Miracle-dz/UniFAR-FTUs huggingface dataset:
Induced Pluripotent Stem Cells Derived From Two Idiopathic Azoospermia Patients Display Compromised Differentiation Potential for Primordial Germ Cell Fate

At present, the etiology of most non-obstructive azoospermia (NOA) remains unclear. In vitro generation of patient-specific induced pluripotent stem cells (iPSCs) is an effective approach for exploring the mechanisms of human disease. Here, we established iPSCs from two patients with idiopathic NOA and differentiated them into primordial germ cell–like cells (PGCLCs) in vitro. Compared with iPSCs derived from normal fertile men, the NOA patient-specific iPSCs show decreased efficiency of PGCLC formation in vitro. Particularly, the embryoids derived from NOA patient-specific iPSCs show defects in the expression of early primordial germ cell (PGC) genes. The transcriptome analysis reveals the expression patterns of key human PGC genes are generally similar in PGCLCs differentiated from all iPSC lines, and the differentially expressed genes were enriched with gene ontology (GO) of cell cycle and apoptosis regulation. Moreover, the PGCLCs derived from NOA patient-specific iPSCs might have initiated epigenetic reprogramming at a very early stage. Thus, the NOA patient-specific iPSCs exhibit poor response to germ cell induction in vitro, which may be related to the regulation of apoptotic process. These findings provide a foundation for future research on mechanism of male infertility.
Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer

Significance Rev-Erbβ is a heme-responsive transcription factor. Yet, the critical role of heme redox chemistry in regulating the protein’s heme occupancy and function as a repressor and gas sensor remains elusive. We show that the heme in Rev-Erbβ exists in the Fe3+-state to be replete under the limiting labile heme pool in cellulo. However, binding and sensing gases require Fe2+-heme. We show that signaling gases can drive Fe3+-heme reduction by electrochemically coupling heme reduction to the tight binding of CO/NO to Fe2+-heme. Our work describes a mechanism to explain how and why Fe3+-hemoproteins like Rev-Erbβ are ideal for in cellulo gas signaling. Rev-Erbβ is a nuclear receptor that couples circadian rhythm, metabolism, and inflammation. Heme binding to the protein modulates its function as a repressor, its stability, its ability to bind other proteins, and its activity in gas sensing. Rev-Erbβ binds Fe3+-heme more tightly than Fe2+-heme, suggesting its activities may be regulated by the heme redox state. Yet, this critical role of heme redox chemistry in defining the protein’s resting state and function is unknown. We demonstrate by electrochemical and whole-cell electron paramagnetic resonance experiments that Rev-Erbβ exists in the Fe3+ form within the cell allowing the protein to be heme replete even at low concentrations of labile heme in the nucleus. However, being in the Fe3+ redox state contradicts Rev-Erb’s known function as a gas sensor, which dogma asserts must be Fe2+. This paper explains why the resting Fe3+ state is congruent both with heme binding and cellular gas sensing. We show that the binding of CO/NO elicits a striking increase in the redox potential of the Fe3+/Fe2+ couple, characteristic of an EC mechanism in which the unfavorable Electrochemical reduction of heme is coupled to the highly favorable Chemical reaction of gas binding, making the reduction spontaneous. Thus, Fe3+-Rev-Erbβ remains heme-loaded, crucial for its repressor activity, and undergoes reduction when diatomic gases are present. This work has broad implications for proteins in which ligand-triggered redox changes cause conformational changes influencing its function or interprotein interactions (e.g., between NCoR1 and Rev-Erbβ). This study opens up the possibility of CO/NO-mediated regulation of the circadian rhythm through redox changes in Rev-Erbβ.
The first chromosomal analysis of bisexual populations of the Brazilian scorpion Tityus serrulatus (Scorpiones: Buthidae)

Abstract. The scorpion Tityus serrulatus Lutz & Mello, 1922 (Buthidae) is endemic to Brazil and is considered the most toxic South American scorpion species. The ample distribution of this species and its occurrence in urban areas has been attributed primarily to the parthenogenetic mode of reproduction. For a long time, only all-female T. serrulatus populations were known. Male specimens are very rare and have been recently discovered in natural environments within the Brazilian semi-arid zone. In the present study, we investigated cytogenetically bisexual populations of T. serrulatus, and compared the data with those available for parthenogenetic specimens. The diploid number (2n=12) and the general configuration of the chromosomes in male and female specimens were similar to those recorded for parthenogenetic populations. Male postpachytene cells contained chromosomes in a parallel arrangement with no differentiation of the bivalents, indicating the absence of heteromorphic sex chromosomes. However, the number of 28S rDNA sites varied between male and female specimens. Females invariably presented only one rDNA cistron, while all the males had two. This finding seems to indicate the existence of a sex-specific heteromorphism in T. serrulatus, in which the females are heterogametic and the males are the homogametic sex.
Effects of Planting Density on Water Use and Productivity of Pearl Millet (Pennisetum Typhoides) Grown on Stored Water. I. Growth of Roots and Shoots

SUMMARY Pearl millet (Pennisetum typhoides) was grown on stored water at Niamey, Niger, using three row spacings (38, 75 and 150 cm), to determine the physiological basis of exploitation and conservation of water by crops during drought Between 18 and 32 days after sowing, roots grew rapidly beneath all crops reaching 140 cm in the narrow spacing, but there were differences between crops in the pattern of growth. Soil cores and trench profiles indicated that plants in wider rows had fewer, deeper roots. Substantial differences in both the amount and pattern of shoot growth were recorded in the different populations. Initially growth was fastest at the narrow spacing but stopped by day 45 and eventually the wide spacing produced most dry matter due mainly to greater survival of tillers. The partitioning of above ground dry matter into vegetative and reproductive fractions was similar at all three spacings and was consistent with figures for comparable crops elsewhere. The important role of tillers is discussed in relation to the development and maintenance of a canopy.
Media Bias, the Social Sciences, and NLP: Automating Frame Analyses to Identify Bias by Word Choice and Labeling

Media bias can strongly impact the public perception of topics reported in the news. A difficult to detect, yet powerful form of slanted news coverage is called bias by word choice and labeling (WCL). WCL bias can occur, for example, when journalists refer to the same semantic concept by using different terms that frame the concept differently and consequently may lead to different assessments by readers, such as the terms “freedom fighters” and “terrorists,” or “gun rights” and “gun control. ” In this research project, I aim to devise methods that identify instances of WCL bias and estimate the frames they induce, e.g., not only is “terrorists” of negative polarity but also ascribes to aggression and fear. To achieve this, I plan to research methods using natural language processing and deep learning while employing models and using analysis concepts from the social sciences, where researchers have studied media bias for decades. The first results indicate the effectiveness of this interdisciplinary research approach. My vision is to devise a system that helps news readers to become aware of the differences in media coverage caused by bias.
Characterization of Beauveria sp.1 Isolates and their Virulence against the Yellow Mealworm, Tenebrio molitor 2

Abstract. Strains of Beauveria from different areas of Nuevo Leon State were isolated, characterized morphologically, morphometrically, and enzymatically, and evaluated against yellow mealworm, Tenebrio molitor L. (Coleoptera: Tenebrionidae), in a laboratory. Twenty-four soil samples were collected. Greater wax moth, Galleria mellonella (L.) (Lepidoptera: Pyralidae), larvae were used as bait. Solid media were used to estimate the production of extra-cellular fungal enzymes. Fifty-eight percent of the soil samples were positive for entomopathogenic Beauveria sp. The activity of strains varied for all enzymes evaluated (proteases ranged from 20.6 to 39.8, chitinases 25.6 to 40.8 and lipases 65.0 to 74.8 mm), as did the number of insects killed (30.0 to 75%). Large amounts of native entomopathogenic Beauveria sp. were found with greater sensitivity than commercial GHA strain against mealworm beetles, with possible better biological control against agricultural pests in Mexico.
Identification of a Human SOCS1 Polymorphism That Predicts Rheumatoid Arthritis Severity

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by an autoimmune response in the joints and an exacerbation of cytokine responses. A minority of patients with RA experience spontaneous remission, but most will show moderate/high disease activity, with aggressive joint damage and multiple systemic manifestations. There is thus is a great need to identify prognostic biomarkers for disease risk to improve diagnosis and prognosis, and to inform on the most appropriate therapy. Here we focused on suppressor of cytokine signaling 1 (SOCS1), a physiological negative regulator of cytokines that modulates cell activation. Using four independent cohorts of patients with arthritis, we characterized the correlation between SOCS1 mRNA levels and clinical outcome. We found a significant inverse correlation between SOCS1 mRNA expression and disease activity throughout the follow-up of patients with RA. Lower baseline SOCS1 levels were associated with poorer disease control in response to methotrexate and other conventional synthetic disease-modifying anti-rheumatic drugs in early arthritis, and to rituximab in established (active) RA. Moreover, we identified several single nucleotide polymorphisms in the SOCS1 gene that correlated with SOCS1 mRNA expression, and that might identify those patients with early arthritis that fulfill RA classification criteria. One of them, rs4780355, is in linkage disequilibrium with a microsatellite (TTTTC)3−5, mapped 0.9 kb downstream of the SNP, and correlated with reduced SOCS1 expression in vitro. Overall, our data support the association between SOCS1 expression and disease progression, disease severity and response to treatment in RA. These observations underlie the relevance of SOCS1 mRNA levels for stratifying patients prognostically and guiding therapeutic decisions.
The Mediating Role of Non-reactivity to Mindfulness Training and Cognitive Flexibility: A Randomized Controlled Trial

Mindfulness training has been shown to have a beneficial effect on cognitive flexibility. However, little is known about the mediators that produce this effect. Cross-sectional studies show that there might be a link between Non-judgment, Non-reactivity and cognitive flexibility. Longitudinal studies examining whether Non-judgment or Non-reactivity mediate the effectiveness of mindfulness training on improving cognitive flexibility are lacking. The present study aims to test the effect of mindfulness training on increasing cognitive flexibility and to test whether this effect is mediated by Non-judgment or Non-reactivity. We conducted a single-blind randomized controlled trial in 54 nonclinical high-stress participants between October 2018 and January 2019. Participants were randomly assigned to a Mindfulness Based Stress Reduction (MBSR) group or a waitlist control group. The experimenters were blind to the group assignment of participants. The MBSR group received 8-weekly sessions (2.5-h per week) and a one-day retreat (6-h), and was required to accomplish a 45-min daily formal practice during the intervention. The waitlist control group did not receive any intervention during the waiting period and received a 2-day (6-h per day) mindfulness training after the post-intervention. The primary outcome was self-report cognitive flexibility and perceived stress administered before and after MBSR. The secondary outcome was self-report mindfulness skills (including Non-reactivity and Non-judgment) measured at pre-treatment, Week 3, Week 6, and post-intervention. For cognitive flexibility, mixed-model repeated-measure ANOVA results showed that there were significant main effects of Time, Group and a significant interaction of Time by Group. Follow-up ANOVA indicated that the MBSR group was associated with greater improvements in cognitive flexibility than the waitlist. Path analysis results showed that the effect of the treatment on cognitive flexibility at post-treatment was fully mediated by Non-reactivity at Week 6. The mediation effects of Non-reactivity at Week 3, and Non-judgment at Week 3 and Week 6 were not significant. Our findings support the efficacy of MBSR on improving cognitive flexibility. Non-reactivity is an important element of the effectiveness of MBSR training on cognitive flexibility.
Efficient Neural Machine Translation for Low-Resource Languages via Exploiting Related Languages

A large percentage of the world’s population speaks a language of the Indian subcontinent, comprising languages from both Indo-Aryan (e.g. Hindi, Punjabi, Gujarati, etc.) and Dravidian (e.g. Tamil, Telugu, Malayalam, etc.) families. A universal characteristic of Indian languages is their complex morphology, which, when combined with the general lack of sufficient quantities of high-quality parallel data, can make developing machine translation (MT) systems for these languages difficult. Neural Machine Translation (NMT) is a rapidly advancing MT paradigm and has shown promising results for many language pairs, especially in large training data scenarios. Since the condition of large parallel corpora is not met for Indian-English language pairs, we present our efforts towards building efficient NMT systems between Indian languages (specifically Indo-Aryan languages) and English via efficiently exploiting parallel data from the related languages. We propose a technique called Unified Transliteration and Subword Segmentation to leverage language similarity while exploiting parallel data from related language pairs. We also propose a Multilingual Transfer Learning technique to leverage parallel data from multiple related languages to assist translation for low resource language pair of interest. Our experiments demonstrate an overall average improvement of 5 BLEU points over the standard Transformer-based NMT baselines.
Perinatal Opioid Exposure Primes the Peripheral Immune System Toward Hyperreactivity

The increased incidence of opioid use during pregnancy warrants investigation to reveal the impact of opioid exposure on the developing fetus. Exposure during critical periods of development could have enduring consequences for affected individuals. Particularly, evidence is mounting that developmental injury can result in immune priming, whereby subsequent immune activation elicits an exaggerated immune response. This maladaptive hypersensitivity to immune challenge perpetuates dysregulated inflammatory signaling and poor health outcomes. Utilizing an established preclinical rat model of perinatal methadone exposure, we sought to investigate the consequences of developmental opioid exposure on in vitro activation of peripheral blood mononuclear cells (PBMCs). We hypothesize that PBMCs from methadone-exposed rats would exhibit abnormal chemokine and cytokine expression at baseline, with exaggerated chemokine and cytokine production following immune stimulation compared to saline-exposed controls. On postnatal day (P) 7, pup PMBCs were isolated and cultured, pooling three pups per n. Following 3 and 24 h, the supernatant from cultured PMBCs was collected and assessed for inflammatory cytokine and chemokine expression at baseline or lipopolysaccharide (LPS) stimulation using multiplex electrochemiluminescence. Following 3 and 24 h, baseline production of proinflammatory chemokine and cytokine levels were significantly increased in methadone PBMCs (p < 0.0001). Stimulation with LPS for 3 h resulted in increased tumor necrosis factor (TNF-α) and C-X-C motif chemokine ligand 1 (CXCL1) expression by 3.5-fold in PBMCs from methadone-exposed PBMCs compared to PBMCs from saline-exposed controls (p < 0.0001). Peripheral blood mononuclear cell hyperreactivity was still apparent at 24 h of LPS stimulation, evidenced by significantly increased TNF-α, CXCL1, interleukin 6 (IL-6), and IL-10 production by methadone PMBCs compared to saline control PBMCs (p < 0.0001). Together, we provide evidence of increased production of proinflammatory molecules from methadone PBMCs at baseline, in addition to sustained hyperreactivity relative to saline-exposed controls. Exaggerated peripheral immune responses exacerbate inflammatory signaling, with subsequent consequences on many organ systems throughout the body, such as the developing nervous system. Enhanced understanding of these inflammatory mechanisms will allow for appropriate therapeutic development for infants who were exposed to opioids during development. Furthermore, these data highlight the utility of this in vitro PBMC assay technique for future biomarker development to guide specific treatment for patients exposed to opioids during gestation.
Personalized PageRank with Syntagmatic Information for Multilingual Word Sense Disambiguation

Exploiting syntagmatic information is an encouraging research focus to be pursued in an effort to close the gap between knowledge-based and supervised Word Sense Disambiguation (WSD) performance. We follow this direction in our next-generation knowledge-based WSD system, SyntagRank, which we make available via a Web interface and a RESTful API. SyntagRank leverages the disambiguated pairs of co-occurring words included in SyntagNet, a lexical-semantic combination resource, to perform state-of-the-art knowledge-based WSD in a multilingual setting. Our service provides both a user-friendly interface, available at http://syntagnet.org/, and a RESTful endpoint to query the system programmatically (accessible at http://api.syntagnet.org/).
Integrating and interrogating diverse Brassica data within an EnsEMBL structured database

There is a vast quantity of data being produced by Brassica researchers throughout the world. Genomic data include gene or Expressed Sequence Tag (EST) sequences and genomic sequences from bacterial artificial chromosomes and whole genome shotgun approaches. Associated gene expression or transcriptome data are being produced using various formats of microarray, Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signal Sequencing (MPSS). Molecular marker data such as Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) are providing insights into genetic structure and genetic diversity as well as inherited traits within Brassica species. Phenotypic data are also increasing in complexity through the characterisation of broad diverse germplasm collections and the development of advanced techniques in proteomics and metabolomics. There is a significant challenge in bringing this diverse set of data together in an integrated bioinformatics platform to permit interrogation across these broad fields. The most advanced genome database structure currently available uses the EnsEMBL format. EnsEMBL permits both broad data integration, comparative analysis between related organisms and efficient data interrogation. We have established a Brassica-centric EnsEMBL database founded on the current Arabidopsis thaliana EnsEMBL database, incorporating tracks for Brassica genes, genomic sequences and molecular markers. This database is publicly available to the Brassica research community and can be used as the foundation of a Brassica based EnsEMBL database on completion of the B. rapa genome sequencing under the Multinational Brassica Genome Project.
NAIST’s Machine Translation Systems for IWSLT 2020 Conversational Speech Translation Task

This paper describes NAIST’s NMT system submitted to the IWSLT 2020 conversational speech translation task. We focus on the translation disfluent speech transcripts that include ASR errors and non-grammatical utterances. We tried a domain adaptation method by transferring the styles of out-of-domain data (United Nations Parallel Corpus) to be like in-domain data (Fisher transcripts). Our system results showed that the NMT model with domain adaptation outperformed a baseline. In addition, slight improvement by the style transfer was observed.
Singapore Grouper Iridovirus (SGIV) Inhibited Autophagy for Efficient Viral Replication

Autophagy is a conserved catabolic process that occurs at basal levels to maintain cellular homeostasis. Most virus infections can alter the autophagy level, which functions as either a pro-viral or antiviral pathway, depending on the virus and host cells. Singapore grouper iridovirus (SGIV) is a novel fish DNA virus that has caused great economic losses for the marine aquaculture industry. In this study, we found that SGIV inhibited autophagy in grouper spleen (GS) cells which was evidenced by the changes of LC3-II, Beclin1 and p-mTOR levels. Further study showed that SGIV developed at least two strategies to inhibit autophagy: (1) increasing the cytoplasmic p53 level; and (2) encoding viral proteins (VP48, VP122, VP132) that competitively bind autophagy related gene 5 and mediately affect LC3 conversion. Moreover, activation of autophagy by rapamycin or overexpressing LC3 decreased SGIV replication. These results provide an antiviral strategy from the perspective of autophagy.