Miracle-dz/UniFAR-FTUs huggingface dataset:
The fission yeast non-coding transcriptome

Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression, although it remains unclear to what extent they contribute overall to the information flow from genotype to phenotype. Using strand-specific RNAsequencing, I identify thousands of novel unstable, or cryptic, lncRNAs in Schizosaccharomyces pombe. The nuclear exosome, the RNAi pathway and the cytoplasmic exonuclease Exo2 represent three key pathways regulating lncRNAs in S. pombe, defining the overlapping classes of CUTs, RUTs and XUTs, respectively. The nuclear exosome and the RNAi pathway act cooperatively to control nuclear lncRNA expression, while the cytoplasmic Exo2 pathway is more distinct. Impairing both the nuclear exosome and the cytoplasmic exonuclease Exo2 is lethal in S. pombe. Importantly, I show that CUTs, RUTs and XUTs are stabilised under physiologically relevant growth conditions, with three key groups emerging: late meiotic RUTs/XUTs, early meiotic CUTs and quiescent CUTs. Late meiotic RUTs/XUTs tend to be antisense to protein-coding genes, and anti-correlate in expression with their sense loci. In contrast, early meiotic and quiescent CUTs tend to be transcribed divergently from protein-coding genes and positively correlate in expression with their mRNA partners. The current study provides an in-depth survey of the lncRNA repertoire of S. pombe, and the pathways that regulate their expression. It seems likely that any regulatory functions mediated by most of these lncRNAs are in cis, nuclear and cotranscriptional. The current study provides a rich and comprehensive resource for future studies of lncRNA function.
ScholarlyRead: A New Dataset for Scientific Article Reading Comprehension

We present ScholarlyRead, span-of-word-based scholarly articles’ Reading Comprehension (RC) dataset with approximately 10K manually checked passage-question-answer instances. ScholarlyRead was constructed in semi-automatic way. We consider the articles from two popular journals of a reputed publishing house. Firstly, we generate questions from these articles in an automatic way. Generated questions are then manually checked by the human annotators. We propose a baseline model based on Bi-Directional Attention Flow (BiDAF) network that yields the F1 score of 37.31%. The framework would be useful for building Question-Answering (QA) systems on scientific articles.
On Context Span Needed for Machine Translation Evaluation

Despite increasing efforts to improve evaluation of machine translation (MT) by going beyond the sentence level to the document level, the definition of what exactly constitutes a “document level” is still not clear. This work deals with the context span necessary for a more reliable MT evaluation. We report results from a series of surveys involving three domains and 18 target languages designed to identify the necessary context span as well as issues related to it. Our findings indicate that, despite the fact that some issues and spans are strongly dependent on domain and on the target language, a number of common patterns can be observed so that general guidelines for context-aware MT evaluation can be drawn.
The roles of language use and vocabulary size in the emergence of word-combining in children with complex neurodevelopmental disabilities

Abstract Parent report data on 82 preschool children with complex neurodevelopmental disabilities including Down syndrome, dyspraxia, autism, and global developmental delay suggests communicative language use must reach a threshold level before vocabulary size becomes the best predictor of word combining. Using the Language Use Inventory and the MacArthur-Bates CDI (with sign vocabulary option), statistical modelling using regression trees and random forests suggests that, despite high linear correlations between variables, (1) pragmatic ability, particularly children's emerging ability to talk about things, themselves and others is a significantly better predictor of the earliest word combining than vocabulary size; and (2) vocabulary size becomes a better predictor of later word combining, once this pragmatic base has been established.
Toxic effects of phosphoramidate on Paramecium sp. with special emphasis on respiratory metabolism, growth, and generation time

The toxicological impacts of the increasing number of synthetic compounds present in the aquatic environment are assessed predominantly in laboratory studies where test organisms are exposed to a range of concentrations of single compounds. Protozoan cells are often used as bioindicators for the presence of xenobiotic compounds. In this article, we describe the inhibitory effect of a synthetic phosphoramidate derivative at different concentrations (40, 60, and 80 µmol L−1) on Paramecium sp. , affecting its growth (proliferation) in concentration-dependent manner, as well as the generation time and response percentage. The LC50 value determined for these protozoa was estimated at 60 µmol L−1 on 24 h of exposure. The respiratory metabolism of protozoan is perturbed at three concentrations, noting that the oxygen consumption was significantly increased at high concentrations after 18 h of exposure. In addition, the data can be used as reference values in further testing with other pesticides.
Not Taking a Joke: The Influence of Target Status, Sex, and Age on Reactions to Workplace Humor

The current study tasked undergraduates with serving as hypothetical human resource workers to evaluate complaints of offensive and inoffensive humor used by male and female employees in a fictitious company who varied in employment status and age. Offensive humor was deemed more problematic in its usage, particularly among female perceivers. Contrary to hypotheses, its usage was more problematic for male and older employees than for female and younger employees. In addition, participants were more averse to both offensive and inoffensive humor from high-status and older men relative to women with similar characteristics. We frame results with consideration of recent social trends.
Compatibility of X-ray computed tomography with plant gene expression profiling, rhizosphere bacterial community composition and enzyme activity analyses.

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil-root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 h and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities, or the composition of rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to revert any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impacts on the investigated processes should be conducted.
INOCULATION OF MAN WITH INCLUSION BLENNORRHEA VIRUS

Virus isolated from the cervix of a woman whose baby developed neonatal inclusion blennorrhea produced an acute follicular conjunctivitis, with Halberstaedter-Prowazek inclusions, when inoculated into baboon eyes after eight yolk sac passages (Jones et al., 1959). This was good evidence that the agent was etiologically related to inclusion blennorrhea, but final proof could come only from the inoculation of man. A study of patients presenting in London with trachoma or inclusion blennorrhea showed that it is not possible to divide them neatly into two clear-cut diseases (Jones, 1961). A spectrum of clinical pictures is seen ranging from typical trachoma to typical adult inclusion conjunctivitis, with intermediate and indeterminate types lying between. If this were the result of there being a spectrum of viruses rather than two entirely separate agents, some strains inhabiting the genital tract would probably be capable of producing the ocular picture of trachoma. In London, as the result of investigating the genital tract of patients presenting with either inclusion conjunctivitis or trachoma, a woman with inclusionand virus-positive trachoma I11 was found to have cervicitis with inclusions (Jones, 1961). In the Gambia a woman with inclusionand viruspositive trachoma I11 gave birth to twins who developed inclusion-positive ophthalmia neonatorum. Before they died a t the age of 10 months, one had developed pannus; virus was isolated from the mother's cervix (Collier, 1960). These observations gave support to the concept of the genital tract being infected by a spectrum of strains of varying ocular pathogenicity and made i t imperative to assess the virulence for the adult eye of a number of strains of genital origin, by having recourse to the inoculation of man. The details of materials and methods have been kept to a minimum.
RELATIONSHIP BETWEEN WEATHER FACTORS AND DOLLAR SPOT OF CREEPING BENTGRASS

In 1981 and 1982 epidemics of dollar spot of creeping bentgrass, caused by Sclerotinia homoeocarpa, proceeded in a series of steps. Each step began at a point where a decline in the epidemic rate was followed by an increase in the epidemic rate and continued until a new step began. A step in the epidemic occurred after two consecutive wet days if the average temperature for the period was at or above 22 °C or after three or more consecutive wet days if the average temperature for the period was 15 °C or greater. These weather conditions were referred to as "infection periods. " In 1982, an application of Tersan 1991 (benomyl) 1 and 2 days after two infection periods provided an acceptable level of disease control as effective as that obtained from a regular preventive schedule of seven sprays.Key words: Agrostis palustris, disease control, Sclerotinia homoeocarpa, weather-timed spray
Comparative analysis of programmed death ligand 1 expression in paired cytologic and histologic specimens of non-small cell lung cancer.

BACKGROUND In advanced non-small cell lung cancer (NSCLC), cytologic specimens from transbronchial needle aspiration (TBNA) or transthoracic needle aspiration are often the only cancer tissue material available for the analysis of programmed death ligand 1 (PD-L1) expression. This study was aimed at assessing the concordance of PD-L1 expression in histologic and cytologic samples and at evaluating interobserver agreement on specimens in this setting. METHODS One hundred and thirty-eight specimens from 60 patients with NSCLC were analyzed. Histologic specimens were represented by endoscopic samples obtained with forceps (biopsies), whereas cytologic specimens were from TBNA and bronchial lavage (BL). PD-L1 expression was quantified with the immunohistochemistry (IHC)-based Ventana SP263 assay. For cytologic specimens, IHC was performed on cell block sections. Two independent pathologists who were blinded to the clinical data evaluated partial or complete membrane IHC staining. Concordance between 2 methods and between 2 pathologists was evaluated with normal and weighted Cohen's κ coefficients, overall agreement, and Bland-Altman plots. RESULTS PD-L1 expression was quantified in 138 specimens from 60 patients. Concordance between cytologic and histologic approaches was moderate (κ = 0.56; weighted κ = 0.55). Also, concordance in the biopsy-TBNA and biopsy-BL subgroups was moderate (κ = 0.43 and κ = 0.47, respectively), whereas interobserver agreement was substantial (weighted κ = 0.72). A Bland-Altman plot showed an underestimation in PD-L1 values from cytologic samples in comparison with histologic ones. CONCLUSIONS The results demonstrate that in the absence of available histologic specimens, PD-L1 positivity in cytologic samples could be a reliable data for the oncologist to consider immune checkpoint inhibitor therapy. However, a comparison of cytologic and histologic samples has shown an underestimation of PD-L1 values in cytologic samples.
Increased therapeutic effect on medullary thyroid cancer using a combination of radiation and tyrosine kinase inhibitors

Since patients with medullary thyroid cancer (MTC) often have metastatic disease at the time of diagnosis, the development of efficient systemic treatment options for MTC is important. Vandetanib and cabozantinib are two tyrosine kinase inhibitors (TKIs) that were recently approved by FDA and EMA for systemic treatment of metastatic MTC. Additionally, since MTC is of a neuroendocrine tumour type, treatment with radiolabelled somatostatin analogues (e.g. 177Lu-octreotate) is a valid option for patients with MTC. The aim of this study was to investigate the potentially increased therapeutic effect of combining radiation therapy with these TKIs for treatment of MTC in a mouse model. Nude mice carrying patient-derived MTC tumours (GOT2) were treated with external beam radiotherapy (EBRT) and/or one of the two TKIs vandetanib or cabozantinib. The tumour volume was determined and compared with that of mock-treated controls. The treatment doses were chosen to give a moderate effect as monotherapy to be able to detect any increased therapeutic effect from the combination therapy. At the end of follow-up, tumours were processed for immunohistochemical (IHC) analyses. The animals in the combination therapy groups showed the largest reduction in tumour volume and the longest time to tumour progression. Two weeks after start of treatment, the tumour volume for these mice was reduced by about 70–75% compared with controls. Furthermore, also EBRT and TKI monotherapy resulted in a clear anti-tumour effect with a reduced tumour growth compared with controls. The results show that an increased therapeutic effect could be achieved when irradiation is combined with TKIs for treatment of MTC. Future studies should evaluate the potential of using 177Lu-octreotate therapy in combination with TKIs in patients.
Childhood Maltreatment and Psychosis: A Comparative Validity Study of Maltreatment Indices

Childhood maltreatment is a robust risk factor for psychosis, but it remains unclear whether different measurement methods provide equivalent validity in predicting psychotic symptoms. This study compared the predictive validity of two common indices of maltreatment at age 12—children’s self-report and Child Protective Services (CPS) reports—on the development of psychotic symptoms at age 18 using data from a large, multisite longitudinal study (N = 629). Consistent with prior research, agreement was low between indices, with the prevalence of self-reported maltreatment being 2–3 times higher. A quarter of the sample endorsed at least one psychotic symptom at age 18, most commonly delusions. While CPS-indicated maltreatment was generally not associated with later psychotic symptoms, all forms of self-reported maltreatment were. Sexual abuse demonstrated a particularly strong relationship with psychosis, especially hallucinations. These results suggest that self-reports may provide stronger predictive validity than CPS indications of maltreatment in the assessment of psychosis risk, indicating that a child’s interpretation of trauma matters more than the traumatic event itself in this regard.
Computational modeling of the auditory brainstem response to continuous speech

Objective. The auditory brainstem response can be recorded non-invasively from scalp electrodes and serves as an important clinical measure of hearing function. We have recently shown how the brainstem response at the fundamental frequency of continuous, non-repetitive speech can be measured, and have used this measure to demonstrate that the response is modulated by selective attention. However, different parts of the speech signal as well as several parts of the brainstem contribute to this response. Here we employ a computational model of the brainstem to elucidate the influence of these different factors. Approach. We developed a computational model of the auditory brainstem by combining a model of the middle and inner ear with a model of globular bushy cells in the cochlear nuclei and with a phenomenological model of the inferior colliculus. We then employed the model to investigate the neural response to continuous speech at different stages in the brainstem, following the methodology developed recently by ourselves for detecting the brainstem response to running speech from scalp recordings. We compared the simulations with recordings from healthy volunteers. Main results. We found that the auditory-nerve fibers, the cochlear nuclei and the inferior colliculus all contributed to the speech-evoked brainstem response, although the dominant contribution came from the inferior colliculus. The delay of the response corresponded to that observed in experiments. We further found that a broad range of harmonics of the fundamental frequency, up to about 8 kHz, contributed to the brainstem response. The response declined with increasing fundamental frequency, although the signal-to-noise ratio was largely unaffected. Significance. Our results suggest that the scalp-recorded brainstem response at the fundamental frequency of speech originates predominantly in the inferior colliculus. They further show that the response is shaped by a large number of higher harmonics of the fundamental frequency, reflecting highly nonlinear processing in the auditory periphery and illustrating the complexity of the response.
Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia

The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions.
Mechanisms underlying selective coupling of endothelial Ca2+ signals with eNOS vs. IK/SK channels in systemic and pulmonary arteries

Endothelial cell TRPV4 (TRPV4EC) channels exert a dilatory effect on the resting diameter of resistance mesenteric and pulmonary arteries. Functional intermediate‐ and small‐conductance K+ (IK and SK) channels and endothelial nitric oxide synthase (eNOS) are present in the endothelium of mesenteric and pulmonary arteries. TRPV4EC sparklets preferentially couple with IK/SK channels in mesenteric arteries and with eNOS in pulmonary arteries. TRPV4EC channels co‐localize with IK/SK channels in mesenteric arteries but not in pulmonary arteries, which may explain TRPV4EC‐IK/SK channel coupling in mesenteric arteries and its absence in pulmonary arteries. The presence of the nitric oxide‐scavenging protein, haemoglobin α, limits TRPV4EC‐eNOS signalling in mesenteric arteries. Spatial proximity of TRPV4EC channels with eNOS and the absence of haemoglobin α favour TRPV4EC‐eNOS signalling in pulmonary arteries.
Contribution of NKT cells to the immune response and pathogenesis triggered by respiratory viruses

ABSTRACT Human respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) cause acute respiratory tract infections in children worldwide. Natural killer T (NKT) cells are unconventional T lymphocytes, and their TCRs recognize glycolipids bound to the MHC-I-like molecule, CD1d. These cells modulate the inflammatory response in viral infections. Here, we evaluated the contribution of NKT cells in both hRSV and hMPV infections. A significant decrease in the number of neutrophils, eosinophils, and CD103+DCs infiltrating to the lungs, as well as an increased production of IFN-γ, were observed upon hRSV-infection in CD1d-deficient BALB/c mice, as compared to wild-type control mice. However, this effect was not observed in the CD1d-deficient BALB/c group, upon infection with hMPV. Importantly, reduced expression of CD1d in CD11b+ DCs and epithelial cells was found in hRSV -but not hMPV-infected mice. Besides, a reduction in the expression of CD1d in alveolar macrophages of lungs from hRSV- and hMPV-infected mice was found. Such reduction of CD1d expression interfered with NKT cells activation, and consequently IL-2 secretion, as characterized by in vitro experiments for both hRSV and hMPV infections. Furthermore, increased numbers of NKT cells recruited to the lungs in response to hRSV- but not hMPV-infection was detected, resulting in a reduction in the expression of IFN-γ and IL-2 by these cells. In conclusion, both hRSV and hMPV might be differently impairing NKT cells function and contributing to the immune response triggered by these viruses.
Analysis of the Structure-stability Relationship of Cold-adapted Lipase PsLip1 from Homology Modeling

Two initial models of cold-adapted lipase PsLip1 have been constructed, based on homology with the bacterial lipases Chromobacterium viscosum (CvLip) and Pseudomonas cepacia (PcLip), whose X-ray structures have been solved and refined to high resolution. The mature polypeptide chains of these lipases have 84% similarity. The models of Mod1 and Mod2 have been compared with the tertiary structures of CvLip and PcLip, respectively, and analyzed in terms of stabilizing interactions. Several structural aspects that are believed to contribute to protein stability have been compared: the number of conserved salt bridges, aromatic interactions, hydrogen bonds, helix capping, and disulfide bridges. The 3-dimensional structural model of PsLip1 has been constructed in order to elucidate the structural reasons for the decreased thermostability of the enzyme in comparison with its mesophilic counterparts.
A Phylogenetic Study of Korean Rodents (Muridae, Sciuridae) Based on Mitochondrial and Nuclear DNA

The subfamily Murinae is a very controversial group concerning their phylogenetic relationship. Previous studies could not resolve phylogeny among four genera Apodemus, Micromys, Mus and Rattus of the Muridae. In the present study, eight rodent species resident in South Korea were collected and phylogenetically analyzed based on sequence data of five mitochondrial and nuclear DNA regions: 12S rRNA, cytochrome b gene (cyt b), cytochrome oxidase II (COII), control region of mitochondrial DNA, and a thyroglobulin (Tg) of nuclear DNA. According to the phylogeny of the concatenated data, M. musculus separated early in Murinae (ML 100%; BA 1.00 pp) and the genus Rattus grouped with the harvest mouse, M. minutes; these were separated from the genus Apodemus with relatively strong support (ML 74%; BA 0.76 pp). The Siberian chipmunk population was also examined using the five genes to obtain better resolution. The phylogeny for Korean rodents determined using the 12S rRNA, cyt b, COII and control regions discriminated the Siberian chipmunk populations from Korea, Russia, and China.