Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Simple Summary The aim of this work is to identify CNVs and perform a CNV-based population genetics analysis in five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs and 365 CNV regions (CNVRs). The different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups. Gene enrichment was described for the 37 CNVRs selected considering the top 10%. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. CNVs represent valuable molecular resources to provide useful information for separating the population. Abstract Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
Definition of an Inflammatory Biomarker Signature in Plasma-Derived Extracellular Vesicles of Glioblastoma Patients

Glioblastoma (GB) is an aggressive type of tumour for which therapeutic options and biomarkers are limited. GB diagnosis mostly relies on symptomatic presentation of the tumour and, in turn, brain imaging and invasive biopsy that can delay its diagnosis. Description of easily accessible and effective biomarkers present in biofluids would thus prove invaluable in GB diagnosis. Extracellular vesicles (EVs) derived from both GB and stromal cells are essential to intercellular crosstalk in the tumour bulk, and circulating EVs have been described as a potential reservoir of GB biomarkers. Therefore, EV-based liquid biopsies have been suggested as a promising tool for GB diagnosis and follow up. To identify GB specific proteins, sEVs were isolated from plasma samples of GB patients as well as healthy volunteers using differential ultracentrifugation, and their content was characterised through mass spectrometry. Our data indicate the presence of an inflammatory biomarker signature comprising members of the complement and regulators of inflammation and coagulation including VWF, FCGBP, C3, PROS1, and SERPINA1. Overall, this study is a step forward in the development of a non-invasive liquid biopsy approach for the identification of valuable biomarkers that could significantly improve GB diagnosis and, consequently, patients’ prognosis and quality of life.
Reinfection with SARS-CoV-2 among previously infected healthcare personnel and first responders

Abstract Background SARS-CoV-2 virus testing among first responders and healthcare personnel who participated in a May-August 2020 serosurvey which assessed spike protein antibodies (S1 region) provided an opportunity to assess reinfection. Methods Serology survey data were merged with virus testing results from Rhode Island (March 1, 2020-February 17, 2021) and New York City (March 10-December 14, 2020). Participants with a positive virus test ≥14 days before their serology test were included. Reinfection was defined as a second positive SARS-CoV-2 test result ≥90 days after the first positive test. The association between serostatus and reinfection was assessed with a proportional hazards model adjusting for demographics, exposures, and virus testing frequency. Results Among 1,572 previously infected persons, 40 (2.5%) were reinfected. Reinfection differed by serostatus: 8.4% among seronegative versus 1.9% among seropositive participants (p<0.0001). Most reinfections occurred among Rhode Island nursing home and corrections (RINHC) personnel (n=30) who were most frequently tested (mean 30.3 tests versus 4.6 for other Rhode Island and 2.3 for New York City participants). The adjusted hazard ratio (aHR) for reinfection in seropositive versus seronegative persons was 0.41 (95% CI 0.20, 0.81). Exposure to a household member with COVID-19 before the serosurvey was also protective (aHR 0.34, 95% CI 0.13, 0.89). Conclusions Reinfections were uncommon among previously infected persons over a 9-month period that preceded widespread variant circulation. Seropositivity decreased reinfection risk. Lower reinfection risk associated with exposure to a household member with COVID-19 before the serosurvey may reflect subsequently reduced household transmission among members of previously infected households.
Creating a Natural Vascular Scaffold by Photochemical Treatment of the Extracellular Matrix for Vascular Applications

The development of bioscaffolds for cardiovascular medical applications, such as peripheral artery disease (PAD), remains to be a challenge for tissue engineering. PAD is an increasingly common and serious cardiovascular illness characterized by progressive atherosclerotic stenosis, resulting in decreased blood perfusion to the lower extremities. Percutaneous transluminal angioplasty and stent placement are routinely performed on these patients with suboptimal outcomes. Natural Vascular Scaffolding (NVS) is a novel treatment in the development for PAD, which offers an alternative to stenting by building on the natural structural constituents in the extracellular matrix (ECM) of the blood vessel wall. During NVS treatment, blood vessels are exposed to a photoactivatable small molecule (10-8-10 Dimer) delivered locally to the vessel wall via an angioplasty balloon. When activated with 450 nm wavelength light, this therapy induces the formation of covalent protein–protein crosslinks of the ECM proteins by a photochemical mechanism, creating a natural scaffold. This therapy has the potential to reduce the need for stent placement by maintaining a larger diameter post-angioplasty and minimizing elastic recoil. Experiments were conducted to elucidate the mechanism of action of NVS, including the molecular mechanism of light activation and the impact of NVS on the ECM.
Reuse of Wasted Bread as Soil Amendment: Bioprocessing, Effects on Alkaline Soil and Escarole (Cichorium endivia) Production

In an era characterized by land degradation, climate change, and a growing population, ensuring high-yield productions with limited resources is of utmost importance. In this context, the use of novel soil amendments and the exploitation of plant growth-promoting microorganisms potential are considered promising tools for developing a more sustainable primary production. This study aimed at investigating the potential of bread, which represents a large portion of the global food waste, to be used as an organic soil amendment. A bioprocessed wasted bread, obtained by an enzymatic treatment coupled with fermentation, together with unprocessed wasted bread were used as amendments in a pot trial. An integrated analytical plan aimed at assessing (i) the modification of the physicochemical properties of a typical Mediterranean alkaline agricultural soil, and (ii) the plant growth-promoting effect on escarole (Cichorium endivia var. Cuartana), used as indicator crop, was carried out. Compared to the unamended soils, the use of biomasses raised the soil organic carbon content (up to 37%) and total nitrogen content (up to 40%). Moreover, the lower pH and the higher organic acid content, especially in bioprocessed wasted bread, determined a major availability of Mn, Fe, and Cu in amended soils. The escaroles from pots amended with raw and bioprocessed bread had a number of leaves, 1.7- and 1.4-fold higher than plants cultivated on unamended pots, respectively, showing no apparent phytotoxicity and thus confirming the possible re-utilization of such residual biomasses as agriculture amendments.
Is the future near or far depending on the verb tense markers used? An experimental investigation into the effects of the grammaticalization of the future

Psycholinguistic approaches that study the effects of language on mental representations have ignored a potential role of the grammaticalization of the future (i.e., how the future manifests linguistically). We argue that the grammaticalization of the future may be an important aspect, as thinking about the future is omnipresent in our everyday life. The aim of this study was to experimentally manipulate the degree of future time references (i.e., present and future verb tense and temporal adverbials) to address their impact on the perceived location of future events. Across four experiments, two in French and two in German, no effect was found, irrespective of our verb and adverbial manipulations, and contrary to our hypotheses. Bayes factors confirmed that our null effects were not due to a lack of power. We present one of the first empirical accounts investigating the role of the grammaticalization of the future on effects of mental representations. We discuss possible reasons for these null results and illustrate further avenues for future research.
Assessment of Sleep Quality and Quality of Life in Hypertensive Subjects at a Tertiary Care Hospital in Uttarakhand, India

Background: Hypertension is a leading risk factor for cardiovascular diseases with prevalence of 33% in urban and 25% in rural population in India. Studies have suggested that hypertension significantly affects the sleep quality and quality of life of subjects. Therefore, this study aimed to establish a correlation between sleep quality, quality of life, and hypertension in Uttarakhand. Methods: This observational cross-sectional study was carried out on hypertensive subjects at a tertiary care hospital in Uttarakhand following ethics approval. After taking consent from participants, blood pressure and anthropometric measurements were recorded. Then, their sleep quality and quality of life was assessed using Pittsburgh sleep quality index (PSQI) and WHO-QOL BREF questionnaire respectively. Statistical analysis was then carried out to correlate these parameters. Results: 168 participants were recruited for this study, with 43.5% males and 56.5% females. It was found that 77.4% of these subjects were having poor sleep quality with the mean global PSQI score as 7.90 ± 3.713. These subjects assessed their Quality of life to be worst in physical domain (12.68 ± 3.13), followed by psychological, social relationship domain and environment domain. A significant association was found between sleep quality and different stages of hypertension (P value = 0.039) but quality of life and stages of hypertension have no significant association (P value > 0.05). Conclusions: Sleep quality, quality of life and blood pressure are correlated. So, clinicians should also focus on improving their patient's sleep quality and quality of life besides pharmacological treatment.
In Vivo Confocal Microscopy Evaluation in Patients with Keratoconus

Keratoconus is the most common primary corneal ectasia characterized by progressive focal thinning. Patients experience increased irregular astigmatism, decreased visual acuity and corneal sensitivity. Corneal collagen crosslinking (CXL), a minimally invasive procedure, is effective in halting disease progression. Historically, keratoconus research was confined to ex vivo settings. In vivo confocal microscopy (IVCM) has been used to examine the corneal microstructure clinically. In this review, we discuss keratoconus cellular changes evaluated by IVCM before and after CXL. Cellular changes before CXL include decreased keratocyte and nerve densities, disorganized subbasal nerves with thickening, increased nerve tortuosity and shortened nerve fibre length. Repopulation of keratocytes occurs up to 1 year post procedure. IVCM also correlates corneal nerve status to functional corneal sensitivity. Immediately after CXL, there is reduced nerve density and keratocyte absence due to mechanical removal of the epithelium and CXL effect. Nerve regeneration begins after 1 month, with nerve fibre densities recovering to pre-operative levels between 6 months to 1 year and remains stable up to 5 years. Nerves remain tortuous and nerve densities are reduced. Corneal sensitivity is reduced immediately postoperatively but recovers with nerve regeneration. Our article provides comprehensive review on the use of IVCM imaging in keratoconus patients.
Nursing Students’ Knowledge, Awareness, and Experiences of Emergency Contraception Pills’ Use

The emergency contraception pill (ECP) is a non-prescribed medication in Spain. However, there is not enough evidence of its use among young people to define sex education contents. The aims of this research were to describe the experiences of the use of the ECP in university students and analyze their knowledge, attitude, and awareness regarding the ECP. The cross-sectional, analytic study was conducted with nursing degree students at the University of Seville. A total of 478 students answered the questionnaire. All of the students (100%) had heard about the ECP and had a positive attitude towards this contraceptive. A total of 25.7% had used the ECP, mainly because a condom had failed or because they did not use any contraceptive at all. Deficiencies in knowledge are related with the ECPs’ mechanism of action, efficacy after repeated use, and the type of ECP available. Female students who used no method at all or withdrawal, and who were over 20 years old, used ECP to a greater extent (p < 0.005). Further education initiatives focused on the use of the ECP, its efficacy, and typology are needed, particularly among future health professionals who will later educate other young people.
Multiphoton Bleaching of Red Fluorescent Proteins and the Ways to Reduce It

Red fluorescent proteins and biosensors built upon them are potentially beneficial for two-photon laser microscopy (TPLM) because they can image deeper layers of tissue, compared to green fluorescent proteins. However, some publications report on their very fast photobleaching, especially upon excitation at 750–800 nm. Here we study the multiphoton bleaching properties of mCherry, mPlum, tdTomato, and jREX-GECO1, measuring power dependences of photobleaching rates K at different excitation wavelengths across the whole two-photon absorption spectrum. Although all these proteins contain the chromophore with the same chemical structure, the mechanisms of their multiphoton bleaching are different. The number of photons required to initiate a photochemical reaction varies, depending on wavelength and power, from 2 (all four proteins) to 3 (jREX-GECO1) to 4 (mCherry, mPlum, tdTomato), and even up to 8 (tdTomato). We found that at sufficiently low excitation power P, the rate K often follows a quadratic power dependence, that turns into higher order dependence (K~Pα with α > 2) when the power surpasses a particular threshold P*. An optimum intensity for TPLM is close to the P*, because it provides the highest signal-to-background ratio and any further reduction of laser intensity would not improve the fluorescence/bleaching rate ratio. Additionally, one should avoid using wavelengths shorter than a particular threshold to avoid fast bleaching due to multiphoton ionization.
Food Insecurity and Associated Factors in Brazilian Undergraduates during the COVID-19 Pandemic

Undergraduates may face challenges to assure food security, related to economic and mental distress, especially during the COVID-19 pandemic. This study aimed to assess food insecurity and its associated factors in undergraduates during the COVID-19 pandemic. An online cross-sectional study was conducted from August 2020 to February 2021 with 4775 undergraduates from all Brazilian regions. The questionnaire contained socio-economic variables, the validated Brazilian food insecurity scale, and the ESQUADA scale to assess diet quality. The median age of the students was 22.0 years, and 48.0% reported income decreasing with the pandemic. Food insecurity was present in 38.6% of the students, 4.5% with severe food insecurity and 7.7% moderate. Logistic regressions showed students with brown and black skin color/race presented the highest OR for food insecurity; both income and weight increase or reduction during the pandemic was also associated with a higher OR for food insecurity, and better diet quality was associated with decreased OR for food insecurity. Our study showed a considerable presence of food insecurity in undergraduates. Policy for this population must be directed to the most vulnerable: those with brown and black skin color/race, who changed income during the pandemic, and those presented with difficulties maintaining weight and with poor diet quality.
Two Decades of Active Surveillance for Prostate Cancer in a Single-Center Cohort: Favorable Outcomes after Transurethral Resection of the Prostate

Simple Summary Prostate cancer is the most commonly diagnosed cancer in men. Active surveillance—repeated measurements of prostate specific antigen, digital rectal examination, and prostate biopsies—is an alternative treatment option to active therapy, such as radical prostatectomy or radiotherapy, for patients with low grade prostate cancer. It aims to reduce overtreatment and negative side effects of active treatment. However, long-term outcome data is rare. As we prospectively collected data since the beginning of active surveillance in our clinic in 1999, our study provides insights into long-term outcomes after two decades of active surveillance. Abstract Objective: To report the outcomes of active surveillance (AS) for low-risk prostate cancer (PCa) in a single-center cohort. Patients and Methods: This is a prospective, single-center, observational study. The cohort included all patients who underwent AS for PCa between December 1999 and December 2020 at our institution. Follow-up appointments (FU) ended in February 2021. Results: A total of 413 men were enrolled in the study, and 391 had at least one FU. Of those who followed up, 267 had PCa diagnosed by transrectal ultrasound (TRUS)-guided biopsy (T1c: 68.3%), while 124 were diagnosed after transurethral resection of the prostate (TURP) (T1a/b: 31.7%). Median FU was 46 months (IQR 25–90). Cancer specific survival was 99.7% and overall survival was 92.3%. Median reclassification time was 11.2 years. After 20 years, 25% of patients were reclassified within 4.58 years, 6.6% opted to switch to watchful waiting, 4.1% died, 17.4% were lost to FU, and 46.8% remained on AS. Those diagnosed by TRUS had a significantly higher reclassification rate than those diagnosed by TURP (p < 0.0001). Men diagnosed by targeted MRI/TRUS fusion biopsy tended to have a higher reclassification probability than those diagnosed by conventional template biopsies (p = 0.083). Conclusions: Our single-center cohort spanning over two decades revealed that AS remains a safe option for low-risk PCa even in the long term. Approximately half of AS enrollees will eventually require definitive treatment due to disease progression. Men with incidental prostate cancer were significantly less likely to have disease progression.
Deep Ensemble Learning-Based Models for Diagnosis of COVID-19 from Chest CT Images

Novel coronavirus (COVID-19) has been endangering human health and life since 2019. The timely quarantine, diagnosis, and treatment of infected people are the most necessary and important work. The most widely used method of detecting COVID-19 is real-time polymerase chain reaction (RT-PCR). Along with RT-PCR, computed tomography (CT) has become a vital technique in diagnosing and managing COVID-19 patients. COVID-19 reveals a number of radiological signatures that can be easily recognized through chest CT. These signatures must be analyzed by radiologists. It is, however, an error-prone and time-consuming process. Deep Learning-based methods can be used to perform automatic chest CT analysis, which may shorten the analysis time. The aim of this study is to design a robust and rapid medical recognition system to identify positive cases in chest CT images using three Ensemble Learning-based models. There are several techniques in Deep Learning for developing a detection system. In this paper, we employed Transfer Learning. With this technique, we can apply the knowledge obtained from a pre-trained Convolutional Neural Network (CNN) to a different but related task. In order to ensure the robustness of the proposed system for identifying positive cases in chest CT images, we used two Ensemble Learning methods namely Stacking and Weighted Average Ensemble (WAE) to combine the performances of three fine-tuned Base-Learners (VGG19, ResNet50, and DenseNet201). For Stacking, we explored 2-Levels and 3-Levels Stacking. The three generated Ensemble Learning-based models were trained on two chest CT datasets. A variety of common evaluation measures (accuracy, recall, precision, and F1-score) are used to perform a comparative analysis of each method. The experimental results show that the WAE method provides the most reliable performance, achieving a high recall value which is a desirable outcome in medical applications as it poses a greater risk if a true infected patient is not identified.
The influence of mitral valve pathology on the concomitant tricuspid valve repair

The influence of the etiology of mitral valve (MV) lesion on outcomes of concomitant repair for functional tricuspid regurgitation (TR) is not well studied. Our objectives were to compare long‐term survival and TR recurrence after tricuspid valve (TV) repair concomitant with surgery for rheumatic versus degenerative MV disease.