bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urban scaling theory: Answers to frequent questions
Authors: Lobo José , Bettencourt Luís , Ortman Scott G 
Published: December 2024

Since its start about 15 years ago, urban scaling research has become a vibrant component of the emerging field of urban science. Initially, this work focused on the identification of nonlinear relationships in urban quantities relative to population size, but more recently it has expanded to include efforts to explain observed scaling relationships in terms of new theory. We find that some misunderstandings have arisen in the literature concerning the nature and purpose of this work. Here, we address several persistent questions that have been raised with respect to urban scaling theory, clarify what we perceive to be its achievements and distinctiveness, and highlight questions and areas of opportunity for future work.
Investigation of the effect of green walking and intelligence games on the cognitive skills of individuals between the ages of 50–70 survived COVID-19 disease: A randomized controlled study
Authors: Akeren Zahide , Hintistan Sevilay 
Published: December 2024

Background Mild cognitive impairment can be considered as the preclinical stage of Alzheimer's disease. With the addition of COVID-19 disease to the cognitive decline that occurs with aging, it may cause dementia with severe cognitive losses such as Alzheimer's disease in some people. Physical activity and brain-occupying practices can significantly improve the risk factors for cognitive disorders and Alzheimer's disease. Objective The aim of study was to examine the effect of green walking and intelligence game on the cognitive skills of individuals aged 50–70 years with COVID-19. Methods The randomized controlled study was completed with 40 individuals, 20 in the experimental and 20 in the control group. Individuals in the experimental group green walking for 30 min three days a week for one month in two groups of 10 people, accompanied by the researcher. In addition, these individuals played intelligence games (brain games-memory thinking and brain exercise) via their smartphones for 15 min every day for a month. Results The cognitive skills and cognitive dimensions of “attention, concentration, memory, language and orientation” of the individuals in the experimental group were significantly increased compared to the control group individuals (p < 0.05). Conclusions It was found that green walk and intelligence game practice increased the cognitive skills of individuals aged 50–70 years who had outpatient COVID-19.
MRI-based mild cognitive impairment and Alzheimer's disease classification using an algorithm of combination of variational autoencoder and other machine learning classifiers
Authors: Bit Subhrangshu , Dey Pritam , Maji Arnab ,   for the Alzheimer’s Disease Neuroimaging Initiative, Khan Tapan K 
Published: December 2024

Background Correctly diagnosing mild cognitive impairment (MCI) and Alzheimer's disease (AD) is important for patient selection in drug discovery. Research outcomes on stage diagnosis using neuroimages combined with cerebrospinal fluid and genetic biomarkers are expensive and time-consuming. Only structural magnetic resonance imaging (sMRI) scans from two internationally recognized datasets are employed as input as well as test and independent validation to determine the classification of dementia by the machine learning algorithm. Objective We extract the reduced dimensional latent feature vector from the sMRI scans using a variational autoencoder (VAE). The objective is to classify AD, MCI, and control (CN) using MRI and without any other information. Methods The extracted feature vectors from MRI scans by VAE are used as input conditions for different advanced machine-learning classifiers. Classification of AD/CN/MCI are conducted using the output of VAE from MRI images and different artificial intelligence/machine learning classifier models in two cohorts. Results Using only MRI scans, the primary goal of the study is to test the ability to classify AD from CN and MCI cases. The current study achieved classification accuracies of AD versus CN 75.45% (F1-score = 79.52%), AD versus MCI 81.41% (F1-Score = 87.06%), and autopsy-confirmed AD versus MCI 92.75% (F1-Score = 95.52%) in test sets and AD versus CN 86.16% (F1-score = 92.03%) and AD versus MCI 70.03% (F1-Score = 82.1%) in validation data set. Conclusions By overcoming the data leakage problem, the autopsy-confirmed machine learning classification model is tested in two independent cohorts. External validation by an independent cohort improved the quality and novelty of the classification algorithm.
Determinants of adequate antenatal care among immediate postpartum mothers in Eastern Uganda: a multicenter cross-sectional study
Authors: Lee Seungwon , Nantale Ritah , Wani Solomon , Kasibante Samuel , Kanyike Andrew Marvin 
Published: December 2024

Background: Antenatal care is essential for reducing maternal and neonatal mortality, particularly in low-income regions. However, the adequacy of the care provided is crucial for achieving maternal health goals. Maternal mortality rates in Uganda are still among the highest globally. Thus, evaluating the adequacy of antenatal care (ANC) services, especially in high-risk regions is imperative. Objective: To determine the prevalence of adequate ANC and associated factors in Eastern Uganda. Design: A multicenter quantitative cross-sectional study was conducted at four healthcare facilities in Eastern Uganda from July to August 2022. Methods: We included immediate postpartum mothers who had given birth within 48 h with a record of their ANC information on a card or book. Adequate ANC was measured by a composite index of 10 core components per WHO guidelines on ANC for a positive pregnancy experience. Data were collected using a structured questionnaire designed with Kobo Toolbox and analyzed using Stata 15.0. Bivariable and multivariable logistic regression analyses assessed factors associated with receiving adequate ANC. Statistical significance was determined by a p value <0.05. Results: We recruited 1104 postnatal mothers, most aged 20–34 years ( n = 805, 72.9%). Only 5.9% received adequate ANC, with most mothers receiving an average of 6.9 (±2.0) of the 10 assessed ANC components. Receiving adequate ANC was associated with urban residency (AOR: 2.3; 95% CI: 1.16–4.38, p = 0.017), age between 20 and 34 years (AOR: 3.5; 95% CI: 1.07–11.30, p = 0.038), current or previous complications (AOR: 1.8; 95% CI: 1.02–3.29, p = 0.043), and delivery at a general hospital (AOR: 4.8; 95% CI: 2.60–8.83, p < 0.001). Conclusion: There is a critical gap in providing adequate ANC in Eastern Uganda, especially for rural and younger mothers. Policy efforts should focus on expanding access, enhancing maternal education, and strengthening healthcare infrastructure to meet the recommended ANC standards.
Alternative splicing induces sample-level variation in gene–gene correlations
Authors: Lu Yihao , Pierce Brandon L. , Wang Pei , Yang Fan , Chen Lin S. 
Published: December 2024

Abstract
Background
The vast majority of genes in the genome are multi-exonic, and are alternatively spliced during transcription, resulting in multiple isoforms for each gene. For some genes, different mRNA isoforms may have differential expression levels or be involved in different pathways. Bulk tissue RNA-seq, as a widely used technology for transcriptome quantification, measures the total expression (TE) levels of each gene across multiple isoforms in multiple cell types for each tissue sample. With recent developments in precise quantification of alternative splicing events for each gene, we propose to study the effects of alternative splicing variation on gene–gene correlation effects. We adopted a variance-component model for testing the TE–TE correlations of one gene with a co-expressed gene, accounting for the effects of splicing variation and splicing-by-TE interaction of one gene on the other.

Results
We analyzed data from the Genotype-Tissue Expression (GTEx) project (V8). At the 5% FDR level, 38,146 pairs of genes out of ∼10 M examined pairs from GTEx lung tissue showed significant TE-splicing interaction effects, implying isoform-specific and/or sample-specific TE–TE correlations. Additional analysis across 13 GTEx brain tissues revealed strong tissue-specificity of TE-splicing interaction effects. Moreover, we showed that accounting for splicing variation across samples could improve the reproducibility of results and could reduce potential confounding effects in studying co-expressed gene pairs with bulk tissue data. Many of those gene pairs had correlation effects specific to only certain isoforms and would otherwise be undetected. By analyzing gene–gene co-expression variation within functional pathways accounting for splicing, we characterized the patterns of the “hub” genes with isoform-specific regulatory effects on multiple other genes.

Conclusions
We showed that splicing variation of a gene may interact with TE of the gene and affect the TE of co-expressed genes, resulting in substantial tissue-specific inter-sample variability in gene–gene correlation effects. Accounting for TE-splicing interaction effects could reduce potential confounding effects and improve the robustness of estimation when estimating gene–gene correlations from bulk tissue expression data.
Prediction of gene expression-based breast cancer proliferation scores from histopathology whole slide images using deep learning
Authors: Ekholm Andreas , Wang Yinxi , Vallon-Christersson Johan , Boissin Constance , Rantalainen Mattias 
Published: December 2024

Abstract
Background
In breast cancer, several gene expression assays have been developed to provide a more personalised treatment. This study focuses on the prediction of two molecular proliferation signatures: an 11-gene proliferation score and the MKI67 proliferation marker gene. The aim was to assess whether these could be predicted from digital whole slide images (WSIs) using deep learning models.

Methods
WSIs and RNA-sequencing data from 819 invasive breast cancer patients were included for training, and models were evaluated on an internal test set of 172 cases as well as on 997 cases from a fully independent external test set. Two deep Convolutional Neural Network (CNN) models were optimised using WSIs and gene expression readouts from RNA-sequencing data of either the proliferation signature or the proliferation marker, and assessed using Spearman correlation (r). Prognostic performance was assessed through Cox proportional hazard modelling, estimating hazard ratios (HR).

Results
Optimised CNNs successfully predicted the proliferation score and proliferation marker on the unseen internal test set (ρ = 0.691(p < 0.001) with R2 = 0.438, and ρ = 0.564 (p < 0.001) with R2 = 0.251 respectively) and on the external test set (ρ = 0.502 (p < 0.001) with R2 = 0.319, and ρ = 0.403 (p < 0.001) with R2 = 0.222 respectively). Patients with a high proliferation score or marker were significantly associated with a higher risk of recurrence or death in the external test set (HR = 1.65 (95% CI: 1.05–2.61) and HR = 1.84 (95% CI: 1.17–2.89), respectively).

Conclusions
The results from this study suggest that gene expression levels of proliferation scores can be predicted directly from breast cancer morphology in WSIs using CNNs and that the predictions provide prognostic information that could be used in research as well as in the clinical setting.
Effect of GFRP Stirrup Confinement on the Bond Strength of GFRP-RC Beams
Authors: Hussain Zahid , Ortiz Jesús D. , Hosseini Seyed Arman , Benmokrane Brahim , Nanni Antonio 
Published: December 2024

AbstractThe current provisions for development length in the ACI 440.11 code disregard the confinement effect provided by stirrups on the bond strength of longitudinal bars and require splice lengths that pose implementation challenges. Given the significant improvement in GFRP material properties, this study investigated the bond strength of sand-coated GFRP bars and proposed a new factor to include the effect of stirrup confinement on the bond-strength provisions. The experimental program involved 16 GFRP-reinforced concrete (RC) beams having a width of 300 mm, and depth 440 mm, consisting of two repetitions for every configuration, subjected to four-point loading. The test parameters comprised lap-splice length and stirrup spacing in the lap-spliced zone. Out of 16 GFRP-RC beams, two beams were reinforced with two M16 (No. 5) continuous bars and six with varying lap-splice lengths [i.e., 40, 60, and 80 bar diameters (db)] without confining stirrups. To evaluate the effect of confining stirrups, eight beams were reinforced with two M16 (No. 5) lap-spliced longitudinal bars (i.e., 40 and 60 db) and M13 (No. 4) stirrups spaced at 100 mm (4 in.) and 200 mm (8 in.) center-to-center. Based on experimental results, stirrup confinement clearly increased the bond strength, reduced longitudinal bar slippage, and increased splitting stress. The beams with a splice length of 60 db and stirrups on 100 mm (4 in.) centers achieved 57% higher capacity than those with the same lap-splice length but without stirrups. Further, the ACI 440.11 equation overestimated the bond strength of sand-coated GFRP bars but yielded conservative results with closely spaced stirrups. CSA S6:25 predicted bond-strength values that were close to the experimental results compared to CSA S6:19, and CSA S806:12.
Impact of meteorological and processing factors on metabolite composition of Darjeeling tea
Authors: De Dwaipee , Sarkar Sreerupa , Chhetri Himashree , Chatterjee Jhelam , Sinha Nitu , Das Sujit , Sarkar Abhijit , Das Susmita , Ray Sonali 
Published: December 2024

AbstractMeteorological and edaphic factors significantly affect the first flush metabolite composition of Darjeeling tea, impacting flavor, nutrition, and customer preferences. The Camellia sinensis var. sinensis grown in the Darjeeling hills was sampled at different stages of processing. 75 metabolites were identified using a GC/MS-based metabolomic and chemometric technique. The study aimed to pinpoint quality markers and create a database for Darjeeling tea authenticity, India’s first geographical indication product. Principal component analysis and partial least squares discriminant analysis revealed changes in tea metabolites during processing, while the chemometric study demonstrated variations in key compounds. Antioxidant activity exhibited significant variations among the samples with final processed showing highest antioxidant potential. The concentration of amino acids increased significantly (p < 0.05) from fresh tea leaves to the final processed product. Conversely, the content of organic acids, inorganic acids, and fatty acids was observed to decrease. Additionally, caffeic acids, epicatechin, epigallocatechin, chlorogenic acid, 3, 4-dihydroxybenzoic acid, and 4-hydroxycinnamic acid increased in concentration, while catechin, (-)-epicatechin, gallic acid, pyrogallol, quinic acid, shikimic acid, and arbutin decreased significantly in concentration in the final processed tea. Meteorological parameters were documented during the study period, showing variation in the levels of PM2.5, PM10, O3, NO2, and SO2. The findings of this study offer insightful information on the variables influencing Darjeeling tea metabolite composition, which tea producers and processors can use to raise the standard and authenticity of this beverage.
Graphical abstract
Predictors of VILI risk: driving pressure, 4DPRR and mechanical power ratio—an experimental study
Authors: Galizia Mauro , Ghidoni Valentina , Catozzi Giulia , Giovanazzi Stefano , Nocera Domenico , Donati Beatrice , Pozzi Tommaso , D’Albo Rosanna , Busana Mattia , Romitti Federica , Herrmann Peter , Moerer Onnen , Meissner Konrad , Quintel Michael , Camporota Luigi , Gattinoni Luciano 
Published: December 2024

Abstract
Background
Ventilator-induced lung injury (VILI) is one of the side effects of mechanical ventilation during ARDS; a prerequisite for averting it is the quantification of its risk factors associated with a given ventilatory setting. Many clinical variables have been proposed as predictors of VILI, of which driving pressure is the most widely used. In this study, we compared the performance of driving pressure, four times the driving pressure added to respiratory rate (4DPRR) and mechanical power ratio.

Results
In a study population of 121 previously healthy pigs exposed to harmful ventilation, we compared the association of driving pressure, 4DPRR and mechanical power ratio to lung weight, lung wet-to-dry and total histological score. All the three variables were associated with these outcomes. Driving pressure, 4DPRR and mechanical power ratio increase linearly with the lung weight (adjusted R2 of 0.27, 0.36 and 0.40, respectively), the lung wet-to-dry ratio (adjusted R2 of 0.19, 0.25 and 0.37) and the total histological score (adjusted R2 of 0.26, 0.38 and 0.26). Using a multiple linear regression model with forward analysis, starting with tidal volume and progressively adding respiratory rate and positive end-expiratory pressure, and comparing the topic with the outcome variables, we obtained R2 values, respectively, of 0.07, 0.20, 0.42 for lung weight, 0.09, 0.19, 0.26 for lung wet-to-dry ratio and 0.07, 0.27, 0.43 for total histological score.

Conclusions
Driving pressure, 4DPRR and mechanical power ratio, were all associated with lung injury in healthy animals undergoing mechanical ventilation.
Enhancing synthetic vinasse treatment efficiency using an integrated UASB-Modified Bardenpho Process
Authors: Mazaheri Afsaneh , Doosti Mohamad Reza , Zoqi Mohammad javad 
Published: December 2024

AbstractVinasse poses considerable environmental problems due to its complex composition of organic matter, minerals, and toxic compounds. If discharged into the environment without treatment, it can cause adverse impacts on ecosystems. This research investigated the effectiveness of an integrated treatment system involving an upflow anaerobic sludge blanket (UASB) reactor and the modified Bardenpho process (MBP) for purifying synthetic vinasse. The study lasted for 167 days, during which the integrated UASB-MBP system processed untreated synthetic vinasse with organic loading rates (OLR) ranging from 1.6 to 12.5 kgCOD/m3 day. The UASB-MBP system impressively achieved a COD removal efficiency of 99.41%. Removal efficiencies of approximately 98.14, 99.91, and 99.63% were also achieved for total nitrogen (TN), total phosphorus (TP) and total ammonium (NH4+-N), respectively. The final discharge was 51.06 mg/L. The concentrations of NH4+-N and TN in the outflow of the settlement tank were 0.8–1.2 mg/L and 5.1–7.9 mg/L, respectively. Optimal performance was achieved when the HRT and nitrate recycle ratio were 15.5 h and 200%, respectively. The temperature was kept in the mesophilic range (33–35 °C) during the experiments. These results underscores the potential of the integrated UASB reactor and modified Bardenpho process to provide an effective and eco-friendly approach for concurrent removal of COD and nutrients from vinasse treatment, offering broad prospects for implementation in wastewater treatment.
Susceptibility of Aedes aegypti mosquitoes to pyrethroid insecticides and characterization of breeding habitats in selected districts of Mwanza, Tanzania
Authors: Emidi Basiliana , Kiwanuka Ziada , Antony Selina , Kajeguka Debora , Manjurano Alphaxard 
Published: December 2024

Abstract
Background
Tanzania has experienced outbreaks of dengue fever in major cities. The main vectors of the dengue virus in Tanzania are Aedes aegypti mosquitoes. The control of this mosquito vector is based on insecticide, and yet, the insecticide susceptibility of this species is not well known in many places in Tanzania. Conversely, the breeding habitats mostly preferred by this species are not well documented in the study area. Therefore, the present study aimed to determine the pyrethroid insecticide susceptibility status and breeding habitats preference of Ae. aegypti mosquito in the three sites from three districts in Mwanza, Tanzania. The assessment of Ae. aegypti mosquito 24-h percentage mortality was based on WHO criteria.

Results
A total of 850 Ae. aegypti were exposed to three pyrethroid insecticides. In Bwiru site, 100% mortality was observed for all three pyrethroids, indicating full susceptibility. At Igekemaja and Mwagagala villages, Ae. aegypti were resistant to all the three pyrethroid insecticides tested. In Igekemaja, there were variations in Ae. aegypti mortality rates induced by different insecticides, with mortality rates ranging from 72% for alphacypermethrin to 86% for deltamethrin. Although the mortality rates were lower than in Bwiru site, they were still substantial and statistically significant. The mortality rates in Mwagagala were lowest across the three insecticides, with mortality rates ranging from 60% for deltamethrin to 86% for alphacypermethrin. In Mwagagala, the Ae. aegypti mosquitoes were less susceptible to the insecticides tested. Aedes aegypti mosquito prefer breeding in abandoned old tires in urban area and in small containers and uncovered water storage containers in rural settings.

Conclusion
The study has revealed pyrethroid insecticide susceptibility status and breeding habitats of Ae. aegypti in the rural and urban settings in Mwanza, Tanzania. The study findings imply the need for public health interventions with focus on community education on mosquito control.
Impact of COVID-19 vaccination in patients with epilepsy
Authors: Elshebawy Haidy , Kishk Nirmeen A. , Alaa Nouran , Hussein Mona , Abdelghaffar Mohamed , Magdy Rehab 
Published: December 2024

Abstract
Background
The risk of seizure aggravation following coronavirus disease 2019 (COVID-19) vaccines is a major cause behind vaccine hesitancy among patients with epilepsy (PWE), resulting in lower immunization rates. This work aimed to investigate the impact of COVID-19 different vaccines on seizure control in PWE.

Results
This study was conducted on 110 PWE who received at least the first dose of any COVID-19 vaccine. Sixty-one (55.5%) patients did not develop any side effects from vaccination. There was no statistically significant change in seizure frequency following receiving COVID-19 vaccines, either adenoviral vector vaccines, inactivated vaccines, or mRNA vaccines (P = 0.733, 0.778, respectively). Twelve patients (10.9%) experienced seizure exacerbation following COVID-19 vaccination; seizure occurrence in the first 24 h immediately after the vaccine was reported in only one patient. There were no statistically significant differences between patients who developed seizure exacerbation following COVID-19 vaccination and those who did not develop regarding age, age at onset, seizure etiology, type of vaccine, or seizure exacerbation following COVID-19 infection.

Conclusions
There is a low likelihood of COVID-19 vaccine-related seizure exacerbations in PWE. This data can be utilized to counsel PWE regarding the safety of COVID-19 vaccination.