Miracle-dz/UniFAR-FTUs huggingface dataset:
Pan-genome analyses of model fungal species

The concept of the species ‘pan-genome’, the union of ‘core’ conserved genes and all ‘accessory’ non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining ‘accessory’ gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.
Lymphomas associated with chronic hepatitis C virus infection: A prospective multicenter cohort study from the Rete Ematologica Lombarda (REL) clinical network

Chronic hepatitis C virus (HCV) infection is related with an increased risk of non‐Hodgkin lymphomas (NHL). In indolent subtypes, regression of NHL was reported after HCV eradication with antiviral therapy (AT). In 2008 in Lombardy, a region of Northern Italy, the “Rete Ematologica Lombarda” (REL, Hematology Network of Lombardy—Lymphoma Workgroup) started a prospective multicenter observational cohort study on NHL associated with HCV infection, named “Registro Lombardo dei Linfomi HCV‐positivi” (“Lombardy Registry of HCV‐associated non‐Hodgkin lymphomas”). Two hundred fifty patients with a first diagnosis of NHL associated with HCV infection were enrolled; also in our cohort, diffuse large B cell lymphoma (DLBCL) and marginal zone lymphoma (MZL) are the two most frequent HCV‐associated lymphomas. Two thirds of patients had HCV‐positivity detection before NHL; overall, NHL was diagnosed after a median time of 11 years since HCV survey. Our data on eradication of HCV infection were collected prior the recent introduction of the direct‐acting antivirals (DAAs) therapy. Sixteen patients with indolent NHL treated with interferon‐based AT as first line anti‐lymphoma therapy, because of the absence of criteria for an immediate conventional treatment for lymphoma, had an overall response rate of 90%. After a median follow‐up of 7 years, the overall survival (OS) was significantly longer in indolent NHL treated with AT as first line (P = 0.048); this confirms a favorable outcome in this subset. Liver toxicity was an important adverse event after a conventional treatment in 20% of all patients, in particular among DLBCL, in which it is more frequent the coexistence of a more advanced liver disease. Overall, HCV infection should be consider as an important co‐pathology in the treatment of lymphomas and an interdisciplinary approach should be always considered, in particular to evaluate the presence of fibrosis or necroinflammatory liver disease.
Global occurrence of deoxynivalenol in food commodities and exposure risk assessment in humans in the last decade: a survey

Abstract Preventing food from fungal infestation has become a cause of great concern as food safety is of particular importance to public health globally. Recently International Agency for Research on Cancer (IARC) and the World Health Organization (WHO) in its 2016 press release has urged to take action against widespread mycotoxin contamination in developing countries. Deoxynivalenol (DON) is a group B trichothecene mycotoxin, produced by common field pathogens such as Fusarium graminearum and Fusarium culmorum, and reported to be the predominant contaminant of food commodities. At present, no detailed/systematic review regarding the global occurrence of DON in various food and grain samples is available in the literature. Considering DON’s cosmopolitan behavior and toxicological manifestations, the present review summarizes the region-wise reports and surveys conducted across the globe during the last decade, on the occurrence of DON in the food commodities intended for human consumption. Studies conducted on DON metabolites either in food, urine or blood samples from humans have also been reviewed. The present review indicates that the current exposure levels of DON might pose a health risk for the consumers, especially in growing children, necessitating to take vigilant steps to guarantee food safety.
Vesicular GABA Transporter Is Necessary for Transplant-Induced Critical Period Plasticity in Mouse Visual Cortex

The maturation of GABAergic inhibitory circuits is necessary for the onset of the critical period for ocular dominance plasticity (ODP) in the postnatal visual cortex (Hensch, 2005; Espinosa and Stryker, 2012). When it is deficient, the critical period does not start. When inhibitory maturation or signaling is precocious, it induces a precocious critical period. Heterochronic transplantation of GABAergic interneuron precursors derived from the medial ganglionic eminence (MGE) can induce a second period of functional plasticity in the visual cortex (Southwell et al., 2010). Although the timing of MGE transplantation-induced plasticity is dictated by the maturation of the transplanted cells, its mechanisms remain largely unknown. Here, we sought to test the effect of blocking vesicular GABA loading and subsequent release by transplanted interneurons on the ability to migrate, integrate, and induce plasticity in the host circuitry. We show that MGE cells taken from male and female donors that lack vesicular GABA transporter (Vgat) expression disperse and differentiate into somatostatin- and parvalbumin-expressing interneurons upon heterochronic transplantation in the postnatal mouse cortex. Although transplanted Vgat mutant interneurons come to express mature interneuron markers and display electrophysiological properties similar to those of control cells, their morphology is significantly more complex. Significantly, Vgat mutant MGE transplants fail to induce ODP, demonstrating the pivotal role of vesicular GABAergic transmission for MGE transplantation-induced plasticity in the postnatal mouse visual cortex. SIGNIFICANCE STATEMENT Embryonic inhibitory neurons thrive when transplanted into postnatal brains, migrating and differentiating in the host as they would have done if left in the donor. Once integrated into the host, these new neurons can have profound effects. For example, in the visual cortex, such neurons induce a second critical period of activity-dependent plasticity when they reach the appropriate stage of development. The cellular mechanism by which these transplanted GABAergic interneurons induce plasticity is unknown. Here, we show that transplanted interneurons that are unable to fill synaptic vesicles with GABA migrate and integrate into the host circuit, but they do not induce a second period of plasticity. These data suggest a role for the vesicular GABA transporter in transplantation-mediated plasticity.
Rhinovirus infection induces degradation of antimicrobial peptides and secondary bacterial infection in chronic obstructive pulmonary disease.

RATIONALE Chronic obstructive pulmonary disease (COPD) exacerbations are associated with virus (mostly rhinovirus) and bacterial infections, but it is not known whether rhinovirus infections precipitate secondary bacterial infections. OBJECTIVES To investigate relationships between rhinovirus infection and bacterial infection and the role of antimicrobial peptides in COPD exacerbations. METHODS We infected subjects with moderate COPD and smokers and nonsmokers with normal lung function with rhinovirus. Induced sputum was collected before and repeatedly after rhinovirus infection and virus and bacterial loads measured with quantitative polymerase chain reaction and culture. The antimicrobial peptides secretory leukoprotease inhibitor (SLPI), elafin, pentraxin, LL-37, α-defensins and β-defensin-2, and the protease neutrophil elastase were measured in sputum supernatants. MEASUREMENTS AND MAIN RESULTS After rhinovirus infection, secondary bacterial infection was detected in 60% of subjects with COPD, 9.5% of smokers, and 10% of nonsmokers (P < 0.001). Sputum virus load peaked on Days 5-9 and bacterial load on Day 15. Sputum neutrophil elastase was significantly increased and SLPI and elafin significantly reduced after rhinovirus infection exclusively in subjects with COPD with secondary bacterial infections, and SLPI and elafin levels correlated inversely with bacterial load. CONCLUSIONS Rhinovirus infections are frequently followed by secondary bacterial infections in COPD and cleavage of the antimicrobial peptides SLPI and elafin by virus-induced neutrophil elastase may precipitate these secondary bacterial infections. Therapy targeting neutrophil elastase or enhancing innate immunity may be useful novel therapies for prevention of secondary bacterial infections in virus-induced COPD exacerbations.
Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Synechococcus, a genus of unicellular cyanobacteria found throughout the global surface ocean, is a large driver of Earth's carbon cycle. Developing a better understanding of its diversity and distributions is an ongoing effort in biological oceanography. Here, we introduce 12 new draft genomes of marine Synechococcus isolates spanning five clades and utilize ~100 environmental metagenomes largely sourced from the TARA Oceans project to assess the global distributions of the genomic lineages they and other reference genomes represent. We show that five newly provided clade-II isolates are by far the most representative of the recovered in situ populations (most 'abundant') and have biogeographic distributions distinct from previously available clade-II references. Additionally, these isolates form a subclade possessing the smallest genomes yet identified of the genus (2.14 ± 0.05Mbps; mean ± 1SD) while concurrently hosting some of the highest GC contents (60.67 ± 0.16%). This is in direct opposition to the pattern in Synechococcus's nearest relative, Prochlorococcus - wherein decreasing genome size has coincided with a strong decrease in GC content - suggesting this new subclade of Synechococcus appears to have convergently undergone genomic reduction relative to the rest of the genus, but along a fundamentally different evolutionary trajectory.
Understanding physical activity behavior of Chinese female college students with/without vulnerable conditions: a theory of planned behavior perspective

ABSTRACT Guided by the theory of planned behavior (TPB), this study examined the relationships between three constructs of TPB (attitude, subjective norm, perceived behavioral control [PBC]) and physical activity intention and behavior among Chinese female college students, and evaluated whether the relationships differed between healthy and vulnerable individuals within this population. Participants included 436 female college students (301 healthy and 135 vulnerable; Mean age = 19.24 years; SD = 0.97 years) recruited from five universities in China, and the data collection was completed in Fall 2015. Path analysis supported the direct and indirect relations of TPB constructs to physical activity intention and behavior among female college students, and the path model was invariant across the two groups. The vulnerable group reported significantly lower attitude, subjective norm, intention, and physical activity behavior than the healthy group but not for PBC. These findings suggest fostering positive attitudes and intention toward physical activity are important among Chinese female college students, regardless of their health status.
The North American Listening in Spatialized Noise-Sentences test (NA LiSN-S): normative data and test-retest reliability studies for adolescents and young adults.

BACKGROUND The Listening in Spatialized Noise-Sentences test (LiSN-S; Cameron and Dillon, 2009) was originally developed to assess auditory stream segregation skills in children aged 6 to 11 yr with suspected central auditory processing disorder. The LiSN-S creates a three-dimensional auditory environment under headphones. A simple repetition-response protocol is used to assess a listener's speech reception threshold (SRT) for target sentences presented in competing speech maskers. Performance is measured as the improvement in SRT in dB gained when either pitch, spatial, or both pitch and spatial cues are incorporated in the maskers. A North American-accented version of the LiSN-S (NA LiSN-S) is available for use in the United States and Canada. PURPOSE To develop normative data for adolescents and adults on the NA LiSN-S, to compare these data with those of children aged 6 to 11 yr as documented in Cameron et al (2009), and to consolidate the child, adolescent, and adult normative and retest data to allow the software to be used with a wider population. RESEARCH DESIGN In a descriptive design, normative data and test-retest reliability data were collected. STUDY SAMPLE One hundred and twenty normally hearing participants took part in the normative data study (67 adolescents aged 12 yr, 1 mo, to 17 yr, 10 mo, and 53 adults aged 19 yr, 10 mo, to 30 yr, 30 mo). Forty-nine participants returned between 1 and 4 mo after the initial assessment for retesting. Participants were recruited from sites in Cincinnati, Dallas, and Calgary. RESULTS When combined with data collected from children aged 6 to 11 yr, a trend of improved performance as a function of increasing age was found across performance measures. ANOVA (analysis of variance) revealed a significant effect of age on performance. Planned contrasts revealed that there were no significant differences between adults and children aged 13 yr and older on the low-cue SRT; 14 yr and older on talker and spatial advantage; 15 yr and older on total advantage; and 16 yr and older on the high-cue SRT. Mean test-retest differences on the various NA LiSN-S performance measures for the combined child, adult, and adolescent data ranged from 0.05 to 0.5 dB. Paired comparisons revealed test-retest differences were not significant on any measure of the NA LiSN-S except low-cue SRT. Test-retest differences across measures did not differ as a function of age. Test and retest scores were significantly correlated for all NA LiSN-S measures. CONCLUSIONS The ability to use either spatial or talker cues in isolation becomes adultlike by about 14 yr of age, whereas the ability to combine spatial and talker cues does not fully mature until closer to adulthood. By consolidating child, adolescent, and adult normative and retest data the NA LiSN-S can now been utilized to assess auditory processing skills in a wider population.
Does bilateral versus single thoracic artery grafting provide survival benefit in female patients?

OBJECTIVES Bilateral internal thoracic artery (BITA) grafting is associated with improved survival, but this technique is reluctantly used in women due to an increased risk of sternal wound infection. The aim of this study was to compare the long-term survival of women who underwent BITA grafting and single internal thoracic artery (SITA) grafting. METHODS We performed a retrospective analysis of 556 consecutive female BITA patients and 685 female SITA patients. RESULTS SITA patients were older and more likely to have comorbidities (diabetes mellitus, chronic lung disease, chronic renal failure, peripheral vascular disease and cerebral vascular disease). Operative mortality showed a trend towards a benefit for BITA (2.9% vs 5.0% for SITA, P = 0.06). The sternal wound infection rates were similar (3.4% vs 2.9%, P = 0.6); however, the occurrence of stroke was significantly lower in the SITA group (3.4% vs 1.2%, P = 0.007). The median survival of the BITA group was significantly better {13.8 years [95% confidence interval (CI) 12.8-14.9] vs 10.3 years [95% CI 9.6-11.1], P = 0.001}. After propensity score matching (491 pairs), the assignment to BITA was not associated with increased early mortality or complication rates, and the choice of BITA grafting was associated with better survival [14.5 years (95% CI 13.3-15.6) vs 11.8 years (95% CI 10.7-12.9)]. Only the choice of conduits was associated with increased late mortality (multivariable analysis, hazard ratio 1.28, 95% CI 1.024-1.591; P = 0.03). CONCLUSIONS The low early mortality and complication rate, and the long-term survival benefit of BITA compared to SITA grafting, support the use of BITA grafting in women.
Comparison of the Efficacy of Holmium Laser Enucleation of the Prostate in Treating Prostate Volumes of ≤80 and > 80 mL

Introduction: Holmium laser enucleation of the prostate (HoLEP) is becoming the new standard procedure for treating benign prostatic hyperplasia (BPH), a common condition in aging men. Most studies have focused on proving its efficacy in treating large prostates. In this study, we compared its efficacy in treating small (< 80 mL) and large (> 80 mL) prostates. Methods: This prospective study included 119 patients with BPH who underwent HoLEP by the same surgeon between June 2015 and December 2017. They were divided into 2 groups according to their prostate volumes (≤80 mL: Group 1; > 80 mL: Group 2). Various pre- and postoperative parameters were compared within and between the groups. Results: International Prostate Symptom Score (IPSS), postvoid residual (PVR) volume, and voiding time (VT) significantly decreased, and the peak urinary flow rate (Qmax), average urinary flow rate (Qave), and quality of life (QoL) score significantly increased postoperatively in both groups. The postoperative changes in IPSS, QoL score, Qmax, Qave, VT, PVR volume, and hemoglobin levels were not significantly different between the groups. In addition, no significant difference was observed in postoperative complications between the groups. Conclusions: Our results indicate that HoLEP is an effective procedure for treating both small and large prostates.
The Impact of Dual Health Care System Use for Obtaining Prescription Medications on Nonadherence in Veterans With Type 2 Diabetes

Background: Dual health system use may provide increased access to physicians, medications, and other health care resources but may also increase the complexity and coordination of medication regimens. Thus, it is important to elucidate the impact of dual use on medication adherence. Objective: The objective of this study was to evaluate the impact on medication adherence for veterans with dual health care system use (VA and Medicare) when obtaining prescription antihyperglycemic medications to treat diabetes. Methods: This was a longitudinal cohort study using VA and Medicare data from 2006 to 2010. Medication adherence was estimated by calculating annualized drug class-level proportion of days covered (PDC), where PDC >80% was considered adherent. Generalized linear models were used for estimations, accounting for correlation over time. Results: In total, 254 267 veterans with diabetes were included, with 71 057 (27.9%) defined as pharmacy system dual users. Mean age was 77.5 years, and nearly all had multiple comorbidities (mean count 10.2). During follow-up, 75% of VA-only users were deemed adherent to diabetes prescriptions, compared with 63% of dual users. In adjusted models, dual prescription benefit use from VA/Medicare was associated with 39% lower odds of medication adherence (odds ratio [OR] = 0.61; 95% CI = 0.60-0.61). Medication adherence significantly worsened with each additional diabetes medication (OR = 0.65; 95% CI = 0.64-0.65) and significantly decreased over time (OR = 0.95 per year; 95% CI = 0.95-0.96). Conclusion and Relevance: These data suggest that veterans utilizing VA and Medicare to obtain diabetes prescriptions are significantly less likely to be adherent.
Diurnal variations of postural stability and attentional capacities in 5–6-year-old tennis players

ABSTRACT The present study aimed to investigate the diurnal variation of postural stability, attentional capacities, and oral temperature in 5–6-year-old tennis players. A total of 24 young children were divided into two groups: Twelve tennis players with 2 years of training experience and twelve sedentary children without previous experience in any type of sport. They were asked to maintain an upright bipedal stance on a static force platform with eyes open (EO) and eyes closed (EC) at 07:00, 10:00, 14:00, and 18:00 h. Postural stability was evaluated by the center of pressure (CoP), surface area (CoPArea), CoP mean velocity (CoPVm), and Romberg’s index (RI). Oral temperature and simple reaction time (SRT) were also recorded at the beginning of each test session. Postural stability in 5–6-year-old tennis players was low at 07:00 h and improved at 10:00 h (p < 0.001); then, it worsened at 14:00 h (p < 0.001) and improved again at 18:00 h (p < 0.001) as found in sedentary children. This rhythm was also close to that of SRT in both groups. Body temperature increased significantly (p < 0.001) from the morning to the afternoon in both groups. However, the peak of postural performance, the peak of attentional capacities, and the greatest vision contribution to maintain balance observed at 18:00 h were only found in the trained group. Moreover, young tennis players were more stable (p < 0.001) and more attentive (p < 0.01) than sedentary ones at 18:00 h. The amplitude of the diurnal rhythm of CoP parameters was significantly larger (p < 0.01) in trained children compared to sedentary ones (43.1 ± 8.5 vs 31.7 ± 8.3 for the CoPArea; 27.5 ± 7.4 vs 17.7 ± 8.2 for the CoPVm). Therefore, time-of-day has a significant effect on static postural stability and attentional capacities in young tennis players with better performances in the late afternoon (habitual hour of training). Thus, we recommend planning some training sessions at 07:00 and/or 14:00 h to optimize postural stability at the time of its batyphase and to reduce the incidence of fall-related injury risks during this critical age in athletic environments.
A Brief Review on the Resistance-in-Series Model in Membrane Bioreactors (MBRs)

The cake layer deposited on the membrane modules of membrane bioreactors (MBRs), especially under a submerged configuration, represents a relevant and fundamental mechanism deeply influencing the development of membrane fouling. It negatively affects the total resistance to filtration, while exerting a positive effect as a “pre-filter” promoting the “dynamic membrane” that protects the physical membrane from internal fouling. These two opposite phenomena should be properly managed, where the submerged membranes are usually subjected to a periodical cake layer removal through ordinary (permeate backwashing and air scouring) and/or irregular cleaning actions (manual physical cleaning). In this context, the physical removal of the cake layer is needed to maintain the design filtration characteristics. Nevertheless, the proper evaluation of the effect of physical cleaning operations is still contradictory and under discussion, referring in particular to the correct evaluation of fouling mechanisms. The aim of the present work was to summarize the different aspects that influence the fouling investigations, based on simple models for the evaluation of the resistance to filtration due to the cake layer, through physical cleaning operations.