Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic and Molecular Characterization of Infectious Bursal Disease Virus in China From Layer Chicken Flocks

Five field isolates of infectious bursal disease virus (IBDV) were isolated from bursae of sick young chickens by inoculating chicken embryo fibroblasts (CEF) while the morphological and physiochemical properities of these isolates were detected. Subtype of the virus isolates were analysed by cross virus neutralization. Virulence of IBDV isolates was determined with specific pathogen-free (SPF) chicken inoculation. Nucleotide sequence of genomic segment A of the isolate NB was further sequenced and analysed. All bursal suspensions produced cytopathic effects (CPE) in CEF after 2~14 passages. The physiochemical and morphological properties of IBDV isolates were in accordance with that of typical IBDV. The three CEF-adapted virus isolates JD1, JD2 and NB were divided into 3 subtypes of serotype Ⅰ IBDV except IBDV isolates HZ1 and HZ2 belonged to classical IBDV. In a pathogenicity experiment, the clinical signs and bursal atrophy resembling those of field outbreaks were produced and microscopic bursa lesions revealed that there was degeneration, necrosis and disappearance of lymphocytes in the medullary area of bursal follicles. Sequence data demonstrated that genomic A-segment of the isolate NB was composed of 3 259 nucleotides, encoding VP5 of 145 amino acid residues and the polyprotein (VP243) of 1 012 amino acid residues. Compared with serotype Ⅰ IBDV strains from GenBank, within serotype Ⅰ IBDV strains, the isolate NB has the highest identity to the polyprotein of the isolate JD1 (99.5%), VP2 of the isolates JD1, CEF94 and D78 (99.8%), VP3 of the isolate JD1 (99.2%), VP4 of the isolate JD1 (100%) and VP5 of the isolates JD1, HZ2, P2, CEF94, CT, Cu-1 and D78 (99.3%). In the VP2-predicted amino acid sequence of the isolate NB, amino acid residues at positions 253, 280 and 284 were consistent with and other published variant and classical IBDV strains, and different from very virulent IBDV. These results indicated that antigenic epitopes of IBDV are conformational and subtype forming of IBDV isolates originated from classical IBDV attenuated vaccine strains.
Genetic and morphological identification of pelagic juvenile rockfish collected from the Gulf of Alaska

Pelagic juvenile rockfish (Sebastes spp.) collected in surveys designed to assess juvenile salmonids and other species in the Gulf of Alaska in 1998 and 2000–2003 provide an opportunity to document the occurrence of the pelagic juveniles of several species of rockfish. Often, species identification of rockfish is difficult or impossible at this stage of development (~20 to 60 mm), and few species indigenous to Alaska waters have been described. Use of mitochondrial DNA markers for rockfish species allowed unequivocal identification of ten species (S. aleutianus, S. alutus, S. borealis, S. entomelas, S. flavidus, S. melanops, S. pinniger, S. proriger, S. reedi, and S. ruberrimus) in subsamples from the collections. Other specimens were genetically assignable to groups of two or three species. Sebastes borealis, S. crameri, and S. reedi were identified using morphological data. Combining genetic and morphological data allowed successful resolution of the other species as S. emphaeus, probably S. ciliatus (although S. polyspinis cannot be totally ruled out), and S. polyspinis. Many specimens were initially morphologically indistinguishable from S. alutus, and several morphological groups included fish genetically identified as S. alutus. This paper details the characteristics of these pelagic juveniles to facilitate morphological identification of these species in future collections. (PDF file contains 32 pages.)
Finding the direction of a sound source using a vector sound‐intensity probe

Good spatial resolution of a sound source can be achieved with the four closely spaced pressure transducers in a vector sound‐intensity probe. In contrast, a receiving array generally requires an extensive distribution of transducer elements. Experimental results are presented that demonstrate the ability of a vector probe to determine the direction of a sound source in water, both without and with noise interference. Measurements of the sound‐intensity vector, or sound‐power flux, were performed using the cross‐spectral method. Spectral subtraction and averaging over the frequency range of a source were found to be effective tools for determining the direction of a source when there is uncorrelated interference and background noise.
ForecastQA: A Question Answering Challenge for Event Forecasting with Temporal Text Data

Event forecasting is a challenging, yet important task, as humans seek to constantly plan for the future. Existing automated forecasting studies rely mostly on structured data, such as time-series or event-based knowledge graphs, to help predict future events. In this work, we aim to formulate a task, construct a dataset, and provide benchmarks for developing methods for event forecasting with large volumes of unstructured text data. To simulate the forecasting scenario on temporal news documents, we formulate the problem as a restricted-domain, multiple-choice, question-answering (QA) task. Unlike existing QA tasks, our task limits accessible information, and thus a model has to make a forecasting judgement. To showcase the usefulness of this task formulation, we introduce ForecastQA, a question-answering dataset consisting of 10,392 event forecasting questions, which have been collected and verified via crowdsourcing efforts. We present our experiments on ForecastQA using BERTbased models and find that our best model achieves 61.0% accuracy on the dataset, which still lags behind human performance by about 19%. We hope ForecastQA will support future research efforts in bridging this gap.
Ultrasonic and Brillouin scattering measurements of the elastic constants of SrFCl

The six elastic constants of BaFCl which is a crystal of the matlockite family have been measured using ultrasonic and Brillouin scattering techniques. The values obtained are compared with those of BaF2 crystals which exhibit some structural similarities with BaFCl. Because of the layer structure of BaFCl, the 'transverse' elastic constants C66, C44, C12 and C13 and the 'longitudinal' elastic constants C33 and C11 are smaller than the corresponding constants of BaF2. The linear and volume compressibilities are deduced from these measurements. An elastic Debye temperature is calculated ( Theta el=246.5 K) and compared with other experimental (calorimetric) and theoretical (shell model) determinations. Finally, the effect of the dipole moments of the halide ions on the elastic constants for materials of the matlockite family is discussed.
Aging Memories Generate More Fluent Dialogue Responses with Memory Augmented Neural Networks.

Memory Networks have emerged as effective models to incorporate Knowledge Bases (KB) into neural networks. By storing KB embeddings into a memory component, these models can learn meaningful representations that are grounded to external knowledge. However, as the memory unit becomes full, the oldest memories are replaced by newer representations. In this paper, we question this approach and provide experimental evidence that conventional Memory Networks store highly correlated vectors during training. While increasing the memory size mitigates this problem, this also leads to overfitting as the memory stores a large number of training latent representations. To address these issues, we propose a novel regularization mechanism named memory dropout which 1) Samples a single latent vector from the distribution of redundant memories. 2) Ages redundant memories thus increasing their probability of overwriting them during training. This fully differentiable technique allows us to achieve state-of-the-art response generation in the Stanford Multi-Turn Dialogue and Cambridge Restaurant datasets.
Grids of stellar models. II. From 0.8 to 120 M_solar at Z=0.008

Continuing the effort to provide a homogeneous base of extensive and accurate grids of stellar models covering a wide range of metallicities we present a new grid of stellar models at metallicity Z = 0.008 - roughly corresponding to the Large Magellanic Cloud composition. The models have been computed for 0.8 to 120 M ○ . using up-to-date input physics and the new radiative opacities from Rogers & Iglesias (1992) and Kurucz (1991). Mass loss and moderate core overshooting are taken into account. The resulting HR diagram and the lifetimes in the H − , He- and C-burning phase as well as some general results on massive stars are discussed and compared to complementary grids using the same input physics at metallicities Z = 0.020 and Z = 0.001 by Schaller et al. (1992)
Memory for positive versus negative life events : theories for the differences between happy and unhappy persons

Three studies examined the following hypotheses for the relation of subjective well-being (SWB) with memory for positive versus negative life events: (a) differences in retrieval mood, (b) the incidence of positive and negative events, (c) the interpretation of events, and (d) frequency of rehearsal. In Studies 1 (n = 420) and 2 (n = 94), the partial correlation of retrieval mood with recall, controlling for SWB, was trivial, suggesting that mood had little or no effect on recall. Endorsement frequencies of positive minus negative concrete events and interpretive events on checklists in Studies 2 and 3 each correlated with SWB (ps < .001), suggesting that both incidence and interpretation contributed to the recall differences. In Study 3, the recall of 55 Ss from Study 2 was retested after an 11-month interval. The lack of an interaction between SWB and recall change suggested that rehearsal did not contribute to the recall differences.
Transcriptional Regulation of Müllerian Inhibiting Substance (MIS) and Establishment of a Gonadal Somatic Cell Line Using mis-GFP Transgenic Medaka (Oryzias latipes)

In vertebrate germ cell differentiation, gonadal somatic cells and germ cells are closely related. By analyzing this relationship, it has recently been reported in mammals that primordial germ cells (PGCs), induced from pluripotent stem cells and germline stem cells, can differentiate into functional gametes when co-cultured in vitro with fetal gonadal somatic cells. In some fish species, differentiation into functional sperm by reaggregation or co-culture of gonadal somatic cells and germ cells has also been reported; however, the relationship between gonadal somatic cells and germ cells in these species is not well-understood. Here, we report the transcriptional regulation of Müllerian inhibiting substance (MIS) and the establishment of a gonadal somatic cell line using mis-GFP transgenic fish, in medaka (Oryzias latipes)—a fish model which offers many advantages for molecular genetics. MIS is a glycoprotein belonging to the transforming growth factor β superfamily. In medaka, mis mRNA is expressed in gonadal somatic cells of both sexes before sex differentiation, and MIS regulates the proliferation of germ cells during this period. Using luciferase assays, we found that steroidogenic factor 1 (SF1) and liver receptor homolog 1 (LRH1) activate medaka mis gene transcription, probably by binding to the mis promoter. We also report that mis-GFP transgenic medaka emit GFP fluorescence specific to gonadal somatic cells in the gonads. By fusing Sertoli cells from transgenic medaka with a cell line derived from medaka hepatoma cancer, we produced a hybridoma cell line that expresses gonadal somatic cell-specific markers, including Sertoli and Leydig cell markers. Moreover, embryonic PGCs co-cultured with the established hybridoma, as feeder cells, proliferated and formed significant colonies after 1 week. PGCs cultured for 3 weeks expressed a germ cell marker dnd, as well as the meiotic markers sycp1 and sycp3. Thus, we here provide the first evidence in teleosts that we have successfully established a gonadal somatic cell-derived hybridoma that can induce both the proliferation and meiosis of germ cells.
Novel Cyclovirus Identified in Broiler Chickens With Transmissible Viral Proventriculitis in China

In October 2018, an outbreak of transmissible viral proventriculitis (TVP) occurred in 30-day-old commercial broiler chickens on a farm in Weifang, China. TVP, an infectious viral disease characterized by runting and stunting, is associated with many viruses, and has a significant economic impact on the global poultry industry. TVP is diagnosed according to clinical symptoms, gross and histological lesions, and negative PCR results for pathogenic bacteria, avian leukosis virus subgroup J, Marek's disease virus, reticuloendotheliosis virus, infectious bursa disease virus, avian reovirus, chicken anemia virus, infectious bronchitis virus, chicken proventricular necrosis virus, gyrovirus 3 and chicken circovirus. To further detect the possible causative pathogens of TVP, we used PacBio third-generation sequencing to examine proventricular samples. A dominant abundance of the novel cyclovirus (CyCV), chCyCV-SDAU-1, was identified in broilers with TVP. The complete chCyCV-SDAU-1 genome was verified via inverse PCR, was 1936 bp long, and consisted of Rep, Cp, and two intergenic regions. Phylogenetic tree analysis showed that chCyCV-SDAU-1 formed an independent branch with other cycloviruses. The homology of chCyCV-SDAU-1 with 20 others known cycloviruses was < 40%. Retrospective investigation showed that the CyCV infection rate in the broilers with TVP was 80% (16/20), while no CyCV was found in healthy chickens. In conclusion, a novel CyCV was identified in chickens with TVP, though its role in this disease is unclear.
The Polyphenol Pterostilbene Ameliorates the Myopathic Phenotype of Collagen VI Deficient Mice via Autophagy Induction

The induction of autophagy, the catabolic pathway by which damaged or unnecessary cellular components are subjected to lysosome-mediated degradation and recycling, is impaired in Collagen VI (COL6) null mice and COL6-related myopathies. This autophagic impairment causes an accumulation of dysfunctional mitochondria, which in turn leads to myofiber degeneration. Our previous work showed that reactivation of autophagy in COL6-related myopathies is beneficial for muscle structure and function both in the animal model and in patients. Here we show that pterostilbene (Pt)—a non-toxic polyphenol, chemically similar to resveratrol but with a higher bioavailability and metabolic stability—strongly promotes in vivo autophagic flux in the skeletal muscle of both wild-type and COL6 null mice. Reactivation of autophagy in COL6-deficient muscles was also paralleled by several beneficial effects, including significantly decreased incidence of spontaneous apoptosis, recovery of ultrastructural defects and muscle remodeling. These findings point at Pt as an effective autophagy-inducing nutraceutical for skeletal muscle with great potential in counteracting the major pathogenic hallmarks of COL6-related myopathies, a valuable feature that may be also beneficial in other muscle pathologies characterized by defective regulation of the autophagic machinery.
Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides

Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes

Cardiovascular disease is the leading global health concern and responsible for more deaths worldwide than any other type of disorder. Atherosclerosis is a chronic inflammatory disease in the arterial wall, which underpins several types of cardiovascular disease. It has emerged that a strong relationship exists between alterations in amino acid (AA) metabolism and the development of atherosclerosis. Recent studies have reported positive correlations between levels of branched-chain amino acids (BCAAs) such as leucine, valine, and isoleucine in plasma and the occurrence of metabolic disturbances. Elevated serum levels of BCAAs indicate a high cardiometabolic risk. Thus, BCAAs may also impact atherosclerosis prevention and offer a novel therapeutic strategy for specific individuals at risk of coronary events. The metabolism of AAs, such as L-arginine, homoarginine, and L-tryptophan, is recognized as a critical regulator of vascular homeostasis. Dietary intake of homoarginine, taurine, and glycine can improve atherosclerosis by endothelium remodeling. Available data also suggest that the regulation of AA metabolism by indoleamine 2,3-dioxygenase (IDO) and arginases 1 and 2 are mediated through various immunological signals and that immunosuppressive AA metabolizing enzymes are promising therapeutic targets against atherosclerosis. Further clinical studies and basic studies that make use of animal models are required. Here we review recent data examining links between AA metabolism and the development of atherosclerosis.
Light-Driven Biosynthesis of myo-Inositol Directly From CO2 in Synechocystis sp. PCC 6803

myo-inositol (MI) is an essential growth factor, nutritional source, and important precursor for many derivatives like D-chiro-inositol. In this study, attempts were made to achieve the “green biosynthesis” of MI in a model photosynthetic cyanobacterium Synechocystis sp. PCC 6803. First, several genes encoding myo-inositol-1-phosphate synthases and myo-inositol-1-monophosphatase, catalyzing the first or the second step of MI synthesis, were introduced, respectively, into Synechocystis. The results showed that the engineered strain carrying myo-inositol-1-phosphate synthase gene from Saccharomyces cerevisiae was able to produce MI at 0.97 mg L–1. Second, the combined overexpression of genes related to the two catalyzing processes increased the production up to 1.42 mg L–1. Third, to re-direct more cellular carbon flux into MI synthesis, an inducible small RNA regulatory tool, based on MicC-Hfq, was utilized to control the competing pathways of MI biosynthesis, resulting in MI production of ∼7.93 mg L–1. Finally, by optimizing the cultivation condition via supplying bicarbonate to enhance carbon fixation, a final MI production up to 12.72 mg L–1 was achieved, representing a ∼12-fold increase compared with the initial MI-producing strain. This study provides a light-driven green synthetic strategy for MI directly from CO2 in cyanobacterial chassis and represents a renewable alternative that may deserve further optimization in the future.
Circadian Changes of Dendritic Spine Geometry in Mouse Barrel Cortex

The circadian rhythmicity changes the density and shape of dendritic spines in mouse somatosensory barrel cortex, influencing their stability and maturation. In this study, we analyzed the main geometric parameters of dendritic spines reflecting the strength of synapses located on these spines under light/dark (12:12) and constant darkness conditions, in order to distinguish between endogenously regulated and light-driven parameters. Using morphological analysis of serial electron micrographs, as well as three-dimensional reconstructions, we found that the light induces elongation of single-synapse spine necks and increases in the diameter of double-synapse spine necks, increasing and decreasing the isolation of synapses from the parent dendrite, respectively. During the subjective night of constant darkness, we observed an enlargement of postsynaptic density area in inhibitory synapses and an increase in the number of polyribosomes inside double-synapse spines. The results show that both endogenous effect (circadian clock/locomotor activity) and light affect the morphological parameters of single- and double-synapse spines in the somatosensory cortex: light reduces the efficiency of excitatory synapses on single-synapse spines, increases the effect of synaptic transmission in double-synapse spines, and additionally masks the endogenous clock-driven enlargement of inhibitory synapses located on double-synapse spines. This indicates a special role of double-synapse spines and their inhibitory synapses in the regulation of synaptic transmission during both circadian and diurnal cycles in the mouse somatosensory cortex.