Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of mindfulness-based interventions on depressive symptoms in patients with substance use disorders: a systematic review and meta-analysis

Abstract Objective We examined the effects of mindfulness-based interventions (MBIs) on depressive symptoms in patients with substance use disorders (SUDs) and explored the moderating effects of participant, method, and intervention characteristics. Methods We systematically searched 8 databases from their inception till November 2021. The inclusion criteria were primary studies evaluating MBIs in patients with SUDs with depression measured as an outcome, those including a control group, and those written in English. We used a random-effects model to compute effect sizes (ESs) using Hedges’ g, a forest plot, and Q and I2 statistics as measures of heterogeneity; we also examined moderator analyses. Results Nineteen studies included 1352 participants (age: 38.6 ± 7.0 years). Overall, MBIs showed significantly improved depression (g = 0.67, 95% confidence interval [CI]: 0.29, 1.05, I2 = 89%) compared to controls. With regard to moderators, providing MBIs as an individual plus group intervention had a greater effect (g = 2.13) on reducing depressive symptoms than providing MBIs as a group intervention (g = 0.64) or an individual intervention only (g = 0.33, P = 0.034). Using concealed allocation tended to reduce depressive symptoms (g = 1.22) as compared to not using concealed allocation (g = 0.48, P = 0.086). No other quality indicators were demonstrated to have a moderating influence on the value of the ES. Conclusions MBIs improved depressive symptoms in patients with SUDs. MBIs might be used as an adjunctive or alternative to conventional treatment for depressed patients with SUDs.
A Course Sequence as a Model to Teach Cultural Humility to MSW Students

ABSTRACT This paper discusses the utilization of a cultural humility model to educate social work students in understanding the importance of diversity, power, privilege, oppression, marginalization and social and economic justice in an increasingly diverse society. Social work programs are required to teach students to effectively engage a diversity of clients in practice as well as to take action to resolve issues of oppression and discrimination. While the cultural humility model is gaining acceptance in social work and in social work education, there are few models of how to effectively teach it within the social work curriculum. One model that includes a two-course sequence is presented. The paper discusses components in creating a culturally humble classroom environment as well as specific materials and classroom assignments aimed at providing students with the knowledge, tools and skills essential to practicing with cultural humility. The power of utilizing materials that are representative of a diversity of voices is emphasized with appendices providing written and audio resources.
APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants

APOGEE 2 is a mitochondrially-centered ensemble method designed to improve the accuracy of pathogenicity predictions for interpreting missense mitochondrial variants. Built on the joint consensus recommendations by the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP), APOGEE 2 features an improved machine learning method and a curated training set for enhanced performance metrics. It offers region-wise assessments of genome fragility and mechanistic analyses of specific amino acids that cause perceptible long-range effects on protein structure. With clinical and research use in mind, APOGEE 2 scores and pathogenicity probabilities are precompiled and available in MitImpact. APOGEE 2’s ability to address challenges in interpreting mitochondrial missense variants makes it an essential tool in the field of mitochondrial genetics.
Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking

The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
Prognostic impact of peripheral natural killer cells in primary central nervous system lymphoma

Background Primary central nervous system lymphoma (PCNSL) is an aggressive extranodal non-Hodgkin lymphoma with a poor prognosis. We aimed to evaluate the prognostic impact of circulating NK cells in PCNSL. Materials and methods Patients diagnosed with PCNSL who were treated at our institution between December 2018 and December 2019 were retrospectively screened. Patient variables including age, sex, Karnofsky performance status, diagnostic methods, location of lesions, lactate dehydrogenase, cerebrospinal fluids (CSF), and vitreous fluids involvement or not were documented. NK cell count and NK cell proportion (NK cell count/lymphocyte count) in the peripheral blood were evaluated by flow cytometry. Some patients underwent two consecutive NK cell tests before and three weeks after chemotherapy (before the next chemotherapy). The fold change in NK cell proportion and NK cell counts were calculated. CD56-positive NK cells in tumor tissue were assessed by immunohistochemistry. NK cell cytotoxicity assay was performed using flow cytometry. Results A total of 161 patients with PCNSL were included in this study. The median NK cell count of all NK cell tests was 197.73/μL (range 13.11–1889.90 cells/μL). The median proportion of NK cells was 14.11% (range 1.68–45.15%) for all. Responders had a higher median NK cell count (p<0.0001) and NK cell proportion (p<0.0001) than non-responders. Furthermore, Responders had a higher median fold change in NK cell proportion than non-responders (p=0.019) or patients in complete remission/partial remission (p<0.0001). A higher median fold change in NK cell count was observed in responders than in non-responders (p=0.0224) or patients in complete remission/partial remission (p=0.0002). For newly diagnosed PCNSL, patients with a high NK cell count (>165 cells/μL) appeared to have a longer median overall survival than those with a low NK cell count (p=0.0054). A high fold change in the proportion of NK cells (>0.1957; p=0.0367) or NK cell count (>0.1045; p=0.0356) was associated with longer progression-free survival. Circulating NK cells from newly-diagnosed PCNSL demonstrated an impaired cytotoxicity capacity compared to those from patients with PCNSL in complete remission or healthy donors. Conclusion Our study indicated that circulating NK cells had some impact on the outcome of PCNSL.
Molecular identification of Trypanosoma theileri (Laveran, 1902) in cattle from two slaughterhouses in Ecuador and its relation with other haemotropic agents

Trypanosoma theileri is a worldwide distributed haemoparasite that has been reported throughout the American continent in various species, including bovines, buffaloes and bats. In bovines, high incidence of T. theileri can be harmful when associated with other infections or under stress situations. There is little information on this hemoflagellate in Ecuador, which prompted the study and molecular identification of the trypanosomes collected in two slaughtering centers. Between February and April 2021, a total of 218 samples of bovine blood were collected in abattoirs located in the Andean region of Quito (n = 83) and in the coastal region, in Santo Domingo (n = 135). Quito public Slaughterhouse is the biggest in Ecuador, and for that, they receive animals from all country; on the other hand, Santo Domingo's Slaughterhouse is a small one where mainly females from the region are sacrificed and some males. The samples were evaluated using two molecular tests, the PCR cathepsin L-like (CatL) specific for T. theileri and for the positive samples, a Nested PCR that targets the ITS of the 18S gene. The corresponding PCR products were sequenced, analyzed by BLAST/NCBI and the sequences were used to build a concatenated phylogenetic tree, using the MEGA XI software. Overall, 34 out of the 218 samples, (15.6%) were positive to T. theileri by PCR CatL, resulting from 20/83 (24.1%) positives from the Quito abattoir and 14/135 (10.4%) from the Santo Domingo slaughterhouse. These prevalence rates were found to be significantly different (p = 0.006). According to the phylogenetic tree based on the CatL and ITS concatenated sequences (n = 13), the two novel Equatorial T. theileri isolates, ThI (n = 7) and ThII (n = 6) are closely related and associated to the IC, IB and IIB genotypes, present in Brazil, Venezuela and Colombia. Thirty-one out of the thirty-four T. theileri-positive bovines were co-infected with other haemotropic pathogens, Anaplasma marginale Babesia spp and T. vivax. This coinfection could be responsible for additional pathologies and harmful effects on the affected cattle. This study presents the molecular identification and genotypification of T. theileri isolated from cattle in Ecuador through the analysis of CAtL and ITS sequences, and the high frequency of coinfection of this hemoflagellate with other blood haemotropic organisms.
Identifying risk factors affecting exercise behavior among overweight or obese individuals in China

Background The disease burden caused by obesity has increased significantly in China. Less than 30% of those who are obese meet the weekly physical activity standards recommended by the WHO. Risk factors that influence exercise behavior in people with obesity remain unclear. Methods Based on the survey from the Chinese General Social Survey program (CGSS) in 2017, 3,331 subjects were identified and enrolled in the univariate and multiple probit regression models. We aimed to identify the association between SRH and the exercise behavior of obese people and further explore the influencing factors of active physical activity in this group of people. Results The proportion of active physical activity in obese people was 25%. Groups with better SRH, higher education and income were more likely to participate in sports. Obese people who lived in rural areas, were unmarried or divorced, or fell within the age range of 35–40 had a significantly lower percentage of engagement in active physical activity. Conclusions The proportion of people with obesity who meet the WHO recommendation for physical activity in China is not ideal. Health promotion programs for those who are obese need to be further strengthened and targeted, especially for rural areas, low-income families, and middle-aged obese people.
Treatment-associated mRNA co-expression changes in monocytes of patients with posttraumatic stress disorder

PTSD is a prevalent mental disorder that results from exposure to extreme and stressful life events and comes at high costs for both the individual and society. Therapeutic treatment presents the best way to deal with PTSD-the mechanisms underlying change after treatment, however, remain poorly understood. While stress and immune associated gene expression changes have been associated with PTSD development, studies investigating treatment effects at the molecular level so far tended to focus on DNA methylation. Here we use gene-network analysis on whole-transcriptome RNA-Seq data isolated from CD14+ monocytes of female PTSD patients (N = 51) to study pre-treatment signatures of therapy response and therapy-related changes at the level of gene expression. Patients who exhibited significant symptom improvement after therapy showed higher baseline expression in two modules involved in inflammatory processes (including notable examples IL1R2 and FKBP5) and blood coagulation. After therapy, expression of an inflammatory module was increased, and expression of a wound healing module was decreased. This supports findings reporting an association between PTSD and dysregulations of the inflammatory and the hemostatic system and mark both as potentially treatment sensitive.
The relationship between young children’s personal values and their teacher-rated behaviors in the classroom

There has been little research on the relationships between children’s personal values and the behaviors that express such values in the school context. In the present study, we examined for the first time with children at this young age, the relations between values and their value-related behaviors, i.e., supportive, disciplined, learning-oriented, and achievement-oriented, in the primary school context. The sample consisted of 952 primary school children (51.5% boys; Mage = 7.93; SD = 0.35). Data used in this study were collected in 2022 in Switzerland. A multilevel analysis confirmed the hypothesis that systematic relationships between values and teacher-rated behaviors can be demonstrated with young children. However, gender was the strongest predictor of teacher-rated children’s classroom behaviors. The results highlight the significance of understanding children’s value-behavior relations, teachers’ possible gender stereotypes of children’s behaviors, and its practical importance in the school context.
Generation of a monoclonal antibody against duck circovirus capsid protein and its potential application for native viral antigen detection

Introduction Duck circovirus (DuCV) infection is currently recognized as an important immunosuppressive disease in commercial duck flocks in China. Specific antibodies against DuCV viral proteins are required to improve diagnostic assays and understand the pathogenesis of DuCV infection. Methods and results To generate DuCV-specific monoclonal antibodies (mAbs), a recombinant DuCV capsid protein without the first 36 N-terminal amino acids was produced in Escherichia coli. Using the recombinant protein as an immunogen, a mAb was developed that reacted specifically with the DuCV capsid protein, expressed in E. coli and baculovirus systems. Using homology modeling and recombinant truncated capsid proteins, the antibody-binding epitope was mapped within the region of 144IDKDGQIV151, which is exposed to solvent in the virion capsid model structure. To assess the applicability of the mAb to probe the native virus antigen, the murine macrophage cell line RAW267.4 was tested for DuCV replicative permissiveness. Immunofluorescence and Western blot analysis revealed that the mAb recognized the virus in infected cells and the viral antigen in tissue samples collected from clinically infected ducks. Discussion This mAb, combined with the in vitro culturing method, would have widespread applications in diagnosing and investigating DuCV pathogenesis.
Advanced methods and novel biomarkers in autoimmune diseases ‑ a review of the recent years progress in systemic lupus erythematosus

There are several autoimmune and rheumatic diseases affecting different organs of the human body. Multiple sclerosis (MS) mainly affects brain, rheumatoid arthritis (RA) mainly affects joints, Type 1 diabetes (T1D) mainly affects pancreas, Sjogren’s syndrome (SS) mainly affects salivary glands, while systemic lupus erythematosus (SLE) affects almost every organ of the body. Autoimmune diseases are characterized by production of autoantibodies, activation of immune cells, increased expression of pro-inflammatory cytokines, and activation of type I interferons. Despite improvements in treatments and diagnostic tools, the time it takes for the patients to be diagnosed is too long, and the main treatment for these diseases is still non-specific anti-inflammatory drugs. Thus, there is an urgent need for better biomarkers, as well as tailored, personalized treatment. This review focus on SLE and the organs affected in this disease. We have used the results from various rheumatic and autoimmune diseases and the organs involved with an aim to identify advanced methods and possible biomarkers to be utilized in the diagnosis of SLE, disease monitoring, and response to treatment.
Development and evaluation of a COVID tracking system to support provision of social service in Wyandotte County, Kansas

Background In addition to the state-mandated case investigation and contact tracing, the Unified Government Public Health Department of Wyandotte County, Kansas implemented social support services for COVID-19 cases and contacts; however, did not have the systems in place to document the provision of these services. Our team worked with the health department to develop and implement the COVID Tracking System (CTS), an eHealth system that linked multiple involved teams. Here, we describe the development and evaluation of the CTS. The objective of this manuscript is to describe and evaluate the development and implementation process of the Covid Tracking System. Methods Drawing from concepts of user-centered design, we took a 4-phase approach to development: understanding context, specifying needs, designing solutions, and evaluating. A mixed-methods evaluation of the development and implementation process using RE-AIM was conducted. Quantitative CTS data captured between February 1, 2021, and September 30, 2021 were exported. Descriptive statistics were calculated for categorical variables and means (SD, range) or median (IQR) for continuous variables. Qualitative discussions with key users supplemented the quantitative data. Results There were 1,152 cases entered into the CTS, of whom 307 (26.6%) requested a letter be sent to their workplace to excuse them during their quarantine period, 817 (70.9%) requested and had food and cleaning supplies delivered, 21 (1.8%) requested guidance on applying for federal assistance, and 496 (43.1%) requested to be contacted by a community health worker. While a few technical glitches slowed down early implementation, these were quickly resolved and key users felt that the CTS streamlined client referral and simplified their workflow, allowing them to spend more time on patient care and follow up, rather than documentation. After study implementation ended, the Unified Government Public Health Department of Wyandotte County continued using the CTS for client tracing and follow up. Discussion This project provides a roadmap of how user centered design can be applied to the development and evaluation of eHealth software to support program intervention implementation, even in situations where urgent action is needed.
Antiprotozoal activity of natural products from Nigerien plants used in folk medicine

In the course of the screening of plants from Niger for antiprotozoal activity, the methanol extract of Cassia sieberiana, and the dichloromethane extracts of Ziziphus mauritiana and Sesamun alatum were found to be active against protozoan parasites, namely Trypanosoma brucei rhodesiense, Trypanosoma cruzi, Leishmania donovani and/or Plasmodium falciparum. Myricitrin (1), quercitrin (2) and 1-palmitoyl-lysolecithin (3) were isolated from C. sieberiana. From Z. mauritiana, the three triterpene derivatives 13, 15, and 16 are described here for the first time. Their chemical structures were determined by 1D and 2D NMR experiments, UV, IR and HRESIMS data. The absolute configurations were assigned via comparison of the experimental and calculated ECD spectra. In addition, eight known cyclopeptide alkaloids (4, 5, 7–12), and five known triterpenoids (6, 14, 17–19) were isolated. The antiprotozoal activity of the isolated compounds, as well as of eleven quinone derivatives (20–30) previously isolated from S. alatum was determined in vitro. The cytotoxicity in L6 rat myoblast cells was also evaluated. Compound 18 showed the highest antiplasmodial activity (IC50 = 0.2 µm) and compound 24 inhibited T. b. rhodesiense with an IC50 value of 0.007 µM. However, it also displayed significant cytotoxicity in L6 cells (IC50 = 0.4 µm).
From salty to thriving: plant growth promoting bacteria as nature’s allies in overcoming salinity stress in plants

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.
Developing and validating a Japanese version of the Plymouth Sensory Imagery Questionnaire

Mental imagery refers to the representation of stimuli that are not physically present and has long been a subject of interest in psychology. However, most research on mental imagery has been limited to visual images, with other types of imagery, such as sound and smell, receiving little attention. A possible reason for this is the lack of appropriate scales to measure the vividness of multisensory imagery. The Plymouth Sensory Imagery Scale (Psi-Q) has been developed to address this issue and has been used in several studies to measure the vividness of seven imageries: vision, sound, smell, taste, touch, body, and feeling. In this study of 400 participants in Japan, the Psi-Q was translated into Japanese and tested for reliability and validity. The results showed good internal reliability and retest reliability and moderate to high correlations with other measures of construct validity, including mindfulness, Big Five, and life satisfaction. Additionally, there is no significant difference in total Psi-Q scores between the Japanese and British samples, although some differences are found in individual sensory imagery abilities. This study provides valuable insights into multisensory mental imagery, and it is expected that research dealing simultaneously with the responses of multisensory modalities will further accumulate.