bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an ADME-related gene for forecasting the prognosis and responding to immunotherapy in sarcomas
Authors: Wang Jianlong , Wang Guowei , Hu Tianrui , Wang Hongyi , Zhou Yong 
Published: January 2024

AbstractThere are more than 170 subtypes of sarcomas (SARC), which pose a challenge for diagnosis and patient management. Relatively simple or complex karyotypes play an indispensable role in the early diagnosis and effective treatment of SARC. The genes related to absorption, distribution, metabolism, and excretion (ADME) of a drug can serve as prognostic biomarkers of cancer and potential drug targets. In this study, a risk score signature was created. The SARC cohort was downloaded from The Cancer Genome Atlas (TCGA) database, and divided into high-risk group and low-risk group according to the median value of risk score. Compared with high-risk group, low-risk group has a longer survival time, which is also verified in osteosarcoma cohort from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. In addition, the relationship between the signature and immunophenotypes, including status of immune cell infiltration and immune checkpoint expression, was explored. Then, we found that high-risk group is in immunosuppressive status. Finally, we verified that PPARD played a role as a carcinogen in osteosarcoma, which provided a direction for targeted treatment of osteosarcoma in the future. Generally speaking, the signature can not only help clinicians predict the prognosis of patients with SARC, but also provide a theoretical basis for developing more effective targeted drugs in the future.
Identification of potential crucial genes and therapeutic targets for epilepsy
Authors: Wang Shitao , Xie Zhenrong , Jun Tian , Ma Xuelu , Zhang Mengen , Rao Feng , Xu Hui , Lu Jinghong , Ding Xiangqian , Li Zongyou 
Published: January 2024

Abstract
Background
Epilepsy, a central neurological disorder, has a complex genetic architecture. There is some evidence suggesting that genetic factors play a role in both the occurrence of epilepsy and its treatment. However, the genetic determinants of epilepsy are largely unknown. This study aimed to identify potential therapeutic targets for epilepsy.

Methods
Differentially expressed genes (DEGs) were extracted from the expression profiles of GSE44031 and GSE1834. Gene co-expression analysis was used to confirm the regulatory relationship between newly discovered epilepsy candidate genes and known epilepsy genes. Expression quantitative trait loci analysis was conducted to determine if epilepsy risk single-nucleotide polymorphisms regulate DEGs’ expression in human brain tissue. Finally, protein–protein interaction analysis and drug–gene interaction analysis were performed to assess the role of DEGs in epilepsy treatment.

Results
The study found that the protein tyrosine phosphatase receptor-type O gene (PTPRO) and the growth arrest and DNA damage inducible alpha gene (GADD45A) were significantly upregulated in epileptic rats compared to controls in both datasets. Gene co-expression analysis revealed that PTPRO was co-expressed with RBP4, NDN, PAK3, FOXG1, IDS, and IDS, and GADD45A was co-expressed with LRRK2 in human brain tissue. Expression quantitative trait loci analysis suggested that epilepsy risk single-nucleotide polymorphisms could be responsible for the altered PTPRO and GADD45A expression in human brain tissue. Moreover, the protein encoded by GADD45A had a direct interaction with approved antiepileptic drug targets, and GADD45A interacts with genistein and cisplatin.

Conclusions
The results of this study highlight PTPRO and GADD45A as potential genes for the diagnosis and treatment of epilepsy.
Salsal: blockchain for vetting cultural object collections
Authors: Khelifi Adel , Altaweel Mark , Hashir Mohammad , Hadjitofi Tasoula , Ghazal Mohammad 
Published: January 2024

Abstract
Many modern cultural object collections suffer from the problem of being obtained in unethical and illegal circumstances. Additionally, information about collections, including their status, object descriptions, and other data need up-to-date information presented to users. We propose a novel blockchain tool called Salsal that enables the vetting of objects, individually or as part of more extensive collections, to meet required ethical and legal guidelines while informing users about relevant information regarding collections. Blockchain provides a better and more rapid way for users to know about collections using a decentralized and immutable ledger technology. Blockchain can be used to incentivize or even pressure collections to vet their objects for ethical and legal guidelines that can benefit the public who use object collections. The prototype software we have made is presented and compared to other blockchains, with code and demonstration provided. We present how our blockchain can enable benefit, providing a useful vetting process for cultural objects, and allowing a user community to contribute to collections in a transparent and secure manner.
Nonlinear dimensionality reduction based visualization of single-cell RNA sequencing data
Authors: Yousuff Mohamed , Babu Rajasekhara , Rathinam Anand 
Published: January 2024

AbstractSingle-cell multi-omics technology has catalyzed a transformative shift in contemporary cell biology, illuminating the nuanced relationship between genotype and phenotype. This paradigm shift hinges on the understanding that while genomic structures remain uniform across cells within an organism, the expression patterns dictate physiological traits. Leveraging high throughput sequencing, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool, enabling comprehensive transcriptomic analysis at unprecedented resolution. This paper navigates through a landscape of dimensionality reduction techniques essential for distilling meaningful insights from the scRNA-seq datasets. Notably, while foundational, Principal Component Analysis may fall short of capturing the intricacies of diverse cell types. In response, nonlinear techniques have garnered traction, offering a more nuanced portrayal of cellular relationships. Among these, Pairwise Controlled Manifold Approximation Projection (PaCMAP) stands out for its capacity to preserve local and global structures. We present an augmented iteration, Compactness Preservation Pairwise Controlled Manifold Approximation Projection (CP-PaCMAP), a novel advancement for scRNA-seq data visualization. Employing benchmark datasets from critical human organs, we demonstrate the superior efficacy of CP-PaCMAP in preserving compactness, offering a pivotal breakthrough for enhanced classification and clustering in scRNA-seq analysis. A comprehensive suite of metrics, including Trustworthiness, Continuity, Mathew Correlation Coefficient, and Mantel test, collectively validate the fidelity and utility of proposed and existing techniques. These metrics provide a multi-dimensional evaluation, elucidating the performance of CP-PaCMAP compared to other dimensionality reduction techniques.
Minimum acceptable diet and associated factors among children aged 6–23 months in Jig-Jiga, Somali region, eastern Ethiopia, 2022
Authors: Farah Shukri , Derese Tariku , Abera Legesse 
Published: January 2024

Abstract
Background
The minimum acceptable diet is the proportion of children aged 6–23 months who consumed the minimum meal frequency and minimum dietary diversity during the previous day or night. The minimum acceptable diet assesses both micronutrient adequacy and the quantity of food consumed during the previous day or night. Inappropriate infant and young child feeding practices during this period result in significant threats to child health through impaired cognitive development. Therefore, this study aims to assess the minimum acceptable diet and associated factors among children aged 6–23 months in Jig-Jiga, Somali region, Eastern Ethiopia.

Methods
A community-based, cross-sectional study was conducted in Jig-Jiga town. A systematic random sampling technique was used to select 536 children aged 6–23 months with their mothers. Data were collected using a pre-tested, structured questionnaire. The data were entered into Epi-data 3.1. The data were cleaned and analyzed using SPSS v20. Bi-variable and multivariable logistic regression analyses were done, and model fitness was checked and tested by the Hosmer-Lemeshow goodness of fit test. The results of the adjusted odds ratio with 95% confidence intervals and P < 0.05 were considered statistically significant.

Result
The overall prevalence of a minimum acceptable diet was 47.2% (95% CI: 43.1–51.6). Occupation of fathers (AOR = 0.5, 95%CI: 0.3–0.8), child age of 6–11 months (AOR = 3.6, 95%CI: 1.7–7.7), age of the mother 15–24 years (AOR = 7.6, 95%CI: 1.5–38.146), 25–34 years (AOR = 5.56, 95%CI: 1.17–26.325), mothers who had only one under-five child (AOR = 2.1, 95%CI: 1.298–3.471), and media as a source of information (AOR = 0.16, 95%CI: 0.061–0.433) were associated with the minimum acceptable diet.

Conclusion
This study showed that the prevalence of a minimum acceptable diet was low. Factors associated with a minimum acceptable diet included the father’s occupation, the child’s age, the mother’s age, having one under-five child, and the media as a source of information. Therefore, interventional strategies that focus on family planning and advocacy for infant and young child feeding are required to improve the provision of a minimum acceptable diet.
Activity provider-facilitated patient and public involvement with care home residents
Authors: Micklewright Kerry , Killett Anne , Akdur Gizdem , Biswas Priti , Blades Pamela , Irvine Lisa , Jones Liz , Meyer Julienne , Ravenscroft Natalie , Woodhead Hilary , Goodman Claire 
Published: January 2024

AbstractBackgroundIn care home research, residents are rarely included in patient and public involvement and engagement (PPIE) despite their lived experiences of day-to-day care. This paper reports on a novel approach to PPIE, developed in response to Covid-19, and utilised in a large UK-based study focused on care homes. PPIE sessions were facilitated on behalf of the research team by Activity Providers (APs) already working within the care homes. This paper provides an account of how PPIE with care home residents can be achieved.MethodsAn exploratory design was used to see if it was possible to support “in-house” PPIE, with researchers working at a distance in partnership with care home staff. The National Activity Providers Association recruited five APs working in care homes. A series of optional discussion or activity sessions were developed by the research team in partnership with APs, tailored to reflect the research topics of interest and to make sessions accessible to residents with differing needs.ResultsAPs facilitated four rounds of PPIE with up to 56 residents per topic, including individuals living with cognitive and communication impairments. Topics discussed included residents’ views on data use, measuring quality of life and the prioritisation of care-related data for study collection. Feedback from the residents was observed to have unexpected and positive changes to participating care homes’ practice. APs valued participation and working with researchers. They identified acquisition of new skills and insights into residents’ thoughts and preferences as direct benefits. Challenges included time pressures on APs and managing emotive feedback. APs were able to approach residents at times convenient to them and in ways that best suited their individual needs. PPIE with residents provided different perspectives, particularly with respect to the importance of different types of data, and constructive challenge about some of the research team’s assumptions.ConclusionsPPIE with APs as research partners is a promising approach to working in an inclusive and participatory way with care home residents. The voices of older care home residents, including those living with cognitive or communicative impairments, are important for the successful and meaningful completion of research.
Choroidal measurements in decision making for retinopathy of prematurity: a decision tree analysis
Authors: Bahar Mohammadreza Mehrabi , Salari Farhad , Dastjanifarahani Afsar , Ghassemi Fariba , Harper C. Armitage , Bazvand Fatemeh 
Published: January 2024

Abstract
Background
To compare the choroidal thickness and vascular profile of premature infants with ROP (retinopathy of prematurity) using a handheld SD-OCT device.

Methods
We performed horizontal SD-OCT scans through the fovea in 115 eyes of 66 premature infants. Premature infants included 2 groups [infants with ROP requiring treatment (as treatment group) vs. infants without ROP or with ROP not- requiring treatment (as no-treatment group)] Choroidal thicknesses (CT) were measured at 5 points, including the fovea, 250 µm, and 500 µm mm nasal and temporal to the fovea. The choroidal vascularity index (CVI) and choroidal stromal index (CSI) were also calculated. The classification and regression tree (CRT) algorithm was used to predict the need for treatment based on all OCT characteristics.

Results
Mean CT was higher in 500 µm nasal to the fovea compared to temporal CT (275.8 ± 64.8 and 257.1 ± 57.07, P value < 0.03). No statistically significant difference was found regarding CVI, corrected CVI, and temporal and nasal CT in the treatment group versus the no-treatment group. The foveal CT was significantly lower in ROP patients with the plus disease compared to not-plus ROP (P value = 0.03. ANOVA, Bonferroni posthoc test). CT was not significantly different between plus and pre-plus patients (P-value = 0.9, ANOVA, Bonferroni posthoc test). No significant relationship was found between the stage of ROP and choroidal thickness (P value > 0.05, GEE). The decision tree analysis showed that in infants with ROP, the most important predictor for the need for treatment is CSI.

Conclusion
This study delineated the possible effectiveness of choroidal measurements as an additive to decision-making for ROP. We also demonstrated that choroidal involution is associated with the presence of plus disease, not with the stage of ROP. We demonstrated that choroidal measurements are very sensitive but not specific tools for assessing the need for treatment in ROP patients.
Financial Toxicity and Health-Related Quality of Life Profile of Patients With Hematologic Malignancies Treated in a Universal Health Care System
Authors: Sparano Francesco , Giesinger Johannes M. , Gaidano Gianluca , Anota Amelie , Cavo Michele , Brini Alberto , Voso Maria Teresa , Venditti Adriano , Perrone Francesco , Di Maio Massimo , Luppi Mario , Baron Frederic , Platzbecker Uwe , Fazi Paola , Vignetti Marco , Efficace Fabio 
Published: January 2024

PURPOSE We investigated the association of financial toxicity (FT) with the health-related quality of life (HRQoL) profile of patients with hematologic malignancies treated in a universal health care system. METHODS We did a secondary analysis of six multicenter studies enrolling patients with hematologic malignancies. FT was evaluated using the financial difficulties item of the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 (EORTC QLQ-C30). Multivariable linear regression models were used to assess the mean differences in HRQoL scores between patients with or without FT, while adjusting for key potential confounding factors. We also examined the prevalence of clinically important problems and symptoms by the experience of FT, using established thresholds for the EORTC QLQ-C30. Multivariable binary logistic regression analysis was performed to explore the risk factors associated with FT. RESULTS Overall, 1,847 patients were analyzed, of whom 441 (23.9%) reported FT. We observed statistically and clinically relevant worse scores for patients with FT compared with those without FT for all the EORTC QLQ-C30 scales. The three largest clinically relevant mean differences between patients with and without FT were observed in pain (∆ = 19.6 [95% CI, 15.7 to 23.5]; P < .001), social functioning (∆ = –18.9 [95% CI, –22.5 to –15.2]; P < .001), and role functioning (Δ = –17.7 [95% CI, –22.1 to –13.3]; P < .001). Patients with FT tended to report a higher prevalence of clinically important problems and symptoms across all EORTC QLQ-C30 scales. In the univariable and multivariable analyses, the presence of FT was associated with the presence of comorbidities, an Eastern Cooperative Oncology Group performance status ≥1, and not receiving a salary. CONCLUSION Patients with hematologic malignancies treated in the setting of a universal health care system who experience FT have a worse HRQoL profile compared with those without FT.
A rheological model for spheroids including extra-cellular matrix
Authors: Verdier Claude , Palade Liviu I. 
Published: January 2024

Abstract
The rheology of spheroids has been studied intensively recently and it was shown that the presence of the Extra-Cellular Matrix (ECM) can have significant effects on the overall behaviour of these biological systems. Collagen I can indeed be a proxy between cells and bring new intriguing effects, as its content increases. To investigate these effects further, a two-phase emulsion model is proposed including interactions between cells and the ECM. Starting with the single cell and collagen individual viscoelastic properties, the model can be tested against previously obtained data for spheroids. The model has interesting features and capabilities for it covers a variety of behaviours and uses fitting parameters such as collagen and cell concentration, as well as adhesion energy. It is shown that the final intercellular collagen content can be large as compared to the initial one, and that this increase in collagen content induces a larger packing of cells, together with a larger adhesion energy.
Non-equilibrium attractor for non-linear stochastic dynamics
Authors: Patrón A. , Sánchez-Rey B. , Trizac E. , Prados A. 
Published: January 2024

Abstract
We study the dynamical behaviour of mesoscopic systems in contact with a thermal bath, described either via a non-linear Langevin equation at the trajectory level —or the corresponding Fokker-Planck equation for the probability distribution function at the ensemble level. Our focus is put on one-dimensional —or d-dimensional isotropic— systems in confining potentials, with detailed balance —fluctuation-dissipation thus holds, and the stationary probability distribution has the canonical form at the bath temperature. When quenching the bath temperature to low enough values, a far-from-equilibrium state emerges that rules the dynamics over a characteristic intermediate timescale. Such a long-lived state has a Dirac-delta probability distribution function and attracts all solutions over this intermediate timescale, in which the initial conditions are immaterial while the influence of the bath is still negligible. Numerical evidence and qualitative physical arguments suggest that the above picture extends to higher-dimensional systems, with anisotropy and interactions.
Microtubule polyglutamylation is an essential regulator of cytoskeletal integrity in Trypanosoma brucei
Authors: Jentzsch Jana , Wunderlich Hannes , Thein Marinus , Bechthold Julia , Brehm Lucas , Krauss Sebastian W. , Weiss Matthias , Ersfeld Klaus 
Published: January 2024

ABSTRACT
Tubulin polyglutamylation, catalysed by members of the tubulin tyrosine ligase-like (TTLL) protein family, is an evolutionarily highly conserved mechanism involved in the regulation of microtubule dynamics and function in eukaryotes. In the protozoan parasite Trypanosoma brucei, the microtubule cytoskeleton is essential for cell motility and maintaining cell shape. In a previous study, we showed that T. brucei TTLL6A and TTLL12B are required to regulate microtubule dynamics at the posterior cell pole. Here, using gene deletion, we show that the polyglutamylase TTLL1 is essential for the integrity of the highly organised microtubule structure at the cell pole, with a phenotype distinct from that observed in TTLL6A- and TTLL12B-depleted cells. Reduced polyglutamylation in TTLL1-deficient cells also leads to increased levels in tubulin tyrosination, providing new evidence for an interplay between the tubulin tyrosination and detyrosination cycle and polyglutamylation. We also show that TTLL1 acts differentially on specific microtubule doublets of the flagellar axoneme, although the absence of TTLL1 appears to have no measurable effect on cell motility.
Pedaling to Performance: Exploring the Effects of Pre-Tournament Cycling on Rocket League Esports Performance
Authors: Gaige Connor J. , Allen Leah E. , Krieger Joesi M. , Hagele Anthony M. , Sunderland Kyle L. , Kerksick Chad M. , Mumford Petey W. 
Published: January 2024

ABSTRACTPurposeExercise has been well documented to elicit cognitive benefits; therefore, we aimed to examine the effect on performance of a single bout of cycling exercise before an esports tournament.MethodsTwenty healthy males (age, 24 ± 6 yr; height, 177.3 ± 7.3 cm; body mass, 80.7 ± 20.9 kg; ranked between Gold 1 and Champion 3) participated in a randomized, counterbalanced crossover study involving 1) a 20-min cycling exercise bout at 60%–70% heart rate reserve or 2) 20 min of rest before competing in an esports tournament. Tournaments consisted of 10 paired, rank-matched Rocket League 1 vs. 1 matches played in three series. Participants were assessed before and after the tournament for hemodynamics, cognition, and gameplay mechanics. Heart rate was monitored throughout the tournament, with gameplay performance and post-match surveys completed after each match.ResultsExercising before the tournament led to higher initial fatigue (P= 0.002), higher average heart rates throughout the tournament (P< 0.001), lower perceived individual performance in series 1 (P= 0.03), lower overall perceived opponent performance (P= 0.03), and improved goal percentage in series 3 (P= 0.04) compared with rest. Participant save percentage decreased over time in both conditions (P= 0.04). No differences were observed in cognition measures, gameplay mechanics, or hemodynamics.ConclusionsA single bout of cycling exercise completed before a Rocket League 1 vs. 1 tournament had no negative effects on performance or wins. It did, however, lower perceived match performance and fatigue at the beginning of the tournament while improving goal percentage during the last series.