bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of uniformity in coronary artery enhancement using a bolus tracking technique with a dual region of interest in coronary computed tomographic angiography
Authors: Xiao Huawei , Wang Xiangquan , Yang Panfeng , Wang Ling , Xu Jian 
Published: December 2023

Background Consistent coronary artery enhancement is essential to achieve accurate and reproducible quantification of coronary plaque composition. Purpose To optimize coronary artery uniformity of enhancement using a bolus tracking technique with a dual region of interest (ROI) in coronary computed tomography angiography (CCTA) on a 320-detector CT scanner. Material and Methods This prospective study recruited 100 consecutive patients who underwent CCTA and were randomly divided into two groups, namely, a manual trigger group (n = 50), in which a manual fast start technique was used to start the diagnostic scan with the visual evaluation of attenuation in the left atrium and left ventricle, and an automatic trigger group (n = 50), in which a bolus tracking technique was used to automatically start the breath-holding command and diagnostic scan with two ROIs placed in the right and left ventricles. Coronary artery image quality was assessed using quantitative and qualitative scores. The enhancement uniformity was characterized by attenuation variability of the ascending aorta (AAO) and coronary arteries. Results No statistically significant differences in the image quality of the coronary arteries were observed between the two groups (all P > 0.05). The coefficients of variation (COVs) of arterial attenuation in the automatic trigger group were significantly smaller than in the manual trigger group (AAO: 9.89% vs. 17.93%; LMA: 10.35% vs. 18.98%; LAD proximal: 12.09% vs. 20.84%; LCX proximal: 11.85% vs. 20.95%; RCA proximal: 12.13% vs. 20.84%; all P < 0.05). Conclusion The automatic trigger technique accompanied with dual ROI provides consistent coronary artery enhancement and optimizes coronary artery enhancement uniformity in CCTA on a 320-detector CT scanner.
Enhancing Bone Cancer Diagnosis Through Image Extraction and Machine Learning: A State-of-the-Art Approach
Authors: Shrivastava Abhishek , Nag Mukesh Kumar 
Published: December 2023

Background: Bone cancer is a severe condition often leading to patient mortality. Diagnosis relies on X-rays, MRIs, or CT scans, which require time-consuming manual review by experts. Thus, developing an automated system is crucial for accurate classification of malignant and healthy bone. Methods: Differentiating between them poses a challenge as they may exhibit similar physical characteristics. The initial step is selecting the optimal edge detection method. Two feature sets are then generated: one with the histogram of oriented gradients (HOG) and one without. Performance evaluation involves two machine learning models: Support Vector Machine (SVM) and Random Forest. Results: Including HOG consistently yields superior results. The SVM model with HOG achieves an F-1 score of 0.92, outperforming the Random Forest model’s .77. This study aims to develop reliable methods for bone cancer classification. The proposed automated method assists surgeons in accurately detecting malignant bone regions using modern image analysis techniques and machine learning models. Incorporating HOG significantly enhances performance, improving differentiation between malignant and healthy bone. Conclusion: Ultimately, this approach supports precise diagnoses and informed treatment decisions for bone cancer patients.
pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods
Authors: Behdenna Abdelkader , Colange Maximilien , Haziza Julien , Gema Aryo , Appé Guillaume , Azencott Chloé-Agathe , Nordor Akpéli 
Published: December 2023

Abstract
Background
Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data.

Results
In this technical note, we present a new Python implementation of ComBat and ComBat-Seq. While the mathematical framework is strictly the same, we show here that our implementations: (i) have similar results in terms of batch effects correction; (ii) are as fast or faster than the original implementations in R and; (iii) offer new tools for the bioinformatics community to participate in its development. pyComBat is implemented in the Python language and is distributed under GPL-3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html) license as a module of the inmoose package. Source code is available at https://github.com/epigenelabs/inmoose and Python package at https://pypi.org/project/inmoose.

Conclusions
We present a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq for the correction of batch effects in microarray and RNA-Seq data. This new implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq, offers similar power for batch effect correction, at reduced computational cost.
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Authors: Xu Xuechun , Bhalla Nayanika , Ståhl Patrik , Jaldén Joakim 
Published: December 2023

Abstract
Background
Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov models (HMMs) that relied on pre-segmenting ion current measurements. However, the CTC-RNN model operates independently of prior biological and physical insights.

Results
We present a novel basecaller named Lokatt: explicit duration Markov model and residual-LSTM network. It leverages an explicit duration HMM (EDHMM) designed to model the nanopore sequencing processes. Trained on a newly generated library with methylation-free Ecoli samples and MinION R9.4.1 chemistry, the Lokatt basecaller achieves basecalling performances with a median single read identity score of 0.930, a genome coverage ratio of 99.750%, on par with existing state-of-the-art structure when trained on the same datasets.

Conclusion
Our research underlines the potential of incorporating prior knowledge into the basecalling processes, particularly through integrating HMMs and recurrent neural networks. The Lokatt basecaller showcases the efficacy of a hybrid approach, emphasizing its capacity to achieve high-quality basecalling performance while accommodating the nuances of nanopore sequencing. These outcomes pave the way for advanced basecalling methodologies, with potential implications for enhancing the accuracy and efficiency of nanopore-based DNA sequencing protocols.
Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress
Authors: Ma Li , Tao Xiaolei , Wang Wangtian , Jiao Jintang , Pu Yuanyuan , Yang Gang , Liu Lijun , Fang Yan , Wu Junyan , Sun Wancang 
Published: December 2023

Abstract
Background
The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability.

Results
In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I–XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars ‘Longyou 7’ and ‘Longyou 99’ following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the ‘Longyou 7’ variety were found to be significantly higher than those observed in the ‘Longyou 99’ variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana.

Conclusions
This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.
Solitary atrial Rhabdomyoma in an infant with tuberous sclerosis: a case report and review of the literature
Authors: Jawad Ali , Hannouneh Zein Alabdin , Salame Hadi , Jaber Rida , Eid Nader 
Published: December 2023

Abstract
Background
Despite its rare incidence of 1/40,000, fetal cardiac rhabdomyoma (CR) represents the prevailing type of benign cardiac fetal tumors, which commonly affects the ventricles. Fetal CRs rarely occur in the right atrium. Thus, the presentation of atrial fibrillation and premature atrial contractions (PAC) due to a solitary cardiac rhabdomyoma is an extremely rare scenario. Our literature review found that only 2% (1 out of 61) of rhabdomyoma cases were found in the right atrium. The majority of fetal cardiac rhabdomyomas are associated with tuberous sclerosis complex (TSC).

Case presentation
A 7-day-old male neonate presented with arrhythmias and an atrial mass for further evaluation. Echocardiography revealed a hyperechoic, round, uniform right atrial mass (25 mm). An abdominal and testicular ultrasound showed multiple thin-walled cortical cysts in both kidneys and a scrotal hydrocele, respectively. His laboratory workup was insignificant except for hypomagnesemia. Electrocardiography revealed junctional rhythm and PACs with wave distortions. A brain magnetic resonance imaging scan revealed multiple subependymal lesions on the frontal and occipital horns of the lateral ventricles. These findings (Fig. 1), along with a family history of TSC, confirmed the diagnosis of TSC with associated CR. The patient was treated symptomatically with an anti-convulsant and monitored with regular follow-ups. Surgical resection was not required.

Conclusion
Despite CR’s predominance in the ventricles, a diagnosis of rhabdomyoma should be kept in mind in the presence of a solitary atrial mass and PACs. Physicians should evaluate systemic findings related to TSC and provide appropriate follow-up and family screening. Surgical resection is not always required, and symptom management can be achieved through medical treatment alone.
On the use of multiple imputation to address data missing by design as well as unintended missing data in case-cohort studies with a binary endpoint
Authors: Middleton Melissa , Nguyen Cattram , Carlin John B. , Moreno-Betancur Margarita , Lee Katherine J. 
Published: December 2023

Abstract
Background
Case-cohort studies are conducted within cohort studies, with the defining feature that collection of exposure data is limited to a subset of the cohort, leading to a large proportion of missing data by design. Standard analysis uses inverse probability weighting (IPW) to address this intended missing data, but little research has been conducted into how best to perform analysis when there is also unintended missingness. Multiple imputation (MI) has become a default standard for handling unintended missingness and is typically used in combination with IPW to handle the intended missingness due to the case-control sampling. Alternatively, MI could be used to handle both the intended and unintended missingness. While the performance of an MI-only approach has been investigated in the context of a case-cohort study with a time-to-event outcome, it is unclear how this approach performs with a binary outcome.

Methods
We conducted a simulation study to assess and compare the performance of approaches using only MI, only IPW, and a combination of MI and IPW, for handling intended and unintended missingness in the case-cohort setting. We also applied the approaches to a case study.

Results
Our results show that the combined approach is approximately unbiased for estimation of the exposure effect when the sample size is large, and was the least biased with small sample sizes, while MI-only and IPW-only exhibited larger biases in both sample size settings.

Conclusions
These findings suggest that a combined MI/IPW approach should be preferred to handle intended and unintended missing data in case-cohort studies with binary outcomes.
Prevalence of obesity, hypertension and diabetes among people living with HIV in South Africa: a systematic review and meta-analysis
Authors: Gizamba Jacob M. , Davies Jess , Africa Chad , Choo-Kang Candice , Goedecke Julia H. , Madlala Hlengiwe , Lambert Estelle V. , Rae Dale E. , Myer Landon , Luke Amy , Dugas Lara R. 
Published: December 2023

Abstract
Background
HIV has become a manageable chronic condition due to the success and scale-up of antiretroviral therapy (ART). Globally, South Africa has the highest number of people living with HIV (PLHIV) and research evidence indicates that countries with the highest burden of PLHIV have a substantial burden of obesity, hypertension (HPT) and type 2 diabetes (T2D). We sought to summarize the burden of these three common NCDs among PLHIV in South Africa.

Methods
In this systematic review, multiple databases were searched for articles reporting on the prevalence of obesity, HPT, and T2D among PLHIV in South Africa published since journal inception until March 2022. A meta-analysis was conducted using random-effects models to obtain pooled prevalence estimates of the three NCDs. Heterogeneity was assessed using X2 test on Cochran’s Q statistic.

Results
We included 32 studies, with 19, 22 and 18 studies reporting the prevalence of obesity, HPT, and T2D among PLHIV, respectively. The overall prevalence of obesity, HPT, and T2D was 23.2% [95% CI 17.6; 29.9], 25.5% [95% CI 15.6; 38.7], and 6.1% [95% CI 3.8; 9.7] respectively. The prevalence of obesity was significantly higher among women (P = 0.034) compared to men, however the prevalence of HPT and T2D did not differ by sex. The prevalence of each of the three NCDs did not differ significantly between rural, urban, and peri-urban areas. The prevalence of obesity and T2D was higher in studies conducted between 2013 and 2022 compared to studies conducted between 2000 and 2012, while the prevalence of HPT was higher between 2000 and 2012 compared to between 2013 and 2022.

Conclusions
These findings suggest that South Africa is experiencing a syndemic of NCDs among people PLHIV highlighting the need to increase cost-effective interventions and management strategies that involve integrated HIV and NCD care in the South African setting.
Associations of Wnt5a expression with liver injury in chronic hepatitis B virus infection
Authors: Ji Xiang-Fen , Zhou Qi , Wang Jing-Wei , Sun Fei , Gao Shuai , Wang Kai 
Published: December 2023

Abstract
Background
Aberrant Wnt5a expression contributes to immunity, inflammation and tissue damage. However, it remains unknown whether Wnt5a is associated with liver injury in chronic hepatitis B virus (HBV) infection. We aimed to explore the potential role of Wnt5a expression in liver injury caused by chronic HBV infection.

Methods
Wnt5a mRNA levels in peripheral blood mononuclear cells (PBMCs) were analyzed in 31 acute-on-chronic hepatitis B liver failure (ACHBLF) patients, 82 chronic hepatitis B (CHB) patients, and 20 healthy controls using quantitative real-time polymerase chain reaction. Intrahepatic Wnt5a protein expression from 32 chronic HBV infection patients and 6 normal controls was evaluated by immunohistochemical staining.

Results
Wnt5a mRNA expression was increased in CHB patients and ACHBLF patients compared to healthy controls and correlated positively with liver injury markers. Additionally, there was a significant correlation between Wnt5a mRNA expression and HBV DNA load in all patients and CHB patients but not in ACHBLF patients. Furthermore, intrahepatic Wnt5a protein expression was elevated in chronic HBV infection patients compared to that in normal controls. Moreover, chronic HBV infection patients with higher hepatic inflammatory grades had increased intrahepatic Wnt5a protein expression compared with lower hepatic inflammatory grades. In addition, the cut-off value of 12.59 for Wnt5a mRNA level was a strong indicator in predicting ACHBLF in CHB patients.

Conclusions
We found that Wnt5a expression was associated with liver injury in chronic HBV infection patients. Wnt5a might be involved in exacerbation of chronic HBV infection.
Luteibacter jiangsuensis blood stream infection: a first case report
Authors: Horiguchi Takanori , Sumiyoshi Makoto , Nagatomo Eri , Sakamoto Kazuki , Ogawa Souichiro , Ichinari Naoki , Yamada Akiteru , Rikitake Yuki , Iwao Chihiro , Kawaguchi Takeshi , Umekita Kunihiko , Takajo Ichiro , Yamamoto Shojiro , Miyazaki Taiga 
Published: December 2023

Abstract
Background
Luteibacter jiangsuensis is a gram-negative aerobic bacillus that was first isolated from soil samples at a pesticide factory in China and reported in 2011. Here, we describe the first case of L. jiangsuensis infection in human.

Case presentation
A 59-year-old Japanese woman undergoing treatment for Crohn’s disease was admitted to our hospital with fever. Clinical examination indicated catheter-related bloodstream infection. The catheter was removed and meropenem was initiated. Morphologically identical glucose non-fermentative gram-negative bacilli were detected from two sets of aerobic blood culture and catheter-tip cultures. MALDI-TOF mass spectrometry failed to identify the bacterium, which was later identified as L. jiangsuensis by 16 S rRNA gene sequencing. Antimicrobial susceptibility test revealed that the isolate was resistant to carbapenem, therefore meropenem was switched to intravenous levofloxacin (500 mg/day). After 14 days of treatment with levofloxacin, the patient was discharged.

Conclusions
This is the first case of L. jiangsuensis infection in human. The strain was identified by 16 S rRNA gene sequence analysis.
Validation of the phenol red thread test in a Chinese population
Authors: Hao Yiran , Jin Tao , Zhu Lei , Zhao Mengnan , Wang Silu , Li Zhongying , Tian Lei , Jie Ying 
Published: December 2023

Abstract
Background
To investigate the validation of phenol red thread (PRT) test in a Chinese population by evaluating the intraobserver repeatability and interobserver reproducibility, determining correlations between the PRT test and other dry eye disease (DED) parameters including tear meniscus height (TMH) and Schirmer I test, and testing the accuracy of diagnosing DED when using the PRT test alone.

Methods
A total of 108 eyes were involved in this prospective and diagnostic study, and were divided into two groups (with and without DED). Each subject underwent a series of ocular surface examinations, including Ocular Surface Disease Index (OSDI) questionnaire, non-invasive tear breakup time (NIBUT), tear meniscus height (TMH) assessment, PRT test, fluorescein tear breakup time (FBUT), corneal fluorescein staining and Schirmer I test.

Results
In the experimental group and the control group, the intra-class correlation coefficients (ICCs) of the repeatability were 0.747 and 0.723, respectively (all P < 0.05). The ICCs of the reproducibility in both groups were 0.588 and 0.610, respectively (all P < 0.05). The PRT test correlated weakly with the Schirmer I test and the tear meniscus height, with Spearman coefficients of 0.385 and 0.306, respectively (all P < 0.05). The PRT test is available to diagnose DED, with an area under the curve of 0.806 and a Youden index of 0.556 at the cutoff point of 8.83 mm.

Conclusions
The PRT test can provide patients a comfortable, timesaving and less irritating approach to screening and diagnosing DED compared to Schirmer I test.
Age and sex-related comparison of referral-based telemedicine service utilization during the COVID-19 pandemic in Ontario: a retrospective analysis
Authors: Wong Hubert , Razvi Yasmeen , Hamid Muhammad Akhter , Mistry Niraj , Filler Guido 
Published: December 2023

Abstract
Background
The COVID-19 pandemic has led to increased utilization of telemedicine services.

Methods
A retrospective analysis of all referral-based ambulatory telemedicine services in Ontario from November 2019 to June 2021 was collected from the Ontario Health Insurance Plan (OHIP) billing database. Only fee-for-service billings were included in the present analysis. Coincident COVID-19 cases were obtained from Public Health Ontario. Comparisons were made based on age bracket, sex, telemedicine and in-person care.

Results
Billings for telemedicine services in Ontario increased from $1.7 million CAD in November 2019 to $64 million CAD in April 2020 and the proportions reached a mean peak of 72% in April 2020 and declined to 46% in June 2021. A positive correlation was found between the use of telemedicine and COVID-19 cases (p = 0.05). The age group with the highest proportion of telemedicine use was the 10–20-year-olds, followed by the 20–50-year-olds (61 ± 9.0%, 55 ± 7.3%, p = 0.01). Both age groups remained above 50% telemedicine services at the end of the study period. There seemed to be higher utilization by females (females 54.2 ± 8.0%, males 47.9 ± 7.7%, ANCOVA p = 0.05) for all specialties, however, after adjusting for male to female ratio m:f of 0.952:1.0 according to the 2016 census, this was no longer significant.

Conclusions
The use of telemedicine services remained at a high level across groups, particularly the 10–50-year-olds. There were clear age preferences for using telemedicine. Studying these differences may provide insights into how the delivery of non-hospital-based medicine has changed during the COVID-19 pandemic.