bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent validity of skin carotenoid status as a concentration biomarker of vegetable and fruit intake compared to multiple 24-h recalls and plasma carotenoid concentrations across one year: a cohort study
Authors: Jahns Lisa , Johnson LuAnn K. , Conrad Zach , Bukowski Michael , Raatz Susan K. , Jilcott Pitts Stephanie , Wang Youfa , Ermakov Igor V. , Gellermann Werner 
Published: November 2019

Abstract
Background
Biological markers of vegetable and fruit (VF) intake are needed both for nutrition surveillance and for the evaluation of nutrition interventions. Optically assessed skin carotenoid status (SCS) has been proposed as a marker of intake but there are few published validity studies to date. Therefore, the objective of the study was to examine the concurrent validity of multiple methods of assessing VF intake cross-sectionally and seasonally over one year and to discuss the relative merits and limitations of each method.

Methods
Fifty-two 40–60 y old women completed a 1-year longitudinal study that included 1) SCS assessment using resonance Raman spectroscopy (RRS) and using pressure-mediated reflection spectroscopy (RS) at 12 timepoints, 2) thirty-six 24-h recalls using the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24; total 1866 recalls), and 3) plasma carotenoid concentrations measured every 3 months. Pearson correlation coefficients and mixed linear models were used to estimate pairwise correlations between RRS, RS, ASA24, and plasma carotenoids.

Results
RS and RRS were strongly correlated at baseline and over the year (r = 0.86 and 0.76; respectively, P < 0.001). RS was strongly correlated with plasma carotenoids at baseline (r = 0.70) and moderately across the year (r = 0.65), as was RRS (r = 0.77 and 0.69, respectively, all P < 0.001). At baseline, self-reported VF was weakly correlated with RRS (r = 0.33; P = 0.016), but not with RS or plasma carotenoids. Across the year, self-reported VF intake was weakly correlated with both RS (r = 0.37; P = 0.008), RRS (r = 0.37; P = 0.007), and with plasma carotenoids (r = 0.36; P < 0.008).

Conclusions
SCS as measured by RS and RRS is moderately to strongly correlated with plasma carotenoid concentrations both cross-sectionally and longitudinally, indicating that it can be a powerful tool to assess carotenoid-rich VF intake in populations.

Clinical trial registry
This trial was registered at ClinicalTrials.gov as NCT01674296.
Effects of school-based physical activity on mathematics performance in children: a systematic review
Authors: Sneck S. , Viholainen H. , Syväoja H. , Kankaapää A. , Hakonen H. , Poikkeus A.-M. , Tammelin T. 
Published: November 2019

AbstractBackgroundThe benefits of physical activity (PA) on children’s health and wellbeing are well established. However, the benefits of PA on academic performance and particularly on mathematics performance warrant systematic analysis. Mathematics is one of the core subjects in school education globally.MethodsWe systematically searched, analysed and synthesized the literature on the effects of school-based PA interventions on mathematics performance in children aged 4–16. A total of 29 studies consisting of randomised trials and other interventions with control groups were identified through a systematic search, and 11 of them provided sufficient data and appropriate design for a meta-analysis.ResultsOf the 29 studies involving 11,264 participants, positive overall effects of a PA intervention on mathematics performance were found in 13 studies (45%) and neutral overall effects in 15 studies (52%). Only one study reported a significant negative result for a subgroup of children in the first half of the intervention. In a risk-of-bias assessment, 12 studies had low, 17 moderate, and none had a high risk of bias. The meta-analysis of 11 studies suggested an overall small positive effect (ES = 0.23) of the interventions. Only one study in the meta-analysis indicated a negative effect in one of the intervention groups.ConclusionsAdding PA to the school day may enhance children’s mathematics performance or has no negative effects on performance. Several types of PA interventions can be recommended to be added to the school day.
Systematic review of interventions in the childcare setting with direct parental involvement: effectiveness on child weight status and energy balance-related behaviours
Authors: van de Kolk I. , Verjans-Janssen S. R. B. , Gubbels J. S. , Kremers S. P. J. , Gerards S. M. P. L. 
Published: November 2019

AbstractBackgroundThe early years are a crucial period to promote healthy energy balance-related behaviours in children and prevent overweight and obesity. The childcare setting is important for health-promoting interventions. Increasingly, attention has been paid to parental involvement in childcare-based interventions. The aim of this systematic review is to evaluate the effectiveness of these interventions with direct parental involvement on the children’s weight status and behavioural outcomes.MethodsA systematic search was conducted in four electronic databases to include studies up until January 2019. Studies written in English, describing results on relevant outcomes (weight status, physical activity, sedentary behaviour and/or nutrition-related behaviour) of childcare-based interventions with direct parental involvement were included. Studies not adopting a pre-post-test design or reporting on pilot studies were excluded. To improve comparability, effect sizes (Cohen’s d) were calculated. Information on different types of environment targeted (e.g., social, physical, political and economic) was extracted in order to narratively examine potential working principles of effective interventions.ResultsA total of 22 studies, describing 17 different interventions, were included. With regard to the intervention group, 61.1% found some favourable results on weight status, 73.3% on physical activity, 88.9% on sedentary behaviour, and all on nutrition-related behaviour. There were studies that also showed unfavourable results. Only a small number of studies was able to show significant differences between the intervention and control group (22.2% weight status, 60.0% physical activity, 66.6% sedentary behaviour, 76.9% nutrition behaviour). Effect sizes, if available, were predominantly small to moderate, with some exceptions with large effect sizes. The interventions predominantly targeted the socio-cultural and physical environments in both the childcare and home settings. Including changes in the political environment in the intervention and a higher level of intensity of parental involvement appeared to positively impact intervention effectiveness.ConclusionChildcare-based interventions with direct parental involvement show promising effects on the children’s energy balance-related behaviours. However, evidence on effectiveness is limited, particularly for weight-related outcomes. Better understanding of how to reach and involve parents may be essential for strengthening intervention effectiveness.
Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy
Authors: Weiss Rebecca J. , Bates Sara V. , Song Ya’nan , Zhang Yue , Herzberg Emily M. , Chen Yih-Chieh , Gong Maryann , Chien Isabel , Zhang Lily , Murphy Shawn N. , Gollub Randy L. , Grant P. Ellen , Ou Yangming 
Published: November 2019

AbstractBackgroundSecondary and retrospective use of hospital-hosted clinical data provides a time- and cost-efficient alternative to prospective clinical trials for biomarker development. This study aims to create a retrospective clinical dataset of Magnetic Resonance Images (MRI) and clinical records of neonatal hypoxic ischemic encephalopathy (HIE), from which clinically-relevant analytic algorithms can be developed for MRI-based HIE lesion detection and outcome prediction.MethodsThis retrospective study will use clinical registries and big data informatics tools to build a multi-site dataset that contains structural and diffusion MRI, clinical information including hospital course, short-term outcomes (during infancy), and long-term outcomes (~ 2 years of age) for at least 300 patients from multiple hospitals.DiscussionWithin machine learning frameworks, we will test whether the quantified deviation from our recently-developed normative brain atlases can detect abnormal regions and predict outcomes for individual patients as accurately as, or even more accurately, than human experts.Trial RegistrationNot applicable. This study protocol mines existing clinical data thus does not meet the ICMJE definition of a clinical trial that requires registration
Sequencing of animal viruses: quality data assurance for NGS bioinformatics
Authors: Zamperin Gianpiero , Lucas Pierrick , Cano Irene , Ryder David , Abbadi Miriam , Stone David , Cuenca Argelia , Vigouroux Estelle , Blanchard Yannick , Panzarin Valentina 
Published: November 2019

AbstractBackgroundNext generation sequencing (NGS) is becoming widely used among diagnostics and research laboratories, and nowadays it is applied to a variety of disciplines, including veterinary virology. The NGS workflow comprises several steps, namely sample processing, library preparation, sequencing and primary/secondary/tertiary bioinformatics (BI) analyses. The latter is constituted by a complex process extremely difficult to standardize, due to the variety of tools and metrics available. Thus, it is of the utmost importance to assess the comparability of results obtained through different methods and in different laboratories. To achieve this goal, we have organized a proficiency test focused on the bioinformatics components for the generation of complete genome sequences of salmonid rhabdoviruses.MethodsThree partners, that performed virus sequencing using different commercial library preparation kits and NGS platforms, gathered together and shared with each other 75 raw datasets which were analyzed separately by the participants to produce a consensus sequence according to their own bioinformatics pipeline. Results were then compared to highlight discrepancies, and a subset of inconsistencies were investigated more in detail.ResultsIn total, we observed 526 discrepancies, of which 39.5% were located at genome termini, 14.1% at intergenic regions and 46.4% at coding regions. Among these, 10 SNPs and 99 indels caused changes in the protein products. Overall reproducibility was 99.94%. Based on the analysis of a subset of inconsistencies investigated more in-depth, manual curation appeared the most critical step affecting sequence comparability, suggesting that the harmonization of this phase is crucial to obtain comparable results. The analysis of a calibrator sample allowed assessing BI accuracy, being 99.983%.ConclusionsWe demonstrated the applicability and the usefulness of BI proficiency testing to assure the quality of NGS data, and recommend a wider implementation of such exercises to guarantee sequence data uniformity among different virology laboratories.
Prognostic and diagnostic validity of p16/Ki-67, HPV E6/E7 mRNA, and HPV DNA in women with ASCUS: a follow-up study
Authors: Ren Chenchen , Zhu Yuanhang , Yang Li , Zhang Xiaoan , Liu Ling , Wang Zhaoxin , Jiang Dongyuan 
Published: November 2019

AbstractBackgroundWe evaluated the prognostic and diagnostic ability of p16/Ki-67 immunocytochemistry, HPV E6/E7 mRNA testing and HPV DNA assay in triaging ASCUS to find a way to manage cervical lesions more effectively.MethodsWe conducted a prospective study through follow-up. The detection methods of the three factors: p16/Ki-67 immunocytochemistry conducted by using the CINtec® Plus Kit, E6/E7 mRNA testing by QuantiVirus®HPV E6/E7 mRNA assay and DNA by Hybrid Capture 2 assay.ResultsOne hundred three women with ASCUS satisfied requirements and completed the entire follow-up process. All CIN2+ occurred in women who were mRNA positive at baseline, none in mRNA negative. 100% (6/6) patients with CIN2+ were HPV DNA assay positive, 100% (6/6) were HPV E6/E7 mRNA testing positive and 50.0% (3/6) were p16/Ki-67 immunocytochemistry positive. The risk ratio of E6/E7 mRNA test was 57.306 (95% CI 0.077–42,400.545). For endpoint of CIN2+, the sensitivity between HPV DNA assay and HPV E6/E7 mRNA testing is no statistical difference, but statistical difference exists between HPV E6/E7 mRNA testing vs. p16/Ki-67 immunocytochemistry (χ2 = 5.718,P = 0.023) and HPV DNA assay vs. p16/Ki-67 immunocytochemistry (χ2 = 5.718,P = 0.023). The specificity of E6/E7 mRNA testing, p16/Ki-67 and DNA assay in triaging ASCUS was 44.33, 75.26 and 11.34% respectively and is all statistical difference (χ2 = 26.277,P < 0.001(HPV DNA assay vs. HPV E6/E7 mRNA testing),χ2 = 19.297,P < 0.001(HPV E6/E7 mRNA testing vs. p16/Ki-67 immunocytochemistry),χ2 = 80.707,P < 0.001(HPV DNA assay vs. p16/Ki-67 immunocytochemistry). The expression level of 2097.09 copies/ml was the optimal cut-off value for HPV E6/E7 mRNA testing to diagnose CIN2+, the sensitivity and specificity was 61.1 and 68.2%.ConclusionsHigh expression of HPV E6/E7 mRNA could be a good candidate as a diagnostic biomarker to triage ASCUS superseding HPV DNA. p16/Ki-67 immunocytochemistry is suggested to be a good tool to triage ASCUS, but it reduced the sensitivity of diagnosis when improves the diagnostic specificity.
Chiropractic maintenance care - what’s new? A systematic review of the literature
Authors: Axén Iben , Hestbaek Lise , Leboeuf-Yde Charlotte 
Published: November 2019

Abstract
Background
Maintenance Care is a traditional chiropractic approach, whereby patients continue treatment after optimum benefit is reached. A review conducted in 1996 concluded that evidence behind this therapeutic strategy was lacking, and a second review from 2008 reached the same conclusion. Since then, a systematic research program in the Nordic countries was undertaken to uncover the definition, indications, prevalence of use and beliefs regarding Maintenance Care to make it possible to investigate its clinical usefulness and cost-effectiveness. As a result, an evidence-based clinical study could be performed. It was therefore timely to review the evidence.

Method
Using the search terms “chiropractic OR manual therapy” AND “Maintenance Care OR prevention”, PubMed and Web of Science were searched, and the titles and abstracts reviewed for eligibility, starting from 2007. In addition, a search for “The Nordic Maintenance Care Program” was conducted. Because of the diversity of topics and study designs, a systematic review with narrative reporting was undertaken.

Results
Fourteen original research articles were included in the review. Maintenance Care was defined as a secondary/tertiary preventive approach, recommended to patients with previous pain episodes, who respond well to chiropractic care. Maintenance Care is applied to approximately 30% of Scandinavian chiropractic patients. Both chiropractors and patients believe in the efficacy of Maintenance Care. Four studies investigating the effect of chiropractic Maintenance Care were identified, with disparate results on pain and disability of neck and back pain. However, only one of these studies utilized all the existing evidence when selecting study subjects and found that Maintenance Care patients experienced fewer days with low back pain compared to patients invited to contact their chiropractor ‘when needed’. No studies were found on the cost-effectiveness of Maintenance Care.

Conclusion
Knowledge of chiropractic Maintenance Care has advanced. There is reasonable consensus among chiropractors on what Maintenance Care is, how it should be used, and its indications. Presently, Maintenance Care can be considered an evidence-based method to perform secondary or tertiary prevention in patients with previous episodes of low back pain, who report a good outcome from the initial treatments. However, these results should not be interpreted as an indication for Maintenance Care on all patients, who receive chiropractic treatment.
Factors affecting the incidence of surgical site infection after geriatric hip fracture surgery: a retrospective multicenter study
Authors: Liu Xiaopo , Dong Zhijie , Li Jun , Feng Yunbo , Cao Guolong , Song Xin , Yang Jie 
Published: November 2019

Abstract
Background
Geriatric hip fracture is a common type of osteoporotic fracture with high mortality and disability; surgical site infection (SSI) can be a devastating complication of this injury. By far, only a few studies identified easily remediable factors to reduce infection rates following hip fracture and less researches have focused on geriatric patients. The objective of this study was to identify potentially modifiable factors associated with SSI following geriatric hip fracture surgery.

Methods
This retrospective, multicenter study involves three level I hospitals. A total of 1240 patients (60 years or older) underwent hip surgery with complete data were recruited between January 2016 and June 2018. Demographics information, medications and additional comorbidities, operation-related variables, and laboratory indexes were extracted and analyzed. Receiver operating characteristic (ROC) analysis was performed to detect the optimum cut-off value for quantitative data. Univariate and multivariate logistic analysis model were performed respectively to identify the independent predictors.

Results
Ninety-four (7.58%) patients developed SSI in this study, and 76 (6.13%) had superficial infection, while 18 (1.45%) were diagnosed with deep infection. Results of univariate and multivariate analysis showed age > 79 years (OR, 2.60; p < 0.001), BMI > 26.6 kg/m2 (OR, 2.97; p < 0.001), operating time > 107 min (OR, 2.18; p = 0.001), and ALB < 41.6 g/L (OR, 2.01; p = 0.005) were associated with an increased incidence of SSI; drainage use (OR, 0.57; p = 0.007) could reduce the incidence of wound infection for patients after geriatric hip fracture.

Conclusion
Accurate modifiable variables, operating time > 107 min, serum albumin < 41.6 g/L, BMI > 26.6 kg/m2, and age > 79 years could be applied to distinguish geriatric patients with high-risk of postoperative surgical site infection.
Arf6-driven endocytic recycling of CD147 determines HCC malignant phenotypes
Authors: Qi Shanshan , Su Linjia , Li Jing , Zhang Chuanshan , Ma Zhe , Liu Guiqiu , Zhang Qing , Jia Guhe , Piao Yongjun , Zhang Sihe 
Published: November 2019

AbstractBackgroundAdhesion molecules distributed on the cell-surface depends upon their dynamic trafficking that plays an important role during cancer progression. ADP-ribosylation factor 6 (Arf6) is a master regulator of membrane trafficking. CD147, a tumor-related adhesive protein, can promote the invasion of liver cancer. However, the role of Arf6 in CD147 trafficking and its contribution to liver cancer progression remain unclear.MethodsStable liver cancer cell lines with Arf6 silencing and over-expression were established. Confocal imaging, flow cytometry, biotinylation and endomembrane isolation were used to detect CD147 uptake and recycling. GST-pull down, gelatin zymography, immunofluorescence, cell adhesion, aggregation and tight junction formation, Transwell migration, and invasion assays were used to examine the cellular phenotypes. GEPIA bioinformatics, patient’s specimens and electronic records collection, and immunohistochemistry were performed to obtain the clinical relevance for Arf6-CD147 signaling.ResultsWe found that the endocytic recycling of CD147 in liver cancer cells was controlled by Arf6 through concurrent Rab5 and Rab22 activation. Disruption of Arf6-mediated CD147 trafficking reduced the cell-matrix and cell-cell adhesion, weakened cell aggregation and junction stability, attenuated MMPs secretion and cytoskeleton reorganization, impaired HGF-stimulated Rac1 activation, and markedly decreased the migration and invasion of liver cancer cells. Moreover, high-expression of the Arf6-CD147 signaling components in HCC (hepatocellular carcinoma) was closely correlated with poor clinical outcome of patients.ConclusionsOur results revealed that Arf6-mediated CD147 endocytic recycling is required for the malignant phenotypes of liver cancer. The Arf6-driven signaling machinery provides excellent biomarkers or therapeutic targets for the prevention of liver cancer.
Association between hospital mortality and inspiratory airway pressures in mechanically ventilated patients without acute respiratory distress syndrome: a prospective cohort study
Authors:   Society of Critical Care Medicine Discovery Network Critical Illness Outcomes Study Investigators, Sahetya Sarina K. , Mallow Christopher , Sevransky Jonathan E. , Martin Greg S. , Girard Timothy D. , Brower Roy G. , Checkley William 
Published: November 2019

Abstract
Background
Higher inspiratory airway pressures are associated with worse outcomes in mechanically ventilated patients with the acute respiratory distress syndrome (ARDS). This relationship, however, has not been well investigated in patients without ARDS. We hypothesized that higher driving pressures (ΔP) and plateau pressures (Pplat) are associated with worse patient-centered outcomes in mechanically ventilated patients without ARDS as well as those with ARDS.

Methods
Using data collected during a prospective, observational cohort study of 6179 critically ill participants enrolled in 59 ICUs across the USA, we used multivariable logistic regression to determine whether ΔP and Pplat at enrollment were associated with hospital mortality among 1132 mechanically ventilated participants. We stratified analyses by ARDS status.

Results
Participants without ARDS (n = 822) had lower average severity of illness scores and lower hospital mortality (27.3% vs. 38.7%; p <  0.001) than those with ARDS (n = 310). Average Pplat (20.6 vs. 23.9 cm H2O; p <  0.001), ΔP (14.3 vs. 16.0 cm H2O; p <  0.001), and positive end-expiratory pressure (6.3 vs. 7.9 cm H2O; p <  0.001) were lower in participants without ARDS, whereas average tidal volumes (7.2 vs. 6.8 mL/kg PBW; p <  0.001) were higher. Among those without ARDS, higher ΔP (adjusted OR = 1.36 per 7 cm H2O, 95% CI 1.14–1.62) and Pplat (adjusted OR = 1.42 per 8 cm H2O, 95% CI 1.17–1.73) were associated with higher mortality. We found similar relationships with mortality among those participants with ARDS.

Conclusions
Higher ΔP and Pplat are associated with increased mortality for participants without ARDS. ΔP may be a viable target for lung-protective ventilation in all mechanically ventilated patients.
EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
Authors: Lhoumaud Priscillia , Sethia Gunjan , Izzo Franco , Sakellaropoulos Theodore , Snetkova Valentina , Vidal Simon , Badri Sana , Cornwell Macintosh , Di Giammartino Dafne Campigli , Kim Kyu-Tae , Apostolou Effie , Stadtfeld Matthias , Landau Dan Avi , Skok Jane 
Published: November 2019

AbstractActivation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.