bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technologies for Diabetes Self-Monitoring: A Scoping Review and Assessment Using the REASSURED Criteria
Authors: Zafra-Tanaka Jessica Hanae , Beran David , Vetter Beatrice , Sampath Rangarajan , Bernabe-Ortiz Antonio 
Published: March 2021

Background: Self-management is an important pillar for diabetes control and to achieve it, glucose self-monitoring devices are needed. Currently, there exist several different devices in the market and many others are being developed. However, whether these devices are suitable to be used in resource constrained settings is yet to be evaluated. Aims: To assess existing glucose monitoring tools and also those in development against the REASSURED which have been previously used to evaluate diagnostic tools for communicable diseases. Methods: We conducted a scoping review by searching PubMed for peer-review articles published in either English, Spanish or Portuguese in the last 5 years. We selected papers including information about devices used for self-monitoring and tested on humans with diabetes; then, the REASSURED criteria were used to assess them. Results: We found a total of 7 continuous glucose monitoring device groups, 6 non-continuous, and 6 devices in development. Accuracy varied between devices and most of them were either invasive or minimally invasive. Little to no evidence is published around robustness, affordability and delivery to those in need. However, when reviewing publicly available prices, none of the devices would be affordable for people living in low- and middle-income countries. Conclusions: Available devices cannot be considered adapted for use in self-monitoring in resource constraints settings. Further studies should aim to develop less-invasive devices that do not require a large set of components. Additionally, we suggest some improvement in the REASSURED criteria such as the inclusion of patient-important outcomes to increase its appropriateness to assess non-communicable diseases devices.
“Lighten This Burden of Ours”: Acceptability and Preferences Regarding Injectable Antiretroviral Treatment Among Adults and Youth Living With HIV in Coastal Kenya
Authors: Simoni Jane M. , Beima-Sofie Kristin , Wanje George , Mohamed Zahra H. , Tapia Kenneth , McClelland R. Scott , Ho Rodney J. Y. , Collier Ann C. , Graham Susan M. 
Published: March 2021

Background: Long-acting injectable (LAI) antiretroviral therapy (ART) may offer persons living with HIV (PLWH) an attractive alternative to pill-based treatment options, yet acceptability data remain scant, especially in sub-Saharan Africa. Methods: We conducted 6 focus group discussions with PLWH, including key stake holder groups, and analyzed data with content analysis. Results: Initial reactions to the idea of LAI-ART were often positive. The primary advantages voiced were potential to facilitate improved adherence and alleviate the burden of daily pill-taking while avoiding inadvertent disclosure and HIV stigma. Potential side effects were a particular concern of the women. Most participants preferred clinic-based administration over self-injections at home due to concerns about safety, privacy, and potential need for refrigeration. Conclusions: LAI-ART may be acceptable in Kenya, provided injections are infrequent and delivered in a clinic setting. However, HIV stigma, fear of potential side effects, and limited clinical capacity would need to be addressed.
COVID-19 pandemic-induced physical inactivity: the necessity of updating the Global Action Plan on Physical Activity 2018-2030
Authors: Amini H. , Habibi S. , Islamoglu A. H. , Isanejad E. , Uz C. , Daniyari H. 
Published: March 2021

AbstractTo prevent and reduce inactivity, the World Health Organization (WHO) designed a global plan called Global Action Plan on Physical Activity 2018–2030 (GAPPA) in 2017. In this plan and according to the state of physical activity in 2016, actions and goals were set. However, the world is facing a COVID-19 pandemic, which has affected various aspects of lifestyle, including physical activity. Some studies have shown that physical activity reduced during the pandemic. For this reason, the WHO should review the GAPPA and update goals and actions according to the state of physical activity in 2020.
Enhancing backcross programs through increased recombination
Authors: Tourrette Elise , Falque Matthieu , Martin Olivier C. 
Published: March 2021

AbstractBackgroundIntrogression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters.ResultsIn this paper, we assess, by simulations in the context ofBrassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental.ConclusionsDepending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Authors: Chen Hao , Lu Yan , Lu Dongsheng , Xu Shuhua 
Published: March 2021

AbstractBackgroundY-chromosome DNA (Y-DNA) has been used for tracing paternal lineages and offers a clear path from an individual to a known, or likely, direct paternal ancestor. The advance of next-generation sequencing (NGS) technologies increasingly improves the resolution of the non-recombining region of the Y-chromosome (NRY). However, a lack of suitable computer tools prevents the use of NGS data from the Y-DNA studies.ResultsWe developed Y-LineageTracker, a high-throughput analysis framework that not only utilizes state-of-the-art methodologies to automatically determine NRY haplogroups and identify microsatellite variants of Y-chromosome on a fine scale, but also optimizes comprehensive Y-DNA analysis methods for NGS data. Notably, Y-LineageTracker integrates the NRY haplogroup and Y-STR analysis modules with recognized strategies to robustly suggest an interpretation for paternal genetics and evolution. NRY haplogroup module mainly covers haplogroup classification, clustering analysis, phylogeny construction, and divergence time estimation of NRY haplogroups, and Y-STR module mainly includes Y-STR genotyping, statistical calculation, network analysis, and estimation of time to the most recent common ancestor (TMRCA) based on Y-STR haplotypes. Performance comparison indicated that Y-LineageTracker outperformed existing Y-DNA analysis tools for the high performance and satisfactory visualization effect.ConclusionsY-LineageTracker is an open-source and user-friendly command-line tool that provide multiple functions to efficiently analyze Y-DNA from NGS data at both Y-SNP and Y-STR level. Additionally, Y-LineageTracker supports various formats of input data and produces high-quality figures suitable for publication. Y-LineageTracker is coded with Python3 and supports Windows, Linux, and macOS platforms, and can be installed manually or via the Python Package Index (PyPI). The source code, examples, and manual of Y-LineageTracker are freely available athttps://www.picb.ac.cn/PGG/resource.phpor CodeOcean (https://codeocean.com/capsule/7424381/tree).
Transcriptional expression of secondary resistance genes ccdB and repA2 is enhanced in presence of cephalosporin and carbapenem in Escherichia coli
Authors: Baishya Somorita , Deshamukhya Chandrayee , Wangkheimayum Jayalaxmi , Das Bhaskar Jyoti , Anbarasu Anand , Talukdar Anupam Das , Bhattacharjee Amitabha , Choudhury Manabendra Dutta 
Published: March 2021

Abstract
Background
The issue of carbapenem resistance in E.coli is very concerning and it is speculated that cumulative effect of both primary resistance genes and secondary resistance genes that act as helper to the primary resistance genes are the reason behind their aggravation. Therefore, here we attempted to find the role of two secondary resistance genes (SRG) ccdB and repA2 in carbapenem resistance in E. coli (CRE). In this context influential genes belonging to secondary resistome that act as helper to the primary resistance genes like blaNDM and blaCTX-M in aggravating β-lactam resistance were selected from an earlier reported in silico study. Transcriptional expression of the selected genes in clinical isolates of E.coli that were discretely harboring blaNDM-1, blaNDM-4, blaNDM-5, blaNDM-7 and blaCTX-M-15 with and without carbapenem and cephalosporin stress (2 μg/ml) was determined by real time PCR. Cured mutants sets that were lacking (i) primary resistance genes, (ii) secondary resistance genes and (iii) both primary and secondary resistance genes were prepared by SDS treatment. These sets were then subjected to antibiotic susceptibility testing by Kirby Bauer disc diffusion method.

Results
Out of the 21 genes reported in the in silico study, 2 genes viz.repA2 and ccdB were selected for transcriptional expression analysis. repA2, coding replication regulatory protein, was downregulated in response to carbapenems and cephalosporins. ccdB, coding for plasmid maintenance protein, was also downregulated in response to carbapenems except imipenem and cephalosporins. Following plasmid elimination assay increase in diameter of zone of inhibition under stress of both antibiotics was observed as compared to uncured control hinting at the reversion of antibiotic susceptibility by the-then resistant bacteria.

Conclusion
SRGs repA2 and ccdB help sustenance of blaNDM and blaCTX-M under carbapenem and cephalosporin stress.
Healthcare professionals’ perspective on treatment burden and patient capacity in low-income rural populations: challenges and opportunities
Authors: Hardman Ruth , Begg Stephen , Spelten Evelien 
Published: March 2021

Abstract
Background
The challenges of chronic disease self-management in multimorbidity are well-known. Shippee’s Cumulative Complexity Model provides useful insights on burden and capacity factors affecting healthcare engagement and outcomes. This model reflects patient experience, but healthcare providers are reported to have a limited understanding of these concepts. Understanding burden and capacity is important for clinicians, since they can influence these factors both positively and negatively. This study aimed to explore the perspectives of healthcare providers using burden and capacity frameworks previously used only in patient studies.

Methods
Participants were twelve nursing and allied health providers providing chronic disease self-management support in low-income primary care settings. We used written vignettes, constructed from interviews with multimorbid patients at the same health centres, to explore how clinicians understood burden and capacity. Interviews were recorded and transcribed verbatim. Analysis was by the framework method, using Normalisation Process Theory to explore burden and the Theory of Patient Capacity to explore capacity.

Results
The framework analysis categories fitted the data well. All participants clearly understood capacity and were highly conscious of social (e.g. income, family demands), and psychological (e.g. cognitive, mental health) factors, in influencing engagement with healthcare. Not all clinicians recognised the term ‘treatment burden’, but the concept that it represented was familiar, with participants relating it both to specific treatment demands and to healthcare system deficiencies. Financial resources, health literacy and mental health were considered to have the biggest impact on capacity. Interaction between these factors and health system barriers (leading to increased burden) was a common and challenging occurrence that clinicians struggled to deal with.

Conclusions
The ability of health professionals to recognise burden and capacity has been questioned, but participants in this study displayed a level of understanding comparable to the patient literature. Many of the challenges identified were related to health system issues, which participants felt powerless to address. Despite their awareness of burden and capacity, health providers continued to operate within a single-disease model, likely to increase burden. These findings have implications for health system organisation, particularly the need for alternative models of care in multimorbidity.
High inter-rater reliability of Japanese bedriddenness ranks and cognitive function scores: a hospital-based prospective observational study
Authors: Tago Masaki , Katsuki Naoko E. , Yaita Shizuka , Nakatani Eiji , Yamashita Shun , Oda Yoshimasa , Yamashita Shu-ichi 
Published: March 2021

Abstract
Background
The statistical validities of the official Japanese classifications of activities of daily living (ADLs), including bedriddenness ranks (BR) and cognitive function scores (CFS), have yet to be assessed. To this aim, we evaluated the ability of BR and CFS to assess ADLs using inter-rater reliability and criterion-related validity.

Methods
New inpatients aged ≥75 years were enrolled in this hospital-based prospective observational study. BR and CFS were assessed once by an attending nurse, and then by a social worker/medical clerk. We evaluated inter-rater reliability between different professions by calculating the concordance rate, kappa coefficient, Cronbach’s α, and intraclass correlation coefficient. We also estimated the relationship of the Barthel Index and Katz Index with the BR and CFS using Spearman’s correlation coefficients.

Results
For the 271 patients enrolled, BR at the first assessment revealed 66 normal, 10 of J1, 15 of J2, 18 of A1, 31 of A2, 37 of B1, 35 of B2, 22 of C1, and 32 of C2. The concordance rate between the two BR assessments was 68.6%, with a kappa coefficient of 0.61, Cronbach’s α of 0.91, and an intraclass correlation coefficient of 0.83, thus showing good inter-rater reliability. BR was negatively correlated with the Barthel Index (r = − 0.848, p < 0.001) and Katz Index (r = − 0.820, p < 0.001), showing justifiable criterion-related validity.
Meanwhile, CFS at the first assessment revealed 92 normal, 47 of 1, 19 of 2a, 30 of 2b, 60 of 3a, 8 of 3b, 8 of 4, and 0 of M. The concordance rate between the two CFS assessments was 70.1%, with a kappa coefficient of 0.62, Cronbach’s α of 0.87, and an intraclass correlation coefficient 0.78, thus also showing good inter-rater reliability. CFS was negatively correlated with the Barthel Index (r = − 0.667, p < 0.001) and Katz Index (r = − 0.661, p < 0.001), showing justifiable criterion-related validity.

Conclusions
BR and CFS could be reliable and easy-to-use grading scales of ADLs in acute clinical practice or large-scale screening, with high inter-rater reliabilities among different professions and significant correlations with well-established, though complicated to use, instruments to assess ADLs.

Trial registration
UMIN000041051 (2020/7/10).
Poor health-related physical fitness performance increases the overweight and obesity risk in older adults from Taiwan
Authors: Ho Chien-Chang , Lee Po-Fu , Chen Hui-Ling , Tseng Ching-Yu , Hsieh Xin-Yu , Chiu Chih-Hui 
Published: March 2021

Abstract
Background
The purpose of the present study was to investigate the associations between health-related physical fitness performance and overweight/obesity risk among Taiwanese healthy older adults.

Methods
A secondary dataset from the nationwide survey was applied in this study. Data from a total of 21,630 respondents aged 65–96 years were collected in this study. Demographic characteristics, life habits, perceived health status, anthropometric assessments, and health-related physical fitness measurements from this dataset were analyzed using the chi-square test, one-way analysis of variance, and logistic regression analysis.

Results
The results indicated that overweight and obesity significantly associated with health-related physical fitness performance in the Taiwanese older adult population. In particular, the upper extremity muscular endurance scores of older adults with poor activity and physical fitness scores revealed obesity as a critical indicator of health-related physical fitness performance.

Conclusions
Future studies can use muscle quality or body fat classification to predict obesity in older adults, which could more precisely portray the relationship between obesity and health-related physical fitness performance.
Development of a recombinase-aided amplification assay for rapid detection of human norovirus GII.4
Authors: Qin Zhiwei , Xue Liang , Cai Weicheng , Gao Junshan , Jiang Yueting , Yang Jiale , Liang Yanhui , Wang Linping , Zhang Jumei , Hu Yongdan , Wu Qingping 
Published: March 2021

Abstract
Background
Human noroviruses are one of the main causes of foodborne illnesses and represent a serious public health concern. Rapid and sensitive assays for human norovirus detection are undoubtedly necessary for clinical diagnosis, especially in regions without more sophisticated equipment.

Method
The rapid reverse transcription recombinase-aided amplification (RT-RAA) is a fast, robust and isothermal nucleic acid detection method based on enzyme reaction. This method can complete the sample detection at 39 °C in 30 min. In this study, we successfully established a rapid reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of human norovirus GII.4 and applied this assay to clinical samples, as well as comparison with commercial reverse transcription real-time fluorescence quantitative PCR (RT-qPCR).

Results
At 95% probability, the detection sensitivity of RT-RAA was 3.425 log10 genomic copies (LGC)/reaction. Moreover, no cross-reaction was observed with other norovirus genogroups and other common foodborne viruses. Stool samples were examined by RT-RAA and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). Compared of RT-qPCR, kappa values for human norovirus detection with RT-RAA were 0.894 (p < 0.001), indicating that both assays were in agreement.

Conclusion
This RT-RAA assay provides a rapid, specific, and sensitive assay for human norovirus detection and is suitable for clinical testing.
A new machine learning approach for predicting likelihood of recurrence following ablation for atrial fibrillation from CT
Authors: Atta-Fosu Thomas , LaBarbera Michael , Ghose Soumya , Schoenhagen Paul , Saliba Walid , Tchou Patrick J. , Lindsay Bruce D. , Desai Milind Y. , Kwon Deborah , Chung Mina K. , Madabhushi Anant 
Published: March 2021

Abstract
Objective
To investigate left atrial shape differences on CT scans of atrial fibrillation (AF) patients with (AF+) versus without (AF−) post-ablation recurrence and whether these shape differences predict AF recurrence.

Methods
This retrospective study included 68 AF patients who had pre-catheter ablation cardiac CT scans with contrast. AF recurrence was defined at 1 year, excluding a 3-month post-ablation blanking period. After creating atlases of atrial models from segmented AF+ and AF− CT images, an atlas-based implicit shape differentiation method was used to identify surface of interest (SOI). After registering the SOI to each patient model, statistics of the deformation on the SOI were used to create shape descriptors. The performance in predicting AF recurrence using shape features at and outside the SOI and eight clinical factors (age, sex, left atrial volume, left ventricular ejection fraction, body mass index, sinus rhythm, and AF type [persistent vs paroxysmal], catheter-ablation type [Cryoablation vs Irrigated RF]) were compared using 100 runs of fivefold cross validation.

Results
Differences in atrial shape were found surrounding the pulmonary vein ostia and the base of the left atrial appendage. In the prediction of AF recurrence, the area under the receiver-operating characteristics curve (AUC) was 0.67 for shape features from the SOI, 0.58 for shape features outside the SOI, 0.71 for the clinical parameters, and 0.78 combining shape and clinical features.

Conclusion
Differences in left atrial shape were identified between AF recurrent and non-recurrent patients using pre-procedure CT scans. New radiomic features corresponding to the differences in shape were found to predict post-ablation AF recurrence.
Early prediction of putamen imaging features in HIV-associated neurocognitive impairment syndrome
Authors: Qi Yu , Xu Man , Wang Wei , Wang Yuan-Yuan , Liu Jiao-Jiao , Ren Hai-Xia , Liu Ming-Ming , Li Rui-Li , Li Hong-Jun 
Published: March 2021

Abstract
Background
To explore the correlation between the volume of putamen and brain cognitive impairment in patients with HIV and to predict the feasibility of early-stage HIV brain cognitive impairment through radiomics.

Method
Retrospective selection of 90 patients with HIV infection, including 36 asymptomatic neurocognitive impairment (ANI) patients and 54 pre-clinical ANI patients in Beijing YouAn Hospital. All patients received comprehensive neuropsychological assessment and MRI scanning. 3D Slicer software was used to acquire volume of interest (VOI) and radiomics features. Clinical variables and volume of putamen were compared between patients with ANI and pre-clinical ANI. The Kruskal Wallis test was used to analysis multiple comparisons between groups. The relationship between cognitive scores and VOI was compared using linear regression. For radiomics, principal component analysis (PCA) was used to reduce model overfitting and calculations and then a support vector machine (SVM) was used to build a binary classification model. For model performance evaluation, we used an accuracy, sensitivity, specificity and receiver operating characteristic curve (ROC).

Result
There were no significant differences in clinical variables between ANI group and pre-clinical-ANI group (P>0.05). The volume of bilateral putamen was significantly different between AHI group and pre-clinical group (P<0.05), but there was only a trend in the left putamen between ANI-treatment group and pre-clinical treatment group(P = 0.063). Reduced cognitive scores in Verbal Fluency, Attention/Working Memory, Executive Functioning, memory and Speed of Information Processing were negatively correlated with the increased VOI (P<0.05), but the correlation was relatively low. In diagnosing the ANI from pre-clinical ANI, the mean area under the ROC curves (AUC) were 0.85 ± 0.22, the mean sensitivity and specificity were 63.12 ± 5.51 and 94.25% ± 3.08%.

Conclusion
The volumes of putamen in patients with ANI may be larger than patients with pre-clinical ANI, the change of the volume of the putamen may have a certain process; there is a relationship between putamen and cognitive impairment, but the exact mechanism is unclear. Radiomics may be a useful tool for predicting early stage HAND in patients with HIV.