Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits

Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the isolates, among which the most frequently represented were ST76 (16%) and ST70 (11%). Based on LPS structure, serotypes O1 and O3 were the most prevalent, accounting for approximately 63% of all infections. The virulence capsular types K10, K136, and K2 were present in 16, 13, and 8% of the isolates, respectively. Phylogenomic analysis based on virtual genome fingerprints correlated with the MLST data. The phylogenomic reconstruction also denoted association between strains with a higher abundance of virulence genes and virulent serotypes compared to strains that do not possess these traits. This study highlights the value of whole-genomic sequencing in the surveillance of virulence attributes among clinical K. pneumoniae strains.
Rectal Tumor Stiffness Quantified by In Vivo Tomoelastography and Collagen Content Estimated by Histopathology Predict Tumor Aggressiveness

Purpose To investigate the significance of collagen in predicting the aggressiveness of rectal tumors in patients, examined in vivo based on tomoelastography quantified stiffness and ex vivo by histologically measured collagen volume fraction (CVF). Experimental Design 170 patients with suspected rectal cancer were prospectively enrolled and underwent preoperative magnetic resonance imaging (MRI) and rectal tomoelastography, a technique based on multifrequency magnetic resonance elastography. Histopathologic analysis identified eighty patients with rectal cancer who were divided into subgroups by tumor-node (TN) stage, prognostic stage, and risk level. Rectal tumor stiffness was correlated with histopathologic CVF. Area-under-the-curve (AUC) and contingency analysis were used to evaluate the performance of rectal stiffness in distinguishing tumor stages which was compared to standard clinical MRI Results In vivo tomoelastography revealed that rectal tumor stiffened significantly with increased TN stage (p<0.05). Tumors with poorly differentiated status, perineural and lymphovascular invasion also displayed higher stiffness than well-to-moderately differentiated, noninvasive tumors (all p<0.05). Similar to in vivo stiffness, CVF indicated an abnormally high collagen content in tumors with perineural invasion and poor differentiation status. CVF was also positively correlated with stiffness (p<0.05). Most importantly, both stiffness (AUROC: 0.82) and CVF (AUROC: 0.89) demonstrated very good diagnostic accuracy in detecting rectal tumors that have high risk for progressing to an aggressive state with poorer prognosis. Conclusion In human rectal carcinomas, overexpression of collagen is correlated with increased tissue stiffness and high risk for tumor advancing more aggressively. In vivo tomoelastography quantifies rectal tumor stiffness which improves the diagnostic performance of standard MRI in the assessment of lymph nodes metastasis. Therefore, in vivo stiffness mapping by tomoelastography can predict rectal tumor aggressiveness and add diagnostic value to MRI.
Immune Checkpoints Expression in Chronic Lung Allograft Rejection

Chronic lung allograft dysfunction (CLAD) is the main cause of poor survival and low quality of life of lung transplanted patients. Several studies have addressed the role of dendritic cells, macrophages, T cells, donor specific as well as anti-HLA antibodies, and interleukins in CLAD, but the expression and function of immune checkpoint molecules has not yet been analyzed, especially in the two CLAD subtypes: BOS (bronchiolitis obliterans syndrome) and RAS (restrictive allograft syndrome). To shed light on this topic, we conducted an observational study on eight consecutive grafts explanted from patients who received lung re-transplantation for CLAD. The expression of a panel of immune molecules (PD1/CD279, PDL1/CD274, CTLA4/CD152, CD4, CD8, hFoxp3, TIGIT, TOX, B-Cell-Specific Activator Protein) was analyzed by immunohistochemistry in these grafts and in six control lungs. Results showed that RAS compared to BOS grafts were characterized by 1) the inversion of the CD4/CD8 ratio; 2) a higher percentage of T lymphocytes expressing the PD-1, PD-L1, and CTLA4 checkpoint molecules; and 3) a significant reduction of exhausted PD-1-expressing T lymphocytes (PD-1pos/TOXpos) and of exhausted Treg (PD-1pos/FOXP3pos) T lymphocytes. Results herein, although being based on a limited number of cases, suggest a role for checkpoint molecules in the development of graft rejection and offer a possible immunological explanation for the worst prognosis of RAS. Our data, which will need to be validated in ampler cohorts of patients, raise the possibility that the evaluation of immune checkpoints during follow-up offers a prognostic advantage in monitoring the onset of rejection, and suggest that the use of compounds that modulate the function of checkpoint molecules could be evaluated in the management of chronic rejection in LTx patients.
A Path Analysis Model of Protection and Risk Factors for University Academic Stress: Analysis and Psychoeducational Implications for the COVID-19 Emergency

The aim of this research was to empirically validate hypothesized predictive relationships of protection and risk factors for experiencing academic stress. A synthesis of models—the presage–process–product model; the studying, learning and performing under stress competency model; and self- vs. external-regulatory theory—underlies the investigation and is important for assessment and guidance in stress situations within the university context. Over the course of an academic year, a sample of 564 Spanish university students voluntarily completed validated questionnaires, in an online format, on several psychological variables connected to academic stress. Correlational analysis and the path analysis model, within an ex post facto design, were used to build empirical models of the presage–process–product factors that constitute protection or risk factors in academic stress. Two statistically acceptable models appeared: one with protection factors and another with risk factors in predicting and preventing academic stress at a university. These results support the need for psychology units at university that have a preventive, health and education focus, going beyond the merely clinical. Focus on an individual is insufficient, given that there are also contextual factors that predispose academic stress. Discussion, conclusions, and implications for assessment and intervention in academic stress in university students and teachers, within the present COVID-19 crisis, are offered.
Machine Learning Identification of Pro-arrhythmic Structures in Cardiac Fibrosis

Cardiac fibrosis and other scarring of the heart, arising from conditions ranging from myocardial infarction to ageing, promotes dangerous arrhythmias by blocking the healthy propagation of cardiac excitation. Owing to the complexity of the dynamics of electrical signalling in the heart, however, the connection between different arrangements of blockage and various arrhythmic consequences remains poorly understood. Where a mechanism defies traditional understanding, machine learning can be invaluable for enabling accurate prediction of quantities of interest (measures of arrhythmic risk) in terms of predictor variables (such as the arrangement or pattern of obstructive scarring). In this study, we simulate the propagation of the action potential (AP) in tissue affected by fibrotic changes and hence detect sites that initiate re-entrant activation patterns. By separately considering multiple different stimulus regimes, we directly observe and quantify the sensitivity of re-entry formation to activation sequence in the fibrotic region. Then, by extracting the fibrotic structures around locations that both do and do not initiate re-entries, we use neural networks to determine to what extent re-entry initiation is predictable, and over what spatial scale conduction heterogeneities appear to act to produce this effect. We find that structural information within about 0.5 mm of a given point is sufficient to predict structures that initiate re-entry with more than 90% accuracy.
Phylogeography of Blue Corals (Genus Heliopora) Across the Indo-West Pacific

Species delimitation of corals is one of the most challenging issues in coral reef ecology and conservation. Morphology can obscure evolutionary relationships, and molecular datasets are consistently revealing greater within-species diversity than currently understood. Most phylogenetic studies, however, have examined narrow geographic areas and phylogeographic expansion is required to obtain more robust interpretations of within- and among- species relationships. In the case of the blue coral Heliopora, there are currently two valid species (H. coerulea and H. hiberniana) as evidenced by integrated genetic and morphological analyses in northwestern Australia. There are also two distinct genetic lineages of H. coerulea in the Kuroshio Current region that are morphologically and reproductively different from each other. Sampling from all Heliopora spp. across the Indo-Pacific is essential to obtain a more complete picture of phylogeographic patterns. To examine phylogenetic relationships within the genus Heliopora, we applied Multiplexed inter simple sequence repeat (ISSR) Genotyping by sequencing (MIG-seq) on > 1287 colonies across the Indo-West Pacific. Maximum likelihood phylogenetic trees indicated the examined Heliopora samples comprise three genetically distinct groups: H. coerulea group, H. hiberniana group, and a new undescribed Heliopora sp. group with further subdivisions within each group. Geographic structuring is evident among the three species with H. hiberniana group found in the Indo-Malay Archipelago and biased toward the Indian Ocean whilst Heliopora sp. was only found in the Kuroshio Current region and Singapore, indicating that this taxon is distributed in the western Pacific and the Indo-Malay Archipelago. Heliopora coerulea has a wider distribution, being across the Indian Ocean and western Pacific. This study highlights the effectiveness of phylogenetic analysis using genome-wide markers and the importance of examining populations across their distribution range to understand localized genetic structure and speciation patterns of corals.
Clinicopathological Characteristics and Prognosis of Signet Ring Gastric Cancer: A Population-Based Study

Background To better define the clinicopathologic characteristics of signet ring cell (SRC) gastric cancer and build a prognostic model for it. Methods SRC patient information from 2010 to 2015 were identified using Surveillance, Epidemiology, and End Results (SEER) database. Kaplan-Meier method and log-rank test were used to estimate Overall survival (OS) and to determine associations with histologic subtypes. In COX proportional hazards regression model–based univariate and multivariate analyses, significant variables for construction of a nomogram were screened out. The nomogram was validated by means of the concordance index (CI), calibration plots, and receiver operating characteristics (ROCs) curves. Results A total of 11,363 gastric cancer patients were enrolled. On dividing the patients into SRC, well-to-moderately differentiated (WMD) adenocarcinoma, and poorly differentiated (PD) adenocarcinoma, differences among these subgroups emerged. SRC patients were more likely to occur in female and young patients than other histologic subtypes. Larger tumors, stage T4, and node stage N3 were more likely to be found in the SRC group. The survival for SRC patients was better than non-SRC patients in stage I. Univariate and multivariate analyses identified age, tumor site, larger tumor size, advanced T classification, advanced N classification, advanced TNM stage, and surgery of primary site as independent prognostic indicators. Then an OS nomogram was formulated. Conclusions SRC had distinct clinicopathological characteristics. The nomogram provided an accurate tool to evaluate the prognosis of SRC.
Effects of Methyl Salicylate on Host Plant Acceptance and Feeding by the Aphid Rhopalosiphum padi

Methyl salicylate (MeSA) is a volatile shown to act as an inducer of plant defense against pathogens and certain herbivores, particularly aphids. It has been shown to have potential for aphid pest management, but knowledge on its mode of action is lacking, particularly induced plant-mediated effects. This study investigated the effects of exposing plants to MeSA on the host searching, host acceptance and feeding behavior of the bird cherry-oat aphid Rhopalosiphum padi. Barley plants were exposed to volatile MeSA for 24 h, after which biological effects were tested immediately after the exposure (Day 0), and then 1, 3 and 5 days after the end of the exposure. Aphid settling on MeSA-exposed plants was significantly reduced on days 0, 1 and 3, but not on day 5. In olfactometer tests, aphids preferred the odor of unexposed plants on days 1 and 3, but not on day 0 or 5. Analysis of volatiles from exposed and unexposed plants showed higher levels of MeSA from exposed plants, most likely absorbed and re-released from plant surfaces, but also specific changes in other plant volatiles on days 0, 1 and 3. High doses of MeSA did not affect aphid orientation in an olfactometer, but lower doses were repellent. Analysis of aphid feeding by Electronic penetration graph (EPG) showed that MeSA exposure resulted in resistance factors in barley plants, including surface factors and induced systemic factors in other tissues including the phloem. The results support the potential of MeSA as a potential tool for management of aphid pests.
Daily Intravoxel Incoherent Motion (IVIM) In Prostate Cancer Patients During MR-Guided Radiotherapy—A Multicenter Study

Purpose Daily quantitative MR imaging during radiotherapy of cancer patients has become feasible with MRI systems integrated with linear accelerators (MR-linacs). Quantitative images could be used for treatment response monitoring. With intravoxel incoherent motion (IVIM) MRI, it is possible to acquire perfusion information without the use of contrast agents. In this multicenter study, daily IVIM measurements were performed in prostate cancer patients to identify changes that potentially reflect response to treatment. Materials and Methods Forty-three patients were included, treated with 20 fractions of 3 Gy on a 1.5 T MR-linac. IVIM measurements were performed on each treatment day. The diffusion coefficient (D), perfusion fraction (f), and pseudo-diffusion coefficient (D*) were calculated based on the median signal intensities in the non-cancerous prostate and the tumor. Repeatability coefficients (RCs) were determined based on the first two treatment fractions. Separate linear mixed-effects models were constructed for the three IVIM parameters. Results In total, 726 fractions were analyzed. Pre-treatment average values, measured on the first fraction before irradiation, were 1.46 × 10−3 mm2/s, 0.086, and 28.7 × 10−3 mm2/s in the non-cancerous prostate and 1.19 × 10−3 mm2/s, 0.088, and 28.9 × 10−3 mm2/s in the tumor, for D, f, and D*, respectively. The repeatability coefficients for D, f, and D* in the non-cancerous prostate were 0.09 × 10−3 mm2/s, 0.05, and 15.3 × 10−3 mm2/s. In the tumor, these values were 0.44 × 10−3 mm2/s, 0.16, and 76.4 × 10−3 mm2/s. The mixed effects analysis showed an increase in D of the tumors over the course of treatment, while remaining stable in the non-cancerous prostate. The f and D* increased in both the non-cancerous prostate and tumor. Conclusions It is feasible to perform daily IVIM measurements on an MR-linac system. Although the repeatability coefficients were high, changes in IVIM perfusion parameters were measured on a group level, indicating that IVIM has potential for measuring treatment response.
Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.
Performance on verbal fluency in late-onset schizophrenia is more preserved than in early-onset schizophrenia

Introduction According to the literature, cognition may be more preserved in late-onset schizophrenia (LOS) compared to early-onset schizophrenia (EOS), but data are limited. Objectives To compare performance on cognitive tests in LOS and EOS. Methods LOS patients (n=14, mean age 58.1±8.2, 13 females, illness duration 1.07±1.5 years) and age-comparable controls (n=17, mean age 55.3±7.8, 12 females), EOS patients (n=25, mean age 20.7±3.9, 25 males, illness duration 0.75±0.62 years) and age-comparable controls (n=15, mean age 22.9±2.3, 15 males) underwent the Brief Assessment of Cognition in Schizophrenia (BACS) comprised of six subtests: Verbal Memory, Digit Sequencing, Verbal Fluency, Token Motor Task, Symbol Coding, and Tower of London. The Mann-Whitney U test with Bonferroni correction for multiple comparisons was applied (p <.05/8, i.e. p <.006). Results Compared to LOS, EOS patients had lower score on Verbal Fluency (VF): U=78, p=. 004; mean T-scores are 43.5±9.5 and 33.6±12.6 for LOS and EOS, respectively. Additionally, we compared VF performance in each clinical group with age-comparable controls and revealed significantly lower performance in both LOS (U=37.5, p=.001) and EOS (U=56.5, p=.000). Conclusions Performance on VF is deteriorated in clinical groups, but may be more intact in LOS compared to EOS. This result is of particular interest because low performance on VF is considered as a cognitive endophenotype of schizophrenia. Performance on VF requires preserved executive functions, language, and processing speed. Our results are in line with the idea that LOS and EOS may be different subtypes of schizophrenia. Limitation of this study is that the clinical groups are not sex-matched.
Thallium Mass Fraction and Stable Isotope Ratios of Sixteen Geological Reference Materials

Thallium stable isotope ratio and mass fraction measurements were performed on sixteen geological reference materials spanning three orders of magnitude in thallium mass fraction, including both whole rock and partially separated mineral powders. For stable isotope ratio measurements, a minimum of three independent digestions of each reference material was obtained. High‐precision trace element measurements (including Tl) were also performed for the majority of these RMs. The range of Tl mass fractions represented is 10 ng g−1 to 16 μg g−1, and Tl stable isotope ratios (reported for historical reasons as ε205Tl relative to NIST SRM 997) span the range −4 to +2. With the exception – attributed to between‐bottle heterogeneity – of G‐2, the majority of data are in good agreement with published or certified values, where available. The precision of mean of independent measurement results between independent dissolutions suggests that, for the majority of materials analysed, a minimum digested mass of 100 mg is recommended to mitigate the impact of small‐scale powder heterogeneity. Of the sixteen materials analysed, we therefore recommend for use as Tl reference materials the USGS materials BCR‐2, COQ‐1, GSP‐2 and STM‐1; CRPG materials AL‐I, AN‐G, FK‐N, ISH‐G, MDO‐G, Mica‐Fe, Mica‐Mg and UB‐N; NIST SRM 607 and OREAS14P.