Miracle-dz/UniFAR-FTUs huggingface dataset:
Normalization of Showjumping Competition’s Results

Abstract The aim of this study was to verify the newly proposed transformation of penalty points and ranking of showjumping horses for the purpose of genetic evaluation. Genomic information in the transformation of input data was used as well. Data of showjumping competition Global Champions Tour was used. Profit of penalty points was transformed to normally distributed variable using Blom formula (height of obstacles and height of obstacles with single nucleotide polymorphism - SNP effect taken into account). Non-normal distribution was obtained. The rankings of sport horses in competitions were transformed using the Blom formula (height of obstacles taken into account) to normal distribution (tests of normality Kolmogorov-Smirnov (KS) test Pr>D, D 0.011, P>0.150, Cramer-von Mises (CM) test Pr>W-Sq, W-Sq 0.039, P>0.250, Anderson-Darling test (AD) Pr>A-Sq, A-Sq 0.638, P<0.097). Better distributed variable ranking transformed by Blom formula (height of obstacles and SNP effect taken into account) was obtained (KS test Pr>D, D 0.004, P>0.150, CM test Pr>W-Sq, W-Sq 0.004, P>0.250, AD test Pr>A-Sq, A-Sq 0.062, P>0.250). Model where all used fixed effects to equation were applied without any combination of the effects was tested, R2 0.54. Variable ranking was transformed to normal score by Blom formula (height of obstacles was taken into account). In the following model some effects were taken into account in the form of quadratic regression, R2 0.61. Variable ranking was transformed to normal score, the same as in previous model. In the last model we transformed variable ranking to normal score by Blom formula, taking into account height of obstacles and SNP effect. Same effects as in previous model were used, R2 0.60
Impact of migration from an illicit drug scene on hospital outcomes among people who use illicit drugs in Vancouver, Canada.

INTRODUCTION AND AIMS People who use illicit drugs (PWUD) are vulnerable to an array of negative health outcomes, and increased hospital services utilisation. PWUD are also a transient population which poses challenges to the provision of optimal health care. The objective of this study was to identify out-migration patterns from Vancouver's Downtown Eastside (DTES), a neighbourhood where services for PWUD are concentrated, and to estimate the impact of these patterns on hospitalisation events among PWUD. DESIGN AND METHODS Data were collected through three prospective cohorts of PWUD in Vancouver, which were linked with health administrative data. Latent class growth analysis was used to define migration trajectory groups. Poisson regression was used to estimate the effect of migration patterns on hospitalisation events. RESULTS A total of 1180 participants were included in the study. Four latent classes were identified: early migration out (243, 20.6%); frequent revisit (112, 9.5%); late migration out (219, 18.6%); and consistently living in the DTES (606, 51.4%). Compared with those who consistently lived in the DTES, participants in the early migration out group had lower hospitalisation events (adjusted rate ratio = 0.65; 95% confidence interval: 0.48-0.90). DISCUSSION AND CONCLUSION We found that PWUD who migrated out of the DTES early had lower hospitalisation events compared to those who consistently lived in the DTES, which may be a function of lesser addiction severity among this trajectory group. These findings underscore a need to provide transitional health and social service supports for other trajectory groups in an effort to minimise hospitalisation for preventable causes.
Consolidated BRCA1/2 Variant Interpretation by MH BRCA Correlates with Predicted PARP Inhibitor Efficacy Association by MH Guide

BRCA1/2 variants are prognostic biomarkers for hereditary breast and/or ovarian cancer (HBOC) syndrome and predictive biomarkers for PARP inhibition. In this study, we benchmarked the classification of BRCA1/2 variants from patients with HBOC-related cancer using MH BRCA, a novel computational technology that combines the ACMG guidelines with expert-curated variant annotations. Evaluation of BRCA1/2 variants (n = 1040) taken from four HBOC studies showed strong concordance within the pathogenic (98.1%) subset. Comparison of MH BRCA’s ACMG classification to ClinVar submitter content from ENIGMA, the international consortium of investigators on the clinical significance of BRCA1/2 variants, the ARUP laboratories, a clinical testing lab of the University of UTAH, and the German Cancer Consortium showed 99.98% concordance (4975 out of 4976 variants) in the pathogenic subset. In our patient cohort, refinement of patients with variants of unknown significance reduced the uncertainty of cancer-predisposing syndromes by 64.7% and identified three cases with potential family risk to HBOC due to a likely pathogenic variant BRCA1 p.V1653L (NM_007294.3:c.4957G > T; rs80357261). To assess whether classification results predict PARP inhibitor efficacy, contextualization with functional impact information on DNA repair activity were performed, using MH Guide. We found a strong correlation between treatment efficacy association and MH BRCA classifications. Importantly, low efficacy to PARP inhibition was predicted in 3.95% of pathogenic variants from four examined HBOC studies and our patient cohort, indicating the clinical relevance of the consolidated variant interpretation.
PREHENSILE USE OF PERIORAL BRISTLES DURING FEEDING AND ASSOCIATED BEHAVIORS OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS)

The use of perioral bristles (modified vibrissae) by 17 captive Florida manatees and approximately 20 wild manatees was analyzed. Captive manatees were fed six species of aquatic vegetation normally eaten in the wild (four freshwater species and two seagrasses). Inanimate objects were placed in the holding tanks with manatees at Lowry Park Zoological Gardens (Tampa, FL) to determine the degree to which perioral bristles were used in exploration and to define the range of manipulative behavior. In addition, behavioral observations were made on the use of perioral bristles during social interactions with conspecifics. Observations were recorded using a Hi8-format video camera. Florida manatees possess an unusually large degree of fine motor control of the snout and perioral bristles. The large and robust perioral bristle fields of the upper lip were used in a prehensile manner during feeding. Bristle use by manatees feeding on submerged vegetation differed from that seen during feeding on floating vegetation. Other behavioral use of the perioral bristles shows variation depending upon the situation encountered. The degree of plasticity of perioral bristle use supports our hypothesis that the vibrissal-muscular complex of the Florida manatee has evolved to increase the efficiency of grazing and browsing on aquatic vegetation and to fully maximize the potential of the manatee as a generalist feeder. The manipulative and sensitive nature of the manatee snout is likely a manifestation of a complex sensory and motor system which has evolved for marine mammal aquatic herbivores living in shallow turbid habitats.
Synthetic (E)-3-Phenyl-5-(phenylamino)-2-styryl-1,3,4-thiadiazol-3-ium Chloride Derivatives as Promising Chemotherapy Agents on Cell Lines Infected with HTLV-1

Synthesis of four compounds belonging to mesoionic class, (E)-3-phenyl-5-(phenylamino)-2-styryl-1,3,4-thiadiazol-3-ium chloride derivatives (5a–d) and their biological evaluation against MT2 and C92 cell lines infected with human T-cell lymphotropic virus type-1 (HTLV-1), which causes adult T-cell leukemia/lymphoma (ATLL), and non-infected cell lines (Jurkat) are reported. The compounds were obtained by convergent synthesis under microwave irradiation and the cytotoxicity was evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. Results showed IC50 values of all compounds in the range of 1.51–7.70 μM in HTLV-1-infected and non-infected cells. Furthermore, it was observed that 5b could induce necrosis after 24 h for Jurkat and MT2 cell lines. The experimental (fluorimetric method) and theoretical (molecular docking) results suggested that the mechanism of action for 5b could be related to its capacity to intercalate into DNA. Moreover, the preliminary pharmacokinetic profile of the studied compounds (5a–d) was obtained through human serum albumin (HSA) binding affinity using multiple spectroscopic techniques (circular dichroism, steady-state and time-resolved fluorescence), zeta potential and molecular docking calculations. The interaction HSA:5a–d is spontaneous and moderate (Ka ~ 104 M−1) via a ground-state association, without significantly perturbing both the secondary and surface structures of the albumin in the subdomain IIA (site I), indicating feasible biodistribution in the human bloodstream.
Graphite Modified Polylactide (PLA) for 3D Printed (FDM/FFF) Sliding Elements

With the development of 3D printing technology, there is a need to produce printable materials with improved properties, e.g., sliding properties. In this paper, the authors present the possibilities of producing composites based on biodegradable PLA with the addition of graphite. The team created composites with the following graphite weight contents: 1%, 2.5%, 5%, 7.5%, and 10%. Neat material was also subjected to testing. Tribological, mechanical, and chemical properties of the mentioned materials were examined. Measurements were also made after keeping the samples in ageing and climatic ovens. Furthermore, SEM observations of samples before and after friction tests were carried out. It was demonstrated that increasing graphite content caused a significant decrease in wear (PLA + 10% graphite had a wear rate three times lower than for a neat material). The addition of graphite did not adversely affect most of the other properties, but it ought to be noted that mechanical properties changed significantly. After conditioning in a climatic oven PLA + 10% graphite has (in comparison with neat material) 11% lower fracture stress, 47% lower impact strength, and 21% higher Young’s modulus. It can be certainly stated that the addition of graphite to PLA is a step towards obtaining a material that is low-cost and suitable for printing sliding spare parts.
Using EQ-5D Data to Measure Hospital Performance: Are General Population Values Distorting Patients’ Choices?

Background. The English National Health Service publishes hospital performance indicators based on average postoperative EQ-5D index scores after hip replacement surgery to inform prospective patients’ choices of hospital. Unidimensional index scores are derived from multidimensional health-related quality-of-life data using preference weights estimated from a sample of the UK general population. This raises normative concerns if general population preferences differ from those of the patients who are to be informed. This study explores how the source of valuation affects hospital performance estimates. Methods. Four different value sets reflecting source of valuation (general population v. patients), valuation technique (visual analog scale [VAS] v. time tradeoff [TTO]), and experience with health states (currently experienced vs. experimentally estimated) were used to derive and compare performance estimates for 243 hospitals. Two value sets were newly estimated from EQ-5D-3L data on 122,921 hip replacement patients and 3381 members of the UK general public. Changes in hospital ranking (nationally) and performance outlier status (nationally; among patients’ 5 closest hospitals) were compared across valuations. Results. National rankings were stable under different valuations (rank correlations >0.92). Twenty-three (9.5%) hospitals changed outlier status when using patient VAS valuations instead of general population TTO valuations, the current approach. Outlier status also changed substantially at the local level. This was explained mostly by the valuation technique, not the source of valuations or experience with the health states. Limitations. No patient TTO valuations were available. The effect of value set characteristics could be established only through indirect comparisons. Conclusion. Different value sets may lead to prospective patients choosing different hospitals. Normative concerns about the use of general population valuations are not supported by empirical evidence based on VAS valuations.
Boldness, behavioral inhibition and learning

While many studies have examined both boldness and behavioral inhibition from psychological, psychiatric and physiological perspectives, little in the way of controlled experimental work has examined the costs or benefits of boldness and behavioral inhibition. Predator inspection behavior in fish is a model system for just such an approach. Here, we examined one potential benefit to boldness by examining the relationship between boldness/behavioral inhibition (measured by predator inspection behavior) and associative learning in the guppy (Poecilia reticulata). We found a positive relationship between male boldness and a simple associative learning task, in that males that learned to associate a cue with food were bolder than those that did not.
Molecular Patterns in Acute Pancreatitis Reflect Generalizable Endotypes of the Host Response to Systemic Injury in Humans

Supplemental Digital Content is available in the text Objective: Acute Pancreatitis (AP) is sudden onset pancreas inflammation that causes systemic injury with a wide and markedly heterogeneous range of clinical consequences. Here, we hypothesized that this observed clinical diversity corresponds to diversity in molecular subtypes that can be identified in clinical and multiomics data. Summary Background Data: Observational cohort study. n = 57 for the discovery cohort (clinical, transcriptomics, proteomics, and metabolomics data) and n = 312 for the validation cohort (clinical and metabolomics data). Methods: We integrated coincident transcriptomics, proteomics, and metabolomics data at serial time points between admission to hospital and up to 48 hours after recruitment from a cohort of patients presenting with acute pancreatitis. We systematically evaluated 4 different metrics for patient similarity using unbiased mathematical, biological, and clinical measures of internal and external validity. We next compared the AP molecular endotypes with previous descriptions of endotypes in a critically ill population with acute respiratory distress syndrome (ARDS). Results: Our results identify 4 distinct and stable AP molecular endotypes. We validated our findings in a second independent cohort of patients with AP. We observed that 2 endotypes in AP recapitulate disease endotypes previously reported in ARDS. Conclusions: Our results show that molecular endotypes exist in AP and reflect biological patterns that are also present in ARDS, suggesting that generalizable patterns exist in diverse presentations of critical illness.
Mulching with grass-clippings in cauliflower: effects on yield and brassica root flies (Delia spp.).

Abstract The effects of mulching with organic materials on yield and damage by brassica root maggots (Delia floralis and D. radicum) in cauliflower, were studied in field experiments for 3 years. Mulching with grass‐clippings consistently resulted in increased yield and reduced damage by root maggots, as measured by wilting symptoms and root damage. During one of these years, the effects of mulching with grass‐clippings on root fly population dynamics was also studied. Mulching did not reduce egg‐laying but resulted in increased egg‐predation. The number of D. floralis pupae per plant was not reduced by mulching, probably because of higher larval mortality owing to competition in unmulched plots. Mulching decreased the rate of parasitization by Aleochara bilineata (Staphylinidae), resulting in a higher number of healthy pupae per plant in grass‐mulched plots, and these healthy pupae were heavier. All these effects were most pronounced when the mulch material completely covered the ground, even close to th.
Transgenic tobacco plants expressing antimicrobial peptide bovine lactoferricin show enhanced resistance to phytopathogens

Lactoferricin B, the antimicrobially active N-terminal peptide derived from acid pepsin hydrolysis of bovine lactoferrin, has broad spectrum antimicrobial activities. We expressed the lactoferricin gene in tobacco plants to evaluate its antimicrobial activity. e coding region for the chimeric peptide gene of the signal peptide from tobacco pathogenrelated protein (PR-1) and bovine lactoferricin was synthesized using the recombinant polymerase chain reaction (PCR) method. Transgenic tobacco plants expressing the lactoferricin gene were developed using the Agrobacterium-mediated transformation method. e lactoferricin B gene was integrated into the tobacco genome and its transcription was detected by PCR, Southern blot analysis, and reverse transcription PCR (RT-PCR), respectively. e transgenic tobacco plants were challenged with the pathogenic bacteria Pseudomonas syringae pv. tabaci and Botrytis cinerea. At 30 or 28 days postinoculation, the transgenic plants were still green and continued to grow, whereas the control plants were infected with bacterial or fungal pathogens from the roots to the tips, resulting in death of the plants. In conclusion, transgenic tobacco plants that overexpressed the lactoferricin gene, linked to the signal peptide of tobacco PR-1 protein under the control of a high expression constitutive promoter, showed enhanced resistance to bacterial (P. syringae pv. tabaci) and fungal (B. cinerea) diseases.
Hepatitis B Virus DNA is a Substrate for the cGAS/STING Pathway but is not Sensed in Infected Hepatocytes

Hepatitis B virus (HBV) chronic infection is a critical risk factor for hepatocellular carcinoma. The innate immune response to HBV infection is a matter of debate. In particular, viral escape mechanisms are poorly understood. Our study reveals that HBV RNAs are not immunostimulatory in immunocompetent myeloid cells. In contrast, HBV DNA from viral particles and DNA replication intermediates are immunostimulatory and sensed by cyclic GMP-AMP Synthase (cGAS) and Stimulator of Interferon Genes (STING). We show that primary human hepatocytes express DNA sensors to reduced levels compared to myeloid cells. Nevertheless, hepatocytes can respond to HBV relaxed-circular DNA (rcDNA), when transfected in sufficient amounts, but not to HBV infection. Finally, our data suggest that HBV infection does not actively inhibit the DNA-sensing pathway. In conclusion, in infected hepatocytes, HBV passively evades recognition by cellular sensors of nucleic acids by (i) producing non-immunostimulatory RNAs, (ii) avoiding sensing of its DNAs by cGAS/STING without active inhibition of the pathway.
Transcriptome Comparison of Defense Responses in the Rice Variety ‘Jao Hom Nin’ Regarding Two Blast Resistant Genes, Pish and Pik

Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.
Cultivable Bacterial Communities in Brines from Perennially Ice-Covered and Pristine Antarctic Lakes: Ecological and Biotechnological Implications

The diversity and biotechnological potentialities of bacterial isolates from brines of three Antarctic lakes of the Northern Victoria Land (namely Boulder Clay and Tarn Flat areas) were first explored. Cultivable bacterial communities were analysed mainly in terms of bacterial response to contaminants (i.e., antibiotics and heavy metals) and oxidation of contaminants (i.e., aliphatic and aromatic hydrocarbons and polychlorobiphenyls). Moreover, the biosynthesis of biomolecules (antibiotics, extracellular polymeric substances and enzymes) with applications for human health and environmental protection was assayed. A total of 74 and 141 isolates were retrieved from Boulder Clay and Tarn Flat brines, respectively. Based on 16S rRNA gene sequence similarities, bacterial isolates represented three phyla, namely Proteobacteria (i.e., Gamma- and Alphaproteobacteria), Bacteroidetes and Actinobacteria, with differences encountered among brines. At genus level, Rhodobacter, Pseudomonas, Psychrobacter and Leifsonia members were dominant. Results obtained from this study on the physiological and enzymatic features of cold-adapted isolates from Antarctic lake brines provide interesting prospects for possible applications in the biotechnological field through future targeted surveys. Finally, findings on contaminant occurrence and bacterial response suggest that bacteria might be used as bioindicators for tracking human footprints in these remote polar areas.
Light from below matters: Quantifying the consequences of responses to far‐red light reflected upwards for plant performance in heterogeneous canopies

Abstract In vegetation stands, plants receive red to far‐red ratio (R:FR) signals of varying strength from all directions. However, plant responses to variations in R:FR reflected from below have been largely ignored despite their potential consequences for plant performance. Using a heterogeneous rose canopy, which consists of bent shoots down in the canopy and vertically growing upright shoots, we quantified upward far‐red reflection by bent shoots and its consequences for upright shoot architecture. With a three‐dimensional plant model, we assessed consequences of responses to R:FR from below for plant photosynthesis. Bent shoots reflected substantially more far‐red than red light, causing reduced R:FR in light reflected upwards. Leaf inclination angles increased in upright shoots which received low R:FR reflected from below. The increased leaf angle led to an increase in simulated plant photosynthesis only when this low R:FR was reflected off their own bent shoots and not when it reflected off neighbour bent shoots. We conclude that plant response to R:FR from below is an under‐explored phenomenon which may have contrasting consequences for plant performance depending on the type of vegetation or crop system. The responses are beneficial for performance only when R:FR is reflected by lower foliage of the same plants.