bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime
Authors: Zhang Yifan , Tran Duc , Nguyen Tin , Dascalu Sergiu M. , Harris Frederick C. 
Published: February 2023

Abstract
Background
The advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in individual cell resolution. In recent years, many trajectory inference methods have been developed. They have focused on using the graph method to infer the trajectory using single-cell data, and then calculate the geodesic distance as the pseudotime. However, these methods are vulnerable to errors caused by the inferred trajectory. Therefore, the calculated pseudotime suffers from such errors.

Results
We proposed a novel framework for trajectory inference called the single-cell data Trajectory inference method using Ensemble Pseudotime inference (scTEP). scTEP utilizes multiple clustering results to infer robust pseudotime and then uses the pseudotime to fine-tune the learned trajectory. We evaluated the scTEP using 41 real scRNA-seq data sets, all of which had the ground truth development trajectory. We compared the scTEP with state-of-the-art methods using the aforementioned data sets. Experiments on real linear and non-linear data sets demonstrate that our scTEP performed superior on more data sets than any other method. The scTEP also achieved a higher average and lower variance on most metrics than other state-of-the-art methods. In terms of trajectory inference capacity, the scTEP outperforms those methods. In addition, the scTEP is more robust to the unavoidable errors resulting from clustering and dimension reduction.

Conclusion
The scTEP demonstrates that utilizing multiple clustering results for the pseudotime inference procedure enhances its robustness. Furthermore, robust pseudotime strengthens the accuracy of trajectory inference, which is the most crucial component in the pipeline. scTEP is available at https://cran.r-project.org/package=scTEP.
Deafness gene screening based on a multilevel cascaded BPNN model
Authors: Liu Xiao , Teng Li , Zuo Wenqi , Zhong Shixun , Xu Yuqiao , Sun Jing 
Published: February 2023

AbstractSudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in genes for inherited deafness. To identify these genes associated with deafness, researchers have mostly used biological experiments, which are accurate but time-consuming and laborious. In this paper, we proposed a computational method based on machine learning to predict deafness-associated genes. The model is based on several basic backpropagation neural networks (BPNNs), which were cascaded as multiple-level BPNN models. The cascaded BPNN model showed a stronger ability for screening deafness-associated genes than the conventional BPNN. A total of 211 of 214 deafness-associated genes from the deafness variant database (DVD v9.0) were used as positive data, and 2110 genes extracted from chromosomes were used as negative data to train our model. The test achieved a mean AUC higher than 0.98. Furthermore, to illustrate the predictive performance of the model for suspected deafness-associated genes, we analyzed the remaining 17,711 genes in the human genome and screened the 20 genes with the highest scores as highly suspected deafness-associated genes. Among these 20 predicted genes, three genes were mentioned as deafness-associated genes in the literature. The analysis showed that our approach has the potential to screen out highly suspected deafness-associated genes from a large number of genes, and our predictions could be valuable for future research and discovery of deafness-associated genes.
The association between hordein polypeptide banding and agronomic traits in partitioning genetic diversity in six-rowed Ethiopian barley lines (Hordeum vulgare L.)
Authors: Fantahun Basazen , Woldesemayate Tesfaye , Shiferaw Eleni 
Published: February 2023

Abstract
Background
Evaluation of the extent of genetic variation within and between the populations of crop genetic resources are of paramount importance in any breeding program. An experiment aimed at assessing the extent of variation among barley lines and the degree of association between hordein polypeptide and agronomic traits was hence executed.

Methods
Field experiment was conducted in six environments between 2017–2019 involving 19 barley lines. Hordein bands were separated using vertical Sodium Dodecyl Sulphate Poly- acrylamide Gel Electrophoresis (SDS-PAGE).

Results
The analysis of variance revealed significant variation among lines and wider range units were observed for the agronomic traits. The line (Acc# 16,811–6) was superior, producing the highest grain yield (2.97 ton ha−1) across environments, 3.6 ton ha−1 at Holleta, and 1.93 ton ha−1 at Chefedonsa. At Arsi Negelle a different line Acc# 17146–9 was the highest yielding (3.15ton ha−1). SDS-PAGE-based analysis of barley lines separated 12 hordein bands between C (four bands) and B (eight bands) subunits. Interestingly bands 52, 46a, and 46b were uniquely conserved in the four naked barley lines (Acc#16809–14,16956–11, 17240–3, 17244–19). A considerably high proportion of genetic diversity within the populations than among the populations could be a repercussion of high gene flow which substantiates the longstanding and dominant informal seed exchange system among the farmers. The significant positive association between grain yield and band 50 evocates the expression of this allele may code for higher grain yield. The negative association between days to maturity and band 52 perhaps stipulates earliness in barely lines upon the manifestation of the band. Band 52 and 60 appeared to be associated with more than one agronomic trait (days to maturity and thousand kernel weight; grain filling period and grain yield respectively) and could be the result of pleiotropic characteristics of the genes residing in these banding regions.

Conclusion
The barley lines exhibited substantial variation for hordein protein and agronomic traits. However, imparted the need for the implementation of decentralized breeding as a consequence of genotype-by-environment interaction. Significant hordein polypeptide and agronomic traits association advocated the utilization of hordein as a protein marker and perhaps consider them in the parental line selection.
Estimating disease incidence rates and transition probabilities in elderly patients using multi-state models: a case study in fragility fracture using a Bayesian approach
Authors: Llopis-Cardona Fran , Armero Carmen , Sanfélix-Gimeno Gabriel 
Published: February 2023

Abstract
Background
Multi-state models are complex stochastic models which focus on pathways defined by the temporal and sequential occurrence of numerous events of interest. In particular, the so-called illness-death models are especially useful for studying probabilities associated to diseases whose occurrence competes with other possible diseases, health conditions or death. They can be seen as a generalization of the competing risks models, which are widely used to estimate disease-incidences among populations with a high risk of death, such as elderly or cancer patients. The main advantage of the aforementioned illness-death models is that they allow the treatment of scenarios with non-terminal competing events that may occur sequentially, which competing risks models fail to do.

Methods
We propose an illness-death model using Cox proportional hazards models with Weibull baseline hazard functions, and applied the model to a study of recurrent hip fracture. Data came from the PREV2FO cohort and included 34491 patients aged 65 years and older who were discharged alive after a hospitalization due to an osteoporotic hip fracture between 2008-2015. We used a Bayesian approach to approximate the posterior distribution of each parameter of the model, and thus cumulative incidences and transition probabilities. We also compared these results with a competing risks specification.

Results
Posterior transition probabilities showed higher probabilities of death for men and increasing with age. Women were more likely to refracture as well as less likely to die after it. Free-event time was shown to reduce the probability of death. Estimations from the illness-death and the competing risks models were identical for those common transitions although the illness-death model provided additional information from the transition from refracture to death.

Conclusions
We illustrated how multi-state models, in particular illness-death models, may be especially useful when dealing with survival scenarios which include multiple events, with competing diseases or when death is an unavoidable event to consider. Illness-death models via transition probabilities provide additional information of transitions from non-terminal health conditions to absorbing states such as death, what implies a deeper understanding of the real-world problem involved compared to competing risks models.
Evaluation of the advantages of robotic versus laparoscopic surgery in elderly patients with colorectal cancer
Authors: Xue Yonggan , Li Sen , Guo Shaohua , Kuang Yanshen , Ke Mu , Liu Xin , Gong Fangming , Li Peng , Jia Baoqing 
Published: February 2023

Abstract
Background
The incidence of colorectal cancer increases with aging. Curative-intent surgery based on a minimally invasive concept is expected to bring survival benefits to elderly patients (aged over 80 years) with colorectal cancer who are frequently with fragile health status and advanced tumors. The study explored survival outcomes in this patient population who received robotic or laparoscopic surgery and aimed to identify an optimal surgical option for those patients.

Methods
We retrieved the clinical materials and follow-up data on elderly patients with colorectal carcinoma who received robotic or laparoscopic surgery in our institution. The pathological and surgical outcomes were compared to examine the efficacy and safety of the two approaches. The DFS (disease-free survival) and OS (overall survival) results at 3 years after surgery were assessed to explore the survival benefits.

Results
A total of 111 patients were screened for the study, including 55 in the robotic group and 56 in the laparoscopic group. The demographic details were generally similar between the two groups. No statistically significant difference in the number of removed lymph nodes was observed between the two approaches, with a median of 15 versus 14 (P = 0.053). The intraoperative blood loss was significantly reduced by robotic technique when compared to the laparoscopic approach, with a mean of 76.9 ml versus 161.6 ml (P = 0.025). There were no significant differences in operation time, conversion, postoperative complications and recovery, and long-term outcomes between the two groups.

Conclusion
Robotic surgery was prized for elderly patients with colorectal cancer who developed anemia and/or hematological conditions.
Prevalence of extended spectrum beta lactamase and molecular detection of blaTEM, blaSHV and blaCTX-M genotypes among Gram negative bacilli isolates from pediatric patient population in Gaza strip
Authors: El Aila Nabil Abdullah , Al Laham Nahed Ali , Ayesh Basim Mohammed 
Published: February 2023

Abstract
Background
Extended-spectrum β lactamases (ESBLs), have the ability to hydrolyze and cause resistance to various types of the β-lactam antibiotics, including the extended-spectrum (or third-generation) cephalosporins (e.g., cefotaxime, ceftriaxone, ceftazidime) and monobactams (e.g., aztreonam). ESBL-producing Gram negative bacteria is still posing significant therapeutic challenges.

Objectives
To assess the prevalence and molecular characteristics of ESBL producing Gram negative bacilli, isolated from a cohort of pediatric patients in Gaza hospitals.

Methods
A total of 322 isolates of Gram-negative bacilli were collected from four referral pediatric hospitals in Gaza, namely: Al-Nasr, Al-Rantisi, Al-Durra and Beit Hanoun hospitals. These isolates were tested for ESBL production using the double disk synergy and CHROMagar phenotypic methods. Molecular characterization of the ESBL producing strains was performed using PCR targeting the CTX-M, TEM and SHV genes. Antibiotic profile was done using Kirby Bauer method according to Clinical and Laboratory Standard Institute.

Results
Out of 322 isolates tested by phenotypic methods, 166 (51.6%) were ESBL positive. The prevalence of ESBL production in Al-Nasr, Al-Rantisi, Al-Durra and Beit Hanoun hospitals was 54%, 52.5%, 45.5% and 52.8% respectively. The prevalence of ESBL production among Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., Proteus mirabilis, Enterobacter spp., Citrobacter spp., and Serratia marcescens is 55.3%, 63.4%, 17.8%, 57.1%, 33.3%, 28.5%, 38.4%, and 4% respectively.
ESBL production among urine, pus, blood, CSF and sputum was 53.3%, 55.2%, 47.4%, 33.3%, and 25% respectively. Out of the 322 isolates, 144 were screened for CTX-M, TEM and SHV production. Using PCR, 85 (59%) had at least one gene. The prevalence rate of CTX-M, TEM and SHV genes was 60%, 57.6%, and 38.3% respectively.
Meropenem and amikacin were highest rates of susceptibility antibiotics against ESBLs producers (83.1% and 82.5% respectively), while the least effective antibiotics were amoxicillin (3.1%) and cephalexin (13.9%). Moreover, ESBLs producers showed high resistance rate to cefotaxime, ceftriaxone and ceftazidime (79.5%, 78.9% and 79.5% respectively).

Conclusion
Our results show high prevalence of ESBL production among Gram negative bacilli isolated from children in different pediatric hospitals in Gaza strip. A substantial level of resistance to first and second generation cephalosporins was also observed. This ascertains the need for a rational antibiotic prescription and consumption policy.
Incidence, susceptibility and outcomes of candidemia in adults living in Calgary, Alberta, Canada (2010–2018)
Authors: Bourassa-Blanchette Samuel , Biesheuvel Marit M. , Lam John C. , Kipp Alexander , Church Deirdre , Carson Julie , Dalton Bruce , Parkins Michael D. , Barkema Herman W. , Gregson Daniel B. 
Published: February 2023

Abstract
Background
Candidemia is increasing in frequency and is associated with high mortality. We sought to determine the burden of illness, the population it affects and its resistance profile in our region.

Methods
The Calgary Zone (CZ) provides all care for residents of Calgary and surrounding communities (~ 1.69 million) via five tertiary hospitals each served by a common single laboratory for acute care microbiology. All adult patients in the CZ with at least one Candida spp.-positive blood culture between January 1, 2010, and December 31, 2018, were identified using microbiological data from Calgary Lab Services, the laboratory that processes > 95% of all blood culture samples in the CZ, were reviewed for the study.

Results
The overall annual incidence of candidemia among individuals living in the CZ was 3.8 per 100,000 persons (Median age 61 years (IQR 48–72) and 221/455 (47.4%) were female). C. albicans was the most common species (50.6%), followed by C. glabrata, (24.0%). No other species accounted for more than 7% of cases. Overall mortality at 30, 90, and 365 days was 32.2, 40.1, and 48.1% respectively. Mortality rate did not differ by Candida species. Of individuals who developed candidemia, more than 50% died within the next year. No new resistance pattern has emerged in the most common Candida species in Calgary, Alberta.

Conclusions
In Calgary, Alberta, the incidence of candidemia has not increased in the last decade. C. albicans was the most common species and it remains susceptible to fluconazole.
Use machine learning to help identify possible sarcopenia cases in maintenance hemodialysis patients
Authors: Liao Hualong , Yang Yujie , Zeng Ying , Qiu Ying , Chen Yang , Zhu Linfang , Fu Ping , Yan Fei , Chen Yu , Yuan Huaihong 
Published: February 2023

Abstract
Background
Maintenance hemodialysis (MHD) patients often suffer from sarcopenia, which is strongly associated with their long-term mortality. The diagnosis and treatment of sarcopenia, especially possible sarcopenia for MHD patients are of great importance. This study aims to use machine learning and medical data to develop two simple sarcopenia identification assistant tools for MHD patients and focuses on sex specificity.

Methods
Data were retrospectively collected from patients undergoing MHD and included patients’ basic information, body measurement results and laboratory findings. The 2019 consensus update by Asian working group for sarcopenia was used to assess whether a MHD patient had sarcopenia. Finally, 140 male (58 with possible sarcopenia or sarcopenia) and 102 female (65 with possible sarcopenia or sarcopenia) patients’ data were collected. Participants were divided into sarcopenia and control groups for each sex to develop binary classifiers. After statistical analysis and feature selection, stratified shuffle split and Synthetic Minority Oversampling Technique were conducted and voting classifiers were developed.

Results
After eliminating handgrip strength, 6-m walk, and skeletal muscle index, the best three features for sarcopenia identification of male patients are age, fasting blood glucose, and parathyroid hormone. Meanwhile, age, arm without vascular access, total bilirubin, and post-dialysis creatinine are the best four features for females. After abandoning models with overfitting or bad performance, voting classifiers achieved good sarcopenia classification performance for both sexes (For males: sensitivity: 77.50% ± 11.21%, specificity: 83.13% ± 9.70%, F1 score: 77.32% ± 5.36%, the area under the receiver operating characteristic curves (AUC): 87.40% ± 4.41%. For females: sensitivity: 76.15% ± 13.95%, specificity: 71.25% ± 15.86%, F1 score: 78.04% ± 8.85%, AUC: 77.69% ± 7.92%).

Conclusions
Two simple sex-specific sarcopenia identification tools for MHD patients were developed. They performed well on the case finding of sarcopenia, especially possible sarcopenia.
Area postrema syndrome with linear enhancement along the surface of the brainstem and fourth ventricle in autoimmune GFAP astrocytopathy
Authors: Liang Xinming , Shen Yaoyao 
Published: February 2023

Abstract
Background
Glial fibrillary acidic protein (GFAP) astrocytopathy, a novel autoimmune disease of the nervous system, was first defined in 2016. To our knowledge, area postrema syndrome (APS) with linear enhancement along the surface of the brainstem and fourth ventricle is extremely rare in this disorder.

Case presentation
A Chinese woman presented with intractable nausea and vomiting after onset of flu-like symptoms. Brain magnetic resonance imaging (MRI) disclosed abnormal signal intensities in the dorsal medulla oblongata including area postrema. Besides, linear enhancement surrounding the surface of the brainstem and fourth ventricle was visualized after gadolinium injection. Cerebrospinal fluid (CSF) analysis showed increased cell count and protein. A cell-based assay was positive for anti-GFAP IgG in CSF. She was diagnosed with autoimmune GFAP astrocytopathy and treated with high-dose glucocorticoid. The patient received a quick recovery with entire resolution of the initial abnormalities.

Conclusions
Isolated APS can be the initial manifestation of autoimmune GFAP astrocytopathy. Linear enhancement surrounding the surface of the brainstem and fourth ventricle is another neuroradiological hallmark.
Application of the child community health inclusion index for measuring health inclusion of children with disabilities in the community: a feasibility study
Authors: Yejong Yoo Paul , Majnemer Annette , Wilton Robert , Ahmed Sara , Shikako Keiko 
Published: February 2023

Abstract
Background
Participation in the community is a fundamental human right for children with disabilities and is a key component of their health and development. Inclusive communities can enable children with disabilities to participate fully and effectively. The Child Community Health Inclusion Index (CHILD-CHII) is a comprehensive assessment tool developed to examine the extent to which community environments foster healthy, active living for children with disabilities.

Objectives
To assess the feasibility of applying the CHILD-CHII measurement tool across different community settings.

Methods
Participants recruited through maximal representation, and purposeful sampling from four community sectors (Health, Education, Public Spaces, Community Organizations) applied the tool on their affiliated community facility. Feasibility was examined by assessing length, difficulty, clarity, and value for measuring inclusion; each rated on a 5-point Likert scale. Participants provided comments for each indicator through the questionnaire and a follow-up interview.

Results
Of the 12 participants, 92% indicated that the tool was ‘long’ or ‘much too long’; 66% indicated that the tool was clear; 58% indicated that the tool was ‘valuable’ or ‘very valuable’. No clear consensus was obtained for the level of difficulty. Participants provided comments for each indicator.

Conclusion
Although the length of the tool was regarded as long, it was seen to be comprehensive and valuable for stakeholders in addressing the inclusion of children with disabilities in the community. The perceived value and the evaluators’ knowledge, familiarity, and access to information can facilitate use of the CHILD-CHII. Further refinement and psychometric testing will be conducted.