Tag: statistics

Proteins. 2022 Sep 11. doi: 10.1002/prot.26420. Online ahead of print.

ABSTRACT

Antibodies are key proteins produced by the immune system to target pathogen proteins termed antigens via specific binding to surface regions called epitopes. Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computational protocol that uses template-based modeling and docking to predict epitope residues. This protocol is implemented in three major steps. First, a template-based modeling approach is used to build the antibody structures. We tested several options, including generation of models using AlphaFold2. Second, each antibody model is docked to the antigen using the FFT based docking program PIPER. Attention is given to optimally selecting the docking energy parameters depending on the input data. In particular, the van der Waals energy terms are reduced for modeled antibodies relative to X-ray structures. Finally, ranking of antigen surface residues is produced. The ranking relies on the docking results, i.e., how often the residue appears in the docking poses’ interface, and also on the energy favorability of the docking pose in question. The method, called PIPER-Map, has been tested on a widely used antibody-antigen docking benchmark. The results show that PIPER-Map improves upon the existing epitope prediction methods. An interesting observation is that epitope prediction accuracy starting from antibody sequence alone does not significantly differ from that of starting from unbound (i.e., separately crystallized) antibody structure.

PMID:36088633 | DOI:10.1002/prot.26420

Colorectal Dis. 2022 Sep 11. doi: 10.1111/codi.16328. Online ahead of print.

ABSTRACT

The management of malignant polyps is a treatment dilemma in selecting between polypectomy and colorectal resection. To assist clinicians, guidelines have been developed by the Association of Coloproctology of Great Britain and Ireland (ACPGBI) to provide treatment recommendations.

METHODS: This study compared management strategy based on the ACPGBI risk categorisation for malignant polyps. Univariate and multivariable statistical analysis was undertaken to assess the factors predicting management strategy. A population wide analysis was performed of 1,646 malignant polyps, and the factors which predicted their management strategy, from Queensland, Australia from 2011-2019.

RESULTS: Overall 31.55% of patients with very-low or low risk disease proceeded to resection. Of those with high or very-high risk disease, 36.69% did not proceed to resection. In very-low and low risk polyps, age (p=0.003) and polyp location (p<0.001) were significantly different between the colorectal resection group and the polypectomy alone group. In those with very-high or high risk polyps age (p<0.001), type of facility (public or private) for the colonoscopy (p=0.037), right colonic polyps compared to left colonic (p=0.015) and rectal polyps (p<0.001) and mismatch repair mutations present (p=0.027) were predictive of resection in high risk disease using a multivariable model.

CONCLUSION: Over 30% of patients with very-low and low risk malignant polyps proceeded to resection, against the advice of guidelines. Furthermore, over 35% of patients with very-high or high risk malignant polyps did not proceed to resection. Education strategies may improve management decision choices. Furthermore, improvements in data collation will improve understanding management choices into the future.

PMID:36088629 | DOI:10.1111/codi.16328

Orv Hetil. 2022 Sep 11;163(37):1481-1489. doi: 10.1556/650.2022.32573. Print 2022 Sep 11.

ABSTRACT

INTRODUCTION: In international comparison, Hungary is in the forefront of cancer incidence and mortality statistics. Based on paper-based death certificates, mortality statistics are compiled by the Hungarian Central Statistical Office, while population-based measures of cancer incidences are performed by the Hungarian National Cancer Registry.

OBJECTIVE: Linking the records of these two independent databases can highlight their weaknesses and provide an opportunity to reconcile and verify collected data, which may emphasize the need to expand current data exchange protocols.

METHOD: Based on the Hungarian unique health care insurance ID, the mortality database of the Hungarian Central Statistical Office between 2012 and 2020 was compared with the data of the Hungarian National Cancer Registry from 2001 to 2020. Deaths in 2018, in particular those related to lung cancer, were examined in more depth to demonstrate the biases resulting from erroneous data collection.

RESULTS: The mortality database of the Hungarian Central Statistical Office contained 32 586 cases with an underlying cause of death of malignant neoplasm for 2018, of which 29 970 were identified in the Hungarian National Cancer Registry. Out of the 8716 deaths coded to lung cancer, 7957 corresponding individuals were also found in the Registry. From the matches, 7381 cases were marked with lung cancer in the Hungarian National Cancer Registry. For the remaining 576 cases, the Registry recorded different types of cancers, of which in 69 cases with lung metastasis.

DISCUSSION: The differences between the two databases may be caused by methodological differences in data collection, incomplete, inaccurate reporting and differences in processing algorithms. Nevertheless, the majority of the data in the examined databases were found to be appropriate for epidemiological studies.

CONCLUSION: Based on the outcomes of the present analysis, a revision of the data transfer between the two institutions is in order. The introduction of electronic Death certificate recording and validity checks are expected to improve the reliability of ID numbers and may shorten data processing times. Orv Hetil. 2022; 163(37): 1481-1489.

PMID:36088625 | DOI:10.1556/650.2022.32573

Arch Orthop Trauma Surg. 2022 Sep 11. doi: 10.1007/s00402-022-04603-1. Online ahead of print.

ABSTRACT

BACKGROUND: The treatment of periprosthetic femur fractures around a total knee replacement remains a technical challenge for the orthopedic surgeon. Management options include non-operative treatment, plate fixation, intramedullary nailing and distal femur replacement (DFR), with few studies comparing fixation with DFR. This is an up-to-date meta-analysis in the literature to directly compare clinical outcomes between fixation and distal femoral replacement in the treatment of supracondylar periprosthetic femur fractures.

METHODS: A stratified literature search of the Medline, EMBASE and Cochrane databases was performed. All studies in English language were searched from inception to July 2022. The search was performed with the following MeSH terms: Periprosthetic fracture AND ORIF OR Internal Fixation AND Distal Femur Replacement. The search was conducted using a predesigned search strategy where all eligible literature was critically appraised for methodological quality using the Cochrane collaboration tool. We included Level I, II and III studies comparing fixation with DFR in the treatment of periprosthetic supracondylar femur fractures. Data from eligible studies were extracted by two authors (NP and AR) and a table created which included author, year, sample size, mean age, measured parameters, follow-up period, fracture classification, length of stay (days), mortality rate, revision rate and complication rate.

RESULTS: The extracted data were pooled for meta-analysis using RevMan® v5.3.5 software (Nordic Cochrane Centre, Copenhagen, Denmark) and forest plots constructed. A p value < 0.05 was considered statistically significant and confidence intervals (CI) set to 95%. A total of six studies were included in the meta-analysis (n = 406). 153 patients underwent distal femur replacement and 253 patients underwent fixation with a mean follow-up time of 71.4 months. The results of this analysis suggest no statistically significant difference in measured outcomes.

CONCLUSION: The results of this meta-analysis suggest no proven statistically significant difference between DFR and fixation in terms of length of hospital stay, mortality rate, revision rate and complication rate for the treatment of periprosthetic supracondylar femur fractures. Further prospective randomized research may help to define the specific indications for each treatment option which must include fracture configuration. Early functional outcome and cost-effectiveness have yet to be evaluated in the available literature.

PMID:36088601 | DOI:10.1007/s00402-022-04603-1

Folia Med Cracov. 2022;62(1):105-122. doi: 10.24425/fmc.2022.141694.

ABSTRACT

Coronavirus infection (COVID-19) is a highly infectious disease of viral etiology. SARS-CoV-2 virus was first identified during the investigation of the outbreak of respiratory disease in Wuhan, China in December 2019. And already on March 11, 2020 COVID-19 in the world was characterized by the WHO as a pandemic. In Ukraine the situation with incidence COVID-19 remains difficult. The purpose of this study is to to develop a mathematical forecasting model for COVID-19 incidence in Ukraine using an exponential smoothing method. The article analyzes reports on basic COVID-19 incidence rates from 29.02.2019 to 01.10.2021. In order to determine the forecast levels of statistical indicators that characterize the epidemic process of COVID-19 the method of exponential smoothing was used. It is expected that from 29.02.2019 to 01.10.2021 the epidemic situation of COVID-19 incidence will stabilize. The indicator of “active patients” will range from 159.04 to 353.63 per 100 thousand people. The indicator of “hospitalized patients” can reach 15.43 and “fatalities” ‒ 1.87. The use of the method of exponential smoothing based on time series models for modeling the dynamics of COVID-19 incidence allows to develop and implement scientifically sound methods in order to prevent, quickly prepare health care institutions for hospitalization.

PMID:36088596 | DOI:10.24425/fmc.2022.141694

Folia Med Cracov. 2022;62(1):5-17. doi: 10.24425/fmc.2022.141687.

ABSTRACT

INTRODUCTION: The musculus flexor carpi radialis (FCR) is a muscle with an important function for the mechanics and physiology of the hand. Its isolation during intrauterine development occurs relatively late, which may result in the presence of high variability during the fetal period. The aim of this study is to determine the detailed typology of FCR in the fetal period based on the available material.

MATERIAL AND METHODS: A total of 114 human fetuses (53 female, 61 male) aged between 117.0 and 197.0 days of fetal life were included in the study. The research material was derived from the collections of the Department of Anatomy, Medical University of Wrocław. Fetuses were stored in typical conservation solvents. The study incorporated the following methods: anthropological, preparational, and image acquisition, which was obtained using an innovative digital microscope. Statistical analysis was performed using R software.

RESULTS: The typology of FCR was determined based on the characteristics of the distal attachment of the investigated muscle. The statistical analysis revealed a predominance of type I in the examined fetal material – the attachment located on metacarpal bone II (about 82% of cases). Type IV (attachment to the 4th metacarpal bone) occurs with a frequency of less than 10% and the remaining types II and III occur with a frequency of 4-6%. The statistical analysis did not reveal bilateral or dimorphic differences in the prevalence of each FCR type. In respect of the collected anthropometric parameters, no statistically significant dimorphic differences were revealed. For a more complete description, the FCR proportionality index was introduced. The mean value of this index was 0.6 and was independent of the side or sex of the analyzed fetus.

CONCLUSIONS: FCR in the fetal period is characterized by a stable course in both the proximal and distal attachments.

PMID:36088589 | DOI:10.24425/fmc.2022.141687

Hernia. 2022 Sep 11. doi: 10.1007/s10029-022-02670-2. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of this study was to evaluate the safety and effectiveness of a Chinese absorbable tack for mesh fixation in laparoscopic abdominal wall hernia repair compared to a widely used similar imported product.

METHODS: From May 2019 to December 2020, the clinical data of 158 patients with abdominal wall hernias were analyzed. They were divided into two groups: 76 patients underwent surgery with local absorbable tacks for mesh fixation (experimental group) and 82 patients received a similar imported product (control group). Preoperative and postoperative variables, effectiveness of postoperative immediate fixation, and with ease of handling of instruments were analyzed statistically. Complications and adverse events were followed and analyzed statistically. Meanwhile, medical costs were recorded and evaluated.

RESULTS: There were no statistically significant differences between the two groups in terms of demographic data, hernia types, hernia defects, or number of tacks used for mesh fixation during operation. The effect of postoperative immediate fixation and with ease of handling of instruments in both groups were not significantly different. During the follow-up period, no recurrence or adverse events occurred in either group. No significant differences were noted between the two groups for other complications, such as chronic pain, foreign body sensation, infection of the abdominal wall, hematoma and seroma. There was a significant difference in medical costs between the two groups: the costs associated with the experimental group using local tacks were lower.

CONCLUSION: Chinese absorbable tacks for mesh fixation in laparoscopic abdominal wall hernia repair are effective, safe, and economical. They are worthy of clinical application.

PMID:36088587 | DOI:10.1007/s10029-022-02670-2

Health Promot J Austr. 2022 Sep 11. doi: 10.1002/hpja.662. Online ahead of print.

ABSTRACT

ISSUE ADDRESSED: Child and youth participation in physical activity (PA) is fundamental for healthy development and obesity prevention. Government policy requires schools to offer 150 minutes of PA each week, however compliance is low. Race Around Australia (RAA) is a New South Wales (NSW) Department of Education, virtual PA program aimed at assisting schools in meeting the PA guidelines.

METHODS: A pre- and post-intervention, quasi-experimental study was conducted using a mixed-methods approach comprising teacher interviews, a student questionnaire, and a 1.6 kilometre (km) timed run. Data were collected from April-September 2021 among students and teachers in Grades 5-8, from 10 schools in NSW, Australia.

RESULTS: The analytical sample included data from 918 students and 17 teachers. The RAA program was deemed feasible and acceptable in primary schools, whereas there were several systemic and intrapersonal barriers to implementation success for secondary schools. In primary schools, RAA increased PA opportunities and the 1.6 km timed runs revealed a statistically significant treatment by time effect in favour of the intervention group for cardiorespiratory fitness (-36.91 secs, 95% CI [-63.14, -10.68], p=0.006).

CONCLUSIONS: RAA has demonstrated feasibility and potential efficacy in improving cardiorespiratory fitness. We recommend that program refinement be made to deliver an intervention that addresses the unique barriers of the secondary school setting through a multi-level ecological approach.

PMID:36088579 | DOI:10.1002/hpja.662

Brief Bioinform. 2022 Sep 9:bbac399. doi: 10.1093/bib/bbac399. Online ahead of print.

ABSTRACT

Tipping points or critical transitions widely exist during the progression of many biological processes. It is of great importance to detect the tipping point with the measured omics data, which may be a key to achieving predictive or preventive medicine. We present the tipping point detector (TPD), a web tool for the detection of the tipping point during the dynamic process of biological systems, and further its leading molecules or network, based on the input high-dimensional time series or stage course data. With the solid theoretical background of dynamic network biomarker (DNB) and a series of computational methods for DNB detection, TPD detects the potential tipping point/critical state from the input omics data and outputs multifarious visualized results, including a suggested tipping point with a statistically significant P value, the identified key genes and their functional biological information, the dynamic change in the DNB/leading network that may drive the critical transition and the survival analysis based on DNB scores that may help to identify ‘dark’ genes (nondifferential in terms of expression but differential in terms of DNB scores). TPD fits all current browsers, such as Chrome, Firefox, Edge, Opera, Safari and Internet Explorer. TPD is freely accessible at http://www.rpcomputationalbiology.cn/TPD.

PMID:36088546 | DOI:10.1093/bib/bbac399

Int Health. 2022 Sep 10:ihac061. doi: 10.1093/inthealth/ihac061. Online ahead of print.

ABSTRACT

BACKGROUND: Despite a crucial role played by obstetric care providers (OCPs) in providing pain relief methods during labour, the evidence suggests that there is a large number of women in Ethiopia who did not have access to pain relief methods. Moreover, to the best of the investigators’ knowledge, evidence is scarce regarding the utilization of pharmacological labour pain management methods in the study area. Thus this study was carried out to determine the practice of pharmacological labour pain management methods among OCPs in Harari regional state health facilities in Ethiopia.

METHODS: A facility-based cross-sectional study was conducted from 20 May to 10 June 2021 in Harari regional state health facilities. All (n=464) OCPs in Harari regional state health facilities were included in the study. Data were collected using a structured questionnaire adapted from previous studies. The data were entered into Epi-data version 3.1 statistical software. Statistical analysis was carried out using SPSS for Windows version 22. Bivariate and multivariate logistic regression analyses were employed to determine the association between independent variables and the outcome variable. A p-value <0.05 was used to establish statistical significance.

RESULTS: In this study, 464 OCPs participated. The overall utilization of pharmacological labour pain relief methods was 50.9% (95% confidence interval [CI] 45.8 to 55.8). The main barriers to labouring mothers receiving pain relief include high patient flow (54.4%), the limited number of staff (51.9%) and a lack of knowledge and skill (32.9%). Being female (adjusted odds ratio [AOR] 2.07 [95% CI 1.31 to 3.26]), not having training (AOR 1.60 [95% CI 1.02 to 2.53]) and having an unfavourable attitude (AOR 9.1 [95% CI 5.34 to 15.35]) were the predictors of utilization of pharmacological labour pain management methods.

CONCLUSIONS: The study revealed that half of the OCPs utilized the pharmacological labour pain management method. In general, this study identified that variables like sex, training and the attitude of OCPs were factors associated with the utilization of pharmacological labour pain management methods. The health facilities should provide training to enhance the skill of OCPs and equip themselves with sufficient analgesic drugs.

PMID:36088530 | DOI:10.1093/inthealth/ihac061