Miracle-dz/UniFAR-FTUs huggingface dataset:
Multilocus sequence typing analysis of Italian Xanthomonas campestris pv. campestris strains suggests the evolution of local endemic populations of the pathogen and does not correlate with race distribution

P. Bella* , C. Moretti , G. Licciardello, C. P. Strano, A. Pulvirenti, S. Alaimo, M. Zaccardelli, F. Branca, R. Buonaurio, J. G. Vicente and V. Catara Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo; Department of Agricultural, Food and Environmental Sciences University of Perugia, Borgo XX Giugno 74, 06121 Perugia; Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia, 100 95123; Department of Clinical and Experimental Medicine, University of Catania, Viale Andrea Doria, 6 – 95125, Catania; CREA Horticulture and Floriculture Research Centre, Via dei Cavalleggeri, 25 84098, Pontecagnano (SA), Italy; and School of Life Sciences, University of Warwick, Wellesbourne, CV35 9EF, UK
Association of Genes Involved in the Metabolic Pathways of Amyloid-β and Tau Proteins With Sporadic Late-Onset Alzheimer’s Disease in the Southern Han Chinese Population

The genes involved in the metabolic pathways of amyloid-β (Aβ) and tau proteins significantly influence the etiology of Alzheimer’s disease (AD). Various studies have explored the associations between some of these genes and AD in the Caucasian population; however, researches regarding these associations remain limited in the Chinese population. To systematically evaluate the associations of these genes with AD, we investigated 19 genes involved in the metabolism of Aβ and tau based on previous studies selected using the PubMed database. This study included 372 patients with sporadic late-onset AD (sLOAD) and 345 cognitively healthy individuals from southern China. The results were replicated in the International Genomics of Alzheimer’s Project (IGAP). Protein–protein interactions were determined using the STRING v11 database. We found that a single-nucleotide polymorphism, rs11682128, of BIN1 conferred susceptibility to sLOAD after adjusting for age, sex, and APOE ε4 status and performing the Bonferroni correction {corrected P = 0.000153, odds ratio (OR) [95% confidence interval (CI)] = 1.403 (1.079–1.824)}, which was replicated in the IGAP. Protein–protein interactions indicated that BIN1 was correlated with MAPT. Moreover, rare variants of NEP and FERMT2 (0.0026 < corrected P < 0.05), and the Aβ degradation, tau pathology, and tau phosphatase pathways (0.01 < corrected P < 0.05), were nominally significantly associated with sLOAD. This study suggested that the genes involved in the metabolic pathways of Aβ and tau contributed to the etiology of sLOAD in the southern Han Chinese population.
Development and validation of early warning score systems for COVID‐19 patients

COVID-19 is a major, urgent, and ongoing threat to global health. Globally more than 24 million have been infected and the disease has claimed more than a million lives as of October 2020. Predicting which patients will need respiratory support is important to guiding individual patient treatment and also to ensuring sufficient resources are available. We evaluated the ability of six common Early Warning Scores (EWS) to identify respiratory deterioration defined as the need for advanced respiratory support (high-flow nasal oxygen, continuous positive airways pressure, non-invasive ventilation, intubation) within a prediction window of 24 hours. We show these scores perform sub-optimally at this specific task. Therefore, we develop an alternative Early Warning Score based on a Gradient Boosting Trees (GBT) algorithm that is able to predict deterioration within the next 24 hours with high AUROC 94% and an accuracy, sensitivity and specificity of 70%, 96%, 70%, respectively. Our GBT model outperformed the best EWS (LDTEWS:NEWS), increasing the AUROC by 14%. Our GBT model makes the prediction based on the current and baseline measures of routinely available vital signs and blood tests.
Rapid, Quantitative, High-Sensitive Detection of Escherichia coli O157:H7 by Gold-Shell Silica-Core Nanospheres-Based Surface-Enhanced Raman Scattering Lateral Flow Immunoassay

Escherichia coli O157:H7 is regarded as one of the most harmful pathogenic microorganisms related to foodborne diseases. This paper proposes a rapid-detection biosensor for the sensitive and quantitative analysis of E. coli O157:H7 in biological samples by surface-enhanced Raman scattering (SERS)-based lateral flow immunoassay (LFIA). A novel gold-shell silica-core (SiO2/Au) nanosphere (NP) with monodispersity, good stability, and excellent SERS activity was utilized to prepare high-performance tags for the SERS-based LFIA system. The SiO2/Au SERS tags, which were modified with two layers of Raman reporter molecules and monoclonal antibodies, effectively bind with E. coli O157:H7 and form sandwich immune complexes on the test lines. E. coli O157:H7 was quantitatively detected easily by detecting the Raman intensity of the test lines. Under optimal conditions, the limit of detection (LOD) of the SiO2/Au-based SERS-LIFA strips for the target bacteria was 50 cells/mL in PBS solution, indicating these strips are 2,000 times more sensitive than colloidal Au-based LFIA strips. Moreover, the proposed assay demonstrated high applicability in E. coli O157:H7 detection in biological samples, including tap water, milk, human urine, lettuce extract and beef, with a low LOD of 100 cells/mL. Results indicate that the proposed SERS-based LFIA strip is applicable for the sensitive and quantitative determination of E. coli O157:H7.
Divergent geographic patterns of genetic diversity among wild bees: Conservation implications

Genetic diversity is a key factor to species survival. This diversity is unevenly distributed across the species range, delimiting genetic diversity hotspots (GDH). Focusing conservation efforts on regions where GDH of several species overlap (i.e., multispecies GDH) could rationalize conservation efforts by protecting several taxa in one go. However, recent studies suggest the existence of many species‐specific GDH. This would make spatially prioritizing protection even more challenging as it requires the integration of these multiple GDH rather than few hotspots into conservation planning. Here, we characterize GDH of nine co‐distributed bee species through an original comparative mapping approach to assess the suitability of a spatial prioritization strategy to protect their genetic diversity.
Building comprehensive MS-friendly databases for proteomic analysis of bacterial species of unknown genetic background

In proteogenomic analysis of prokaryotes of unknown genetic background, merging different gene annotation from genomic data of all strains for a given species is a valuable strategy to help the characterization of the sample. It is also relevant for identification of important amino acid polymorphisms and validation of coding regions. We designed a bioinformatic tool which constructs fasta databases including conserved and unique sequences of strains of a given species. By using mass spectrometry data collected from 8 clinical strains from Mycobacterium tuberculosis, we checked protein identification performance of three sequence databases, one including all proteins from 65 sequenced strains; one built using our tool using the same 65 strains; and one using the assembly of model strain H37Rv. Finally, we built databases for 10 species with complete sequenced genomes and monitored features which are relevant for probabilistic-based protein identification by proteomics. We observed that as expected increase in database complexity correlates with pangenomic complexity. However Mycobacterium tuberculosis and Bortedella pertusis generated very complex databases even having low pangenomic complexity or no pangenome at all respectively. This indicate that differences in gene annotation is higher than average between strains of those species.
Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G

HLA-G is considered to be an immune checkpoint molecule, a function that is closely linked to the structure and dynamics of the different HLA-G isoforms. Unfortunately, little is known about the structure and dynamics of these isoforms. For instance, there are only seven crystal structures of HLA-G molecules, being all related to a single isoform, and in some cases lacking important residues associated to the interaction with leukocyte receptors. In addition, they lack information on the dynamics of both membrane-bound HLA-G forms, and soluble forms. We took advantage of in silico strategies to disclose the dynamic behavior of selected HLA-G forms, including the membrane-bound HLA-G1 molecule, soluble HLA-G1 dimer, and HLA-G5 isoform. Both the membrane-bound HLA-G1 molecule and the soluble HLA-G1 dimer were quite stable. Residues involved in the interaction with ILT2 and ILT4 receptors (α3 domain) were very close to the lipid bilayer in the complete HLA-G1 molecule, which might limit accessibility. On the other hand, these residues can be completely exposed in the soluble HLA-G1 dimer, due to the free rotation of the disulfide bridge (Cys42/Cys42). In fact, we speculate that this free rotation of each protomer (i.e., the chains composing the dimer) could enable alternative binding modes for ILT2/ILT4 receptors, which in turn could be associated with greater affinity of the soluble HLA-G1 dimer. Structural analysis of the HLA-G5 isoform demonstrated higher stability for the complex containing the peptide and coupled β2-microglobulin, while structures lacking such domains were significantly unstable. This study reports for the first time structural conformations for the HLA-G5 isoform and the dynamic behavior of HLA-G1 molecules under simulated biological conditions. All modeled structures were made available through GitHub (https://github.com/KavrakiLab/), enabling their use as templates for modeling other alleles and isoforms, as well as for other computational analyses to investigate key molecular interactions.
Effect of Different Yam Varieties and Addition on Resistant Starch Type III Formation and Physical Properties of Steamed Rice Bowl Cake

This research aimed to evaluate the effect of different varieties and proportion of yam on the resistant starch type III content (RSC) and physical properties of steamed rice bowl cake. According to the research results, RSC (9.2-11.7%) was significantly increased (p p p p p < 0.05) were observed in some experiment variables of solubility and swelling power.
Prevalence, predictors and prognosis of incidental intracranial aneurysms in patients with suspected TIA and minor stroke: a population-based study and systematic review

Introduction Unruptured intracranial aneurysms (UIAs) are common incidental imaging findings, but there are few data in patients with transient ischaemic attack (TIA)/stroke. The frequency of UIA might be higher due to shared risk factors, but rupture risk might be reduced by intensive secondary prevention. We determined the prevalence and prognosis of UIA in patients with suspected TIA/minor stroke. Methods All patients referred to the population-based Oxford Vascular Study (2011–2020) with suspected TIA/minor stroke and non-invasive angiography were included. We determined the prevalence of incidental asymptomatic UIA and the risk of subsequent subarachnoid haemorrhage (SAH) by follow-up on intensive medical treatment, with guideline-based monitoring/management. We also did a systematic review of UIA prevalence/prognosis in cohorts with TIA/stroke. Findings Among 2013 eligible patients, 95 (4.7%) had 103 previously unknown asymptomatic UIA. Female sex (OR 2.3, 95% CI 1.5 to 3.7), smoking (2.1, 1.2 to 3.6) and hypertension (1.6, 1.0 to 2.5) were independently predictive of UIA, with a prevalence of 11.1% in those with all three risk factors. During mean follow-up of 4.5 years, only one SAH occurred: 2.3 (95% CI 0.3 to 16.6) per 1000 person-years. We identified 19 studies of UIA in TIA/stroke cohorts (n=12 781), all with either symptomatic carotid stenosis or major acute stroke. The pooled mean UIA prevalence in patients with TIA/stroke was 5.1% (95% CI 4.8 to 5.5) and the incidence of SAH was 4.6 (95% CI 1.9 to 11.0) per 1000 person-years. Interpretation The 5% prevalence of UIA in patients with confirmed TIA/minor stroke is likely higher than that in the general population. However, the risk of SAH on intensive medical treatment and guideline-based management/monitoring is low.
IsoSense: frequency enhanced sensorless adaptive optics through structured illumination

We present IsoSense, a wavefront sensing method that mitigates sample dependency in image based sensorless adaptive optics applications in microscopy. Our method employs structured illumination to create additional, high spatial frequencies in the image through custom illumination patterns. This improves the reliability of image quality metric calculations and enables sensorless wavefront measurement even in samples with sparse spatial frequency content. We demonstrate the feasibility of IsoSense for aberration correction in a deformable mirror based structured illumination super-resolution fluorescence microscope.
Carvedilol Inhibits Tumor Necrosis Factor-α–Induced Endothelial Transcription Factor Activation, Adhesion Molecule Expression, and Adhesiveness to Human Mononuclear Cells

Objective— We tested the hypothesis that carvedilol, a β-adrenoceptor and α-adrenoceptor antagonist with potent antioxidant property, could inhibit tumor necrosis factor-α (TNF-α)–induced endothelial adhesiveness to human mononuclear cells (MNCs), an early sign of atherogenesis. Methods and Results— Circulating MNCs were isolated from the peripheral blood of healthy subjects. Compared with control condition, pretreatment of carvedilol (10 μmol/L for 18 hours) or probucol (5 μmol/L for 18 hours), but not propanolol, prazosin, or both propanolol and prazosin significantly decreased TNF-α–stimulated adhesiveness of cultured human aortic endothelial cells (HAECs) to MNCs. Carvedilol inhibited TNF-α–stimulated endothelial vascular cell adhesion molecule-1 (VCAM-1) and E-selectin (66.0±2.0% and 55.60±1.0% of control, P<0.05, respectively) expression, whereas probucol inhibited only VCAM-1 expression (79.0±5.0% of control, P<0.05). Propanolol, prazosin, or both did not alter the expression of adhesion molecules.
Enhancement of Thermonuclear Reaction Rate due to Strong Screening

The calculation of the enhancement factor for the rate of thermonuclear reactions in the strong-screening regime is extended to the cases involving plasmas with two different ion species. The calculation is based on the recent results of Monte Carlo computations for such two-component plasmas. With appropriate definition and combination of the plasma parameters we find that the screening potentials in two-component plasmas exhibit a linear dependence at intermediate distances, quite similar to that found for one-component plasmas. Application to the calculation of carbon ignition in the carbon--oxygen core of a highly evolved star is discussed.
UJI AKTIVITAS ANTIOKSIDAN DAN SIFAT ORGANOLEPTIK TEH HERBAL CAMPURAN DAGING BUAH PARE (MOMORDICA CHARANTIA L.) DAN KULIT BUAH NAGA MERAH (Hylocereus Lemairei (HOOK.) BRITTON & ROSE)

Herbal tea is a herbal mixture made from flowers, leaves, seeds and or roots of various plants. Some of herbal tea consumed for adds energizing, help relaxation, overcome digestive problems and also strengthen the immune system. Research on antioxidant activity and organoleptic characteristic mixflesh of bitter melon fruit (Momordica charantia L.) and red dragon fruit skin (Hylocereus lemairei (Hook.) britton & rose) herbal tea has been done. The objective of this research was to make a herbal tea formulation that has a high antioxidant activity and is preferred from a mixture of bitter melon fruitand red dragon fruit skin that has been dried at 50-60°C. The antioxidant activity were measured by free radical scavenging method with DPPH; whereas organoleptic test was measured by hedonik method. The results of 5 formulas indicate that antioxidant activity is the highest in FIII formula that has the most content of bitter melon fruit. Data were analyzed using one way ANOVA and Tukey method at 99% confidence level. The herbal tea formulation of a coarse powder mixture of 1.75 g of bitter melon fruit and a coarse powder of 0.25 g red dragon fruit showed the highest antioxidant activity with percent inhibition of 98,249% and preferably with the likes after adding 30 mL of honey.
Relationship between ABO blood group and risk of venous thrombosis in cancer patients with peripherally inserted central catheters

Abstract Background: Peripherally inserted central catheter (PICC) is closely related to venous thromboembolism (VTE). It is a common complication of hospitalized patients, and its etiology is complex. How to prevent the occurrence of VTE is the focus of clinical work. In order to provide basis for individual prevention and accurate treatment of VTE, the purpose of this study was to explore the relationship between ABO blood group and the risk of VTE in cancer patients associated with PICC through meta-analysis. Methods: Electronic databases, including Embase, Cochrane Library, Pubmed, Chinese databases SinoMed, Chinese National Knowledge Infrastructure (CNKI), Chinese Scientific Journals Database (VIP), and Wanfang Data, were searched for case-control studies of ABO blood group and PICC-related VTE in cancer patients. The languages were limited to Chinese and English. Two reviewers were responsible for the selection of the study, the extraction of data and the evaluation of the quality of the research. All statistical analyses were carried out with Review Manager 5.3 and Stata 14.0. Results: The results of this meta-analysis would be published in peer-reviewed journals. Conclusion: This study provided evidence to support the relationship between ABO blood group and the risk of PICC-related VTE in cancer patients. OSF Registration number: DOI 10.17605/OSF.IO/6DPFG
The effects of traditional Chinese medicine combined with chemotherapy on immune function and quality of life in patients with non-small cell lung cancer

Abstract Background: This article will evaluate the effects of traditional Chinese medicine (TCM) combined with chemotherapy on the immune function and quality of life of patients with non-small cell lung cancer (NSCLC), and evaluate the published side effects. Methods: The systematic review and meta-analysis will be conducted in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. The databases we will search include: PubMed, EMBASE, Cochrane Library, Web of Science, China National Knowledge Infrastructure, China Biomedicine, Wan fang Data, and Technology Periodical Database. The search date is from inception to June 30, 2020. There are no restrictions on the document language. The literatures included in this study are randomized controlled trials. The main results include ratio of CD3+, CD4+, CD8+, CD4+/CD8+, NK cells, the level of IgA, IgG, IgM, and Karnofsky performance status score. The secondary result is to evaluate various side effects during treatment. We will use the Cochrane Collaboration tool to evaluate each study and use Review Manager software (RevMan, version 5.3) to merge and analyze the data. The 2 researchers will independently cross-screen the literature, extract data, and evaluate the quality. If there are differences, we will resolve them through discussion or consultation with a third reviewer. Results: The results of this study will provide high-quality evidence for the effect of TCM combined with chemotherapy on the immune function and quality of life of patients with NSCLC. Conclusion: This article will comprehensively evaluate the effects of TCM combined with chemotherapy on the immune function and quality of life of patients with NSCLC, and provide evidence-based evidence for clinical practice. Ethics: Since the data used in this study is based on previous trials and does not involve patient privacy, ethical approval is not required. Study registration number: INPLASY202070071
Impact of right ventricular systolic pressure in elderly patients admitted to intensive care unit after femur fracture surgery

Supplemental Digital Content is available in the text Abstract The number of femoral fractures is expected to continue to increase as the size of the older population rapidly grows. However, old age is accompanied by various comorbidities and is an important postoperative risk factor in itself, meaning that patients who undergo surgery for a femur fracture may require admission to an ICU. We investigated pulmonary complications in patients over the age of 65 admitted to the ICU after femur fracture surgery. In this single-center retrospective observational study, 289 patients over 65 years who admitted to the ICU after femur fracture surgery between June 2008 and December 2016 were investigated. Pulmonary complications occurred in 97 of these patients (33.6%) after surgery. Mean hospitalization days (34.1 ± 25.7 vs 23.1 ± 15.7, P < .001) and mean ICU length of stay (8.4 ± 16.1 vs 2.5 ± 1.1, P = .001) were significantly longer for patients with pulmonary complications than for patients without pulmonary complications after femur fracture surgery. Patients with pulmonary complications were significantly more likely to have pulmonary disease (19.6% vs 8.9%, P = .009) and exhibit sequelae on preoperative chest X-rays (9.3% vs 3.6%, P = .048) than were patients without pulmonary complications. In addition, significant differences were observed in the right ventricular systolic pressure (RVSP) measured during preoperative echocardiography (37.4 ± 10.9 mm Hg vs 40.7 ± 9.3 mm Hg for patients without and with pulmonary complications, P = .010) and in the proportion of each group that had an RVSP of >35 mm Hg, which is a marker for pulmonary hypertension (55.2% vs 76.3% for patients without and with pulmonary complications, P < .001). In multivariate analysis, an RVSP of >35 mm Hg during preoperative echocardiography was associated with pulmonary complications after femur fracture surgery (OR, 2.6; 95% CI, 1.45–4.53). In conclusion, Pulmonary complications in older patients admitted to the ICU after femur fracture surgery was associated with longer hospitalization and ICU stays. Preoperative RVSP measurement could identify those older patients with a high risk of pulmonary complications following transferal to the ICU after femur fracture surgery.