bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of shear and rotatory inertia on the bending vibration method without weighing specimens
Authors: Kubojima Yoshitaka , Sonoda Satomi , Kato Hideo , Harada Masaki 
Published: July 2020

AbstractThis study examines the effect of shear and rotatory inertia on the accuracy of the vibration method with additional mass (VAM). Bending vibration tests were performed for rectangular bars with a width of 30 mm, thicknesses ranging from 5 to 60 mm, and a length of 300 mm, small round bars with diameters in the range of 6–36 mm, and lengths of 150–300 mm, and cross beams for timber guardrails with and without a concentrated mass under a free–free condition. The estimation accuracy of the VAM and the effect of shear and rotatory inertia increased and decreased, respectively, as the length/thickness ratio of the rectangular bar and length/diameter ratio of the round bar increased. The estimation accuracy of the VAM decreased with an increase in the effect of shear and rotatory inertia, and it could be corrected. The range of the effect of shear and rotatory inertia for the sufficient estimation accuracy of the VAM was obtained.
Association between surgical procedures under general anesthesia in infancy and developmental outcomes at 1 year: the Japan Environment and Children’s Study
Authors: Kobayashi Yoshiko , Tokuda Narumi , Adachi Sho , Takeshima Yasuhiro , Hirose Munetaka , Shima Masayuki ,   Japan Environment and Children’s Study (JECS) Group, Kamijima Michihiro , Yamazaki Shin , Ohya Yukihiro , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Yamagata Zentaro , Inadera Hidekuni , Nakayama Takeo , Iso Hiroyasu , Kurozawa Youichi , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko 
Published: July 2020

Abstract
Background
The neurotoxicity of general anesthesia to the developing human brains is controversial. We assessed the associations between surgery under general anesthesia in infancy and development at age 1 year using the Japan Environment and Children’s Study (JECS), a large-scale birth cohort study.

Methods
In the JECS, 103,062 pregnancies and 104,065 fetuses were enrolled between January 2011 and March 2014. Of the 100,144 registered live births, we excluded preterm or post-term infants, multiple births, and infants with chromosomal anomalies and/or anomalies of the head or brain. Data on surgical procedures under general anesthesia in infancy were collected from self-administered questionnaires by parents at the 1-year follow-up. Developmental delay at age 1 year was assessed using the Japanese translation of the Ages and Stages Questionnaires, Third Edition (J-ASQ-3), comprising five developmental domains.

Results
Among the 64,141 infants included, 746 infants had surgery under general anesthesia once, 90 twice, and 71 three or more times. The percentage of developmental delay in the five domains of the J-ASQ-3 significantly increased with the number of surgical procedures. After adjusting for potential confounding factors, the risk of developmental delays in all five domains was significantly increased in infants who had surgery under general anesthesia three times or more (adjusted odds ratios: for communication domain 3.32; gross motor domain 4.69; fine motor domain 2.99; problem solving domain 2.47; personal–social domain 2.55).

Conclusions
Surgery under general anesthesia in infancy was associated with an increased likelihood of developmental delay in all five domains of the J-ASQ-3, especially the gross motor domain at age 1 year. The neurodevelopment with the growth should be further evaluated among the children who had surgery under general anesthesia.

Trial registration
UMIN Clinical Trials Registry (number: UMIN000030786)
Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients
Authors: De Maio Flavio , Posteraro Brunella , Ponziani Francesca Romana , Cattani Paola , Gasbarrini Antonio , Sanguinetti Maurizio 
Published: July 2020

AbstractWe analyzed the bacterial communities of the nasopharynx in 40 SARS-CoV-2 infected and uninfected patients. All infected patients had a mild COVID-19 disease. We did not find statistically significant differences in either bacterial richness and diversity or composition. These findings suggest a nasopharyngeal microbiota at least early resilient to SARS-CoV-2 infection.
Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials
Authors: Theilhaber Joachim , Chiron Marielle , Dreymann Jennifer , Bergstrom Donald , Pollard Jack 
Published: July 2020

AbstractBackgroundGene expression signatures for the prediction of differential survival of patients undergoing anti-cancer therapies are of great interest because they can be used to prospectively stratify patients entering new clinical trials, or to determine optimal treatment for patients in more routine clinical settings. Unlike prognostic signatures however, predictive signatures require training set data from clinical studies with at least two treatment arms. As two-arm studies with gene expression profiling have been rarer than similar one-arm studies, the methodology for constructing and optimizing predictive signatures has been less prominently explored than for prognostic signatures.ResultsFocusing on two “use cases” of two-arm clinical trials, one for metastatic colorectal cancer (CRC) patients treated with the anti-angiogenic molecule aflibercept, and the other for triple negative breast cancer (TNBC) patients treated with the small molecule iniparib, we present derivation steps and quantitative and graphical tools for the construction and optimization of signatures for the prediction of progression-free survival based on cross-validated multivariate Cox models. This general methodology is organized around two more specific approaches which we have called subtype correlation (subC) and mechanism-of-action (MOA) modeling, each of which leverage a priori knowledge of molecular subtypes of tumors or drug MOA for a given indication. The tools and concepts presented here include the so-called differential log-hazard ratio, the survival scatter plot, the hazard ratio receiver operating characteristic, the area between curves and the patient selection matrix. In the CRC use case for instance, the resulting signature stratifies the patient population into “sensitive” and “relatively-resistant” groups achieving a more than two-fold difference in the aflibercept-to-control hazard ratios across signature-defined patient groups. Through cross-validation and resampling the probability of generalization of the signature to similar CRC data sets is predicted to be high.ConclusionsThe tools presented here should be of general use for building and using predictive multivariate signatures in oncology and in other therapeutic areas.
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
Authors: Phaneuf Patrick V. , Yurkovich James T. , Heckmann David , Wu Muyao , Sandberg Troy E. , King Zachary A. , Tan Justin , Palsson Bernhard O. , Feist Adam M. 
Published: July 2020

Abstract
Background
Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover mutations that confer phenotypic functions of interest. However, the task of finding and understanding all beneficial mutations of an ALE experiment remains an open challenge for the field. To provide for better results than traditional methods of ALE mutation analysis, this work applied enrichment methods to mutations described by a multiscale annotation framework and a consolidated set of ALE experiment conditions. A total of 25,321 unique genome annotations from various sources were leveraged to describe multiple scales of mutated features in a set of 35 Escherichia coli based ALE experiments. These experiments totalled 208 independent evolutions and 2641 mutations. Additionally, mutated features were statistically associated across a total of 43 unique experimental conditions to aid in deconvoluting mutation selection pressures.

Results
Identifying potentially beneficial, or key, mutations was enhanced by seeking coding and non-coding genome features significantly enriched by mutations across multiple ALE replicates and scales of genome annotations. The median proportion of ALE experiment key mutations increased from 62%, with only small coding and non-coding features, to 71% with larger aggregate features. Understanding key mutations was enhanced by considering the functions of broader annotation types and the significantly associated conditions for key mutated features. The approaches developed here were used to find and characterize novel key mutations in two ALE experiments: one previously unpublished with Escherichia coli grown on glycerol as a carbon source and one previously published with Escherichia coli tolerized to high concentrations of L-serine.

Conclusions
The emergent adaptive strategies represented by sets of ALE mutations became more clear upon observing the aggregation of mutated features across small to large scale genome annotations. The clarification of mutation selection pressures among the many experimental conditions also helped bring these strategies to light. This work demonstrates how multiscale genome annotation frameworks and data-driven methods can help better characterize ALE mutations, and thus help elucidate the genotype-to-phenotype relationship of the studied organism.
Direct acute respiratory distress syndrome after gastric perforation caused by an intragastric balloon: a case report
Authors: Theuerkauf Nils , Weismüller Tobias , Weißbrich Carsten , Schewe Jens-Christian , Putensen Christian , Bode Christian 
Published: July 2020

Abstract
Background
Acute respiratory distress syndrome (ARDS) is a life-threatening condition and the identification of the underlying direct (pulmonary) or indirect (non-pulmonary) cause is mandatory for a successful treatment. Intragastric balloon (IGB) therapy is a minimal invasive and supposedly harmless option to reduce body weight for the growing number of obese people. We present a case of a young patient who developed a direct ARDS due to initially undiagnosed abdominal pathologies caused by an IGB therapy.

Case presentation
A 23-year old woman was admitted because of a direct ARDS for extracorporeal membrane oxygenation (ECMO) therapy. Weeks before, an IGB has been removed because of abdominal pain and free intraabdominal air. Diagnostic work-up of free intraabdominal air, previous pain of the left shoulder and newly developed abscess pneumonia revealed a perforation of the posterior wall of the gastral antrum. This resulted in a left subphrenic abscess with destruction of the diaphragm, development of pneumonia per continuitatem and subsequent direct lung injury. The gastric perforation was endoscopically clipped and the ARDS was successfully treated under ECMO therapy.

Conclusion
This case illustrates that a patient presenting with direct ARDS may have upper abdominal pathologies caused by a rare complication of a supposedly harmless treatment.
New CHA2DS2-VASc-HSF score predicts the no-reflow phenomenon after primary percutaneous coronary intervention in patients with ST-segment elevation myocardial infarction
Authors: Zhang Qin-Yao , Ma Shu-Mei , Sun Jia-Ying 
Published: July 2020

Abstract
Background
The no-reflow phenomenon (NRP) is a serious complication of primary percutaneous coronary intervention (PPCI) and is an independent predictor of poor prognosis. We aimed to find a simple but effective risk stratification method for the prediction of NRP.

Methods
This retrospective single-center study included 454 consecutive patients diagnosed with acute ST-segment elevation myocardial infarction (STEMI) and treated by PPCI, who were admitted to our emergency department between January 2017 and March 2019. The patients were divided according to the post-PPCI thrombolysis in the myocardial infarction flow rate: the NRP group and the control group. The CHADS2, CHA2DS2-VASc, and CHA2DS2-VASc-HSF scores were calculated for all the patients in this study, and multivariable regression and receiver operating characteristic curve analyses were conducted to determine the independent predictors of NRP and the predictive value of the three scores.

Results
A total of 454 patients were analyzed in this study: 80 in the no-reflow group and 374 in the control group. The incidence of NRP was 17.6%. Creatine kinase-myocardial band, Killip class, stent length, and multivessel disease also independently predicted NRP. The CHA2DS2-VASc-HSF score had a higher predictive value than the other two scores, and a CHA2DS2-VASc-HSF score of ≥4 predicted NRP with a sensitivity of 72.5% and specificity of 66.5% (area under the curve: 0.755, 95% confidence interval [0.702–0.808]).

Conclusion
Although the CHADS2, CHA2DS2-VASc, and CHA2DS2-VASc-HSF scores can all be used as simple tools to predict NRP, our findings show that the CHA2DS2-VASc-HSF score had the highest predictive value. Thus, the CHA2DS2-VASc-HSF score may be an optimal tool for predicting high-risk patients.
Risk factors of embolism for the cardiac myxoma patients: a systematic review and metanalysis
Authors: Liu Yanna , Wang Jiwei , Guo Liangyun , Ping Luyi 
Published: July 2020

Abstract
Background
The risk factors contributing to embolism in cardiac myxoma (CM) are yet controversial. This systematic review and meta-analysis aimed to clarify the risk factors of embolism for the CM patients.

Methods
PubMed, Embase, Cochrane library, Web of Science, China National Knowledge Infrastructure, Wan Fang, and Wei Pu databases were searched from inception to June 2019. Statistical analysis was conducted using Stata version 14.0. The pooled odds ratio or mean difference with 95% confidence interval was estimated for each risk factor.

Results
Herein, 12 studies, encompassing 1814 patients, were included. The pooled results suggested that New York Heart Association (NYHA) class I/II (P < 0.01), hypertension (P = 0.03), irregular tumor surface (P < 0.01), tumor in atypical location (P = 0.01), narrow base of tumor (P < 0.01), and increased fibrinogen (FIB) (P < 0.01) are significant risk factors of embolism in CM patients. However, sex, age, body mass index, smoking, left ventricular ejection fraction, diabetes, hyperlipidemia, atrial fibrillation, valvular heart disease, coronary heart disease, tumor size, platelet count, white blood cells, and hemoglobin were not associated with embolism (all P > 0.05).

Conclusions
NYHA class (I/II), hypertension, irregular tumor surface, atypical tumor location, the narrow base of tumor, and increased FIB were significant risk factors of embolism in CM patients. For CM patients with these factors, early surgery might be beneficial to prevent embolism.
Linkage of the CHHiP randomised controlled trial with primary care data: a study investigating ways of supplementing cancer trials and improving evidence-based practice
Authors: Lemanska Agnieszka , Byford Rachel C. , Cruickshank Clare , Dearnaley David P. , Ferreira Filipa , Griffin Clare , Hall Emma , Hinton William , de Lusignan Simon , Sherlock Julian , Faithfull Sara 
Published: July 2020

Abstract
Background
Randomised controlled trials (RCTs) are the gold standard for evidence-based practice. However, RCTs can have limitations. For example, translation of findings into practice can be limited by design features, such as inclusion criteria, not accurately reflecting clinical populations. In addition, it is expensive to recruit and follow-up participants in RCTs. Linkage with routinely collected data could offer a cost-effective way to enhance the conduct and generalisability of RCTs. The aim of this study is to investigate how primary care data can support RCTs.

Methods
Secondary analysis following linkage of two datasets: 1) multicentre CHHiP radiotherapy trial (ISRCTN97182923) and 2) primary care database from the Royal College of General Practitioners Research and Surveillance Centre. Comorbidities and medications recorded in CHHiP at baseline, and radiotherapy-related toxicity recorded in CHHiP over time were compared with primary care records. The association of comorbidities and medications with toxicity was analysed with mixed-effects logistic regression.

Results
Primary care records were extracted for 106 out of 2811 CHHiP participants recruited from sites in England (median age 70, range 44 to 82). Complementary information included longitudinal body mass index, blood pressure and cholesterol, as well as baseline smoking and alcohol usage but was limited by the considerable missing data. In the linked sample, 9 (8%) participants were recorded in CHHiP as having a history of diabetes and 38 (36%) hypertension, whereas primary care records indicated incidence prior to trial entry of 11 (10%) and 40 (38%) respectively. Concomitant medications were not collected in CHHiP but available in primary care records. This indicated that 44 (41.5%) men took aspirin, 65 (61.3%) statins, 14 (13.2%) metformin and 46 (43.4%) phosphodiesterase-5-inhibitors at some point before or after trial entry.

Conclusions
We provide a set of recommendations on linkage and supplementation of trials. Data recorded in primary care are a rich resource and linkage could provide near real-time information to supplement trials and an efficient and cost-effective mechanism for long-term follow-up. In addition, standardised primary care data extracts could form part of RCT recruitment and conduct. However, this is at present limited by the variable quality and fragmentation of primary care data.
Accuracy of random-forest-based imputation of missing data in the presence of non-normality, non-linearity, and interaction
Authors: Hong Shangzhi , Lynn Henry S. 
Published: July 2020

Abstract
Background
Missing data are common in statistical analyses, and imputation methods based on random forests (RF) are becoming popular for handling missing data especially in biomedical research. Unlike standard imputation approaches, RF-based imputation methods do not assume normality or require specification of parametric models. However, it is still inconclusive how they perform for non-normally distributed data or when there are non-linear relationships or interactions.

Methods
To examine the effects of these three factors, a variety of datasets were simulated with outcome-dependent missing at random (MAR) covariates, and the performances of the RF-based imputation methods missForest and CALIBERrfimpute were evaluated in comparison with predictive mean matching (PMM).

Results
Both missForest and CALIBERrfimpute have high predictive accuracy but missForest can produce severely biased regression coefficient estimates and downward biased confidence interval coverages, especially for highly skewed variables in nonlinear models. CALIBERrfimpute typically outperforms missForest when estimating regression coefficients, although its biases are still substantial and can be worse than PMM for logistic regression relationships with interaction.

Conclusions
RF-based imputation, in particular missForest, should not be indiscriminately recommended as a panacea for imputing missing data, especially when data are highly skewed and/or outcome-dependent MAR. A correct analysis requires a careful critique of the missing data mechanism and the inter-relationships between the variables in the data.
Using the Cochrane Central Register of Controlled Trials to identify clinical trial registration is insufficient: a cross-sectional study
Authors: Banno Masahiro , Tsujimoto Yasushi , Kataoka Yuki 
Published: July 2020

Abstract
Background
While conducting systemic reviews, searching for ongoing or unpublished trials is critical to address publication bias. As of April 2019, records of ongoing or unpublished randomized and/or quasi-randomized controlled trials registered in the International Clinical Trials Registry Platform (ICTRP) and ClinicalTrials.gov are available in the Cochrane Central Register of Controlled Trials (CENTRAL). These records registered in CENTRAL include studies published since the inception of ICTRP and ClinicalTrials.gov. Whether systematic reviewers can search CENTRAL to identify ongoing or unpublished trials instead of ICTRP and ClinicalTrials.gov is unknown.

Methods
This was a cross-sectional study. A consecutive sample of ongoing or unpublished studies published from June 1, 2019 to December 27, 2019 was selected from the Cochrane Reviews.
The sensitivity and the number needed to read (NNR) were assessed from among the studies selected from CENTRAL instead of ICTRP and ClinicalTrials.gov and also assessed the characteristics of studies not identified by searching CENTRAL.

Results
In total, 247 records from 50 Cochrane reviews were included; of these, 200 were identified by searching CENTRAL, whereas the remaining 47 records were not. The sensitivity of searching CENTRAL was 0.81 (95% confidence interval [CI]: 0.76, 0.85). The NNR was 115 (95% CI: 101, 133). The 47 unidentified studies were registered through ClinicalTrials.gov or ICTRP. Sixteen unidentified studies were not indexed in CENTRAL.

Conclusions
For systematic reviewers, searching CENTRAL could not substitute for searching ClinicalTrials.gov and/or ICTRP. Systematic reviewers should not only search CENTRAL but also ICTRP and ClinicalTrials.gov to identify unpublished trials.

Trial registration
A pre-specified protocol was applied to conduct this study. The study was registered in the University Hospital Medical Information Network Clinical Trials Registry (UMIN-CTR). Trial registration number: UMIN000038981.