bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes
Authors: Azad Md Fakhrul , Tong Tong , Lau Nelson C. 
Published: October 2024

AbstractRecent studies have suggested that Transposable Elements (TEs) residing in introns frequently splice into and alter primary gene-coding transcripts. To re-examine the exonization frequency of TEs into protein-coding gene transcripts, we re-analyzed a Drosophila neuron circadian rhythm RNAseq dataset and a deep long RNA fly midbrain RNAseq dataset using our Transposon Insertion and Depletion Analyzer (TIDAL) program. Our TIDAL results were able to predict several TE insertions from RNAseq data that were consistent with previous published studies. However, we also uncovered many discrepancies in TE-exonization calls, such as reads that mainly support intron retention of the TE and little support for chimeric mRNA spliced to the TE. We then deployed rigorous genomic DNA-PCR (gDNA-PCR) and RT-PCR procedures on TE-mRNA fusion candidates to see how many of bioinformatics predictions could be validated. By testing a w1118 strain from which the deeper long RNAseq data was derived and comparing to an OreR strain, only 9 of 23 TIDAL candidates (< 40%) could be validated as a novel TE insertion by gDNA-PCR, indicating that deeper study is needed when using RNAseq data as inputs into current TE-insertion prediction programs. Of these validated calls, our RT-PCR results only supported TE-intron retention. Lastly, in the Dscam2 and Bx genes of the w1118 strain that contained intronic TEs, gene expression was 23 times higher than the OreR genes lacking the TEs. This study's validation approach indicates that chimeric TE-mRNAs are infrequent and cautions that more optimization is required in bioinformatics programs to call TE insertions using RNAseq datasets.
Proteomics analysis reveals the differential protein expression of female and male adult Toxocara canis using Orbitrap Astral analyzer
Authors: Qiu Hui-Jie , Zhou Ya-Jia , Li Zhi-Yu , Lv Yi-Han , Zhu Xing-Quan , Zheng Wen-Bin 
Published: October 2024

Abstract
Background
Toxocara canis, the most prevalent helminth in dogs and other canines, is one of the socioeconomically important zoonotic parasites, particularly affecting pediatric and adolescent populations in impoverished communities. However, limited information is available regarding the proteomes of female and male adult T. canis. To address this knowledge gap, we performed a comprehensive proteomic analysis to identify the proteins with differential abundance (PDAs) and gender-specifically expressed proteins between the two sexes adult T. canis.

Methods
The comparative proteomic analysis was carried out by the Orbitrap mass spectrometry (MS) with asymmetric track lossless (Astral) analyzer. The difference analysis was conducted using t-test and the proteins verification was achieved through parallel reaction monitoring (PRM). The potential biological functions of identified adult T. canis proteins and PDAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The domain, transcription factor and subcellular localization of the identified proteins and PDAs were analyzed by InterPro, AnimalTFDB 4.0 and Cell-mPLOC 2.0 databases, respectively.

Results
A total of 8565 somatic proteins of adult T. canis were identified. Compared to male adult, 682 up-regulated PDAs and 844 down-regulated PDAs were identified in female adult with P-values < 0.05 and |log2FC| > 1, including 139 proteins exclusively expressed in female and 272 proteins exclusively expressed in male. The GO annotation analysis using all PDAs revealed that the main biological processes, cellular components and molecular functions corresponded to aminoglycan metabolic process, extracellular region and protein tyrosine phosphatase activity, respectively. The KEGG analysis using all PDAs showed that the pathways were mainly associated with adipocytokine signaling pathway, proximal tubule bicarbonate reclamation and PPAR signaling pathway.

Conclusions
This study reveals the differential protein expression between female and male adult T. canis, providing valuable resource for developing the novel intervention strategies against T. canis infection in humans and animals, especially from the perspective of sexual development and reproduction.

Graphical abstract
Skin-permeable gold nanoparticles with modifications azelamide monoethanolamine ameliorate inflammatory skin diseases
Authors: Zhao He , Zhao Han , Tang Yan , Li Mengfan , Cai Yisheng , Xiao Xin , He Fanping , Huang Hongwen , Zhang Yiya , Li Ji 
Published: October 2024

Abstract
Background
Traditional topical drug delivery for treating inflammatory skin diseases suffers from poor skin penetration and long-term side effects. Metal nanoparticles show promising application in topical drug delivery for inflammatory skin diseases.

Methods
Here, we synthesized a new type of nanoparticles, azelamide monoethanolamine-functionalized gold nanoparticles (Au-MEA NPs), based on citrate-capped gold nanoparticles (Au-CA NPs) via the ligand exchange method. The physical and chemical properties of Au-CA NPs and Au-MEA NPs were characterized. In vivo studies were performed using imiquimod-induced psoriasis and LL37-induced rosacea animal models, respectively. For in vitro studies, a model of cellular inflammation was established using HaCaT cells stimulated with TNF-α. In addition, proteomics, gelatin zymography, and other techniques were used to investigate the possible therapeutic mechanisms of the Au-MEA NPs.

Results
We found that Au-MEA NPs exhibited better stability and permeation properties compared to conventional Au-CA NPs. Transcutaneously administered Au-MEA NPs exerted potent therapeutic efficacy against both rosacea-like and psoriasiform skin dermatitis in vivo without overt signs of toxicity. Mechanistically, Au-MEA NPs reduced the production of pro-inflammatory mediators in keratinocytes by promoting SOD activity and inhibiting the activity of MMP9.

Conclusion
Au-MEA NPs have the potential to be a topical nanomedicine for the effective and safe treatment of inflammatory skin diseases.
A systematic scrutiny of artificial intelligence-based air pollution prediction techniques, challenges, and viable solutions
Authors: Malhotra Meenakshi , Walia Savita , Lin Chia-Chen , Aulakh Inderdeep Kaur , Agarwal Saurabh 
Published: October 2024

AbstractAir is an essential human necessity, and inhaling filthy air poses a significant health risk. One of the most severe hazards to people’s health is air pollution, and appropriate precautions should be taken to monitor and anticipate its quality in advance. Among all the countries, the air quality in India is decreasing daily, which is a matter of concern to the health department. Many studies use machine learning and Deep learning methods to predict atmospheric pollutant levels, prioritizing accuracy over interpretability. Many research studies confuse researchers and readers about how to proceed with further research. This paper aims to give every detail of the considered air pollutants and brief about the techniques used, their advantages, and challenges faced during pollutant prediction, which leads to a better understanding of the techniques before starting any research related to air pollutant prediction. This paper has given numerous prospective questions on air pollution that piqued the study’s interest. This study discussed various machine and deep learning methods and optimization techniques. Despite all the discussed machine learning and deep learning techniques, the paper concluded that more datasets, better learning techniques, and a variety of suggestions would enhance interpretability while maintaining high accuracy for air pollution prediction. The purpose of this review is also to reveal how a family of neural network algorithms has helped researchers across the globe to predict air pollutant(s).
Information quality and students’ academic performance: the mediating roles of perceived usefulness, entertainment and social media usage
Authors: Badr Abdallah M. M. , Al-Abdi Badr Saleh , Rfeqallah Maged , Kasim Rozilah , Ali Faisal A. M. 
Published: October 2024

Abstract

Purpose
This study evaluates the mediating roles of entertainment, perceived usefulness, and social media use on social information (content) and students’ academic performance.

Methodology
Primary data was collected from 445 students at King Khalid University in Saudi Arabia using the snowball sampling strategy was employed. For data analysis, structural equation modeling (PLS-SEM) was used.

Findings
Entertainment partly mediates the link between social information quality “content” (IQ) and social media use (SMU) and SMU mediates the link between IQ and student’s academic performance (SAP). Perceived usefulness mediates the link between IQ and SAP. Suggesting that entertainment and perceived usefulness are crucially necessary for inspiring social media content to obtain optimum performance among graduate students. The study was limited to a single academic institution. Therefore, the results of the investigation cannot be generalized as a whole, and cannot track respondents’ social media activity over time. Thus, longitudinal data may be used in future investigations.

Practical implications
The results of this study indicate that faculties can adapt and adjust their teaching methods and activities to incorporate social media, perceived usefulness, and entertaining content since it affects student performance. Social media (SM) has a significant influence on students’ social and academic performance. Thus, educational stakeholders, such as university authorities, the government, and parents and guardians, should recognize social media as a tool for achieving educational objectives.

Originality/value
The study enhances the application of UTAUT2 by examining how factors that influence the adoption of technology are connected to the subsequent influence of that adoption on students’ learning and conduct.
Investigation of students' use of online information in higher education using eye tracking
Authors: Kunz Ann-Kathrin , Zlatkin-Troitschanskaia Olga , Schmidt Susanne , Nagel Marie-Theres , Brückner Sebastian 
Published: October 2024

AbstractTo successfully learn using freely available (and non-curated) Internet resources, university students need to search for, critically evaluate and select online information, and verify sources (defined as Critical Online Reasoning, COR). Recent research indicates substantial deficits in COR skills among higher education students. To support students in learning how to critically use online information for their learning, it is necessary to better understand the strategies and practices that might elicit less critically-reflective judgments about online information and thus account for such deficits. To this end, using eye tracking data, we investigate how the COR behaviors of students who critically-reflectively evaluate the credibility of online information (‘high performers’) differ from those of students who do not critically-reflectively evaluate it (‘low performers’): 19 students were divided into high and low performers according to their performance in the newly developed Critical Online Reasoning Assessment (CORA). The fixation and dwell times of both groups during CORA task processing were compared regarding time spent on the different processing steps and eye movements on the visited web pages. The results show noticeable differences between the two groups, indicating that low performers indeed approached the task rather heuristically than systematically, and that COR skills require targeted and effective training in higher education.
Dynamic conditions for large shallow intraslab earthquakes: four categories of subduction zones
Authors: Yoshida Masaki 
Published: October 2024

AbstractLarge shallow intraslab earthquakes (LSIEs) of over magnitude-7 rarely occur at shallower depths (≤ 60 km) in the subducting plates of the circum-Pacific and northern margin of the Australian Plate off Indonesia. Previous studies have suggested that most LSIEs occur under surface tectonic conditions with a lateral stress gradient across the back-arc to the fore-arc on the overriding plate based on seismological and geological evidence. In this study, dynamic conditions for the occurrence of LSIEs were studied using the intraslab stress state, stress state of the overriding plate, motion speed of overriding and subducting plates, and trench migration speed determined by plate motion models. LSIEs prefer tectonic conditions under (1) an extensional-to-neutral stress state in the back-arc, (2) a compressional stress state in the fore-arc, and (3) down-dip tension in the shallower part of the subducting plate. The results suggest that the Earth’s subduction zones can be classified into four categories. This categorization is informed by the behavior of underlying mantle flow, i.e., the magnitude of slab suction flow in the mantle under the subducting plates, which is related to the degree of plate-slab coupling, and the scale of return flow in the mantle wedge under the overriding plates, which varies the combination of stress states in the fore-arc and back-arc.
Effect of sequencing platforms on the sensitivity of chemical mutation detection using Hawk-Seq™
Authors: Hosoi Sayaka , Hirose Takako , Matsumura Shoji , Otsubo Yuki , Saito Kazutoshi , Miyazawa Masaaki , Suzuki Takayoshi , Masumura Kenichi , Sugiyama Kei-ichi 
Published: October 2024

Abstract
Background
Error-corrected next-generation sequencing (ecNGS) technologies have enabled the direct evaluation of genome-wide mutations after exposure to mutagens. Previously, we reported an ecNGS methodology, Hawk-Seq™, and demonstrated its utility in evaluating mutagenicity. The evaluation of technical transferability is essential to further evaluate the reliability of ecNGS-based assays. However, cutting-edge sequencing platforms are continually evolving, which can affect the sensitivity of ecNGS. Therefore, the effect of differences in sequencing instruments on mutation data quality should be evaluated.

Results
We assessed the performance of four sequencing platforms (HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400) with the Hawk-Seq™ protocol for mutagenicity evaluation using DNA samples from mouse bone marrow exposed to benzo[a]pyrene (BP). The overall mutation (OM) frequencies per 106 bp in vehicle-treated samples were 0.22, 0.36, 0.46, and 0.26 for HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400, respectively. The OM frequency of NextSeq2000 was significantly higher than that of HiSeq2500, suggesting the difference to be based on the platform. The relatively higher value in NextSeq2000 was a consequence of the G:C to C:G mutations in NextSeq2000 data (0.67 per 106 G:C bp), which was higher than the mean of the four platforms by a ca. of 0.25 per 106 G:C bp. A clear dose-dependent increase in G:C to T:A mutation frequencies was observed in all four sequencing platforms after BP exposure. The cosine similarity values of the 96-dimensional trinucleotide mutation patterns between HiSeq and the three other platforms were 0.93, 0.95, and 0.92 for NovaSeq, NextSeq, and DNBSeq, respectively. These results suggest that all platforms can provide equivalent data that reflect the characteristics of the mutagens.

Conclusions
All platforms sensitively detected mutagen-induced mutations using the Hawk-Seq™ analysis. The substitution types and frequencies of the background errors differed depending on the platform. The effects of sequencing platforms on mutagenicity evaluation should be assessed before experimentation.
Student mobility in Southern Italy: An empirical analysis of preferential patterns
Authors: Genova Vincenzo Giuseppe , Ruiu Gabriele , Attanasio Massimo , Ermacora Matteo , Breschi Marco 
Published: October 2024

AbstractThis paper presents an empirical analysis aimed at identifying chain migration patterns among university students from Sicily, Sardinia, and Apulia. Utilizing data from the national archive of university students enrolled in an Italian university from 2008 to 2017, we construct origin–destination matrixes and calculate residuals from a log-linear model to detect key student routes. Positive residuals between specific origin–destination pairs that persist over time can suggest significant attraction and potential chain migration. The results support a “large to large” and “small to small” city mobility model, particularly for Sicily and Sardinia. Students from Palermo, Catania, Messina, and Cagliari show strong connections with large cities such as Rome and Milan. Furthermore, results show historical links between Sardinia and Tuscany date back to the 1950s, and the enduring connections between Apulian students and universities in Emilia-Romagna, Veneto, and Lombardy have been evident since the 1970s. In Sicily, mobility patterns towards the Polytechnic of Turin began in the 1970s and persist today. These patterns underscore the influence of prior migrants on the mobility decisions of university students in Southern Italy, highlighting a potential chain migration effect.
Water, sanitation, and hygiene (WASH) practices in Africa: exploring the effects on public health and sustainable development plans
Authors: Okesanya Olalekan John , Eshun Gilbert , Ukoaka Bonaventure Michael , Manirambona Emery , Olabode Olaleke Noah , Adesola Ridwan Olamilekan , Okon Inibehe Ime , Jamil Safayet , Singh Amandeep , Lucero-Prisno Don Eliseo , Ali Habib Mohammad , Chowdhury A. B. M. Alauddin 
Published: October 2024

Abstract
Background
Suboptimal water, sanitation, and hygiene (WASH) practices constitute a serious public health risk, affecting one-third of the world's population. Remarkable progress has been made to improve WASH; however, challenges remain, with rapid population growth adding pressure on WASH systems. This study explores the current state of WASH practices and diseases in Africa, identifies challenges, and proposes public health recommendations for sustainable implementation.

Main body
The staggering burden of WASH-related diseases in low- and middle-income countries (LMICs), particularly in Africa, threatens public health, with millions of deaths and disability-adjusted life years (DALYs) attributed to poor WASH practices annually. Notable challenges plaguing WASH practices in the region include poverty, malnutrition, poor data reporting, illiteracy, climate change, and poor healthcare financing. This results in adverse health consequences, including waterborne infections like cholera, typhoid, dysentery, and diarrheal diseases. Additionally, neglected tropical diseases (NTDs) such as intestinal worms, schistosomiasis, trachoma, lost productivity, and environmental pollution from soil and underground water contamination have been implicated. Geographical disparities, cultural norms, and inadequate funding further complicate efforts to improve WASH infrastructure and practices. Globally concerted efforts are required to address these issues and permit WASH practices to protect human health by preventing infectious diseases and contributing to economic growth. Strong financial frameworks, skills training, and tools like WASH Fit are recommended for a stronger WASH approach in Africa.

Conclusion
The consequences of poor WASH extend beyond public health, impacting economic growth, gender equality, and environmental sustainability. WaterAid’s policy recommendations prioritizing government administration, institutional capacity enhancement, and more financial resources are expedient.
Validation of a multi-parameter algorithm for personalized contrast injection protocol in liver CT
Authors: Brat Hugues G. , Dufour Benoit , Heracleous Natalie , Sastre Pauline , Thouly Cyril , Rizk Benoit , Zanca Federica 
Published: October 2024

Abstract
Background
In liver computed tomography (CT), tailoring the contrast injection to the patient’s specific characteristics is relevant for optimal imaging and patient safety. We evaluated a novel algorithm engineered for personalized contrast injection to achieve reproducible liver enhancement centered on 50 HU.

Methods
From September 2020 to August 31, 2022, CT data from consecutive adult patients were prospectively collected at our multicenter premises. Inclusion criteria consisted of an abdominal CT referral for cancer staging or follow-up. For all examinations, a web interface incorporating data from the radiology information system (patient details and examination information) and radiographer-inputted data (patient fat-free mass, imaging center, kVp, contrast agent details, and imaging phase) were used. Calculated contrast volume and injection rate were manually entered into the CT console controlling the injector. Iopamidol 370 mgI/mL or Iohexol 350 mgI/mL were used, and kVp varied (80, 100, or 120) based on patient habitus.

Results
We enrolled 384 patients (mean age 61.2 years, range 21.1–94.5). The amount of administered iodine dose (gI) was not significantly different across contrast agents (p = 0.700), while a significant increase in iodine dose was observed with increasing kVp (p < 0.001) and in males versus females (p < 0.001), as expected. Despite the differences in administered iodine load, image quality was reproducible across patients with 72.1% of the examinations falling within the desirable range of 40–60 HU.

Conclusion
This study validated a novel algorithm for personalized contrast injection in adult abdominal CT, achieving consistent liver enhancement centered at 50 HU.

Relevance statement
In healthcare’s ongoing shift towards personalized medicine, the algorithm offers excellent potential to improve diagnostic accuracy and patient management, particularly for the detection and follow-up of liver malignancies.

Key Points

The algorithm achieves reproducible liver enhancement, promising improved diagnostic accuracy and patient management in diverse clinical settings.

The real-world study demonstrates this algorithm’s adaptability to different variables ensuring high-quality liver imaging.

A personalized algorithm optimizes liver CT, improving the visibility, conspicuity, and follow-up of liver lesions.

Graphical Abstract
Rare primary vasculitis: update on multiple complex diseases and the new kids on the block
Authors: Dantas Joao Gabriel , Biegelmeyer Erika , Zarur Eduarda Bonelli , Pinheiro Frederico Augusto Gurgel 
Published: October 2024

AbstractSystemic vasculitis is a group of rare diseases that share an essential characteristic: inflammation of blood vessel walls. This injury occurs during the disease course, but specific features vary for each entity. In this paper, we will address relevant aspects of the newest monogenic mutation vasculitis, such as deficiency of adenosine deaminase 2 (ADA2) and VEXAS syndrome (UBA1), and other relevant vasculitis, such as Cogan syndrome and Susac syndrome that may share some similarities with them.