Miracle-dz/UniFAR-FTUs huggingface dataset:
A rapid risk analysis tool to prioritise response to infectious disease outbreaks

Epidemics are influenced by both disease and societal factors and can grow exponentially over short time periods. Epidemic risk analysis can help in rapidly predicting potentially serious outcomes and flagging the need for rapid response. We developed a multifactorial risk analysis tool ‘EpiRisk’ to provide rapid insight into the potential severity of emerging epidemics by combining disease-related parameters and country-related risk parameters. An initial set of 18 disease and country-related risk parameters was reduced to 14 following qualitative discussions and the removal of highly correlated parameters by a correlation and clustering analysis. Of the remaining parameters, three risk levels were assigned ranging from low (1) moderate (2) and high (3). The total risk score for an outbreak of a given disease in a particular country is calculated by summing these 14 risk scores, and this sum is subsequently classified into one of four risk categories: low risk (<21), moderate risk (21–29), high risk (30–37) and extreme risk (>37). Total risk scores were calculated for nine retrospective outbreaks demonstrating an association with the actual impact of those outbreaks. We also evaluated to what extent the risk scores correlate with the number of cases and deaths in 61 additional outbreaks between 2002 and 2018, demonstrating positive associations with outbreak severity as measured by the number of deaths. Using EpiRisk, timely intervention can be implemented by predicting the risk of emerging outbreaks in real time, which may help government and public health professionals prevent catastrophic epidemic outcomes.
Mycophagie chez le sanglier et hypothèses sur son rôle dans la dissémination des spores de champignons hypogés

Microscopic study of wild boar (Sus scrofa scrofa) faeces collected in the French Mediterranean zone reveals a frequent consumption of ectomycorrhizal fungi. Hypogeous species are predominant. Mycophagy is more important in forest stands than in open areas. Hypotheses are proposed on the role of the wild boar in the dissemination of hypogeous fungi spores, which is necessary for forest regeneration: the boar would not play an important role in the recolonization of deforested areas, but may favour the genie mixing of spatially separated fungi populations.
Ultrasonographic assessment of the effect of metoclopramide, erythromycin, and exenatide on solid‐phase gastric emptying in healthy cats

Abstract Background Available data on the effect of gastrointestinal motility‐modifying drugs in cats are limited. Most recommendations for drug usage and dosage are based on collective clinical experience. Objectives To assess the effects of metoclopramide, erythromycin, and exenatide on gastric emptying (GE) and gastric motility in comparison to placebo. We hypothesized that metoclopramide and erythromycin would have prokinetic gastric effects, whereas exenatide would prolong GE times and decrease the motility index (MI) of antral contractions. Animals Eight healthy domestic shorthair cats. Methods Each cat had 4 separate ultrasonographic assessments. In a prospective, randomized, double‐blind, 4‐way crossover design, cats received placebo, metoclopramide, erythromycin, or exenatide for 2 days followed by a minimum 5‐day washout period. Ultrasonographic GE times and MI were compared to placebo. Results When compared to placebo, the rate of GE was significantly faster after administration of metoclopramide and erythromycin. Significant differences were found at all fractions of GE after administration of erythromycin and all but 1 fraction after metoclopramide when compared to placebo. The rate of GE in the first half of the GE curve was significantly slower after exenatide administration. The total area under the Ml curve was significantly larger after administration of metoclopramide and erythromycin than after placebo. Conclusions and Clinical Importance Metoclopramide and erythromycin shorten GE times and increase the MI of antral contractions, thus having a prokinetic effect in the stomach of healthy cats, whereas exenatide causes an initial delay in GE.
Shaping Microglial Phenotypes Through Estrogen Receptors: Relevance to Sex-Specific Neuroinflammatory Responses to Brain Injury and Disease

In mammals, 17β-estradiol (E2), the primary endogenous estrogen, maintains normal central nervous system (CNS) function throughout life and influences brain responses to injury and disease. Estradiol-induced cellular changes are mediated through the activation of nuclear and extranuclear estrogen receptors (ERs), which include ERα, ERβ, and the G-protein coupled receptor, GPER1. ERs are widely expressed throughout the brain, acting as transcriptional effectors or rapidly initiating membrane and cytoplasmic signaling cascades in practically all brain cells including microglia, the resident immune cells of the CNS. Activation of ERs by E2 exerts potent anti-inflammatory effects through mechanisms involving the modification of microglial cell responses to acute or chronic brain injury. Recent studies suggest that microglial maturation is influenced by the internal gonadal hormone milieu and that their functions in the normal and diseased brain are sex specific. However, the role that each ER subtype plays in microglial development or in determining microglial function as the primary cellular defense mechanism against pathogens and injury remains unclear. This is partly due to the fact that most studies investigating the mechanisms by which E2-ER signaling modifies microglial cellular phenotypes have been restricted to one sex or age. This review examines the different in vivo and in vitro models used to study the direct and indirect regulation of microglial cell function by E2 through ERs. Ischemic stroke will be used as an example of a neurologic disease in which activation of ERs shapes microglial phenotypes in response to injury in a sex- and age-specific fashion. Significance Statement As the primary immune sensors of central nervous system damage, microglia are important potential therapeutic targets. Estrogen receptor signaling modulates microglial responses to brain injury and disease in a sex- and age-specific fashion. Hence, investigating the molecular mechanisms by which estrogen receptors regulate and shape microglial functions throughout life may result in novel and effective therapeutic opportunities that are tailored for each sex and age.
A new technique for measuring oscillatory and diurnal changes in leaf thickness

A new technique is described for measuring oscillatory and diurnal changes in leaf thickness. Mature leaves of Populusdeltoides × nigra undergo diurnal or oscillatory changes in thickness of up to 20 μm in amplitude; thickness changes were measured to ±0.2 μm and appear to correlate with expected levels of leaf water stress.
The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the betacoronavirus family, which causes COVID-19 disease. SARS-CoV-2 pathogenicity in humans leads to increased mortality rates due to alterations of significant pathways, including some resulting in exacerbated inflammatory responses linked to the “cytokine storm” and extensive lung pathology, as well as being linked to a number of comorbidities. Our current study compared five SARS-CoV-2 sequences from different geographical regions to those from SARS, MERS and two cold viruses, OC43 and 229E, to identify the presence of miR-like sequences. We identified seven key miRs, which highlight considerable differences between the SARS-CoV-2 sequences, compared with the other viruses. The level of conservation between the five SARS-CoV-2 sequences was identical but poor compared with the other sequences, with SARS showing the highest degree of conservation. This decrease in similarity could result in reduced levels of transcriptional control, as well as a change in the physiological effect of the virus and associated host-pathogen responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to the more recent ones, may have led to the emergence of sequence motifs that can be related directly to the pathogenicity of SARS-CoV-2. Importantly, we identified 7 key-microRNAs (miRs 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways linked to viral pathogenicity and host responses. According to Bioproject data (PRJNA615032), SARS-CoV-2 mediated transcriptomic alterations were similar to the target pathways of the selected 7 miRs identified in our study. This mechanism could have considerable significance in determining the symptom spectrum of future potential pandemics. KEGG pathway analysis revealed a number of critical pathways linked to the seven identified miRs that may provide insight into the interplay between the virus and comorbidities. Based on our reported findings, miRNAs may constitute potential and effective therapeutic approaches in COVID-19 and its pathological consequences.
Infectious Bursal Disease

Recently, Indovax undertook a detailed scientific study to examine relevance of currently available IBD vaccines. The study established that there is no variant of IBD in the country as determined by PCR analysis, CEP test and Challenge test. Molecular studies and extensive experimentation have conclusively shown that IBD vaccines of Indovax (Georgia, Bursa B2K and IV 95 ) are homologous to the field challenge and effective under field conditions.
Dark chilling imposes metabolic restrictions on photosynthesis in soybean

Dark chilling inhibited photosynthesis in two soybean [Glycine max (L.) Merr. ] cultivars (Fiskeby V and Maple Arrow). The inhibition of CO2 assimilation was characterized by a simultaneous decrease in stomatal conductance (Gs) and intercellular CO2 concentration (Ci) in Maple Arrow, whereas a similar decrease in Gs in Fiskeby V occurred without any change in Ci. Dark chilling had little effect on total ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) activity, Rubisco protein content or Rubisco activation state in the subsequent light period. Chilling reduced the abundance of the nocturnal Rubisco inhibitor, 2-carboxyarabinitol 1-phosphate, only in Fiskeby V. The abundance of Rubisco small subunit transcripts was enhanced in both cultivars as a result of dark chilling. Dark chilling decreased the maximal extractable activities and activation states of stromal fructose-1,6-bisphosphatase (FBPase) and NADP-malate dehydrogenase but had no effect on sucrose phosphate synthase or leaf sucrose and starch contents. It is concluded that dark chilling-induced limitations on CO2 assimilation are predominantly due to metabolic restrictions rather than to direct effects on electron transport reactions and that stromal FBPase is particularly susceptible to dark chilling.
Cytokinin production by Asparagus shoot apex cultured in vitro

The cytokinin producing capacity of asparagus (Asparagus officinalis L.) shoot apex was examined by means of shoot apex culture in vitro, where adventitious roots were never formed. The cultured shoot apices continued to diffuse a small but constant amount of cytokinin into the medium throughout five passages of subculture. The cytokinin content in the apices at the end of the subculture was not different from that at the beginning of the subculture. These results indicate a production of cytokinin by the apices. However, the finding is not in conflict with the hypothesis that the root tip is the major source of cytokinin supply, because the root tip of asparagus produced more cytokinin than the shoot apex and the decline of shoot growth observed during the subculture was partially restored by an application of zeatin into the medium.
OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.)

The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types—Cpn60α and Cpn60β and the rice genome encodes three α and three β plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60β1, we attempted to disrupt the OsCpn60β1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60β1 knockout rice plants. The OsCpn60β1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60β1 mutant. In addition, OsCpn60β1 was located in the chloroplast and OsCpn60β1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60β1 mutants. These results indicate that OsCpn60β1 is essential for chloroplast development in rice.
What is a successful fish ? Determinants of competitive success in Arctic char (Salvelinus alpinus) in different social contexts

Lors de tests entre paires d'ombles chevaliers (Salvelinus alpinus) d'âge 0+, il est apparu une nette relation entre l'agressivite et la capacite de s'approprier une source limitee de nourriture. Cependant, les indices de la capacite competitive determinee lors d'essais par paires dans des enclos d'observation ou la quantite de nourriture etait tres limitee, n'ont pas permis de predire le rendement (croissance, âge de maturation ou acquisition d'energie alimentaire en vue de la reproduction) lorsque les memes sujets etaient places en enclos dans des conditions ordinaires d'elevage (c.-a-d. en densite elevee et nourris a satiete). Ces resultats sont opposes a ceux obtenus lors d'etudes sur le saumon atlantique (Salmo salar) ou la suppression sociale de la recherche de nourriture s'exerce meme quand celle-ci est abondante. On suggere que des traits comportementaux differents favorisent le succes dans des environnements competitifs differents et qu'ils ne sont pas covariants au niveau des sujets individuels de l'omble chevalier.
Enzymatic diagnosis of resistance to deltamethrin in diapausing larvae of the codling moth, Cydia pomonella (L.)

The resistance to deltamethrin was evaluated in diapausing larvae of 14 field populations of the codling moth (Cydia pomonella L.) From the main French orchard areas using biological assays. Resistance to deltamethrin was compared to mixed-function-oxidase (mfo) activity measured at the individual level through ethoxycoumarin-O-deethylase (ECOD) activity using a fluorescence microplate reader. The larvae were collected in corrugated paper band traps in the autumn of 1995. Analysis was previously performed on two laboratory strains, one susceptible and one resistant to deltamethrin, in order to characterize the changes in resistance during diapause development. Resistance to deltamethrin as well as the ECOD activity were stable during the diapause, and ECOD activity was always significantly lower in the susceptible strain than in the resistant one. The ECOD activity was significantly correlated to the frequency of resistant moths in the field populations. This strongly suggested the involvement of the mfo system in the resistance to deltamethrin in these populations. The intra-strain variabilities in ECOD activity of both laboratory and field resistant insects indicated that other resistance mechanisms might also be involved. Further investigations on these mechanisms are needed in order to develop complete diagnostic methods and to define suitable control strategies against each resistant population. Arch. Insect Biochem. Physiol. 39:55–64, 1998. © 1998 Wiley-Liss, Inc.
Alcohol use and injury risk in Thailand: A case-crossover emergency department study.

INTRODUCTION AND AIMS While injuries and alcohol contribute to a large proportion of the disease burden in Thailand, no well-designed underlying study has yet been published. This study aims to evaluate the relationship between acute alcohol consumption and injury risk in Thailand. DESIGN AND METHODS Using the case-crossover design, this study examined 520 injured patients aged 18 years and older from two emergency departments in Meuang District, Chiang-Mai Province, Thailand, from June to August of 2016. The case period was defined as 6 h prior to injury, the two control periods as the same 6-h period at 1 day and 7 days prior to injury. Alcohol exposure and the amount consumed were measured for these periods. RESULTS Twenty percent of injured patients consumed alcohol within the 6 h prior to injury, averaging 6.9 drinks during that time. The odds of injury for those individuals consuming alcoholic beverages was 5.0 (95% confidence interval 3.0, 8.2) times greater compared to non-exposure individuals; every additional drink consumed increased the odds of injury by 1.3 (95% confidence interval 1.2, 1.4). Alcohol use significantly increased the odds of sustaining an unintentional injury, intentional injury inflicted by someone else or experiencing a road traffic injury (among drivers). The dose-response analysis indicated alcohol use significantly increased the risks of unintentional injury and road traffic injuries (among drivers). DISCUSSION AND CONCLUSIONS Exposure to alcohol increased the odds of injury in a dose-dependent fashion; hence, comprehensive, cost-effective strategies should be implemented in Thailand to reduce alcohol exposure, binge drinking and drunk driving.
Monolayer culture conditions suitable for primitive erythroid cell differentiation from embryonic stem cells in vitro

Embryonic stem (ES) cells effectively differentiated into primitive erythroid/mesodermal cells when grown in the absence of both a feeder layer and leukemia inhibitory factor (LIF). The formation of a three‐dimensional structure, exogenous mesoderm induction factors and exogenous hematopoietic growth factors were not essential for their differentiation. Primitive erythroid cells were first detected on day 5 in the differentiation‐permissive cultures. Differentiation into other mesodermal cells was always preceded by that into primitive erythroid cells. Precursor cells of erythroid cells but of other hematoid cells were also detected in this system. This model system is useful for studying the early steps of mesoderm formation in mouse embryogenesis.
Amalgamating Isatin/Indole/Nitroimidazole with 7‐chloroquinolines via azide‐alkyne cycloaddition: Synthesis, anti‐plasmodial, and cytotoxic evaluation

The present paper describes the synthesis, anti‐plasmodial, and cytotoxic evaluation of 7‐chloroquinoline‐based conjugates with isatins/indoles/ nitroimidazoles, obtained via Cu‐promoted 1,3‐dipolar cycloadditions. On contemplating SAR of the synthesized series, the inclusion of indole and nitroimidazole‐core improved the anti‐plasmodial activities while the isatin seemed to have a lesser effect. The conjugate with a nitroimidazole‐core and hexyl chain length as a spacer between the two pharmacophores was found to be most potent among the synthesized series and displayed an IC50 of 0.12 µM and a selectivity index of 1748.
Route of intestinal absorption and tissue distribution of iron contained in the novel phosphate binder ferric citrate.

BACKGROUND Anemia of chronic kidney disease (CKD) is, in part, caused by hepcidin-mediated impaired iron absorption. However, phosphate binder, ferric citrate (FC) overcomes the CKD-induced impairment of iron absorption and increases serum iron, transferrin saturation, and iron stores and reduces erythropoietin requirements in CKD/ESRD patients. The mechanism and sites of intestinal absorption of iron contained in FC were explored here. METHODS Eight-week old rats were randomized to sham-operated or 5/6 nephrectomized (CKD) groups and fed either regular rat chow or rat chow containing 4% FC for 6 weeks. They were then euthanized, and tissues were processed for histological and biochemical analysis using Prussian blue staining, Western blot analysis to quantify intestinal epithelial tight junction proteins and real-time PCR to measure Fatty Acid receptors 2 (FFA2) and 3 (FFA3) expressions. RESULTS CKD rats exhibited hypertension, anemia, azotemia, and hyperphosphatemia. FC-treated CKD rats showed significant reductions in blood pressure, serum urea, phosphate and creatinine levels and higher serum iron and blood hemoglobin levels. This was associated with marked increase in iron content of the epithelial and subepithelial wall of the descending colon and modest iron deposits in the proximal tubular epithelial cells of their remnant kidneys. No significant difference was found in hepatic tissue iron content between untreated and FC-treated CKD or control groups. Distal colon's epithelial tight Junction proteins, Occludin, JAM-1 and ZO-1 were markedly reduced in the CKD groups. The FFA2 expression in the jejunum and FFA3 expression in the distal colon were significantly reduced in the CKD rats and markedly increased with FC administration. CONCLUSION Iron contained in the phosphate binder, FC, is absorbed by the distal colon of the CKD animals via disrupted colonic epithelial barrier and upregulation of short chain fatty acid transporters.
Selection for food conversion in broilers: Predicted responses to selection for economic efficiency

1. Two selection indices which included a measure of food conversion efficiency in broiler production, were formulated: one index (I1) used individual 9‐week body weight and 5‐ to 9‐week food consumption (FC); the other (I 2) used individual 9‐week weight and sire‐family average food consumption (FC). 2. Three empirical parameter sets and 10 hypothetical data sets were used in calculating the indices and in predicting selection responses. 3. The three empirical parameter sets gave relatively similar index coefficients for I1 which were proportional to the relative economic weightings to the two traits. 4. Predicted economic responses to selection based on I 2 were negligibly superior to selection for body weight alone for nearly all data sets, whereas selection based on I1 was always superior in economic response. 5. Predicted economic response to selection based on I1 calculated from typical published estimates of genetic parameters was 20% greater than predicted response to selection for body weight alone.
Lys694Arg polymorphism leads to blunted responses to LPS by interfering TLR4 with recruitment of MyD88

TLR4 polymorphisms such as Asp299Gly and Thr399Ile related to Gram-negative sepsis have been reported to result in significantly blunted responsiveness to LPS. Our study group previously screened other TLR4 polymorphic variants by checking the NF-κB activation in comparison to wild type (WT) TLR4 in human embryonic kidney 293T cells. In this study, we found that the Lys694Arg (K694R) polymorphism reduced the activation of NF-κB, and the production of downstream inflammatory factors IL-1, TNF-α and IL-6, representing the K694R polymorphism, led to blunted responsiveness to LPS. Then, we examined the influence of the K694R polymorphism on total and cell-surface TLR4 expression by Western blotting and flow cytometry, respectively, but observed no differences between the K694R polymorphism and WT TLR4. We also used co-immunoprecipitation to determine the interaction of the K694R polymorphism and WT TLR4 with their co-receptor myeloid differentiation factor 2 (MD2) and their downstream signal adaptor MyD88. We found that K694R reduced the recruitment of MyD88 in TLR4 signalling but had no impact on the interaction with MD2.