bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-Dimensional Measurements of the Sinus Tarsi and Tarsal Canal in Pediatric Flexible Flatfeet using Weightbearing CT Scans
Authors: Sun Chengyi , Li Shuyuan , Zhu Mingjie , Choudhury Fahim , Myerson Mark S. , Zhang Ming-Zhu 
Published: November 2022

Category: Hindfoot; Other Introduction/Purpose: When the hindfoot is in varus the tarsal canal becomes visible on a lateral Xray (XR) and has been referred to as a 'target sign'. However, the sinus tarsi (ST) and tarsal canal (TC) are not easily visible radiographically when associated with a flatfoot. The dimensions of both the ST and TC in normal and flatfeet are unknown, but if understood, could help with the design and implantation of an arthroereisis, a commonly performed procedure for correction of pediatric flatfoot deformity. Knowing the size of the TC will also reduce postoperative complications of arthroereisis such as stiffness, resulting from too large an implant. The aim of this study was to take three-dimensional (3D) measurements of the TC in pediatric flatfeet under weightbearing (WB) conditions. Methods: This was a prospective IRB approved study in pediatric patients with flexible flatfeet and asymptomatic children without flatfeet who were reviewed and analyzed. Using 3D computer-aided design (CAD) models from weightbearing CT (WBCT) scans, the following parameters were measured: the widest diameter of the posteromedial tarsal canal (WDPTC), the narrowest supero- inferior diameter of the tarsal canal (NSDTC), the length of the tarsal sinus, (LTS), the length of the tarsal canal (LTC) and the tarsal sinus and canal volume (TSCV). Correlations between patient age, Meary's angle, foot and ankle offset (FAO), and each of the above measured parameters were investigated. Both weight bearing and non-weight bearing CT scans were used for study to investigate the effect of bearing weight on the above-mentioned parameters. (Figures 1, 2). Results: Twenty-two children with flexible flatfeet (age range 9-14) and fourteen children with no foot deformity (age 9-15) were included for study. With the WBCT the TSCV decreased by 20% in comparison with non-weightbearing evaluation. The TSCV, the widest diameter of the anterolateral tarsal sinus (WDATS) and LTC decreased in flatfeet both under WB and NWB conditions compared with the control group. A positive linear correlation was found between the TSCV and patient age (r = 0.7307, P < 0.0001), while negative linear correlations were found between the TSCV and FAO (r = -0.5188, P < 0.0001) and Meary's angle (r = -0.3132, P = 0.0019). The tarsal sinus and tarsal canal volume significantly decreased in the flatfoot group during weight bearing, while the volume of the tarsal canal remained unchanged. Older age was not associated with either a wider tarsal canal or its orientation. Conclusion: Although the tarsal sinus and canal volume was positively associated with patient age, there was a negative correlation with both the FAO and Meary's angle. These findings may be very relevant in future study of the subtalar joint in both children and adults, and clearly have an implication for treatment of the pediatric flatfoot with arthroereisis.
Glycoproteomics revealed novel N-glycosylation biomarkers for early diagnosis of lung adenocarcinoma cancers
Authors: Fang Kai , Long Qin , Liao Zhonghua , Zhang Chaoyu , Jiang Zhiqiang 
Published: November 2022

AbstractCirculating biomarkers play important roles in diagnosis of malignant tumors. N-glycosylation is an important post-translation patter and obviously affect biological behaviors of malignant tumor cells. However, the role of N-glycosylation sites in early diagnosis of tumors still remains further investigation. In this study, plasma from 20 lung adenocarcinoma (LUAD), which were all classified as stage I, as well as 20 normal controls (NL) were labeled and screened by mass spectrometry (MS). Total 39 differential N-glycosylation sites were detected in LUAD, 17 were up-regulated and 22 were down-regulated. In all differential sites, ITGB3-680 showed highest potential in LUAD which showed 99.2% AUC, 95.0% SP and 95.0% SN. Besides, APOB-1523 (AUC: 89.0%, SP: 95.0%, SN: 70.0%), APOB-2982 (AUC: 86.8%, SP: 95.0%, SN: 45.0%) and LPAL2-101 (AUC: 81.1%, SP: 95.0%, SN: 47.4%) also acted as candidate biomarkers in LUAD. Combination analysis was then performed by random forest model, all samples were divided into training group (16 cases) and testing group (4 cases) and conducted by feature selection, machine learning, integrated model of classifier and model evaluation. And the results indicated that combination of differential sites could reach 100% AUC in both training and testing group. Taken together, our study revealed multiple N-glycosylation sites which could be applied as candidate biomarkers for early diagnosis diagnosis of LUAD.
USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences
Authors: Wang Xuewen , Budowle Bruce , Ge Jianye 
Published: November 2022

Abstract
Background
Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential.

Results
In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled.

Conclusion
USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs.
SeSAM: software for automatic construction of order-robust linkage maps
Authors: Vidal Adrien , Gauthier Franck , Rodrigez Willy , Guiglielmoni Nadège , Leroux Damien , Chevrolier Nicolas , Jasson Sylvain , Tourrette Elise , Martin Olivier C. , Falque Matthieu 
Published: November 2022

AbstractBackgroundGenotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs.ResultsIn this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustnessframeworkmap which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-densitytotalmap including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++.ConclusionsSeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) athttps://forgemia.inra.fr/gqe-acep/sesam/-/releases
A systematic review and psychometric evaluation of resilience measurement scales for people living with dementia and their carers
Authors: Windle Gill , MacLeod Catherine , Algar-Skaife Katherine , Stott Joshua , Waddington Claire , Camic Paul M. , Sullivan Mary Pat , Brotherhood Emilie , Crutch Sebastian 
Published: November 2022

AbstractPsychometrically sound resilience outcome measures are essential to establish how health and care services or interventions can enhance the resilience of people living with dementia (PLWD) and their carers. This paper systematically reviews the literature to identify studies that administered a resilience measurement scale with PLWD and/or their carers and examines the psychometric properties of these measures. Electronic abstract databases and the internet were searched, and an international network contacted to identify peer-reviewed journal articles. Two authors independently extracted data. They critically reviewed the measurement properties from the available psychometric data in the studies, using a standardised checklist adapted for purpose. Fifty-one studies were included in the final review, which applied nine different resilience measures, eight developed in other populations and one developed for dementia carers in Thailand. None of the measures were developed for use with people living with dementia. The majority of studies (N = 47) focussed on dementia carers, three studies focussed on people living with dementia and one study measured both carers and the person with dementia. All the studies had missing information regarding the psychometric properties of the measures as applied in these two populations. Nineteen studies presented internal consistency data, suggesting seven of the nine measures demonstrate acceptable reliability in these new populations. There was some evidence of construct validity, and twenty-eight studies hypothesised effects a priori (associations with other outcome measure/demographic data/differences in scores between relevant groups) which were partially supported. The other studies were either exploratory or did not specify hypotheses. This limited evidence does not necessarily mean the resilience measure is not suitable, and we encourage future users of resilience measures in these populations to report information to advance knowledge and inform further reviews. All the measures require further psychometric evaluation in both these populations. The conceptual adequacy of the measures as applied in these new populations was questionable. Further research to understand the experience of resilience for people living with dementia and carers could establish the extent current measures -which tend to measure personal strengths -are relevant and comprehensive, or whether further work is required to establish a new resilience outcome measure.
Methods for handling missing data in serially sampled sputum specimens for mycobacterial culture conversion calculation
Authors: Malatesta Samantha , Weir Isabelle R. , Weber Sarah E. , Bouton Tara C. , Carney Tara , Theron Danie , Myers Bronwyn , Horsburgh C. Robert , Warren Robin M. , Jacobson Karen R. , White Laura F. 
Published: November 2022

Abstract
Background
The occurrence and timing of mycobacterial culture conversion is used as a proxy for tuberculosis treatment response. When researchers serially sample sputum during tuberculosis studies, contamination or missed visits leads to missing data points. Traditionally, this is managed by ignoring missing data or simple carry-forward techniques. Statistically advanced multiple imputation methods potentially decrease bias and retain sample size and statistical power.

Methods
We analyzed data from 261 participants who provided weekly sputa for the first 12 weeks of tuberculosis treatment. We compared methods for handling missing data points in a longitudinal study with a time-to-event outcome. Our primary outcome was time to culture conversion, defined as two consecutive weeks with no Mycobacterium tuberculosis growth. Methods used to address missing data included: 1) available case analysis, 2) last observation carried forward, and 3) multiple imputation by fully conditional specification. For each method, we calculated the proportion culture converted and used survival analysis to estimate Kaplan-Meier curves, hazard ratios, and restricted mean survival times. We compared methods based on point estimates, confidence intervals, and conclusions to specific research questions.

Results
The three missing data methods lead to differences in the number of participants achieving conversion; 78 (32.8%) participants converted with available case analysis, 154 (64.7%) converted with last observation carried forward, and 184 (77.1%) converted with multiple imputation. Multiple imputation resulted in smaller point estimates than simple approaches with narrower confidence intervals. The adjusted hazard ratio for smear negative participants was 3.4 (95% CI 2.3, 5.1) using multiple imputation compared to 5.2 (95% CI 3.1, 8.7) using last observation carried forward and 5.0 (95% CI 2.4, 10.6) using available case analysis.

Conclusion
We showed that accounting for missing sputum data through multiple imputation, a statistically valid approach under certain conditions, can lead to different conclusions than naïve methods. Careful consideration for how to handle missing data must be taken and be pre-specified prior to analysis. We used data from a TB study to demonstrate these concepts, however, the methods we described are broadly applicable to longitudinal missing data. We provide valuable statistical guidance and code for researchers to appropriately handle missing data in longitudinal studies.
The impact of funding models on the integration of registered nurses in primary health care teams: protocol for a multi-phase mixed-methods study in Canada
Authors: Mathews Maria , Spencer Sarah , Hedden Lindsay , Lukewich Julia , Poitras Marie-Eve , Marshall Emily Gard , Brown Judith Belle , Sibbald Shannon , Norful Alison A. 
Published: November 2022

AbstractBackgroundFamily practice registered nurses co-managing patient care as healthcare professionals in interdisciplinary primary care teams have been shown to improve access, continuity of care, patient satisfaction, and clinical outcomes for patients with chronic diseases while being cost-effective. Currently, however, it is unclear how different funding models support or hinder the integration of family practice nurses into existing primary health care systems and interdisciplinary practices. This has resulted in the underutilisation of family practice nurses in contributing to high-quality patient care.MethodsThis mixed-methods project is comprised of three studies: (1) a funding model analysis; (2) case studies; and (3) an online survey with family practice nurses. The funding model analysis will employ policy scans to identify, describe, and compare the various funding models used in Canada to integrate family practice nurses in primary care. Case studies involving qualitative interviews with clinic teams (family practice nurses, physicians, and administrators) and family practice nurse activity logs will explore the variation of nursing professional practice, training, skill set, and team functioning in British Columbia, Nova Scotia, Ontario, and Quebec. Interview transcripts will be analysed thematically and comparisons will be made across funding models. Activity log responses will be analysed to represent nurses’ time spent on independent, dependent, interdependent, or non-nursing work in each funding model. Finally, a cross-sectional online survey of family practice nurses in Canada will examine the relationships between funding models, nursing professional practice, training, skill set, team functioning, and patient care co-management in primary care. We will employ bivariate tests and multivariable regression to examine these relationships in the survey results.DiscussionThis project aims to address a gap in the literature on funding models for family practice nurses. In particular, findings will support provincial and territorial governments in structuring funding models that optimise the roles of family practice nurses while establishing evidence about the benefits of interdisciplinary team-based care. Overall, the findings may contribute to the integration and optimisation of family practice nursing within primary health care, to the benefit of patients, primary healthcare providers, and health care systems nationally.
Non-prescribed antibiotic dispensing practices for symptoms of urinary tract infection in community pharmacies and accredited drug dispensing outlets in Tanzania: a simulated clients approach
Authors: Ndaki Pendo M. , Mushi Martha F. , Mwanga Joseph R. , Konje Eveline T. , Mugassa Stella , Manyiri Msilikale W. , Mwita Stanley M. , Ntinginya Nyanda E. , Mmbaga Blandina T. , Keenan Katherine , Sabiiti Wilber , Kesby Mike , Benitez-Paez Fernando , Sandeman Alison , Holden Matthew T. G. , Mshana Stephen E. 
Published: November 2022

Abstract
Background
Antibiotic dispensing without prescription is a major determinant of the emergence of Antimicrobial Resistance (AMR) which has impact on population health and cost of healthcare delivery. This study used simulated clients describing UTI like symptoms to explore compliance with regulation, variations in dispensing practices and drug recommendation, and quality of seller-client interaction on the basis of the gender of the client and the type of drug outlets in three regions in Tanzania.

Method
A total of 672 Accredited Drug Dispensing Outlets (ADDOs) and community pharmacies were visited by mystery clients (MCs). The study was conducted in three regions of Tanzania namely Kilimanjaro (180, 26.79%), Mbeya (169, 25.15%) and Mwanza (323, 48.07%) in March–May 2020. During data collection, information was captured using epicollect5 software before being analyzed using Stata version 13.

Results
Overall, 89.43% (CI: 86.87–91.55%) of drug sellers recommended antibiotics to clients who described UTI like symptoms but held no prescription and 58.93% were willing to sell less than the minimum recommended course. Female clients were more likely than male to be asked if they were taking other medications (27.2% vs 9.8%), or had seen a doctor (27.8% vs 14.7%), and more likely to be advised to consult a doctor (21.6% vs 9.0%); pharmacies addressed these issues more often than ADDOs (17.7% vs 13.2, 23.9% vs 16.6%, 17.7 vs 10.9% respectively). Sellers recommended 32 different drugs to treat the same set of symptoms, only 7 appear in the Tanzanian Standard Treatment Guidelines as recommended for UTI and 30% were 2nd and 3rd line drugs. ADDO sellers recommended 31 drug types (including 2nd and 3rd line) but had permission to stock only 3 (1st line) drugs. The most commonly suggested antibiotics were Azithromycin (35.4%) and ciprofloxacin (20.5%). Azithromycin was suggested more often in pharmacies (40.8%) than in ADDOs (34.4%) and more often to male clients (36.0%) than female (33.1%).

Conclusion
These findings support the need for urgent action to ensure existing regulations are adhered to and to promote the continuing professional development of drug sellers at all outlet levels to ensure compliance with regulation, high quality service and better antibiotic stewardship.
Threshold of main pancreatic duct for malignancy in intraductal papillary mucinous neoplasm at head-neck and body-tail
Authors: Zhou Hao , Li Xiaoshuang , Wang Yajie , Wang Zhiyue , Zhu Jingrong , Wang Zhongqiu , Chen Xiao 
Published: November 2022

Abstract
Background
Main pancreatic duct (MPD) dilation is a high-risk stigmata/worrisome feature of malignancy in intraductal papillary mucinous neoplasms (IPMNs). The threshold of MPD diameter in predicting malignancy may be related to the lesion location. This study aimed to separately identify the thresholds of MPD for malignancy of IPMNs separately for the head-neck and body-tail.

Materials and methods
A total of 185 patients with pathologically confirmed IPMNs were included. Patient demographic information, clinical data, and pathological features were obtained from the medical records. Those IPMNs with high-grade dysplasia or with associated invasive carcinoma were considered as malignant tumor. Radiological data including lesion location, tumor size, diameter of the MPD, mural nodule, and IPMN types (main duct, MD; branch duct, BD; and mixed type, MT), were collected on computed tomography or magnetic resonance imaging. Serum carbohydrate antigen 19-9 levels, serum carcinoembryonic antigen levels, and the medical history of diabetes mellitus, chronic cholecystitis, and pancreatitis were also collected.

Results
Malignant IPMNs were detected in 31.6% of 117 patients with lesions in the pancreatic head-neck and 20.9% of 67 patients with lesions in the pancreatic body-tail. In MPD-involved IPMNs, malignancy was observed in 54.1% of patients with lesions in the pancreatic head-neck and 30.8% of patients with lesions in the pancreatic body-tail (p < 0.05). The cutoff value of MPD diameter for malignancy was 6.5 mm for lesions in the head-neck and 7.7 mm for lesions in the body-tail in all type of IPMNs. In MPD-involved IPMNs, the threshold was 8.2 mm for lesion in pancreatic head-neck and 7.7 mm for lesions in the body-tail. Multivariate analysis confirmed that MPD diameter ≥ 6.5 mm (pancreatic head-neck) and MPD diameter ≥ 7.7 mm (pancreatic body-tail) were independent predictors of malignancy (p < 0.05). Similar results were observed in MPD-involved IPMNs using 8.2 mm as a threshold.

Conclusion
The thresholds of the dilated MPD may be associated with IPMNs locations. Thresholds of 6.5 mm for lesions in the head-neck and 7.7 mm for lesions in the body-tail were observed. For MPD-involved IPMNs alone, threshold for lesions in the head-neck was close to that in the body-tail.