Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-B DNA-Forming Motifs Promote Mfd-Dependent Stationary-Phase Mutagenesis in Bacillus subtilis

Transcription-induced mutagenic mechanisms limit genetic changes to times when expression happens and to coding DNA. It has been hypothesized that intrinsic sequences that have the potential to form alternate DNA structures, such as non-B DNA structures, influence these mechanisms. Non-B DNA structures are promoted by transcription and induce genome instability in eukaryotic cells, but their impact in bacterial genomes is less known. Here, we investigated if G4 DNA- and hairpin-forming motifs influence stationary-phase mutagenesis in Bacillus subtilis. We developed a system to measure the influence of non-B DNA on B. subtilis stationary-phase mutagenesis by deleting the wild-type argF at its chromosomal position and introducing IPTG-inducible argF alleles differing in their ability to form hairpin and G4 DNA structures into an ectopic locus. Using this system, we found that sequences predicted to form non-B DNA structures promoted mutagenesis in B. subtilis stationary-phase cells; such a response did not occur in growing conditions. We also found that the transcription-coupled repair factor Mfd promoted mutagenesis at these predicted structures. In summary, we showed that non-B DNA-forming motifs promote genetic instability, particularly in coding regions in stressed cells; therefore, non-B DNA structures may have a spatial and temporal mutagenic effect in bacteria. This study provides insights into mechanisms that prevent or promote mutagenesis and advances our understanding of processes underlying bacterial evolution.
The Effects of High-Protein Diet and Resistance Training on Glucose Control and Inflammatory Profile of Visceral Adipose Tissue in Rats

High-protein diets (HPDs) are widely accepted as a way to stimulate muscle protein synthesis when combined with resistance training (RT). However, the effects of HPDs on adipose tissue plasticity and local inflammation are yet to be determined. This study investigated the impact of HPDs on glucose control, adipocyte size, and epididymal adipose inflammatory biomarkers in resistance-trained rats. Eighteen Wistar rats were randomly assigned to four groups: normal-protein (NPD; 17% protein total dietary intake) and HPD (26.1% protein) without RT and NPD and HPD with RT. Trained groups received RT for 12 weeks with weights secured to their tails. Glucose and insulin tolerance tests, adipocyte size, and an array of cytokines were determined. While HPD without RT induced glucose intolerance, enlarged adipocytes, and increased TNF-α, MCP-1, and IL1-β levels in epididymal adipose tissue (p < 0.05), RT diminished these deleterious effects, with the HPD + RT group displaying improved blood glucose control without inflammatory cytokine increases in epididymal adipose tissue (p < 0.05). Furthermore, RT increased glutathione expression independent of diet (p < 0.05). RT may offer protection against adipocyte hypertrophy, pro-inflammatory states, and glucose intolerance during HPDs. The results highlight the potential protective effects of RT to mitigate the maladaptive effects of HPDs.
Neutrophil-to-Lymphocyte Ratio as an Independent Predictor of In-Hospital Mortality in Patients with Acute Intracerebral Hemorrhage

Background and Objectives: Neutrophil-to-lymphocyte ratio (NLR), a very low cost, widely available marker of systemic inflammation, has been proposed as a potential predictor of short-term outcome in patients with intracerebral hemorrhage (ICH). Methods: Patients with ICH admitted to the Neurology Department during a two-year period were screened for inclusion. Based on eligibility criteria, 201 patients were included in the present analysis. Clinical, imaging, and laboratory characteristics were collected in a prespecified manner. Logistic regression models and receiver operating characteristics (ROC) curves were used to assess the performance of NLR assessed at admission (admission NLR) and 72 h later (three-day NLR) in predicting in-hospital death. Results: The median age of the study population was 70 years (IQR: 61–79), median admission NIHSS was 16 (IQR: 6–24), and median hematoma volume was 13.7 mL (IQR: 4.6–35.2 mL). Ninety patients (44.8%) died during hospitalization, and for 35 patients (17.4%) death occurred during the first three days. Several common predictors were significantly associated with in-hospital mortality in univariate analysis, including NLR assessed at admission (OR: 1.11; 95% CI: 1.04–1.18; p = 0.002). However, in multivariate analysis admission, NLR was not an independent predictor of in-hospital mortality (OR: 1.04; 95% CI: 0.9–1.1; p = 0.3). The subgroup analysis of 112 patients who survived the first 72 h of hospitalization showed that three-day NLR (OR: 1.2; 95% CI: 1.09–1.4; p < 0.001) and age (OR: 1.05; 95% CI: 1.02–1.08; p = 0.02) were the only independent predictors of in-hospital mortality. ROC curve analysis yielded an optimal cut-off value of three-day NLR for the prediction of in-hospital mortality of ≥6.3 (AUC = 0.819; 95% CI: 0.735–0.885; p < 0.0001) and Kaplan–Meier analysis proved that ICH patients with three-day NLR ≥6.3 had significantly higher odds of in-hospital death (HR: 7.37; 95% CI: 3.62–15; log-rank test; p < 0.0001). Conclusion: NLR assessed 72 h after admission is an independent predictor of in-hospital mortality in ICH patients and could be widely used in clinical practice to identify the patients at high risk of in-hospital death. Further studies to confirm this finding are needed.
Association of Family Nutrition and Physical Activity with Preschooler’s Working Memory: A Cross-Sectional Study among Mexican Children

Healthy eating and active lifestyles are associated with children’s healthy weight and cognitive development. This study examines whether family behaviors relevant for nutrition and activity levels are associated with children’s working memory, independent of their weight status. A convenience sample of child–caregiver dyads (n = 85 dyads) were recruited from a public preschool serving a low-income community in central Mexico. Caregivers reported the frequency of ten family behaviors using the Family Nutrition and Physical Activity screening tool. Children completed a test of their ability to recall four words after a 60-s distraction task, an assessment of working memory. Multiple linear regression models were used to test the association of children’s working memory with each family behavior, adjusting for children’s sex, age, mother’s age and education, and subjective social status and then also adjusting for children’s age- and sex-specific body mass index percentile (BMI-P) and covariates. Higher frequency of breakfast intake was significantly associated with working memory (β = 0.57, p = 0.013). This association was independent of children’s BMI-P. Other family behaviors (frequent family mealtimes, limiting screen time, and others) were not significantly associated with children’s working memory. Frequent breakfast intake could benefit young children’s working memory, regardless of their weight status. This association merits further investigation.
Simulation and Modeling of Novel Electronic Device Architectures with NESS (Nano-Electronic Simulation Software): A Modular Nano TCAD Simulation Framework

The modeling of nano-electronic devices is a cost-effective approach for optimizing the semiconductor device performance and for guiding the fabrication technology. In this paper, we present the capabilities of the new flexible multi-scale nano TCAD simulation software called Nano-Electronic Simulation Software (NESS). NESS is designed to study the charge transport in contemporary and novel ultra-scaled semiconductor devices. In order to simulate the charge transport in such ultra-scaled devices with complex architectures and design, we have developed numerous simulation modules based on various simulation approaches. Currently, NESS contains a drift-diffusion, Kubo–Greenwood, and non-equilibrium Green’s function (NEGF) modules. All modules are numerical solvers which are implemented in the C++ programming language, and all of them are linked and solved self-consistently with the Poisson equation. Here, we have deployed some of those modules to showcase the capabilities of NESS to simulate advanced nano-scale semiconductor devices. The devices simulated in this paper are chosen to represent the current state-of-the-art and future technologies where quantum mechanical effects play an important role. Our examples include ultra-scaled nanowire transistors, tunnel transistors, resonant tunneling diodes, and negative capacitance transistors. Our results show that NESS is a robust, fast, and reliable simulation platform which can accurately predict and describe the underlying physics in novel ultra-scaled electronic devices.
Dynamic Risk Measures for Processes via Backward Stochastic Differential Equations Associated with Lévy Processes

In this paper, we study the dynamic risk measures for processes induced by backward stochastic differential equations driven by Teugel’s martingales associated with Lévy processes (BSDELs). The representation theorem for generators of BSDELs is provided. Furthermore, the time consistency of the coherent and convex dynamic risk measures for processes is characterized by means of the generators of BSDELs. Moreover, the coherency and convexity of dynamic risk measures for processes are characterized by the generators of BSDELs. Finally, we provide two numerical examples to illustrate the proposed dynamic risk measures.
Effects of Different Non-Cage Housing Systems on the Production Performance, Serum Parameters and Intestinal Morphology of Laying Hens

Simple Summary With the increased interest in animal welfare, poultry housing systems have been a concern for the last decade, and conventional cages have been replaced by non-cage systems or enriched cages. However, the environmental conditions in non-cage housing systems and their association with hens’ production performance and health have not been studied extensively. Therefore, the present study compared the indoor environmental microbial content in two different non-caged systems, namely, a plastic-net housing system and floor-litter housing system, and investigated its effects on the production performance, serum parameters and intestinal morphology of hens during the peak laying period. The results indicated that the NRS resulted in better indoor environmental air quality and ground hygiene than the LRS and enhanced the production performance, antioxidant capacity and intestinal health of hens, represented by positive changes in the laying rate, serum parameters and intestinal morphology. Abstract This study investigated the effects of plastic-net housing system (NRS) and floor-litter housing system (LRS) on the production performance, serum parameters and intestinal morphology of Shendan laying hens. A total of 1200 30-week-old hens were randomly allocated to the NRS and LRS groups, each of which included five replicates with 120 chickens in each replicate. The experiment was conducted from 32 to 40 weeks of age. Indoor airborne parameters were measured every 2 weeks, and indoor ground contamination was measured monthly. The laying rate and mortality of hens were recorded daily, and egg quality traits and serum parameters were measured every 2 weeks. At 40 weeks of age, four birds per replicate from each experimental group were selected for intestinal morphological observation. The results showed that the airborne bacteria number in the LRS was significantly higher than that in the NRS (p < 0.05) for most of the experimental period (except at 32 and 38 weeks of age), and the bacterial numbers on the surfaces of the floor and floor eggs in the LRS were approximately 10 times higher than those in the NRS (p < 0.05). Compared with the LRS, the NRS improved the laying rate (p < 0.05), reduced serum malondialdehyde (MDA) (p < 0.05) and corticosterone (CORT) concentrations and increased serum glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) activities, indicating favourable effects on antioxidative status. The NRS was significantly associated with an increased villus height (VH), villus height to crypt depth ratio (VCR) in the small intestine (p < 0.05) and increased VCR in the caecum (p < 0.05). Overall, the lower rate of bacterial contamination in the NRS than in the LRS indicated better environmental hygiene. The NRS enhanced the laying performance and antioxidant capacity of hens and was superior to the LRS in improving intestinal health. The current findings support the advantages of the NRS for the health and welfare of Shendan chickens during the peak laying period.
Adjuvant Transarterial Chemoembolization Following Curative-Intent Hepatectomy Versus Hepatectomy Alone for Hepatocellular Carcinoma: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Simple Summary The role of postoperative transarterial chemoembolization (TACE) after liver resection for hepatocellular carcinoma (HCC) remains unclear. We performed a systematic review of the literature and compared the survival outcomes of TACE vs. no TACE after liver resection for HCC. While the existing evidence suggests a benefit of adjuvant TACE, published trials to date are at significant risk of bias and limited to Eastern Asian patients. High-quality randomized clinical trials are needed to confirm the oncologic benefits of adjuvant TACE. Abstract The role of adjuvant transarterial chemoembolization (TACE) for patients with resectable hepatocellular carcinoma (HCC) undergoing hepatectomy is currently unclear. We performed a systematic review of the literature using the MEDLINE, Embase, and Cochrane Library databases. Random-effects meta-analysis was carried out to compare the overall survival (OS) and recurrence-free survival (RFS) of patients with resectable HCC undergoing hepatectomy followed by adjuvant TACE vs. hepatectomy alone in randomized controlled trials (RCTs). The risk of bias was assessed using the Risk of Bias 2.0 tool. Meta-regression analyses were performed to explore the effect of hepatitis B viral status, microvascular invasion, type of resection (anatomic vs. parenchymal-sparing), and tumor size on the outcomes. Ten eligible RCTs, reporting on 1216 patients in total, were identified. The combination of hepatectomy and adjuvant TACE was associated with superior OS (hazard ratio (HR): 0.66, 95% confidence interval (CI): 0.52 to 0.85; p < 0.001) and RFS (HR: 0.70, 95% CI: 0.56 to 0.88; p < 0.001) compared to hepatectomy alone. There were significant concerns regarding the risk of bias in most of the included studies. Overall, adjuvant TACE may be associated with an oncologic benefit in select HCC patients. However, the applicability of these findings may be limited to Eastern Asian populations, due to the geographically restricted sample. High-quality multinational RCTs, as well as predictive tools to optimize patient selection, are necessary before adjuvant TACE can be routinely implemented into standard practice. PROSPERO Registration ID: CRD42021245758.
Lyme Neuroborreliosis in Children

Lyme neuroborreliosis (LNB) is an infectious disease, developing after a tick bite and the dissemination of Borrelia burgdorferi sensu lato spirochetes reach the nervous system. The infection occurs in children and adults but with different clinical courses. Adults complain of radicular pain and paresis, while among the pediatric population, the most common manifestations of LNB are facial nerve palsy and/or subacute meningitis. Moreover, atypical symptoms, such as fatigue, loss of appetite, or mood changes, may also occur. The awareness of the various clinical features existence presented by children with LNB suspicion remains to be of the greatest importance to diagnose and manage the disease.
Cell Replacement Therapy for Retinal and Optic Nerve Diseases: Cell Sources, Clinical Trials and Challenges

The aim of this review was to provide an update on the potential of cell therapies to restore or replace damaged and/or lost cells in retinal degenerative and optic nerve diseases, describing the available cell sources and the challenges involved in such treatments when these techniques are applied in real clinical practice. Sources include human fetal retinal stem cells, allogenic cadaveric human cells, adult hippocampal neural stem cells, human CNS stem cells, ciliary pigmented epithelial cells, limbal stem cells, retinal progenitor cells (RPCs), human pluripotent stem cells (PSCs) (including both human embryonic stem cells (ESCs) and human induced pluripotent stem cells (iPSCs)) and mesenchymal stem cells (MSCs). Of these, RPCs, PSCs and MSCs have already entered early-stage clinical trials since they can all differentiate into RPE, photoreceptors or ganglion cells, and have demonstrated safety, while showing some indicators of efficacy. Stem/progenitor cell therapies for retinal diseases still have some drawbacks, such as the inhibition of proliferation and/or differentiation in vitro (with the exception of RPE) and the limited long-term survival and functioning of grafts in vivo. Some other issues remain to be solved concerning the clinical translation of cell-based therapy, including (1) the ability to enrich for specific retinal subtypes; (2) cell survival; (3) cell delivery, which may need to incorporate a scaffold to induce correct cell polarization, which increases the size of the retinotomy in surgery and, therefore, the chance of severe complications; (4) the need to induce a localized retinal detachment to perform the subretinal placement of the transplanted cell; (5) the evaluation of the risk of tumor formation caused by the undifferentiated stem cells and prolific progenitor cells. Despite these challenges, stem/progenitor cells represent the most promising strategy for retinal and optic nerve disease treatment in the near future, and therapeutics assisted by gene techniques, neuroprotective compounds and artificial devices can be applied to fulfil clinical needs.
Extraction of Phenolic Compounds and Terpenes from Cannabis sativa L. By-Products: From Conventional to Intensified Processes

Cannabis sativa L. is a controversial crop due to its high tetrahydrocannabinol content varieties; however, the hemp varieties get an increased interest. This paper describes (i) the main categories of phenolic compounds (flavonoids, stilbenoids and lignans) and terpenes (monoterpenes and sesquiterpenes) from C. sativa by-products and their biological activities and (ii) the main extraction techniques for their recovery. It includes not only common techniques such as conventional solvent extraction, and hydrodistillation, but also intensification and emerging techniques such as ultrasound-assisted extraction or supercritical CO2 extraction. The effect of the operating conditions on the yield and composition of these categories of phenolic compounds and terpenes was discussed. A thorough investigation of innovative extraction techniques is indeed crucial for the extraction of phenolic compounds and terpenes from cannabis toward a sustainable industrial valorization of the whole plant.
Brain-Specific Gene Expression and Quantitative Traits Association Analysis for Mild Cognitive Impairment

Transcriptome–wide association studies (TWAS) have identified several genes that are associated with qualitative traits. In this work, we performed TWAS using quantitative traits and predicted gene expressions in six brain subcortical structures in 286 mild cognitive impairment (MCI) samples from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. The six brain subcortical structures were in the limbic region, basal ganglia region, and cerebellum region. We identified 9, 15, and 6 genes that were stably correlated longitudinally with quantitative traits in these three regions, of which 3, 8, and 6 genes have not been reported in previous Alzheimer’s disease (AD) or MCI studies. These genes are potential drug targets for the treatment of early–stage AD. Single–Nucleotide Polymorphism (SNP) analysis results indicated that cis–expression Quantitative Trait Loci (cis–eQTL) SNPs with gene expression predictive abilities may affect the expression of their corresponding genes by specific binding to transcription factors or by modulating promoter and enhancer activities. Further, baseline structure volumes and cis–eQTL SNPs from correlated genes in each region were used to predict the conversion risk of MCI patients. Our results showed that limbic volumes and cis–eQTL SNPs of correlated genes in the limbic region have effective predictive abilities.
Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum

Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.
Exploring the Perspectives of South African Parents and Primary Caregivers Living in Low-Income Communities on What Children Need to Thrive within the First 1000 Days of Life

The first 1000 days is recognised as a critical period for the development of children. What children need to thrive in this particular phase of development may be different from any other phase. In South Africa, parents’ perception of children’s needs within the first 1000 days of life could be considered as emerging. Therefore, this study aims to explore the perspectives of South African parents and primary caregivers on what children need to thrive within the first 1000 days. An exploratory qualitative study design was used to explore the parents’ understanding of what children need to thrive in the first 1000 days. A purposive sampling approach was employed to select parents and primary caregivers in low-income communities. In all, thirty respondents participated in the study. The data were analysed using thematic analysis. During the analysis, four themes emerged. The themes included (1) the importance of parenting, care and support; (2) children’s need for holistic development; (3) parental roles; and (4) sharing responsibilities. Parents and primary caregivers living in low-income communities understand what children need to thrive within the first thousand days of life. The study could assist policymakers and service providers to design appropriate interventions for parents within these communities.