Category: Nevin Manimala

Bioinformatics. 2023 Apr 19:btad214. doi: 10.1093/bioinformatics/btad214. Online ahead of print.

ABSTRACT

SUMMARY: PyHMMER provides Python integration of the popular profile Hidden Markov Model software HMMER via Cython bindings. This allows annotation of protein sequences with profile HMMs and building new ones directly with Python. PyHMMER increases flexibility of use, allowing creating queries directly from Python code, launching searches and obtaining results without I/O, or accessing previously unavailable statistics like uncorrected p-values. A new parallelization model greatly improves performance when running multithreaded searches, while producing the exact same results as HMMER.

AVAILABILITY AND IMPLEMENTATION: PyHMMER supports all modern Python versions (Python 3.6+) and similar platforms as HMMER (x86 or PowerPC UNIX systems). Pre-compiled packages are released via PyPI (https://pypi.org/project/pyhmmer/) and Bioconda (https://anaconda.org/bioconda/pyhmmer). The PyHMMER source code is available under the terms of the open-source MIT licence and hosted on GitHub (https://github.com/althonos/pyhmmer); its documentation is available on ReadTheDocs (https://pyhmmer.readthedocs.io).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37074928 | DOI:10.1093/bioinformatics/btad214

Ann Med. 2023 Dec;55(1):643-651. doi: 10.1080/07853890.2023.2178668.

ABSTRACT

BACKGROUND: To investigate the prevalence and related influencing factors of subclinical hypothyroidism (SCH) in a pre-diabetes (PreDM) population.

PATIENTS AND METHODS: A multi-stage stratified cluster random sampling method was used to select the adult Han population in Gansu Province for investigation. General data and related biochemical indices were recorded and SPSS software was used for statistical analyses.

RESULTS: This study selected 2876 patients, including 548 with SCH and 433 with PreDM. In the PreDM population, the levels of thyroid stimulating hormone (TSH), serum phosphorus, TPOAb and TgAb in the SCH group were higher than those in the euthyroid group (P < 0.05). The level of TPOAb in females of SCH group was higher than that in males (P < 0.05). The positive rates of TPOAb and TgAb in females were higher than those in males in the total population and SCH population. The prevalence of SCH in the PreDM group under 60 was significantly higher than that in the normal glucose tolerance (NGT) group (26.02% vs. 20.40%, χ² = 5.150, P < 0.05). We defined SCH as a TSH level of >4.20 mIU/L. Using this criterion, the prevalence of SCH in the total population of PreDM was higher than that in the NGT population (χ² = 8.611, P < 0.05), the prevalence of SCH in the PreDM population generally showed an upward trend. However, we performed a separate analysis considering the accepted impact of age on TSH redefining SCH as TSH >8.86 mIU/L (for individuals over age 65). However, allowing for the expected rise in TSH levels in individuals over age 65, the prevalence of SCH in the elderly over 65 years of age decreased significantly (NGT population from 27.48% to 9.16%, PreDM population from 34.18% to 6.33%, P < 0.05). Logistic regression analysis showed that the risk factors for SCH in the PreDM population were female gender, fasting plasma glucose and TSH (all P < 0.05). Risk factors for SCH in the impaired fasting glucose (IFG) population were female gender, OGTT 2 h, TSH and TPOAb (all P < 0.05).

CONCLUSION: The prevalence of SCH in the PreDM population not considering the known physiological increase in age related TSH was relatively high and was significant in female and the IFG population. However, the effect of age on these findings needs to attract more attention.

PMID:37074323 | DOI:10.1080/07853890.2023.2178668

J Wildl Dis. 2023 Apr 20. doi: 10.7589/JWD-D-21-00153. Online ahead of print.

ABSTRACT

Antimicrobial resistance (AMR) is a critical challenge of the 21st century for public and animal health. The role of host biodiversity and the environment in the evolution and transmission of resistant bacteria between populations and species, and specifically at the wildlife-livestock-human interface, needs to be further investigated. We evaluated the AMR of commensal Escherichia coli in three mammalian herbivore species-impala (Aepyceros melampus), greater kudu (Tragelaphus strepsiceros), and plains zebra (Equus quagga)-targeting populations living under two conditions: captivity (French zoos) and free ranging (natural and private parks in Zimbabwe). From 137 fecal samples from these three host species, 328 E. coli isolates were isolated. We measured the AMR of each isolate against eight antibiotics, and we assessed the presence of AMR genes and mobile genetic element class 1 integrons (int1). Isolates obtained from captive hosts had a higher probability of being resistant than those obtained from free-ranging hosts (odds ratio, 293.8; confidence interval, 10-94,000). This statistically higher proportion of AMR bacteria in zoos than in natural parks was especially observed for bacteria resistant to amoxicillin. The percentage of int1 detection was higher when isolates were obtained from captive hosts, particularly captive impalas. Ninety percent of bacterial isolates with genes involved in antibiotic resistance also had the int1 gene. The sul1, sul2, blaTEM, and stra genes were found in 14, 19, 0, and 31%, respectively, of E. coli with respective antibiotic resistance. Finally, plains zebra carried AMR significantly more often than the other species.

PMID:37074787 | DOI:10.7589/JWD-D-21-00153

J Dev Behav Pediatr. 2023 Apr 19. doi: 10.1097/DBP.0000000000001183. Online ahead of print.

ABSTRACT

OBJECTIVE: Quality child health research requires multimodal, multi-informant, longitudinal tools for data collection to ensure a holistic description of real-world health, function, and well-being. Although advances have been made, the design of these tools has not typically included community input from families with children whose function spans the developmental spectrum.

METHODS: We conducted 24 interviews to understand how children, youth, and their families think about in-home longitudinal data collection. We used examples of smartphone-based Ecological Momentary Assessment of everyday experiences, activity monitoring with an accelerometer, and salivary stress biomarker sampling to help elicit responses. The children and youth who were included had a range of conditions and experiences, including complex pain, autism spectrum disorder, cerebral palsy, and severe neurologic impairments. Data were analyzed using reflexive thematic analysis and descriptive statistics of quantifiable results.

RESULTS: Families described (1) the importance of flexibility and customization within the data collection process, (2) the opportunity for a reciprocal relationship with the research team; families inform the research priorities and the development of the protocol and also benefit from data being fed back to them, and (3) the possibility that this research approach would increase equity by offering accessible participation opportunities for families who might otherwise not be represented. Most families expressed interest in participating in in-home research opportunities, would find most methods discussed acceptable, and cited 2 weeks of data collection as feasible.

CONCLUSION: Families described diverse areas of complexity that necessitate thoughtful adaptations to traditional research designs. There was considerable interest from families in active engagement in this process, particularly if they could benefit from data sharing. This feedback is being incorporated into pilot demonstration projects to iteratively codesign an accessible research platform.

PMID:37074803 | DOI:10.1097/DBP.0000000000001183

J Magn Reson Imaging. 2023 Apr 19. doi: 10.1002/jmri.28746. Online ahead of print.

ABSTRACT

BACKGROUND: Endometrial fibrosis may cause infertility. Accurate evaluation of endometrial fibrosis helps clinicians to schedule timely therapy.

PURPOSE: To explore T2 mapping for assessing endometrial fibrosis.

STUDY TYPE: Prospective.

POPULATION: Ninety-seven women with severe endometrial fibrosis (SEF) and 21 patients with mild to moderate endometrial fibrosis (MMEF), diagnosed by hysteroscopy, and 37 healthy women.

FIELD STRENGTH/SEQUENCE: 3T, T2-weighted turbo spin echo (T2-weighted imaging) and multi-echo turbo spin echo (T2 mapping) sequences.

ASSESSMENT: Endometrial MRI parameters (T2, thickness [ET], area [EA], and volume [EV]) were measured by N.Z. and Q.H. (9- and 4-years’ experience in pelvic MRI) and compared between the three subgroups. A multivariable model including MRI parameters and clinical variables (including age and body mass index [BMI]) was developed to predict endometrial fibrosis assessed by hysteroscopy.

STATISTICAL TESTS: Kruskal-Wallis; ANOVA; Spearman’s correlation coefficient (rho); area under the receiver operating characteristic curve (AUC); binary logistic regression; intraclass correlation coefficient (ICC). P value <0.05 for statistical significance.

RESULTS: Endometrial T2, ET, EA, and EV of MMEF patients (185 msec, 8.2 mm, 168 mm² , and 2181 mm³ ) and SEF patients (164 msec, 6.7 mm, 120 mm² , and 1762 mm³ ) were significantly lower than those of healthy women (222 msec, 11.7 mm, 316 mm² , and 3960 mm³ ). Endometrial T2 and ET of SEF patients were significantly lower than those of MMEF patients. Endometrial T2, ET, EA, and EV were significantly correlated to the degree of endometrial fibrosis (rho = -0.623, -0.695, -0.694, -0.595). There were significant strong correlations between ET, EA, and EV in healthy women and MMEF patients (rho = 0.850-0.908). Endometrial MRI parameters and the multivariable model accurately distinguished MMEF or SEF from normal endometrium (AUCs >0.800). Age, BMI, and MRI parameters in univariable analysis and age and T2 in multivariable analysis significantly predicted endometrial fibrosis. The reproducibility of MRI parameters was excellent (ICC, 0.859-0.980).

DATA CONCLUSION: T2 mapping has potential to noninvasively and quantitatively evaluate the degree of endometrial fibrosis.

EVIDENCE LEVEL: 2 Technical Efficacy: Stage 2.

PMID:37074789 | DOI:10.1002/jmri.28746

Acta Odontol Scand. 2023 Apr 19:1-9. doi: 10.1080/00016357.2023.2199862. Online ahead of print.

ABSTRACT

PURPOSE: Rapid maxillary expansion (RME) is a routine method for correcting transverse maxillary deficiency. This paper investigated the effect of RME on anchorage alveolar bone and examined the differences between micro-implant-assisted RME and conventional RME.

METHODS: Relevant articles were selected from the PubMed, EMBASE and Cochrane Central Register of Controlled Trials databases. Review Manager software (v.5.3) was used for the pooled analysis and Cochran Q and I² statistic tests were used to assess the heterogeneity.

RESULTS: Following conventional RME, the distal buccal alveolar bone thickness and the mesiobuccal alveolar thickness of the maxillary first molars were significantly reduced. Hyrax (standard mean difference [SMD]: -0.93, 95% confidence interval [CI]: -1.20-0.66) and Haas procedures (SMD: -0.88, 95% CI: -1.40-0.36) significantly reduced the buccal vertical alveolar height of the maxillary first molars. Similar results were obtained for the maxillary first premolars following RME. The thickness of the buccal alveolar bone decreased with conventional RME compared to when using the method assisted by micro-implants.

CONCLUSIONS: Conventional RME can reduce the thickness and vertical height of maxillary alveolar bone, and there is less loss of alveolar bone when using micro-implant-assisted RME. Further research is needed to validate the findings.

PMID:37074788 | DOI:10.1080/00016357.2023.2199862

J Med Internet Res. 2023 Apr 19;25:e41900. doi: 10.2196/41900.

ABSTRACT

BACKGROUND: Positive health behavior changes before pregnancy can optimize perinatal outcomes for mothers, babies, and future generations. Women are often motivated to positively change their behavior in preparation for pregnancy to enhance their health and well-being. Mobile phone apps may provide an opportunity to deliver public health interventions during the preconception period.

OBJECTIVE: This review aimed to synthesize the evidence of the effectiveness of mobile phone apps in promoting positive behavior changes in women of reproductive age before they are pregnant (preconception and interconception periods), which may improve future outcomes for mothers and babies.

METHODS: Five databases were searched in February 2022 for studies exploring mobile phone apps as a prepregnancy intervention to promote positive behavior change. The identified studies were retrieved and exported to EndNote (Thomson Reuters). Using Covidence (Veritas Health Innovation), a PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) study flow diagram was generated to map the number of records identified, included, and excluded. Three independent reviewers assessed the risk of bias and conducted data extraction using the Review Manager software (version 5.4, The Cochrane Collaboration), and the data were then pooled using a random-effects model. The Grades of Recommendation, Assessment, Development, and Evaluation system was used to assess the certainty of the evidence.

RESULTS: Of the 2973 publications identified, 7 (0.24%) were included. The total number of participants across the 7 trials was 3161. Of the 7 studies, 4 (57%) included participants in the interconception period, and 3 (43%) included women in the preconception period. Of the 7 studies, 5 (71%) studies focused on weight reduction, assessing the outcomes of reductions in adiposity and weight. Of the 7 studies, nutrition and dietary outcomes were evaluated in 2 (29%) studies, blood pressure outcomes were compared in 4 (57%) studies, and biochemical and marker outcomes associated with managing disease symptoms were included in 4 (57%) studies. Analysis showed that there were no statistically significant differences in energy intake; weight loss; body fat; and biomarkers such as glycated hemoglobin, total cholesterol, fasting lipid profiles, or blood pressure when compared with standard care.

CONCLUSIONS: Owing to the limited number of studies and low certainty of the evidence, no firm conclusions can be drawn on the effects of mobile phone app interventions on promoting positive behavior changes in women of reproductive age before they are pregnant (preconception and interconception periods).

TRIAL REGISTRATION: PROSPERO CRD42017065903; https://tinyurl.com/2p9dwk4a.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1186/s13643-019-0996-6.

PMID:37074767 | DOI:10.2196/41900

JMIR Form Res. 2023 Apr 19;7:e42868. doi: 10.2196/42868.

ABSTRACT

BACKGROUND: eHealth resources and interventions promise to promote favorable behavior change, self-efficacy, and knowledge acquisition, thereby improving health literacy. However, individuals with limited eHealth literacy may find it difficult to identify, understand, and benefit from eHealth use. It is necessary to identify the self-assessed eHealth literacy of those who use eHealth resources to classify their eHealth literacy levels and to determine the demographic characteristics associated with higher and lower eHealth literacy skills.

OBJECTIVE: This study aimed to identify notable factors closely associated with limited eHealth literacy among Chinese male populations to provide some implications for clinical practice, health education, medical research, and public health policy making.

METHODS: We hypothesized that participants’ eHealth literacy status was associated with various demographic characteristics. Therefore, we elicited the following information in the questionnaire: age and education, self-assessed disease knowledge, 3 well-developed health literacy assessment tools (ie, the All Aspects of Health Literacy Scale, eHealth Literacy Scale, and General Health Numeracy Test), and the 6 Internal items on health beliefs and self-confidence in the Multidimensional Health Locus of Control Scales. Using randomized sampling, we recruited survey participants from Qilu Hospital of Shandong University, China. After validating the data collected through a web-based questionnaire survey via wenjuanxing, we coded all valid data according to predefined coding schemes of Likert scales with different point (score) ranges. We then calculated the total scores of the subsections of the scales or the entire scale. Finally, we used logistic regression modeling to associate the scores of the eHealth Literacy Scale with the scores of the All Aspects of Health Literacy Scale, the General Health Numeracy Test-6, and age and education to ascertain factors considerably associated with limited eHealth literacy among Chinese male populations.

RESULTS: All data from the 543 returned questionnaires were valid according to the validation criteria. By interpreting these descriptive statistics, we found that 4 factors were significantly correlated with participants’ limited eHealth literacy: older age, lower education attainment, lower levels of all aspects of health literacy (functional, communicative, and critical), and weaker beliefs and self-confidence in internal drivers and strengths to stay healthy.

CONCLUSIONS: By applying logistic regression modeling, we ascertained 4 factors that were significantly correlated with limited eHealth literacy among Chinese male populations. These relevant factors identified can inform stakeholders engaging in clinical practice, health education, medical research, and health policy making.

PMID:37074760 | DOI:10.2196/42868

J Sports Sci. 2023 Apr 19:1-8. doi: 10.1080/02640414.2023.2204269. Online ahead of print.

ABSTRACT

Hamstring morphology may play an important role in understanding the aetiology of hamstring injury. Currently, the methods available to capture detailed morphological data such as muscle shape have not been utilized for the hamstring muscles. The aim of this study was to examine the utility of statistical shape modelling (SSM) for describing and comparing hamstring muscle shape in rugby and sprinting athletes. Magnetic resonance images of both thighs of nine elite male rugby players and nine track and field sprinters were analysed. Images were converted to three-dimensional models enabling generation of four statistical shape models. Principal components describing the shape variation in the cohort were derived and evaluated. Six principal components were sufficient to discriminate differences in the shape of the hamstring muscles of rugby and sprinting athletes with 89% classification accuracy. Distinct shape features distinguishing rugby players from sprinters included size, curvature and axial torsion. These data demonstrate that SSM is useful for understanding hamstring muscle shape and that meaningful variation can be identified within a small sample. This method can be used in future research to enhance the anatomical specificity of musculoskeletal modelling and to understand the relationship between hamstring shape and injury.

PMID:37074755 | DOI:10.1080/02640414.2023.2204269