bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical integration of two omics datasets using GO2PLS
Authors: Gu Zhujie , el Bouhaddani Said , Pei Jiayi , Houwing-Duistermaat Jeanine , Uh Hae-Won 
Published: March 2021

Abstract
Background
Nowadays, multiple omics data are measured on the same samples in the belief that these different omics datasets represent various aspects of the underlying biological systems. Integrating these omics datasets will facilitate the understanding of the systems. For this purpose, various methods have been proposed, such as Partial Least Squares (PLS), decomposing two datasets into joint and residual subspaces. Since omics data are heterogeneous, the joint components in PLS will contain variation specific to each dataset. To account for this, Two-way Orthogonal Partial Least Squares (O2PLS) captures the heterogeneity by introducing orthogonal subspaces and better estimates the joint subspaces. However, the latent components spanning the joint subspaces in O2PLS are linear combinations of all variables, while it might be of interest to identify a small subset relevant to the research question. To obtain sparsity, we extend O2PLS to Group Sparse O2PLS (GO2PLS) that utilizes biological information on group structures among variables and performs group selection in the joint subspace.

Results
The simulation study showed that introducing sparsity improved the feature selection performance. Furthermore, incorporating group structures increased robustness of the feature selection procedure. GO2PLS performed optimally in terms of accuracy of joint score estimation, joint loading estimation, and feature selection. We applied GO2PLS to datasets from two studies: TwinsUK (a population study) and CVON-DOSIS (a small case-control study). In the first, we incorporated biological information on the group structures of the methylation CpG sites when integrating the methylation dataset with the IgG glycomics data. The targeted genes of the selected methylation groups turned out to be relevant to the immune system, in which the IgG glycans play important roles. In the second, we selected regulatory regions and transcripts that explained the covariance between regulomics and transcriptomics data. The corresponding genes of the selected features appeared to be relevant to heart muscle disease.

Conclusions
GO2PLS integrates two omics datasets to help understand the underlying system that involves both omics levels. It incorporates external group information and performs group selection, resulting in a small subset of features that best explain the relationship between two omics datasets for better interpretability.
Social prescribing for people with complex needs: a realist evaluation
Authors: Wood Emily , Ohlsen Sally , Fenton Sarah-Jane , Connell Janice , Weich Scott 
Published: March 2021

Abstract
Background
Social Prescribing is increasingly popular, and several evaluations have shown positive results. However, Social Prescribing is an umbrella term that covers many different interventions. We aimed to test, develop and refine a programme theory explaining the underlying mechanisms operating in Social Prescribing to better enhance its effectiveness by allowing it to be targeted to those who will benefit most, when they will benefit most.

Methods
We conducted a realist evaluation of a large Social Prescribing organisation in the North of England. Thirty-five interviews were conducted with stakeholders (clients attending Social Prescribing, Social Prescribing staff and general practice staff). Through an iterative process of analysis, a series of context-mechanism-outcome configurations were developed, refined and retested at a workshop of 15 stakeholders. The initial programme theory was refined, retested and ‘applied’ to wider theory.

Results
Social Prescribing in this organisation was found to be only superficially similar to collaborative care. A complex web of contexts, mechanisms and outcomes for its clients are described. Key elements influencing outcomes described by stakeholders included social isolation and wider determinants of health; poor interagency communication for people with multiple needs. Successful Social Prescribing requires a non-stigmatising environment and person-centred care, and shares many features described by the asset-based theory of Salutogenesis.

Conclusions
The Social Prescribing model studied is holistic and person-centred and as such enables those with a weak sense of coherence to strengthen this, access resistance resources, and move in a health promoting or salutogenic direction.
Epidemiological survey to determine the prevalence of cholecystolithiasis in Uyghur, Kazakh, and Han Ethnic Groups in the Xinjiang Uyghur Autonomous Region of China: cross-sectional studies
Authors: Lv Fujun , Wang Guangjun , Ding Dandan , Shen Caifu , Liu Jiangwei , Ji Feng , Kang Yan 
Published: March 2021

Abstract
Background
This study was performed to understand the prevalence of and possible risk factors for cholecystolithiasis in Uyghur, Kazakh, Han, and other ethnic groups in the Xinjiang Uyghur autonomous region of China.

Methods
Subjects were enrolled using typical case sampling and multistage stratified random sampling. We collected epidemiological data regarding cholecystolithiasis using a standard questionnaire of risk factors for gallbladder disease in Xinjiang. The subjects completed the questionnaire and underwent an abdominal ultrasound examination of the liver and gallbladder.

Results
This study included 5454 Xinjiang residents aged ≥ 18 years. The prevalence of cholecystolithiasis was 15% (11.3% in men and 17.1% in women), and the sex difference was statistically significant (male-to-female odds ratio [OR] 1.867; p < 0.001). The cholecystolithiasis prevalence was also significantly different among the Han, Uyghur, Kazakh, and other ethnic groups (13.1%, 20.8%, 11.5%, and 16.8%, respectively; p < 0.001). The prevalence of cholecystolithiasis in northern Xinjiang was 13.5% and that in southern Xinjiang was 17.5%; this difference was also statistically significant (OR 1.599; p < 0.001). Across all ethnic groups, the cholecystolithiasis prevalence significantly increased with age (all p < 0.01) and body mass index (BMI) (all p < 0.01). A multivariate logistic regression analysis indicated that cholecystolithiasis prevalence was associated with sex, age, BMI, smoking, diabetes, fatty liver disease, and geographical differences between northern and southern Xinjiang.

Conclusions
The prevalence of cholecystolithiasis was significantly higher in the Uyghur ethnic group than in the Han, Kazakh, and other ethnic groups; in women than in men; in southern Xinjiang than in northern Xinjiang; in patients with fatty liver disease; and increased with age and BMI. Our findings could provide a theoretical basis for the formulation of control measures for cholecystolithiasis.
Associations of poor oral health with frailty and physical functioning in the oldest old: results from two studies in England and Japan
Authors: Albani Viviana , Nishio Kensuke , Ito Tomoka , Kotronia Eftychia , Moynihan Paula , Robinson Louise , Hanratty Barbara , Kingston Andrew , Abe Yukiko , Takayama Michiyo , Iinuma Toshimitsu , Arai Yasumichi , Ramsay Sheena E. 
Published: March 2021

Abstract
Background
Very few studies have examined the relationship of oral health with physical functioning and frailty in the oldest old (> 85 years). We examined the association of poor oral health with markers of disability, physical function and frailty in studies of oldest old in England and Japan.

Methods
The Newcastle 85+ Study in England (n = 853) and the Tokyo Oldest Old Survey on Total Health (TOOTH; n = 542) comprise random samples of people aged > 85 years. Oral health markers included tooth loss, dryness of mouth, difficulty swallowing and difficulty eating due to dental problems. Physical functioning was based on grip strength and gait speed; disability was assessed as mobility limitations. Frailty was ascertained using the Fried frailty phenotype. Cross-sectional analyses were undertaken using logistic regression.

Results
In the Newcastle 85+ Study, dry mouth symptoms, difficulty swallowing, difficulty eating, and tooth loss were associated with increased risks of mobility limitations after adjustment for sex, socioeconomic position, behavioural factors and co-morbidities [odds ratios (95%CIs) were 1.76 (1.26–2.46); 2.52 (1.56–4.08); 2.89 (1.52–5.50); 2.59 (1.44–4.65) respectively]. Similar results were observed for slow gait speed. Difficulty eating was associated with weak grip strength and frailty on full adjustment. In the TOOTH Study, difficulty eating was associated with increased risks of frailty, mobility limitations and slow gait speed; and complete tooth loss was associated with increased risk of frailty.

Conclusion
Different markers of poor oral health are independently associated with worse physical functioning and frailty in the oldest old age groups. Research to understand the underlying pathways is needed.
Frailty status as a potential factor in increased postoperative opioid use in older adults
Authors: Auckley Elizabeth D. , Bentov Nathalie , Zelber-Sagi Shira , Jeong Lily , Reed May J. , Bentov Itay 
Published: March 2021

Abstract
Background
Prescription opioids are commonly used for postoperative pain relief in older adults, but have the potential for misuse. Both opioid side effects and uncontrolled pain have detrimental impacts. Frailty syndrome (reduced reserve in response to stressors), pain, and chronic opioid consumption are all complex phenomena that impair function, nutrition, psychologic well-being, and increase mortality, but links among these conditions in the acute postoperative setting have not been described. This study seeks to understand the relationship between frailty and patterns of postoperative opioid consumption in older adults.

Methods
Patients ≥ 65 years undergoing elective surgery with a planned hospital stay of at least one postoperative day were recruited for this cohort study at pre-anesthesia clinic visits. Preoperatively, frailty was assessed by Edmonton Frailty and Clinical Frailty Scales, pain was assessed by Visual Analog and Pain Catastrophizing Scales, and opioid consumption was recorded. On the day of surgery and subsequent hospitalization days, average pain ratings and total opioid consumption were recorded daily. Seven days after hospital discharge, patients were interviewed using uniform questionnaires to measure opioid prescription use and pain rating.

Results
One hundred seventeen patients (age 73.0 (IQR 67.0, 77.0), 64 % male), were evaluated preoperatively and 90 completed one-week post discharge follow-up. Preoperatively, patients with frailty were more likely than patients without frailty to use opioids (46.2 % vs. 20.9 %, p = 0.01). Doses of opioids prescribed at hospital discharge and the prescribed morphine milligram equivalents (MME) at discharge did not differ between groups. Seven days after discharge, the cumulative MME used were similar between cohorts. However, patients with frailty used a larger fraction of opioids prescribed to them (96.7 % (31.3, 100.0) vs. 25.0 % (0.0, 83.3), p = 0.007) and were more likely (OR 3.7, 95 % CI 1.13–12.13) to use 50 % and greater of opioids prescribed to them. Patients with frailty had higher pain scores before surgery and seven days after discharge compared to patients without frailty.

Conclusions
Patterns of postoperative opioid use after discharge were different between patients with and without frailty. Patients with frailty tended to use almost all the opioids prescribed while patients without frailty tended to use almost none of the opioids prescribed.
Associations between antimicrobial susceptibility/resistance of Neisseria gonorrhoeae isolates in European Union/European Economic Area and patients’ gender, sexual orientation and anatomical site of infection, 2009–2016
Authors:   on behalf of The Euro-GASP Network, Jacobsson Susanne , Cole Michelle J. , Spiteri Gianfranco , Day Michaela , Unemo Magnus 
Published: March 2021

AbstractBackgroundThe emergence and spread of antimicrobial resistance (AMR) inNeisseria gonorrhoeae, nationally and internationally, is a serious threat to the management and control of gonorrhoea. Limited and conflicting data regarding the epidemiological drivers of gonococcal AMR internationally have been published. We examined the antimicrobial susceptibility/resistance of gonococcal isolates (n = 15,803) collected across 27 European Union/European Economic Area (EU/EEA) countries in 2009–2016, in conjunction to epidemiological and clinical data of the corresponding patients, to elucidate associations between antimicrobial susceptibility/resistance and patients’ gender, sexual orientation and anatomical site of infection.MethodsIn total, 15,803 N. gonorrhoeaeisolates from the European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP), 2009–2016, were examined. Associations between gonococcal susceptibility/resistance and patients’ gender, sexual orientation and anatomical site of infection were investigated using univariate and multivariate logistic regression analysis. Statistical significance was determined by Pearson χ2-test or Fisher’s exact test with two-tailedp-values of < 0.05 indicating significance.ResultsThe overall gonococcal resistance from 2009 to 2016 was 51.7% (range during the years: 46.5–63.5%), 7.1% (4.5–13.2%), 4.3% (1.8–8.7%), and 0.2% (0.0–0.5%) to ciprofloxacin, azithromycin, cefixime, and ceftriaxone, respectively. The level of resistance combined with decreased susceptibility to ceftriaxone was 10.2% (5.7–15.5%). Resistance to cefixime and ciprofloxacin, and resistance combined with decreased susceptibility to ceftriaxone were positively associated with urogenital infections and heterosexual males, males with sexual orientation not reported and females (except for ciprofloxacin), i.e. when compared to men-who-have-sex-with-men (MSM). Azithromycin resistance was positively associated with heterosexual males, but no association was significant regarding anatomical site of infection.ConclusionsOverall, sexual orientation was the main variable associated with gonococcal AMR. Strongest positive associations were identified with heterosexual patients, particularly males, and not MSM. To provide evidence-based understanding and mitigate gonococcal AMR emergence and spread, associations between antimicrobial susceptibility/resistance and patients’ gender, sexual orientation and anatomical site of infection need to be further investigated in different geographic settings. In general, these insights will support identification of groups at increased risk and targeted public health actions such as intensified screening, 3-site testing using molecular diagnostics, sexual contact tracing, and surveillance of treatment failures.
Health care utilization for patients with stroke: a 3-year cross-sectional study of China’s two urban health insurance schemes across four cities
Authors: Yang Yong , Nicholas Stephen , Li Shuo , Huang Zhengwei , Chen Xiaoping , Ma Yong , Shi Xuefeng 
Published: March 2021

Abstract
Background
Stroke is a devastating disease and a major cause of death and disability in China. While existing studies focused mainly on differences in stroke patients’ health care utilization by insurance type, this study assesses whether health utilization and medical costs differed by insurance type across four cities in China.

Methods
A 5% random sample from the 2014–2016 China Urban Employees’ Basic Medical Insurance (UEBMI) and Urban Residents’ Basic Medical Insurance (URBMI) claims data were collected across four cities, Beijing, Shanghai, Tianjin, and Chongqing. Descriptive statistics and ordinary least squares regression were employed to analyze the data.

Results
We found that differences in healthcare utilization and inpatient and outpatient medical expenses varied more by city-specific insurance type than they did between the UEBMI and URBMI schemes. For example, the median UEBMI medical outpatient costs in Beijing (RMB500.2) were significantly higher than UEBMI patients in Shanghai (RMB260.8), Tianjin (RMB240.8), and Chongqing (RMB293.0), and Beijing URBMI patients had significantly higher outpatient medical costs (RMB356.9) than URBMI patients in Shanghai (RMB233.4) and Chongqing (RMB211.0), which were significantly higher than Tianjin (RMB156.2). Patients in Chongqing had 66.4% (95% CI: − 0.672, − 0.649) fewer outpatient visits, 13.0% (95% CI: − 0.144, − 0.115) fewer inpatient visits, and 34.2% (95% CI: − 0.366, − 0.318) shorter length of stay than patients in Beijing. The divergence of average length of stay and out-of-pocket (OOP) expenses by insurance type was also greater between cities than the UEMBI-URBMI mean difference.

Conclusions
Significant city-specific differences in stroke patients’ healthcare utilization and medical costs reflected inequalities in health care access. The fragmented social health insurance schemes in China should be consolidated to provide patients in different cities equal financial protection and benefit packages and to improve the equity of stroke patient access to health care.
Effect of periodontal therapy on COPD outcomes: a systematic review
Authors: Apessos Ioulianos , Voulgaris Athanasios , Agrafiotis Michalis , Andreadis Dimitrios , Steiropoulos Paschalis 
Published: March 2021

Abstract
Background
Latest evidence suggests that periodontitis is prevalent among patients with chronic obstructive pulmonary disease (COPD), while recent studies have also reported a potential benefit of periodontal treatment on several COPD outcomes. This systematic review aims to determine the impact of periodontal treatment on exacerbation rate, lung function and quality of life of COPD patients.

Methods
A systematic search of electronic databases of PubMed, Scopus, Virtual Health Library, ScienceDirect, Wiley Online Library, Web of Science, ProQuest Dissertation and Theses Global and Google Scholar was conducted. Search restricted to studies involving human subjects which were published from January 2000 to March 2020 in English language. Distiller Systematic Review software was used for data management. Risk of bias was assessed using Risk of Bias 2 (RoB2) and Risk of Bias for non-randomized studies of intervention (ROBINS-I) tools. Overall quality of evidence was judged based on Grading of Recommendations Assessment, Development and Evaluation working group methodology.

Results
Out of 1442 articles retrieved, 7 full text articles were included in the review. Limited evidence suggests that periodontal treatment in patients with COPD and periodontitis is associated with reduced exacerbation frequency and a slower lung function decline rate, while its effects on quality of life remain unclear. In addition, periodontal treatment in COPD is associated with lower hospitalization rates and reduced all-cause mortality. Significant methodological differences were noted amongst included studies, while very low-to-moderate overall quality of evidence was demonstrated.

Conclusions
Although it is reasonable to advise COPD patients not to neglect their dental health, further studies are warranted to determine the role of periodontal therapy on COPD clinical outcomes.
Trial Registration: PROSPERO 2020 (CRD42020158481). https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020158481
A haptic laparoscopic trainer based on affine velocity analysis: engineering and preliminary results
Authors: De Witte Benjamin , Barnouin Charles , Moreau Richard , Lelevé Arnaud , Martin Xavier , Collet Christian , Hoyek Nady 
Published: March 2021

Abstract
Background
There is a general agreement upon the importance of acquiring laparoscopic skills outside the operation room through simulation-based training. However, high-fidelity simulators are cost-prohibitive and elicit a high cognitive load, while low-fidelity simulators lack effective feedback. This paper describes a low-fidelity simulator bridging the existing gaps with affine velocity as a new assessment variable. Primary validation results are also presented.

Methods
Psycho-motor skills and engineering key features have been considered e.g. haptic feedback and complementary assessment variables. Seventy-seven participants tested the simulator (17 expert surgeons, 12 intermediates, 28 inexperienced interns, and 20 novices). The content validity was tested with a 10-point Likert scale and the discriminative power by comparing the four groups’ performance over two sessions.

Results
Participants rated the simulator positively, from 7.25 to 7.72 out of 10 (mean, 7.57). Experts and intermediates performed faster with fewer errors (collisions) than inexperienced interns and novices. The affine velocity brought additional differentiations, especially between interns and novices.

Conclusion
This affordable haptic simulator makes it possible to learn and train laparoscopic techniques. Self-assessment of basic skills was easily performed with slight additional cost compared to low-fidelity simulators. It could be a good trade-off among the products currently used for surgeons' training.
Clinico-pathological study of malignant odontogenic tumours from a national referral centre
Authors: Sathasivam Hans Prakash , Saw Chee Lynn , Lau Shin Hin 
Published: March 2021

Abstract
Background
Malignant odontogenic tumours are extremely rare tumours occurring within the jaws. Our study was performed to determine the demographic and clinico-pathological features of malignant odontogenic tumours amongst a multi-ethnic Asian population.

Methods
This was a retrospective cross-sectional study of malignant odontogenic tumours diagnosed at the Institute for Medical Research, Malaysia, from 2009 to 2019. All cases were independently reviewed and reclassified following the criteria set out in the latest edition of the World Health Organization 2017 reference text. Demographic and clinico-pathological data were recorded for each case.

Results
Twenty-four cases of malignant odontogenic tumours were identified. The patients’ age ranged from 16 to 79 years with the mean age at diagnosis being 50.8 years (SD = 16.18). There was a male predominance (66.7%) in this cohort of patients. The ethnic distribution appeared to reflect the Malaysian population with most cases seen amongst the Malay ethnic group (66.7%). Ameloblastic carcinoma was the most frequently diagnosed malignant odontogenic tumour (45.8%) and was also predominantly seen in males (90.9%). All patients with clear cell odontogenic carcinoma were females. There was no obvious sex predilection in primary odontogenic carcinoma not otherwise specified (NOS). The mandible (79.2%) was more frequently involved compared to the maxilla.

Conclusions
Diagnosis and management of malignant odontogenic tumours are challenging due to the rarity of these tumours. Our study has elucidated the clinico-pathological features of malignant odontogenic tumours seen in a multi-ethnic Asian population.