Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and validation of a qPCR method for species verification and serogroup determination of Listeria monocytogenes isolates.

Listeria monocytogenes (Lm) is one of the leading causes of death due to foodborne illness, affecting the elderly, pregnant women, neonates and the immune compromised. Serologically, Lm can be classified into 13 serotypes, though only four are typically linked with food contamination and illness. Since 2000, a shift in serotypes involved in listeriosis outbreaks was observed, suggesting that tracking of serotypes could help identify emerging trends. A PCR method developed in 2004 allowed detection of the four major serotypes as molecular serogroups, corresponding to broad phylogenetic groups. In this study, a novel qPCR method was developed that uses two multiplex qPCRs, one to confirm the Listeria genus and Lm species, and the second for Lm molecular serogrouping. This method was compared with the FDA Bacteriological Analytical Manual (BAM) method for Lm and the sero-agglutination method, using a 208-strain panel. Comparison of the genus/species qPCR assay with the BAM methods found an equal or slightly higher accuracy for the qPCR method (>98%), as compared to the BAM protocol (>96%), when evaluated against independent characterization data. Molecular serogrouping using the qPCR method (96.6%) was more accurate than the sero-agglutination assay (75.6%). The qPCR method identified Lm 4bV strains, which could not be resolved using sero-agglutination. The qPCR could not identify lineages III and IV serotype 4b strains but did correctly identify 16 of 18 lineage III/IV strains. The qPCR method performed genus identification for Lm, L. innocua, L. welshimeri, L. ivanovii, and L. seeligeri. Additionally, the method performed species identification for Lm, and serogrouped Lm into six molecular serogroups, 2A, 2B, 2C, 4B, NT, and 4bV. This method provided a rapid and accurate confirmation of Lm and serogroup determinations; furthermore, it could help identify otherwise unlinked strains by enabling WGS analysis based on broad phylogeny, independent of other information.
The PANDEMYC Score. An Easily Applicable and Interpretable Model for Predicting Mortality Associated With COVID-19

This study aimed to build an easily applicable prognostic model based on routine clinical, radiological, and laboratory data available at admission, to predict mortality in coronavirus 19 disease (COVID-19) hospitalized patients. Methods: We retrospectively collected clinical information from 1968 patients admitted to a hospital. We built a predictive score based on a logistic regression model in which explicative variables were discretized using classification trees that facilitated the identification of the optimal sections in order to predict inpatient mortality in patients admitted with COVID-19. These sections were translated into a score indicating the probability of a patient’s death, thus making the results easy to interpret. Results. Median age was 67 years, 1104 patients (56.4%) were male, and 325 (16.5%) died during hospitalization. Our final model identified nine key features: age, oxygen saturation, smoking, serum creatinine, lymphocytes, hemoglobin, platelets, C-reactive protein, and sodium at admission. The discrimination of the model was excellent in the training, validation, and test samples (AUC: 0.865, 0.808, and 0.883, respectively). We constructed a prognostic scale to determine the probability of death associated with each score. Conclusions: We designed an easily applicable predictive model for early identification of patients at high risk of death due to COVID-19 during hospitalization.
Protocol, rationale and design of DAbigatran for Stroke PreVention In Atrial Fibrillation in MoDerate or Severe Mitral Stenosis (DAVID-MS): a randomised, open-label study

Introduction Current international guidelines recommend non-vitamin K oral anticoagulants (NOACs) for stroke prevention among patients with non-valvular atrial fibrillation (AF) at significant ischaemic stroke risk given the superior safety and comparable efficacy of NOACs over warfarin. Nonetheless, the safety and effectiveness of NOACs have not been evaluated in patients with AF with underlying moderate or severe mitral stenosis (MS), hence the recommended stroke prevention strategy remains warfarin therapy. Method and analysis MS remains disproportionately prevalent in Asian countries compared with the developed countries. This prospective, randomised, open-label trial with blinded endpoint adjudication aims to evaluate the safety and efficacy of dabigatran for stroke prevention in AF patients with moderate or severe MS. Patients with AF aged ≥18 years with moderate or severe MS not planned for valvular intervention in the coming 12 months will be randomised in a 1:1 ratio to receive dabigatran 110 mg or 150 mg two times per day or warfarin with international normalised ratio 2–3 in an open-label design. Patients with estimated creatinine clearance <30 mL/min, or with a concomitant indication for antiplatelet therapy will be excluded. The primary outcome is a composite of stroke and systemic embolism. Secondary outcomes are ischaemic stroke, systemic embolism, haemorrhagic stroke, intracranial haemorrhage, major bleeding and death. The estimated required sample size is approximately 686 participants. Ethics and dissemination The study protocol has been approved by the Institutional Review Board of the University of Hong Kong and Hong Kong West Cluster, Hospital Authority, Hong Kong for Fung Yiu King Hospital, Grantham Hospital, Queen Mary Hospital and Tung Wah Hospital in Hong Kong. Results will be published in peer-reviewed journals. Trial registration number ClinicalTrials.gov Registry (NCT04045093); pre-results.
Effect of Instrument Design and Technique on the Precision and Accuracy of Objective Refraction Measurement

Background: To evaluate the precision and accuracy of objective refraction measurement obtained with combinations of instrument design and technique. We also compared the performance of the instruments with subjective refraction measurements. Method and analysis: The objective refraction was measured in 71 subjects with three autorefractometers that have different designs and measurement principles (binocular with fogging, binocular without fogging, and monocular with fogging). Repeatability and reproducibility metrics were calculated for the objective refraction measurements. The agreement of the objective refraction measurements between the three instruments and the agreement with the subjective refraction measurements were evaluated. Results: All three autorefractometers had repeatability and reproducibility limits smaller than 0.70D. The smallest difference (0.10D) in the spherical equivalent was seen between the two binocular instruments. Compared with the subjective refraction, the binocular without fogging technique had the smallest mean difference in spherical equivalent (<0.20D) whereas the binocular fogging technique had the smallest limit of agreement interval (1.00D). For all comparisons, the mean difference and limit of agreement interval for the cylindrical components were lower than 0.10D and 0.75D, respectively. Conclusion: All three instruments evaluated had good repeatability and reproducibility. The binocular fogging technique provided the best agreement with subjective refraction.
A survey of psychological practitioner workplace wellbeing.

The wellbeing of the psychological workforce is an area of concern. However, it has been sparsely studied in an holistic manner encompassing workplace wellbeing as well as burnout. This study reports a survey of 1,678 psychological practitioners accessed through professional networks. The short Warwick Edinburgh Mental Wellbeing Scale (SWEMWBS) and the Psychological Practitioner Workplace Wellbeing Measure (PPWWM) were administered with a demographic questionnaire. The mean for the SWEMWBS was below that of a national population survey. The inter-correlation of these tests was.61. Subgroup analyses showed significant differences: assistant psychologists, counsellors and psychological wellbeing practitioners demonstrated better than average workplace wellbeing. But for general wellbeing (SWEMWBS) trainee clinical psychologists and assistant psychologists showed lower than average wellbeing while psychological wellbeing practitioners were higher than average. Other factors associated with wellbeing were: contract type -both measures (higher workplace wellbeing in those with temporary contracts and the self-employed); employment sector -for PPWWM only (private organisation/independent workers and third sector/charitable organisation workers scored above the PPWWM mean); ethnicity - for both measures (Asian groups except Chinese had higher wellbeing than average for the PPWWM and SWEMWBS); disability was strongly associated with lower wellbeing on both measures. Harassment, feeling depressed or a failure and wanting to leave the NHS were associated with lower wellbeing. Greater age, pay and years of service were negatively correlated with wellbeing. A five-factor structure was obtained with this sample. The results confirmed psychological practitioners as an at-risk group and identified a number of factors associated with workplace wellbeing.
Association of CDKAL1 rs4712523 polymorphism with susceptibility to the blood lipid of type 2 diabetes in Han population of Inner Mongolia

Objective To study the association of alleles and genotype frequencies of rs4712523 single nucleotide polymorphism in CDKAL1(CDK5 regulatory subunit associated protein 1-like 1) gene with blood lipid level of type 2 diabetes mellitus(T2DM) in Han population of Inner Mongolia. Methods Based on case-control design methods, using the technology such as fully automatic biochemical analyzer test with biochemical all items, including lipids, blood glucose, plasma insulin, glycosylated hemoglobin levels in type 2 diabetes and normal control group(normal control, NC) in patients; Using allele-specific polymerase chain reaction(AS-PCR), the rs4712523 polymorphism of CDKAL1 gene was genotyped in Han population of Inner Mongolia, including 97 T2DM patients(T2DM group) and 98 normal controls(NC group). Results(1) In T2DM group, the frequencies of G allele and GG genotype of rs4712523 were 49.5% and 8.2% respectively, they were significantly higher than those(39.2% and 5.2%) in the NC group(P0.05). The risk of T2DM was significantly increased by G allele with A allelic odd ratio(OR) of 1.263(OR=1.521, 95% CI=1.018-2.274). (2) Compared with NC group, the BMI, TG, LDL-C, HDL-C of T2DM group was significantly higher, there were significant differences(P0.05), TC levels of the T2DM group were higher than NC group, but no significant difference. (3) The SBP,DBP,TC and LDL of AA,AG,GG genotypes had statistically difference(P0.05), the SBP, DBP, TC, LDL level of G allele were higher than the A allele. (4) Logistic regression analysis showed that TC(OR=98.543, P=0.000), TG(OR=0.014, P= 0.000), LDL-C(OR=0.005, P=0.000) might be independent risk factors of T2DM. Conclusions G allele of rs4712523 polymorphism site in CDKAL1 gene might be a risk factor of T2DM, the A/G polymorphism is associated with T2DM and CDKAL1 gene might be a susceptible gene of T2DM in Han population of Inner Mongolia. The gene mutation of CDKAL1 T allele might be associated with blood pressure and blood lipid levels.
Comparative Morphological Studies on the Lingual Papillae and Their Connective Tissue Cores in the Swamp Wallaby, Wallabia bicolar

有袋類で, カンガルー科に属するオグロワラビーの舌乳頭の微細形態について, 動物種の食性と関連づけて比較解剖学的に検討した。 舌背の後半部には草食性動物に特徴的な左右の臼歯間にわずかな舌隆起部 (臼歯間隆起部) が存在した。 舌背に密集する糸状乳頭は1本の槍先状の主突起と複数の細長い副突起からなっていた。 舌隆起部の糸状乳頭は副突起の数が多く, 長いものが多かった。 糸状乳頭の結合織芯は板状の主突起と6-10本の小杆状突起からなり, それらの形状は舌背の部位により多少異なるが, 基本的には肉食性のイヌ, ネコのものに似た船の舳先状を呈していた。 茸状乳頭は舌背の舌縁部に散在し, 舌尖下面の舌縁に特に多く認められた。 これらの結合織芯は円柱状の細長いものから太めのものまであり, 円柱の頂上には1-数個の味蕾をのせる小陥凹が存在していた。 有郭乳頭は舌後方に3個存在し, 中央乳頭の先端がわずかに表面に出る閉鎖型で, 中央乳頭の溝側上皮内に多数の味蕾が並んでいた。 舌後方の外側縁に葉状乳頭はなく, 数本の円錐乳頭様構造物である外側器官が並んでいたが, 味蕾は欠如していた。 舌根部の表面は乳頭を欠如し平坦であった。 茸状乳頭の結合織芯の形状と3個の有郭乳頭や突出した外側器官の存在などはツパイと基本的に近似していた。 糸状乳頭の外形や結合織芯の形態, それに円錐状の外側器官をもつといった所見から, オグロワラビーはイヌ, ネコなど肉食性の祖先の特徴を保持しながら, オーストラリア大陸でツパイに近縁の草食性の動物へと進化を遂げた動物であることが推測された。
Crosstalk Between Autophagy and Hypoxia-Inducible Factor-1α in Antifungal Immunity

Modern medicine is challenged by several potentially severe fungal pathogens such as Aspergillus fumigatus, Candida albicans, or Histoplasma capsulatum. Though not all fungal pathogens have evolved as primary pathogens, opportunistic pathogens can still cause fatal infections in immuno-compromised patients. After infection with these fungi, the ingestion and clearance by innate immune cells is an important part of the host immune response. Innate immune cells utilize two different autophagic pathways, the canonical pathway and the non-canonical pathway, also called microtubule-associated protein 1A/1B-light chain 3 (LC3) -associated pathway (LAP), to clear fungal pathogens from the intracellular environment. The outcome of autophagy-related host immune responses depends on the pathogen and cell type. Therefore, the understanding of underlying molecular mechanisms of autophagy is crucial for the development and improvement of antifungal therapies. One of those molecular mechanisms is the interaction of the transcription-factor hypoxia-inducible factor 1α (HIF-1α) with the autophagic immune response. During this review, we will focus on a comprehensive overview of the role of autophagy and HIF-1α on the outcome of fungal infections.
Characterization of crude 5'-phosphodiesterase from germinated adzuki (Vigna angularis L.) beans.

BACKGROUND 5'-Phosphodiesterase (5'-PDE) is an enzyme that hydrolyzes RNA to form 5'-inosine monophosphate (5'-IMP) and 5'-guanosine monophosphate (5'-GMP). These 5'-nucleotides can function as flavor enhancers. Adzuki beans (Vigna angularis L.) are found to be high in 5'-PDE. METHODS 5'-phosphodiesterase (5'-PDE) enzyme was characterized from adzuki beans, in which the optimum pH and temperature were determined. In addition, the stability of 5'-PDE was assessed at different pH and temperature. The effects of cations and EDTA were evaluated to characterize the 5'-PDE enzymes further. RESULTS The alkaline 5'-phosphodiesterase has an optimum pH of 8.5. This enzyme is also thermostable, with an optimum temperature of 80°C. The stability in terms of temperature and pH was also determined, and was found to be stable in the pH range of 7.0-8.5. This enzyme was found to retain more than 80% of its activity for 4 days at 60 and 65°C. In addition, the effects of 14 different metal ions, 4 types of detergents and ethylenediaminetetraacetic acid (EDTA) on 5'-PDE were studied. Ca2+, K+, Mg2+ and Li+ activated 5'-PDE while Na+, Zn2+, Ni+, Hg+, Cu2+, Pb2+, Fe2+, Al3+, Ba2+ and Co2+ were inhibitory. EDTA, Triton X-100 and sodium dodecyl sulfate (SDS) were strong inhibitors of 5'-PDE, while Tween 80 and Tween 20 were slightly inhibitory. The effects of cations and EDTA suggest that 5'-PDE from adzuki beans is a metalloenzyme. CONCLUSIONS Although 5'-PDE from adzuki beans has a high temperature optimum of 80°C, the enzyme is more stable at 60°C, and different cations affected the activity of the enzyme differently.
Deltamethrin exposure inhibits adult hippocampal neurogenesis and causes deficits in learning and memory in mice.

Deficits in learning and memory are often associated with disruption of hippocampal neurogenesis, which is regulated by numerous processes, including precursor cell proliferation, survival, migration, and differentiation to mature neurons. Recent studies demonstrate that adult born neurons in the dentate gyrus (DG) in the hippocampus can functionally integrate into the existing neuronal circuitry and contribute to hippocampal-dependent learning and memory. Here, we demonstrate that relatively short-term deltamethrin exposure (3 mg/kg every 3 days for 1 month) inhibits adult hippocampal neurogenesis and causes deficits in learning and memory in mice. Hippocampal-dependent cognitive functions were evaluated using two independent hippocampal-dependent behavioural tests, the novel object recognition task and Morris water maze. We found that deltamethrin-treated mice exhibited profound deficits in novel object recognition and learning and memory in water maze. Deltamethrin exposure significantly decreased bromodeoxyuridine (BrdU)-positive cells (39%) and Ki67+ cells (47%) in the dentate gyrus (DG) of the hippocampus, indicating decreased cellular proliferation. In addition, deltamethrin-treated mice exhibited a 44% decrease in nestin-expressing neural progenitor cells and a 38% reduction in the expression of doublecortin (DCX), an early neuronal differentiation marker. Furthermore, deltamethrin exposed mice exhibited a 25% reduction in total number of granule cells in the DG. These findings indicate that relatively short-term exposure to deltamethrin causes significant deficits in hippocampal neurogenesis that is associated with impaired learning and memory.
Nutritional state and productivity of organic sugarcane in Goiás, Brazil.

In order to study the effect of use organic agriculture avoids the use of synthetic fertilizers and emphasizes the use of organic inputs to provide nutrients to the plants. This study had as aim to evaluate the effect of organic management time on nutrition and productivity of sugarcane. The nutrition levels and the productivity of sugarcane plantations were evaluated in areas cultivated for two, six and ten years in the organic production system compared with a sugarcane plantation cultivated for ten years in the conventional system. The sugarcane organic production system enhanced the nutrition levels of the plants and raised the crops productivity. After ten years of organic cultivation, there was an increase of 43, 42.8 and 32% in the leaf contents of potassium (K), phosphorus (P) and nitrogen (N), respectively, in relation to the conventional production system and an increase of 209% in the sugarcane productivity. The management of the fertilizers inputs used in the sugarcane organic production system is adequate for the plants nutrition, with positive result on the crops productivity. The effects are more visible after six and ten years of management in the organic production system. In the organic production system, after ten and six years, it could be suggested that the productivity was 209 and 98% higher in comparison to the productivity of the cane cultivated under the conventional system, areas Org.10 and Org.6, respectively.
Anterior Segment Inflammation in Pediatric Uveitis Is Associated with Reduced Retinal Vascular Density as Quantified by Optical Coherence Tomography Angiography

ABSTRACT Purpose To analyze the retinal capillary vascular density (VD) as quantified by optical coherence tomography angiography (OCTA) in patients with pediatric uveitis. Methods OCTA images of 32 pediatric uveitis patients and 30 normal controls (NC) were obtained retrospectively. The foveal avascular zone (FAZ) area, VDs in the superficial capillary plexus (SCP) and deep capillary plexus (DCP), the central macular thickness (CMT), and subfoveal choroidal thickness (SFCT) were analyzed and compared between active and quiescent uveitic eyes, contralateral eyes and NC eyes. Results Compared with NCs, the VDs in the SCP and DCP were significantly reduced in eyes with both active and quiescent pediatric uveitis (P < .05). The SFCT was increased significantly in the active group relative to the quiescent group and NC groups (P < .05). In contrast, no significant differences were observed in the FAZ and CMT (all P > .05). Conclusions Our quantitative OCTA findings suggest that the posterior segment is affected during anterior segment recurrence in patients with pediatric uveitis.
Impact of Polypharmacy for Chronic Ailments in Colon Cancer Patients: A Review Focused on Drug Repurposing

Simple Summary Colorectal cancer patients are frequently also affected by various chronic conditions that require specific treatment. Several papers have focused on the role of different classes of drugs such as anti-hypertensive medications, statins, anti-bacterial antibiotics, aspirin and NSAIDs, metformin and anti-depressants, and their impact on colorectal cancer survival. Aim of this review is to summarise this findings as to suggest which drugs might be further explored for therapeutic approaches in this setting. Our review suggests that beta-blockers and statins should be further explored as potentially useful treatment options respectively in metastatic colorectal cancer for the former and in adjuvant setting for the latter. Abstract Colorectal cancer is characterized by high incidence worldwide. Despite increased awareness and early diagnosis thanks to screening programmes, mortality remains high, particularly for patients with metastatic involvement. Immune checkpoint inhibitors or poly (ADP-ribose) polymerase (PARP)-inhibitors have met with disappointing results when used in this setting, opposed to other malignancies. New drugs with different mechanisms of action are needed in this disease. Drug repurposing might offer new therapeutic options, as patients with metastatic colorectal cancer often share risk factors for other chronic diseases and thus frequently are on incidental therapy with these drugs. The aim of this review is to summarise the published results of the activity of drugs used to treat chronic medications in patients affected by colorectal cancer. We focused on antihypertensive drugs, Non-Steroid Anti-inflammatory Drugs (NSAIDs), metformin, antidepressants, statins and antibacterial antibiotics. Our review shows that there are promising results with beta blockers, statins and metformin, whereas data concerning antidepressants and antibacterial antibiotics seem to show a potentially harmful effect. It is hoped that further prospective trials that take into account the role of these drugs as anticancer medications are conducted.
First predation record of Canthecona furcellata (Wolff.) (Hemiptera: Pentatomidae) on spinning stage silkworm Antheraea mylitta (Drury)

A new scientific survey elucidates the preferred attack of stink bug Canthecona furcellata (Wolff.) (Hemiptera: Pentatomidae) on the spinning stage of the tropical tasar silkworm, Antheraea mylitta (Drury) (Lepidoptera: Saturniidae). The silkworm A. mylitta produces an excellent quality of wild silk; however, due to predation by C. furcellata, tasar silk production is reduced. The bug C. furcellata is the most invasive larval predator of A. mylitta and predation is high during early instars as well as the molting stage of the larvae. However, for the first time it is reported that the spinning stage is also preferable for attack by the stink bug. Both the nymphs and adults of C. furcellata attack the spinning silkworm; moreover, stink bug attack is observed in groups under field conditions. It is postulated that feeding preference is due to the concealed, non‐movable and less defensive stage of the tasar larvae during spinning. The predation of C. furcellata includes its approach on target larva of the tasar silkworm during spinning, where it inserts the proboscis inside the larval skin through the moist silk network of newly forming or formed cocoon. Most of the spinning larvae die from the attack and the normal seed cocoon fails to form. The mechano‐ and chemoreceptors, present on the antenna and proboscis of C. furcellata, play an important role in prey locating and the feeding mechanism. The life cycle of C. furcellata is also discussed in the present study.