bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioLegato: a programmable, object-oriented graphic user interface
Authors: Alvare Graham , Roche-Lima Abiel , Fristensky Brian 
Published: August 2023

Abstract
Background
Biologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computing platforms. To resolve the tradeoff between analytical sophistication and usability, we have designed BioLegato, a programmable graphical user interface (GUI) for running external programs.

Results
BioLegato can run any program or pipeline that can be launched as a command. BioLegato reads specifications for each tool from files written in PCD, a simple language for specifying GUI components that set parameters for calling external programs. Thus, adding new tools to BioLegato can be done without changing the BioLegato Java code itself. The process is as simple as copying an existing PCD file and modifying it for the new program, which is more like filling in a form than writing code. PCD thus facilitates rapid development of new applications using existing programs as building blocks, and getting them to work together seamlessly.

Conclusion
BioLegato applies Object-Oriented concepts to the user experience by organizing applications based on discrete data types and the methods relevant to that data. PCD makes it easier for BioLegato applications to evolve with the succession of analytical tools for bioinformatics. BioLegato is applicable not only in biology, but in almost any field in which disparate software tools need to work as an integrated system.
Nonspecific intraventricular conduction delay predicts the prognosis of dilated cardiomyopathy
Authors: Yuan Yong , Yang Kai , Liu Qianjun , Song Weixiang , Jin Dongsheng , Zhao Shihua 
Published: August 2023

Abstract
Purpose
Left bundle branch block (LBBB) has been confirmed to be independently associated with adverse outcomes in dilated cardiomyopathy (DCM). However, prognostic data on nonspecific intraventricular conduction delay (NSIVCD) are still limited and conflicting. We aimed to evaluate the prognosis of DCM with NSIVCD.

Methods
A total of 548 DCM patients who underwent cardiovascular magnetic resonance imaging (CMR) from January 2016 to December 2017 were consecutively enrolled. The cohort was divided into four groups: 87 with LBBB, 27 with RBBB, 61 with NSIVCD, and 373 without intraventricular conduction delay (IVCD). After a median follow-up of 58 months (interquartile range: 47–65), 123 patients reached the composite endpoints, which included cardiovascular death, heart transplantation, and malignant arrhythmias. The associations between different patterns of IVCD and the outcomes of DCM were analysed by Kaplan‒Meier analysis and Cox proportional hazards regression analysis.

Results
Of 548 DCM patients, there were 398 males (72.6%), and the average age was 46 ± 15 years, ranging from 18 to 76 years. In Kaplan‒Meier analysis, patients with NSIVCD and LBBB showed higher event rates than patients without IVCD, while RBBB patients did not. By multivariate Cox regression analysis, LBBB, NSIVCD, NYHA class, left ventricular ejection fraction (LVEF), indexed left ventricular end-diastolic diameter (LVEDDI), percentage of late gadolinium enhancement mass (LGE%), and global longitudinal strain (GLS) were found to be independently associated with the outcomes of DCM.

Conclusions
In addition to LBBB, NSIVCD was an unfavourable prognostic marker in patients with DCM, independent of LVEDDI, NYHA class, LVEF, LGE%, and GLS.
Comparison of Bayesian Networks, G-estimation and linear models to estimate causal treatment effects in aggregated N-of-1 trials with carry-over effects
Authors: Gärtner Thomas , Schneider Juliana , Arnrich Bert , Konigorski Stefan 
Published: August 2023

Abstract
Background
The aggregation of a series of N-of-1 trials presents an innovative and efficient study design, as an alternative to traditional randomized clinical trials. Challenges for the statistical analysis arise when there is carry-over or complex dependencies of the treatment effect of interest.

Methods
In this study, we evaluate and compare methods for the analysis of aggregated N-of-1 trials in different scenarios with carry-over and complex dependencies of treatment effects on covariates. For this, we simulate data of a series of N-of-1 trials for Chronic Nonspecific Low Back Pain based on assumed causal relationships parameterized by directed acyclic graphs. In addition to existing statistical methods such as regression models, Bayesian Networks, and G-estimation, we introduce a carry-over adjusted parametric model (COAPM).

Results
The results show that all evaluated existing models have a good performance when there is no carry-over and no treatment dependence. When there is carry-over, COAPM yields unbiased and more efficient estimates while all other methods show some bias in the estimation. When there is known treatment dependence, all approaches that are capable to model it yield unbiased estimates. Finally, the efficiency of all methods decreases slightly when there are missing values, and the bias in the estimates can also increase.

Conclusions
This study presents a systematic evaluation of existing and novel approaches for the statistical analysis of a series of N-of-1 trials. We derive practical recommendations which methods may be best in which scenarios.
New evidence of trends in cognitive function among middle-aged and older adults in China, 2011-2018: an age-period-cohort analysis
Authors: Guo Shuai , Zheng Xiao-Ying 
Published: August 2023

Abstract
Background
Increasing evidence from high-income countries suggests the risk of cognitive impairment has been declining recently. However, related studies in China have rarely been done, and the results are inconsistent. We analyze the trends in cognitive function among middle-aged and older adults in China between 2011 and 2018.

Methods
We used data from four waves of the China Health and Retirement Longitudinal Study (CHARLS), including 48918 individuals aged 45 years and older. Cognitive function was assessed using the CHARLS cognitive measures containing episodic memory, orientation, attention, and visuospatial abilities. The hierarchical age-period-cohort (APC) model was used to quantify the separate age, period, and cohort effects on trends in cognitive function.

Results
The study sample’s ages ranged from 45 to 105 years (Mean = 59.2, SD = 9.4). Cognitive function declined with age net of period and cohort effects, an apparent acceleration in the rate of cognitive decline after age 65 was found adjusting for individual characteristics. Although period effects on trends in cognitive function remained stable during the study period, hierarchical APC models demonstrated significant cohort variations. Independent of age and period effects, there was a fluctuating trend across cohorts before 1960 and an overall decline across successive cohorts.

Conclusions
Our study indicates that the age effect remains the most crucial factor regarding cognitive decline. Moreover, results demonstrate that cohorts living in social upheaval leading to educational deprivation and/or nutritional deficiency in early life may face a higher risk for cognitive deterioration later in life. Such findings indicate that dementia prevention from a life course perspective and cohort-specific strategies are critical to alleviating the future public-health burdens related to cognitive aging. Ongoing attention should be paid to the role of cross-cohort differences in education on cohort trends in cognition in countries like China that are aging rapidly and have a late start in educational expansion compared to other countries. Other factors, such as environmental stimulation, need to be noticed in younger cohorts.
Study protocol of a cluster-randomised controlled trial assessing a multimodal machine-based exercise training programme in senior care facilities over 6 months – the bestform study (best function of range of motion)
Authors: Siegrist M. , Schaller N. , Weiß M. , Isaak J. , Schmid V. , Köppel E. , Weichenberger M. , Mende E. , Haller B. , Halle M. 
Published: August 2023

Abstract
Background
Physical functioning is a crucial factor for independence and quality of life in old age. The aim of the "bestform—Best function of range of motion" trial is to investigate the effects of a 6 months multimodal machine-based strength, coordination and endurance training on physical function, risk of falls and health parameters in older adults.

Methods
Bestform is a cluster-randomised trial including older adults  ≥ 65 years living in senior care facilities in Southern Germany. Senior care facilities are randomly allocated to the control group with usual care (n ≥ 10 care facilities) and to the intervention group (n ≥ 10 care facilities), overall including  ≥ 400 seniors. Residents belonging to the intervention group are offered a supervised machine-based exercise training programme twice weekly over 45–60 min over six months in small groups, while those in the usual care facilities will not receive active intervention. The primary outcome is the change in Short Physical Performance Battery over six months between groups. Secondary outcomes are change in risk of falling, fear of falling, number of falls and fall-related injuries, physical exercise capacity, handgrip strength, body composition, cardiac function, blood parameters, quality of life, risk of sarcopenia, activities of daily living, and cognition over three and six months.

Discussion
The bestform study investigates the change in physical function between seniors performing exercise intervention versus usual care over six months. The results of the study will contribute to the development of effective physical activity concepts in senior care facilities.

Trial registration
ClinicalTrials.gov: NCT04207307. Registered December 2019.
The metabolic consequences of HIV/TB co-infection
Authors: Herbert Chandré , Luies Laneke , Loots Du Toit , Williams Aurelia A. 
Published: August 2023

Abstract
Background
The synergy between the human immunodeficiency virus (HIV) and Mycobacterium tuberculosis during co-infection of a host is well known. While this synergy is known to be driven by immunological deterioration, the metabolic mechanisms that contribute to the associated disease burden experienced during HIV/tuberculosis (TB) co-infection remain poorly understood. Furthermore, while anti-HIV treatments suppress viral replication, these therapeutics give rise to host metabolic disruption and adaptations beyond that induced by only infection or disease.

Methods
In this study, the serum metabolic profiles of healthy controls, untreated HIV-negative TB-positive patients, untreated HIV/TB co-infected patients, and HIV/TB co-infected patients on antiretroviral therapy (ART), were measured using two-dimensional gas chromatography time-of-flight mass spectrometry. Since no global metabolic profile for HIV/TB co-infection and the effect of ART has been published to date, this pilot study aimed to elucidate the general areas of metabolism affected during such conditions.

Results
HIV/TB co-infection induced significant changes to the host’s lipid and protein metabolism, with additional microbial product translocation from the gut to the blood. The results suggest that HIV augments TB synergistically, at least in part, contributing to increased inflammation, oxidative stress, ART-induced mitochondrial damage, and its detrimental effects on gut health, which in turn, affects energy availability. ART reverses these trends to some extent in HIV/TB co-infected patients but not to that of healthy controls.

Conclusion
This study generated several new hypotheses that could direct future metabolic studies, which could be combined with other research techniques or methodologies to further elucidate the underlying mechanisms of these changes.
Fully automated film mounting in dental radiography: a deep learning model
Authors: Lin Yu-Chun , Chen Meng-Chi , Chen Cheng-Hsueh , Chen Mu-Hsiung , Liu Kang-Yi , Chang Cheng-Chun 
Published: August 2023

Abstract
Background
Dental film mounting is an essential but time-consuming task in dental radiography, with manual methods often prone to errors. This study aims to develop a deep learning (DL) model for accurate automated classification and mounting of both intraoral and extraoral dental radiography.

Method
The present study employed a total of 22,334 intraoral images and 1,035 extraoral images to train the model. The performance of the model was tested on an independent internal dataset and two external datasets from different institutes. Images were categorized into 32 tooth areas. The VGG-16, ResNet-18, and ResNet-101 architectures were used for pretraining, with the ResNet-101 ultimately being chosen as the final trained model. The model’s performance was evaluated using metrics of accuracy, precision, recall, and F1 score. Additionally, we evaluated the influence of misalignment on the model’s accuracy and time efficiency.

Results
The ResNet-101 model outperformed VGG-16 and ResNet-18 models, achieving the highest accuracy of 0.976, precision of 0.969, recall of 0.984, and F1-score of 0.977 (p < 0.05). For intraoral images, the overall accuracy remained consistent across both internal and external datasets, ranging from 0.963 to 0.972, without significant differences (p = 0.348). For extraoral images, the accuracy consistently achieved the highest value of 1 across all institutes. The model’s accuracy decreased as the tilt angle of the X-ray film increased. The model achieved the highest accuracy of 0.981 with correctly aligned films, while the lowest accuracy of 0.937 was observed for films exhibiting severe misalignment of ± 15° (p < 0.001). The average time required for the tasks of image rotation and classification for each image was 0.17 s, which was significantly faster than that of the manual process, which required 1.2 s (p < 0.001).

Conclusion
This study demonstrated the potential of DL-based models in automating dental film mounting with high accuracy and efficiency. The proper alignment of X-ray films is crucial for accurate classification by the model.
A marked elevation in serum creatinine/cystatin C ratio may indicate pseudo-acute kidney injury due to urinary ascites: a case report and literature review
Authors: Jiang Ran , Huang Yumin , Zeng Ming , Xing Changying , Mao Huijuan , Wu Buyun 
Published: August 2023

Abstract
Background
Urinary ascites represents a scarcely observed pseudo-acute kidney injury in clinical settings. Protracted or missed diagnosis may hold grave ramifications for patient outcomes.

Case presentation
We reported a case involving an elderly female patient experiencing pseudo-acute kidney injury accompanied by ascites, wherein her renal dysfunction persisted despite medical intervention and hemodialysis. Urinary ascites was identified via a methylene blue test and by contrasting creatinine levels in serum and ascites. This patient’s kidney function was multiple typified by a marked elevation in serum creatinine/Cystatin C ratio (> 2 L/dL), potentially serving as a clue for the clinical diagnosis of pseudo-acute kidney injury engendered by urinary ascites.

Conclusions
This case suggested the potential diagnostic value of an asynchronous increase in serum creatinine and serum CysC (or an increased ratio of blood creatinine to blood CysC) in patients with pseudo-acute kidney injury.
Estimating cancer incidence in Uganda: a feasibility study for periodic cancer surveillance research in resource limited settings
Authors: Nakaganda Annet , Spencer Angela , Orem Jackson , Mpamani Collins , Wabinga Henry , Nambooze Sarah , Kiwanuka Gertrude N. , Atwine Raymond , Gemmell Isla , Jones Andrew , Verma Arpana 
Published: August 2023

Abstract
Background
Population based cancer registries (PBCRs) are accepted as the gold standard for estimating cancer incidence in any population. However, only 15% of the world’s population is covered by high quality cancer registries with coverage as low as 1.9% in settings such as Africa. This study was conducted to assess the operational feasibility of estimating cancer incidence using a retrospective “catchment population” approach in Uganda.

Methods
A retrospective population study was conducted in 2018 to identify all newly diagnosed cancer cases between 2013 and 2017 in Mbarara district. Data were extracted from the medical records of health facilities within Mbarara and from national and regional centres that provide cancer care services. Cases were coded according to the International Classification of Diseases for Oncology (ICD-0-03). Data was analysed using CanReg5 and Excel.

Results
We sought to collect data from 30 health facilities serving Mbarara district, southwestern Uganda. Twenty-eight sources (93%) provided approval within the set period of two months. Among the twenty-eight sources, two were excluded, as they did not record addresses for cancer cases, leaving 26 sources (87%) valid for data collection. While 13% of the sources charged a fee, ranging from $30 to $100, administrative clearance and approval was at no cost in most (87%) data sources. This study registered 1,258 new cancer cases in Mbarara district. Of the registered cases, 65.4% had a morphologically verified diagnosis indicating relatively good quality of data. The Age-Standardised Incidence Rates for all cancers combined were 109.9 and 91.9 per 100,000 in males and females, respectively. In males, the most commonly diagnosed cancers were prostate, oesophagus, stomach, Kaposi’s sarcoma and liver. In females, the most common malignancies were cervix uteri, breast, stomach, liver and ovary. Approximately, 1 in 8 males and 1 in 10 females would develop cancer in Mbarara before the age of 75 years.

Conclusion
Estimating cancer incidence using a retrospective cohort design and a “catchment population approach” is feasible in Uganda. Periodic studies using this approach are potentially a precious resource for producing quality cancer data in settings where PBCRs are scarce. This could supplement PBCR data to provide a detailed and comprehensive picture of the cancer burden over time, facilitating the direction of cancer control efforts in resource-limited countries.
Traumatic dislocation of the iris into the vitreous cavity with intact lens: a case report
Authors: Xie Hai-Nan , Chen Lan-Lan , Wang Rui , Zhu Zhi-Hong , Huang Hou-Bin 
Published: August 2023

Abstract
Background
Traumatic aniridia occurs when the iris is extruded from the eye and is often accompanied by lens injuries. However, traumatic aniridia due to dislocation of the iris into the vitreous cavity without lens damage has never been reported.

Case presentation
A 30-year-old man presented with visual loss and pain for 6 h after a thin wire injured his right eyeball. Ophthalmologic examinations manifested a 2 mm full-thickness corneal laceration and total hyphema. An intact clear lens, healthy attached retina, and almost complete iris tissue in the vitreous cavity were found after resolution of hyphema the next day. Further examination revealed that the defect in the zonule below the corneal wound was the path for the iris to enter the vitreous cavity. The patient opted for nonsurgical treatment until pigment granules and opacity were observed in the vitreous cavity after 50 days. Vitrectomy was performed to remove the dislocated iris.

Conclusions
The presentation of this unique case indicates that the torn iris was displaced to the vitreous cavity with an intact lens and missing local zonula instead of out the corneal laceration after a penetrating injury. The type of injury, mechanism, and force on the spot may contribute to the occurrence of this rare condition. Instead of artificial irises, tinted glasses were more appropriate treatment option for this patient. Peripheral retinal examination was essential in the management of this case. In such cases, the iris in the vitreous cavity should be resected to prevent complications.
Harsh parenting and suicide ideation among Chinese adolescents: the roles of self-esteem and school social support
Authors: Zhao Jingfei , Wang Yulong 
Published: August 2023

AbstractBackgroundWhile negative parenting style has considered as a risk factor for suicide ideation, little attention has been given to the mechanisms between harsh parenting and suicide ideation in the context of Chinese culture. This study explored the the potential mediating roles of self-esteem and the potential moderating roles of school social support in the relationship between harsh parenting and suicide ideation among Chinese adolescents.MethodsWe conducted a cross-sectional study among 4189 Chinese adolescents who completed measures of harsh parenting, school social support, self-esteem, and suicide ideation. The moderated mediation model was used to test the roles of self-esteem and school social support on the association between harsh parenting and adolescent suicide ideation.Results(1) There were significant positive correlations between harsh parenting and adolescents suicide ideation. (2) Self-esteem mediates the relationship between harsh parenting and suicide ideation in adolescents. (3) School social support moderates the indirect effect of harsh parenting on suicidal ideation.ConclusionsBeyond the direct impact of harsh parenting, harsh parenting also indirectly contributes to adolescent suicide ideation via the mediator of adolescents’ self-esteem. School social support moderates the relationship between harsh parenting and self-esteem as well as the relationship between self-esteem and suicide ideation. The findings suggest potential pathways for suicide prevention and intervention strategies and highlighted that buffering effect of school social support is limited as risk increasing.