrates, and monoterpene more oxidized compounds. These factors display similar mass profiles and diurnal variations between the two sites, revealing similar terpene reaction pathways in these forests. With the distinct characteristics of VOCs and oxygenated VOCs measured by the Vocus PTR-TOF, this study identified various primary emission sources and secondary oxidation processes of atmospheric organic vapors in the European pine forests, providing a more comprehensive understanding of gas-phase atmospheric chemistry.
Anti-müllerian hormone level in patients with polycystic ovary syndrome

Background: Polycystic ovary syndrome (PCOS) is one of the common causes of chronic anovulation and hyperandrogenism in women between the age of 13 and 45 years old. PCOS is characterized by an increased number of follicles at all growing stages particularly in the preantral and small antral follicles, those who primarily produce Anti-Müllerian hormone (AMH). Objective: The aim of the study is to measure the AMH levels in serum of the women with PCOS. Materials and Methods: The study included 90 women (50 cases with PCOS and 40 control cases healthy women). PCOS patients were diagnosed according to the Rotterdam definition; serum AMH was measured using the ultrasensitive AMH enzyme-linked immunosorbent assay. Results: Mean serum of AMH in PCOS patients was 11.52 ng/ml and for the control group was 3.36 ng/ml and was statistically significant with the P < 0.0001. Conclusions: AMH is elevated in PCOS patients, which can be used in the future as a marker for the diagnosis of PCOS.
Cuando la conservación no puede seguir el ritmo del desarrollo: Estado de salud de los ecosistemas coralinos del Pacífico Norte de Costa Rica

When conservation can keep up with development ́s pace: Health status of coral ecosystems in the North Pacific of Costa Rica. Coral reefs are diverse and productive ecosystems, despite this, they are being threatened by human activities that enhance the detrimental impact of the natural phenomenon’s like Harmful Algal Blooms (HAB). The north Pacific of Costa Rica has been characterized as one of the best regions for the coral reefs development in the country. However, many of these ecosystems are being lost as a result of eutrophication, overfishing, invasive species and others impacts that affect the region. In the present study, live coral cover in the north Pacific was 5.0 ± 10.4(s.d.) %, with a domination in the ecosystems by turf algae. Twenty-six invertebrate taxa were registered in the region with the predominance of the sea urchin Diadema mexicanum. Ninety-four species of reef fish were identified. Snappers and some planktivores species were the groups with the highest frequency and abundance. The localities previously studied in the 1990 decade, presented a mean live coral cover between 40-50 %, whereby the actual state of the reef reflect a significant deterioration. This decline in coral cover is due to natural events like the El Niño, as well as the decrease in water quality in the region. In recent years, proliferations of the invasive seaweed Caulerpa sertularioides and high densities of bioerosive sea urchins have been reported, mainly associated with HAB events. Likewise, fish communities have low biomass, especially in the vicinity of fishing villages. The state of the reefs in the North Pacific is worrying and requires actions for its recovery and conservation, for which there must be better planning of the development of projects and activities on the coast. Rev. Biol. Trop. 66(Suppl. 1): S280-S308. Epub 2018 April 01.
Effect of Moringa oleifera Ethanolic Leaf Extract for the Management of Hepatotoxicity and Nephrotoxicity in Mice

Moringa oleifera is a valued medicinal plant. It is a rich source of nutrients, amino acid, antioxidants, anti-ageing and anti-inflammatory compounds. This study was carried out to assess the effect of the ethanolic extract of Moringa oleifera leaves on tetrachloride CCL4 induced liver damage and gentamycin induced kidney damage in albino mice. Twenty-eight (28) mice were divided into seven groups subjected to the different treatments. Results from the serum enzyme assay revealed that the Moringa oleifera leaf ethanolic extract reduced the activities of the hepatic Original Research Article Tariq et al.; JOCAMR, 6(4): 1-10, 2018; Article no.JOCAMR. 44623 2 and renal enzymes voz: ALP, AST, ALT, blood urea nitrogen and creatinine. Moringa oleifera leaf extracts showed significant amelioration of experimentally induced hepatotoxicity and nephrotoxicity which enhanced the recovery from hepatic damage induced by CCL4 and renal damage induced by gentamycin.
Small mammal species richness is directly linked to regional productivity, but decoupled from food resources, abundance, or habitat complexity

Species richness is often strongly correlated with climate. The most commonly invoked mechanism for this climate‐richness relationship is the more‐individuals‐hypothesis (MIH), which predicts a cascading positive influence of climate on plant productivity, food resources, total number of individuals, and species richness. We test for a climate‐richness relationship and an underlying MIH mechanism, as well as testing competing hypotheses including positive effects of habitat diversity and heterogeneity, and the species‐area effect.
Non-CG methylation and multiple epigenetic layers associate child abuse with immune and small GTPase dysregulation

Early-life adversity (ELA) is a major predictor of psychopathology, and is thought to increase lifetime risk by epigenetically regulating the genome. Here, focusing on the lateral amygdala, a major brain site for emotional homeostasis, we described molecular cross-talk among multiple epigenetic mechanisms, including 6 histone marks, DNA methylation and the transcriptome, in subjects with a history of ELA and controls. We first uncovered, in the healthy brain, previously unknown interactions among epigenetic layers, in particular related to non-CG methylation in the CAC context. We then showed that ELA associates with methylomic changes that are as frequent in the CAC as in the canonical CG context, while these two forms of plasticity occur in sharply distinct genomic regions, features, and chromatin states. Combining these multiple data indicated that immune-related and small GTPase signaling pathways are most consistently impaired in the amygdala of ELA individuals. Overall, this work provides new insights into epigenetic brain regulation as a function of early-life experience.
Resveratrol and arctigenin production from polydatin and arctiin respectively by a thermostable β-glucosidase from Thermotoga maritima

Abstract For preparation of resveratrol and arctigenin from peanut hulls and arctium lappa fruits, respectively, a recombinant β-glucosidase (TmBglA) from hyperthermophile Thermotoga maritima was purified and characterized. The hydrolytic activity was the highest at 90 °C and pH 6.2 for arctiin with Km of 1.61 mM and kcat of 197.4 s−1, and 90 °C and 5.8 for polydatin with Km of 0.38 mM and kcat of 47.6 s−1. The enzyme produced 215.4 mg L−1 resveratrol and 355.7 mg L−1 arctigenin from 400 mg L−1 polydatin and 540 mg L−1 arctiin after 60 min of incubation at 80 °C, with capable of hydrolyzing up to 92.1 and 94.9% of polydatin and arctiin, respectively. The enzymatic hydrolysis of peanut hulls and fructus arctii displayed a conversion yield of 3.8 and 0.33 mg resveratrol and arctigenin per gram of substrate material flour, respectively. Of the reported β-glucosidase, TmBglA exhibited the highest thermostability, kcat, kcat/Km, and conversion productivity for hydrolyzing polydatin and arctiin, and has great potential applications in functional food and medicine production. Graphical Abstract
Ionic Mechanisms of Regional Action Potential Heterogeneity in the Canine Right Atrium

Abstract—Atrial action potential heterogeneity is a major determinant of atrial reentrant arrhythmias, but the underlying ionic mechanisms are poorly understood. To evaluate the basis of spatial heterogeneity in canine right atrial repolarization, we isolated cells from 4 regions: the crista terminalis (CT), appendage (APG), atrioventricular ring (AVR) area, and pectinate muscles. Systematic action potential (AP) differences were noted: CT cells had a “spike-and-dome” morphology and the longest AP duration (APD; value to 95% repolarization at 1 Hz, 270±10 ms [mean±SEM]); APG and pectinate muscle cells had intermediate APDs (180±3 and 190±3 ms, respectively; P<0.001 versus CT for each), with APG cells having a small phase 1; and AVR cells had the shortest APD (160±4 ms, P<0.001 versus other regions). The inward rectifier and the slow and ultrarapid delayed rectifier currents were similar in all regions. The transient outward K+ current was significantly smaller in APG cells, explaining their small phase 1 .
Effects of Mexican dwarf mistletoe (Arceuthobium vaginatumsubsp.vaginatum) on the growth ofPinus cooperiin Durango, Mexico-A case study

Mexican dwarf mistletoe (Arceuthobium vaginatum subsp. vaginatum, Viscaceae) is the most widespread and damaging parasitic plant in Mexico. It parasitizes 10 species of pines (Pinus spp., Pinaceae) as principal hosts, including Pinus cooperi, one of the economically most important pines in the state of Durango. As a case study, we used stem analysis to estimate the effects of Mexican dwarf mistletoe on volume and height growth of dwarf mistletoe‐infected P. cooperi in western Durango (Ejido El Brillante, Municipality Pueblo Nuevo). This case study sampled a total of 48 trees, 12 in each of four infection classes estimated using the 6‐class dwarf mistletoe rating system (DMR): uninfected (DMR 0), lightly infected (DMR 1–2), moderately infected (DMR 3–4) and severely infected (DMR 5–6). Significant reductions in both volume and height growth were found for moderately and severely infected trees when compared to uninfected trees. On average, reductions in volume growth and height growth were as high as 50% and 17%, respectively. The largest growth reductions were for moderately infected trees, but large growth reductions also occurred for severely infected trees. Because of the reduced growth associated with moderate to severe infection, Mexican dwarf mistletoe‐infested pine forests in Durango, where timber production is a high priority, should be managed using harvesting practices that reduce dwarf mistletoe infection, and thereby, increase forest productivity.
Concurrent EEG- and fMRI-derived functional connectomes exhibit linked dynamics

Large-scale functional connectivity of the human brain, commonly observed using functional Magnetic Resonance Imaging (fMRI), exhibits a whole-brain spatial organization termed the functional connectome. The fMRI-derived connectome shows dynamic reconfigurations that are behaviorally relevant. Due to the indirect nature of fMRI, it is unclear whether such topographic changes reliably reflect modulation in neuronal connectivity patterns. Here, we directly compared concurrent fMRI-derived and electrophysiological connectivity dynamics on a connection-wise basis across the whole connectome. Dynamic whole-brain functional connectivity (dFC) was assessed during resting-state in two independent concurrent fMRI-electroencephalography (EEG) datasets (42 subjects total) using a sliding window approach. FMRI- and EEG-derived dFC shared significant mutual information in all canonical EEG frequency bands. Notably, this was true for virtually all connections. Across all EEG frequency bands, connections with the strongest link between EEG and fMRI dynamics tied the default mode network (DMN) to the rest of the brain. Beyond this frequency-independent multimodal dFC, fMRI connectivity covaried with EEG connectivity in a frequency-specific manner in two distributed sets of connections for delta and gamma bands, respectively. These results generalized across the two datasets. Our findings promote the DMN as a universal hub of dynamics across frequencies, but also show that spatial distribution of fMRI and EEG dFC differ across the canonical EEG-frequency bands. This study reveals a close relationship between time-varying changes in whole-brain connectivity patterns of electrophysiological and hemodynamic signals. The results support the value of EEG for studying the whole-brain connectome and provide evidence for a neuronal basis of fMRI-derived dFC.
Phospholipid vesicles for enhanced drug delivery in dermatology

Phospholipid vesicles (liposomes) have been widely investigated as carriers for enhancing skin delivery of drugs. The similarity between lipid compositions of liposomes with the skin structures enables liposomes to be used as physiologically acceptable drug delivery nanosystems. By manipulation of their physico-chemical properties the effective skin delivery of the encapsulated/incorporated drug can be achieved. They can be used as carriers to increase the solubility of the poorly soluble drugs or improve the stability of instable compounds. Phospholipid vesicles enable localized skin delivery of lipophilic drugs, enhance the penetration of hydrophilic drugs and help in reducing the drug irritation. Even without entrapped active compound, they have been shown to improve the skin condition by increasing the hydration level of the skin and integrity of the stratum corneum. The potentials and perspectives of different types of phospholipid vesicles have been summarized in this review, including conventional liposomes, deformable liposomes, ethosomes, invasomes and propylene glycol-containing liposomes, with the emphasis on their potential mechanism of action in enhanced skin delivery.
Cytotaxonomic Studies on Thirteen Ferns of Taiwan

Mitotic chromosome numbers of 13 fern taxa collected in Taiwan were counted, and their reproductive modes were estimated by counting the number of spores per sporangium. Four taxa (Pteris angustipinna, P. longipinna, Thelypteris angustifrons×T. glanduligera and Dryopteris enneaphylla var. enneaphylla) were not studied in previous cyotological studies. New cytotypes were recorded for four others (Coniogramme japonica, Pteris dactylina, Blechnum hancockii and Dryopteris varia), and for three taxa (Cyrtomium devexiscapulae, Dryopteris integriloba and D. labordei var. labordei), the present results are the first cytological records of Taiwanese plants of the taxa. The chromosome counts for the remaining two taxa (Stegnogramma tottoides and Acystopteris tenuisecta) matched those previously reported from Taiwan.
Association between XRCC1 exon 10 (Arg399Gln) gene polymorphism and micronucleus as a predictor of DNA damage among radiation workers

Surniyantoro HNE, Lusiyanti Y, Rahardjo T, Nurhayati S, Tetriana D. 2018. Association between XRCC1 exon 10 (Arg399Gln) gene polymorphism and micronucleus as a predictor of DNA damage among radiation workers. Biodiversitas 19: 1676-1682. This study was aimed to examine the association between XRCC1 exon 10 gene polymorphism and micronucleus frequencies in radiation workers and their relation to the confounding factors. This study involved 37 radiation workers and 37 controls from several hospitals in Indonesia. Genotyping of X-ray cross-complementing group 1 (XRCC1) exon 10 gene polymorphism and micronucleus assay were performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Cytokinesis-Block Micronucleus assay (CBMN assay), respectively. The results indicated that MN frequencies were not significantly higher in the exposed workers than in controls (20.46±6.42 versus 16.89 ±9.72; P=0.07). The micronucleus frequencies of radiation workers with mutant genotype showed not significantly higher than controls in the same genotypes (22±6.64 versus 11.75 ± 8.13; P=0.11). The confounding factors, like age, years of employment and equivalent doses were significantly associated with micronucleus frequencies (P<0.05). The equivalent dose has a significantly positive correlation with micronucleus frequencies among radiation workers, increasing the MN frequencies by 16.3 per 1 mSv of equivalent dose (P=0.001). The genetic polymorphism of XRCC1 gene exon 10 demonstrated no association with the extent of DNA damage in the hospital radiation workers. The MN frequencies were strongly associated with age, equivalent dose and years of employment.
Stress Orientations in the Nankai Trough Constrained Using Seismic and Aseismic Slip

The strength of subduction thrust faults is key to understanding seismogenesis at the provenance of Earth's largest earthquakes. Earthquake focal mechanisms are routinely inverted to constrain the stress state at seismogenic depths. However, on some megathrusts, deformation is accommodated by both earthquakes and types of slow fault slip. We employ focal mechanisms of short‐term slow slip events (SSEs), a type of slow fault slip, and earthquakes in a regional stress inversion to investigate the stress state of the Nankai Trough megathrust and interpret the results in the context of regional tectonics Previous studies using earthquake‐only stress inversions found principal stress orientations in this region that are incompatible with thrust faulting on the megathrust. When both SSEs and earthquakes are considered, the stress state of the central and eastern Nankai Trough megathrust is well oriented for thrust faulting. Our results suggest that slow fault slip source regions may appear to have misoriented stress fields if slow fault slip constitutes a substantial proportion of fault slip and the stress field is not well constrained by earthquakes. In the SSE region, we find that faults are well oriented for failure, suggesting they have strengths similar to their surroundings. Combined with low Vp/Vs ratios and sensitivity to small stress changes, our results imply that the megathrust and surroundings operate at low deviatoric stresses in the SSE source region. Further, we show that the coefficient of friction for areas hosting SSEs is low (μ=0.19–0.50), implying frictionally weak materials in the SSE source region.