bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field Services Facilitated Treatment and Prevention: Challenges and Opportunities
Authors: Bachmann Laura Hinkle , Kerani Roxanne P. 
Published: December 2022

Abstract
Assisted partner services (APS) is a longstanding public health strategy to reduce transmission of STI and HIV in the U.S. However, with rapidly increasing rates of STI, innovations to APS are needed to allow health departments to conserve limited public health resources while improving the effectiveness of APS. Disease Intervention Specialists (DIS), public health staff who conduct APS, have a wealth of experience in identifying, locating, and interviewing index patients and their sexual partners, but are currently limited in the services that they are able to provide in the field. While several state and local health departments are working to expand the role of DIS to incorporate less traditional APS activities, such programs are uncommon. We discuss several services that DIS could conceivably provide in the field, such as STI testing, treatment, and vaccination, and identify critical issues to be addressed in order to implement these changes in DIS activities on a larger scale. Broadening the scope of DIS activities may result in multiple benefits to health departments, including more effectively delivering STI testing and treatment to hard to reach populations, imparting more responsibility to DIS, thereby potentially increasing job satisfaction, and building a workforce that is better prepared for public health crises. Effective approaches to address variable state level regulations governing DIS scope of practice are needed.
IDH2-Mutated Sinonasal Tumors: A Review
Authors: Alzumaili Bayan , Sadow Peter M. 
Published: December 2022

Introduction:
Genetic profiling has caused an explosion in the subclassification of sinonasal malignancies. Distinguishing several of these tumor types by histomorphology alone has been quite challenging, and although pathologic classification aims to be as specific as possible, it remains to be seen if this recent move toward tumor speciation bears clinical relevance, most particularly focused on subtyping for the sake of prognostication and treatment. One such recently described cohort, predominantly lumped under the moniker of sinonasal undifferentiated carcinoma (SNUC) is IDH2-mutated sinonasal carcinoma, a high-grade carcinoma associated with mutations in the isocitrate dehydrogenase-2 (IDH2) gene. A hotspot mutation in the R172 codon has been described in 50% to 80% of the tumors classified as SNUC, large cell neuroendocrine carcinomas, and rarely in cases classified as olfactory neuroblastoma. The use of immunohistochemical and molecular approaches is required to correctly identify this subset of sinonasal tumors, with further study necessary to elucidate their unique pathophysiology, ultimately determining whether a revision is required toward the current therapeutic approach.

Aims:
Here, we provide an overview of the IDH2-mutated sinonasal tumors, discuss histopathologic and clinical features, and focus on molecular diagnostics and novel immunohistochemical markers.

Results:
A review of the literature reveals 82 reported cases with IDH2-mutated sinonasal tumors (IST), confirmed either by molecular studies or diagnostic immunohistochemical markers. The mean patient age is 60 years (female/male: 1/1.4), the median tumor size is 5 cm (range: 2.5 to 7.0 cm), and the most common location is the nasal cavity (81%). IST displays tumor necrosis and increased mitotes. Histopathologically, IST shows SNUC-like, large cell neuroendocrine carcinomas-like, or poorly differentiated carcinoma-like features (77%, 12%, and 9%, respectively). The molecular hotspot alterations in mitochondrial IDH2 are: R172S (61%), R172T (19%), R172G (7%), and R172M (3%). Sixty-five percent of tumors are surgically resectable, and all patients received chemotherapy, radiation therapy, or both. Rates of locoregional recurrence and distant metastasis are 60% and 40%, respectively. One-, 3- and 5-year survival rates are 83%, 50%, and 43%, respectively. In all but 1 study, IST is associated with better outcomes than IDH2 wild-type tumors and SMARCB1-deficient sinonasal tumors.
Association of Intraoperative Red Blood Cell Transfusions With Venous Thromboembolism and Adverse Outcomes After Cardiac Surgery
Authors: Raphael Jacob , Feng Xiaoke , Shotwell Matthew S. , Mazzeffi Michael A. , Bollen Bruce A. , Shah Ashish S. , Kertai Miklos D. 
Published: December 2022

Objective:We determined whether intraoperative packed red blood cell (PRBC) transfusion was associated with a higher incidence of hospital-acquired venous thromboembolic (HA-VTE) complications and adverse outcomes after isolated coronary artery bypass grafting (CABG) surgery.Background:Intraoperative PRBC has been associated with increased risk for postoperative deep venous thrombosis after cardiac surgery, but validation of these findings in a large, multi-institutional, national cohort of cardiac surgery patients has been lacking.Methods:A registry-based cohort study of 751,893 patients with isolated CABG between January 1, 2015, to December 31, 2019. Using propensity score-weighted regression analysis, we analyzed the effect of intraoperative PRBC on the incidence of HA-VTE and adverse outcomes.Results:Administration of 1, 2, 3, and ≥4 units of PRBC transfusion was associated with increased odds for HA-VTE [odds ratios (ORs): 1.27 (1.22–1.32), 1.21 (1.16–1.26), 1.93 (1.85–2.00), 1.82 (1.75–1.89)], deep venous thrombosis [ORs: 1.39 (1.33–1.46), 1.38 (1.32–1.44), 2.18 (2.09–2.28), 1.82 (1.74–1.91], operative mortality [ORs: 1.11 (1.08–1.14), 1.16 (1.13–1.19), 1.29 (1.26–1.32), 1.47 (1.43–1.50)], readmission within 30 days [ORs: 1.05 (1.04–1.06), 1.16 (1.13–1.19), 1.29 (1.26–1.32), 1.47 (1.43–1.50)], and a prolonged postoperative length of stay [mean difference in days, 0.23 (0.19–0.27), 0.34 (0.30–0.39), 0.69 (0.64–0.74), 0.77 (0.72–0.820]. The odds of pulmonary venous thromboembolism were lower for patients transfused with 1 or 2 units [ORs: 0.98 (0.91–1.06), 0.75 (0.68–0.81)] of PRBC but remained significantly elevated for those receiving 3 and ≥4 units [ORs: 1.19 (1.09–1.29), 1.35 (1.25–1.48)].Conclusions:Intraoperative PRBC transfusion was associated with HA-VTE and adverse outcomes after isolated CABG surgery.
Impact of the Percentage of Overlapping Surgery on Patient Outcomes
Authors: Pitts Charles C. , Ponce Brent A. , Arguello Alexandra M. , Willis Joseph G. , McGwin Gerald , Vatsia Sohrab , Parks Chris T. , Wills Brad W. 
Published: December 2022

Objectives:
The primary objective of this study was to analyze the relationship of percentage of surgical overlap with patient outcomes to determine if a detrimental level of overlap exists.

Background:
Overlapping surgery is defined as 1 attending physician supervising 2 or more operative cases simultaneously, without the critical portions of the cases occurring concurrently. To date, no study has examined the relationship of percent overlap, or the percentage of 1 case that is spent overlapping with another, to outcomes, efficiency, safety, and complications.

Methods:
This study is a retrospective cohort study conducted at a large tertiary referral center. The primary outcomes of interest included operative duration, in-hospital mortality, 30-day readmission, and patient safety indicators (PSIs). The Cochran-Armitage test for trend was used to evaluate the outcomes of interest. P values of ≤0.05 were considered statistically significant.

Results:
A total of 87,426 cases were included in this study. There were 62,332 cases without overlap (Group 0), 10,514 cases with 1% to 25% overlap (Group 1), 5303 cases with 26% to 50% overlap (Group 2), 4296 cases with 51% to 75% overlap (Group 3), and 4981 cases with >75% overlap (Group 4). In-hospital mortality decreased as overlap increased (P
trend<0.0001). Operative time increased with increasing overlap (P
trend<0.0001) while readmission rates showed no statistical significance between groups (P
trend=0.5078). Rates of PSIs were lower for Groups 1, 2, and 3 (1.69%, 2.01%, and 2.08%) when compared to Group 0 (2.24%). Group 4 had the highest rate of PSIs at 2.35% (P=0.0086).

Conclusion:
Overlapping surgery was shown to have reduced in-hospital mortality and similar PSI and readmission rates when compared to nonoverlapping cases. Operative time was shown to increase in overlapping surgeries when compared to nonoverlapping surgeries. The results from this study indicate that the percentage of surgical overlap does not detrimentally affect most patient outcomes, especially with overlap of <75%.
Optimal Timing of Perioperative Chemical Thromboprophylaxis in Elective Major Abdominal Surgery
Authors: Klonis Christopher , Ashraf Hamza , Cabalag Carlos S. , Wong Darren J. , Stevens Sean G. , Liu David S. 
Published: December 2022

Objective:
To investigate the effect of the timing of chemoprophylaxis on venous thromboembolisms (VTEs) and bleeding rates in patients undergoing major abdominal surgery.

Background:
Postoperative bleeding and VTE incur significant morbidity, mortality, and health care costs. Chemoprophylaxis is used routinely to prevent VTEs but increases bleeding risk. The perioperative timing of chemoprophylaxis initiation may influence both VTE and bleeding risks. The optimal window for commencing chemoprophylaxis in the perioperative period is unclear.

Methods:
MEDLINE, EMBASE, Cochrane Library, and Web of Science databases were searched using PRISMA guidelines. Randomized trials and cohort studies published between January 1, 2000 to May 10, 2022, which reported on chemoprophylaxis timing as well as the incidence of VTE and bleeding after elective abdominal surgery were meta-analyzed.

Results:
From 6175 studies, 14 (24,922 patients) were meta-analyzed. Bariatric (4 studies), antireflux (1 study), hepato-pancreatic-biliary (5 studies), colorectal (1 study), ventral hernia (1 study), and major intra-abdominal surgeries (2 studies) were included. Chemoprophylaxis was initiated before skin closure in 10,403 patients, and postoperatively in 14,519 patients. Both symptomatic [risk ratios (RR), 0.81; 95% CI, 0.45-1.43; P=0.460] and overall (RR, 0.74; 95% CI, 0.45-1.24; P=0.250) VTE rates were comparable between study groups. Compared with postoperative chemoprophylaxis, early usage increased the risk of all bleeding (RR, 1.56; 95% CI, 1.13-2.15; P=0.007), major bleeding (RR, 1.63; 95% CI, 1.16-2.28; P=0.005), blood transfusion (RR, 1.48; 95% CI, 1.24-1.76; P<0.001), and reintervention (RR, 1.94; 95% CI, 1.19-3.18; P=0.008).

Conclusions:
Our findings advocate for initiating chemoprophylaxis postoperatively in elective abdominal surgery to minimize bleeding risk without compromising VTE protection.
Just What the Doctor Ordered
Authors: Baimas-George Maria R. , Ross Samuel W. , Yang Hongmei , Matthews Brent D. , Nimeri Abdelrahman , Reinke Caroline E. 
Published: December 2022

Objective:
To define the impact of missed ordering of venous thromboembolism (VTE) chemoprophylaxis in high-risk general surgery populations.

Background:
The primary cause of preventable death in surgical patients is VTE. Although guidelines and validated risk calculators assist in dosing recommendations, there remains considerable variability in ordering and adherence to recommended dosing.

Methods:
All adult inpatients who underwent a general surgery procedure between 2016 and 2019 and were entered into Atrium Health National Surgical Quality Improvement Program registry were identified. Patients at high risk for VTE (2010 Caprini score ≥5) and without bleeding history and/or acute renal failure were included. Primary outcome was 30-day postoperative VTE. Electronic medical record identified compliance with “perfect” VTE chemoprophylaxis orders (pVTE): no missed orders and no inadequate dose ordering. Multivariable analysis examined association between pVTE and 30-day VTE events.

Results:
A total of 19,578 patients were identified of which 4252 were high-risk inpatients. Hospital compliance of pVTE was present in 32.4%. pVTE was associated with shorter postoperative length of stay and lower perioperative red blood cell transfusions. There was 50% reduced odds of 30-day VTE event with pVTE (odds ratio: 0.50; 95% CI, 0.30−0.80) and 55% reduction in VTE event/mortality (odds ratio: 0.45; 95% CI, 0.31–0.63). After controlling for relevant covariates, pVTE remained significantly associated with decreased odds of VTE event and VTE event/mortality.

Conclusions:
pVTE ordering in high-risk general surgery patients was associated with 42% reduction in odds of postoperative 30-day VTE. Comprehending factors contributing to missed or suboptimal ordering and development of quality improvement strategies to reduce them are critical to improving outcomes.
Aqueous Povidone-Iodine Versus Normal Saline For Intraoperative Wound Irrigation on The Incidence of Surgical Site Infection in Clean-Contaminated Wounds After Gastroenterological Surgery: A Single-Institute, Prospective, Blinded-Endpoint, Randomized Controlled Trial
Authors: Maemoto Ryo , Noda Hiroshi , Ichida Kosuke , Miyakura Yasuyuki , Kakizawa Nao , Machida Erika , Aizawa Hidetoshi , Kato Takaharu , Iseki Masahiro , Fukui Taro , Muto Yuta , Fukai Shota , Tsujinaka Shingo , Hatsuzawa Yuuri , Watanabe Fumiaki , Nagamori Masakazu , Takahashi Jun , Kimura Yasuaki , Maeda Shimpei , Takayama Noriya , Sakio Ryotaro , Takahashi Rei , Takenami Tsutomu , Matsuzawa Natsumi , Mieno Makiko , Rikiyama Toshiki 
Published: December 2022

Objective:
This trial evaluated the superiority of intraoperative wound irrigation (IOWI) with aqueous povidone-iodine (PVP-I) compared with that with saline for reducing the incidence of surgical site infection (SSI).

Background:
IOWI with aqueous PVP-I is recommended for the prevention of SSI by the World Health Organization and the Centers for Disease Control and Prevention, although the evidence level is low.

Methods:
This single institute in Japan, prospective, randomized, blinded-endpoint trial was conducted to assess the superiority of IOWI with aqueous PVP-I in comparison with IOWI with saline for reducing the incidence of SSI in clean-contaminated wounds after gastroenterological surgery. Patients 20 years or older were assessed for eligibility, and the eligible participants were randomized at a 1:1 ratio using a computer-generated block randomization. In the study group, IOWI was performed for 1 minute with 40 mL of aqueous 10% PVP-I before skin closure. In the control group, the procedure was performed with 100 mL of saline. Participants, assessors, and analysts were masked to the treatment allocation. The primary outcome was the incidence of incisional SSI in the intention-to-treat set.

Results:
Between June 2019 and March 2022, 941 patients were randomized to the study group (473 patients) or the control group (468 patients). The incidence of incisional SSI was 7.6% in the study group and 5.1% in the control group (risk difference 0.025, 95% CI -0.006 to 0.056; risk ratio 1.484, 95% CI 0.9 to 2.448; P=0.154).

Conclusion:
The current recommendation of IOWI with aqueous PVP-I should be reconsidered.
Antidepressant drug prescription and incidence of COVID-19: a retrospective cohort study
Authors: Glebov Oleg O. , Mueller Christoph , Stewart Robert , Aarsland Dag , Perera Gayan 
Published: December 2022

AbstractWhile antidepressant drugs (ADs) have shown some efficacy in treatment of COVID-19, their preventative potential remains unexplored. To investigate association between AD and COVID-19 incidence in the community, we analysed data from community-living, non-hospitalized adults admitted to inpatient care of the South London&’Maudsley (SLaM) NHS Foundation Trust during the 1st wave of COVID-19 pandemic in the UK. Prescription of ADs within the period of 1 to 3 months before admission was associated with an approximately 40% decrease in positive COVID-19 test results when adjusted for socioeconomic parameters and physical health. This association was specifically observed for ADs of the Selective Serotonin Reuptake Inhibitor (SSRI) class. These results suggest that ADs, specifically SSRIs, may help prevent COVID-19 infection in the community. Definitive determination of AD preventative potential warrants prospective studies in the wider general population.Key pointsQuestionIs there an association between prescription of antidepressants and incidence of COVID-19 in the general population?FindingsIn this retrospective cohort study of mental health outpatients with a recent (1-3 months) antidepressant prescription, there was a statistically significant 40% decrease in positive COVID-19 tests. This association was specifically observed for the most commonly prescribed antidepressant class, Selective Serotonin Reuptake Inhibitors, and remained when adjusted for socioeconomic parameters and physical health.MeaningAntidepressant prescription was associated with lower incidence of COVID-19 in the community, warranting further investigation as prophylactics in prospective clinical studies.
Codon language embeddings provide strong signals for protein engineering
Authors: Outeiral Carlos , Deane Charlotte M. 
Published: December 2022

AbstractProtein representations from deep language models have yielded state-of-the-art performance across many tasks in computational protein engineering. In recent years, progress has primarily focused on parameter count, with recent models’ capacities surpassing the size of the very datasets they were trained on. Here, we propose an alternative direction. We show that large language models trained on codons, instead of amino acid sequences, provide high-quality representations that outperform comparable state-of-the-art models across a variety of tasks. In some tasks, like species recognition, prediction of protein and transcript abundance, or melting point estimation, we show that a language model trained on codons outperforms every other published protein language model, including some that contain over 50 times more parameters. These results suggest that, in addition to commonly studied scale and model complexity, the information content of biological data provides an orthogonal direction to improve the power of machine learning in biology.
An improved habitat suitability index for the great crested newt
Authors: Seccombe Emily , Salguero-Gomez Roberto 
Published: December 2022

ABSTRACTGreat crested newts (GCN) are a protected species whose conservation depends on the provision and protection of their breeding habitat. A habitat suitability index (HSI) developed in 2000 is extensively used in GCN conservation to assess breeding habitat quality. This two-decade old index is based on limited data and validation.Here, we introduce a new HSI with an improved ability to reflect GCN presence/absence in UK ponds. This proposed HSI is easier, requires less data, and predicts GCN presence/absence better than the previous index.To inform the new index, we used a dual approach to identify the relative importance of environmental criteria to predict GCN presence/absence. Firstly, we conducted a survey of 288 users of the GCN HSI to assess the perceived strengths and limitations of the existing index. Secondly, we analysed national datasets of GCN presence/absence and associated environmental data. Using these findings, we then tested various index modifications. The final modifications of the new HSI include: (i) using an arithmetic mean to combine variables, rather than a geometric mean, to reduce calculation errors and allow compensation between variables; (ii) excluding water quality and waterfowl impact as these lacked significant power to predict GCN presence/absence and were deemed inaccurate by HSI users; and (iii) changing the scoring relationship for pond area to better reflect current data and provide scores for ponds over 2000m2. Additionally, we present modified graphs to reduce errors in the calculation of pond density scores. We compared scores from the new and original HSIs using an independent dataset for validation, showing that the new HSI better reflects GCN present/absence (larger effect sizes and R-squared values) in comparison to the old HSI. Adopting this improved HSI will enable more effective conservation of the protected species via better-informed decision-making and monitoring.
Towards Cloud-Native, Machine Learning Based Detection of Crop Disease with Imaging Spectroscopy
Authors: Rubambiza Gloire , Galvan Fernando Romero , Pavlick Ryan , Weatherspoon Hakim , Gold Kaitlin M. 
Published: December 2022

AbstractDeveloping actionable early detection and warning systems for agricultural stakeholders is crucial to reduce the annual $200B USD losses and environmental impacts associated with crop diseases. Agricultural stakeholders primarily rely on labor-intensive, expensive scouting and molecular testing to detect disease. Spectroscopic imagery (SI) can improve plant disease management by offering decision-makers accurate risk maps derived from Machine Learning (ML) models. However, training and deploying ML requires significant computation and storage capabilities. This challenge will become even greater as global scale data from the forthcoming Surface Biology & Geology (SBG) satellite becomes available. This work presents a cloud-hosted architecture to streamline plant disease detection with SI from NASA’s AVIRIS-NG platform, using grapevine leafroll associated virus complex 3 (GLRaV-3) as a model system. Here, we showcase a pipeline for processing SI to produce plant disease detection models and demonstrate that the underlying principles of a cloud-based disease detection system easily accommodate model improvements and shifting data modalities. Our goal is to make the insights derived from SI available to agricultural stakeholders via a platform designed with their needs and values in mind. The key outcome of this work is an innovative, responsive system foundation that can empower agricultural stakeholders to make data-driven plant disease management decisions, while serving as a framework for others pursuing use-inspired application development for agriculture to follow that ensures social impact and reproducibility while preserving stakeholder privacy.Key PointsCloud-based plant disease detection system, easily accommodates newly developed and/or improved models, as well as diverse data modalities.Empower agricultural stakeholders to use hyperspectral data for decision support while preserving stakeholder data privacy.Outline framework for researchers interested in designing geospatial/remote sensing applications for agricultural stakeholders to follow.