bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inpatient Neurology Deaths and Factors Associated With Discharge to Hospice
Authors: Dujari Shefali , Wei Janet , Kraler Lironn , Goyal Tarini , Bernier Eric , Schwartz Neil , Hirsch Karen , Gold Carl A. 
Published: May 2023

Background and Purpose The Neurology Mortality Review Committee at our institution identified variability in location of death for patients on our inpatient neurology services. Hospice may increase the number of patients dying in their preferred locations. This study aimed to characterize patients who die on inpatient neurology services and explore barriers to discharge to hospice. Methods This retrospective study was completed at a single, quaternary care medical center that is a Level I Trauma Center and Comprehensive Stroke Center. Patients discharged by an inpatient neurology service between 6/2019-1/2021 were identified and electronic medical record review was performed on patients who died in the hospital and who were discharged to hospice. Results 69 inpatient deaths and 74 discharges to hospice occurred during the study period. Of the 69 deaths, 54 occurred following withdrawal of life sustaining treatment (WLST), of which 14 had a referral to hospice placed. There were 88 “hospice-referred” patients and 40 “hospice-eligible” patients. Hospice-referred patients were less likely to require the intensive care unit than hospice-eligible patients. Hospice-referred patients had their code status changed to Do Not Intubate earlier and were more likely to have advanced directives available. Conclusion Our data highlight opportunities for further research to improve discharge to hospice including interhospital transfers, advanced directives, earlier goals of care discussions, palliative care consultations, and increased hospice bed availability. Importantly, it highlights the limitations of using in-hospital mortality as a quality indicator in this patient population.
The early diagnostic value of optical coherence tomography (OCT) and OCT angiography in thyroid-associated ophthalmopathy
Authors: Xu Bei , Wang Sha , Chen Lu , Tan Jia 
Published: May 2023

Background: The retinal microvascular density changes have been identified in thyroid-associated ophthalmopathy (TAO) patients. Whereas a lack of research has been done on the diagnostic ability of optical coherence tomography (OCT) combined with optical coherence tomography angiography (OCTA) parameters. Objectives: This study aims to evaluate the retina perfusion variations in eyes with active and stable TAO and its diagnostic abilities using OCT and OCTA. Design: This is cohort longitudinal retrospective study. Methods: A total of 51 patients with TAO and 39 healthy controls (HCs) were recruited. The TAO eyes were divided into active and stable stage groups. The foveal avascular zone (FAZ), macular perfusion density (mPD), and peripapillary PD were measured by OCTA. The peripapillary retinal nerve fiber layer (RNFL), central retinal thickness (CRT), and whole macular volume (wMV) were measured by OCT. Visual evoked potential (VEP) and visual field (VF) were also assessed. Results: The mPD of the superficial retinal capillary plexus (SRCP) was significantly different in all subfields among active, stable, and HC groups ( p < 0.05) except for the temporal inner ( p = 0.137), and the active group achieved the lowest PD. The FAZ size increased significantly in the active and stable groups compared with the HC group ( p < 0.001). Significant difference was observed in mPD of deep retinal capillary plexus (DRCP) in all quadrants among three groups ( p < 0.05). Moreover, PD parameters of optic nerve head (ONH) and radial peripapillary capillary plexus (RPCP) showed a different trend among three groups ( p < 0.05). The r-value of visual field-mean deviation (VF-MD) of TAO with DRCP-whole PD (wPD) and RPCP-wPD was 0.421 and 0.299, respectively ( p < 0.05). The DRCP-wPD in OCTA and RNFL in OCT were significantly higher in area under the receiver operating characteristic curve (AUC) than that of HC eyes. Conclusion: OCT and OCTA can noninvasively detect the peripapillary and macular changes in various stages of TAO patients, and it might be a high diagnostic value tool to monitor the TAO progression.
Active chitosan- poly (vinyl alcohol) film reinforced with zinc oxide nanoparticles for food packaging applications
Authors: Coneo Natalia , Ramos Yulieth , De Ávila Gezira , Herrera Adriana , Cremades Ana 
Published: May 2023

Active packaging represents an innovative alternative to improve the quality of food and extend the shelf life of the product. The main aim of this research is to develop antibacterial films based on chitosan (Cs), polyvinyl alcohol (PVA), and zinc oxide nanoparticles (ZnONps) to find a solution of food deterioration due to the presence of pathogenic microorganisms. ZnONps were synthesized by green chemistry using the leaves extract of Petroselinum crispum. The films were fabricated with 0; 0.5; and 1% w/v of ZnONps using different proportions of Cs: PVA by the casting method. The mechanical, physicochemical, antimicrobial, and antifungal properties were assessed. Moreover, the influence of the Cs/PVA/ZnONps films in the conservation of the Isabella grape was analyzed (pH, titratable acidity, weight loss, total soluble solids, and decay rate) and it was compared to commercial coating and uncoated grapes. Results showed the increase in the content of PVA improved the mechanical properties and increased the water absorption. Besides, Young’s Module, and tensile strength of the films improved with ZnO nanoparticles addition. The antimicrobial activity of the nanocomposite films against Escherichia Coli was demonstrated. Finally, it was corroborated the nanocomposite films preserve the quality and extend the shelf life of Isabella grapes 6 days more than the commercial coating affirming their use in food packaging. To the best of our knowledge, no previous work related with the development of films based on Cs/PVA reinforced with ZnONPs has tested its application as fruits packaging, determining its effect on the ripening process through physic-chemical assays.
Rate of Conversion to Matrix-Induced Autologous Chondrocyte Implantation After a Biopsy: A Multisurgeon Study
Authors: Pasic Nicholas , Bradsell Hannah L. , Barandiaran Andres , Robinson Avi S. , Cole Brian J. , Vidal Armando F. , Frank Rachel M. 
Published: May 2023

Background: Autologous chondrocyte implantation (ACI) and matrix-induced autologous chondrocyte implantation (MACI) are performed to treat focal chondral defects (FCDs); both are 2-step procedures involving a biopsy, followed by transplantation. There is little published research evaluating ACI/MACI in patients who undergo a biopsy alone. Purpose: To determine (1) the value of ACI/MACI cartilage biopsies and concomitant procedures in patients with FCDs of the knee and (2) the conversion rate to cartilage transplantation as well as the rate of reoperation. Study Design: Case series; Level of evidence, 4. Methods: A retrospective review was performed of 46 patients (63% female) who underwent a MACI (or ACI) biopsy between January 2013 and January 2018. Preoperative data, intraoperative data, and postoperative outcomes were assessed at a minimum of 2 years after the biopsy. The conversion rate from a biopsy to transplantation and the reoperation rate were calculated and analyzed. Results: Among the 46 patients included, 17 (37.0%) underwent subsequent surgery, with only 12 undergoing cartilage restoration surgery, for an overall transplantation rate of 26.1%. Of these 12 patients, 9 underwent MACI/ACI, 2 underwent osteochondral allograft transplantation (OCA), and 1 underwent particulated juvenile articular cartilage implantation at 7.2 ± 7.5 months after the biopsy. The reoperation rate was 16.7% (1 patient after MACI/ACI and 1 patient after OCA) at 13.5 ± 2.3 months after transplantation. Conclusion: Arthroscopic surgery with debridement, chondroplasty, loose body removal, meniscectomy/meniscal repair, and other treatment approaches of knee compartment abnormalities at the time of a biopsy appeared to be sufficient in improving function and reducing pain in patients with knee FCDs.
Effectiveness of a New Clinical and Communication Curriculum for Medical Students: Result of a Double-Blinded Randomized Controlled Educational Trial
Authors: Nguyen Sang Ngoc , Pham Hanh Thi , Vu Lam Tung , Pham Truong Xuan , Gottlieb Barbara 
Published: May 2023

OBJECTIVES To improve 4 skills (communication, history-taking, past history-taking, and documentation) in medical students, we designed and pilot-tested a curriculum to teach a sample of Year 4 (Y4) students these skills and compared the clinical performance of these students with students not receiving the intervention. METHODS The study focused on the new curriculum's effectiveness in enhancing students’ performance of these skills. To minimize exposure across groups, participants were divided into intervention and control groups at random and placed in various classrooms. We evaluated each group's clinical competency 3 times: prior to the intervention, 9 weeks afterward, and 2 years later. RESULTS There was no difference at baseline between the 2 groups. Immediately following the intervention, the mean score of the intervention group's skills was significantly higher than before and higher than the control group in each clinical skill. The performance difference between the 2 groups was maintained for 2 years following the intervention. CONCLUSIONS Following a 9-week curriculum, evaluators rated students’ performance higher than their counterparts who learned these skills through standard informal exposure in the clinical setting. The fact that this performance advantage was maintained for 2 years following the intervention is a testament to the durability of the intervention and the value of dedicated training in these critical areas at an early point in students’ clinical careers.
Descending serotonergic modulation from rostral ventromedial medulla to spinal trigeminal nucleus is involved in experimental occlusal interference-induced chronic orofacial hyperalgesia
Authors: Mo Si-Yi , Xue Yang , Li Yuan , Zhang Yao-Jun , Xu Xiao-Xiang , Fu Kai-Yuan , Sessle Barry J. , Xie Qiu-Fei , Cao Ye 
Published: May 2023

Abstract
Background
Dental treatment associated with unadaptable occlusal alteration can cause chronic primary myofascial orofacial pain. The serotonin (5-HT) pathway from the rostral ventromedial medulla (RVM) exerts descending modulation on nociceptive transmission in the spinal trigeminal nucleus (Sp5) and facilitates chronic pain. The aim of this study was to investigate whether descending 5-HT modulation from the RVM to the Sp5 is involved in the maintenance of primary myofascial orofacial hyperalgesia after persistent experimental occlusal interference (PEOI) or after delayed removal of experimental occlusal interference (REOI).

Methods
Expressions of 5-HT3A and 5-HT3B receptor subtypes in the Sp5 were assessed by immunofluorescence staining and Western blotting. The release and metabolism of 5-HT in the Sp5 were measured by high-performance liquid chromatography. Changes in the pain behavior of these rats were examined after specific pharmacologic antagonism of the 5-HT3 receptor, chemogenetic manipulation of the RVM 5-HT neurons, or selective down-regulation of 5-HT synthesis in the RVM.

Results
Upregulation of the 5-HT3B receptor subtype in the Sp5 was found in REOI and PEOI rats. The concentration of 5-HT in Sp5 increased significantly only in REOI rats. Intrathecal administration of Y-25130 (a selective 5-HT3 receptor antagonist) dose-dependently reversed the hyperalgesia in REOI rats but only transiently reversed the hyperalgesia in PEOI rats. Chemogenetic inhibition of the RVM 5-HT neurons reversed the hyperalgesia in REOI rats; selective down-regulation of 5-HT in advance also prevented the development of hyperalgesia in REOI rats; the above two manipulations did not affect the hyperalgesia in PEOI rats. However, chemogenetic activation of the RVM 5-HT neurons exacerbated the hyperalgesia both in REOI and PEOI rats.

Conclusions
These results provide several lines of evidence that the descending pathway from 5-HT neurons in the RVM to 5-HT3 receptors in the Sp5, plays an important role in facilitating the maintained orofacial hyperalgesia after delayed EOI removal, but has a limited role in that after persistent EOI.

Graphical Abstract
Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data
Authors: Claeys Arne , Merseburger Peter , Staut Jasper , Marchal Kathleen , Van den Eynden Jimmy 
Published: May 2023

Abstract
Background
The Human Leukocyte Antigen (HLA) genes are a group of highly polymorphic genes that are located in the Major Histocompatibility Complex (MHC) region on chromosome 6. The HLA genotype affects the presentability of tumour antigens to the immune system. While knowledge of these genotypes is of utmost importance to study differences in immune responses between cancer patients, gold standard, PCR-derived genotypes are rarely available in large Next Generation Sequencing (NGS) datasets. Therefore, a variety of methods for in silico NGS-based HLA genotyping have been developed, bypassing the need to determine these genotypes with separate experiments. However, there is currently no consensus on the best performing tool.

Results
We evaluated 13 MHC class I and/or class II HLA callers that are currently available for free academic use and run on either Whole Exome Sequencing (WES) or RNA sequencing data. Computational resource requirements were highly variable between these tools. Three orthogonal approaches were used to evaluate the accuracy on several large publicly available datasets: a direct benchmark using PCR-derived gold standard HLA calls, a correlation analysis with population-based allele frequencies and an analysis of the concordance between the different tools. The highest MHC-I calling accuracies were found for Optitype (98.0%) and arcasHLA (99.4%) on WES and RNA sequencing data respectively, while for MHC-II HLA-HD was the most accurate tool for both data types (96.2% and 99.4% on WES and RNA data respectively).

Conclusion
The optimal strategy for HLA genotyping from NGS data depends on the availability of either WES or RNA data, the size of the dataset and the available computational resources. If sufficient resources are available, we recommend Optitype and HLA-HD for MHC-I and MHC-II genotype calling respectively.
The landscape of the long non-coding RNAs in developing mouse retinas
Authors: Yu Dongliang , Wu Yuqing , Zhu Leilei , Wang Yuying , Sheng Donglai , Zhao Xiaofeng , Liang Guoqing , Gan Lin 
Published: May 2023

Abstract
Background
The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available.

Results
Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways.

Conclusions
In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.
Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data
Authors: Chen Jiao , Wang Yunjian , Yang Zhi , Liu Danwen , Jin Yao , Li Xixi , Deng Yuhang , Wang Boya , Zhang Zhifeng , Ma Yubin 
Published: May 2023

Abstract
Background
Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes.

Results
In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct =  − 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data.

Conclusion
Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
The effect of lidocaine intraoperative infusion on quality of postoperative sleep in patients undergoing thyroidectomy: a randomized controlled trial
Authors: Shao Caiqun , Lin Longxiang , Chen Mengmeng , Wang Ning , Shangguan Wangning 
Published: May 2023

Abstract
Background
The incidence of thyroid nodules has increased significantly in recent years, and surgical removal is a common treatment. Postoperative sleep disturbance is still a serious problem in the current surgical environment. In this study, we explored whether intraoperative lidocaine infusion could improve the quality of sleep over 7 days and 30 days after surgery and postoperative recovery for patients undergoing thyroid surgery.

Methods
Seventy patients who underwent thyroid surgery from October 2020 to June 2021 were randomly assigned to the lidocaine or the normal saline group, 35 cases in each group. Patients enrolled in this study were randomized to receive either system lidocaine (a bolus of 1.5 mg·kg− 1, followed by an infusion of 2 mg·kg− 1·h− 1 until the end of the surgical procedure) or identical volumes and rates of normal saline. The primary endpoint was the Pittsburgh Sleep Quality Index (PSQI) scores. Secondary endpoints included intraoperative remifentanil consumption, whether there was a cough within 5 min after extubation and the cough scores, postoperative pain scores, the incidence of postoperative nausea and vomiting (PONV).

Results
Totally seventy cases were enrolled and eventually sixty-eight cases were analyzed. PSQI scores did not change significantly over time (F = 2.799, P = 0.069); also, there was no significant difference in PSQI scores between two groups in the entire 30 days follow-up period (F = 0.174, P = 0.678). Further, there was no interaction between the time points and the intervention (F = 0.649, P = 0.513). Similarly, intraoperative remifentanil consumption, the incidence of cough and postoperative pain scores, were comparable between the two groups (all P > 0.05); while patients in the lidocaine group showed significantly lower cough scores (P = 0.042) and lower incidence of PONV (P = 0.015).

Conclusions
Systemic lidocaine infusion might not improve the sleep quality and reduce postoperative pain over 7 days or 30 days after the operation of patients who underwent thyroid surgery, but it can reduce postoperative complications and improve the quality of recovery. Furthermore, sleep quality of patients wasn’t impaired significantly in the entire 30 days follow-up period after thyroid surgery compared with baseline values.

Trial registration
Registered in the Chinese Clinical Trial Registry (http://www.chictr.org.cn, identifier: ChiCTR2000039764, date: 08/11/2020)
Multiple imputation methods for missing multilevel ordinal outcomes
Authors: Dong Mei , Mitani Aya 
Published: May 2023

AbstractBackgroundMultiple imputation (MI) is an established technique for handling missing data in observational studies. Joint modelling (JM) and fully conditional specification (FCS) are commonly used methods for imputing multilevel data. However, MI methods for multilevel ordinal outcome variables have not been well studied, especially when cluster size is informative on the outcome. The purpose of this study is to describe and compare different MI strategies for dealing with multilevel ordinal outcomes when informative cluster size (ICS) exists.MethodsWe conducted comprehensive Monte Carlo simulation studies to compare the performance of five strategies: complete case analysis (CCA), FCS, FCS+CS (including cluster size (CS) in the imputation model), JM, and JM+CS under various scenarios. We evaluated their performance using a proportional odds logistic regression model estimated with cluster weighted generalized estimating equations (CWGEE).ResultsThe simulation results showed that including CS in the imputation model can significantly improve estimation accuracy when ICS exists. FCS provided more accurate and robust estimation than JM, followed by CCA for multilevel ordinal outcomes. We further applied these strategies to a real dental study to assess the association between metabolic syndrome and clinical attachment loss scores. The results based on FCS + CS indicated that the power of the analysis would increase after carrying out the appropriate MI strategy.ConclusionsMI is an effective tool to increase the accuracy and power of the downstream statistical analysis for missing ordinal outcomes. FCS slightly outperforms JM when imputing multilevel ordinal outcomes. When there is plausible ICS, we recommend including CS in the imputation phase.