bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bariatric Surgery in Medicare Patients
Authors: Chao Grace F. , Chhabra Karan R. , Yang Jie , Thumma Jyothi R. , Arterburn David E. , Ryan Andrew M. , Telem Dana A. , Dimick Justin B. 
Published: November 2020

Objective:
To compare safety and healthcare utilization after sleeve gastrectomy versus Roux-en-Y gastric bypass in a national Medicare cohort.

Summary Background Data:
Though bariatric surgery is increasing among Medicare beneficiaries, no long-term, national studies examining comparative effectiveness between procedures exist. Bariatric outcomes are needed for shared decision-making and coverage policy concerns identified by the cMS Medicare Evidence Development and Coverage Advisory Committee.

Methods:
Retrospective instrumental variable analysis of Medicare claims (2012–2017) for 30,105 bariatric surgery patients entitled due to disability or age. We examined clinical safety outcomes (mortality, complications, and reinterventions), healthcare utilization [Emergency Department (ED) visits, rehospitalizations, and expenditures], and heterogeneity of treatment effect. We compared all outcomes between sleeve and bypass for each entitlement group at 30 days, 1 year, and 3 years.

Results:
Among the disabled (n = 21,595), sleeve was associated with lower 3-year mortality [2.1% vs 3.2%, absolute risk reduction (ARR) 95% confidence interval (CI): –2.2% to –0.03%], complications (22.2% vs 27.7%, ARR 95%CI: –8.5% to –2.6%), reinterventions (20.1% vs 27.7%, ARR 95%CI: –10.7% to –4.6%), ED utilization (71.6% vs 77.1%, ARR 95%CI: –8.5% to –2.4%), and rehospitalizations (47.4% vs 52.3%, ARR 95%Ci: –8.0% to –1.7%). Cumulative expenditures were $46,277 after sleeve and $48,211 after bypass (P = 0.22). Among the elderly (n = 8510), sleeve was associated with lower 3-year complications (20.1% vs 24.7%, ARR 95%CI: –7.6% to –1.7%), reinterventions (14.0% vs 21.9%, ARR 95%CI: –10.7% to –5.2%), ED utilization (51.7% vs 57.2%, ARR 95%CI: –9.1% to –1.9%), and rehospitalizations (41.8% vs 45.8%, ARR 95%Ci: –7.5% to –0.5%). Expenditures were $38,632 after sleeve and $39,270 after bypass (P = 0.60). Procedure treatment effect significantly differed by entitlement for mortality, revision, and paraesophageal hernia repair.

Conclusions:
Bariatric surgery is safe, and healthcare utilization benefits of sleeve over bypass are preserved across both Medicare elderly and disabled subpopulations.
Association Between Preoperative HbA1c Levels and Complications after Esophagectomy
Authors: Okamura Akihiko , Yamamoto Hiroyuki , Watanabe Masayuki , Miyata Hiroaki , Kanaji Shingo , Kamiya Kinji , Kakeji Yoshihiro , Doki Yuichiro , Kitagawa Yuko 
Published: November 2020

Objective:
To elucidate the association between preoperative hemoglobin A1c (HbAlc) levels and short-term outcomes after oncologic esophagectomy.

Summary Background Data:
Although diabetes mellitus is associated with an increased risk of postoperative morbidity in several types of surgery, the association of diabetes mellitus with short-term outcomes after esophagectomy has shown conflicting results.

Methods:
We analyzed 15,801 patients who underwent oncologic esophagectomy between 2015 and 2017 from the National Clinical Database. We evaluated the associations between preoperative HbA1c levels and short-term outcomes, using multivariable logistic regression and restricted cubic spline models.

Results:
The cohort included 12,074, 1361, 1097, 909, and 360 patients with HbA1c levels of ≤5.9%, 6.0% to 6.4%, 6.5% to 6.9%, 7.0% to 7.9%, and ≥8.0%, respectively. There were value-dependent associations between HbA1c values and odds ratios for anastomotic leakage, surgical site infections, pneumonia, and composite outcomes. Compared with the HbA1c category of ≤5.9%, the categories of 7.0% to 7.9% and ≥8.0% were at higher risk for anastomotic leakage (P < 0.001 and 0.031, respectively), the category of ≥8.0% was at higher risk for surgical site infections (P = 0.001), the categories of 6.5% to 6.9% and 7.0% to 7.9% were at higher risk for pneumonia (P = 0.016 and 0.002, respectively), and the categories of 7.0 to 7.9 and > 8.0% were at higher risk for composite outcomes (P < 0.001 and 0.001, respectively).

Conclusions:
Preoperative HbA1c levels are associated with the risk of postoperative complications after esophagectomy, and the threshold values differed among the outcomes. Preoperative HbA1c is useful in predicting the risk of postoperative complications.
Thoracic Endovascular Aortic Repair Practice in 13 Countries
Authors: Hellgren Tina , Beck Adam W. , Behrendt Christian-Alexander , Becker Daniel , Beiles Barry , Boyle Jonathan R. , Jormalainen Mikko , Koncar Igor , Lopez Espada Cristina , Setacci Carlo , Settembre Nicla , Sutzko Danielle C. , Szeberin Zoltan , Thomson Ian , Venermo Maarit , Mani Kevin 
Published: November 2020

Objective:To assess practice patterns and short-term outcome after thoracic endovascular aortic repair (TEVAR), based on an international vascular registry collaboration.Summary Background Data:TEVAR has become the primary surgical treatment modality for descending aortic pathologies, and has expanded to new patient cohorts, including the elderly.Methods:Data on thoracic aortic aneurysms (TAA), type B aortic dissections (TBAD), and traumatic aortic injuries (TAI) treated with TEVAR from 2012 to 2016 were retrieved from registries and centers in 13 countries.Results:Nine-thousand five-hundred eighteen TEVAR for TAA (n= 4436), TBAD (n= 3976) and TAI (n= 1106) were included. The distribution of TEVAR procedures per pathology varied, with TAA repair constituting from 40% of TEVARs in the US to 72% in the UK (P< 0.001).Mean intact TAA (iTAA) diameter varied from 59 (US) to 69 mm (Nancy, France) (P< 0.001), 25.3% of patients having a diameter of <60 mm. Perioperative mortality after iTAA repair was 4.9%; combined mortality, stroke, paraplegia, and renal replacement therapy outcome was 12.8%. 18.6% of iTAA patients were ≥80 years old. Mortality was higher in this group (7.2%) than in patients <80 (3.8%) (P< 0.001). After rTAA repair, perioperative mortality was 26.8%.Mortality was 9.7% after acute (within 14 days from onset of dissection) and 3.0% after chronic TBAD repair (P< 0.001). Mortality after TAI was 7.8%, and depended on injury severity (grade IV (free rupture) 20.9%).Conclusions:This registry collaboration provides a unique platform to evaluate cross-border patterns of use and outcomes of TEVAR. A common core dataset is proposed, to achieve harmonization of registry-based quality outcome measures for TEVAR.
Outcomes of Laparoscopic Redo Fundoplication in Patients With Failed Antireflux Surgery
Authors: Schlottmann Francisco , Laxague Francisco , Angeramo Cristian A. , Sadava Emmanuel E. , Herbella Fernando A. M. , Patti Marco G. 
Published: November 2020

Objective:
The aim of this meta-analysis was to summarize the current available evidence regarding the surgical outcomes of laparoscopic redo fundoplication (LRF).

Summary of Background Data:
Although antireflux surgery is highly effective, a minority of patients will require a LRF due to recurrent symptoms, mechanical failure, or intolerable side-effects of the primary repair.

Methods:
A systematic electronic search on LRF was conducted in the Medline database and Cochrane Central Register of Controlled Trials. Conversion and postoperative morbidity were used as primary endpoints to determine feasibility and safety. Symptom improvement, QoL improvement, and recurrence rates were used as secondary endpoints to assess efficacy. Heterogeneity across studies was tested with the Chi-square and the proportion of total variation attributable to heterogeneity was estimated by the inconsistency (I
2) statistic. A random-effect model was used to generate a pooled proportion with 95% confidence interval (CI) across all studies.

Results:
A total of 30 studies and 2,095 LRF were included. The mean age at reoperation was 53.3 years. The weighted pooled proportion of conversion was 6.02% (95% CI, 4.16%–8.91%) and the meta-analytic prevalence of major morbidity was 4.98% (95% CI, 3.31%–6.95%). The mean follow-up period was 25 (6–58) months. The weighted pooled proportion of symptom and QoL improvement was 78.50% (95% CI, 74.71%–82.03%) and 80.65% (95% CI, 75.80%–85.08%), respectively. The meta-analytic prevalence estimate of recurrence across the studies was 10.71% (95% CI, 7.74%–14.10%).

Conclusions:
LRF is a feasible and safe procedure that provides symptom relief and improved QoL to the vast majority of patients. Although heterogeneously assessed, recurrence rates seem to be low. LRF should be considered a valuable treatment modality for patients with failed antireflux surgery.
Evaluating the association between American Association for the Surgery of Trauma emergency general surgery anatomic severity grades and clinical outcomes using national claims data
Authors: Scott John W. , Staudenmayer Kristan , Sangji Naveen , Fan Zhaohui , Hemmila Mark , Utter Garth 
Published: November 2020

BACKGROUND
Emergency general surgery (EGS) encompasses a heterogeneous population of acutely ill patients, and standardized methods for determining disease severity are essential for comparative effectiveness research and quality improvement initiatives. The American Association for the Surgery of Trauma (AAST) has developed a grading system for the anatomic severity of 16 EGS conditions; however, little is known regarding how well these AAST EGS grades can be approximated by diagnosis codes in administrative databases.

METHODS
We identified adults admitted for 16 common EGS conditions in the 2012 to 2017q3 National Inpatient Sample. Disease severity strata were assigned using International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) and International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) diagnosis codes based on AAST EGS anatomic severity grades. We evaluated whether assigned EGS severity (multiple strata or dichotomized into less versus more complex) were associated with in-hospital mortality, complications, length of stay, discharge disposition, and costs. Analyses were adjusted for age, sex, comorbidities, hospital traits, geography, and year.

RESULTS
We identified 10,886,822 EGS admissions. The number of anatomic severity strata derived from ICD-9/10-CM codes varied by EGS condition and by year. Four conditions mapped to four strata across all years. Two conditions mapped to four strata with ICD-9-CM codes but only two or three strata with ICD-10-CM codes. Others mapped to three or fewer strata. When dichotomized into less versus more complex disease, patients with more complex disease had worse outcomes across all 16 conditions. The addition of multiple strata beyond a binary measure of complex disease, however, showed inconsistent results.

CONCLUSION
Classification of common EGS conditions according to anatomic severity is feasible with International Classification of Diseases codes. No condition mapped to five distinct severity grades, and the relationship between increasing grade and outcomes was not consistent across conditions. However, a standardized measure of severity, even if just dichotomized into less versus more complex, can inform ongoing efforts aimed at optimizing outcomes for EGS patients across the nation.

LEVEL OF EVIDENCE
Prognostic, level III.
Immunosuppression Regimen Use and Outcomes in Older and Younger Adult Kidney Transplant Recipients: A National Registry Analysis
Authors: Lentine Krista L. , Cheungpasitporn Wisit , Xiao Huiling , McAdams-DeMarco Mara , Lam Ngan N. , Segev Dorry L. , Bae Sunjae , Ahn JiYoon B. , Hess Gregory P. , Caliskan Yasar , Randall Henry B. , Kasiske Bertram L. , Schnitzler Mark A. , Axelrod David A. 
Published: November 2020

Background.
Although the population of older transplant recipients has increased dramatically, there are limited data describing the impact of immunosuppression regimen choice on outcomes in this recipient group.

Methods.
National data for US Medicare-insured adult kidney recipients (N = 67 362; 2005–2016) were examined to determine early immunosuppression regimen and associations with acute rejection, death-censored graft failure, and mortality using multivariable regression analysis in younger (18–64 y) and older (>65 y) adults.

Results.
The use of antithymocyte globulin (TMG) or alemtuzumab (ALEM) induction with triple maintenance immunosuppression (reference) was less common in older compared with younger (36.9% versus 47.0%) recipients, as was TMG/ALEM + steroid avoidance (19.2% versus 20.1%) and mammalian target of rapamycin inhibitor (mTORi)-based (6.7% versus 7.7%) treatments. Conversely, older patients were more likely to receive interleukin (IL)-2-receptor antibody (IL2rAb) + triple maintenance (21.1% versus 14.7%), IL2rAb + steroid avoidance (4.1% versus 1.8%), and cyclosporine-based (8.3% versus 6.6%) immunosuppression. Compared with older recipients treated with TMG/ALEM + triple maintenance (reference regimen), those managed with TMG/ALEM + steroid avoidance (adjusted odds ratio [aOR], 0.440.520.61) and IL2rAb + steroid avoidance (aOR, 0.390.550.79) had lower risk of acute rejection. Older patients experienced more death-censored graft failure when managed with Tac + antimetabolite avoidance (adjusted hazard [aHR], 1.411.782.25), mTORi-based (aHR, 1.702.142.71), and cyclosporine-based (aHR, 1.411.782.25) regimens, versus the reference regimen. mTORi-based and cyclosporine-based regimens were associated with increased mortality in both older and younger patients.

Conclusions.
Lower-intensity immunosuppression regimens (eg, steroid-sparing) appear beneficial for older kidney transplant recipients, while mTORi and cyclosporine-based maintenance immunosuppression are associated with higher risk of adverse outcomes.
DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning
Authors: Jiang Yuepeng , Rensi Stefano , Wang Sheng , Altman Russ B. 
Published: November 2020

AbstractMassively accumulated pharmacogenomics, chemogenomics, and side effect datasets offer an unprecedented opportunity for drug response prediction, drug target identification and drug side effect prediction. Existing computational approaches limit their scope to only one of these three tasks, inevitably overlooking the rich connection among them. Here, we propose DrugOrchestra, a deep multi-task learning framework that jointly predicts drug response, targets and side effects. DrugOrchestra leverages pre-trained molecular structure-based drug representation to bridge these three tasks. Instead of directly fine-tuning on an individual task, DrugOrchestra uses deep multi-task learning to obtain a phenotype-based drug representation by simultaneously fine-tuning on drug response, target and side effect prediction. By coupling these three tasks together, DrugOrchestra is able to make predictions for unseen drugs by only knowing their molecular structures. We constructed a heterogeneous drug discovery dataset of over 21k drugs by integrating 8 datasets across three tasks. Our method obtained significant improvement in comparison to methods that were trained on a single task or a single dataset. We further revealed the transferability across 8 datasets and 3 tasks, providing novel insights for understanding drug mechanisms.Availabilityhttps://github.com/jiangdada1221/DrugOrchestra
COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory
Authors: Guerra Geno , Nielsen Rasmus 
Published: November 2020

2AbstractGenome-scale data are increasingly being used to infer phylogenetic trees. A major challenge in such inferences is that different regions of the genome may have local topologies that differ from the species tree due to incomplete lineage sorting (ILS). Another source of gene tree discrepancies is estimation errors arising from the randomness of the mutational process during sequence evolution. There are two major groups of methods for estimating species tree from whole-genome data: a set of full likelihood methods, which model both sources of variance, but do not scale to large numbers of independent loci, and a class of faster approximation methods which do not model the mutational variance.To bridge the gap between these two classes of methods, we present COAL_PHYRE (COmposite Approximate Likelihood for PHYlogenetic REconstruction), a composite likelihood based method for inferring population size and divergence time estimates of rooted species trees from aligned gene sequences. COAL_PHYRE jointly models coalescent variation across loci using the MSC and variation in local gene tree reconstruction using a normal approximation. To evaluate the accuracy and speed of the method, we compare against BPP, a powerful MCMC full-likelihood method, as well as ASTRAL-III, a fast approximate method. We show that COAL_PHYRE’s divergence time and population size estimates are more accurate than ASTRAL, and comparable to those obtained using BPP, with an order of magnitude decrease in computational time. We also present results on previously published data from a set of Gibbon species to evaluate the accuracy in topology and parameter inference on real data, and to illustrate the method’s ability to analyze data sets which are prohibitively large for MCMC methods.
Bell-shaped dose response for a system with no IFFLs
Authors: Sontag Eduardo D. 
Published: November 2020

AbstractIt is well known that the presence of an incoherent feedforward loop (IFFL) in a network may give rise to a steady state non-monotonic dose response. This note shows that the converse implication does not hold. It gives an example of a three-dimensional system that has no IFFLs, yet its dose response is bell-shaped. It also studies under what conditions the result is true for two-dimensional systems, in the process recovering, in far more generality, a result given in the T-cell activation literature.
Meta-Prism 2.0: Enabling algorithm for ultra-fast, accurate and memory-efficient search among millions of microbial community samples
Authors: Kang Kai , Chong Hui , Ning Kang 
Published: November 2020

AbstractMotivationMicrobial community samples and sequencing data have been accumulated at a speed faster than ever, with tens of thousands of samples been sequenced each year. Mining such a huge amount of multi-source heterogeneous data is becoming more and more difficult. Among several sample mining bottlenecks, efficient and accurate search of samples is one of the most prominent: Faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy.ResultsHere we proposed Meta-Prism 2.0, a microbial community sample search method based on smart pair-wise sample comparison, which pushed the time and memory efficiency to a new limit, without the compromise of accuracy. Based on memory-saving data structure, time-saving instruction pipeline, and boost scheme optimization, Meta-Prism 2.0 has enabled ultra-fast, accurate and memory-efficient search among millions of samples. Meta-Prism 2.0 has been put to test on several datasets, with largest containing one million samples. Results have shown that firstly, as a distance-based method, Meta-Prism 2.0 is not only faster than other distance-based methods, but also faster than unsupervised methods. Its 0.00001s per sample pair search speed, as well as 8GB memory needs for searching against one million samples, have enabled it to be the most efficient method for sample comparison. Additionally, Meta-Prism 2.0 could achieve the comparison accuracy and search precision that are comparable or better than other contemporary methods. Thirdly, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking.ConclusionIn summary, Meta-Prism 2.0 can perform accurate searches among millions of samples with very low memory cost and fast speed, enabling knowledge discovery from samples at a massive scale. It has changed the traditional resource-intensive sample comparison and search scheme to a cheap and effective procedure, which could be conducted by researchers everyday even on a laptop, for insightful sample search and knowledge discovery. Meta-Prism 2.0 could be accessed at:https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0.
Cognitive Aids for Operating Room Crises – A Thematic Analysis of Implementer Experiences
Authors: Henrich Natalie , Benotti Emily , Berry William , Hannenberg Alexander , Hepner David , Karlage Ami , Goldhaber-Fiebert Sara 
Published: November 2020

AbstractBackgroundStrategies for the implementation of evidence-based interventions have proliferated, but it remains unclear how these strategies are operationalized for different types of interventions and contexts. Here, we examine seven implementation strategies--initially developed for implementing the World Health Organization (WHO) Surgical Safety Checklist (SSC)--for implementing cognitive aids for operating room (OR) crises.MethodsWe conducted semi-structured interviews with implementers of these aids exploring the use of each of the strategies previously studied with WHO SSC implementation as well as barriers and facilitators to implementation. We conducted a thematic analysis to identify and describe the use of the strategies. We mapped barriers and factors helping facilitate (facilitators) onto corresponding constructs from the Consolidated Framework for Implementation Research.ResultsWe conducted interviews with 37 implementers across the United States. Most interviewees identified similar strategies in their implementation process, and none offered additional strategies that fell outside existing categories. There was substantial variation among implementers in how the strategies were deployed. Many of the barriers and facilitators were common across implementations.ConclusionInterviewees used a core set of strategies to implement cognitive aids for OR crises, but there was substantial variation in how implementers used these strategies, suggesting the flexibility of the strategies and the value of deliberately adapting strategies to local context. The transferability of implementation strategies from the WHO SSC to other OR-based cognitive aids demonstrates the utility of informing novel implementations with prior successful ones that share similar attributes with respect to intervention and/or context.