bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple-testing Correction in Metabolome-wide Association Studies
Authors: Peluso Alina , Glen Robert , Ebbels Timothy M D 
Published: October 2020

Abstract
The search for statistically signiﬁcant relationships between molecular markers and outcomes is challenging when dealing with high-dimensional, noisy and collinear multivariate omics data. Permutation procedures allow for the estimation of adjusted signiﬁcance levels without assuming independence among the metabolomic variables. Nevertheless, the complex non-normal structure of the metabolic proﬁles and outcomes may bias the permutation results leading to overly conservative threshold estimates i.e. lower than a Bonferroni or Sidak correction. Within a univariate permutation procedure we employ parametric simulation methods based on the multivariate (log-)Normal distribution to obtain adjusted signiﬁcance levels which are consistent across phenotypes while eﬀectively controlling the type I error rate at the α level. Next, we derive an alternative closed-form expression for the estimation of the number of non-redundant metabolic variates based on the spectral decomposition of their correlation matrix. The eﬃcacy of our methods is tested for diﬀerent model parametrizations and across a wide range of correlation levels of the variates using both synthetic and real data sets. Both the permutation-based formulation and the more practical closed form expression are found to give an eﬀective indication of the number of indipendent metabolic eﬀects exhibited by the system.
Surgery for Primary Tumor Benefits Survival for Breast Cancer Patients With Bone Metastases: A Large Cohort Retrospective Study
Authors: Huang Zhangheng , Zhou Xin , Tong Yuexin , Zhu Lujian , Zhao Ruhan , Zhao Chengliang 
Published: October 2020

Abstract
Background: The role of surgery for the primary tumor in breast cancer patients with bone metastases (BM) remains unclear. The purpose of this study was to determine the impact of surgery for the primary tumor in breast cancer patients with BM and to develop prognostic nomograms to predict the overall survival (OS) of breast cancer patients with BM.Methods: A total of 3,956 breast cancer patients with BM from the Surveillance, Epidemiology, and End Results database between 2010 and 2016 were included. Propensity score matching (PSM) was used to eliminate the bias between the surgery and non-surgery groups. The Kaplan-Meier analysis and the log-rank test were performed to compare the OS between two groups. Cox proportional risk regression models were used to identify independent prognostic factors. Two nomograms were constructed for predicting the OS of patients in the surgery and non-surgery groups, respectively. In addition, calibration curve, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA) were used to evaluate the performance of nomograms.Result: The survival analysis showed that the surgery of the primary tumor significantly improved the OS for breast cancer patients with BM. Based on independent prognostic factors, separate nomograms were constructed for the surgery and non-surgery groups. The calibration and ROC curves of these nomograms indicated that both two models have high predictive accuracy, with the area under the curve values ≥0.700 on both the training and validation cohorts. Moreover, DCA showed that nomograms have strong clinical utility. Based on the results of the X-tile analysis, all patients were classified in the low-risk-of-death subgroup had a better prognosis.Conclusion: The surgery of the primary tumor can provide survival benefits for breast cancer patients with BM. Furthermore, these prognostic nomograms we constructed can be used as a tool to accurately assess the long-term prognosis of patients and help clinicians to develop individualized treatment strategies.
Additive Value of Texture Analysis Based on Breast MRI for Distinguishing Between Benign and Malignant Non-mass Enhancement in Premenopausal Women
Authors: Tan Yu , Mai Hui , Huang Zhiqing , Zhang Li , Li Chengwei , Wu Songxin , Huang Huang , Tang Wen , Liu Yongxi , Jiang Kuiming 
Published: October 2020

Abstract
Background: Non-mass enhancement (NME) is a diagnostic dilemma. Texture analysis (TA) could serve as an objective method to quantify tumor characteristics and growth patterns. However, there are few reports about TA use in NME diagnosis. To our knowledge, NME diagnosis based on the combination of the features noted on routine MRI and TA has not been reported.. The purpose of this study was to explore the value of TA in distinguishing between benign and malignant NME in premenopausal women. Methods: Women in whom NME was histologically proven (n = 147) were enrolled (benign: 58; malignant: 89) was retrospective. Then, 102 and 45 patients were classified as the training and validation groups, respectively. Scanning sequences included Fat-suppressed T2-weighted and fat-suppressed contrast-enhanced T1-weighted which were acquired on a 1.5T MRI system. Clinical and routine MR characteristics (CRMC) were evaluated by two radiologists according to the Breast Imaging and Reporting and Data system (2013). Texture features were extracted from all post-contrast sequences in the training group. The combination model was built and then assessed in the validation group. Pearson’s chi-square test and Mann-Whitney U test were used to compare categorical variables and continuous variables, respectively. Logistic regression analysis and receiver operating characteristic curve were employed to assess the diagnostic performance of CRMC, TA, and their combination model in NME diagnosis.Results: The combination model showed a superior diagnostic performance in differentiating between benign and malignant NME compared to that of CRMC or TA alone (AUC, 0.887 vs 0.832 vs 0.74). Moreover, compared to CRMC, the model showed high specificity (72.5% vs 80%). The results obtained in the validation group confirmed the model was promising.Conclusion: The combined use of TA and CRMC could afford an improved diagnostic performance in differentiating between benign and malignant NME.
Alleviation of EGFR Tyrosine Kinase Inhibitor-induced Skin Toxicity by Modified Huang-Lian-Jie-Du Decoction Cream in Cancer Patients
Authors: Lee Ming-Yang , Lin Mei-Yi , Chang Yu-Ju , Tseng Yu-Ting , Huang I-An , Siao Ying-Yu , Liu Yi-Wen 
Published: October 2020

Abstract
Background: The EGFRIs and TKIs are effective for cancer target therapy, but the acneiform rashes or called inflammatory papulopustular exanthemas are common (50% to 100%). The conventional therapy for EGFRIs/TKIs-induced skin toxicity is steroids and antibiotics, but their effect is still limited. In this study, a modified Chinese herbal medicine Huang Lian Jie Du decoction cream with Yin-Cold (YC) medicine characteristic was investigated for the effect on patients suffering EGFRIs/TKIs-induced skin toxicity.Methods: The modified Huang Lian Jie Du (mHLJD) decoction cream was made from 10 herbal medicines including 4 major medicines (Huanglian, Huangqin, Huangbo, and Zhizi) in traditional HLJD decoction. Patients with EGFRIs/TKIs-induced skin toxicity were enrolled. Patients were excluded if they also used other cream for the skin toxicity. Skin conditions were follow up every 2 weeks. The patients’ characteristics, the skin toxicities and treatment response were recorded and analyzed after using mHLJD decoction cream for 1~2 months.Results: The mHLJD decoction cream and its subpackages were stored at 4℃ before use. Thirty-four patients who had grade 1-3 skin toxicities after receiving EGFRIs or TKIs were enrolled. Five patients were withdrawal or excluded, 2 patients with paronychia syndrome had no improvement and were excluded, too. Finally, data from 27 patients were analyzed. The mean grade of rash acneiform was decreased from 2.23 (ranged 1 to 3) to 0.38 (ranged 0 to 1) after mHLJD decoction cream treatment for 1~2 months. And the mean grade of dry skin was decreased from 1.57 (ranged 1 to 2) to 0.77 (ranged 0 to 1). The changes of skin toxicity were significant and no obvious adverse events.Conclusions: In summary, the mHLJD decoction cream is effective for alleviation of EGFRIs/TKIs-induced skin rash acneiform and dry skin. And mHLJD decoction cream has no effect in patients with paronychia syndrome.Trial registration: CYCH, CYCH-IRB No. 2019023. Registered 14 May 2019, http://www.cych.org.tw/irbweb/
Association of Risk Factors With Hepatitis B &amp; C Infection Among Pregnant Women Visiting a Private Tertiary Care Hospitals- Peshawar (An Un Matched Pilot Case Control Study)
Authors: Farooqi Jalwa Javed , Malik Farhat Rehana , Farooqi Kanza Javed , Mudassar Owais 
Published: October 2020

Abstract
Background; Viral hepatitis causes devastating health issues to everyone globally and specifically the most vulnerable groups like pregnant ladies. The aim of this study was to identify risk factors for hepatitis B and C virus infection with univariate association of virus seropositivity among pregnant women and comparison of public with private hospital data.Study Design; An Unmatched Case Control Pilot Study.Place and Duration; Gynaecology wards of Two Public Tertiary Care Hospitals of Peshawar and equal number of Private clinics, from September- 2018 to February- 2019.Methods; This study enrolled 21 cases and controls as 1:1 ratio via consecutive sampling. A validated questionnaire was used. Cases included were HBsAg and ELISA positive HCV females, while anti HBsAg and Anti HCV ELISA negative were the controls. The collected data was entered and analysed in SPSS version- 19. Descriptive statistics were computed by frequency and percentages while inferential statistics through Odd ratio and 95% confidence interval. P value cut of limit was set at <0.05. Results; The mean age was 37±9 for the cases and 28±6 years for controls respectively. The risk factors with increase occurrence of disease were past history of abortion OR=1.23 (95% Cl=0.34-4.35), past hospitalization OR=2.90 (Cl=0.77-10.8), past surgical procedure OR=3.69 (Cl=0.81-16.6), dental extraction OR=1.25 (Cl=0.33-4.63), delivery in hospital OR=4.26 (Cl=1.13-16.05), injection in hospitals OR=1.47 (Cl=0.43-5.04), household contact with jaundice OR=5.66 (Cl=1.41-22.7). Normal vaginal delivery OR=1.96 (Cl=0.51-7.48) and history of sexually transmitted infections OR=2.23 (Cl=0.36-13.7) were independently associated with HBV, HCV.Conclusion; Iatrogenic exposures of injections, blood transfusions, tooth extractions, home deliveries with past history of sexually transmitted infections, abortion, hepatitis infection and hospital admissions were the risk factors among the pregnant women.
Changes in the Taxonomic and Functional Structure of Microbial Communities During Vegetable Waste Silage Fermentation
Authors: Zhang Juntao , Huang Xiying , Ma Menggen , Xiang Quanju , Zhao Ke , Penttinen Petri , Gu Yunfu 
Published: October 2020

Abstract
Background：Silage fermentation, a sustainable way to use vegetable waste resources, is a complex process driven by a variety of microorganisms. We used lettuce waste as the raw material for silage, analyzed changes in the physico-chemical characteristics and bacterial community composition of silage during a 60 day fermentation, identified differentially abundant taxa, predicted the functional profiles of bacterial communities, and determined the associated effects on the quality of silage. Results: The biggest changes occurred in the early stage of silage fermentation. Changes in the physico-chemical characteristics included a decrease in pH and increases in ammonia nitrogen to total nitrogen ratio and lactic acid content. The numbers of lactic acid bacteria increased and those of molds, yeasts and aerobic bacteria decreased. The bacterial communities and their predicted functions on day 0 were clearly different from those on day 7 to day 60. The relative abundances of phylum Firmicutes and genus Lactobacillus increased. Nitrite ammonification and nitrate ammonification were more prevalent after day 0. The differences in the predicted functions were associated with differences in pH and amino acid, protein, carbohydrate, NH3-N, ether extract and crude ash contents. Conclusion: Firmicutes and Lactobacillus were the dominant taxa during vegetable waste silage fermentation. The microbial communities and the predicted functions changed in different stages of silage fermentation, and the changes were accompanied with changes in the physico-chemical characteristics, especially with a decrease in pH and increases in ammonia nitrogen to total nitrogen ratio and lactic acid content.
LOCATE: A Prospective Evaluation of the Value of Leveraging Ongoing Citation Acquisition Techniques for Living Evidence Syntheses
Authors: Gates Michelle , Elliott Sarah A , Gates Allison , Sebastianski Meghan , Pillay Jennifer , Bialy Liza , Hartling Lisa 
Published: October 2020

Abstract
Background. Living systematic reviews (LSRs) can expedite evidence synthesis by incorporating new evidence in real time. However, the methods needed to identify new studies in a timely manner are not well established. Objectives. To explore the value of complementary search approaches in terms of search performance, impact on results and conclusions, screening workload and feasibility compared to the reference standard.Methods. We developed three complementary search approaches for a systematic review on treatments for bronchiolitis: Automated Full Search, Pubmed Similar Articles, and Scopus Citing References. These were automated to retrieve results monthly; pairs of reviewers screened the records and commented on feasibility. After one year, we conducted a full update search (reference standard). For each complementary approach, we compared search performance (proportion missed, number needed to read [NNR]) and reviewer workload (number of records screened, time required) to the reference standard. We investigated the impact of the new trials on the effect estimate and certainty of evidence for the primary outcomes. We summarized comments about feasibility. Results. Via the reference standard, reviewers screened 505 titles/abstracts, 24 full texts, and identified four new trials (NNR 126.6; 12.4 hours). Of the complementary approaches, only the Automated Full Search located all four trials; these were located six to 12 months sooner than via the reference standard but did not alter the results nor certainty in the evidence. The Automated Full Search was the most resource-intensive approach (816 records screened; NNR 204.1; 17.1 hours). The Pubmed Similar Articles and Scopus Citing References approaches located far fewer records (452 and 244, respectively), thereby requiring less screening time (9.4 and 5.2 hours); however, each approach located only one of the four new trials. Reviewers found it feasible and convenient to conduct monthly screening for searches of this yield (median 15-65 records/month). Conclusions. The Automated Full Search was the most resource-intensive approach, but also the only to locate all of the newly published trials. Although the monthly screening time for the Pubmed Similar Articles and Scopus Citing Articles was far less, most relevant records were missed. These approaches were feasible to integrate into reviewer work processes.Study Protocol. Posted 25 October 2018 on the Open Science Framework, https://osf.io/wxebg/ doi: 10.17605/OSF.IO/6M28H.
The Clinical Effects of Cerebral Near-Infrared Spectroscopy Monitoring (NIRS) Versus No Monitoring in Children and Adults: A Protocol for a Systematic Review With Meta-Analysis and Trial Sequential Analysis
Authors: Hansen Mathias Lühr , Hyttel-Sørensen Simon , Jakobsen Janus Christian , Gluud Christian , Kooi Elisabeth M.W. , Mintzer Jonathan , de Boode Willem P. , Fumagalli Monica , Allen Ana Alarcon , Alderliesten Thomas , Greisen Gorm 
Published: October 2020

Abstract
BackgroundMultiple clinical conditions are associated with cerebral hypoxia/ischaemia and thereby an increased risk of hypoxic-ischaemic brain injury. Cerebral near-infrared spectroscopy monitoring (NIRS) is a tool to monitor brain oxygenation and perfusion, and the clinical uptake of NIRS has expanded over recent years. Specifically, NIRS is used in the perioperative and neonatal, paediatric, and adult intensive care settings. However, the available literature suggests that clinical benefits and harms of cerebral NIRS monitoring are uncertain. As rates of clinically significant hypoxic-ischaemic brain injuries are typically low, it is difficult for randomised clinical trials to capture a sufficiently large number of events to evaluate the clinical effect of cerebral NIRS monitoring, when focusing on specific clinical settings. MethodsWe will conduct a systematic review with meta-analysis and Trial Sequential Analysis to evaluate the benefits and harms of clinical care with cerebral NIRS monitoring versus clinical care without cerebral NIRS monitoring in children and adults across all clinical settings. We will only include randomised clinical trials and the primary outcomes are all-cause mortality, moderate or severe persistent cognitive or neurological deficit, and proportion of participants with one or more serious adverse events. The review will be conducted according to the methodology described in The Cochrane Handbook for Systematic Reviews of Interventions, including GRADE. An eight-step procedure by Jakobsen et al. will be used to assess if thresholds for statistical and clinical significance are crossed.DiscussionAs we include trials across multiple clinical settings, there is an increased probability of reaching a sufficient information size. However, heterogeneity between the included trials may impair our ability to interpret results to specific clinical settings. In this situation, we may have to depend on subgroup analyses with inherent increased risks of type I and II errors. Systematic review registrationThis systematic review protocol has been submitted for registration in the International Prospective Register of Systematic Reviews (PROSPERO) (http://www.crd.york.ac.uk/prospero) (1,2) on 12th of October 2020.
Inflammation Scores as Prognostic Biomarkers in Small Cell Lung Cancer: A Systematic Review and Meta-Analysis
Authors: Winther-Larsen Anne , Aggerholm-Pedersen Ninna , Sandfeld-Paulsen Birgitte 
Published: October 2020

Abstract
Background: Inflammation scores based on general inflammation markers as leucocyte count or C-reactive protein have been evaluated as prognostic markers of inferior survival in several cancers. In small cell lung cancer (SCLC), however, inflammation scores are less studied. In the present study, we set out to perform a systematic review and meta-analysis investigating reported associations between inflammation scores and overall survival (OS) in SCLC. Methods: A literature search was performed in PubMed, Embase, Scopus, and Web of Science following the Preferred Reporting Items for Systematic and Meta-Analyses (PRISMA) guidelines. Of the identified publications, only studies in English containing original data evaluating inflammation scores as a prognostic factor in SCLC patients were included. Hazard ratios (HRs) for OS were pooled in a random-effects model. Results: In total, 33 articles were included evaluating eight different inflammation scores in 7762 SCLC patients. Seven of the identified scores were based on leucocyte count. Neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte (PLR) ratio were the most frequently evaluated scores (NLR: n=23; PLR: n=22). For NLR, a meta-analysis including 16 studies demonstrated that patients with a high NLR had a significantly shorter OS compared to patients with a low NLR (pooled HR=1.39 (95 % CI, 1.23 – 1.56)). For PLR, an association with survival could not be confirmed in a meta-analysis performed based on eight studies (pooled HR=1.20 (95 % CI, 0.96 – 1.51)). Conclusions: This review identifies that inflammation scores based on general inflammation markers have some potential as prognostic biomarkers in SCLC. The meta-analyses indicated that NLR is associated with inferior OS, whereas an association between PLR and OS could not be confirmed. Thus, NLR could be a useful biomarker of OS in SCLC patients. Systematic Review Registrations: The protocol for the study was submitted to the PROSPERO database (registration number CRD42020188553).
Adverse Health Manifestations in the Hands of Vibration Exposed Carpenters - A Cross Sectional Study
Authors: Tekavec Eva , Löfqvist Lotta , Larsson Anna , Fisk Karin , Riddar Jakob , Nilsson Tohr , Nordander Catarina 
Published: October 2020

Abstract
BackgroundDespite EU regulatory standards, many workers suffer injury as a result of working with hand-held vibrating tools. Our aim of this study was to investigate whether carpenters, a highly exposed group, suffer more injuries to their hands than painters, a group assumed to be less exposed to vibration. Methods193 carpenters and 72 painters, all men, answered a questionnaire and underwent a clinical examination to identify manifestations of neural and vascular origin in hands. Neurosensory affection was defined as having at least one symptom in the fingers/hands (impaired perception of touch, warmth, or cold, impaired dexterity, increased sensation of cold, numbness or tingling, or pain in the fingers/hands when cold) and at least one clinical finding (impaired perception of touch, warmth, cold, vibration, or two-point discrimination). Logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI). ResultsNeurosensory affection was fulfilled for 31% of the carpenters and 17% of the painters, age-adjusted OR 3.3 (CI 1.6–7.0). Among carpenters with neurosensory affection 18% reported interference with daily life activities, the most common symptoms being increased sensation of cold, numbness and pain in the fingers/hands when cold, the most common clinical findings were impaired perception of touch and vibration. Neurosensory affection was found in 12 % of young carpenters (≤ 30 years old). No difference was found in the prevalence of white fingers between carpenters and painters. ConclusionsCarpenters showed more symptoms and clinical findings of neurosensory affection than painters, probably due to vibration exposure. Also young carpenters showed signs of neurosensory affection, which indicates that workers at today´s working conditions are not protected against injury. This underlines the importance of reducing exposure to vibration, and conducting regular medical check-ups to detect early signs of neural and vascular manifestations indicating hand-arm vibration injuries. Special attention should be given to symptoms of increased sensation of cold, pain in the fingers when cold, and numbness, as these were the most common initiating ones, and should be addressed as early as possible in the preventive sentinel process. It is also important to test clinically for small- and large-fibre neuropathy, as the individual may be unaware of any pathology.