bluuebunny/crossref_metadata_2025_split huggingface dataset:
Percutaneous spine biopsy under cone beam computed tomography guidance for spondylodiscitis: Time is diagnosis
Authors: Cannavale Alessandro , Nardis Piergiorgio , Lucatelli Pierleone , Corona Mario , Santoni Mariangela , Cannavale Giuseppe , Teodoli Leonardo , Bezzi Mario , Catalano Carlo 
Published: May 2021

Background and purpose Percutaneous spine biopsies for spondylodiscitis have been long discussed due to the low microbiologic yield. This retrospective study evaluated factors of cone beam computed tomography-guided spine biopsies that may affect microbiologic yield. Methods We retrospectively reviewed percutaneous spine biopsies under cone beam computed tomography for spondylodiscitis performed from January 2015–December 2020. Clinical and technical features such as the time from initial symptoms to biopsy, level biopsied, biopsy needle type/gauge, technical approach, radiation dose, technical success and microbiologic yield were recorded. Pre-procedure magnetic resonance imaging findings were also recorded such as the number of vertebral bodies involved, and disc morphology. Univariate logistic regression analysis and Receiver operating characteristic analysis were performed to assess any relationship between relevant factors and positive cultures. Results A total of 50 patients underwent cone beam computed tomography-guided biopsies for spondylodiscitis, with resulted positive cultures in 18 patients (36%). The mean time from the initial referral of spinal symptoms to procedure in the positive culture group was the most influential finding for positive cultures (odds ratio 56.3, p < 0.001). Among magnetic resonance imaging findings, thin or degenerated intervertebral disc was a negative factor for positive cultures (odds ratio 0.09, p = 0.006). Univariate analysis showed that percutaneous approach (transpedicular vs posterolateral/interlaminar) needle size (11–13 g vs 16–18G, odds ratio 1.2, p = 0.7) and site of biopsy (disc vs bone vs disc plus endplate) did not significantly affect the microbiologic yield of spine biopsy. Conclusion Percutaneous cone beam computed tomography-guided biopsy for spondylodiscitis is a reliable and safe technique and its microbiologic yield may increase if biopsy is performed within the acute phase of infection.
Body Mass Index, Multi-Morbidity, and COVID-19 Risk Factors as Predictors of Severe COVID-19 Outcomes
Authors: Nanda Sanjeev , Chacin Suarez Audry S. , Toussaint Loren , Vincent Ann , Fischer Karen M. , Hurt Ryan , Schroeder Darrell R. , Medina Inojosa Jose R. , O’Horo John C. , DeJesus Ramona S. , Abu Lebdeh Haitham S. , Mundi Manpreet S. , Iftikhar Salma , Croghan Ivana T. 
Published: May 2021

Purpose The purpose of the present study was to investigate body mass index, multi-morbidity, and COVID-19 Risk Score as predictors of severe COVID-19 outcomes. Patients Patients from this study are from a well-characterized patient cohort collected at Mayo Clinic between January 1, 2020 and May 23, 2020; with confirmed COVID-19 diagnosis defined as a positive result on reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assays from nasopharyngeal swab specimens. Measures Demographic and clinical data were extracted from the electronic medical record. The data included: date of birth, gender, ethnicity, race, marital status, medications (active COVID-19 agents), weight and height (from which the Body Mass Index (BMI) was calculated, history of smoking, and comorbid conditions to calculate the Charlson Comorbidity Index (CCI) and the U.S Department of Health and Human Services (DHHS) multi-morbidity score. An additional COVID-19 Risk Score was also included. Outcomes included hospital admission, ICU admission, and death. Results Cox proportional hazards models were used to determine the impact on mortality or hospital admission. Age, sex, and race (white/Latino, white/non-Latino, other, did not disclose) were adjusted for in the model. Patients with higher COVID-19 Risk Scores had a significantly higher likelihood of being at least admitted to the hospital (HR = 1.80; 95% CI = 1.30, 2.50; P < .001), or experiencing death or inpatient admission (includes ICU admissions) (HR = 1.20; 95% CI = 1.02, 1.42; P = .028). Age was the only statistically significant demographic predictor, but obesity was not a significant predictor of any of the outcomes. Conclusion Age and COVID-19 Risk Scores were significant predictors of severe COVID-19 outcomes. Further work should examine the properties of the COVID-19 Risk Factors Scale.
Biomechanical Properties of Double-Row Transosseous Rotator Cuff Repair Combined With the Cinch Stitch in the Lateral Row
Authors: Ito Kentaro , Sakaguchi Katsunobu , Sekihata Hirosi , Sugita Naoki , Kadono Yuho 
Published: May 2021

Background: The self-cinching stitch has been verified to have high mechanical strength. The mechanical strength of combining transosseous rotator cuff repair (RCR) and the self-cinching stitch in the lateral row is unknown. Purpose/Hypothesis: The purpose of this study was to evaluate the biomechanical properties of transosseous RCR combined with the cinch stitch in the lateral row. We hypothesized that this construct would have better mechanical strength than would transosseous repair using a vertical cinch stitch or simple stitch. Study Design: Controlled laboratory study. Methods: Rotator cuff tears were simulated in 48 porcine shoulder specimens. The tears were repaired using 1 of 6 repair configurations: 2–simple stitch transosseous repair alone (group 2TO), with a vertical cinch stitch (group 2TO-VC), or with a horizontal cinch stitch (group 2TO-HC) or 4–simple stitch transosseous repair alone (group 4TO), with a vertical cinch stitch (group 4TO-VC), or with a horizontal cinch stitch (group 4TO-HC). All specimens were set at a 45° angle from the footprint and underwent cyclic loading from 10 to 160 N for 200 cycles, followed by a load-to-failure test at 10 mm/min. Results: During cyclic loading, all specimens in group 2TO and half of the specimens in group 2TO-VC failed by suture pullout. In the other groups, none of the specimens failed before 200 cycles. The yield load in group 2TO-HC was significantly greater than that in group 2TO-VC (261.43 vs 219.54 N, respectively; P < .05). There were significant differences between groups 4TO-HC and 4TO with regard to elongation (3.92 vs 5.68 mm, respectively), yield load (304.04 vs 246.94 N, respectively), and linear stiffness (63.44 vs 52.28 N/mm, respectively) ( P < .01 for all). Group 4TO-HC also had shorter elongation and a superior yield load and linear stiffness compared with group 2TO-HC ( P < .05 for all), and group 4TO-VC had shorter elongation and a stronger maximum load to failure and yield load than did group 2TO-VC ( P < .05 for all). Conclusion: Increasing the number of medial simple stitches can prevent suture pullout. Adding the horizontal cinch stitch to the lateral row in transosseous repair can further improve biomechanical properties through a self-cinching mechanism. Clinical Relevance: Transosseous RCR with a horizontal cinch stitch in the lateral row may reduce the retear rate.
Decision Making from the Experience of Orthognathic Surgery Patients: A Grounded Theory Approach
Authors: Paul N.R. , Baker S.R. , Gibson B.J. 
Published: May 2021

Introduction: Patients’ decisions to undergo major surgery such as orthognathic treatment are not just about how the decision is made but what influences the decision. Objectives: The primary objective of the study was to identify the key processes involved in patients’ experience of decision making for orthognathic treatment. Methods: This study reports some of the findings of a larger grounded theory study. Data were collected through face-to-face interviews of patients who were seen for orthognathic treatment at a teaching hospital in the United Kingdom. Twenty-two participants were recruited (age range 18–66 y), of whom 12 (male = 2, female = 10) were 6 to 8 wk postsurgery, 6 (male = 2, female = 4) were in the decision-making stage, and 4 (male = 0, female = 4) were 1 to 2 y postsurgery. Additional data were also collected from online blogs and forums on jaw surgery. The data analysis stages of grounded theory methodology were undertaken, including open and selective coding. Results: The study identified the central role of dental care professionals (DCPs) in several underlying processes associated with decision making, including legitimating, mediating, scheduling, projecting, and supporting patients’ decisions. Six categories were related to key aspects of decision making. These were awareness about their underlying dentofacial problems and treatment options available, the information available about the treatment, the temporality of when surgery would be undertaken, the motivations and expectation of patients, social support, and fear of the surgery, hospitalization, and potentially disliking their new face. Conclusion: The decision-making process for orthognathic treatment is complex, multifactorial, and heavily influenced by the role of DCPs in patient care. Understanding the magnitude of this role will enable DCPs to more clearly participate in improving patients’ decision-making process. The findings of this study can inform future quantitative studies. Knowledge Transfer Statement: The results of this study can be used both for informing clinical practice around enabling decision making for orthognathic treatment and also for designing future research. The findings can better inform clinicians about the importance of their role in the patients’ decision-making process for orthognathic treatment and the means to improve the patient experience. It is suggested that further research could be conducted to measure some of the key constructs identified within our grounded theory and assess how these change during the treatment process.
The Influence of Applicant and Reviewer Gender on Resident Selection for Internal Medicine
Authors: Katz Steven J 
Published: May 2021

Background: While gender bias in medicine, including physician training, has been well described, less is known about gender bias in the selection process for post graduate residency training programs. This analysis reviews the potential role of gender on resident selection for an internal medicine residency program. Methods: File review and interview overall and component scores were analyzed based on the gender of the applicant. File review scores were further analyzed based on the reviewer’s gender. Results: Women applicants scored higher than men applicants on their file review. There were no differences in any one component score except for leadership in art. Women file reviewers scored applicants higher than men file reviewers, but there was no difference between gender scores. There was no difference in overall or component interview scores between men or women applicants. Scoring did not impact the expected rank performance of applicants based on gender at any stage of the selection process. Conclusions: While higher scores were observed in women applicants upon their file review, and women reviewers provided higher file review scores, this did not appear to impact the expected number of women and men applicants at each stage of the applicant process. This suggests a potential lack of gender bias at these stages of applicant selection.
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data
Authors: Ülgen Ege , Sezerman O. Uğur 
Published: May 2021

AbstractBackgroundCancer develops due to “driver” alterations. Numerous approaches exist for predicting cancer drivers from cohort-scale genomics data. However, methods for personalized analysis of driver genes are underdeveloped. In this study, we developed a novel personalized/batch analysis approach for driver gene prioritization utilizing somatic genomics data, called driveR.ResultsCombining genomics information and prior biological knowledge, driveR accurately prioritizes cancer driver genes via a multi-task learning model. Testing on 28 different datasets, this study demonstrates that driveR performs adequately, achieving a median AUC of 0.684 (range 0.651–0.861) on the 28 batch analysis test datasets, and a median AUC of 0.773 (range 0–1) on the 5157 personalized analysis test samples. Moreover, it outperforms existing approaches, achieving a significantly higher median AUC than all of MutSigCV (Wilcoxon rank-sum test p < 0.001), DriverNet (p < 0.001), OncodriveFML (p < 0.001) and MutPanning (p < 0.001) on batch analysis test datasets, and a significantly higher median AUC than DawnRank (p < 0.001) and PRODIGY (p < 0.001) on personalized analysis datasets.ConclusionsThis study demonstrates that the proposed method is an accurate and easy-to-utilize approach for prioritizing driver genes in cancer genomes in personalized or batch analyses. driveR is available on CRAN:https://cran.r-project.org/package=driveR.
Applied comparison of large‐scale propensity score matching and cardinality matching for causal inference in observational research
Authors: Fortin Stephen P. , Johnston Stephen S , Schuemie Martijn J 
Published: May 2021

Abstract
Background
Cardinality matching (CM), a novel matching technique, finds the largest matched sample meeting prespecified balance criteria thereby overcoming limitations of propensity score matching (PSM) associated with limited covariate overlap, which are especially pronounced in studies with small sample sizes. The current study proposes a framework for large-scale CM (LS-CM); and compares large-scale PSM (LS-PSM) and LS-CM in terms of post-match sample size, covariate balance and residual confounding at progressively smaller sample sizes.

Methods
Evaluation of LS-PSM and LS-CM within a comparative cohort study of new users of angiotensin-converting enzyme inhibitor (ACEI) and thiazide or thiazide-like diuretic monotherapy identified from a U.S. insurance claims database. Candidate covariates included patient demographics, and all observed prior conditions, drug exposures and procedures. Propensity scores were calculated using LASSO regression, and candidate covariates with non-zero beta coefficients in the propensity model were defined as matching covariates for use in LS-CM. One-to-one matching was performed using progressively tighter parameter settings. Covariate balance was assessed using standardized mean differences. Hazard ratios for negative control outcomes perceived as unassociated with treatment (i.e., true hazard ratio of 1) were estimated using unconditional Cox models. Residual confounding was assessed using the expected systematic error of the empirical null distribution of negative control effect estimates compared to the ground truth. To simulate diverse research conditions, analyses were repeated within 10 %, 1 and 0.5 % subsample groups with increasingly limited covariate overlap.

Results
A total of 172,117 patients (ACEI: 129,078; thiazide: 43,039) met the study criteria. As compared to LS-PSM, LS-CM was associated with increased sample retention. Although LS-PSM achieved balance across all matching covariates within the full study population, substantial matching covariate imbalance was observed within the 1 and 0.5 % subsample groups. Meanwhile, LS-CM achieved matching covariate balance across all analyses. LS-PSM was associated with better candidate covariate balance within the full study population. Otherwise, both matching techniques achieved comparable candidate covariate balance and expected systematic error.

Conclusions
LS-CM found the largest matched sample meeting prespecified balance criteria while achieving comparable candidate covariate balance and residual confounding. We recommend LS-CM as an alternative to LS-PSM in studies with small sample sizes or limited covariate overlap.
Type of tea consumption and depressive symptoms in Chinese older adults
Authors: Yao Yao , Chen Huashuai , Chen Lele , Ju Sang-Yhun , Yang Huazhen , Zeng Yi , Gu Danan , Ng Tze Pin 
Published: May 2021

Abstract
Background
Existing research indicates that tea drinking may exert beneficiary effects on mental health. However, associations between different types of tea intake and mental health such as depression have not been fully examined. The purpose of this study was to examine the associations of green tea, fermented tea, and floral tea consumption with depressive symptoms.

Methods
We used data from the 2018 wave of the Chinese Longitudinal Healthy Longevity Survey, a nationwide survey on older adults in mainland China. A total of 13,115 participants (mean age 83.7 years, 54.2% were women) with valid responses were included in the analysis. The type (green, fermented [black, Oolong, white, yellow, dark, and compressed teas], and floral) and the frequency of tea consumption were recorded, and depressive symptoms were assessed using 10-item of the Center for Epidemiologic Studies Depression Scale (CES-D-10). We examined the associations between the type and the frequency of tea intake and depression, controlling for a set of demographic, socioeconomic, psychosocial, behavioral, and health-related variables.

Results
Overall, intakes of green tea, fermented tea, and floral tea were all significantly associated with lower prevalence of depressive symptoms, independent of other risk factors. Compared with the group of no tea intake, the adjusted ORs of depressive symptoms for daily green tea, fermented tea, and floral tea intake were 0.85 (95% CI: 0.76–0.95), 0.87 (95% CI: 0.76–0.99), and 0.70 (95% CI: 0.59–0.82), respectively. Linear associations were observed between the frequencies of all three types of tea intake and depressive symptoms (P < 0.05 for trends for all three types). The associations of the type and the frequency of tea intake and depressive symptoms were robust in several sensitivity analyses.

Conclusions
Among Chinese older adults, regularly consumed any type of tea (green, fermented, or floral) were less likely to show depressive symptoms, the associations seemed more pronounced among floral tea and green tea drinkers.
Expression of mRNAs for pro-and anti-apoptotic factors in granulosa cells and follicular fluid of women undergoing in vitro fertilization. A pilot study
Authors: Bódis József , Sulyok Endre , Várnagy Ákos , Prémusz Viktória , Gödöny Krisztina , Makai Alexandra , Szenczi Ágnes , Varjas Timea 
Published: May 2021

Abstract
Background
This observational clinical study evaluated the expression levels and predictive values of some apoptosis-related genes in granulosa cells (GCs) and follicular fluid (FF) of women undergoing in vitro fertilization (IVF).

Methods
GCs and FF were obtained at oocyte retrieval from 31 consecutive patients with heterogeneous infertility diagnosis (age: 34.3 ± 5.8 years, body mass index: 24.02 ± 3.12 kg/m2, duration of infertility: 4.2 ± 2.1 years). mRNA expression of pro-apoptotic (BAX, CASP3, CASP8) and anti-apoptotic (BCL2, AMH, AMHR, FSHR, LHR, CYP19A1) factors was determined by quantitative RT-PCR using ROCHE LightCycler 480.

Results
No significant difference in GC or FF mRNA expression of pro- and anti-apoptotic factors could be demonstrated between IVF patients with (9 patients) or without (22 patients) clinical pregnancy. Each transcript investigated was detected in FF, but their levels were markedly reduced and independent of those in GCs. The number of retrieved oocytes was positively associated with GC AMHR (r = 0.393, p = 0.029), but the day of embryo transfer was negatively associated with GC LHR (r = − 0.414, p = 0.020) and GC FSHR transcripts (r = − 0.535, p = 0.002). When pregnancy positive group was analysed separately the impact of apoptosis- related gene expressions on some selected measures of IVF success could be observed. Strong positive relationship was found between gene expression levels of pro- and anti-apoptotic factors in GCs.

Conclusion
Our study provides only marginal evidences for the apoptosis dependence of IVF outcome and suggests that the apoptosis process induces adaptive increases of the anti-apoptotic gene expression to attenuate apoptosis and to protect cell survival.
Co-relation with novel phosphorylation sites of IκBα and necroptosis in breast cancer cells
Authors: Choi Sung Hoon , Yoon Hee-Sub , Yoo Shin-Ae , Yun Sung Ho , Park Joo-Hee , Han Eun Hee , Chi Sung-Gil , Chung Young-Ho 
Published: May 2021

Abstract
Background
Phosphorylation of NF-kappaB inhibitor alpha (IκBα) is key to regulation of NF-κB transcription factor activity in the cell. Several sites of IκBα phosphorylation by members of the IκB kinase family have been identified, but phosphorylation of the protein by other kinases remains poorly understood. We investigated a new phosphorylation site on IκBα and identified its biological function in breast cancer cells.

Methods
Previously, we observed that aurora kinase (AURK) binds IκBα in the cell. To identify the domains of IκBα essential for phosphorylation by AURK, we performed kinase assays with a series of IκBα truncation mutants. AURK significantly promoted activation of IκBα at serine 32 but not serine 36; by contrast, IκB kinase (IKK) family proteins activated both of these residues. We also confirmed phosphorylation of IκBα by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and nano-liquid chromatography hybrid quadrupole orbitrap mass spectrometer (nanoLC-MS/MS; Q-Exactive).

Results
We identified two novel sites of serine phosphorylation, S63 and S262. Alanine substitution of S63 and S262 (S63A and S262A) of IκBα inhibited proliferation and suppressed p65 transcription activity. In addition, S63A and/or S262A of IκBα regulated apoptotic and necroptotic effects in breast cancer cells.

Conclusions
Phosphorylation of IκBα by AURK at novel sites is related to the apoptosis and necroptosis pathways in breast cancer cells.
Initiation of Somatostatin analogues for neuroendocrine tumor patients: a cost-effectiveness analysis
Authors: Rustgi Sheila D. , Oh Aaron , Yang Jeong Yun , Kang Dasol , Wolin Edward , Kong Chung Y. , Hur Chin , Kim Michelle K. 
Published: May 2021

Abstract
Background & Aims
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are heterogeneous neoplasms. Although some have a relatively benign and indolent natural history, others can be aggressive and ultimately fatal. Somatostatin analogues (SSAs) improve both quality of life and survival for these patients once they develop metastatic disease. However, these drugs are costly and their cost-effectiveness is not known.

Methods
A decision-analytic model was developed and analyzed to compare two treatment strategies for patients with Stage IV GEP-NETs. The first strategy had all patients start SSA immediately while the second strategy waited, reserving SSA initiation until the patient showed signs of progression. Sensitivity analysis was performed to explore model parameter uncertainty.

Results
Our model of patients age 60 with metastatic GEP-NETs suggests empiric initiation of SSA led to an increase 0.62 unadjusted life-years and incremental increase in quality-adjusted life years (QALYs) of 0.44. The incremental costs were $388,966 per QALY and not cost-effective at a willingness-to-pay threshold of $100,000. Death was attributed to GEP-NETs for 94.1% of patients in the SSA arm vs. 94.9% of patients in the DELAY SSA arm. Sensitivity analysis found that the model was most sensitive to costs of SSAs. Using probabilistic sensitivity analysis, the SSA strategy was only cost-effective 1.4% of the time at a WTP threshold of $100,000 per QALY.

Conclusions
Our modeling study finds it is not cost-effective to initiate SSAs at time of presentation for patients with metastatic GEP-NETs. Further clinical studies are needed to identify the optimal timing to initiate these drugs.