Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors

Esters are organic compounds widely represented in cellular structures and metabolism, originated by the condensation of organic acids and alcohols. Esterification reactions are also used by chemical industries for the production of synthetic plastic polymers. Polyester plastics are an increasing source of environmental pollution due to their intrinsic stability and limited recycling efforts. Bioremediation of polyesters based on the use of specific microbial enzymes is an interesting alternative to the current methods for the valorization of used plastics. Microbial esterases are promising catalysts for the biodegradation of polyesters that can be engineered to improve their biochemical properties. In this work, we analyzed the structure-activity relationships in microbial esterases, with special focus on the recently described plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. Our analysis, based on structure-alignment, molecular docking, coevolution of amino acids and surface electrostatics determined the specific characteristics of some polyester hydrolases that could be related with their efficiency in the degradation of aromatic polyesters, such as phthalates.
Automated Spore Measurements Using Microscopy, Image Analysis, and Peak Recognition of Near-Monodisperse Aerosols

Rapid detection of airborne fungal and bacterial spores would enable public agencies to respond quickly and appropriately to intentional releases of hazardous aerosols. Automated analysis of microscope images and automated detection of near-monodisperse peaks in aerosol size distribution data offer complementary approaches to traditional methods for the identification and counting of fungal and bacterial spores. First, spores of the fungus Scopulariopsis brevicaulis were aerosolized in a chamber and then collected with a slit impactor; later, digital microscope images were analyzed manually to determine spore cluster distributions. The images also were analyzed with ImageJ, a program that automatically outlined objects and measured Feret's diameter, area, perimeter, and circularity. These characteristics were used to identify spore clusters automatically using two data analysis methods. Second, a computer program was developed to discriminate near-monodisperse bioaerosol peaks from those for polydisperse ambient particulate matter (PM) and was successfully tested using simulated and real aerosol mixtures. The observed agreement between manual and automated spore counts and the ability to detect spore peaks suggest that it may be possible to develop a system to recognize intentional releases rapidly through examination of particle morphology and size distributions. The peak detection procedure is potentially the fastest technique when used with real-time instrument data, but assumes that intentional releases would consist of large numbers of uniformly sized particles in the respirable size range. Copyright 2012 American Association for Aerosol Research
Targeting the Autonomic Nervous System for Risk Stratification, Outcome Prediction and Neuromodulation in Ischemic Stroke

Ischemic stroke is a worldwide major cause of mortality and disability and has high costs in terms of health-related quality of life and expectancy as well as of social healthcare resources. In recent years, starting from the bidirectional relationship between autonomic nervous system (ANS) dysfunction and acute ischemic stroke (AIS), researchers have identified prognostic factors for risk stratification, prognosis of mid-term outcomes and response to recanalization therapy. In particular, the evaluation of the ANS function through the analysis of heart rate variability (HRV) appears to be a promising non-invasive and reliable tool for the management of patients with AIS. Furthermore, preclinical molecular studies on the pathophysiological mechanisms underlying the onset and progression of stroke damage have shown an extensive overlap with the activity of the vagus nerve. Evidence from the application of vagus nerve stimulation (VNS) on animal models of AIS and on patients with chronic ischemic stroke has highlighted the surprising therapeutic possibilities of neuromodulation. Preclinical molecular studies highlighted that the neuroprotective action of VNS results from anti-inflammatory, antioxidant and antiapoptotic mechanisms mediated by α7 nicotinic acetylcholine receptor. Given the proven safety of non-invasive VNS in the subacute phase, the ease of its use and its possible beneficial effect in hemorrhagic stroke as well, human studies with transcutaneous VNS should be less challenging than protocols that involve invasive VNS and could be the proof of concept that neuromodulation represents the very first therapeutic approach in the ultra-early management of stroke.
Assessment of anammox, microalgae and white-rot fungi-based processes for the treatment of textile wastewater

The treatability of seven wastewater samples generated by a textile digital printing industry was evaluated by employing 1) anammox-based processes for nitrogen removal 2) microalgae (Chlorella vulgaris) for nutrient uptake and biomass production 3) white-rot fungi (Pleurotus ostreatus and Phanerochaete chrysosporium) for decolorization and laccase activity. The biodegradative potential of each type of organism was determined in batch tests and correlated with the main characteristics of the textile wastewaters through statistical analyses. The maximum specific anammox activity ranged between 0.1 and 0.2 g N g VSS-1 d-1 depending on the sample of wastewater; the photosynthetic efficiency of the microalgae decreased up to 50% during the first 24 hours of contact with the textile wastewaters, but it improved from then on; Pleurotus ostreatus synthetized laccases and removed between 20–62% of the colour after 14 days, while the enzymatic activity of Phanerochaete chrysosporium was inhibited. Overall, the findings suggest that all microbes have great potential for the treatment and valorisation of textile wastewater after tailored adaptation phases. Yet, the depurative efficiency can be probably enhanced by combining the different processes in sequence.
A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ2 test p < 0.001, Fisher’s exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).
SIMULATION OF DRYING SUSPENSIONS IN SPOUT-FLUID BEDS OF INERT PARTICLES

In spouted and spout fluid bed dryers, the suspension is spread into the bed of inert particles, covering these particles with a thin layer. As the inert particles circulate, this suspension layer is dried and must become brittle enough to break off by the particle attrition. The powder produced is then carried out by air. Problems with the spout stability, particle agglomeration and powder deposits inside the column should be overcome by controlling the drying operation. The present work is aimed at modeling and simulating the drying of suspensions, such as organic and biological pastes, in conical spout-fluid beds of inert particles. A computer program has been developed combining the air flow and particle circulation models with the mass and energy balances and the drying kinetic equations in order to describe this drying process. The effect of cohesive forces is also incorporated to the fluid flow model. Simulation results are analyzed and compared with experimental data reported in the literature. Implication of these results in drying suspensions is also discussed.
Loss of childcare and classroom teaching during the Covid-19-related lockdown in spring 2020: A longitudinal study on consequences on leisure behavior and schoolwork at home

Aim In spring 2020, the first Covid-19-related lockdown included the closing of kindergartens and schools. Home schooling, the lack of social contacts with peers and the care of the children at home posed an enormous challenge for many families. Methods The present study investigated the leisure behavior of 285 one- to 10-year-old German children at two time points (t1 and t2) during the Covid-19-related lockdown in spring 2020. In the subsample of primary school children (n = 102), we also explored children’s attitudes towards schoolwork at home. Analyses focused on the change of behavior from t1 to t2, on differences in these changes depending on socio-economic status (SES), and on associations of behavior with SES, the number of children at home, and the frequency of receiving learning materials from school. Results While the frequency of playing outside increased significantly from t1 to t2, the frequency of handicrafts, playing board games, indoor sports, and motivation to do schoolwork decreased. The observed changes between t1 and t2 did not differ depending on SES. However, a lower SES was associated with higher media use, less outdoor activity, and (though only marginally significant) a reduced time doing schoolwork and a reduced ability to concentrate on schoolwork at t1. In households with more children, children played outside more often, but were read to less frequently and (though only marginally significant) watched movies and series less frequently. Children receiving learning materials from school on a regular basis spent significantly more time doing schoolwork at home than children receiving materials only irregularly. Conclusions A continuing loss of childcare in day-care facilities and schools entails the danger of declining education in the form of (inter)active indoor activities and schoolwork.
Predictors of patient satisfaction and perceived quality of healthcare: College healthcare providers and students’ communication

Abstract Background: Prior research indicates that healthcare provider-patient communication influences health outcomes such as patient satisfaction, compliance with diagnosis or treatment, and general health quality. However, little is known about this type of inquiry in the context of healthcare centers on college and university campuses. Aim: The objective of this study was to examine the influence of students’ perception of college healthcare providers’ affective and instrumental behaviors on student patient satisfaction and perceived quality of healthcare at a university health center. Methods: 349 participants who were college students took an online survey. Regression analyses were conducted. Results: Affective and instrumental behaviors were important communicative behaviors predicting student patient satisfaction and perceived quality of healthcare. However, directions of these predictions differed between student patient satisfaction and perceived quality of healthcare. Conclusion: Healthcare providers at the university health center are recognizing student patients as partners in the healthcare decision-making processes.
Prognostic and comparative performance of cardiovascular risk markers in patients with type 2 diabetes

Diagnostic tests including echocardiography, albuminuria, electrocardiogram (ECG), high‐sensitivity troponin I (hs‐TnI), and N‐terminal prohormone brain natriuretic peptide (NT‐proBNP) have been suggested as cardiovascular (CV) risk predictors in type 2 diabetes. We studied the separate and combined prognostic yield of these risk markers.
Second window ICG predicts gross-total resection and progression-free survival during brain metastasis surgery.

OBJECTIVE Metastases are the most common intracranial malignancies and complete resection can provide relief of neurological symptoms and reduce recurrence. The authors' prospective pilot study in 2017 demonstrated promising results for the application of high-dose, delayed imaging of indocyanine green (ICG), known as second window ICG (SWIG), in patients undergoing surgery for brain metastases. In this prospective cohort study, the authors evaluated intraoperative imaging and clinical outcomes of treatment using SWIG. METHODS Patients were prospectively enrolled in an approved study of high-dose, delayed ICG (SWIG) and received 5 mg/kg (2014-2018) or 2.5 mg/kg (2018-2019) ICG 24 hours preoperatively. Intraoperatively, near-infrared (NIR) imaging was performed using a dedicated NIR exoscope. NIR images were analyzed and the signal-to-background ratio (SBR) was calculated to quantify fluorescence. Residual fluorescence on the postresection NIR view was compared and correlated to the residual gadolinium enhancement on postoperative MRI. Patient survival and predictive factors were analyzed. RESULTS In total, 51 intracranial metastases were surgically treated in 47 patients in this cohort. All 51 metastatic tumors demonstrated strong NIR fluorescence (mean SBR 4.9). In tumors ≤ 10 mm from the cortical surface, SWIG with 5 mg/kg ICG produced enhanced transdural tumor visibility (91.3%) compared to 2.5 mg/kg (52.9%; p = 0.0047). Neoplastic margin detection using NIR fluorescence compared to white light improved sensitivity, albeit lowered specificity; however, increasing the SBR cutoff for positive fluorescence significantly improved specificity without sacrificing sensitivity, increasing the overall accuracy from 57.5% to 72.5%. A lack of residual NIR fluorescence after resection was closely correlated with a lack of residual enhancement on postoperative MRI (p = 0.007). Among the 16 patients in whom tumor recurred at the site of surgery, postoperative MRI successfully predicted 8 cases, whereas the postresection NIR view predicted 12 cases. Progression-free survival rate at 12 months was greater for patients without residual NIR fluorescence (38%) than for those without residual enhancement on postoperative MRI (29%). CONCLUSIONS The current study demonstrates the clinical benefits of the SWIG technique in surgery for patients with brain metastases. Specifically, this technique allows for dose-dependent, transdural localization of neoplasms and improved sensitivity in neoplastic margin detection. Postresection residual fluorescence can be a powerful tool to evaluate extent of resection in conjunction with MRI, and it may guide decisions on brain metastasis management.
Using deep neural networks to evaluate object vision tasks in rats

In the last two decades rodents have been on the rise as a dominant model for visual neuroscience. This is particularly true for earlier levels of information processing, but a number of studies have suggested that also higher levels of processing such as invariant object recognition occur in rodents. Here we provide a quantitative and comprehensive assessment of this claim by comparing a wide range of rodent behavioral and neural data with convolutional deep neural networks. These networks have been shown to capture hallmark properties of information processing in primates through a succession of convolutional and fully connected layers. We find that performance on rodent object vision tasks can be captured using low to mid-level convolutional layers only, without any convincing evidence for the need of higher layers known to simulate complex object recognition in primates. Our approach also reveals surprising insights on assumptions made before, for example, that the best performing animals would be the ones using the most abstract representations–which we show to likely be incorrect. Our findings suggest a road ahead for further studies aiming at quantifying and establishing the richness of representations underlying information processing in animal models at large.
Association Between Cardiovascular Risk Factors and Cognitive Impairment in People With Schizophrenia: A Systematic Review and Meta-analysis.

Importance Schizophrenia is associated with cognitive dysfunction and cardiovascular risk factors, including metabolic syndrome (MetS) and its constituent criteria. Cognitive dysfunction and cardiovascular risk factors can worsen cognition in the general population and may contribute to cognitive impairment in schizophrenia. Objective To study the association between cognitive dysfunction and cardiovascular risk factors and cognitive impairment in individuals with schizophrenia. Data Sources A search was conducted of Embase, Scopus, MEDLINE, PubMed, and Cochrane databases from inception to February 25, 2020, using terms that included synonyms of schizophrenia AND metabolic adversities AND cognitive function. Conference proceedings, clinical trial registries, and reference lists of relevant publications were also searched. Study Selection Studies were included that (1) examined cognitive functioning in patients with schizophrenia or schizoaffective disorder; (2) investigated the association of cardiovascular disease risk factors, including MetS, diabetes, obesity, overweight, obesity or overweight, hypertension, dyslipidemia, and insulin resistance with outcomes; and (3) compared cognitive performance of patients with schizophrenia/schizoaffective disorder between those with vs without cardiovascular disease risk factors. Data Extraction and Synthesis Extraction of data was conducted by 2 to 3 independent reviewers per article. Data were meta-analyzed using a random-effects model. Main Outcomes and Measures The primary outcome was global cognition, defined as a test score using clinically validated measures of overall cognitive functioning. Results Twenty-seven studies involving 10 174 individuals with schizophrenia were included. Significantly greater global cognitive deficits were present in patients with schizophrenia who had MetS (13 studies; n = 2800; effect size [ES] = 0.31; 95% CI, 0.13-0.50; P = .001), diabetes (8 studies; n = 2976; ES = 0.32; 95% CI, 0.23-0.42; P < .001), or hypertension (5 studies; n = 1899; ES = 0.21; 95% CI, 0.11-0.31; P < .001); nonsignificantly greater deficits were present in patients with obesity (8 studies; n = 2779; P = .20), overweight (8 studies; n = 2825; P = .41), and insulin resistance (1 study; n = 193; P = .18). Worse performance in specific cognitive domains was associated with cognitive dysfunction and cardiovascular risk factors regarding 5 domains in patients with diabetes (ES range, 0.23 [95% CI, 0.12-0.33] to 0.40 [95% CI, 0.20-0.61]) and 4 domains with MetS (ES range, 0.15 [95% CI, 0.03-0.28] to 0.40 [95% CI, 0.20-0.61]) and hypertension (ES range, 0.15 [95% CI, 0.04-0.26] to 0.27 [95% CI, 0.15-0.39]). Conclusions and Relevance In this systematic review and meta-analysis, MetS, diabetes, and hypertension were significantly associated with global cognitive impairment in people with schizophrenia.
Epiretinal membrane: A review

The prevalence of epiretinal membrane (ERM) is 7% to 11.8%, with increasing age being the most important risk factor. Although most ERM is idiopathic, common secondary causes include cataract surgery, retinal vascular disease, uveitis and retinal tears. The myofibroblastic pre‐retinal cells are thought to transdifferentiate from glial and retinal pigment epithelial cells that reach the retinal surface via defects in the internal limiting membrane (ILM) or from the vitreous cavity. Grading schemes have evolved from clinical signs to ocular coherence tomography (OCT) based classification with associated features such as the cotton ball sign. Features predictive of better prognosis include absence of ectopic inner foveal layers, cystoid macular oedema, acquired vitelliform lesions and ellipsoid and cone outer segment termination defects. OCT‐angiography shows reduced size of the foveal avascular zone. Vitrectomy with membrane peeling remains the mainstay of treatment for symptomatic ERMs. Additional ILM peeling reduces recurrence but is associated with anatomical changes including inner retinal dimpling.
Effects of 4-phenylbutyric acid on the development of diabetic retinopathy in diabetic rats: regulation of endoplasmic reticulum stress-oxidative activation

Abstract There are good evidences suggesting that endoplasmic reticulum (ER) stress can be one of the contributing factors in the development of diabetic retinopathy. The present study was designed to investigate the effect of chemical chaperone 4-phenylbutyric acid (4-PBA) in alleviating the ER stress, and diabetic retinopathy in type 2 diabetic rats. Treatment of diabetic rats with 4-PBA, increased the antioxidant capacity, reduced the levels of lipid peroxidation, organised the state of apoptosis and regulated the ER stress – oxidative activation in retinal tissue. Also there was an improvement in the histological picture of retinal specimens compared to untreated diabetic rats. It was concluded that 4-PBA is a promising therapeutic agent for ER stress diseases such as diabetic retinopathy.
SARS-CoV-2 Infection and Disease Modelling Using Stem Cell Technology and Organoids

In this Review, we briefly describe the basic virology and pathogenesis of SARS-CoV-2, highlighting how stem cell technology and organoids can contribute to the understanding of SARS-CoV-2 cell tropisms and the mechanism of disease in the human host, supporting and clarifying findings from clinical studies in infected individuals. We summarize here the results of studies, which used these technologies to investigate SARS-CoV-2 pathogenesis in different organs. Studies with in vitro models of lung epithelia showed that alveolar epithelial type II cells, but not differentiated lung alveolar epithelial type I cells, are key targets of SARS-CoV-2, which triggers cell apoptosis and inflammation, while impairing surfactant production. Experiments with human small intestinal organoids and colonic organoids showed that the gastrointestinal tract is another relevant target for SARS-CoV-2. The virus can infect and replicate in enterocytes and cholangiocytes, inducing cell damage and inflammation. Direct viral damage was also demonstrated in in vitro models of human cardiomyocytes and choroid plexus epithelial cells. At variance, endothelial cells and neurons are poorly susceptible to viral infection, thus supporting the hypothesis that neurological symptoms and vascular damage result from the indirect effects of systemic inflammatory and immunological hyper-responses to SARS-CoV-2 infection.