bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perioperative Supplemental Oxygen and Postoperative Nausea and Vomiting: Subanalysis of a Trial, Systematic Review, and Meta-analysis
Authors: Markwei Metabel T. , Babatunde Ifeoluwa O. , Kutlu-Yalcin Esra , Essber Hani A. , Mascha Edward J. , Liu Liu , Kurz Andrea M. , Sessler Daniel I. 
Published: November 2022

Background
Intraoperative supplemental oxygen may reduce postoperative nausea and vomiting by mitigating hypoxic stress on the gastrointestinal tract. The authors therefore tested the hypothesis that supplemental oxygen reduces nausea and vomiting in adults recovering from colorectal surgery at the Cleveland Clinic between January 28, 2013, and March 11, 2016.

Methods
Initially, the authors conducted an unplanned subanalysis of a previous trial that evaluated the effect of 80% versus 30% intraoperative inspired oxygen on surgical site infection. Specifically, they assessed the effect of 80% versus 30% oxygen concentration on the incidence of postoperative nausea and/or vomiting. Thereafter, the authors conducted a systematic review and meta-analysis of the effect of supplemental oxygen on postoperative nausea and vomiting.

Results
The authors’ underlying analysis included 5,057 colorectal surgeries on 4,001 patients. For 2,554 surgeries, assignment was to 80% oxygen, and in 2,503 surgeries, to 30%. Postoperative nausea and vomiting was 852 of 2,554 (33%) in 80% oxygen and 814 of 2,503 (33%) in 30% oxygen. The estimated relative risk (95% CI) of 80% versus 30% oxygen on postoperative nausea and vomiting was 1.04 (0.96 to 1.12) in a generalized estimating equation model adjusting for within-patient correlation for patients with multiple surgeries, P = 0.355. Furthermore, supplemental oxygen did not reduce antiemetic use (P = 0.911) or the severity of nausea and vomiting (P = 0.924). The authors’ meta-analysis included 10 qualifying trials (6,749 patients) and did not find a difference in postoperative nausea and vomiting: relative risk, 0.97 [95% CI, 0.86 to 1.08], P = 0.55, I2 = 52%.

Conclusions
The incidence of postoperative nausea and vomiting did not differ in patients assigned to 80% or 30% inspired oxygen. A meta-analysis of available trials similarly indicated that supplemental intraoperative oxygen does not reduce postoperative nausea and vomiting. Therefore, supplemental oxygen should not be given in the expectation that it will reduce nausea and vomiting.

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What This Article Tells Us That Is New
Preoperative Computed Tomography Radiomics Analysis for Predicting Receptors Status and Ki-67 Levels in Breast Cancer
Authors: Fan Yuan , Pan Xuelin , Yang Fan , Liu Siyun , Wang Zhu , Sun Jiayu , Chen Jie 
Published: November 2022

Background:
To assess the prediction performance of preoperative chest computed tomography (CT) based radiomics features for estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2+), and Ki-67 status of breast cancer.

Materials and Methods:
This study enrolled 108 breast cancer patients who received preoperative chest CT examinations in our institution from July 2018 to January 2020. Radiomics features were separately extracted from nonenhanced, arterial, and portal-venous phases CT images. The least absolute shrinkage and selection operator logistic regression was used for feature selection. Then the radiomics signatures for each phase and a combined model of 3 phases were built. Finally, the receiver operating characteristic curves and calibration curves were used to confirm the performance of the radiomics signatures and combined model. In addition, the decision curves were performed to estimate the clinical usefulness of the combined model.

Results:
The 20 most predictive features were finally selected to build radiomics signatures for each phase. The combined model achieved the overall best performance than using either of the nonenhanced, arterial and portal-venous phases alone, achieving an area under the receiver operating characteristic curve of 0.870 for ER+ versus ER−, 0.797 for PR+ versus PR−, 0.881 for HER2+ versus HER2−, and 0.726 for Ki-67. The decision curve demonstrated that the CT-based radiomics features were clinically useful.

Conclusion:
This study indicated preopreative chest CT radiomics analysis might be able to assess ER, PR, HER2+, and Ki-67 status of breast cancer. The findings need further to be verified in future larger studies.
Predicting Factors for a Favorable Pathologic Response to Neoadjuvant Therapy in Esophageal Cancer
Authors: Wiesel Ory , Zlotnik Oran , Morgenstern Sarah , Tsur Maya , Menasherov Nikolai , Feferman Yael , Ben-Aharon Irit , Kashtan Hanoch 
Published: November 2022

Background:
Favorable pathologic response(FPR) is a significant predictor for improved survival following Neoadjuvant therapy(NAT) in esophageal and gastroesophageal cancer(GEJ). Preoperative prediction of FPR could modify treatment plans. No reliable method for predicting FPR exists. We sought to identify preoperative predicting factors for FPR.

Materials and Methods:
Retrospective analysis of patients with esophageal and GEJ cancer who underwent esophagectomy following (NAT). Univariate and multivariate analysis was used to identify preoperative predicting factors for FPR. A comparison of Tumor Regression Grade(TRG) was used to assess treatment response on overall survival(OS).

Results:
Out of 121 patients, 82(67.8%) had neoadjuvant chemoradiation. FPR was observed in 60(49.6%). Female sex, Radiation therapy(RT), squamous cell carcinoma(SCC), lack of signet ring feature, and FDG avidity posttreatment were associated with FPR on univariate analysis. RT and SCC were associated with FPR (OR=3.9 and 4.0, respectively) on multivariate analysis. OS was lower among patients who did not achieve FPR to NAT(P=0.027).

Conclusions:
FPR is a predictor of improved OS. SCC and radiation therapy-based protocol were identified as major prediction factors of FPR in patients with esophageal and GEJ cancers.
Communicating With Unconscious Patients
Authors: Lawrence Madelaine M. , Ramirez Rebecca P. , Bauer Paul J. 
Published: November 2022

Background
Nurses are told to speak to their unconscious patients because hearing is said to be the last sense to depart. There was little reliable evidence before the 1990s that patients in an unconscious state could hear and understand what was being said. That led to reluctance on the part of health professionals to communicate with these unresponsive patients.

Objective
This historical overview aims to present researched evidence from the 1990s to the present detailing awareness that occurs in unconscious patients, when that awareness increases, and how to detect that awareness. It also includes research about the benefits of communicating with unconscious patients and descriptions of how registered nurses and other health care professionals, from a postsurvey after a continuing education course on experiences of unconscious patients, plan to communicate with unconscious patients.

Methods
A literature search was conducted, which included more than 150 articles and books about experiences of unconscious patients in several electronic databases, including PubMed, CINAHL, and the British Nursing Index. In addition, an analysis of 105 postcourse responses by registered nurses (89%) and other health professionals (11%), licensed practical nurses, emergency medical technicians, and cardiac technicians after taking a continuing education course on experiences of previously unconscious patients were analyzed.

Results
The Glasgow Coma Scale and the Full Outline of Unresponsiveness scale are helpful behavioral tools to identify levels of coma but miss detecting awareness in patients who can hear and understand but cannot move. The estimates are that 25% to 40% (J Trauma. 1975;15:94-98; J Neurosci Nurs. 1988;20:223-228; J Neurosci Nurs. 1990;22(1):52-53; Am J Crit Care. 1995;3:227-232) of patients diagnosed with a disorder of consciousness can hear and understand what is being said in their environment. Substantial evidence supports that isolation and loneliness, such as experienced by some patients perceived to be unaware, can be physically and psychologically harmful.

Conclusions
Strong evidence shows that some patients diagnosed as being in a vegetative state can hear and understand what is being said in their environment. Interviews with previously unconscious patients and electrophysiological methods show that awareness can be detected in patients perceived to be unconscious. There is documented evidence that patients experience awareness when going into unconsciousness, even when they appear unaware and when moved. To our knowledge, these times have not been researched using electrophysiological devices but established from interviews.
Nurse-Led Motor Function Rehabilitation Program for Acute Ischemic Stroke: A Randomized Pilot Study
Authors: WANG Jianmiao , ZHANG Yuping , CHEN Yuanyuan , LI Mei , JIN Jingfen 
Published: November 2022

ABSTRACT

Background
Rehabilitation care for patients with stroke in the acute stage must be strengthened. However, the evidence on how to strengthen this care is insufficient.

Purpose
This article was designed to evaluate the feasibility and effectiveness of implementing a nurse-led motor function rehabilitation program on patients with acute ischemic stroke.

Methods
From January to October 2018, patients with initial acute ischemic stroke were assigned to one of two groups using a pilot randomized controlled trial design, with one group receiving a nurse-led motor function intervention program developed based on Orem's theory (7 consecutive days, twice daily for 30 minutes, experimental group) and the other receiving usual care (control group). The effectiveness measures included changes in the Motor Assessment Scale, the modified Barthel Index, and the National Institutes of Health Stroke Scale. The feasibility measures included patient retention rate, incidence of adverse events, and acceptance of nurses and patients.

Results
We assigned 104 patients (male: 55.7%; age: 62.8 ± 13.2 years) to receive either a nurse-led motor function rehabilitation program or usual care. Eighty-eight patients were evaluated after 7 days (87% retention rate), including 43 (83% retention rate) in the experimental group. Patients accepted the intervention well, and no severe adverse events were reported. Nurses had good fidelity and showed high acceptance. The experimental group showed significantly higher postintervention Motor Assessment Scale and modified Barthel Index scores than the control group (p < .001), whereas postintervention National Institutes of Health Stroke Scale scores did not differ significantly between the two groups.

Conclusions/Implications for Practice
The nurse-led rehabilitation program used in this study was shown to be feasible and effective in improving motor function in patients with acute ischemic stroke. Further study is recommended to determine related clinical recommendations.
Update of surgical treatment of polydactyly
Authors: Tawfeeq Yaser , Hendry J. Michael , Wood Kristi Sue 
Published: November 2022

Purpose of review
Polydactyly presents with variable extent of duplication and may involve preaxial/radial (hand)/medial (foot), postaxial/ulnar (hand)/lateral (foot) or central duplication. This review will summarize recent advancements in the surgical management of this common entity.

Recent findings
Modifications to classification systems aim to help guide surgical management of polydactyly. Attempts have been made at quantifying preoperative angulation of the duplicated digits to minimize the chance of residual or recurrent deformity after surgical reconstruction. As a result, consideration should be given to the need for soft tissue correction vs. osteotomy to optimize the clinical outcome. On-top plasty is an option that may be beneficial in ‘unequal’ preaxial polydactyly, where neither duplicate is preferred on its own.

Summary
Polydactyly is one of the most common congenital anomalies in the hands and feet. Determination of surgical intervention often begins with classification systems that exist, which primarily separate these into preaxial, postaxial, and central. Referral for surgical consideration is indicated, given the management is often surgical.
Decoding Single-cell Landscape and Intercellular Crosstalk in the Transplanted Liver
Authors: Huang Haitao , Chen Ruihan , Lin Yimou , Jiang Jingyu , Feng Shi , Zhang Xueyou , Zhang Cheng , Ji Qinghua , Chen Hui , Xie Haiyang , Zheng Shusen , Ling Qi 
Published: November 2022

Background.
Liver transplantation (LT) is the most effective treatment for various end-stage liver diseases. However, the cellular complexity and intercellular crosstalk of the transplanted liver have constrained analyses of graft reconstruction after LT.

Methods.
We established an immune-tolerated orthotopic LT mouse model to understand the physiological process of graft recovery and intercellular crosstalk. We employed single-cell RNA sequencing and cytometry by time-of-flight to comprehensively reveal the cellular landscape.

Results.
We identified an acute and stable phase during perioperative graft recovery. Using single-cell technology, we made detailed annotations of the cellular landscape of the transplanted liver and determined dynamic modifications of these cells during LT. We found that 96% of graft-derived immune cells were replaced by recipient-derived cells from the preoperative to the stable phase. However, CD206+MerTK+ macrophages and CD49a+CD49b- natural killer cells were composed of both graft and recipient sources even in the stable phase. Intriguingly, the transcriptional profiles of these populations exhibited tissue-resident characteristics, suggesting that recipient-derived macrophages and natural killer cells have the potential to differentiate into ‘tissue-resident cells’ after LT. Furthermore, we described the transcriptional characteristics of these populations and implicated their role in regulating the metabolic and immune remodeling of the transplanted liver.

Conclusions.
In summary, this study delineated a cell atlas (type-proportion-source-time) of the transplanted liver and shed light on the physiological process of graft reconstruction and graft-recipient crosstalk.
Structural analysis of Toxoplasma gondiisortilin
Authors: Honfozo Ariane , Ghouil Rania , Alayi Tchilabalo Dilezitoko , Ouldali Malika , Arteni Ana-Andreea , Atindehou Cynthia Menonve , Fanou Lucie Ayi , Hathout Yetrib , Zinn-Justin Sophie , Tomavo Stanislas 
Published: November 2022

ABSTRACTRhoptries and micronemes are essential for host cell invasion and survival of all apicomplexan parasites, which are composed of numerous obligate intracellular protozoan pathogens includingPlasmodium falciparum(malaria) andToxoplasma gondii(toxoplasmosis) that infect humans and animals causing severe diseases. We identifiedToxoplasma gondiiTgSORT as an essential cargo receptor, which drives the transport of rhoptry (ROP) and microneme (MIC) proteins to ensure the biogenesis of these secretory organelles. The luminal ectodomain of 752 amino acid long situated at the N-terminus end of TgSORT has been described to bind to MIC and ROP proteins. Here, we present an optimized protocol for expression of the entire luminal ectodomain of TgSORT (Tg-NSORT) in the yeastPichia pastoris.Optimization of its coding sequence, cloning and transformation of the yeastP. pastorisallowed the secretion of Tg-NSORT. The protein was purified and further analyzed by negative staining electron microscopy. In addition, molecular modeling using AlphaFold identified key differences between human andT gondiisortilin. The structural features that are only present inT. gondiiand other apicomplexan parasites were highlighted. Elucidating the roles of these specific structural features may be useful for designing new therapeutic agents against apicomplexan parasites
Maximum Classifier Discrepancy Generative Adversarial Network for Jointly Harmonizing Scanner Effects and Improving Reproducibility of Downstream Tasks
Authors: Yan Weizheng , Fu Zening , Jiang Rongtao , Sui Jing , Calhoun Vince D. 
Published: November 2022

AbstractObjectiveMulti-site collaboration is essential for overcoming small-sample problems when exploring reproducible biomarkers in MRI studies. However, various scanner-specific factors dramatically reduce the cross-scanner replicability. Moreover, existing harmony methods mostly could not guarantee the improved performance of downstream tasks.Methodswe proposed a new multi-scanner harmony framework, called ‘maximum classifier discrepancy generative adversarial network’, or MCD-GAN, for removing scanner effects in the original feature space while preserving substantial biological information for downstream tasks. Specifically, the adversarial generative network was utilized for persisting the structural layout of each sample, and the maximum classifier discrepancy module was introduced for regulating GAN generators by incorporating the downstream tasks.ResultsWe compared the MCD-GAN with other state-of-the-art data harmony approaches (e.g., ComBat, CycleGAN) on simulated data and the Adolescent Brain Cognitive Development (ABCD) dataset. Results demonstrate that MCD-GAN outperformed other approaches in improving cross-scanner classification performance while preserving the anatomical layout of the original images.SignificanceTo the best of our knowledge, the proposed MCD-GAN is the first generative model which incorporates downstream tasks while harmonizing, and is a promising solution for facilitating cross-site reproducibility in various tasks such as classification and regression. The codes of the MCD-GAN are available athttps://github.com/trendscenter/MCD-GAN.
SUMO –In SilicoSequence Assessment Using Multiple Optimization Parameters
Authors: Evers Andreas , Malhotra Shipra , Bolick Wolf-Guido , Najafian Ahmad , Borisovska Maria , Warszawski Shira , Nanfack Yves Fomekong , Kuhn Daniel , Rippmann Friedrich , Crespo Alejandro , Sood Vanita 
Published: November 2022

AbstractTo select the most promising screening hits from antibody and VHH display campaigns for subsequent in-depth profiling and optimization, it is highly desirable to assess and select sequences on properties beyond only their binding signals from the sorting process. In addition, developability risk criteria, sequence diversity and the anticipated complexity for sequence optimization are relevant attributes for hit selection and optimization. Here, we describe an approach for thein silicodevelopability assessment of antibody and VHH sequences. This method not only allows for ranking and filtering multiple sequences with regard to their predicted developability properties and diversity, but also visualizes relevant sequence and structural features of potentially problematic regions and thereby provides rationales and starting points for multi-parameter sequence optimization.
Use of whole genome sequencing to identify low-frequency mutations in COVID-19 patients treated with remdesivir
Authors: Nirmalarajah Kuganya , Maguire Finlay , Yim Winfield , Aftanas Patryk , Li Angel X. , Shigayeva Altynay , Yip Lily , Zhong Xi Zoe , McGeer Allison J. , Muberka Samira , Kozak Robert 
Published: November 2022

AbstractBackgroundWe investigate the effects of remdesivir (RDV) treatment on intra-host SARS-CoV-2 diversity and low-frequency mutations in moderately ill hospitalized COVID-19 patients and compare them to patients without RDV treatment.MethodsSequential collections of nasopharyngeal and mid-turbinate swabs were obtained from 16 patients with and 31 patients without RDV treatment. A total of 113 samples were sequenced and mutation analyses were performed.ResultsWe did not identify any drug resistant mutations during RDV therapy. In genes encoding and associated with the replication complex, low-frequency minority variants that do not reach fixation within the sampling period were detected in 6/16 (37.5%) and 14/31 (45%) patients with and without RDV treatment respectively. We did not detect significant differences in within-host diversity and positive selection between the RDV-treated and untreated groups.ConclusionsMinimal intra-host variability and stochastic low-frequency variants detected in moderately ill patients suggests little selective pressure in patients receiving short courses of RDV. Patients undergoing short regimens of RDV therapy should continue to be monitored.
The interaction of polygenic risk for depression and age on white blood cell count
Authors: Tio Earvin , Felsky Daniel 
Published: November 2022

AbstractRecent epidemiological studies suggest that polygenic risk for depression is associated with elevated white blood cell count, indicating shared genetic mechanisms between depression as a psychiatric disorder and the pro-inflammatory states often observed in clinical depression. However, the effects of aging on depressive symptoms and inflammation are not often fully appreciated in these studies, despite known variation across the human lifespan. To investigate the interaction of polygenic risk for depression and age on white blood cell count, we calculated depression polygenic risk scores (PRS) in 324,098 individuals from the UK Biobank (UKB) and 22,758 individuals from the Canadian Longitudinal Study on Aging (CLSA). Linear regression models of white blood cell count were fit to each sample, including interaction effects between age and the depression PRS. Significant age by PRS interaction effects were found in both samples (UKB interaction term: t=-2.9,p=3.7×10−3; CLSA interaction term: t=-2.6,p=9.0×10−3). While the previously reported main positive association between PRS and increasing white blood cell count was observed, we show in this study that the strength of the association diminishes with increasing age. Considering this potential age-dependency, these findings should encourage efforts to uncover genome-wide markers of late-life depression, which are needed to fully understand these age-related interaction effects.
Computational Pipeline to Identify Gene signatures that Define Cancer Subtypes
Authors: Mittal Ekansh , Parikh Vatsal , Kirchgaessner Raphael 
Published: November 2022

AbstractMotivationThe heterogeneous nature of cancers with multiple subtypes makes them challenging to treat. However, multi-omics data can be used to identify new therapeutic targets and we established a computational strategy to improve data mining.ResultsUsing our approach we identified genes and pathways specific to cancer subtypes that can serve as biomarkers and therapeutic targets. Using a TCGA breast cancer dataset we applied the ExtraTreesClassifier dimensionality reduction along with logistic regression to select a subset of genes for model training. Applying hyperparameter tuning, increased the model accuracy up to 92%. Finally, we identified 20 significant genes using differential expression. These targetable genes are associated with various cellular processes that impact cancer progression. We then applied our approach to a glioma dataset and again identified subtype specific targetable genes.ConclusionOur research indicates a broader applicability of our strategy to identify specific cancer subtypes and targetable pathways for various cancers.