Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Stocking Sequence on Survival of Fingerling Channel Catfish Cultured in Mixed‐Size Populations

Abstract Replacement channel catfish Ictalurus punctatus are typically stocked as fingerlings into commercial grow-out ponds following partial harvest of large fish. To determine if timing of subsequent stocking of fingerlings into mixed-size populations influences fingerling survival, we examined the effects of stocking large and small fish 2 weeks after initial stocking of large fish. Fifty large (mean weight = 374 g) and 50 small (25 g) catfish were stocked into two 1,323-L tanks. Tank 1 was stocked with large fish and maintained for 14 d; on day 14, small fish were added. Tank 2 was stocked with large and small fish simultaneously on day 14. A third tank was stocked with 100 small fish only on day 14. Three ponds (0.05-ha each) were also used in the same design with large fish (240 g) and small fish (30 g). On day 15, all fish were harvested and counted to determine 24-h survival. This procedure was replicated over three trials in both the tank and pond studies. Survival of small fish stocked 14 d aft.
THE RELATIONSHIP BETWEEN VALVE DIAMETER AND NUMBER OF CENTRAL FULTOPORTULAE IN THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE) 1

Cells well below the reported minimum size for Thalassiosira weisslogii (Grunow) Fryxell et Hasle were observed in two unialgal cultures. The relationship between diameter and number of central fultoportulae was found to be very regular. Regresion analysis of three different populations showed equivalent slopes and r2 values above 80%. The y‐intercepts were significantly different and support observations in the litrature that nonmarine valeve of T. Weissflogii have fewer central fultoportulae than marine forms.
Relative proportion of antioxidative enzyme activity in locally grown Indian rice cultivars (Oryza sativa L.) under submergence condition

Abstract Breeders are trying to develop true submergence-tolerant genotypes for lowland irrigated and/or rainfed areas, where rice is often affected by short-term submergence. This study was conducted to evaluate the submergence tolerance, response of antioxidative defense systems to hypoxic and re-aerated conditions, and growth and survival percentage among 19 rice genotypes. The rice seedlings submerged into concrete tanks for 10 days exhibited decreased activities of antioxidant enzymes. The antioxidant enzymes, superoxide dismutase, catalase, and ascorbate peroxidase increased, whereas polyphenol oxidase and glutathione reductase decreased in subsequent re-aerated situation in tolerant genotypes. On the other hand, the activities of enzymes decreased greatly in susceptible genotypes under hypoxic and re-aerated conditions. Complete submergence of the seedling increased the plant height of 12 genotypes. However, it decreased the dry matter production. Genotypes having better root and shoot growth maintained higher dry weight and exhibited better survival than did others. The results indicated that genotypes tolerant of flash flood maintained higher activities of antioxidant enzymes and dry matter accumulation to protect against postanoxic injury.
Understanding the psychological impact of the COVID-19 pandemic and containment measures: An empirical model of stress

Research suggests that epidemics and corresponding containment measures have negative consequences to the individual and cause stress. The psychological mechanisms that determine stress, caused by the COVID-19 pandemic and containment measures, are not yet clear. In a survey during the lockdown in Switzerland (n=1565), we found substantially increased levels of stress in the population. In particular, individuals who did not agree with the containment measures, as well as those who saw nothing positive in the crisis, experienced even higher levels of stress. In contrast, individuals who are part of a risk group or who are working in healthcare or in essential shops experienced similar stress levels as the general public. We conducted a path analysis to gain a deeper understanding of the psychological mechanisms during lockdown. Experiencing fear of the disease is a key driver for being worried. Our model further shows that worries about the individual, social, and economic consequences of the crisis, strongly boost stress. The infection rate in the canton (i.e. state) of residence also contributes to stress. Positive thinking and perceived social, organizational, and governmental support mitigate worries and stress. To prevent stress, authorities should explain containment measures well, highlight positive aspects of the crisis, address worries, and facilitate support.
COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status

Previous studies suggest a role for systemic reprogramming of host metabolism during viral pathogenesis to fuel rapidly expanding viral proliferation, for example by providing free amino acids and fatty acids as building blocks. In addition, general alterations in metabolism can provide key understanding of pathogenesis. However, little is known about the specific metabolic effects of SARS-COV-2 infection. The present study evaluated the serum metabolism of COVID-19 patients (n=33), identified by a positive nucleic acid test of a nasopharyngeal swab, as compared to COVID-19-negative control patients (n=16). Targeted and untargeted metabolomics analyses specifically identified alterations in the metabolism of tryptophan into the kynurenine pathway, which is well-known to be involved in regulating inflammation and immunity. Indeed, the observed changes in tryptophan metabolism correlated with serum interleukin-6 (IL-6) levels. Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). Increased circulating levels of glucose and free fatty acids were also observed, consistent with altered carbon homeostasis in COVID-19 patients. Metabolite levels in these pathways correlated with clinical laboratory markers of inflammation and disease severity (i.e., IL-6 and C-reactive protein) and renal function (i.e., blood urea nitrogen). In conclusion, this initial observational study of the metabolic consequences of COVID-19 infection in a clinical cohort identified amino acid metabolism (especially kynurenine and cysteine/taurine) and fatty acid metabolism as correlates of COVID-19, providing mechanistic insights, potential markers of clinical severity, and potential therapeutic targets.
Evaluating the determinants of COVID-19 mortality: A cross-country study

As the COVID-19 pandemic has spread to the entire world, a race to understand the virus and to find an effective and safe vaccine or treatment has triggered interest in the factors contributing to mortality. For instance, some studies have suggested that the BCG vaccine could protect from COVID-19 and nicotine patches could be therapeutic against the virus. This study makes use of data for about 140 countries to evaluate the determinants of COVID-19 mortality. It finds that a country's share of spending on health care (as a measure of a country's effectiveness in tracking, recording, and reporting COVID-19 deaths) is positively associated with COVID-19 deaths. It also finds that the share of people above 65 years of age, obesity, and urbanization are all positively associated with COVID-19 mortality. There is no evidence that BCG vaccination, smoking prevalence, and PM25 pollution have any link to COVID-19 mortality. These estimation results are robust to alternative specifications and after controlling for confounding factors and excluding outliers. Policymakers should allocate resources towards the protection of the elderly and those suffering from underlying conditions such as obesity. They should also exercise caution about administering nicotine patches or the BCG vaccine to fight COVID-19 without the backing of concrete scientific evidence.
The first 100 days of SARS-CoV-2 control in Vietnam

Background: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23rd, 270 cases have been confirmed, with no deaths. We describe the control measures used and their relationship with imported and domestically-acquired case numbers. Methods: Data on the first 270 SARS-CoV-2 infected cases and the timing and nature of control measures were captured by Vietnam's National Steering Committee for COVID-19 response. Apple and Google mobility data provided population movement proxies. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. Results: After the first confirmed case on January 23rd, the Vietnamese Government initiated mass communications measures, contact tracing, mandatory 14-day quarantine, school and university closures, and progressive flight restrictions. A national lockdown was implemented between April 1st and 22nd. Around 200,000 people were quarantined and 266,122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections were asymptomatic. 21 developed severe disease, with no deaths. The serial interval was 3.24 days, and 27.5% (95% confidence interval, 15.7%-40.0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1.15 (95% confidence interval, 0.37-2.36). No community transmission has been detected since April 15th. Conclusions: Vietnam has controlled SARS-CoV-2 spread through the early introduction of communication, contact-tracing, quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic cases and imported cases, and evidence for substantial pre-symptomatic transmission.
Root strength in some Populus and Salix clones

Abstract The tensile strength of the roots of six Populus and Salix clones, and its relation to their anatomy and chemical composition, was investigated to assist selection of improved varieties for soil conservation planting. The amount of stele in the roots and its specific gravity were the most important factors determining tensile strength. Variation in specific gravity accounted for 79% of the intra-clonal variation in the tensile strength of the stele, and was also correlated with inter-clonal and seasonal variation. Fibre wall strength and specific tensile strength were correlated with S2 microfibril angle intra-clonally, cellulose content inter-clonally, and the lignin/cellulose ratio seasonally. The load required to break the roots did not increase linearly with the diameter of the roots. The results show that, in future, tensile testing is not essential in the selection of clones with the strongest roots, because these can be identified from the amount of stele in their roots and its specific gr.
Children’s Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools

Effective response to the Coronavirus Disease 2019 (COVID-19) pandemic requires genomic resources and bioinformatics tools for genomic epidemiology and surveillance studies that involve characterizing full-length viral genomes, identifying origins of infections, determining the relatedness of viral infections, performing phylogenetic analyses, and monitoring the continuous evolution of the SARS-CoV-2 viral genomes. The Children’s Hospital, Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) (https://covid19.cpmbiodev.net/) is a comprehensive genomic resource that provides access to full-length SARS-CoV-2 viral genomes and associated meta-data for over 30,000 (as of May 20, 2020) isolates collected from global sequencing repositories and the sequencing performed at the Center for Personalized Medicine (CPM) at CHLA. Reference phylogenetic trees of global and USA viral isolates were constructed and are periodically updated using selected high quality SARS-CoV-2 genome sequences. These provide the baseline and analytical context for identifying the origin of a viral infection, as well as the relatedness of SARS-CoV-2 genomes of interest. A web-based and interactive Phylogenetic Tree Browser supports flexible tree manipulation and advanced analysis based on keyword search while highlighting time series animation, as well as subtree export for graphical representation or offline exploration. A Virus Genome Tracker accepts complete or partial SARS-CoV-2 genome sequence, compares it against all available sequences in the database (>30,000 at time of writing), detects and annotates the variants, and places the new viral isolate within the global or USA phylogenetic contexts based upon variant profiles and haplotype comparisons, in a few seconds. The generated analysis can potentially aid in genomic surveillance to trace the transmission of any new infection. Using CHLA CARD, we demonstrate the identification of a candidate outbreak point where 13 of 31 CHLA internal isolates may have originated. We also discovered multiple indels of unknown clinical significance in the orf3a gene, and revealed a number of USA-specific variants and haplotypes.
Retrograde transport defects in Munc18-1 null neurons explain abnormal Golgi morphology

Loss of the exocytic Sec1/MUNC18 protein MUNC18-1 or its t-SNARE partners SNAP25 and syntaxin-1 results in rapid, cell-autonomous and unexplained neurodegeneration, which is independent of their known role in synaptic vesicle exocytosis. cis-Golgi abnormalities are the earliest cellular phenotypes before degeneration occurs. Here, we investigated whether these Golgi abnormalities cause defects in the constitutive and regulated secretory pathway that may explain neurodegeneration. Electron microscopy confirmed that loss of MUNC18-1 expression results in a smaller cis-Golgi. In addition, we now show that medial-Golgi and the trans-Golgi Network are also affected. However, stacking and cisternae ultrastructure of the Golgi were normal. Overall ultrastructure of null mutant neurons was remarkably normal just hours before cell death occurred. Anterograde ER-to-Golgi and Golgi exit of endogenous and exogenous proteins were normal. In contrast, loss of MUNC18-1 caused reduced retrograde Cholera Toxin transport from the plasma membrane to the Golgi. In addition, MUNC18-1-deficiency resulted in abnormalities in retrograde TrkB trafficking. We conclude that MUNC18-1 deficient neurons have normal anterograde yet reduced retrograde transport to the Golgi. This imbalance in transport routes provides a plausible explanation for the observed Golgi abnormalities and cell death in MUNC18-1 deficient neurons. Significance statement Loss of MUNC18-1 or its t-SNAREs SNAP25 and syntaxin-1 leads to massive, yet unexplained, neurodegeneration. Previous research showed that Golgi abnormalities are the earliest, shared phenotype. Golgi abnormalities are also an early feature in neurodegenerative diseases, such as Alzheimer’s Disease or Amyotrophic Lateral Sclerosis. This study elucidates the mechanism underlying the Golgi phenotype upon loss of MUNC18-1. By systematically assessing transport routes to and from the Golgi, we show that retrograde endosome-to-Golgi, but not anterograde transport from the Golgi, is disturbed. This imbalance in transport routes provides a plausible explanation for the Golgi phenotype, and may explain the neurodegeneration. The findings in this study contributes to new insights in cellular mechanisms of neurodegeneration.
Effect of drying time, bean depth and temperature on free amino acid, peptide‐N, sugar and pyrazine concentrations of Malaysian cocoa beans

The effect of drying time on free amino acid, peptide-N, sugar and pyrazine concentrations as well as the influence of bean depth and temperature on these compounds during cocoa drying was studied. Drying time, bean depth and temperature significantly decreased the concentration of free amino acids, peptide-N, total reducing sugars and sucrose and increased the concentration of trimethyl-, tetramethylpyrazine and total pyrazines in cocoa beans. The best drying treatment was obtained at the combination of bean depth/drying temperature of 8.3 cm/40 °C. This was based on the fact that it produced significantly high concentrations of hydrophobic free amino acids, peptide-N and total reducing sugars and significantly low concentration of trimethyl-, tetramethylpyrazine and total pyrazines. Drying treatment of 1.5 cm/60 °C significantly produced the lowest concentration of free amino acids, peptide-N and total reducing sugars and the highest concentration of pyrazines. © 1999 Society of Chemical Industry
Potential Antiviral Options against SARS-CoV-2 Infection

As of May 2020, the number of people infected with SARS-CoV-2 continues to skyrocket, with more than 4,5 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. Developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent plasma and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here we developed a neutralization assay using SARS-CoV-2 virus and monkey Vero-E6 cells. We identified most potent sera from recovered patients for treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against SARS-CoV-2 infection in Vero-E6 cells and identified antiviral activity of nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that combinations of virus-directed drug nelfinavir with host-directed drugs, such as salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine exhibit synergistic effect against SARS-CoV-2 in vitro. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19.
Acute effects of prolactin on hypothalamic prolactin receptor expressing neurones in the mouse

The anterior pituitary hormone, prolactin, is a fundamental regulator of lactation, and also plays a role in many other physiological processes including maternal behaviour, reproduction, immune response and even energy balance. Indeed, prolactin receptors (Prlr) are widely distributed throughout the body, including a number of different brain regions, further attesting to its pleiotropic nature. Within the brain, previous research has identified key areas upon which prolactin exerts effects on gene transcription through the canonical JAK2/STAT5 pathway downstream of the Prlr. In some neurones, however, such as the tuberoinfundibular dopamine neurones that control prolactin secretion, prolactin can also exert rapid actions to stimulate neuronal activity. While prolactin-induced activation of STAT5 has been described in a wide variety of brain regions, its capacity for acute modulation of electrical properties of many Prlr-expressing neurones remains to be elucidated. To investigate how widespread these rapid actions of prolactin are in various Prlr-expressing neurones, we utilised a transgenic mouse line in which Cre recombinase is specifically expressed in the coding region of the prolactin long form receptor gene (Prlr-iCre). This mouse line was crossed with a Cre-dependent calcium indicator (GCaMP6f) transgenic mouse, allowing us to visually monitor the electrical activity of Prlr-expressing neurones in ex vivo 200μm brain slice preparations. Here, we survey hypothalamic regions implicated in prolactin’s diverse physiological functions such as: the arcuate (ARC) and paraventricular nuclei of the hypothalamus (PVN), and the medial preoptic area (MPOA). We observe that in both males and virgin and lactating females, bath application of prolactin is able to induce electrical changes in a subset of Prlr-expressing cells in all of these brain regions. The effects we detected ranged from rapid or sustained increases in intracellular calcium to inhibitory effects, indicating a heterogeneous nature of these Prlr-expressing populations. These results enhance our understanding of mechanisms by which prolactin acts on hypothalamic neurones and provide insights into how prolactin might influence neuronal circuits in the mouse brain.
A miR-494 dependent feedback loop regulates ER stress

Defects in stress responses are important contributors in many chronic conditions including cancer, cardiovascular disease, diabetes, and obesity-driven pathologies like non-alcoholic steatohepatitis (NASH). Specifically, endoplasmic reticulum (ER) stress is linked with these pathologies and control of ER stress can ameliorate tissue damage. MicroRNAs have a critical role in regulating diverse stress responses including ER stress. Here we show that miR-494 plays a functional role during ER stress. ER stress inducers (tunicamycin & thapsigargin) robustly increase the expression of miR-494 in vitro in an ATF6 dependent manner. Surprisingly, miR-494 pretreatment dampens the induction and magnitude of ER stress in response to tunicamycin in endothelial cells. Conversely, inhibition of miR-494 increases ER stress de novo and amplifies the effects of ER stress inducers. Using Mass Spectrometry (TMT-MS) we identified 23 proteins that are downregulated by both tunicamycin and miR-494. Among these, we found 6 transcripts which harbor a putative miR-494 binding site. We validated the anti-apoptotic gene BIRC5 (survivin) as one of the targets of miR-494 during ER stress. Finally, induction of ER stress in vivo increases miR-494 expression in the liver. Pretreatment of mice with a miR-494 plasmid via hydrodynamic injection decreased ER stress in response to tunicamycin in part by decreasing inflammatory chemokines and cytokines. In summary, our data indicates that ER stress driven miR-494 may act in a feedback inhibitory loop to dampen downstream ER stress signaling. We propose that RNA-based approaches targeting miR-494 or its targets may be attractive candidates for inhibiting ER stress dependent pathologies in human disease.