bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local data commons: the sleeping beauty in the community of data commons
Authors: Jeong Jong Cheol , Hands Isaac , Kolesar Jill M. , Rao Mahadev , Davis Bront , Dobyns York , Hurt-Mueller Joseph , Levens Justin , Gregory Jenny , Williams John , Witt Lisa , Kim Eun Mi , Burton Carlee , Elbiheary Amir A. , Chang Mingguang , Durbin Eric B. 
Published: September 2022

Abstract
Background
Public Data Commons (PDC) have been highlighted in the scientific literature for their capacity to collect and harmonize big data. On the other hand, local data commons (LDC), located within an institution or organization, have been underrepresented in the scientific literature, even though they are a critical part of research infrastructure. Being closest to the sources of data, LDCs provide the ability to collect and maintain the most up-to-date, high-quality data within an organization, closest to the sources of the data. As a data provider, LDCs have many challenges in both collecting and standardizing data, moreover, as a consumer of PDC, they face problems of data harmonization stemming from the monolithic harmonization pipeline designs commonly adapted by many PDCs. Unfortunately, existing guidelines and resources for building and maintaining data commons exclusively focus on PDC and provide very little information on LDC.

Results
This article focuses on four important observations. First, there are three different types of LDC service models that are defined based on their roles and requirements. These can be used as guidelines for building new LDC or enhancing the services of existing LDC. Second, the seven core services of LDC are discussed, including cohort identification and facilitation of genomic sequencing, the management of molecular reports and associated infrastructure, quality control, data harmonization, data integration, data sharing, and data access control. Third, instead of commonly developed monolithic systems, we propose a new data sharing method for data harmonization that combines both divide-and-conquer and bottom-up approaches. Finally, an end-to-end LDC implementation is introduced with real-world examples.

Conclusions
Although LDCs are an optimal place to identify and address data quality issues, they have traditionally been relegated to the role of passive data provider for much larger PDC. Indeed, many LDCs limit their functions to only conducting routine data storage and transmission tasks due to a lack of information on how to design, develop, and improve their services using limited resources. We hope that this work will be the first small step in raising awareness among the LDCs of their expanded utility and to publicize to a wider audience the importance of LDC.
Genetic architecture of berry aroma compounds in a QTL (quantitative trait loci) mapping population of interspecific hybrid grapes (Vitis labruscana × Vitis vinifera)
Authors: Koyama Kazuya , Kono Atsushi , Ban Yusuke , Bahena-Garrido Sharon Marie , Ohama Tomoko , Iwashita Kazuhiro , Fukuda Hisashi , Goto-Yamamoto Nami 
Published: September 2022

Abstract
Background
Although grapes accumulate diverse groups of volatile compounds, their genetic regulation in different cultivars remains unelucidated. Therefore, this study investigated the volatile composition in the berries of an interspecific hybrid population from a Vitis labruscana ‘Campbell Early’ (CE) × Vitis vinifera ‘Muscat of Alexandria’ (MA) cross to understand the relationship among volatile compounds and their genetic regulation. Then, a quantitative trait locus (QTL) analysis of its volatile compounds was conducted.

Results
While MA contained higher concentrations of monoterpenes and norisoprenoids, CE contained higher concentrations of C6 compounds, lactones and shikimic acid derivatives, including volatiles characteristic to American hybrids, i.e., methyl anthranilate, o-aminoacetophenone and mesifurane. Furthermore, a cluster analysis of volatile profiles in the hybrid population discovered ten coordinately modulated free and bound volatile clusters. QTL analysis identified a major QTL on linkage group (LG) 5 in the MA map for 14 monoterpene concentrations, consistent with a previously reported locus. Additionally, several QTLs detected in the CE map affected the concentrations of specific monoterpenes, such as linalool, citronellol and 1,8-cineol, modifying the monoterpene composition in the berries. As for the concentrations of five norisoprenoids, a major common QTL on LG2 was discovered first in this study. Several QTLs with minor effects were also discovered in various volatile groups, such as lactones, alcohols and shikimic acid derivatives.

Conclusions
An overview of the profiles of aroma compounds and their underlying QTLs in a population of interspecific hybrid grapes in which muscat flavor compounds and many other aroma compounds were mixed variously were elucidated. Coordinate modulation of the volatile clusters in the hybrid population suggested an independent mechanism for controlling the volatiles of each group. Accordingly, specific QTLs with significant effects were observed for terpenoids, norisoprenoids and some volatiles highly contained in CE berries.
Increased risk of preterm delivery with high cortisol during pregnancy is modified by fetal sex: a cohort study
Authors: Oaks Brietta M. , Adu-Afarwuah Seth , Ashorn Per , Lartey Anna , Laugero Kevin D. , Okronipa Harriet , Stewart Christine P. , Dewey Kathryn G. 
Published: September 2022

Abstract
Background
Previous studies show an association between maternal plasma and salivary cortisol and preterm birth but have been primarily conducted in high-income countries. It is unknown whether salivary cortisol is a risk factor for preterm birth in Ghana. Our objective was to determine whether maternal salivary cortisol during pregnancy was associated with pregnancy duration and preterm delivery in Ghana.

Methods
We conducted a cohort study of 783 pregnant women in Ghana. We measured salivary cortisol at baseline (mean 16 wk), 28 wk., and 36 wk. gestation. Pregnancy duration was determined primarily by ultrasound. We used adjusted linear regression models to examine the association between cortisol and pregnancy duration and Poisson regression models to determine the risk of preterm delivery among women with high cortisol at baseline or 28 wk. gestation.

Results
Mean pregnancy duration was 39.4 ± 1.8 wk. and 6.6% had a preterm delivery. Mean maternal cortisol increased throughout pregnancy, from 4.9 ± 2.7 nmol/L at baseline (16 wk) to 6.4 ± 3.2 nmol/L at 28 wk. and 7.9 ± 3.0 nmol/L at 36 wk. gestation. In adjusted analyses, higher cortisol concentrations at baseline (β = − 0.39, p = .002) and 28 wk. (β = − 0.49, p = .001), but not 36 wk. (β = − 0.23, p = .084) were associated with a shorter pregnancy duration. Women with high cortisol at baseline (> 6.3 nmol/L) had an increased relative risk of preterm delivery (RR (95% CI): 1.96 (1.13, 3.40)), but the association between high cortisol at 28 wk. and preterm delivery was not significant. There was a significant interaction with fetal sex (p-for-interaction = 0.037): among women carrying male fetuses, high cortisol at baseline increased the risk of preterm delivery threefold (3.18 (1.51, 6.71)) while there was no association (1.17 (0.50, 2.74)) among women carrying female fetuses.

Conclusion
Higher maternal cortisol is associated with a shorter pregnancy duration and an increased risk of preterm delivery. Subgroup analysis by fetal sex revealed that this association is evident primarily among women carrying male fetuses. Future studies of cortisol and preterm delivery should include consideration of fetal sex as a potential effect modifier.
Association between dietary knowledge and overweight/obesity in Chinese children and adolescents aged 8–18 years: a cross-sectional study
Authors: Wang Lihong , Zhuang Jielian , Zhang Heng , Lu Weijuan 
Published: September 2022

AbstractBackgroundA lack of adequate dietary knowledge may result in poor health. The purpose of this study was to study the association between dietary knowledge and overweight/obesity in children and adolescents. MethodData from the China Health and Nutrition Survey (CHNS) 2004, 2006, 2009, 2011, and 2015 were used in this cross-sectional study. The dietary knowledge of children and adolescents was evaluated by the questionnaire in the database. The overweight and obesity status was evaluated by body mass index (BMI). Cluster analysis was performed to establish different groups based on dietary knowledge level. Logistic regression analysis and subgroup analysis were conducted.ResultsA total of 2,701 children and adolescents were finally selected. Cluster A (n = 837, 30.99%), Cluster B (n = 1,264, 46.80%) and Cluster C (n = 600, 22.21%) were high, medium and low dietary knowledge level, respectively. Participants with high dietary knowledge levels [OR = 0.56 (95%CI: 1.40–0.78)] may be negatively associated with overweight and obesity. Similar results were found among adolescents, males, females, people living in eastern and northeastern China, and rural areas, after adjusting for age, gender, geographic region, maternal education level, alcohol consumption, waist-to-hip ratio, systolic blood pressure and diastolic blood pressure.ConclusionImproving the dietary knowledge level of children and adolescents was associated with decreased risk of overweight and obesity. Our study provided a theoretical basis for the relationship between dietary knowledge and overweight/obesity in Chinese children and adolescents and suggested strengthening the publicity and popularization of dietary knowledge in schools and communities.
The clinical course of comorbid substance use disorder and attention deficit/hyperactivity disorder: protocol and clinical characteristics of the INCAS study
Authors: Brynte Christoffer , Aeschlimann Myriam , Barta Csaba , Begeman Alex Hendikus Abraham , Bäcker Amanda , Crunelle Cleo Lina , Daigre Constanza , De Fuentes-Merillas Laura , Demetrovics Zsolt , Dom Geert , López Lara Grau , Icick Romain , Johnson Brian , Joostens Peter , Kapitány-Fövény Máté , Karsinti Emily , Kiefer Falk , Konstenius Maija , Levin Frances R. , Luderer Mathias , Markus Wiebren , Matthys Frieda , Moggi Franz , Palma-Alvarez Raul Felipe , Paraskevopoulou Maria , Ramos-Quiroga J. Antoni , Schellekens Arnt , Soravia Leila M. , Therribout Norman , Thomas Anil , van de Glind Geurt , van Kernebeek Michiel Willem , Vollstädt-Klein Sabine , Vorspan Florence , van den Brink Wim , Franck Johan 
Published: September 2022

Abstract
Background
Substance use disorders (SUD) often co-occur with attention deficit hyperactivity disorder (ADHD). Although the short-term effects of some specific interventions have been investigated in randomized clinical trials, little is known about the long-term clinical course of treatment-seeking SUD patients with comorbid ADHD.

Aims
This paper presents the protocol and baseline clinical characteristics of the International Naturalistic Cohort Study of ADHD and SUD (INCAS) designed and conducted by the International Collaboration on ADHD and Substance Abuse (ICASA) foundation. The overall aim of INCAS is to investigate the treatment modalities provided to treatment-seeking SUD patients with comorbid ADHD, and to describe the clinical course and identify predictors for treatment outcomes.
This ongoing study employs a multicentre observational prospective cohort design. Treatment-seeking adult SUD patients with comorbid ADHD are recruited, at 12 study sites in nine different countries. During the follow-up period of nine months, data is collected through patient files, interviews, and self-rating scales, targeting a broad range of cognitive and clinical symptom domains, at baseline, four weeks, three months and nine months.

Results
A clinically representative sample of 578 patients (137 females, 441 males) was enrolled during the recruitment period (June 2017-May 2021). At baseline, the sample had a mean age (SD) of 36.7 years (11.0); 47.5% were inpatients and 52.5% outpatients; The most prevalent SUDs were with alcohol 54.2%, stimulants 43.6%, cannabis 33.1%, and opioids 14.5%. Patients reported previous treatments for SUD in 71.1% and for ADHD in 56.9%. Other comorbid mental disorders were present in 61.4% of the sample: major depression 31.5%, post-traumatic stress disorder 12.1%, borderline personality disorder 10.2%.

Conclusions
The first baseline results of this international cohort study speak to its feasibility. Data show that many SUD patients with comorbid ADHD had never received treatment for their ADHD prior to enrolment in the study. Future reports on this study will identify the course and potential predictors for successful pharmaceutical and psychological treatment outcomes.

Trial registration
ISRCTN15998989 20/12/2019.
An analysis of time trends in breast and prostate cancer mortality rates in Lithuania, 1986–2020
Authors: Everatt Rūta , Gudavičienė Daiva 
Published: September 2022

Abstract
Background
Breast cancer (BC) and prostate cancer (PC) mortality rates in Lithuania remain comparatively high despite the ongoing BC and PC screening programmes established in 2006. The aim of this study was to investigate time trends in BC and PC mortality rates in Lithuania evaluating the effects of age, calendar period of death, and birth-cohort over a 35-year time span.

Methods
We obtained death certification data for BC in women and PC in men for Lithuania during the period 1986–2020 from the World Health Organisation database. Age-standardised mortality rates were analysed using Joinpoint regression. Age-period-cohort models were used to assess the independent age, period and cohort effects on the observed mortality trends.

Results
Joinpoint regression analysis indicated that BC mortality increased by 1.6% annually until 1996, and decreased by − 1.2% annually thereafter. The age-period-cohort analysis suggests that temporal trends in BC mortality rates could be attributed mainly to cohort effects. The cohort effect curvature showed the risk of BC death increased in women born prior to 1921, remained stable in cohorts born around 1921–1951 then decreased; however, trend reversed in more recent generations. The period effect curvature displayed a continuous decrease in BC mortality since 1991–1995. For PC mortality, after a sharp increase by 3.0%, rates declined from 2007 by − 1.7% annually. The period effect was predominant in PC mortality, the curvature displaying a sharp increase until 2001–2005, then decrease.

Conclusions
Modestly declining recent trends in BC and PC mortality are consistent with the introduction of widespread mammography and PSA testing, respectively, lagging up to 10 years. The study did not show that screening programme introduction played a key role in BC mortality trends in Lithuania. Screening may have contributed to favourable recent changes in PC mortality rates in Lithuania, however the effect was moderate and limited to age groups < 65 years. Further improvements in early detection methods followed by timely appropriate treatment are essential for decreasing mortality from BC and PC.
Selected coffee (Coffea arabica L.) extracts inhibit intestinal α-glucosidases activities in-vitro and postprandial hyperglycemia in SD Rats
Authors: Mitiku Haimanot , Kim Tae Yang , Kang Hanna , Apostolidis Emmanouil , Lee Jung-Yun , Kwon Young-In 
Published: September 2022

AbstractOne of the therapeutic approaches for decreasing postprandial hyperglycemia is to retard absorption of glucose by the inhibition of carbohydrate hydrolyzing enzymes, α-amylase, and α-glucosidases, in the digestive organs. Coffee consumption has been reported to beneficial effects for controlling calorie and cardiovascular diseases, however, the clear efficacy and mode of action are yet to be proved well. Therefore, in this study we evaluated in- vitro rat intestinal α-glucosidases and porcine α-amylase inhibitory activities as well as in vivo (Sprague–Dawley rat model) blood glucose lowering effects of selected coffee extracts. The water extracted Sumatra coffee (SWE) showed strong α-glucosidase inhibitory activity (IC50, 4.39 mg/mL) in a dose-dependent manner followed by Ethiopian water extract (EWE) (IC50, 4.97) and Guatemala water extract (GWE) (IC50, 5.19). Excepted for GWE all the coffee types significantly reduced the plasma glucose level at 0.5 h after oral intake (0.5 g/kg-body weight) in sucrose and starch-loaded SD rats. In sucrose loading test SWE (p < 0.001) and EWE (p < 0.05) had significantly postprandial blood glucose reduction effect, when compared to control. The maximum blood glucose levels (Cmax) of EWE administration group were decreased by about 18% (from 222.3 ± 16.0 to 182.5 ± 15.4, p < 0.01) and 19% (from 236.2 ± 25.1 to 191.3 ± 13.2 h·mg/dL, p < 0.01) in sucrose and starch loading tests, respectively. These results indicate that selected coffee extract may improve exaggerated postprandial spikes in blood glucose via inhibition of intestinal sucrase and thus delays carbohydrate absorption. These in vitro and in vivo studies therefore could provide the biochemical rationale for the benefit of coffee-based dietary supplement and the basis for further clinical study.
Exploring healthcare workers’ perspectives of video feedback for training in the use of powered air purifying respirators (PAPR) at the onset of the COVID-19 pandemic
Authors: Wyer Mary , Barratt Ruth , Hor Su-yin , Ferguson Patricia E. , Gilbert Gwendolyn L. 
Published: September 2022

Abstract
Background
With the advent of COVID-19, many healthcare workers (HWs) in Australia requested access to powered air purifying respirators (PAPR) for improved respiratory protection, comfort and visibility. The urgency of the response at our hospital required rapid deployment of innovative training to ensure the safe use of PAPRs, in particular, a video-feedback training option to prepare HWs for PAPR competency.

Aim
To explore the feasibility, acceptability, and utility of video-feedback in PAPR training and competency assessment.

Methods
Semi-structured interviews were conducted with 12 HWs, including clinicians from Intensive Care, Anaesthetics and Respiratory Medicine, at a large teaching hospital in Australia.

Findings
Participants believed that the use of video-feedback in PAPR training was feasible, acceptable and useful. They described a variety of benefits to learning and retention, from a variety of ways in which they engaged with the personal video-feedback. Participants also described the impact of reviewing personalised practice footage, compared to generic footage of an ideal performance.

Conclusion
By conceptualising video-feedback using a pedagogical approach, this study contributes to knowledge around optimising methods for training HWs in PPE use, particularly when introducing a new and complex PPE device during an infectious disease outbreak.
Community perspectives on ideal bacterial STI testing services for gay, bisexual, and other men who have sex with men in Toronto, Canada: a qualitative study
Authors: Rana Jayoti , Burchell Ann N. , Wang Susan , Logie Carmen H. , Lisk Ryan , Gesink Dionne 
Published: September 2022

Abstract
Background
Innovation is needed to produce sustained improvements in bacterial sexually transmitted infections (STI) testing given suboptimal access and uptake among sexually active gay, bisexual or other men who have sex with men (GBM). Yet, the STI testing processes and technologies that best address local testing barriers among GBM in Toronto is unknown. We aimed to explore men’s perspectives regarding STI testing services for GBM to identify and prioritize new STI testing interventions in Toronto, Ontario, Canada.

Methods
We conducted four focus groups with twenty-seven GBM in 2017: two with cisgender men living with HIV, one with cisgender HIV-negative men, and one with transgender men. Twenty-seven men participated in the focus groups with 40% 18–30 years of age, 48% self-identifying as white, and the remainder self-identifying as Middle Eastern, Latino/Hispanic, Asian/Pacific Islander, South Asian, First Nations, African/Caribbean/Black, or mixed race. 59% of participants self-identified as living with HIV. Participants were asked about their STI testing experiences in Toronto, barriers and facilitators to testing, and ideal STI testing process. Focus groups were audio recorded, transcribed verbatim, and analyzed using thematic analysis.

Results
Core concepts included how clinical context, bacterial STI testing delivery, and interactions with healthcare providers can create barriers and recommendations for ways to improve. Regarding clinical context, participants desired more clinics with accessible locations/hours; streamlined testing that minimized use of waiting rooms and wait times; and improved clinic ambience. Bacterial STI testing delivery recommendations included standardization to ensure consistency in sexual history intake, tests offered, follow-up and public health reporting between clinics. Men also recommended reducing the multistep process testing by offering components such as lab requisitions and results online. Participants also recommended interactions with healthcare providers be professional and non-judgmental, offer compassionate and competent care with destigmatizing and lesbian, gay, bisexual and trans (LGBT) affirming communication.

Conclusion
Concrete and practical solutions for improving existing sexual health services and facilitating optimal STI testing include streamlining testing options and providing patient-centred, LGBT-affirming care to enable optimal STI testing.
The taTME learning curve for mid-low rectal cancer: a single-center experience in China
Authors: Xu Fengming , Zhang Yiqiao , Yan Jiafu , Xu Bowen , Wu Guocong , Yang Zhengyang , Sun Liting , Zhang Xiao , Yao Hongwei , Zhang Zhongtao 
Published: September 2022

Abstract
Purpose
As transanal total mesorectal excision (taTME) is performed worldwide, the optimization of existing training and guidance programs to enhance new taTME learners’ competence in performing this procedure is warranted. This study aimed to evaluate the taTME learning curve in patients with mid-low rectal cancer.

Methods
Patients who underwent taTME for mid-low rectal cancer between October 2015 and August 2021 at a single center were included. A cumulative sum (CUSUM) learning curve analysis was performed with the total operation time as the study outcome. The learning curve was analyzed using risk-adjusted CUSUM analysis, with postoperative complications and anastomotic leakage (AL) as outcomes.

Results
In total, 104 consecutive patients were included in this study. The CUSUM learning curve for total operative time started declining after 42 cases (309.1 ± 84.4 vs. 220.2 ± 46.4, P < 0.001). The risk-adjusted CUSUM (RA-CUSUM) learning curve for postoperative complications fluctuated in cases 44–75 and declined significantly after case 75. The RA-CUSUM learning curve for AL declined after 68 cases.

Conclusions
taTME had learning curves of 42, 75, and 68 cases for total operative time, postoperative complications, and AL, respectively. A surgeon may require 42 and 75 cases to achieve “proficiency” and “mastery” in taTME procedures, respectively.