bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-aware deep model for MHC-II peptide binding affinity prediction
Authors: Yu Ying , Zu Lipeng , Jiang Jiaye , Wu Yafang , Wang Yinglin , Xu Midie , Liu Qing 
Published: January 2024

AbstractThe prediction of major histocompatibility complex (MHC)-peptide binding affinity is an important branch in immune bioinformatics, especially helpful in accelerating the design of disease vaccines and immunity therapy. Although deep learning-based solutions have yielded promising results on MHC-II molecules in recent years, these methods ignored structure knowledge from each peptide when employing the deep neural network models. Each peptide sequence has its specific combination order, so it is worth considering adding the structural information of the peptide sequence to the deep model training. In this work, we use positional encoding to represent the structural information of peptide sequences and validly combine the positional encoding with existing models by different strategies. Experiments on three datasets show that the introduction of position-coding information can further improve the performance built upon the existing model. The idea of introducing positional encoding to this field can provide important reference significance for the optimization of the deep network structure in the future.
OTSUCNV: an adaptive segmentation and OTSU-based anomaly classification method for CNV detection using NGS data
Authors: Xie Kun , Ge Xiaojun , Alvi Haque A.K. , Liu Kang , Song Jianfeng , Yu Qiang 
Published: January 2024

AbstractCopy-number variations (CNVs), which refer to deletions and duplications of chromosomal segments, represent a significant source of variation among individuals, contributing to human evolution and being implicated in various diseases ranging from mental illness and developmental disorders to cancer. Despite the development of several methods for detecting copy number variations based on next-generation sequencing (NGS) data, achieving robust detection performance for CNVs with arbitrary coverage and amplitude remains challenging due to the inherent complexity of sequencing samples. In this paper, we propose an alternative method called OTSUCNV for CNV detection on whole genome sequencing (WGS) data. This method utilizes a newly designed adaptive sequence segmentation algorithm and an OTSU-based CNV prediction algorithm, which does not rely on any distribution assumptions or involve complex outlier factor calculations. As a result, the effective detection of CNVs is achieved with lower computational complexity. The experimental results indicate that the proposed method demonstrates outstanding performance, and hence it may be used as an effective tool for CNV detection.
Norepinephrine protects against cochlear outer hair cell damage and noise-induced hearing loss via α2A-adrenergic receptor
Authors: Tian Chaoyong , Yang Yang , Wang Renfeng , Li Yao , Sun Fei , Chen Jun , Zha Dingjun 
Published: January 2024

Abstract
Background
The cochlear sympathetic system plays a key role in auditory function and susceptibility to noise-induced hearing loss (NIHL). The formation of reactive oxygen species (ROS) is a well-documented process in NIHL. In this study, we aimed at investigating the effects of a superior cervical ganglionectomy (SCGx) on NIHL in Sprague-Dawley rats.

Methods
We explored the effects of unilateral and bilateral Superior Cervical Ganglion (SCG) ablation in the eight-ten weeks old Sprague-Dawley rats of both sexes on NIHL. Auditory function was evaluated by auditory brainstem response (ABR) testing and Distortion product otoacoustic emissions (DPOAEs). Outer hair cells (OHCs) counts and the expression of α2A-adrenergic receptor (AR) in the rat cochlea using immunofluorescence analysis. Cells culture and treatment, CCK-8 assay, Flow cytometry staining and analysis, and western blotting were to explore the mechanisms of SCG fibers may have a protective role in NIHL.

Results
We found that neither bilateral nor unilateral SCGx protected the cochlea against noise exposure. In HEI-OC1 cells, H2O2-induced oxidative damage and cell death were inhibited by the application of norepinephrine (NE). NE may prevent ROS-induced oxidative stress in OHCs and NIHL through the α2A-AR.

Conclusion
These results demonstrated that sympathetic innervation mildly affected cochlear susceptibility to acoustic trauma by reducing oxidative damage in OHCs through the α2A-AR. NE may be a potential therapeutic strategy for NIHL prevention.
Comprehensive analysis of annexin gene family and its expression in response to branching architecture and salt stress in crape myrtle
Authors: Wei Hui , Chen Jinxin , Zhang Xingyue , Lu Zixuan , Lian Bilin , Liu Guoyuan , Chen Yanhong , Zhong Fei , Yu Chunmei , Zhang Jian 
Published: January 2024

Abstract
Background
Annexin (ANN) is calcium (Ca2+)-dependent and phospholipid binding protein family, which is involved in plant growth and development and response to various stresses. However, little known about ANN genes were identified from crape myrtle, an ornamental horticultural plant widely cultivated in the world.

Results
Here, 9 LiANN genes were identified from Lagerstroemia indica, and their characterizations and functions were investigated in L. indica for the first time. The LiANN genes were divided into 2 subfamilies. The gene structure, chromosomal location, and collinearity relationship were also explored. In addition, the GO annotation analysis of these LiANNs indicated that they are enriched in molecular functions, cellular components, and biological processes. Moreover, transcription factors (TFs) prediction analysis revealed that bHLH, MYB, NAC, and other TFs can interact with the LiANN promoters. Interestingly, the LiANN2/4/6–9 were demonstrated to play critical roles in the branching architecture of crape myrtle. Furthermore, the LiANN2/6/8/9 were differentially expressed under salt treatment, and a series of TFs regulating LiANN2/6/8/9 expression were predicted to play essential roles in salt resistance.

Conclusions
These results shed light on profile and function of the LiANN gene family, and lay a foundation for further studies of the LiANN genes.
The 50% effective dose of hydromorphone and morphine for epidural analgesia in the hemorrhoidectomy: a double-blind, sequential dose-finding study
Authors: Cao Xianghua , Gui Qiangjun , Wei Yujiao , Lan Lanhui , Xiao Huiling , Wen Shihong , Li Xueping 
Published: January 2024

Abstract
Background
Although previous studies have showed that epidural morphine can be used as a complement to local anesthetics for analgesia after postcesarean delivery under spinal anesthesia, there is little known about the analgesic dosage of epidural morphine and hydromorphone for hemorrhoidectomy. Therefore, we conducted this study to examine the potency ratio of hydromorphone to epidural morphine as well as effective analgesic dose for 50% patients (ED50) undergoing elective hemorrhoidectomy.

Methods
80 patients under elective hemorrhoidectomy with combined spinal and epidural anesthesia(CSEA) in department of anesthesia, Dongguan Tungwah hospital. To assess the ED50, patients were treated with epidural morphine or epidural hydromorphone randomly using a biased coin method-determined dose with a sequential allocation procedure. Following surgery, standardized multimodal analgesia was administered to all patients. A pain response score of ≤ 3 (on a scale of 0–10) was determined to be the effective dose after 24 h following CSEA. The ED50 in both groups were determined using the probit regression and isotonic regression method. We also measured pain intensity by patient interview using a 10 point verbal numeric rating scale prospectively at 6, 12 and 24 h after CSEA, and adverse effects were also noted.

Results
The ED50 was 0.350 mg (95% CI, 0.259–0.376 mg) in hydromorphone group and 1.129 mg (95% CI, 0.903–1.187 mg) in morphine group, respectively, estimated by isotonic regression method. Regression analysis with the probit, the ED50 of epidural hydromorphone was 0.366 mg (95% CI, 0.276–0.388 mg) and epidural morphine was 1.138 mg (95% CI, 0.910–1.201 mg). Exploratory findings showed that there was no difference between the most frequent dosages of epidural hydromorphone or epidural morphine in the occurrence of nausea, vomiting and pruritus. When administered with epidural opioids at ED50 doses or higher, 97.5% (39/40) of epidural morphine patients and 97.5% (39/40) epidural hydromorphone of patients were satisfied with their analgesia.

Conclusion
Effective hemorrhoidectomy analgesia requires a 3:1 ratio of epidural morphine to epidural hydromorphone. Both drugs provide excellent patient satisfaction.
Effect of exercise on sleep quality in Parkinson’s disease: a mini review
Authors: Shafiq M. Abdullah , Singh Jyotpal , Khan Zain A. , Neary J. Patrick , Bardutz Holly A. 
Published: January 2024

AbstractThe growing incidence of Parkinson’s Disease (PD) is a major burden on the healthcare system. PD is caused by the degeneration of dopaminergic neurons and is known for its effects on motor function and sleep. Sleep is vital for maintaining proper homeostasis and clearing the brain of metabolic waste. Adequate time spent in each sleep stage can help maintain homeostatic function; however, patients with PD appear to exhibit sleep impairments. Although medications enhance the function of remaining dopaminergic neurons and reduce motor symptoms, their potential to improve sleep is still under question. Recently, research has shifted towards exercise protocols to help improve sleep in patients with PD. This review aims to provide an overview of how sleep is impaired in patients with PD, such as experiencing a reduction in time spent in slow-wave sleep, and how exercise can help restore normal sleep function. A PubMed search summarized the relevant research on the effects of aerobic and resistance exercise on sleep in patients with PD. Both high and low-intensity aerobic and resistance exercises, along with exercises related to balance and coordination, have been shown to improve some aspects of sleep. Neurochemically, sleeping leads to an increase in toxin clearance, including α-synuclein. Furthermore, exercise appears to enhance the concentration of brain-derived neurotrophic factors, which has preliminary evidence to suggest correlations to time spent in slow-wave sleep. More research is needed to further elucidate the physiological mechanism pertaining to sleep and exercise in patients with PD.
Transcutaneous canine breast cancer detection in Tunisia: a pilot study
Authors: Belaid Imtinene , Baya Mohamed Fedy , Ben Ayed Saif , Ben Ayed Ali , Maatoug Jihen , Zommit Nawel , Trabelsi Mohamed Anas , Ben Chida Noureddine , Khairi Hedi , Ben Fatma Leila , Chabchoub Imene , Ammar Nouha , Bourigua Rym , Hochlaf Makrem , Ezzaari Faten , Ben Ahmed Slim 
Published: January 2024

Abstract
Background
Breast cancer in Tunisia is often diagnosed at a late stage with long delay in time to consultation and to diagnosis.The aim of this study is to estimate the sensitivity and specificity of the transcutaneous breast cancer detection by canine olfactionin Tunisian women and to identify the potential confounding factors.

Methods
This is a diagnostic case control study that took place from October 2021 to November 2022 in the Department of Medical Oncology at the University Hospital Farhat Hached of Sousse and in the security and training dog center located in Sousse (K9 Dog Center Security & Training). A two-year-old male Belgian Malinois was trained to detect breast cancer on skin secretion samples in compresses that had been worn overnight by women on their breast and then a double-blind testing was performed. There was no contact between women and the dog. From the mentioned responses of the dog, four parameters were calculated: sensitivity, specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV).

Results
Two hundred women were included in this trial: 100 breast cancer (BC) patients recruited from Farhat Hached University Hospital of Sousse and 100 healthy volunteers (HV).The calculated sensitivity was 84% (95% CI 78–89%) and the calculated specificity was 81% (95% CI 75–86%). The calculated predictive values were: PPV = 83,51% (95% CI 78,37–88,65%) and NPV = 81,55% (95% CI 76.17–86.93%). In the multivariate study, only four confounding factors of test’s sensitivity were retained: age (OR = 1.210 [95% CI = 1.085–1.349]; p = 0.001), history of diabetes(OR = 0.017 [95% CI = 0.001–0.228]; p = 0.002), sampling at hospital (OR = 0.010 [95% CI = 0.003–0.464]; p = 0.010) and testing during chemotherapy courses (OR = 0.034 [95% CI = 0.003–0.404]; p = 0.007).For test’s specificity, we retained the three following confounding factors: age (OR = 1,104 [95% CI = 1.021–1.195]; p = 0.014), history of benign mastopathy (OR = 0.243 [95% CI = 0.074–0.805]; p = 0.021)and history of arterial hypertension (OR = 0.194 [95% CI = 0.053–0.707]; p = 0.013).

Conclusion
This is a pilot study that opens new avenues in developing a reliable cancer diagnostic tool that integrates the dog's olfactory ability to detect breast cancer using a transcutaneous sampling method. It could be a pre-test to select patients who are eligible to a screening mammogram, especially in low-income countries where there is no national mammography screening program.

Pactr.org identifier
PACTR202201864472288, registration date 11/01/2022.
Dietary Inflammatory Index and diabetic retinopathy risk in US adults: findings from NHANES (2005–2008)
Authors: Liu Rong , Zhang Jiechang , Gu Wen , Zhao Xiujuan , Xiao Lishun , Yang Chengcheng 
Published: January 2024

Abstract
Background
Inflammation is associated with the pathophysiology of diabetic retinopathy (DR). Within the framework of complete dietary patterns, the Dietary Inflammatory Index (DII) was formulated to evaluate the inflammatory properties inherent in a diet. The main purpose of the current study was to assess the relationship between DII and DR using National Health and Nutrition Examination Survey (NHANES).

Methods
The original sample size included 1,148 diabetes patients out of 2005–2008 NHANES surveys. Twenty-four-hour dietary consumptions were used to calculate the DII scores. Demographic characteristics and retina examinations were collected for the comparison between DR and non-DR groups in diabetes patients. The relationship between DII and DR was analyzed by a logistic regression model.

Results
227 subjects (110 non-DR and 117 DR) were selected in the analyses by using undersampling method to balance the sample size. Compared with non-DR group, DR group had higher DII values (1.14 ± 0.29 vs. 1.49 ± 0.21, p = 0.32), higher levels of HbA1c (6.8 ± 1.1% vs. 7.7 ± 2.6%, p < 0.001), longer duration of diabetes (6.52 ± 12 years vs. 14 ± 11 years, p < 0.001). The odds rate (OR) of DII for DR from the logistic regression was 1.38 (95%CI 1.06–1.81, p < 0.001). HbA1c, diabetes duration and obesity were important influencing factors, and their ORs were 1.81 (95% CI:1.31–2.50), 1.12 (95%CI:1.04–1.20), 4.01 (95%CI:1.12–14.32), respectively. In addition, the most important dietary indices for DR were different across males and females.

Conclusions
The current study demonstrates that a higher DII is associated with an increased risk of DR in US adults. Considering diet as a modifiable factor, limiting pro-inflammatory diets or encouraging an anti-inflammatory diet may be a promising and cost-effective method in the management of DR.
Source of SARS-CoV-2 infection: results from a series of 584,846 cases in France from October 2020 to August 2022
Authors: Rakover Arthur , Galmiche Simon , Charmet Tiffany , Chény Olivia , Omar Faïza , David Christophe , Martin Sophie , Mailles Alexandra , Fontanet Arnaud 
Published: January 2024

Abstract
Background
We aimed to study the source of infection for recently SARS-CoV-2-infected individuals from October 2020 to August 2022 in France.

Methods
Participants from the nationwide ComCor case–control study who reported recent SARS-CoV-2 infection were asked to document the source and circumstances of their infection through an online questionnaire. Multivariable logistic regression was used to identify the factors associated with not identifying any source of infection.

Results
Among 584,846 adults with a recent SARS-CoV-2 infection in France, 46.9% identified the source of infection and an additional 22.6% suspected an event during which they might have become infected. Known and suspected sources of infection were household members (30.8%), extended family (15.6%), work colleagues (15.0%), friends (11.0%), and possibly multiple/other sources (27.6%). When the source of infection was known, was not a household member, and involved a unique contact (n = 69,788), characteristics associated with transmission events were indoors settings (91.6%), prolonged (> 15 min) encounters (50.5%), symptomatic source case (64.9%), and neither the source of infection nor the participant wearing a mask (82.2%). Male gender, older age, lower education, living alone, using public transportation, attending places of public recreation (bars, restaurants, nightclubs), public gatherings, and cultural events, and practicing indoor sports were all independently associated with not knowing the source of infection.

Conclusion
Two-thirds of infections were attributed to interactions with close relatives, friends, or work colleagues. Extra-household indoor encounters without masks were commonly reported and represented avoidable circumstances of infection.

Trial registration
ClinicalTrials.gov registration number: NCT04607941.
Berberine alleviates ischemia reperfusion injury induced AKI by regulation of intestinal microbiota and reducing intestinal inflammation
Authors: Huo Aijing , Wang Fengmei 
Published: January 2024

Abstract
Background
It has been found that a variety of host disease states can exacerbate intestinal inflammation, leading to disruption of intestinal barrier function. Changes in the composition of the intestine microbiota, which affect downstream metabolites in turn, ultimately react against the host.

Objectives
We revealed the mechanism of berberine as an intestinal protective agent in rats with renal ischemia–reperfusion injury acute kidney injury (AKI).

Methods
HE staining was performed to evaluate the pathological changes in the colon and kidney. 16 S rRNA analysis was performed to assess the intestinal microbiota. Intestine TLR4/NF-κB expression was assessed by western blot. Q-RT-PCR was performed to detect TLR4 in intestine and IL-6 and KIM-1 gene expression in the kidney. SPSS 22.0 was used to compare the data.

Results
Rats with AKI exhibited increased relative abundances of Proteobacteria and Bacteroidetes and decreased relative abundances of Lactobacillus, Ruminococcus and Lachnospiraceae belonging to the phylum Firmicutes. The Sirt1-NF-κB-TLR4 pathway was involved in the occurrence process, accompanied by intestinal inflammation and oxidation. Berberine reversed the appeal change.

Conclusion
Berberine inhibits the intestinal biological barrier of Proteobacteria, reduces LPS production, exerts an anti-inflammatory effect, and delays the progression of AKI.
Gender trends in Canadian medicine and surgery: the past 30 years
Authors: Pickel Lauren , Sivachandran Nirojini 
Published: January 2024

Abstract
Background
While the number of women entering medicine has steadily increased since the 1970s in Canada, the gender composition along each stage of the medical training pathway has not been comprehensively reported. We therefore sought to systematically examine the gender composition of students, residents, and practicing physicians over the past 30 years in Canada.

Results
In this cross-sectional analysis of Canadian medical trainees including MD applicants (137,096 male, 169,099 female), MD students (126,422 male, 152, 967 female), MD graduates (29,413 male, 34,173 female), residents by the decade (24,425 male, 28,506 female) and practicing surgeons (total 7,457 male, 3,457 female), we find that increased female representation in medicine is not matched by representation in surgery, with the key being the specialty choice process. The likelihood of female applicants matriculating to medical school was less than male applicants in the 90s (OR 0.92, 95% CI 0.92–0.93), greater in the early 2000s (OR 1.03, 95% CI 1.03–1.04), and has since balanced out (OR 1.00, 95% CI 1.00-1.01), with medical school classes being nearly 60% female for the past two decades. Despite this, females have remained underrepresented in most surgical residency programs, with odds of female medical students entering surgical residency other than Ob/Gyn being about half that of male students (OR 0.56, 95% CI 0.44–0.71), resulting in a slow increase in practicing female surgeons of less than 0.5% per year in many surgical disciplines and projected parity decades or centuries in the future.

Conclusions
While undergraduate medical education has been majority female in Canada for nearly three decades, females remain greatly underrepresented in the physician workforce within surgical specialties. To build a representative medical workforce equipped to care for diverse patient populations, factors influencing the specialty choices of early career physicians will need to be examined and addressed.
Application of machine learning models on predicting the length of hospital stay in fragility fracture patients
Authors: Lai Chun-Hei , Mok Prudence Kwan-Lam , Chau Wai-Wang , Law Sheung-Wai 
Published: January 2024

Abstract
Background
The rate of geriatric hip fracture in Hong Kong is increasing steadily and associated mortality in fragility fracture is high. Moreover, fragility fracture patients increase the pressure on hospital bed demand. Hence, this study aims to develop a predictive model on the length of hospital stay (LOS) of geriatric fragility fracture patients using machine learning (ML) techniques.

Methods
In this study, we use the basic information, such as gender, age, residence type, etc., and medical parameters of patients, such as the modified functional ambulation classification score (MFAC), elderly mobility scale (EMS), modified Barthel index (MBI) etc, to predict whether the length of stay would exceed 21 days or not.

Results
Our results are promising despite the relatively small sample size of 8000 data. We develop various models with three approaches, namely (1) regularizing gradient boosting frameworks, (2) custom-built artificial neural network and (3) Google’s Wide & Deep Learning technique. Our best results resulted from our Wide & Deep model with an accuracy of 0.79, with a precision of 0.73, with an area under the receiver operating characteristic curve (AUC-ROC) of 0.84. Feature importance analysis indicates (1) the type of hospital the patient is admitted to, (2) the mental state of the patient and (3) the length of stay at the acute hospital all have a relatively strong impact on the length of stay at palliative care.

Conclusions
Applying ML techniques to improve the quality and efficiency in the healthcare sector is becoming popular in Hong Kong and around the globe, but there has not yet been research related to fragility fracture. The integration of machine learning may be useful for health-care professionals to better identify fragility fracture patients at risk of prolonged hospital stays. These findings underline the usefulness of machine learning techniques in optimizing resource allocation by identifying high risk individuals and providing appropriate management to improve treatment outcome.