bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retinograd-AI: An Open-source Automated Fundus Autofluorescence Retinal Image Gradability Assessment for Inherited Retinal Dystrophies
Authors: Naik Gunjan , Al-Khuzaei Saoud , Moghul Ismail , de Guimaraes Thales A. C. , Sen Sagnik , Daich Varela Malena , Liu Yichen , Bagga Pallavi , Fu Dun Jack , Moosajee Mariya , Madhusudhan Savita , Webster Andrew , De Silva Samantha , Patel Praveen J. , Mahroo Omar , Downes Susan M , Michaelides Michel , Balaskas Konstantinos , Pontikos Nikolas , Woof William 
Published: August 2024

AbstractPurposeTo develop an automated system for assessing the quality of Fundus Autofluorescence (FAF) images in patients with inherited retinal diseases (IRD).MethodsWe annotated a dataset of 2445 FAF images from patients with Inherited Retinal Dystrophies which were assessed by three different expert graders. Graders marked images as either gradable (acceptable quality) or ungradable (poor quality), following a strict grading protocol. This dataset was used to train a Convolutional Neural Network (CNN) classification model to predict the gradability label of FAF images.ResultsRetinograd-AI achieves a performance of 91% accuracy on our held-out dataset of 133 images with an Area Under the Receiver Operator Characteristic (AUROC) of 0.94, indicating high performance in distinguishing between gradable and ungradable images. Applying Retinograd-AI to our full internal dataset, the highest proportion of gradable images was found in the 30-50 years age group, where 84.3% of images were rated as gradable, while the lowest was in 0-15 year olds, where only 45.2% of images were rated as gradable. 83.4% of images from male patients were rated as gradable, and 90.6% of images from female patients. By genotype, from the 30 most common genetic diagnoses, the highest proportion of gradable images was in patients with disease causing variants inPRPH2(93.9%), while the lowest wasRDH12(28.6%). Eye2Gene single-image gene classification top-5 accuracy on images rated by Retinograd-AI was 69.2%, while top-5 accuracy on images rated as ungradable was 39.0%. Retinograd-AI is open-sourced, and the source code and network weights are available under an MIT licence on GitHub athttps://github.com/Eye2Gene/retinograd-aiConclusionsRetinograd-AI is the first open-source AI model for automated retinal image quality assessment of FAF images in IRDs. Automated gradability assessment through Retinograd AI enables large scale analysis of retinal images, which is an essential part of developing good analysis pipelines, and real-time quality assessment, which is essential for deployment of AI algorithms, such as Eye2Gene, into clinical settings. Due to the diverse nature of IRD pathologies, Retinograd-AI may also be applicable to FAF imaging for other conditions, either in its current form or through transfer learning and fine-tuning.
Mass spectrometric profiling of estrogen and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling
Authors: Li Vince W. , Dong Tien S. , Funes Diana , Hernandez Laura , Reddy Srinivasa T. , Mayer Emeran , Chang Lin , Meriwether David 
Published: August 2024

AbstractEstrogen and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no reports of estrogen measured in human stool. This methodological limitation in turn limits our understanding of the relationship between systemic and intestinal estrogen. We thus developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method for measuring free and conjugated forms of 15 estrogens and estrogen metabolites in human stool and plasma. We first investigated human stool and plasma estrogen in healthy control males; follicular and luteal phase premenopausal females; and postmenopausal females. Most estrogens were present in the plasma and stool of all groups, and plasma estrogen levels correlated with stool estrogen levels. In stool, estrogens were higher in premenopausal females, with estrogen levels rising across the menstrual cycle. We further combined these measures with shotgun metagenomic sequencing of the stool microbiomes. The level of estrogen deconjugation enzyme gene copy number (beta-glucuronidase + arylsulfatase) was higher in premenopausal females; while the gene copy numbers of beta-glucuronidase + arylsulfatase, but not beta-glucuronidase alone, correlated with reactivated stool estrogen in all groups. Moreover, deconjugation enzyme gene copy number correlated with plasma total estrogen in males and with individual plasma estrogen metabolites in all groups. These results support the hypothesis that gut microbial beta-glucuronidase and arylsulfatase control the reactivation of gut estrogen while modulating systemic levels through the uptake and recirculation of reactivated estrogen.
Biased recruitment of H3.3 by HIRA is dictated by de-/acetylation and determines transcription memory and response
Authors: Usha Satheesan Sandra , Chakrabarti Sourankur , Fulzele Amit , Marcellin Marlène , Locard-Paulet Marie , Peredo Anne Gonzalez-de , Kolthur-Seetharam Ullas 
Published: August 2024

AbstractChromatin plasticity and epigenetic memory, fundamental for eukaryotic biology, are determined by differential/regulatedde novodeposition or recycling of pre-existing histones, which in turn dictate transcriptional programs. Recruitment of the histone-H3 variant, H3.3, mediated by the HIRA chaperone complex, is both causally and consequentially associated with transcription. Despite decades of work, endogenous regulatory mechanisms that differentiate betweende novodeposition and recycling activities of HIRA are still unknown. Here, we have investigated the pivotal role of HIRA de-/acetylation in regulating its function. Our results unequivocally establish function separation effects of acetyl and deacetyl mimic mutations of lysine-600, vis-à-visde novodeposition or recycling of H3.3, respectively. Importantly, we demonstrate that HIRA deacetylation-dependent biased H3.3 recycling determines transcriptional output, possibly through preferential enrichment of H3.3-K36me3. Besides unraveling tunable regulatory mechanism that governs HIRA function, we illustrate a causal link between the chaperone activity, biased recruitment of pre-existing histones, and gene expression.
AnIn-VitroStandardized Protocol for Preparing Smoke Extract Media from Cigarette, Electronic Cigarette and Waterpipe
Authors: Al-Hashimi Amel , Shah Jagrut , Carpenter Roger , Morgan Winston , Meah Mohammed , Ruchaya Prashant J. 
Published: August 2024

AbstractCigarette smoke exposure is a major risk factor for various diseases, and in vitro studies using smoke medium (SM) are crucial for elucidating underlying mechanisms. However, the lack of standardized protocols for SM preparation has led to inconsistencies in experimental results. This paper presents an optimized protocol for reproducible generation of SM from conventional cigarette smoke extract (CSE), electronic cigarette smoke (ECS), and waterpipe vapour (WPV). The protocol involves:A custom-built apparatus for smoke capture in a cell culture mediumSpecific parameters mimicking human smoking topographyRigorous aseptic techniques and safety measuresExtensive details are provided for material preparation, apparatus setup, smoke generation procedures, and post-processing steps. This standardized method enables reliable in vitro exposure models, easing comparative studies across different tobacco products. To prove protocol consistency, we present optical. Additionally, we highlight the protocol’s utility by figuring out the SM quality through analysing O.D. data and morphological changes, cell viability assays, ELISA and gene expression analyses i.e., RNA sequencing through severalin-vitromodels, i.e., Human Umbilical Vein Endothelial Cells, (HUVECs,Merck), human leukaemia monocytic cell line (THP-1, Sigma) and induced pluripotent stem cells differentiated to cardiomyocytes(iPSC-CMs,Axol)respectively. This optimized protocol addresses variability in SM preparation, enabling consistent investigations into smoke-induced pathologies and potential therapeutic interventions.Graphical abstractSpecifications table
DROSHA, DICER and Damage-Induced long ncRNA control BMI1-dependent transcriptional repression at DNA double-strand break
Authors: Esposito Francesca , Capozzo Ilaria , Modafferi Stefania , Gioia Ubaldo , Manfredi Letizia , Iannelli Fabio , Colantoni Alessio , Riccardi Adelaide , di Lillo Alessia , Tavella Sara , Cabrini Matteo , d’Adda di Fagagna Fabrizio , Francia Sofia 
Published: August 2024

AbstractGenome integrity is safeguarded by the DNA damage response (DDR). Controlled transcriptional dampening of genes surrounding DNA double-strand breaks (DSBs) has been shown to facilitate DNA repair. This phenomenon, defined as DSB-induced silencing incis(DISC), involves the DDR apical kinase ATM and the Polycomb Repressive Complex 1 (PRC1). Conversely, DSBs have also been reported to inducede novotranscription of damaged-induced long non-coding RNAs (dilncRNAs) in a MRE11-RAD50-NBS1 (MNR) complex-dependent manner. MRN also controls the recruitment to DSB of the ribonuclease DROSHA, which together with DICER, stimulates DDR signaling and DNA repair. Here, we reconcile these apparently contrasting observations by showing that dilncRNA, together with DROSHA and DICER, but not GW182-like proteins required for miRNA-mediated gene silencing, controls DISC. Indeed, similarly to ATM, MRN inhibition abolishes DISC while pharmacological enhancement of DICER ribonuclease activity by Enoxacin improves DISC. Importantly, Enoxacin administration restores DISC upon ATM inhibition, demonstrating that DICER promotes DISC independently from ATM. Differently, Enoxacin does not restore DISC upon MRN inhibition, suggesting that DICER acts downstream to dilncRNA biogenesis and DROSHA recruitment. Mechanistically, we show that DROSHA and DICER control the recruitment of the PRC1 component BMI1 at DSBs and the consequent H2A-K119 ubiquitination. Upon DSBs formation, BMI1 and DROSHA interact in an RNA-dependent manner. Indeed, BMI1 associates to dilncRNA and do so in a DROSHA- and DICER-dependent manner. Importantly, inhibition of dilncRNA function by antisense oligonucleotides or Cas13-mediated targeting is sufficient to reduce BMI1 recruitment and DISC at individual loci. We propose that dilncRNAs together with DROSHA and DICER control DISC at genomic DSB by supporting PRC1 recruitment and chromatin ubiquitination.
A modified decision tree improves generalization across multiple brains proteomic data sets and reveals the role of ferroptosis in Alzheimer’s disease
Authors: Ivanov Mark V. , Kopeykina Anna S. , Kazakova Elizaveta M. , Tarasova Irina A. , Sun Zhao , Postoenko Valeriy I. , Yang Jinghua , Gorshkov Mikhail V. 
Published: August 2024

AbstractLow generalization to the patient cohort and variety of experimental conditions in the proteomic search for disease biomarkers are among the main reasons for the bumpy road of quantitative proteomics from discovery stage to clinical validation. Only a small fraction of biomarkers discovered so far by proteomic analysis reaches clinical trials. Here, we presented a machine learning-based workflow for proteomics data analysis, which partially solves some of these issues. In particular, we used a customized decision tree model, which was regulated using a newly introduced parameter, min_cohorts_leaf, that resulted in better generalization of trained models. Further, we analyzed the trend of feature importance’s curve as a function of min_cohorts_leaf parameter and found that it could be used for accurate feature selection to obtain a list of proteins with significantly improved generalization. Finally, we demonstrated that the recently introduced DirectMS1 search algorithm for protein identification and quantitation provides a simple, yet, a highly efficient solution for the problem of combining multiple data sets obtained using different experimental settings. The developed workflow was tested using five published LC-MS/MS data sets obtained in the large consortia studies of Alzheimer’s disease brain samples. The selected data sets consist of 535 files in total analyzed using label-free single-shot data-dependent or data-independent acquisitions. Using the proposed modified ExtraTrees model we found that the expressions of two proteins involved in ferroptosis Serotransferrin TRFE and DNA repair nuclease/redox regulator APEX1, are important for explaining a lack of dementia for patients with the presence of neuritic plaques and neurofibrillary tangles.
Ωc→π+(π0,η)πΞ*
,
π+(π0,η)K¯Σ*
reactions and the two
Ξ(1820)
states
Authors: Liang Wei-Hong , Molina Raquel , Oset Eulogio 
Published: August 2024

We have studied the Ωc→π+(π0,η)πΞ* and Ωc→π+(π0,η)K¯Σ* decays, where the final πΞ* or K¯Σ* comes from the decay of two resonances around the nominal Ξ(1820), which are generated from the interaction of coupled channels made of a pseudoscalar and a baryon of the decuplet. The πΞ* mass distributions obtained in the six different reactions studied are quite different, and we single out four of them, which are free of a tree level contribution, showing more clearly the effect of the resonances. The lower mass resonance is clearly seen as a sharp peak, but the higher mass resonance manifests itself through an interference with the lower one that leads to a dip in the mass distribution around 1850 MeV. Such a feature is similar to the dip observed in the S-wave ππ cross section around the 980 MeV coming from the interference of the f0(500) and f0(980) resonances. Its observation in coming upgrades of present facilities will shed light on the existence of these two resonances and their nature. On the other hand, when the Ωc→π+(π0,η)K¯Σ* reactions are studied, both peaks are observed.

Published by the American Physical Society
2024
Astrophysical constraints from synchrotron emission on very massive decaying dark matter
Authors: Munbodh Pankaj , Profumo Stefano 
Published: August 2024

If the cosmological dark matter (DM) couples to Standard Model (SM) fields, it can decay promptly to SM states in a highly energetic hard process, which subsequently showers and hadronizes to give stable particles including e±, γ, p±, and νν¯ at lower energy. If the DM particle is very heavy, the high-energy e±, due to the Klein-Nishina cross section suppression, preferentially lose energy via synchrotron emission which, in turn, can be of unusually high energies. Here, we present previously unexplored bounds on heavy decaying DM up to the Planck scale, by studying the synchrotron emission from the e± produced in the ambient Galactic magnetic field. In particular, we explore the sensitivity of the resulting constraints on the DM decay width to (i) different SM decay channels, to (ii) the Galactic magnetic field configurations, and to (iii) various different DM density profiles proposed in the literature. We find that constraints from the synchrotron component complement and improve on constraints from very high-energy cosmic-ray and gamma-ray observatories targeting the prompt emission when the DM is sufficiently massive, most significantly for masses in excess of 1012  GeV.

Published by the American Physical Society
2024
Search for two-body
B
meson decays to
Λ0
and
Ωc(*)0
Authors: Savinov V. , Adachi I. , Ahn J. K. , Aihara H. , Asner D. M. , Atmacan H. , Ayad R. , Banerjee Sw. , Bennett J. , Bessner M. , Bhardwaj V. , Biswas D. , Bobrov A. , Bodrov D. , Borah J. , Bračko M. , Branchini P. , Browder T. E. , Budano A. , Červenkov D. , Chang M.-C. , Chang P. , Cheon B. G. , Cho K. , Choi S.-K. , Choi Y. , Choudhury S. , Dash N. , De Nardo G. , De Pietro G. , Dhamija R. , Di Capua F. , Dingfelder J. , Doležal Z. , Dubey S. , Ecker P. , Epifanov D. , Farino M. , Ferlewicz D. , Fulsom B. G. , Gaur V. , Giri A. , Goldenzweig P. , Graziani E. , Gu T. , Guan Y. , Gudkova K. , Hadjivasiliou C. , Hayashii H. , Hazra S. , Hedges M. T. , Hou W.-S. , Inami K. , Ipsita N. , Ishikawa A. , Itoh R. , Iwasaki M. , Jacobs W. W. , Jin Y. , Kalita D. , Kim C. H. , Kim D. Y. , Kim K.-H. , Kim Y.-K. , Kinoshita K. , Kodyš P. , Korobov A. , Korpar S. , Kovalenko E. , Križan P. , Krokovny P. , Kuhr T. , Kumar R. , Kumita T. , Kuzmin A. , Kwon Y.-J. , Lai Y.-T. , Lam T. , Lange J. S. , Li L. K. , Li Y. , Li Y. B. , Li Gioi L. , Libby J. , Liventsev D. , Luo T. , Ma Y. , Masuda M. , Matsuda T. , Maurya S. K. , Meier F. , Merola M. , Nakamura I. , Nakao M. , Natkaniec Z. , Nayak L. , Nayak M. , Nishida S. , Ogawa S. , Ono H. , Pakhlov P. , Pakhlova G. , Pardi S. , Park H. , Park J. , Park S.-H. , Passeri A. , Patra S. , Pedlar T. K. , Pestotnik R. , Piilonen L. E. , Podobnik T. , Prencipe E. , Prim M. T. , Russo G. , Sandilya S. , Santelj L. , Schnell G. , Schwanda C. , Seino Y. , Senyo K. , Shan W. , Sharma C. , Shiu J.-G. , Solovieva E. , Starič M. , Sumihama M. , Takizawa M. , Tamponi U. , Tanida K. , Tenchini F. , Tiwary R. , Trabelsi K. , Uchida M. , Unno Y. , Uno S. , Varvell K. E. , Wang E. , Watanuki S. , Won E. , Xu X. , Yabsley B. D. , Yan W. , Yin J. H. , Yuan C. Z. , Yuan L. , Yusa Y. , Zhang Z. P. , Zhilich V. , Zhukova V. ,   The Belle Collaboration
Published: August 2024

We report the results of the first search for Standard Model and baryon-number-violating two-body decays of the neutral B mesons to Λ0 and Ωc(*)0 using 711  fb−1 of data collected at the ϒ(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e− collider. We observe no evidence of signal from any such decays and set 95% confidence-level upper limits on the products of B0 and B¯0 branching fractions for these two-body decays with B(Ωc0→π+Ω−) in the range between 9.5×10−8 and 31.2×10−8.

Published by the American Physical Society
2024
Factors affecting citizen intention toward AI acceptance and adoption: the moderating role of government regulations
Authors: Alzebda Said , Matar Mohammed A.I. 
Published: August 2024

Purpose
This paper aims to explore factors impacting citizen intention toward artificial intelligence (AI) adoption, considering government regulation as a moderating variable. It focuses on the Palestinian Cellular Communications Sector in Gaza Strip, providing insights into the citizen-AI relationship dynamics. The research contributes to enhancing comprehension of AI technology from clients’ perspective.

Design/methodology/approach
To test the hypotheses, a questionnaire was used in an empirical study to collect primary data. In total, 347 Palestinian citizens responded to the survey.

Findings
The findings of this paper reveal that perceived usefulness, perceived ease of use, perceived risks, social influence, user experience and privacy and security concerns significantly influence citizen intention toward AI adoption. Furthermore, government regulations as a moderating variable strengthen the impact of perceived usefulness, perceived ease of use, perceived risks, social influence, user experience and privacy and security concerns on citizen intention toward AI acceptance and adoption. Thus, further research should explore specific domains and cultural contexts to gain a more comprehensive understanding of the factors shaping acceptance and adoption.

Research limitations/implications
The findings of the study should be understood in the context of their limitations. First, the study ignored cultural or domain-specific subtleties in favor of generic characteristics, which calls for more research in these particular circumstances. Second, relying on self-reported data might result in biases and limitations due to subjectivity in reporting, indicating the necessity for alternate data gathering methods and approaches in future research.

Practical implications
Policymakers, developers and organizations working to promote the acceptability and implementation of AI applications should consider the practical implications of this study’s results. To secure the long-term use of AI technologies in a responsible and user-centric way, policymakers should give priority to public education and awareness, user-centered design and ethical AI development techniques. They should also stimulate partnerships and create monitoring systems.

Originality/value
This paper investigates the originality of factors that influence citizen intention toward AI acceptance and adoption. It uniquely examines the moderating role of government regulations in shaping this intention. By addressing this novel aspect, the paper contributes to advancing our understanding of the complex dynamics surrounding citizen intentions toward AI applications.
Development of ancient Chinese inscription rubbings knowledge base in the context of cultural communication and art appreciation
Authors: Qiu Kaiyu , Xia Cuijuan , Liu QianQian 
Published: August 2024

PurposeTo promote the cultural communication and art appreciation of Inscriptions and calligraphy which are important cultural heritages in China, with a broad crowd base and educational appreciation value, by using digital humanities methods and technologies, the paper aims to discuss how to develop a new user-oriented knowledge base according to user needs for inscription rubbings research and appreciation.Design/methodology/approachThe paper investigates user needs and current problems on the basis of status quo and summation of extensive service experience; validates the rationality of requirements and user scenarios with user research methods including focus groups, interviews and behavior observations; then designs and develops the technical solution of data process, knowledge base construction and service platform through experimental research methods based on agile project management.FindingsThe paper proposes a new reading mode for browsing and appreciation inscription rubbing works, a diverse knowledge-integrated knowledge organizational structure, a systematic user experience and service guiding framework which can be widely applicable to the development of other cultural heritage knowledge bases. Apart from that, the paper puts forward intelligent service development goals for the future.Originality/valueThe paper proposes a new reading mode with the overall functions and user experience design and development for browsing and appreciation inscription rubbing works, a diverse knowledge-integrated knowledge organizational structure, a systematic user experience and service guiding framework which can be widely applicable to the development of other cultural heritage knowledge bases. Apart from that, the paper puts forward intelligent service development goals for the future.