bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Physical Function and Neighborhood Environment in Healthy, Older Adults: An Exploratory Study Using Regression Tree Analysis
Authors: Ando Masataka , Kamide Naoto , Shiba Yoshitaka , Sakamoto Miki , Sato Haruhiko , Murakami Takeshi , Watanabe Shuichiro 
Published: October 2021

The aim of this study was to perform an exploratory investigation of the individual characteristics of older adults that affect the relationships between physical function and neighborhood environment. A total of 624 community-dwelling older adults living independently, aged ≥65 years, participated in this cross-sectional study. Physical function was assessed by muscle strength (grip strength and knee extension strength) and physical performance (5-m walking time and Timed Up and Go Test). The neighborhood environment was assessed using the International Physical Activity Questionnaire Environmental Module. The individual characteristics that affect the association between both were analyzed using multiple regression analysis and Classification and Regression tree (CaRT) analysis. In both older men and women, multiple regression analysis showed that neighborhood environment was significantly associated with physical function. On the other hand, on CaRT analyses, older men ≤80 years of age without low back pain and depressive symptoms and perceived good access to recreational facilities had the shortest 5-m walking time. However, CaRT analyses found no relationship between physical function and neighborhood environment in older women. The relationships between physical function and neighborhood environment may be altered by sex, age, and physical and mental health conditions.
Removable Denture Wearing as a Risk Predictor for Pneumonia Incidence and Time to Event in Older Adults
Authors: Alzamil H. , Wu T.T. , van Wijngaarden E. , Mendoza M. , Malmstrom H. , Fiscella K. , Kopycka-Kedzierawski D.T. , Billings R.J. , Xiao J. 
Published: October 2021

Introduction: Older adults are more susceptible to a common respiratory infection: pneumonia. Nearly 1 million older adults per year are hospitalized for community-acquired pneumonia in the United States. Objective: To examine whether wearing removable dentures are associated with an increased risk of pneumonia incidence in a geriatric population. Methods: We conducted a retrospective cohort study among patients >65 y of age within a large academic health system (University of Rochester Medical Center). The medical and dental electronic records from 2010 to 2018 were reviewed and used for data collection. The exposure was removable denture wearing. The main outcome variables were the incidence of pneumonia and time to event of pneumonia. A Cox proportional hazards regression was used to examine the association between pneumonia onset and wearing removable dentures, adjusting for demographics, socioeconomic status, and medical and dental conditions. Results: A total of 2,364 patients were included, with 1,189 (50.29%) in the denture-wearing group and 1,175 (49.70%) in the non–denture wearing group. The annual pneumonia incidence rate per 100,000 persons was 1,191 in the denture-wearing group and 128 per 100,000 persons in the non–denture wearing group, with a crude incidence rate ratio of 9.33 (95% CI, 5.41 to 18.81; P < 0.0001). The mean ± SD age of the pneumonia onset was 78.0 ± 10.0 and 78.6 ± 9.0 y among denture-wearing and nonwearing groups (P = 0.84). The time to event of pneumonia was associated with removable denture wearing (yes/no; hazard ratio, 7.68 [95% CI, 3.91 to 15.08]; P < 0.001) after adjusting for covariates. Conclusions: Wearing removable dentures was found to be a risk predictor for pneumonia incidence among the geriatric population even after accounting for other risk factors. Knowledge Transfer Statement: Wearing removable dentures was found to be a risk predictor of pneumonia incidence among older adults. Although the current study does not imply a causal relationship between denture wearing and pneumonia, clinicians and older patients could reference the study results when choosing dental prostheses to restore missing teeth.
TAGOPSIN: collating taxa-specific gene and protein functional and structural information
Authors: Bundhoo Eshan , Ghoorah Anisah W. , Jaufeerally-Fakim Yasmina 
Published: October 2021

Abstract
Background
The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way.

Results
Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus.

Conclusion
TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License.
Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features
Authors: Fan Yongxian , Wang Wanru 
Published: October 2021

Abstract
Background
The origin is the starting site of DNA replication, an extremely vital part of the informational inheritance between parents and children. More importantly, accurately identifying the origin of replication has great application value in the diagnosis and treatment of diseases related to genetic information errors, while the traditional biological experimental methods are time-consuming and laborious.

Results
We carried out research on the origin of replication in a variety of eukaryotes and proposed a unique prediction method for each species. Throughout the experiment, we collected data from 7 species, including Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, Kluyveromyces lactis, Pichia pastoris and Schizosaccharomyces pombe. In addition to the commonly used sequence feature extraction methods PseKNC-II and Base-content, we designed a feature extraction method based on TF-IDF. Then the two-step method was utilized for feature selection. After comparing a variety of traditional machine learning classification models, the multi-layer perceptron was employed as the classification algorithm. Ultimately, the data and codes involved in the experiment are available at https://github.com/Sarahyouzi/EukOriginPredict.

Conclusions
The prediction accuracy of the training set of the above-mentioned seven species after 100 times fivefold cross validation reach 92.60%, 90.80%, 91.22%, 96.15%, 96.72%, 99.86%, 96.72%, respectively. It denotes that compared with other methods, the methods we designed could accomplish superior performance. In addition, our experiments reveals that the models of multiple species could predict each other with high accuracy, and the results of STREME shows that they have a certain common motif.
Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
Authors: Rafter Pierce , Gormley Isobel Claire , Purfield Deirdre , Parnell Andrew C. , Naderi Saeid , Berry Donagh P. 
Published: October 2021

Abstract
Background
The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.

Results
A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.

Conclusions
The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
Long-term survival of a patient with microsatellite-stable refractory colorectal cancer with regorafenib and PD-1 inhibitor sintilimab: a case report and review of literature
Authors: Zhang Yong , Zhang Fang , Zhao Lingdi , Fu Xiaomin , Shang Yiman , Gao Quanli 
Published: October 2021

Abstract
Background
Colorectal cancer (CRC) is the third most prevalent cancer worldwide and poses a serious challenge for clinicians. Previous studies have shown promising results in patients with Microsatellite Stable microsatellite-stable CRC refractory to chemotherapy upon treating with (Programmed Cell Death Protein 1) PD-1 inhibitor combined with regorafenib. Herein, we report a unique case of a patient for whom the conventional chemotherapy and radiotherapy were ineffective, but showed a prolonged stable disease with third-line treatment with regorafenib and PD-1 inhibitor, sintilimab.

Case presentation
A 64-year-old East Asian female patient was admitted to a regional cancer hospital presenting with abdominal unease due to increased stool frequency and bloody stool. Digital anal examination revealed adenocarcinoma, while genetic profiling of the tumor resections detected wild-type KRAS mutations in codon 12 and 13. Microsatellite instability (MSI) analysis for detecting germline mutations of (Mismatch-repair) MMR genes showed stable phenotype. In December 2016, Miles’ resection for intestinal adhesion release and iliac vessel exploration in the rectum was performed (Tumor, Node, Metastasis [TNM]: T3N0M0; stage IIA). The adjuvant chemotherapeutic regimen consisted of a combination of capecitabine at 1.5 g (twice daily) and oxaliplatin therapy at 200 mg for three cycles from February 2016; followed by administering capecitabine tablets orally (1.5 g bid) for five cycles as post-operative palliative care. The patient tested positive for hepatic C virus, which was managed by oral antiviral agents. Following recurrence of rectal adenocarcinoma after 4 years and disease progression with a previous chemotherapeutic regimen, regorafenib was administered at 120 mg once daily combined with sintilimab 200 mg, and the patient's progress was monitored. A follow-up computerized tomography imaging in March 2020 showed disease progression, additionally presented nodule formation (TNM: T3NxM1b; stage IVB). According to Response Evaluation Criteria in Solid Tumors criteria (RECIST), the patient showed a complete response (CR) after treatment with regorafenib and sintilimab immunotherapy.

Conclusion
Data from this clinical case report support future exploration of combination treatment of the oral multi-kinase inhibitor regorafenib with PD-1 targeted monoclonal antibodies in patients with metastatic microsatellite-stable CRC.
Implementing supportive exercise interventions in the colorectal cancer care pathway: a process evaluation of the PREPARE-ABC randomised controlled trial
Authors: Murdoch Jamie , Varley Anna , McCulloch Jane , Jones Megan , Thomas Laura B. , Clark Allan , Stirling Susan , Turner David , Swart Ann Marie , Dresser Kerry , Howard Gregory , Saxton John , Hernon James 
Published: October 2021

Abstract
Background
A colorectal resection is standard treatment for patients with colorectal cancer (CRC). However, the procedure results in significant post-operative mortality and reduced quality of life. Maximising pre-operative cardiopulmonary fitness could improve post-surgical outcomes. PREPARE-ABC is a multi-centre, three-armed, randomised controlled trial investigating the effects of exercise interventions, with motivational support on short and longer-term recovery outcomes in CRC patients undergoing major lower-gastrointestinal surgery. The trial included an internal pilot phase with parallel process evaluation. The aim of the process evaluation was to optimise intervention implementation for the main trial.

Methods
Mixed methods process evaluation conducted in 14 UK hospitals between November 2016 and March 2018. Data included a site profile questionnaire and telephone scoping interview with hospital staff, 34 qualitative observations of standard care and 14 observations of intervention delivery, 13 semi-structured interviews with healthcare professionals (HCPs) and 28 semi-structured interviews with patients. Data analysis focused on describing intervention delivery within each arm, assessing fidelity, acceptability and how variation in delivery was linked to contextual characteristics.

Results
Standard care exercise advice was typically limited to maintaining current activity levels, and with lead-in time to surgery affecting whether any exercise advice was provided. Variation in HCP capacity affected the ability of colorectal units to deploy staff to deliver the intervention. Patients’ exercise history and motivation prior to surgery influenced HCP perceptions and delivery of the motivational components. Observations indicated a high level of fidelity to delivery of the exercise interventions. All but one of the 28 interviewed patients reported increasing exercise levels as a result of receiving the intervention, with most finding them motivational and greatly valuing the enhanced level of social support (versus standard care) provided by staff.

Conclusion
Hospital-supervised and home-based exercise interventions were highly acceptable for most patients undergoing surgery for CRC. Delivery of pre- and post-operative exercise within the CRC care pathway is feasible but systematic planning of capacity and resources is required to optimise implementation.
Thelazia callipaeda infection during phacoemulsification cataract surgery: a case report
Authors: Li Yang , Liu Jie , Tian Qingmei , Guo Dadong , Liu Dongmei , Ma Xianzhen , Bi Hongsheng 
Published: October 2021

Abstract
Background
In August 2020, we found one case of thelazia callipaeda infection during phacoemulsification cataract surgery. This maybe the first report for thelazia callipaeda discovered during phacoemulsification cataract surgery in China.

Case presentation
An 85 years old farmer was found thelazia callipaeda infection during phacoemulsification cataract surgery. The patient admitted whose foreign body sensation was often found in the right eye in recent 2 months. The worm was then taken out with ophthalmic forceps and put into sterile normal saline. The worm was sent to the Eye Institute of Shandong University of Traditional Chinese Medicine for identification. After identification, the worm was regarded as the male thelazia callipaeda. The head is blunt and round, the tail end curls to the abdomen, and the long copulation spines protrudes from the cloaca. The conjunctival sac was washed carefully with a large amount of Sodium Lactate Ringer ‘s Solution. After operation, antibiotics, pranoprofen eye drops, and tobramycin dexamethasone eye drops were further applied. After continuous examination of conjunctival sac for 2 weeks, the patient’s visual acuity maintained 20/20, confirming that there was no residual thelazia.

Conclusions
This report highlights the physician should ask the patient’s history carefully before operation and it is necessary to strengthen health publicity and education, maintaining clean environment and keeping personal eye hygiene.
Mapping geographic clusters of new HIV diagnoses to inform granular-level interventions for HIV epidemic control in western Kenya
Authors: Muttai Hellen , Guyah Bernard , Achia Thomas , Musingila Paul , Nakhumwa Jesse , Oyoo Rose , Olweny Wilfrida , Odeny Redempter , Ohaga Spala , Agot Kawango , Oruenjo Kennedy , Awino Bob , Joseph Rachael H. , Miruka Fredrick , Zielinski-Gutierrez Emily 
Published: October 2021

AbstractBackgroundAs countries make progress towards HIV epidemic control, there is increasing need to identify finer geographic areas to target HIV interventions. We mapped geographic clusters of new HIV diagnoses, and described factors associated with HIV-positive diagnosis, in order to inform targeting of HIV interventions to finer geographic areas and sub-populations.MethodsWe analyzed data for clients aged> 15 years who received home-based HIV testing as part of a routine public health program between May 2016 and July 2017 in Siaya County, western Kenya. Geospatial analysis using Kulldorff’s spatial scan statistic was used to detect geographic clusters (radius < 5 kilometers) of new HIV diagnoses. Factors associated with new HIV diagnosis were assessed in a spatially-integrated Bayesian hierarchical model.ResultsOf 268,153 clients with HIV test results, 2906 (1.1%) were diagnosed HIV-positive. We found spatial variation in the distribution of new HIV diagnoses, and identified nine clusters in which the number of new HIV diagnoses was significantly (1.56 to 2.64 times) higher than expected. Sub-populations with significantly higher HIV-positive yield identified in the multivariable spatially-integrated Bayesian model included: clients aged 20–24 years [adjusted relative risk (aRR) 3.45, 95% Bayesian Credible Intervals (CI) 2.85–4.20], 25–35 years (aRR 4.76, 95% CI 3.92–5.81) and > 35 years (aRR 2.44, 95% CI 1.99–3.00); those in polygamous marriage (aRR 1.84, 95% CI 1.55–2.16), or separated/divorced (aRR 3.36, 95% CI 2.72–4.08); and clients who reported having never been tested for HIV (aRR 2.35, 95% CI 2.02–2.72), or having been tested > 12 months ago (aRR 1.53, 95% CI 1.41–1.66).ConclusionOur study used routine public health program data to identify granular geographic clusters of higher new HIV diagnoses, and sub-populations with higher HIV-positive yield in the setting of a generalized HIV epidemic. In order to target HIV testing and prevention interventions to finer granular geographic areas for maximal epidemiologic impact, integrating geospatial analysis into routine public health programs can be useful.
A historical overview of legislated alcohol policy in the Northern Territory of Australia: 1979–2021
Authors: Clifford Sarah , Smith James A. , Livingston Michael , Wright Cassandra J. C. , Griffiths Kalinda E. , Miller Peter G. 
Published: October 2021

Abstract
Background
The Northern Territory (NT) has the highest levels of alcohol consumption and harms in Australia. Since the creation of the NT Liquor Act 1978, which came into effect in 1979, numerous legislated alcohol policies have been introduced to attempt to address these harms. We present a narrative historical overview of alcohol policies implemented in the NT from 1979 to 2021.

Methods
Using scoping review methodology, databases were searched from 1979 to 2021. Of 506 articles screened, 34 met inclusion criteria. Reference lists of all included articles were searched, resulting in the inclusion of another 41 articles and reports, totalling 75 final documents. Policies were organised using Babor and colleagues (2010) established framework: 1. pricing/ taxation; 2. regulating physical availability; 3. modifying drinking environments; 4. drink-driving countermeasures; 5. restrictions on marketing; 6. education/persuasion; 7. treatment/early intervention.

Results
Two pricing/taxation policies have been implemented, Living With Alcohol (LWA) and Minimum Unit Price, both demonstrating evidence of positive effects on health and consumption outcomes. Eight policies approaches have focused on regulating physical availability, implemented at both individual and local area levels. Several of these policies have varied by location and been amended over time. There is some evidence demonstrating reduction in harms attributable to Liquor Supply Plans, localised restrictions, and General Restricted Areas, although these have been site specific. Of the three policies which targeted modifying the drinking environment; one was evaluated, finding a relocation of social harms, rather than a reduction. The literature outlines a range of controversies, particularly regarding policies in domain 2–3, including racial discrimination and a lack of policy stability. No policies relating to restricting marketing or education/persuasion programs were found. The only drink-driving legislated policy was considered to have contributed to the success of the LWA program. Three policies relating to treatment were described; two were not evaluated and evidence showed no ongoing benefits of Alcohol Mandatory Treatment.

Discussion
The NT has implemented a large number of alcohol policies, several of which have evidence of positive effects. However, these policies have often existed in a context of clear politicisation of alcohol policy, frequently with an implicit focus on Aboriginal people’s consumption.