Tag: pubmed

Brief Bioinform. 2021 Dec 27:bbab541. doi: 10.1093/bib/bbab541. Online ahead of print.

ABSTRACT

The study of genetic minority variants is fundamental to the understanding of complex processes such as evolution, fitness, transmission, virulence, heteroresistance and drug tolerance in Mycobacterium tuberculosis (Mtb). We evaluated the performance of the variant calling tool LoFreq to detect de novo as well as drug resistance conferring minor variants in both in silico and clinical Mtb next generation sequencing (NGS) data. The in silico simulations demonstrated that LoFreq is a conservative variant caller with very high precision (≥96.7%) over the entire range of depth of coverage tested (30x to1000x), independent of the type and frequency of the minor variant. Sensitivity increased with increasing depth of coverage and increasing frequency of the variant, and was higher for calling insertion and deletion (indel) variants than for single nucleotide polymorphisms (SNP). The variant frequency limit of detection was 0.5% and 3% for indel and SNP minor variants, respectively. For serial isolates from a patient with DR-TB; LoFreq successfully identified all minor Mtb variants in the Rv0678 gene (allele frequency as low as 3.22% according to targeted deep sequencing) in whole genome sequencing data (median coverage of 62X). In conclusion, LoFreq can successfully detect minor variant populations in Mtb NGS data, thus limiting the need for filtering of possible false positive variants due to sequencing error. The observed performance statistics can be used to determine the limit of detection in existing whole genome sequencing Mtb data and guide the required depth of future studies that aim to investigate the presence of minor variants.

PMID:34962257 | DOI:10.1093/bib/bbab541

Brief Bioinform. 2021 Dec 27:bbab533. doi: 10.1093/bib/bbab533. Online ahead of print.

ABSTRACT

Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confirmed that some TFs have capability to interact with methylated DNA fragments to further regulate gene expression. Although biochemical experiments could recognize TFs binding to methylated DNA sequences, these wet experimental methods are time-consuming and expensive. Machine learning methods provide a good choice for quickly identifying these TFs without experimental materials. Thus, this study aims to design a robust predictor to detect methylated DNA-bound TFs. We firstly proposed using tripeptide word vector feature to formulate protein samples. Subsequently, based on recurrent neural network with long short-term memory, a two-step computational model was designed. The first step predictor was utilized to discriminate transcription factors from non-transcription factors. Once proteins were predicted as TFs, the second step predictor was employed to judge whether the TFs can bind to methylated DNA. Through the independent dataset test, the accuracies of the first step and the second step are 86.63% and 73.59%, respectively. In addition, the statistical analysis of the distribution of tripeptides in training samples showed that the position and number of some tripeptides in the sequence could affect the binding of TFs to methylated DNA. Finally, on the basis of our model, a free web server was established based on the proposed model, which can be available at https://bioinfor.nefu.edu.cn/TFPM/.

PMID:34962264 | DOI:10.1093/bib/bbab533

Sports Biomech. 2021 Dec 28:1-10. doi: 10.1080/14763141.2021.2016927. Online ahead of print.

ABSTRACT

Turnout is a key technical and aesthetic element in competitive Irish dance involving external rotation of the lower limb and must be sustained during landings. ‘Forced’ turnout, aided by floor friction rather than active hip rotation, is likely to result in large internal rotation moments at the knee and ankle, which may increase the risk of injury. The aim of the current study was to establish the relationship between the hip and ankle external rotation vector field and maximum internal rotation moments of the ankle and knee. Thirteen (12 female) competitive Irish dancers performed 10 flys (common Irish dance leap) onto a force plate while being recorded by a ten-camera motion capture system. Time-continuous data were analysed over the duration of landing using statistical parametric mapping (SPM). A positive correlation (p < 0.05) was found between the hip-ankle turnout vector field and maximum ankle internal rotation moments throughout most of the landing. Post-hoc analyses showed that hip external rotation contributed the most to the maximum ankle internal rotation moment (p < 0.05). Increasing hip turnout during landing could reduce internal rotation moments, assuming hip turnout brings the thigh and foot axial orientation more in line with each other.

PMID:34962189 | DOI:10.1080/14763141.2021.2016927

Pathog Glob Health. 2021 Dec 28:1-32. doi: 10.1080/20477724.2021.1993676. Online ahead of print.

ABSTRACT

We analyze risk factors correlated with the initial transmission growth rate of the recent COVID-19 pandemic in different countries. The number of cases follows in its early stages an almost exponential expansion; we chose as a starting point in each country the first day di with 30 cases and we fitted for 12 days, capturing thus the early exponential growth. We looked then for linear correlations of the exponents α with other variables, for a sample of 126 countries. We find a positive correlation, i.e. faster spread of COVID-19, with high confidence level with the following variables, with respective p-value: low Temperature (4⋅10–7), high ratio of old vs. working-age people (3⋅10–6), life expectancy (8⋅10–6), number of international tourists (1⋅10–5), earlier epidemic starting date di (2⋅10–5), high level of physical contact in greeting habits (6⋅10–5), lung cancer prevalence (6⋅10–5), obesity in males (1⋅10–4), share of population in urban areas (2⋅10–4), cancer prevalence (3⋅10–4), alcohol consumption (0.0019), daily smoking prevalence (0.0036), and UV index (0.004, 73 countries). We also find a correlation with low Vitamin D serum levels (0.002–0.006), but on a smaller sample, ∼50 countries, to be confirmed on a larger sample. There is highly significant correlation also with blood types: positive correlation with types RH- (3⋅10–5) and A+ (3⋅10–3), negative correlation with B+ (2⋅10–4). We also find positive correlation with moderate confidence level (p-value of 0.02∼0.03) with: CO₂/SO emissions, type-1 diabetes in children, low vaccination coverage for Tuberculosis (BCG). Several of the above variables are correlated with each other, and so they are likely to have common interpretations. We thus performed a Principal Component Analysis, to find the significant independent linear combinations of such variables. The variables with loadings of at least 0.3 on the significant PCA are: greeting habits, urbanization, epidemic starting date, number of international tourists, temperature, lung cancer, smoking, and obesity in males. We also analyzed the possible existence of a bias: countries with low GDP-per capita might have less intense testing, and we discuss correlation with the above variables.

PMID:34962231 | DOI:10.1080/20477724.2021.1993676

J Sch Nurs. 2021 Dec 28:10598405211069601. doi: 10.1177/10598405211069601. Online ahead of print.

ABSTRACT

Menstrual hygiene management (MHM) among female students is a neglected public health issue in the U.S. This study documented period product insecurity, school absenteeism, and use of school resources to obtain period products among high-school students in St. Louis, MO. Female students completed an anonymous, self-administered survey in English (n = 119). Descriptive statistics were used to determine the prevalence of period product need, resources used to obtain period products, and period-related absenteeism. The mean age of participants was 15.78 ± 1.28. Nearly two-thirds (64.4% (95% CI 55.1%-73.0%)) reported period product insecurity. Two-thirds (66.9% (95% CI 57.7%-75.3%)) reported using at least one of the school’s resources to obtain period products. One-third of the participants (33.6% (95% CI 25.0%-43.1%)) reported missing school due to a lack of period products. School nurses need to be cognizant of how MHM affects their students’ attendance at school and what measures they can take to help reduce menstruation-related absenteeism.

PMID:34962178 | DOI:10.1177/10598405211069601

Eur J Ophthalmol. 2021 Dec 28:11206721211066196. doi: 10.1177/11206721211066196. Online ahead of print.

ABSTRACT

PURPOSE: To evaluate the occurrence of transient central retinal artery occlusion following intravitreal anti-vascular endothelial growth factor injection.

METHODS: Prospective, observational study of 807 patients (807 eyes) who were given intravitreal injections of ranibizumab or aflibercept to treat any cause of retinal vascular diseases between 1 January 2017 and 30 November 2018 at the Federal Fluminense University Hospital in Niteroi, and a private facility in Rio de Janeiro, Brazil. Patients who did not present transient central retinal artery occlusion were excluded.

RESULTS: Among 4069 injections, only 18 patients (0.44%) presented transient central retinal artery occlusion, 14 mild cases (77.7%), and 4 severe cases (22.3%). The clinical factors associated with more severe cases of transient central retinal artery occlusion were the duration of the transient central retinal artery occlusion (p = 0.001), number of prior injections (p = 0.01), and a positive carotid Doppler test (p = 0.01). Twelve cases (66.6%) had positive carotid artery obstruction (atheroma plaque size ≥70%) while 6 cases (33.3%) had negative carotid artery obstruction (atheroma plaque size <70%). The age group >60 years old (p = 0.06), cup/disc ratio >0.6 (p = 0.06), and pseudophakic lens status were also factors with association with transient central retinal artery occlusion, although did not meet criteria for statistical significance. The only patient who experienced a recurrent episode of transient central retinal artery occlusion had diabetic macular edema, positive carotid Doppler test, and cup/optic disc ratio >0.6.

CONCLUSION: Transient central retinal artery occlusion is a rare adverse event that can appear in patients with retinal vascular disease receiving anti-vascular endothelial growth factor therapy. The atheroma plaque size and the number of prior injections can be associated with the severity of the event.

PMID:34962172 | DOI:10.1177/11206721211066196

Int J Soc Psychiatry. 2021 Dec 28:207640211067677. doi: 10.1177/00207640211067677. Online ahead of print.

ABSTRACT

BACKGROUND: Previous studies have demonstrated the positive effects of film screening for raising awareness and improving treatment in various clinical groups. This study not only focused on film screening but also paid special attention to pre-screening group analysis to explore the effectiveness of group movie analysis on mothers with schizophrenic sons.

METHODS: The present study was conducted using a quasi-experimental design with pre-test and post-test and a control group. The research population included all mothers with schizophrenic sons who had enrolled in the Iranian Society Supporting Individuals with Schizophrenia in Tehran in 2021. The participants were 30 mothers with schizophrenic sons who were selected based on the inclusion criteria and were randomly assigned to intervention and control groups. The participants in the intervention group attended 12 film therapy analysis sessions (one session per week). The data were collected using the Connor-Davidson Resilience Scale (CD-RISC). Statistical analyses were performed using the analysis of covariance (ANCOVA).

RESULTS: The results showed a significant difference between the mean scores of resilience for the participants before (M = 28.89) and after the film therapy analysis intervention (M = 52.56, F = 6.15, p = .0001).

CONCLUSION: Film therapy analysis was effective in improving the resilience of mothers with schizophrenic sons. It seems that movie screening with the group analysis afterward contributed to sharing the experiences of caring for the sick child and creating a sense of empathy in mothers. Thus, group movie analysis can be used as a suitable option to reduce the psychological distress of mothers with schizophrenic sons and improve their quality of life.

PMID:34962176 | DOI:10.1177/00207640211067677

J Laparoendosc Adv Surg Tech A. 2021 Dec 28. doi: 10.1089/lap.2021.0520. Online ahead of print.

ABSTRACT

Objectives: To evaluate the impact of body mass index (BMI), preoperative risk classification, previous inguinal herniotomy, and abdominal operations on several steps of robot-assisted radical prostatectomy (RARP) and lymph node (LN) involvement. Methods: A total number of 225 consecutive patients were included in the study who underwent transperitoneal RARP by 1 surgeon. We defined the following parameters as dependent variables: duration of prostatectomy, duration of pelvic lymphadenectomy, incision to suture time, console time, number of dissected LNs and number of positive LNs for metastasis. We assessed the impact of the following covariates using univariate nonparametric and multivariate analysis: BMI, preoperative D’Amico risk classification, history of inguinal herniotomy, and previous abdominal operations. Results: We observed a statistically significant difference among our three BMI groups (<25, ≥25 and <30, and ≥30 kg/m²) regarding pelvic lymphadenectomy and LN metastasis. Moreover, among the three risk groups (low, intermediate, and high) duration of prostatectomy, pelvic lymphadenectomy, and LN metastasis were statistically different. Previous abdominal operations have been also demonstrated to significantly influence the pelvic lymphadenectomy. In addition, our multivariate model proved the impact of our covariates on pelvic lymphadenectomy. Conclusions: Our findings highlight the impact of BMI and preoperative risk on various steps of RARP. We revealed longer duration of pelvic lymphadenectomy and more nodal yield in patients with higher BMI and high-risk disease. Therefore, we suggest that BMI and risk classification according to D’Amico should be taken into account while a RARP is being planned.

PMID:34962160 | DOI:10.1089/lap.2021.0520

Surg Obes Relat Dis. 2021 Nov 13:S1550-7289(21)00544-X. doi: 10.1016/j.soard.2021.11.011. Online ahead of print.

ABSTRACT

BACKGROUND: Major concerns years after the sleeve gastrectomy (SG) include weight regain, development of hiatal hernia (HH) and gastroesophageal reflux disease, with esophagitis and Barrett’s esophagus (BE). Both problems could be related, and the incidence of asymptomatic patients is troubling.

OBJECTIVE: To study the incidence of reflux symptoms, esophagitis, BE, HH, and asymptomatic pathology and their relationship with weight regain in patients 5 years after undergoing SG at different bariatric centers in Spain.

SETTING: Public and private hospitals with bariatric surgery units.

METHODS: Prospective, multicenter, nonrandomized study involving 13 Spanish hospitals with a cumulative experience of 4,500 patients having undergone the SG procedure and patients who had been subjected to the procedure at least 5 years previously along with preoperative gastroscopy. The clinical history, preoperative gastroscopy, and technical details of the SG were recorded. A specific clinical questionnaire was given that recorded the intake volume, perception of satiety, and gastroesophageal reflux (GER) symptoms. Gastroscopy, pH-metry, and manometry studies were carried out, and the data were analyzed statistically. The study has been authorized by the official Spanish ethics committee CEI/CEIm Hospital Universitario Gran Canaria Dr Negrín (code 2019-216-1).

RESULTS: One hundred and five patients who underwent SG and who had with at least 5 years of follow-up were included. All procedures were performed laparoscopically. The mean age of patients was 51.1 years, and 70.5% were women. The mean characteristics of the SG procedure were a 37.2F probe, at 4.6 cm from the pylorus, and a crura closure was performed in 5 cases. There were no major complications (Clavien-Dindo grade >3) or deaths. The average preoperative body mass index was 46.3 kg/m², the minimum reached was 20.6 kg/m², whereas the average after 5 years was of 34.5 kg/m². GER, HH, and esophagitis symptoms went from 17.1%, 28.6%, and 5.7%, respectively, before the SG to 76%, 30.5%, and 31.4%, respectively, 5 years after the procedure. Symptoms persisted over the years in 37.1% of cases and presented de novo in 52.8% of cases. Fifty-three percent of manometries (n = 27, total 51) and 64% of pH-metries (n = 32, total 53; DeMeester average score was 65) were pathologic 5 years after the procedure. Concerning gastroscopies, 5 years after the procedure, HH was found in 33 patients (30.5% of total) and esophagitis in 32 patients (31.4% of total). Eighty patients (76%) had GER symptoms, and 25 patients (24%) were asymptomatic. Only 1 patient (.9%) developed BE.

CONCLUSIONS: Our study has confirmed a high rate of both persistent and de novo esophagitis and hiatal hernia, many of which were asymptomatic, 5 years after SG had been performed. Weight regain and a striking increase in gastric capacity are risk factors indicative of esophagitis, even when patients are asymptomatic. We consider a control gastroscopy and the preventive use of proton pump inhibitors necessary in these cases regardless of symptoms. We recommend that a control gastroscopy should be performed in all cases regardless of symptoms 5 years after SG. Further studies are needed to validate these recommendations.

PMID:34961735 | DOI:10.1016/j.soard.2021.11.011

J Med Imaging Radiat Sci. 2021 Dec 24:S1939-8654(21)00302-7. doi: 10.1016/j.jmir.2021.12.001. Online ahead of print.

ABSTRACT

INTRODUCTION: The idea of radiographer image interpretation has not been fully explored in Fiji despite the great shortage of radiologists in the country. This is a feasibility study of radiographer image interpretation aimed at assessing the accuracy of radiographers in interpreting adult chest X-ray images at the Colonial War Memorial Hospital (CWMH) in Fiji.

METHODS: Forty PA chest X-ray images were interpreted in terms of correctly commenting on the presence/ absence of pathology, the name of the pathology, and the location of the pathology on the data sheets by the CWMH diagnostic radiographers (n = 14). The radiographers were grouped according to their years of work experience (≤ 5 vs > 5) and the Mann Whitney U test on a two-tailed p-value of 0.05 was used to compare this grouping.

RESULTS: The data analysis was conducted using the Statistical Package for Social Sciences (SPSS) v.25 and Microsoft Excel. The diagnostic performance of all radiographers in terms of triaging normal and abnormal in the images shows sensitivity ranging from 71.4 to 100%, with specificity ranging from 47.4 to 100%. The mean sensitivity, specificity, and the overall accuracy of radiographers in triaging normal and abnormal on the images were 89.5%, 72.9%, and 81.6%, respectively. The mean accuracy in naming the pathology was 33.6% and the location sensitivity was 45.7%. There was no statistically significant difference in results between the radiographers’ years of experience.

CONCLUSION: Without any formal qualification, training, and practice, the current results suggest that the cohort of radiographers can perform normal/abnormal triage of CXRs within a test setting. With a significant reduction in the radiographers’ accuracy in terms of naming and locating the abnormality, the study results do not support image interpretation by the radiographers at this stage.

IMPLICATIONS FOR PRACTICE: This feasibility study provides baseline information about the accuracy of image interpretation by diagnostic radiographers at CWMH and provides a platform for further research in image interpretation in Fiji.

PMID:34961703 | DOI:10.1016/j.jmir.2021.12.001