Plant Dis. 2022 Dec 31:PDIS08221788A. doi: 10.1094/PDIS-08-22-1788-A. Online ahead of print.
NO ABSTRACT
PMID:36587246 | DOI:10.1094/PDIS-08-22-1788-A
Category: Nevin Manimala
BMC Complement Med Ther. 2022 Dec 31;23(1):1. doi: 10.1186/s12906-022-03814-8.
ABSTRACT
BACKGROUND AND OBJECTIVE: Restless legs syndrome/Willis-Ekbom Disease (RLS/WED) is one of the most prevalent sleep disorders. There are contradicting data about the effectiveness of magnesium and vitamin B6 in alleviating the symptoms of this condition. Therefore, this study aimed to assess the efficacy of magnesium and vitamin B6 in alleviating the symptoms of RLS/WED.
METHODS: A single-blind study was conducted on individuals with this illness for at least three months. Randomly, 75 patients were assigned into three groups: magnesium, vitamin B6, and placebo. The experimental group received daily doses of 40 mg vitamin B6 or 250 mg magnesium oxide. While others in the control group merely received a placebo. Patients’ disease severity and sleep quality were evaluated three times using standard questionnaires (at the beginning of the study, one and two months after therapy). Utilizing SPSS22 software and the ANOVA, t-test, and repeated measure tests, statistical analysis was conducted.
RESULTS: The mean and standard deviation of sleep quality and disease severity at the beginning of the trial and throughout the first month following the intervention did not differ statistically between the three groups. In the second month following the intervention, the mean and standard deviation of sleep quality and disease severity were significantly different (P = 0.001).
CONCLUSION: Taking magnesium and vitamin B6 supplements can reduce the severity of symptoms of RLS/WED patients and improve their sleep quality.
PMID:36587225 | DOI:10.1186/s12906-022-03814-8
BMC Bioinformatics. 2022 Dec 31;23(1):567. doi: 10.1186/s12859-022-05122-x.
ABSTRACT
BACKGROUND: Gene set enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) plays an important role in bioinformatics focused on diseases of genetic basis. To facilitate phenotype-oriented gene set analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases.
RESULTS: PhenoExam generates sensitive and accurate phenotype enrichment analyses. It is also effective in segregating gene sets or Mendelian diseases with very similar phenotypes. We tested the tool with two similar diseases (Parkinson and dystonia), to show phenotype-level similarities but also potentially interesting differences. Moreover, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy.
CONCLUSIONS: We developed PhenoExam, a freely available R package and Web application, which performs phenotype enrichment and disease enrichment analysis on gene set G, measures statistically significant phenotype similarities between pairs of gene sets G and G’ and detects statistically significant exclusive phenotypes or disease terms, across different databases. We proved with simulations and real cases that it is useful to distinguish between gene sets or diseases with very similar phenotypes. Github R package URL is https://github.com/alexcis95/PhenoExam . Shiny App URL is https://alejandrocisterna.shinyapps.io/phenoexamweb/ .
PMID:36587217 | DOI:10.1186/s12859-022-05122-x
Int J Ment Health Syst. 2022 Dec 31;16(1):58. doi: 10.1186/s13033-022-00567-2.
ABSTRACT
BACKGROUND: Internalized stigma has been found to be high among people with mental illness (PWMI) and it results in poor treatment outcome, increased disability and high economic burden. So, this study was designed to determine the prevalence and associated factors of high internalized stigma among PWMI attending psychiatric follow-up at University of Gondar Comprehensive Specialized Hospital, Northwest, Ethiopia, 2021.
METHODS: A cross-sectional study was conducted among PWMI (n = 365), and internalized stigma was measured by using internalized stigma of mental illness 29 (ISMI-29) scale. The data was entered in to EPI DATA software (4.6.0.2) and analyzed by Statistical Package for Social Sciences version 20. A binary logistic regression was used to identify factors associated with internalized stigma and reported with 95% confidence interval (CI). P-value < 0.05 was considered as statistically significant.
RESULTS: The prevalence of high internalized stigma was found to be 27.9% (95% CI 23.1-32.6). A male gender (AOR = 0.332; 95% CI 0.175-0.629), occupation, specifically government employee (AOR = 0.309; 95% CI 0.118-0.809), life time substance use (AOR = 3.561; 95% CI 1.867-6.793), low self-esteem (AOR = 8.313; 95% CI 3.641-18.977), and history of hospitalization (AOR = 4.236; 95% CI 1.875, 9.570) were factors significantly associated with higher internalized stigma.
CONCLUSION: The result of this study showed that there was an intermediate prevalence of high internalized stigma among PWMI at University of Gondar Comprehensive Specialized Hospital. The hospital needs to take immediate action to fight internalized stigma by focusing on females, people with low self-esteem, individuals with history of lifetime substance use, and people who have history of hospital admission.
PMID:36587213 | DOI:10.1186/s13033-022-00567-2
BMC Oral Health. 2022 Dec 31;22(1):661. doi: 10.1186/s12903-022-02562-y.
ABSTRACT
BACKGROUND: This study aims at identifying the microbiota in traumatized immature permanent teeth with periapical lesions using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).
METHODS: The study included 16 immature maxillary central incisors with periapical lesions in 13 patients. Field decontamination and negative control samples were performed before and after access cavity preparation. Root canal samples were taken using sterile stainless-steel hand files following field decontamination. In-office inoculation and pure sub-cultures were performed. Bacterial isolates were prepared for MALDI-TOF MS (Bruker, Billerica, MA USA) analysis using the formic acid extraction method. A comparison of the prevalence of isolated microorganisms was done using a one-sample chi-square test. Comparisons between identified microbial species with the, cone beam computed tomography periapical index (CBCT PAI) scores and lesion volume were also conducted. The Chi-square test was applied to investigate the association between the categorical variables .
RESULTS: Out of the forty isolates recovered from the 16 traumatized teeth included in the present study with the mean patients’ age of 10.93 ± 1.77, 37 isolates were reliably identified by MALDI-TOF MS. Twelve teeth (62.5%) were polymicrobial. The recovered bacteria belonged to five phyla, 15 genera and 25 species. Firmicutes were the predominant phylum (P < 0.001) over Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria. Gram positive bacteria were significantly more prevalent than Gram negative (p = 0.03). Facultative anaerobes were the most prevalent (P < 0.001) compared to the obligate anaerobes and the obligate aerobes. The latter were the least prevalent. Statistically, significant differences existed in the comparison between CBCT PAI scores according to bacterial gram staining.
CONCLUSION: Traumatized immature permanent teeth with periapical lesions showed a significant predominance of Gram-positive facultative anaerobes. MALDI-TOF MS provided accurate identification of numerous viable endodontic microbes.
PMID:36587207 | DOI:10.1186/s12903-022-02562-y
BMC Public Health. 2022 Dec 31;22(1):2460. doi: 10.1186/s12889-022-14781-7.
ABSTRACT
BACKGROUND: Despite widespread restrictions on residents’ mobility to limit the COVID-19 pandemic, controlled impact evaluations on such restrictions are rare. While Colombia imposed a National Lockdown, exceptions and additions created variations across municipalities and over time. METHODS: We analyzed how weekend and weekday mobility affected COVID-19 cases and deaths. Using GRANDATA from the United Nations Development Program (UNDP) we examined movement in 76 Colombian municipalities, representing 60% of Colombia’s population, from March 2, 2020 through October 31, 2020. We combined the mobility data with Colombia’s National Epidemiological Surveillance System (SIVIGILA) and other databases and simulated impacts on COVID-19 burden. RESULTS: During the study period, Colombians stayed at home more on weekends compared to weekdays. In highly dense municipalities, people moved less than in less dense municipalities. Overall, decreased movement was associated with significant reductions in COVID-19 cases and deaths two weeks later. If mobility had been reduced from the median to the threshold of the best quartile, we estimate that Colombia would have averted 17,145 cases and 1,209 deaths over 34.9 weeks, reductions of 1.63% and 3.91%, respectively. The effects of weekend mobility reductions (with 95% confidence intervals) were 6.40 (1.99-9.97) and 4.94 (1.33-19.72) times those of overall reductions for cases and deaths, respectively.
CONCLUSIONS: We believe this is the first evaluation of day-of-the week mobility on COVID-19. Weekend behavior was likely riskier than weekday behavior due to larger gatherings and less social distancing or protective measures. Reducing or shifting such activities outdoors would reduce COVID-19 cases and deaths.
PMID:36587205 | DOI:10.1186/s12889-022-14781-7
Cardiovasc Diabetol. 2022 Dec 31;21(1):293. doi: 10.1186/s12933-022-01726-y.
ABSTRACT
OBJECTIVE: High-density lipoproteins (HDL) comprise particles of different size, density and composition and their vasoprotective functions may differ. Diabetes modifies the composition and function of HDL. We assessed associations of HDL size-based subclasses with incident cardiovascular disease (CVD) and mortality and their prognostic utility.
RESEARCH DESIGN AND METHODS: HDL subclasses by nuclear magnetic resonance spectroscopy were determined in sera from 1991 fasted adults with type 2 diabetes (T2D) consecutively recruited from March 2014 to February 2015 in Hong Kong. HDL was divided into small, medium, large and very large subclasses. Associations (per SD increment) with outcomes were evaluated using multivariate Cox proportional hazards models. C-statistic, integrated discrimination index (IDI), and categorial and continuous net reclassification improvement (NRI) were used to assess predictive value.
RESULTS: Over median (IQR) 5.2 (5.0-5.4) years, 125 participants developed incident CVD and 90 participants died. Small HDL particles (HDL-P) were inversely associated with incident CVD [hazard ratio (HR) 0.65 (95% CI 0.52, 0.81)] and all-cause mortality [0.47 (0.38, 0.59)] (false discovery rate < 0.05). Very large HDL-P were positively associated with all-cause mortality [1.75 (1.19, 2.58)]. Small HDL-P improved prediction of mortality [C-statistic 0.034 (0.013, 0.055), IDI 0.052 (0.014, 0.103), categorical NRI 0.156 (0.006, 0.252), and continuous NRI 0.571 (0.246, 0.851)] and CVD [IDI 0.017 (0.003, 0.038) and continuous NRI 0.282 (0.088, 0.486)] over the RECODe model.
CONCLUSION: Small HDL-P were inversely associated with incident CVD and all-cause mortality and improved risk stratification for adverse outcomes in people with T2D. HDL-P may be used as markers for residual risk in people with T2D.
PMID:36587202 | DOI:10.1186/s12933-022-01726-y
BMC Health Serv Res. 2022 Dec 31;22(1):1602. doi: 10.1186/s12913-022-08985-1.
ABSTRACT
BACKGROUND: Inflammatory bowel disease (IBD), consisting of Crohn’s disease (CD) and ulcerative colitis (UC), is a chronic disorder with a considerable negative impact on health-related quality of life (HRQoL). During the past decade, IBD nurse specialists have been increasingly involved in follow-up care of IBD outpatients, in a consultative and coordinating role, closely cooperating with gastroenterologists. Whether patients’ HRQoL differs between nurses’ follow-up care (NF) and conventional follow-up care (CF) has not been widely researched and the aim of this study was to compare two different follow-up regimes with respect to patients’ HRQoL.
METHODS: This cross-sectional, multicenter study involved seven centers; five organized as CF, two as NF.
RESULTS: A total of 304 patients aged 18-80 years, 174 females and 130 males, were included, of whom 140 received care under the NF model and 164 under the CF model. Participants in the NF group had a statistically significant higher median total score on the Inflammatory Bowel Disease Questionnaire (IBDQ) (p-value < .001). This pattern could also be seen in the sub-scores of the different IBDQ domains. Despite a trend of higher IBDQ score in all domains in the NF model, the overall result in our study did not reach the limit of 16 points, defined as clinically significant. A higher proportion of NF patients had IBDQ scores defined as remission, as well as a statistically significant higher frequency of outpatient check-ups during a two-year follow-up period.
CONCLUSIONS: Nurse-led models are not inferior to conventional models with regards to patient reported HRQoL except in the social domain where the model showed to be clinically significant better. Further studies are needed to advance efforts to implement these models and increase access to IBD care.
PMID:36587197 | DOI:10.1186/s12913-022-08985-1
AIDS Res Ther. 2022 Dec 31;19(1):69. doi: 10.1186/s12981-022-00493-w.
ABSTRACT
INTRODUCTION: Incident syphilis leads to changes in plasma HIV-1 RNA and CD4 + T-cell level in people with HIV (PWH) with viraemia. Its effect in PWH on suppressive antiretroviral therapy (ART) is less clear.
METHODS: PWH on suppressive ART (plasma HIV-1 RNA < 50copies/mL) followed at the Queen Elizabeth Hospital, Hong Kong, China were regularly screened for syphilis. Their plasma HIV-1 RNA, CD4 + and CD8 + T-cell, and total lymphocyte levels before syphilis, during syphilis, and after successful treatment were compared.
RESULTS: Between 2005 and 2020, 288 syphilis episodes from 180 individuals were identified; 287 episodes were related to male, with a median age of 41 at diagnosis; 221 (77%) were syphilis re-infection. The rates of plasma HIV-1 suppression were statistically unchanged across the time-points (97% pre-syphilis, 98% during syphilis, and 99% post-treatment). Total lymphocyte, CD4+ and CD8+ T-cell levels decreased during incident syphilis (p<0.01), and rebounded post-treatment (p<0.01). VDRL titre was associated with declines in CD4+ T-cell (p=0.045), CD8+ T-cell (p=0.004), and total lymphocyte levels (p=0.021). Pre-syphilis CD4/CD8 ratio was associated with increases in CD8+ T-cell (p=0.001) and total lymphocyte levels (p=0.046) during syphilis. Syphilis re-infection was associated with an increase in total lymphocyte level (p=0.037). In the multivariable analysis, only pre-syphilis CD4/CD8 ratio was independently associated with increases in CD8+ T-cell (p=0.014) and total lymphocyte levels (p=0.039) during syphilis.
CONCLUSIONS: Among virally-suppressed PWH, total lymphocyte, CD4+, and CD8+ T-cell levels declined during incident syphilis but rebounded post-treatment. The status of plasma HIV suppression was unaffected by syphilis.
PMID:36587188 | DOI:10.1186/s12981-022-00493-w
Nat Methods. 2022 Dec 31. doi: 10.1038/s41592-022-01687-w. Online ahead of print.
ABSTRACT
Nonnegative matrix factorization (NMF) is widely used to analyze high-dimensional count data because, in contrast to real-valued alternatives such as factor analysis, it produces an interpretable parts-based representation. However, in applications such as spatial transcriptomics, NMF fails to incorporate known structure between observations. Here, we present nonnegative spatial factorization (NSF), a spatially-aware probabilistic dimension reduction model based on transformed Gaussian processes that naturally encourages sparsity and scales to tens of thousands of observations. NSF recovers ground truth factors more accurately than real-valued alternatives such as MEFISTO in simulations, and has lower out-of-sample prediction error than probabilistic NMF on three spatial transcriptomics datasets from mouse brain and liver. Since not all patterns of gene expression have spatial correlations, we also propose a hybrid extension of NSF that combines spatial and nonspatial components, enabling quantification of spatial importance for both observations and features. A TensorFlow implementation of NSF is available from https://github.com/willtownes/nsf-paper .
PMID:36587187 | DOI:10.1038/s41592-022-01687-w