Miracle-dz/UniFAR-FTUs huggingface dataset:
Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
Mesoporous starch aerogels production as drug delivery matrices: synthesis optimization, ibuprofen loading, and release property

The aim of this work was to prepare biodegradable starch aerogels as drug carriers. The effective parameters in the synthesis and the optimal values of these parameters were determined using Minitab experimental design software. Ibuprofen was selected as a model drug for the dissolution study and loaded into optimized aerogel during the last solvent exchange step. The Fourier Transform Infrared Spectroscopy (FTIR) analysis showed that ibuprofen has been successfully loaded into the aerogel matrix without any effect on the aerogel nature. The drug loading was calculated to be 29%. The isotherm of ibuprofen adsorption into aerogels matrices followed from the Freundlich isotherm. The in vitro release tests of crystalline ibuprofen and ibuprofen-loaded potato starch aerogel were investigated with simulated gastric and intestinal fluids in USP 2 apparatus. It was shown that the dissolution rate of ibuprofen could be dramatically changed. Also, an improvement in the dissolution rate of ibuprofen was achieved by performing the dissolution test first in the gastric medium for 120 min and then in the intestinal medium for up to 270 min. A higher release rate (100%) was observed at the end of the in vitro experiment.
tRNA biogenesis and specific aminoacyl-tRNA synthetases regulate senescence stability under the control of mTOR

Oncogenes or chemotherapy treatments trigger the induction of suppressive pathways such as apoptosis or senescence. Senescence was initially defined as a definitive arrest of cell proliferation but recent results have shown that this mechanism is also associated with cancer progression and chemotherapy resistance. Senescence is therefore much more heterogeneous than initially thought. How this response varies is not really understood, it has been proposed that its outcome relies on the secretome of senescent cells and on the maintenance of their epigenetic marks. Using experimental models of senescence escape, we now described that the stability of this suppression relies on specific tRNAs and aminoacyl-tRNA synthetases. Following chemotherapy treatment, the DNA binding of the type III RNA polymerase was reduced to prevent tRNA transcription and induce a complete cell cycle arrest. By contrast, during senescence escape, specific tRNAs such as tRNA-Leu-CAA and tRNA-Tyr-GTA were up-regulated. Reducing tRNA transcription appears necessary to control the strength of senescence since RNA pol III inhibition through BRF1 depletion maintained senescence and blocked cell persistence. mTOR inhibition also prevented CIS escape in association with a reduction of tRNA-Leu-CAA and tRNA-Tyr-GTA expression. Further confirming the role of the tRNA-Leu-CAA and tRNA-Tyr-GTA, their corresponding tRNA ligases, YARS and LARS, were necessary for senescence escape. This effect was specific since the CARS ligase had no effect on persistence. YARS and LARS inactivation reduced cell emergence and proteomic analysis indicated that this effect was associated with the down-regulation of E2F1 target genes. Overall, these findings highlight a new regulation of tRNA biology during senescence and suggest that specific tRNAs and ligases contribute to the strength and heterogeneity of this suppression.
Role of predation and parasitism in growth and mortality of yellow perch in Dauphin Lake, Manitoba.

Abstract Total mortality, mortality due to predation, and the contribution of parasite-induced mortality were estimated for yellow perch Perca flavescens infected with the nematode Raphidascaris acus. Total annual natural mortality of yellow perch in Dauphin Lake, Manitoba, was approximately 61%; predation by northern pike Esox lucius accounted for 19% and 45% of natural mortality for female and male yellow perch, respectively. Yellow perch harbored 18 species of parasites, of which R. acus was the most abundant; 95% of all R. acus larvae inhabited the liver. The number of free and encapsulated larvae and nodules in the liver of yellow perch varied seasonally and with fish gender, but it was not correlated with water temperature or fish habitat. Mean intensity but not recruitment increased with age of yellow perch. Density of R. acus (larvae per gram of liver) was highest in young, immature yellow perch and decreased with age in mature yellow perch. Yellow perch with high-density infections had lower cond.
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches

Large-scale serological testing in the population is essential to determine the true extent of the current SARS-CoV-2 pandemic. Serological tests measure antibody responses against pathogens and use predefined cutoff levels that dichotomize the quantitative test measures into sero-positives and negatives and use this as a proxy for past infection. With the imperfect assays that are currently available to test for past SARS-CoV-2 infection, the fraction of seropositive individuals in serosurveys is a biased estimator of the cumulative incidence and is usually corrected to account for the sensitivity and specificity. Here we use an inference method—referred to as mixture-model approach—for the estimation of the cumulative incidence that does not require to define cutoffs by integrating the quantitative test measures directly into the statistical inference procedure. We confirm that the mixture model outperforms the methods based on cutoffs, leading to less bias and error in estimates of the cumulative incidence. We illustrate how the mixture model can be used to optimize the design of serosurveys with imperfect serological tests. We also provide guidance on the number of control and case sera that are required to quantify the test’s ambiguity sufficiently to enable the reliable estimation of the cumulative incidence. Lastly, we show how this approach can be used to estimate the cumulative incidence of classes of infections with an unknown distribution of quantitative test measures. This is a very promising application of the mixture-model approach that could identify the elusive fraction of asymptomatic SARS-CoV-2 infections. An R-package implementing the inference methods used in this paper is provided. Our study advocates using serological tests without cutoffs, especially if they are used to determine parameters characterizing populations rather than individuals. This approach circumvents some of the shortcomings of cutoff-based methods at exactly the low cumulative incidence levels and test accuracies that we are currently facing in SARS-CoV-2 serosurveys.
Short-term responses to ocean acidification: effects on relative abundance of eukaryotic plankton from the tropical Timor Sea

Anthropogenic carbon dioxide (CO2) emissions drive climate change and pose one of the major challenges of our century. The effects of increased CO2 in the form of ocean acidification (OA) on the communities of marine planktonic eukaryotes in tropical regions such as the Timor Sea are barely understood. Here, we show the effects of high CO2 (pCO2=1823±161 μatm, pHT=7.46±0.05) versus in situ CO2 (pCO2=504±42 μatm, pHT=7.95±0.04) seawater on the community composition of marine planktonic eukaryotes immediately and after 48 hours of treatment exposure in a shipboard microcosm experiment. Illumina sequencing of the V9 hypervariable region of 18S rRNA (gene) was used to study the eukaryotic community composition. Down-regulation of extracellular carbonic anhydrase occurred faster in the high CO2 treatment. Increased CO2 significantly suppressed the relative abundances of different eukaryotic operational taxonomic units (OTUs), including important primary producers. These effects were consistent between abundant (DNA-based) and active (cDNA-based) taxa after 48 hours, e.g., for the diatoms Trieres chinensis and Stephanopyxis turris. Effects were also very species-specific among different diatoms. Planktonic eukaryotes showed adaptation to the CO2 treatment over time, but many OTUs were adversely affected by decreasing pH. OA effects might fundamentally impact the base of marine biodiversity, suggesting profound outcomes for food web functioning in the future ocean.
Bacteria culturing and isolation under field conditions of Moukalaba-Doudou National Park, Gabon, and preliminary survey on bacteria carrying antibiotic resistance genes

Culturing the intestinal bacteria of wild animals is a difficult task under field conditions, although isolation and characterization of bacteria are absolutely necessary to evaluate the transmission of bacteria from human to animal or vice versa. We have developed a protocol for intestinal bacteria culturing from feces of wild animals such as gorillas in Moukalaba-Doudou National Park in Gabon, where no laboratory settings were available. The prevalence of resistance genes in Enterobacteriaceae isolates estimated by real time PCR array was higher for aminoglycosides resistance, followed by tetracycline resistance, except for possible naturally occurring β-lactam resistance. The detection level of resistance genes was higher for isolates from humans than those from gorillas. Occasional monitoring of this prevalence may help to measure the intensity of introduction of humanborne bacteria to wildlife.
Competition between three species of Glomus used as spatially separated introduced and indigenous mycorrhizal inocula for leek (Allium porrum L.)

SUMMARY The ability of three vesicular-arbuscular (VA) mycorrhizal fungi - Glomus caledonium (Nicol. and Gerd.) Trappe and Gerd. , Glomus sp. type E3 and Glomus mosseae (Nicol. and Schenck) Gerd. and Trappe - to infect leek (Allium porrum L.), when used as spatially separated pairs of inocula was assessed by analysing the roots for the presence of diagnostic fungal enzymes after separation of root proteins by gel electrophoresis. A difference in competitiveness was observed, such that Glomus sp. E3 was unable to infect a root system if either G. caledonium or G. mosseae were also present. When the latter two fungi were used as a pair of inocula, the one which had been placed to simulate an indigenous strain predominated in the root to the almost total exclusion of the one placed as an introduced inoculum. These results suggest that the successful establishment of VA mycorrhizal inocula in field soils will depend on the indigenous species present, the species being introduced and its placement in the soil. The use of diagnostic fungal isozyme analysis offers a method of monitoring the outcome of an inoculation programme by detecting the presence of the introduced species in the host roots.
Minocycline exerts inhibitory effects on multiple mitogen‐activated protein kinases and IκBα degradation in a stimulus‐specific manner in microglia

CNS inflammation mediated by microglial activation can result in neuronal and glial cell death in a variety of neurodegenerative and demyelinating diseases. Minocycline, a second‐generation tetracycline, has profound anti‐inflammatory properties in the CNS mediated, in part, by inhibition of microglia. MAPK and nuclear factor‐κB (NF‐κB) activation are hallmarks of activated microglia and they are critical for the expression of many inflammatory mediators. In the present study, we investigated minocycline effects on activation of p38, c‐Jun‐N‐terminal activated protein kinase (JNK) 1/2 and extracellular signal regulated kinase (ERK) 1/2 MAPKs and inhibitor α of NF‐κB (IκBα) degradation in BV‐2 and primary microglial cells. Our results demonstrate that minocycline has the ability to inhibit all MAPKs but these effects strongly depend on the stimulus used for MAPK activation. Minocycline significantly decreased activation of all lipopolysaccharide‐stimulated MAPKs but it was without effect on MAPKs activated by H2O2. Minocycline inhibited JNK1/2 and ERK1/2 but not p38 when stimulated by 2′,3′‐O‐(4‐benzoylbenzoyl)‐adenosine 5′‐triphosphate, indicating that minocycline affects only certain upstream signaling target(s) that are stimulus‐specific. Our data also suggest that protein kinase C (PKC) inhibition may be partially involved in the minocycline mechanism of MAPK inhibition. In addition, minocycline attenuated lipopolysaccharide‐stimulated degradation of IκBα implying a possible inhibitory role on NF‐κB transcriptional activity.
The “Magic Action” of Stock Splits: Evidence from the Warsaw Stock Exchange 2003–2017

Abstract Purpose: Many researchers claim that split has a positive effect on stock returns. However, if we observe more closely, we notice that this is only an accounting procedure. Therefore, the question arises as to whether stock prices should change. To answer this problem, we checked the market reaction to the division of shares on the Warsaw Stock Exchange. Methodology: To verify our hypotheses, we used the event study analysis. Based on the Sharpe market model, we assumed that the price of the asset determines systematic risk and specific risk. Findings: On the basis of conducted analyses, we found a positive market reaction to the first split information, while the announcement of General Meeting of Shareholders (GMS) resolutions generated a price correction. Moreover, split events initially caused an increase in abnormal returns. The research results are consistent with the efficient market hypothesis. Research limitations: The sample size does not give an opportunity to check the impact of economic cycles. During the last 15 years, we found only 75 events of splits without any disruption event. Originality: Analysis of three dates: information about the planned general meeting of shareholders regarding the split, publication of decisions taken at the general meeting, and the day of the split.
Sichuanosuchus shuhanensis, a new ?early Cretaceous protosuchian (Archosauria: Crocodyliformes) from Sichuan (China), and the monophyly of Protosuchia

ABSTRACT A new protosuchian, Sichuanosuchus shuhanensis, sp. nov. from the ? Lower Cretaceous of Sichuan (China), is distinguished from other known basal crocodyliform archosaurs primarily by the subdivision of the small antorbital fenestra into anterior and posterior openings, the presence of a large, caniniform first maxillary tooth, followed by seven teeth with low, chisel-like crowns, and the posterior palpebrai being larger than the anterior one. Phylogenetic analysis using 128 characters for 29 crocodyliform taxa supports the monophyly of Protosuchia. Sichuanosuchus is most closely related to Shantungosuchus from the Upper Jurassic and Lower Cretaceous of China. These two taxa, together with Gobiosuchus from the Upper Cretaceous of Mongolia, appear to form a clade of late Mesozoic basal crocodyliform reptiles.
A Facile H2SO4-SiO2–Catalyzed Ferrier Rearrangement of 3,4,6-Tri-O-benzyl-d-glucal

Sulfuric acid immobilized on silica gel (H2SO4-SiO2) was used as an efficient and convenient promoter for Ferrier-type rearrangement of 3,4,6-tri-O-benzyl-d-glucal in CH2Cl2, which is a difficult donor for this type of reaction. The acceptors include primary alcohols, secondary alcohols, pentanol, halogenated alcohol, sterols, thiol, and 2-naphthol. Thus, 2,3-unsaturated glycosides were obtained rapidly (<2 h) and efficiently (>62%) in good α-selectivity (α/β>4.2:1) under mild conditions.
The Impact of Auditor Specialization and Banks’ Listing Status on Earnings Management in Vietnamese Commercial Banks

Abstract This study investigates the impact of auditor specialization and listing status on earnings management in Vietnamese commercial banks. Discretionary loan loss provisions (LLP) is used as a proxy for earnings management. Based on a sample of 21 banks in the period 2008–2017, the findings show that: First, auditor specialization does not have a significant impact on constraining earnings management in the banks. Second, listed banks engage more in earnings management. In addition, listed banks report more income-increasing LLP, while non-listed banks report more income-decreasing LLP. The results are consistent with a number of prior studies that find no evidence of specialist auditors curtailing earnings management, and listed firms participating more in managing income. The results have important implications for government authorities in improving the legal framework over the preparation of banks’ financial statements, including revision of the accounting standards and alignment of the accounting standards with other banking regulations.
Regulation of Somatic Embryogenesis in Higher Plants

Somatic embryogenesis is the developmental process by which somatic cells undergo restructuring to generate embryogenic cells. These cells then go through a series of morphological and biochemical changes that result in the formation of a somatic or non-zygotic embryo capable of regenerating plants. Somatic embryogenesis represents a unique developmental pathway that includes a number of characteristic events: dedifferentiation of cells, activation of cell division, and reprogramming of their physiology, metabolism, and gene expression patterns. Valuable studies have elucidated the developmental processes pertaining to the control parameters of somatic embryogenesis. These studies have emphasized the transitional state from somatic to embryogenic cells, identified differentially expressed genes in nonembryogenic and embryogenic calli, isolated varieties of genes that are likely involved in the embryogenic pathway, compared specific gene products that accumulate during different stages of somatic embryogenesis, and discovered molecular or protein markers for somatic embryogenesis. An understanding of embryogenic pathway initiation, and origin of somatic embryos (unicellular or multicellular) is critical to scientific and biotechnological applications. Cell tracking has been successfully applied to determine the fate of embryogenic cells. Identification of hormone-inducible genes has yielded clues to the control of gene expression during embryogenic development. Characterization of genes taking part in signal transduction pathways, such as somatic embryogenesis receptor-like kinases, has generated great interest in the switching of several signal cascades during somatic embryogenesis, and has identified how genes encoding transcription factors such as BBM, LEC1, and LEC2 could be used to regulate somatic embryo development. Protein markers are useful probes for defining embryogenic potential and for marking different phases in plant development. This review provides a systematic and comprehensive analysis of current advances in the development of somatic embryogenesis, as well as the cellular and molecular mechanism of somatic embryogenesis in higher plants. The developmental pathway, differential gene expression, and extracellular protein markers during somatic embryogenesis are especially emphasized.
Increased abundance and depth distribution of pelagic crustacean zooplankton during hypolimnetic oxygenation in a deep, eutrophic Alberta Lake

Since June 1988, the north basin of eutrophic Amisk Lake has been treated by hypolimnetic oxygenation, while the south basin has served as a reference. In summer 1989, hypolimnetic dissolved oxygen (DO) concentrations were >=>1 mg ·L-1 in the treatment basin, while they fell to <1 mg ·L-1 in the reference basin by early July. There were no apparent treatment effects on biomass, abundance, or distribution of zooplankton in surface waters (0-10 m). However, in summer 1989, hypolimnetic abundances of two of four species (Daphnia longiremis and Daphnia pulex) were greater in the treatment than in the reference basin (P < 0.03) and than in the north basin in summer 1984 (4 years pretreatment). In the hypolimnion, D. longiremis, D. pulex, Bosmina longirostris, and Diacyclops bicuspidatus thomasi were found at greater median depths (P < 0.001) in the treatment than in the reference basin. Median depths of these four species in the hypolimnion tracked species-specific DO concentrations of between 1.5 and 2.3 mg ·.
Formation of native arsenic in hydrothermal base metal deposits and related supergene U6+ enrichment: The Michael vein near Lahr, SW Germany

Abstract Native arsenic is an occasional ore mineral in some hydrothermal base metal deposits. Its rarity (compared to pyrite, arsenopyrite, galena, sphalerite, or chalcopyrite, for example) is surprising, as arsenic is a common constituent of upper crustal fluids. Hence, the conditions of formation must be quite special to precipitate native arsenic. An ideal location to investigate the formation of native As and to explore the parameters constraining its crystallization is the Michael vein near Lahr, Schwarzwald, southwest (SW) Germany. Here, galena, sphalerite, and native arsenic are the most abundant ore minerals. The two important ore stages comprise (1) galena-barite and (2) sphalerite-native arsenicquartz, the latter with a general mineral succession of pyrite → sphalerite ± jordanite-gratonite solid solution → galena → native As. The native arsenic-bearing mineralization formed by cooling of an at least 130 °C hot saline fluid accompanied by a reduction due to the admixing of a sulfide-bearing fluid. Thermodynamic calculations reveal that for the formation of native arsenic, reduced conditions in combination with very low concentrations of the transition metals Fe, Co, and Ni, as well as low sulfide concentrations, are essential. “Typical” hydrothermal fluids do not fulfill these criteria, as they typically can contain significant amounts of Fe and sulfide. This results in the formation of arsenides, sulfarsenides, or As-bearing sulfides instead of native arsenic. Very minor amounts of pyrite, sulfarsenides, and arsenides record the very low concentrations of Fe, Co, and Ni present in the oreforming fluid. High concentrations of aqueous Zn and Pb lead to early saturation of sphalerite and galena that promoted native arsenic precipitation by decreasing the availability of sulfide and hence suppressing realgar formation. Interestingly, native arsenic in the Michael vein acted as a trap for uranium during supergene weathering processes. Infiltrating oxidizing, U+VI-bearing fluids from the host lithologies reacted under ambient conditions with galena and native arsenic, forming a variety of U+VI (±Pb)-bearing arsenates such as hügelite, hallimondite, zeunerite, heinrichite, or novacekite together with U-free minerals like mimetite or anglesite. Some parts of the vein were enriched to U concentrations of up to 1 wt% by this supergene process. Reduced (hypogene) uranium phases like uraninite were never observed.