Nevin Manimala

Brief Bioinform. 2023 Jan 18:bbad013. doi: 10.1093/bib/bbad013. Online ahead of print.

ABSTRACT

Spatially resolved transcriptomics technologies enable comprehensive measurement of gene expression patterns in the context of intact tissues. However, existing technologies suffer from either low resolution or shallow sequencing depth. Here, we present DIST, a deep learning-based method that imputes the gene expression profiles on unmeasured locations and enhances the gene expression for both original measured spots and imputed spots by self-supervised learning and transfer learning. We evaluate the performance of DIST for imputation, clustering, differential expression analysis and functional enrichment analysis. The results show that DIST can impute the gene expression accurately, enhance the gene expression for low-quality data, help detect more biological meaningful differentially expressed genes and pathways, therefore allow for deeper insights into the biological processes.

PMID:36653906 | DOI:10.1093/bib/bbad013

Brief Bioinform. 2023 Jan 18:bbad002. doi: 10.1093/bib/bbad002. Online ahead of print.

ABSTRACT

In longitudinal studies variables are measured repeatedly over time, leading to clustered and correlated observations. If the goal of the study is to develop prediction models, machine learning approaches such as the powerful random forest (RF) are often promising alternatives to standard statistical methods, especially in the context of high-dimensional data. In this paper, we review extensions of the standard RF method for the purpose of longitudinal data analysis. Extension methods are categorized according to the data structures for which they are designed. We consider both univariate and multivariate response longitudinal data and further categorize the repeated measurements according to whether the time effect is relevant. Even though most extensions are proposed for low-dimensional data, some can be applied to high-dimensional data. Information of available software implementations of the reviewed extensions is also given. We conclude with discussions on the limitations of our review and some future research directions.

PMID:36653905 | DOI:10.1093/bib/bbad002

Biol Res Nurs. 2023 Jan 18:10998004231152849. doi: 10.1177/10998004231152849. Online ahead of print.

ABSTRACT

BACKGROUND: Metabolic syndrome (MetS) is a prognostic cluster of physiologic risk factors that may develop into cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM). Electrocardiogram abnormalities (ECGA) can be instrumental in identifying the early stages of disease and may be associated with MetS in Hispanic Americans.

OBJECTIVE: To explore the relationships between MetS and major and minor ECGA in the Hispanic population (Hypothesis 1) and determine whether gender-ethnic subgroups moderate these relationships (Hypothesis 2).

METHODS: This secondary data analysis was conducted using large-scale data from the cohort study Hispanic Community Health Study/Study of Latinos (N = 13,628; 59% women and 41% men). Major ECGA encompassed 9 abnormalities including pathologic Q waves and left ventricular hypertrophy. Minor ECGA were tested independently of major ECGA. MetS was classified into 4 categories delineating metabolic abnormalities and related medication use. Multinomial logistic regression and Hayes’ PROCESS macro were used for statistical analysis.

RESULTS: Major ECGA were significantly associated with the presence of MetS and/or related medication use, whereas minor ECGA abnormalities were associated with MetS for participants who also took MetS-related medications only. Gender moderated the association between MetS and minor ECGA such that women with minor ECGA had a higher likelihood of MetS when compared to men.

CONCLUSIONS: Findings suggest that early recognition and associated treatment of major and minor ECGA can be important to prevent MetS and further morbidities in the Hispanic population.

PMID:36653902 | DOI:10.1177/10998004231152849

Diabetes Metab J. 2023 Jan 19. doi: 10.4093/dmj.2022.0001. Online ahead of print.

ABSTRACT

BACKGROUND: Background: Body mass index (BMI) is a risk factor for the type 2 diabetes (T2DM), and T2DM accompanies various complications, such as fractures. We investigated the effects of BMI and T2DM on fracture risk and analyzed whether the association varied with fracture locations.

METHODS: This study is a nationwide population-based cohort study that included all people with T2DM (n=2,746,078) who received the National Screening Program during 2009-2012. According to the anatomical location of the fracture, the incidence rate and hazard ratio (HR) were analyzed by dividing it into four categories: vertebra, hip, limbs, and total fracture.

RESULTS: The total fracture had higher HR in the underweight group (HR, 1.268; 95% CI, 1.228 to 1.309) and lower HR in the obese group (HR, 0.891; 95% CI, 0.882 to 0.901) and the morbidly obese group (HR, 0.873; 95% CI, 0.857 to 0.89), compared to reference (normal BMI group). Similar trends were observed for HR of vertebra fracture. The risk of hip fracture was most prominent, the risk of hip fracture increased in the underweight group (HR, 1.896; 95% CI, 1.178 to 2.021) and decreased in the obesity (HR, 0.643; 95% CI, 0.624 to 0.663) and morbidly obesity group (HR, 0.627; 95% CI, 0.591 to 0.665). Lastly, fracture risk was least affected by BMI for limbs.

CONCLUSION: In T2DM patients, underweight tends to increase fracture risk, and overweight tends to lower fracture risk, but association between BMI and fracture risk varied depending on the affected bone lesions.

PMID:36653892 | DOI:10.4093/dmj.2022.0001

Eur J Med Res. 2023 Jan 18;28(1):35. doi: 10.1186/s40001-022-00981-9.

ABSTRACT

BACKGROUND: The use of central venous pressure (CVP) measurements among (intensive care unit) ICU patients with severe coma has been questioned. This study aimed to investigate the application value of CVP in this population.

METHODS: Data stored in the ICU Collaborative Research Database (eICU-CRD) and Medical Information Mart for Intensive Care III (MIMIC-III) database were reviewed. Critically ill patients with a Glasgow Coma Scale (GCS) score of 3-8 were included. The primary outcome was the in-hospital mortality rate. The statistical approaches used included multivariable Cox regression, propensity score matching (PSM), inverse probability treatment weighting (IPTW), stabilized IPTW, and restricted cubic splines (RCS) to ensure the robustness of our findings.

RESULTS: In total, 7386 patients were included in the study. Early CVP measurement was independently associated with in-hospital mortality [hazard ratio, 0.63; p < 0.001] in patients with severe-to-moderate coma. This result was robust in the PSM, sIPTW, and IPTW cohorts. For all patients with CVP measurements, the RCS curves showed that the risk of in-hospital mortality increased as the initial CVP time was delayed. In addition, early CVP measurement was significantly associated with lower ICU mortality, 28-day mortality, and 365-day mortality and a significantly higher number of ventilator-free days.

CONCLUSION: Early CVP measurement could improve clinical outcomes in critically ill patients with severe coma.

PMID:36653881 | DOI:10.1186/s40001-022-00981-9

J Anim Sci Biotechnol. 2023 Jan 18;14(1):14. doi: 10.1186/s40104-022-00812-1.

ABSTRACT

BACKGROUND: Growth-promoting antibiotics have been banned by law in the livestock and poultry breeding industry in many countries. Various alternatives to antibiotics have been investigated for using in livestock. Epimedium (EM) is an herb rich in flavonoids that has many beneficial effects on animals. Therefore, this study was planned to explore the potential of EM as a new alternative antibiotic product in animal feed.

METHODS: A total of 720 1-day-old male broilers (Arbor Acres Plus) were randomly divided into six groups and fed basal diet (normal control; NC), basal diet supplemented with antibiotic (75 mg/kg chlortetracycline; CTC), and basal diet supplemented with 100, 200, 400 or 800 mg/kg EM extract for 6 weeks (EM100, EM200, EM400 and EM800 groups). The growth performance at weeks 3 and 6 was measured. Serum, intestinal tissue and feces were collected to assay for antioxidant indexes, intestinal permeability, lactic acid and short-chain fatty acids (SCFAs) profiles, microbial composition, and expression of intestinal barrier genes.

RESULTS: The average daily feed intake in CTC group at 1-21 d was significantly higher than that in the NC group, and had no statistical difference with EM groups. Compared with NC group, average daily gain in CTC and EM200 groups increased significantly at 1-21 and 1-42 d. Compared with NC group, EM200 and EM400 groups had significantly decreased levels of lipopolysaccharide and D-lactic acid in serum throughout the study. The concentrations of lactic acid, acetic acid, propionic acid, butyric acid and SCFAs in feces of birds fed 200 mg/kg EM diet were significantly higher than those fed chlortetracycline. The dietary supplementation of chlortetracycline and 200 mg/kg EM significantly increased ileal expression of SOD1, Claudin-1 and ZO-1 genes. Dietary supplemented with 200 mg/kg EM increased the relative abundances of g_NK4A214_group and Lactobacillus in the jejunal, while the relative abundances of Microbacterium, Kitasatospora, Bacteroides in the jejunal and Gallibacterium in the ileum decreased.

CONCLUSION: Supplementation with 200 mg/kg EM extract improved the composition of intestinal microbiota by regulating the core bacterial genus Lactobacillus, and increased the concentration of beneficial metabolites lactic acid and SCFAs in the flora, thereby improving the antioxidant capacity and intestinal permeability, enhancing the function of tight junction proteins. These beneficial effects improved the growth performance of broilers.

PMID:36653873 | DOI:10.1186/s40104-022-00812-1

World J Emerg Surg. 2023 Jan 18;18(1):7. doi: 10.1186/s13017-022-00471-7.

ABSTRACT

BACKGROUND: Frailty is associated with poor post-operative outcomes in emergency surgical patients. Shared multidisciplinary models have been developed to provide a holistic, reactive model of care to improve outcomes for older people living with frailty. We aimed to describe current perioperative practices, and surgeons’ awareness and perception of perioperative frailty management, and barriers to its implementation.

METHODS: A qualitative cross-sectional survey was sent via the World Society of Emergency Surgery e-letter to their members. Responses were analysed using descriptive statistics and reported by themes: risk scoring systems, frailty awareness and assessment and barriers to implementation.

RESULT: Of 168/1000 respondents, 38% were aware of the terms “Perioperative medicine for older people undergoing surgery” (POPS) and Comprehensive Geriatric Assessment (CGA). 66.6% of respondents assessed perioperative risk, with 45.2% using the American Society of Anaesthesiologists Physical Status Classification System (ASA-PS). 77.8% of respondents mostly agreed or agreed with the statement that they routinely conducted medical comorbidity management, and pain and falls risk assessment during emergency surgical admissions. Although 98.2% of respondents agreed that frailty was important, only 2.4% performed CGA and 1.2% used a specific frailty screening tool. Clinical frailty score was the most commonly used tool by those who did. Screening was usually conducted by surgical trainees. Key barriers included a lack of knowledge about frailty assessment, a lack of clarity on who should be responsible for frailty screening, and a lack of trained staff.

CONCLUSIONS: Our study highlights the ubiquitous lack of awareness regarding frailty assessment and the POPS model of care. More training and clear guidelines on frailty scoring, alongside support by multidisciplinary teams, may reduce the burden on surgical trainees, potentially improving rates of appropriate frailty assessment and management of the frailty syndrome in emergency surgical patients.

PMID:36653865 | DOI:10.1186/s13017-022-00471-7

BMC Public Health. 2023 Jan 18;23(1):126. doi: 10.1186/s12889-022-14355-7.

ABSTRACT

BACKGROUND: Allergic diseases are highly prevalent in the women of childbearing age. As we know, the immune system could change when pregnancy, which may affect the course of allergic diseases. Meanwhile, they also can affect the course and outcome of pregnancy. The data on incidence of allergies during pregnancy is lacking and conducting clinical trials in pregnant women was limited, therefore, we observed a prebirth cohort to supplement the relevant data and strengthen concerned research conductions.

OBJECTIVE: We aim to obtain the incidence of allergies in urban pregnancy and explore the relevant factors of allergic diseases in urban pregnancy.

METHODS: We design a multicenter and prospective cohort in 20 institutions above municipal level which were eligible according to the study design from 14 provinces covering all-side of China. This cohort was conducted from 13⁺⁶ weeks of gestation to 12 months postpartum and in our study, we chose the prenatal part to analyze. The outcome was developing allergies during pregnancy, which were diagnosed by clinicians according to the uniform criterion from National Health Commission. All the data was collected by electronic questionnaires through tablet computers.

RESULTS: The incidence of allergic diseases in urban pregnant women was 21.0% (95%CI 20.0% ~ 22.0%). From social demography data, the history of allergies of pregnant women and their parents had statistical significance(p < 0.01); For exposure to living or working environment, house decoration for less than half a year, exposure to plush toys, disinfectants, insecticides, antihistamines, glucocorticoids, antipyretic analgesics, tocolytic agent and probiotics had statistical significance (all p < 0.05); For psychological status, self-rated depression and anxiety had statistical significance (p = 0.026;p = 0.006).

CONCLUSION: The incidence of allergic diseases in urban pregnant women was similar to the former study and kept a medium-high level. The history of allergies of pregnant women and their parents, house decoration time, exposure to plush toys, disinfectants, insecticides, antihistamines, glucocorticoids, antipyretic analgesics, tocolytic agents, probiotics, self-rated depression, and anxiety were relevant factors of allergic diseases during pregnancy.

PMID:36653837 | DOI:10.1186/s12889-022-14355-7

Trials. 2023 Jan 18;24(1):37. doi: 10.1186/s13063-022-07049-3.

ABSTRACT

BACKGROUND: A randomized clinical trial assessing plasma rich in growth factors (PRGF) versus hyaluronic acid for knee osteoarthritis was published in 2012 (sponsor trial ID BTI-01-EC/07/ART). Evidence of misreporting was discovered following access to unpublished materials. In accordance with the principles of the Restoring Invisible and Abandoned Trials (RIAT) initiative, we sought to re-analyse Study PRGF based on the unpublished trial materials.

METHODS: Reanalysis was made possible primarily based on two unpublished study documents (original trial protocol and final report) obtained from the authors of the original publication. A call to action, calling on the authors to correct the original publication, was publicly issued. The involved ethics committee was repeatedly approached and extensive discussion with the authors ensued. After no agreement to correct the paper was reached, we embarked on this restoration. Reanalysis was focused on providing updated analyses for efficacy and safety.

RESULTS: The efficacy of PRGF was not statistically different from hyaluronic acid for any prespecified primary or secondary efficacy outcomes. For the primary endpoint, the percent of patients on PRGF compared to hyaluronic acid with a decrease >40% in WOMAC pain subscale score was 5.4% higher; 95% confidence interval (CI) -10.4% to 21.3%; p = 0.505. This differs from the original publication that reported a non-prespecified primary endpoint (decrease >50% in WOMAC pain subscale score) which was 14.1% higher; 95% CI 0.5 to 27.6%; p=0.044. Furthermore, in contrast to the article statement that all the adverse events disappeared in 48 h, at least two patients in the hyaluronic arm and five patients in the PRGF arm reported persistent adverse events. Inadequate disclosure of conflicts of interest in the original publication was also noted.

CONCLUSIONS: This reanalysis of Study PRGF found no clinically or statistically significant benefit from PRGF compared to hyaluronic acid. The restoration of Study PRGF shows the urgency of important changes to trial reporting and oversight practices. In the future, timely access to all clinical trial documents is needed to minimize the risk of reporting bias. Similarly, ethics committees should be ready to intervene whenever a case of potential misconduct arises.

TRIAL REGISTRATION: This is a RIAT project, whose original trial was approved and registered on 19 December 2007 by the Ethics Committee of the Basque Country, Spain, as BTI-01-EC/07/ART.

PMID:36653802 | DOI:10.1186/s13063-022-07049-3

BMC Pediatr. 2023 Jan 19;23(1):29. doi: 10.1186/s12887-022-03829-7.

ABSTRACT

BACKGROUND: This study aimed to evaluate the implementation of the prevention of mother-to-child transmission (PMTCT) of the HIV-PMTCT program in Kermanshah, west of Iran, from 2014 to 2021.

METHODS: The data of all HIV-infected mothers and their infants who were monitored by the Kermanshah behavioral diseases counseling center was extracted and recorded in a checklist.

RESULTS: Out of 95 included infant, 45 (47.4%) were girls and 50 (52.6%) were boys. The mothers were mostly infected with HIV via their infected spouse. The pregnancies of 77 cases (82.1%) were in accordance with the national guideline. The average length of treatment for this group was 185 days. Of the 18 mothers who did not receive treatment, nine were diagnosed during childbirth and nine had no available information. All infants born from infected mothers underwent after-birth-antiretroviral prophylaxis, and all remained healthy. There was no statistically significant relationship between the birth weight and height of neonates with maternal age, maternal last viral load, disease stage, education, and maternal CD4 levels. Only a statistically significant relationship was observed between the duration of treatment and the infants’ weight.

CONCLUSION: The results suggest the feasibility and effectiveness of the PMTCT program for HIV-positive mothers in Kermanshah. It seems that if pregnant HIV-positive women are diagnosed early and covered by a good prevention program on time, the risk of HIV to their babies will be reduced, significantly.

PMID:36653794 | DOI:10.1186/s12887-022-03829-7