Quality and redox state of bovine sperm cryopreserved with resveratrol use of resveratrol in bovine semen.

The use of antioxidants for semen preservation prevents oxidative damage caused by reactive oxygen species (ROS). One of the most promising natural antioxidants is resveratrol, a phytoalexin derived from plants, grapes, berries, peanuts and red wine. To evaluate the effect of resveratrol on the quality and redox status of cryopreserved bovine semen. Five bulls were subjected to electroejaculation to obtain 15 ejaculates. Each ejaculate was extended with a tris-egg yolk-glycerol-based medium and divided into six aliquots supplemented with 0 (control), 10, 20, 30, 40 and 50 µM of resveratrol. Semen was frozen with liquid nitrogen vapours. Post-thawing, motility and kinetics were evaluated using a computer-assisted sperm analysis (CASA) system, membrane integrity using the hypoosmotic test (HOST), morphology by staining with eosin-nigrosin, sperm vitality by fluorescence microscopy with the SYBR14/IP probes. Total antioxidant capacity (TAC) was evaluated using the ABTS•+ assay and ROS was evaluated using spectrofluorimetry with the H2 DCFDA probe. For the statistical analysis linear models were adjusted and means were compared using the Tukey test. All concentrations of resveratrol reduced post-thawed motility and kinetics of sperm. Supplementation with 40 and 50 µM of resveratrol reduced sperm kinetics, and between 30 and 50 µM of resveratrol alterations in the sperm membrane and morphology were observed. However, using resveratrol at 50 µM increased TAC and at 20 µM, it reduced ROS production of cryopreserved bovine semen. Resveratrol appears to have a dose-dependent effect in which higher doses produce greater sperm alterations, however, it can increase semen TAC during freezing. It is concluded that resveratrol can increase antioxidant capacity and reduce ROS production in cryopreserved bovine semen. However, its use between 10 and 50 µM reduces post-thawing semen quality.

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.

Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes. We standardized 203 attributes, based on standardized ontologies, describing host characteristics (e.g. sex, age and body mass index), diagnosis information (e.g. cancer, Crohn's disease and Parkinson), location (e.g. country, longitude and latitude), sampling site (e.g. gut, lung and skin) and sequencing attributes (e.g. sequencing platform, average length and sequence quality). Further, HumanMetagenomeDB version 1.0 metagenomes encompass 58 countries, 9 main sample sites (i.e. body parts), 58 diagnoses and multiple ages, ranging from just born to 91 years old. The HumanMetagenomeDB is publicly available at https://webapp.ufz.de/hmgdb/.

Structure and functional capacity of a benzene-mineralizing, nitrate-reducing microbial community.

AIMS: How benzene is metabolized by microbes under anoxic conditions is not fully understood. Here, we studied the degradation pathways in a benzene-mineralizing, nitrate-reducing enrichment culture. METHODS AND RESULTS: Benzene mineralization was dependent on the presence of nitrate and correlated to the enrichment of a Peptococcaceae phylotype only distantly related to known anaerobic benzene degraders of this family. Its relative abundance decreased after benzene mineralization had terminated, while other abundant taxa-Ignavibacteriaceae, Rhodanobacteraceae and Brocadiaceae-slightly increased. Generally, the microbial community remained diverse despite the amendment of benzene as single organic carbon source, suggesting complex trophic interactions between different functional groups. A subunit of the putative anaerobic benzene carboxylase previously detected in Peptococcaceae was identified by metaproteomic analysis suggesting that benzene was activated by carboxylation. Detection of proteins involved in anaerobic ammonium oxidation (anammox) indicates that benzene mineralization was accompanied by anammox, facilitated by nitrite accumulation and the presence of ammonium in the growth medium. CONCLUSIONS: The results suggest that benzene was activated by carboxylation and further assimilated by a novel Peptococcaceae phylotype. SIGNIFICANCE AND IMPACT OF THE STUDY: The results confirm the hypothesis that Peptococcaceae are important anaerobic benzene degraders.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.

Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.

Lymphocyte Populations in the Adventitial Layer of Hydatid Cysts in Cattle: Relationship With Cyst Fertility Status and Fasciola Hepatica Co-Infection.

Cystic echinococcosis is a worldwide zoonosis caused by the cestode Echinococcus granulosus. Two types of hydatid cysts occur in intermediate hosts: fertile cysts that generate protoscoleces from the germinal layer of the cyst, and infertile cysts that do not produce protoscoleces and are unable to continue the life cycle of the parasite. The adventitial layer, a host-derived fibrous capsule surrounding the hydatid cyst, is suggested to play an important role in local immune regulation during infection and in fertility of the cysts. Fasciola hepatica, another important parasite of cattle, induces a characteristic Th2-like immune response that could modulate the immune response against E. granulosus. Natural co-infection of both parasites is common in cattle, but no reports describe the local immune response against E. granulosus with F. hepatica infection in the same host. This study analyzed the number and distribution of T and B cells in the adventitial layer of liver and lung cysts and the relationship with cyst fertility and F. hepatica co-infection. T lymphocytes were the predominant cell type in the adventitial layer of infertile hydatid cysts and were more numerous in infertile hydatid cysts. B lymphocyte numbers were not associated with hydatid cyst fertility. Mast cells were infrequent in the adventitial layer. The number of T and B cells was not associated with F. hepatica co-infection. The present study contributes to the understanding of local immune responses in bovine cystic echinococcosis.

MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy.

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.

Jealousy, sexism, and romantic love myths: the role of beliefs in online dating violence.

With the massification of the Internet and social networks, a new form of dating violence called cyber-violence has emerged, which involves behaviors of control, humiliation, intimidation and threats towards the partner or ex-partner. Using a non-probabilistic sample of 1,001 participants aged 18 to 25 years, the present study used an ex post facto, retrospective, cross-sectional, single-group design to analyze the joint effects that beliefs associated with dating violence such as romantic love myths, jealousy, and sexism have on the victimization and perpetration of cyber-violence. The results evidenced that jealousy is involved in both Cyber-victimization and Cyber-harassment perpetrated, while sexist beliefs are only involved in perpetration. In the discussion section, it is postulated that cyber-violence is a phenomenon that is more related to the probability of aggression, but not to the probability of being a victim. Finally, limitations and implications for future research are discussed.

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.

The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.

StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins.

Motivation: Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis. Results: StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways. Availability and implementation: StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Nanoporous Amorphous Carbon with Exceptional Ultra-High Strength.

Nanoporous materials show a promising combination of mechanical properties in terms of their relative density; while there are numerous studies based on metallic nanoporous materials, here we focus on amorphous carbon with a bicontinuous nanoporous structure as an alternative to control the mechanical properties for the function of filament composition.Using atomistic simulations, we study the mechanical response of nanoporous amorphous carbon with 50% porosity, with sp3 content ranging from 10% to 50%. Our results show an unusually high strength between 10 and 20 GPa as a function of the %sp3 content. We present an analytical analysis derived from the Gibson-Ashby model for porous solids, and from the He and Thorpe theory for covalent solids to describe Young's modulus and yield strength scaling laws extremely well, revealing also that the high strength is mainly due to the presence of sp3 bonding. Alternatively, we also find two distinct fracture modes: for low %sp3 samples, we observe a ductile-type behavior, while high %sp3 leads to brittle-type behavior due to high high shear strain clusters driving the carbon bond breaking that finally promotes the filament fracture. All in all, nanoporous amorphous carbon with bicontinuous structure is presented as a lightweight material with a tunable elasto-plastic response in terms of porosity and sp3 bonding, resulting in a material with a broad range of possible combinations of mechanical properties.

Defining recovery in schizophrenia: A review of outcome studies.

Schizophrenia is a chronic disorder with a heterogenous course and different ways in which recovery is measured or perceived. Recovery in schizophrenia is a complex process that it can be defined either from a clinical perspective focused on sustained symptom and functional remission, or from a patient-focused one, as a self-broadening process aimed at living a meaningful life beyond mental illness. Until now, studies analysed these domains separately, without examining their mutual relations and changes over time. Therefore, this meta-analysis aimed to examine the relationship of global measures of subjective recovery with each of the components of clinical recovery such as symptom severity and functioning, in patients with schizophrenia spectrum disorders. The results showed that the association between different indicators of personal recovery and remission are weak and inverse (dIG+ = -0.18, z = -2.71, p < 0.01), however, this finding is not substantial according to the sensitivity indicators. With respect to functionality and personal recovery, there was a moderate relationship (dIG+ = 0.26, z = 7.894, p < 0.01) with adequate sensitivity indices. In addition, a low consensus exists between subjective measures that are more related to the patient's perspective and clinical measures based on experts and clinician's viewpoint.

Pre and Post Pandemic Depressive and Anxious Symptoms in Children and Adolescents in Northern Chile.

The psychological effects of the COVID-19 pandemic still represent a focus of concern, especially in children and adolescents who are a group particularly vulnerable to the psychological consequences of the COVID-19 pandemic, mainly due to the loss of socialization and leisure spaces. The aim of the study is to determine the variation in the levels of depressive and anxious symptomatology in children and adolescents in the North of Chile. METHODS: A Repeated cross-sectional design (RCS) was used. The sample consisted of a total of 475 students aged 12 to 18 years (high school) from educational establishments in the city of Arica. To evaluate the changes in the mental health of students associated with the COVID-19 pandemic, the same mental health measures applied to students were compared in two waves (2018-2021). RESULTS: An increase in the symptomatology levels of depression, anxiety, social anxiety, and problems with the family, while a decrease in problems with school and peers was observed. CONCLUSIONS: The results show that there is an increase in mental health problems associated with the periods of time in which the COVID-19 pandemic transformed the social relation spaces and classrooms of secondary school students. The observed changes point to future challenges, which include that it may be important to improve the coordination and integration of mental health professionals in educational centers and schools.

Effectiveness of Self-Affirmation Interventions in Educational Settings: A Meta-Analysis.

School and university can be stressful contexts that can become an important source of identity threats when social prejudices or stereotypes come into play. Self-affirmation interventions are key strategies for mitigating the negative consequences of identity threat. This meta-analysis aims to provide an overview of the effectiveness of self-affirmation interventions in educational settings. A peer-reviewed article search was conducted in January 2023. A total of 144 experimental studies that tested the effect of self-affirmation interventions in educational contexts among high school and university students from different social and cultural backgrounds were considered. The average effect of self-affirmation interventions was of low magnitude (dIG+ = 0.41, z = 16.01, p < 0.00), with a 95% confidence interval whose values tended to lie between 0.36 and 0.45 (SE = 0.0253). In addition, moderators such as identity threat, participants' age, and intervention procedure were found. Through a meta-analysis of the impact of self-affirmation interventions in educational contexts, this study suggests that interventions are effective, resulting in a small mean effect size. Thus, self-affirmation interventions can be considered useful, brief, and inexpensive strategies to improve general well-being and performance in educational settings.

Meeting report: The first soil viral workshop 2022.

Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.

Electrochemical and Microbial Dissection of Electrified Biotrickling Filters.

Electrified biotrickling filters represent sustainable microbial electrochemical technology for treating organic carbon-deficient ammonium-contaminated waters. However, information on the microbiome of the conductive granule bed cathode remains inexistent. For uncovering this black box and for identifying key process parameters, minimally invasive sampling units were introduced, allowing for the extraction of granules from different reactor layers during reactor operation. Sampled granules were analyzed using cyclic voltammetry and molecular biological tools. Two main redox sites [-288 ± 18 mV and -206 ± 21 mV vs. standard hydrogen electrode (SHE)] related to bioelectrochemical denitrification were identified, exhibiting high activity in a broad pH range (pH 6-10). A genome-centric analysis revealed a complex nitrogen food web and the presence of typical denitrifiers like Pseudomonas nitroreducens and Paracoccus versutus with none of these species being identified as electroactive microorganism so far. These are the first results to provide insights into microbial structure-function relationships within electrified biotrickling filters and underline the robustness and application potential of bioelectrochemical denitrification for environmental remediation.

Root anatomy, growth, and development of Typha domingensis Pers. (Typhaceae) and their relationship with cadmium absorption, accumulation, and tolerance.

Typha domingensis Pers. is a plant that grows in marshy environments, where cadmium (Cd) accumulates. The root is the first organ that comes into contact with the metal. The aim of this study was to evaluate the effect of Cd on the roots of T. domingensis. The experiment was conducted in a greenhouse using different Cd concentrations: (1) 0 µM (control), (2) 10 µM, and (3) 50 µM, with 10 replicates for 90 days. The plants were placed in plastic containers containing 5 L of nutrient solution modified with the different Cd concentrations. At the end of the experiment, the roots were measured, sampled, fixed, and subjected to usual plant microtechniques. The slides were observed and photographed under light microscopy and analyzed in ImageJ software. To measure Cd absorption, atomic-absorption spectrometry was used. The data were subjected to analysis of variance and comparison of means by the Scott-Knott test at P < 0.05. When exposed to 50 µM of Cd, the roots accumulated 99.35% of the Cd. At this concentration, there was a reduction in the exodermis but there was an increase in the diameter of the cortical cells and in the proportion of aerenchyma in the cortex. There was an increase in the root cap, which guaranteed the protection of the primary meristems. Therefore, T. domingensis adjusts its root anatomy improving the Cd tolerance and shows potential for phytoremediation purposes.

Latent Profiles of Premorbid Adjustment in Schizophrenia and Their Correlation with Measures of Recovery.

Premorbid adjustment (PA) has classically been defined as psychosocial functioning in the areas of education, occupation, social and interpersonal relationships prior to evidence of characteristic positive symptomatology. It is a concept which possesses ample evidence regarding its predictive nature for the course of Schizophrenia. The study aimed to analyze the latent profiles of premorbid adjustment and their relationship with symptomatology, functionality, subjective recovery, stigma resistance and years of untreated psychosis. Latent class analysis (LCA) was used to elaborate a solution of three premorbid adjustment profiles in a sample of 217 patients diagnosed with Schizophrenia from Public Mental Health Centers in the city of Arica, Chile. The results show that premorbid adjustment was significantly correlated with recovery indicators and that latent profiles of better premorbid adjustment predict better outcomes in subjective recovery and stigma resistance. The results show that premorbid adjustment not only has implications for the severity of the disorder, but that psychosocial functioning prior to psychosis affects the patient's subjectivity, the representation of the disorder and the recovery process.

Predictors of Internalized Stigma in Patients with Schizophrenia in Northern Chile: A Longitudinal Study.

The study aim was to longitudinally assess internalized stigma in a sample of patients from Northern Chile with a diagnosis of schizophrenia along with indicators of patient recovery, including quality of life, psychotic symptomatology, social cognition, premorbid adjustment, and years of untreated psychosis. The 10-year follow-up of stigma measures and predictors were assessed at public outpatient mental health centers in the city of Arica, Chile, during the months of March-July 2012. A total of 26 patients successfully completed the evaluation. The results revealed that, with the exception of the self-stigma subdimension, no clinically significant changes were seen in the trajectories of internalized stigma ratings between baseline and 10-year follow-up, underscoring the importance of assessing global components such as quality of life and premorbid adjustment during the process of internalizing stigma.

Equine Antebrachial Compartment Syndrome Secondary to Flexor Muscle Myopathy With Subsequent Muscle Atrophy And Tendonitis: A Case Report.

This case report describes a 16-year-old jumping stallion that had a marked swelling over the left antebrachial area along with substantial lameness after a fall. The horse was weight bearing but lame (4/5; AAEP scale) at the walk with marked enlargement in the caudal aspect of the antebrachial region. After a static musculoskeletal examination, radiography and ultrasonography the horse was diagnosed with flexor muscle myopathy and presumptive extremity compartment syndrome. Following medical treatment, the horse improved clinically over several days. Six-months post injury the horse showed flexor muscle atrophy but was sound at the walk and trot. The horse was presented again 3 months later with an enlargement of the palmar left metacarpus that was diagnosed as a superficial digital flexor tendonitis. This report describes the episodes from the onset of extremity compartment syndrome until the superficial digital flexor tendonitis, discusses anatomical features of the region, physiopathology of compartment syndrome and the possible biomechanics behind the flexor muscle atrophy and the tendonitis.

Aerenchyma, gas diffusion, and catalase activity in Typha domingensis: a complementary model for radial oxygen loss.

Radial oxygen loss is a physical phenomenon that occurs naturally in aquatic plants. Typha domingensis was chosen as a model plant because it possesses basic morphological characteristics, such as a stem (rhizome) that produces leaves and adventitious roots, which are present in many aquatic plants. This study aimed to evaluate the following: the relevance of the anatomy of T. domingensis on gas diffusion among organs; the influence of plant parts on radial oxygen loss; the role of catalase in radial oxygen loss; and the proposition of a novel explanation for the downward diffusion of oxygen through the organs of this aquatic macrophyte and into the environment. Typha domingensis plants were cultivated in a greenhouse under different conditions: plants with intact leaves, plants with leaves cut in half, and plants without leaves. Furthermore, we evaluated the percentage of aerenchyma in different vegetative organs, the minimum pressure required for radial oxygen loss, the daily variations of dissolved oxygen, and the roots' catalase activity. The results demonstrated that certain cellular features contributed to decreased oxygen diffusion among the organs, specifically, those found in the leaf-rhizome and root-rhizome interfaces as well as the suberin and lignin layers in these regions. Additionally, our experiments with a catalase activator and inhibitor validated that a significant amount of the oxygen released in radial oxygen loss could not, in fact, be exclusively supplied by the atmosphere. Thus, a complementary model is proposed in which catalase activity is an important component of radial oxygen loss.