bluuebunny/crossref_metadata_2025_split huggingface dataset:
iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model
Authors: Peng Binchao , Sun Guicong , Fan Yongxian 
Published: June 2024

AbstractPromoters are essential elements of DNA sequence, usually located in the immediate region of the gene transcription start sites, and play a critical role in the regulation of gene transcription. Its importance in molecular biology and genetics has attracted the research interest of researchers, and it has become a consensus to seek a computational method to efficiently identify promoters. Still, existing methods suffer from imbalanced recognition capabilities for positive and negative samples, and their recognition effect can still be further improved. We conducted research on E. coli promoters and proposed a more advanced prediction model, iProL, based on the Longformer pre-trained model in the field of natural language processing. iProL does not rely on prior biological knowledge but simply uses promoter DNA sequences as plain text to identify promoters. It also combines one-dimensional convolutional neural networks and bidirectional long short-term memory to extract both local and global features. Experimental results show that iProL has a more balanced and superior performance than currently published methods. Additionally, we constructed a novel independent test set following the previous specification and compared iProL with three existing methods on this independent test set.
Diabetes mellitus and risk of incident dementia in APOE ɛ4 carriers: an updated meta-analysis
Authors: Rashtchian Ava , Etemadi Mohammad Hossein , Asadi Elham , Binaei Sara , Abbasi Mina , Bayani Maedeh , Izadi Erfan , Sadat-Madani Sayedeh-Fatemeh , Naziri Mahdyieh , khoshravesh Sahar , shirani Mahsa , Asadi Anar Mahsa , Deravi Niloofar 
Published: June 2024

Abstract
Background and aim
Diabetes raises the risk of dementia, mortality, and cognitive decline in the elderly, potentially because of hereditary variables such as APOE. In this study, we aim to evaluate Diabetes mellitus and the risk of incident dementia in APOE ɛ4 carriers.

Method
We thoroughly searched PubMed (Medline), Scopus, and Google Scholar databases for related articles up to September 2023. The titles, abstracts, and full texts of articles were reviewed; data were extracted and analyzed.

Result
This meta-analysis included nine cohorts and seven cross-sectional articles with a total of 42,390 population. The study found that APOE ɛ4 carriers with type 2 diabetes (T2D) had a 48% higher risk of developing dementia compared to non-diabetic carriers (Hazard Ratio;1.48, 95%CI1.36–1.60). The frequency of dementia was 3 in 10 people (frequency: 0.3; 95%CI (0.15–0.48). No significant heterogeneity was observed. Egger’s test, which we performed, revealed no indication of publication bias among the included articles (p = 0.2).

Conclusion
Overall, diabetes increases the risk of dementia, but further large-scale studies are still required to support the results of current research.
Perceived but not objective measures of neighborhood safety and food environments are associated with longitudinal changes in processing speed among urban older adults
Authors: Hyun Jinshil , Lovasi Gina S. , Katz Mindy J. , Derby Carol A. , Lipton Richard B. , Sliwinski Martin J. 
Published: June 2024

Abstract
Background
Although a growing body of literature documents the importance of neighborhood effects on late-life cognition, little is known about the relative strength of objective and subjective neighborhood measures on late-life cognitive changes. This study examined effects of objective and subjective neighborhood measures in three neighborhood domains (neighborhood safety, physical disorder, food environments) on longitudinal changes in processing speed, an early marker of cognitive aging and impairment.

Methods
The analysis sample included 306 community-dwelling older adults enrolled in the Einstein Aging Study (mean age = 77, age range = 70 to 91; female = 67.7%; non-Hispanic White: 45.1%, non-Hispanic Black: 40.9%). Objective and subjective measures of neighborhood included three neighborhood domains (i.e., neighborhood safety, physical disorder, food environments). Processing speed was assessed using a brief Symbol Match task (unit: second), administered on a smartphone device six times a day for 16 days and repeated annually for up to five years. Years from baseline was used as the within-person time index.

Results
Results from mixed effects models showed that subjective neighborhood safety (β= -0.028) and subjective availability of healthy foods (β= -0.028) were significantly associated with less cognitive slowing over time. When objective and subjective neighborhood measures were simultaneously examined, subjective availability of healthy foods remained significant (β= -0.028) after controlling for objective availability of healthy foods. Associations of objective neighborhood crime and physical disorder with processing speed seemed to be confounded by individual-level race and socioeconomic status; after controlling for these confounders, none of objective neighborhood measures showed significant associations with processing speed.

Conclusion
Subjective neighborhood safety and subjective availability of healthy foods, rather than objective measures, were associated with less cognitive slowing over time over a five-year period. Perception of one’s neighborhood may be a more proximal predictor of cognitive health outcomes as it may reflect one’s experiences in the environment. It would be important to improve our understanding of both objective and subjective neighborhood factors to improve cognitive health among older adults.
Measuring pain intensity in older patients: a comparison of five scales
Authors: Nimmaanrat Sasikaan , Thepsuwan Arpawan , Tipchatyotin Suttipong , Jensen Mark P. 
Published: June 2024

Abstract
Background and aims
Pain is common in older individuals. In order to understand and treat pain in this group, reliable and valid measures are needed. This study aimed to evaluate: (1) the validity, utility, incorrect response rates and preference rates of 5 pain rating scales in older individuals; and (2) the associations between age, education level, and cognitive function and both (a) incorrect response and (b) preference rates.

Methods
Two hundred and one orthopedic clinic outpatients ≥ 65 years old were asked to rate their current pain, and least, average, and worst pain intensity in the past week using 5 scales: Verbal Numerical Rating Scale (VNRS), Faces Pain Scale - Revised (FPS-R), Verbal Rating Scale (VRS), Numerical Rating Scale (NRS), and Visual Analogue Scale (VAS). Participants were also asked to indicate scale preference. We computed the associations between each measure and a factor score representing the shared variance among the scales, the incorrect response and scale preference rates, and the associations between incorrect response and preference rates and age, education level, and cognitive function. The incorrect responses included being unable to respond, providing more than one response, responses outside a range, providing range answers rather than fixed answers, and responses indicating ‘least > average,’ ‘least > worst,’ and ‘average > worst’.

Results
The findings support validity of all 5 scales in older individuals who are able to use all measures. The VNRS had the lowest (2%) and the VAS had the highest (6%) incorrect response rates. The NRS was the most (35%) and the VAS was the least (5%) preferred. Age was associated with the incorrect response rates of the VRS and VAS, such that older individuals were less likely to use these scales correctly. Education level was associated with the incorrect response rates of the FPS-R, NRS and VAS, such that those with less education were less likely to use these measures correctly. Cognitive function was not significantly associated with incorrect response rates. Age, education level and cognitive function were not significantly associated with scale preference.

Conclusions
Although all five scales are valid, the VNRS evidences the best overall utility in this sample of older individuals with pain. The NRS or FPS-R would be fine alternatives if it is not practical or feasible to use the VNRS.
A simple machine learning model for the prediction of acute kidney injury following noncardiac surgery in geriatric patients: a prospective cohort study
Authors: Peng Xiran , Zhu Tao , Chen Qixu , Zhang Yuewen , Zhou Ruihao , Li Ke , Hao Xuechao 
Published: June 2024

Abstract
Background
Surgery in geriatric patients often poses risk of major postoperative complications. Acute kidney injury (AKI) is a common complication following noncardiac surgery and is associated with increased mortality. Early identification of geriatric patients at high risk of AKI could facilitate preventive measures and improve patient prognosis. This study used machine learning methods to identify important features and predict AKI following noncardiac surgery in geriatric patients.

Methods
The data for this study were obtained from a prospective cohort. Patients aged ≥ 65 years who received noncardiac surgery from June 2019 to December 2021 were enrolled. Data were split into training set (from June 2019 to March 2021) and internal validation set (from April 2021 to December 2021) by time. The least absolute shrinkage and selection operator (LASSO) regularization algorithm and the random forest recursive feature elimination algorithm (RF-RFE) were used to screen important predictors. Models were trained through extreme gradient boosting (XGBoost), random forest, and LASSO. The SHapley Additive exPlanations (SHAP) package was used to interpret the machine learning model.

Results
The training set included 6753 geriatric patients. Of these, 250 (3.70%) patients developed AKI. The XGBoost model with RF-RFE selected features outperformed other models with an area under the precision-recall curve (AUPRC) of 0.505 (95% confidence interval [CI]: 0.369–0.626) and an area under the receiver operating characteristic curve (AUROC) of 0.806 (95%CI: 0.733–0.875). The model incorporated ten predictors, including operation site and hypertension. The internal validation set included 3808 geriatric patients, and 96 (2.52%) patients developed AKI. The model maintained good predictive performance with an AUPRC of 0.431 (95%CI: 0.331–0.524) and an AUROC of 0.845 (95%CI: 0.796–0.888) in the internal validation.

Conclusions
This study developed a simple machine learning model and a web calculator for predicting AKI following noncardiac surgery in geriatric patients. This model may be a valuable tool for guiding preventive measures and improving patient prognosis.

Trial registration
The protocol of this study was approved by the Committee of Ethics from West China Hospital of Sichuan University (2019–473) with a waiver of informed consent and registered at www.chictr.org.cn (ChiCTR1900025160, 15/08/2019).
Development of machine learning models for patients in the high intrahepatic cholangiocarcinoma incidence age group
Authors: Shen Jie , Yang Dashuai , Zhou Yu , Pei Junpeng , Wu Zhongkai , Wang Xin , Zhao Kailiang , Ding Youming 
Published: June 2024

Abstract
Background
Intrahepatic cholangiocarcinoma (ICC) has a poor prognosis and is understudied. Based on the clinical features of patients with ICC, we constructed machine learning models to understand their importance on survival and to accurately determine patient prognosis, aiming to develop reference values to guide physicians in developing more effective treatment plans.

Methods
This study used machine learning (ML) algorithms to build prediction models using ICC data on 1,751 patients from the SEER (Surveillance, Epidemiology, and End Results) database and 58 hospital cases. The models’ performances were compared using receiver operating characteristic curve analysis, C-index, and Brier scores.

Results
A total of eight variables were used to construct the ML models. Our analysis identified the random survival forest model as the best for prognostic prediction. In the training cohort, its C-index, Brier score, and Area Under the Curve values were 0.76, 0.124, and 0.882, respectively, and it also performed well in the test cohort. Kaplan–Meier survival analysis revealed that the model could effectively determine patient prognosis.

Conclusions
To our knowledge, this is the first study to develop ML prognostic models for ICC in the high-incidence age group. Of the ML models, the random survival forest model was best at prognosis prediction.
Clinical results with a multifocal intraocular lens with a novel optical design
Authors: Goldman Gustavo 
Published: June 2024

Abstract

Background
To evaluate the optical performance and safety of a new multifocal lens with a novel optical design featuring two additional foci (or intensifiers) in patients with cataract and presbyopia.

Methods
In this single-center, non-randomized prospective observational study, 31 patients underwent implantation of the new multifocal IOL between March 2020 and November 2021 at a tertiary clinical center in Buenos Aires and Ramos Mejia, Argentina. Postoperative examinations with emphasis on uncorrected and corrected visual acuity at distance and near and at two different intermediate distances (80 cm and 60 cm) were performed during the 3 postoperative months.

Results
Of the 31 patients who underwent implantation of the new IOL, 30 underwent bilateral surgery (61 eyes in total). At 3 months, all 61 eyes had an uncorrected distance visual acuity (UCDVA) of at least 0.15 logMAR; 57 eyes (93%) had an uncorrected distance visual acuity (UCDVA) of 0.1 logMAR and 27 eyes (44%) had an UCDVA of 0.0 logMAR. At 80 cm, 60 eyes (98%) had an uncorrected intermediate visual acuity (UCIVA) of at least 0.1 log MAR and 48 eyes (79%) had an UCIVA of 0.0 logMAR.

Conclusion
The new multifocal IOL with a novel optical concept (5 foci) showed a wide range of visual acuity especially at intermediate and near distances in patients undergoing cataract surgery. Uncorrected visual acuity was excellent at all tested distances, monocularly and binocularly, spectacle independence and patient satisfaction were high.
The association between dental and dentoalveolar arch forms of children with normal occlusion and malocclusion: a cross-sectional study
Authors: Luo Jiaqing , Liu Taiqi , Wang Yi , Li Xiaobing 
Published: June 2024

Abstract
Background
Symmetrical and coordinated dental and alveolar arches are crucial for achieving proper occlusion. This study aimed to explore the association between dental and dentoalveolar arch forms in children with both normal occlusion and malocclusion.

Methods
209 normal occlusion subjects (5–13 years, mean 8.48 years) and 199 malocclusion subjects (5–12 years, mean 8.19 years) were included. The dentoalveolar arch form was characterized by the smoothest projected curve representing the layered contour of the buccal alveolar bone, referred to as the LiLo curve. Subsequently, a polynomial function was utilized to assess dental and dentoalveolar arch forms. To facilitate separate analyses of shape (depth/width ratio) and size (depth and width), the widths of dental and dentoalveolar arch forms were normalized. The normalized dental and dentoalveolar arch forms (shapes) were further classified into 6 groups, termed dental/dentoalveolar arch clusters, using the k-means algorithm.

Results
The association between dental and dentoalveolar arch clusters was found to be one-to-many rather than one-to-one. The mismatch between dental and dentoalveolar arch forms is common in malocclusion, affecting 11.4% of the maxilla and 9.2% of the mandible, respectively.

Conclusions
There are large individual variations in the association between dental and dentoalveolar arch forms. Early orthodontic treatment may play an active role in coordinating the relationship between the dental and dentoalveolar arch forms.
Too much time or not enough? An observational study of teacher wait time after questions in case-based seminars
Authors: Häusler Janina , Gartmeier Martin , Grünewald Marc Georg , Hapfelmeier Alexander , Pfurtscheller Theresa , Seidel Tina , Berberat Pascal Oliver 
Published: June 2024

Abstract
Background
We define teacher wait time (TWT) as a pause between a teacher question and the following response given by a student. TWT is valuable because it gives students time to activate prior knowledge and reflect on possible answers to teacher questions. We seek to gain initial insights into the phenomenon of TWT in medical education and give commensurate recommendations to clinical teachers.

Methods
We observed n = 719 teacher questions followed by wait time. These were video-recorded in 29 case-based seminars in undergraduate medical education in the areas of surgery and internal medicine. The seminars were taught by 19 different clinical teachers. The videos were coded with satisfactory reliability. Time-to-event data analysis was used to explore TWT overall and independently of question types.

Results
In our sample of case-based seminars, about 10% of all teacher questions were followed by TWT. While the median duration of TWT was 4.41 s, we observed large variation between different teachers (median between 2.88 and 10.96 s). Based on our results, we recommend that clinical teachers wait for at least five, but not longer than 10–12 s after initial questions. For follow-up and reproduction questions, we recommend shorter wait times of 5–8 s.

Conclusions
The present study provides insights into the frequency and duration of TWT and its dependence on prior questions in case-based seminars. Our results provide clinical teachers with guidance on how to use TWT as an easily accessible tool that gives students time to reflect on and respond to teacher questions.
Health care accessibility and mobility in breast cancer: a Latin American perspective
Authors: Azeredo-da-Silva André Ferreira , Zanotto Bruna Stella , Martins Flavia , Navarro Nádia , Alencar Rafaela , Medeiros Clarissa 
Published: June 2024

Abstract
Background
Latin America (LATAM) encompasses a vast region with diverse populations. Despite publicly funded health care systems providing universal coverage, significant socioeconomic and ethno-racial disparities persist in health care access across the region. Breast cancer (BC) incidence and mortality rates in Brazil are comparable to those in other LATAM countries, supporting the relevance of Brazilian data, with Brazil’s health care policies and expenditures often serving as models for neighboring countries. We evaluated the impact of mobility on oncological outcomes in LATAM by analyzing studies of patients with BC reporting commuting routes or travel distances to receive treatment or diagnosis.

Methods
We searched MEDLINE (PubMed), Embase, Cochrane CENTRAL, LILACS, and Google Scholar databases. Studies eligible for inclusion were randomized controlled trials and observational studies of patients with BC published in English, Portuguese, or Spanish and conducted in LATAM. The primary outcome was the impact of mobility or travel distance on oncological outcomes. Secondary outcomes included factors related to mobility barriers and access to health services. For studies meeting eligibility, relevant data were extracted using standardized forms. Risk of bias was assessed using the Newcastle-Ottawa Scale. Quantitative and qualitative evidence synthesis focused on estimating travel distances based on available data. Heterogeneity across distance traveled or travel time was addressed by converting reported travel time to kilometers traveled and estimating distances for unspecified locations.

Results
Of 1142 records identified, 14 were included (12 from Brazil, 1 from Mexico, and 1 from Argentina). Meta-analysis revealed an average travel distance of 77.8 km (95% CI, 49.1-106.48) to access BC-related diagnostic or therapeutic resources. Nonetheless, this average fails to precisely encapsulate the distinct characteristics of each region, where notable variations persist in travel distance, ranging from 88 km in the South to 448 km in the North.

Conclusion
The influence of mobility and travel distance on access to BC care is multifaceted and should consider the complex interplay of geographic barriers, sociodemographic factors, health system issues, and policy-related challenges. Further research is needed to comprehensively understand the variables impacting access to health services, particularly in LATAM countries, where the challenges women face during treatment remain understudied.

Trial registration
CRD42023446936.
Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes
Authors: Wu Chung-Shien , Wang Rui-Jiang , Chaw Shu-Miaw 
Published: June 2024

Abstract
Background
Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.

Results
We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots—mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.

Conclusions
Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.