bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds
Authors: Zhao Qiangsen , Yin Zhongtao , Hou Zhuocheng 
Published: January 2025

Abstract

Background
Chickens and ducks are vital sources of animal protein for humans. Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species, highlighting the need for more comprehensive genomes. The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. We aim to complete the chicken and duck genomes, recover missing genes, and reveal common and unique chromosomal features between birds.

Results
The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies, with quality values of 36.65 and 44.17 for Silkie and Mallard, respectively; and BUSCO scores of 96.55% and 96.97% for Silkie and Mallard, respectively; the mapping rates reached over 99.52% for both assembled genomes, these evaluation results ensured high completeness and accuracy. We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard, respectively, and assembled gap-free sex chromosomes in Mallard for the first time. Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content, repetitive sequence abundance, gene density, and levels of 5mC methylation. Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes, with Mallard centromeres being invaded by CR1. The highly heterochromatic W chromosome, which serves as a refuge for ERVs, contains disproportionately long ERVs. Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes, and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome. Finally, we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time, revealing conserved protein structures and tissue-specific expression.

Conclusions
The near telomere-to-telomere assemblies in Mallard and Silkie, with the first gap-free sex chromosomes in ducks, significantly enhanced our understanding of genetic structures in birds, specifically highlighting the distinctive chromosome features between the chicken and duck genomes. This foundational work also provides a series of newly identified missing genes for further investigation.
Evaluation of EGFR-TKIs and ICIs treatment stratification in non-small cell lung cancer using an encrypted multidimensional radiomics approach
Authors: Zhang Xingping , Qiu Xingting , Zhang Yue , Lai Qingwen , Zhang Yanchun , Zhang Guijuan 
Published: January 2025

Abstract

Background
Radiomics holds great potential for the noninvasive evaluation of EGFR-TKIs and ICIs responses, but data privacy and model robustness challenges limit its current efficacy and safety. This study aims to develop and validate an encrypted multidimensional radiomics approach to enhance the stratification and analysis of therapeutic responses.

Materials and methods
This multicenter study incorporated various data types from 506 NSCLC patients, which underwent preprocessing through anonymization methods and were securely encrypted using the AES-CBC algorithm. We developed one clinical model and three radiomics models based on clinical factors and radiomics scores (RadScore) of three distinct regions to evaluate treatment response. Additionally, an integrated radiomics-clinical model was created by combining clinical factors with RadScore. The study also explored the association between different EGFR mutations and PD-1/PD-L1 expression in radiomics biomarkers.

Findings
The radiomics-clinical model demonstrated high performance, with AUC values as follows: EGFR (0.884), 19Del (0.894), L858R (0.881), T790M (0.900), and PD-1/PD-L1 expression (0.893) in the test set. This model outperformed both clinical and single radiomics models. Decision curve analysis further supported its superior clinical utility. Additionally, our findings suggest that the efficacy of EGFR-TKIs and ICIs therapy may not depend on detecting a singular tumor feature or cell type.

Conclusion
The proposed method effectively balances the level of evidence with privacy protection, enhancing the study’s validity and security. Therefore, radiomics biomarkers are expected to complement molecular biology analyses and guide therapeutic strategies for EGFR-TKIs, ICIs, and their combinations.
Dual-modal radiomics ultrasound model to diagnose cervical lymph node metastases of differentiated thyroid carcinoma: a two-center study
Authors: Tang Jiajia , Tian Yan , Ma Jiaojiao , Xi Xuehua , Wang Liangkai , Sun Zhe , Liu Xinyi , Yu Xuejiao , Zhang Bo 
Published: January 2025

Abstract

Objectives
To establish and validate a dual-modal radiomics nomogram from grayscale ultrasound and color doppler flow imaging (CDFI) of cervical lymph nodes (LNs), aiming to improve the diagnostic accuracy of metastatic LNs in differentiated thyroid carcinoma (DTC).

Methods
DTC patients with suspected cervical LNs in two medical centers were retrospectively enrolled. Pathological results were set as gold standard. We extracted radiomic characteristics from grayscale ultrasound and CDFI images, then applied lasso (least absolute shrinkage and selection operator) regression analysis to analyze radiomics features and calculate the rad-score. A nomogram based on rad-score, clinical data, and ultrasound signs was developed. The performance of the model was evaluated using AUC and calibration curve. We also assessed the model’s diagnostic ability in European Thyroid Association (ETA) indeterminate LNs.

Results
377 DTC patients and 726 LNs were enrolled. 37 radiomics features were determined and calculated as rad-score. The dual-modal radiomics model showed good calibration capabilities. The radiomics model displayed higher diagnostic ability than the traditional ultrasound model in the training set [0.871 (95% CI: 0.839–0.904) vs. 0.848 (95% CI: 0.812–0.884), p<0.01], internal test set [0.804 (95% CI: 0.741–0.867) vs. 0.803 (95% CI: 0.74–0.866), p = 0.696], and external validation cohort [0.939 (95% CI: 0.893–0.984) vs. 0.921 (95% CI: 0.857–0.985), p = 0.026]. The radiomics model could also significantly improve the detection rate of metastatic LNs in the ETA indeterminate LN category.

Conclusions
The dual-modal radiomics nomogram can improve the diagnostic accuracy of metastatic LNs of DTC, especially for LNs in ETA indeterminate classification.
Effect of doping Mn ion on the crystal structure and cation distribution in Co1-xMnxFe2O4 compounds
Authors: Tran T. A. , Tran H. C. , Nghiem N. T. , Truong-Son L. V. , Imanova G. T. , Jabarov S. H. 
Published: January 2025

Abstract
In this study, we investigated the effect of Mn doping on the crystal structure and the distribution of cations at tetrahedral and octahedral sites in Co1-x
Mn
x
Fe2O4 compounds (0 ≤ x ≤ 0.4), synthesized utilizing a solid phase reaction method, utilizing X-ray diffraction (XRD) and Raman spectroscopy measurements. The surface morphology and chemical composition of the compounds were studied using scanning electron microscope and X-ray energy dispersive spectroscopy. The Rietveld refinement of XRD data using the Fullprof package demonstrate that all studied samples are single phase spinels with no other detectable phases and have a cubic structure with the space group of Fd-3 m. The lattice constant and unit-cell volume increased with increased Mn doping concentration, which are attributed to the larger ionic radius of Mn in comparison with Co. Both the X-ray diffraction and Raman spectroscopy results demonstrated that doping Mn at the Co-site leads to the movement of Fe cations from the tetrahedral sites to the octahedral ones.
Developing a data pricing framework for data exchange
Authors: Majumdar Rupsa , Gurtoo Anjula , Maileckal Minnu 
Published: January 2025

Abstract
Despite emergence of data markets such as Windows Azure Marketplace and India Urban Data Exchange (IUDX), comprehensive frameworks to determine data pricing and/or determine parameters for profit maximization remain a gap. Data valuation often gets guided by the sellers, ignoring the interests of the buyers. The information asymmetry results in lopsided pricing. The data sellers fail to price optimally, and the buyers are unable to optimize their purchasing decisions, thus, reinforcing the need for a structured data pricing framework. The paper reviews literature and applies the stages as reported by Ritchie and Spencer (in: Bryman, Burgess (eds) Analysing qualitative data, Routledge, London, 1994) for applied policy research to determine the main approaches of data pricing and develop a comprehensive pricing framework. Literature selection on pricing attributes and content analysis classifies data pricing models into five broad but distinct themes, based on the data pricing method, namely data characteristics-based pricing, quality-based pricing, query-based pricing, privacy-based pricing, and organizational value-based pricing. Application of the Ritchie and Spencer stages identifies eight factors, namely customer need, customer assigned value, market maturity, market structure, usable data, data quality, seller reputation and seller objectives as defining and intersecting with the five pricing models. A framework is hence developed to guide data pricing. Thereby, the paper creates a platform for prescribing data pricing formulas.
Posterior reversible encephalopathy syndrome in a young male with IgA nephropathy and chronic kidney disease: a case report from the Maldives
Authors: Dey Rajib Kumar , Khadka Gunjan , Ishaq Shifa , Jaleel Aishath Zeena Abdul , Moosa Aminath Shafeenaz , Muslim Saifullah , Nazeem Ali 
Published: January 2025

Abstract

Background
Posterior reversible encephalopathy syndrome (PRES) is a clinico-radiological condition which is commonly associated with chronic kidney disease (CKD), hypertensive encephalopathy, eclampsia, and the use of cytotoxic drugs. It can cause vasogenic edema of the brain and is characterized by nausea, vomiting, headache, seizures, visual changes, and other focal neurological deficits. Acute hypertension is a predisposing factor for PRES which can occur in CKD patients due to fluid overload. Uremia in CKD patients is also one of the factors for developing PRES. Neuroimaging findings involve posterior white matter edema commonly affecting the parietal and occipital lobes. However, involvement of a non-posterior distribution, mainly in watershed areas, including within the frontal, inferior temporal, cerebellar, and brainstem regions, has been reported.

Case presentation
This case report discusses a case of a 27-year-old male with underlying IgA nephropathy, who presented with generalized throbbing headache, along with 1-day history of nausea and vomiting. This was followed by blurring of vision and 2 episodes of abnormal jerky movements of the body on the first day of admission. On examination, he was found to be hypertensive with no focal neurological deficits. Magnetic resonance imaging (MRI) T2/fluid-attenuated inversion recovery (FLAIR) findings showed hyperintense areas on the right frontal periventricular and right parietal and bilateral occipitotemporal lobes which was suggestive of PRES. The patient was treated with antiepileptics and antihypertensives and was started on dialysis following which his condition improved, and he was discharged in stable condition.

Conclusion
Symptoms of PRES are usually reversible unless cerebral hemorrhage or ischemia has occurred which can result in irreversible neurological deficit or death. Hence, it is crucial to identify and manage PRES promptly. Clinical suspicion and radiological findings aid in early diagnosis. It is also important to be aware of uncommon radiological findings (involvement of the right frontal periventricular area) as in our case.
Allelic variation in an expansin, MdEXP-A1, contributes to flesh firmness at harvest in apples
Authors: Su Qiufang , Feng Yifeng , Li Xianglu , Wang Zidun , Zhong Yuanwen , Zhao Zhengyang , Yang Huijuan 
Published: January 2025

Abstract
Flesh firmness is a core quality trait in apple breeding because of its correlation with ripening and storage. Quantitative trait loci (QTLs) were analyzed through bulked segregant analysis sequence (BSA-seq) and comparative transcriptome analysis (RNA-seq) to explore the genetic basis of firmness formation. In this study, phenotypic data were collected at harvest from 251 F1 hybrids derived from ‘Ruiyang’ and ‘Scilate’, the phenotype values of flesh firmness at harvest were extensively segregated for two consecutive years. A total of 11 candidate intervals were identified on chromosomes 03, 05, 06, 07, 13, and 16 via BSA-seq analysis. We characterized a major QTL on chromosome 16 and selected a candidate gene encoding expansin MdEXP-A1 by combining RNA-seq analysis. Furthermore, the genotype of Del-1166 (homozygous deletion) in the MdEXP-A1 promoter was closely associated with the super-hard phenotype of F1 hybrids, which could be used as a functional marker for marker-assisted selection (MAS) in apple. Functional identification revealed that MdEXP-A1 positively expedited fruit softening in both apple fruits and tomatoes that overexpressed MdEXP-A1. Moreover, the promoter sequence of TE-1166 was experimentally validated containing two binding motifs of MdNAC1, and the absence of the MdEXP-A1 promoter fragment reduced its transcription activity. MdNAC1 also promotes the expression of MdEXP-A1, indicating its potential modulatory role in quality breeding. These findings provide novel insight into the genetic control of flesh firmness by MdEXP-A1.
The Bell Jar: allow the humanities to humanise
Authors: Pushkar Piyush 
Published: January 2025

SUMMARY
This commentary responds to Carona & Atanázio's discussion of Sylvia Plath's novel The Bell Jar in this issue of BJPsych Advances. Although I agree with their emphasis on empathy and sensitivity in medical practice, I argue that they overlook the broader insights of the medical humanities. By examining themes of suicide and patriarchy in The Bell Jar, I highlight how the novel itself, and the humanities scholars who have studied it, provide a counternarrative to the biomedical model, urging a more holistic understanding of psychological distress. I advocate engaging with Plath's work beyond diagnostic criteria, appreciating its cultural and structural dimensions.
Emotional and sleep disturbances among patients previously hospitalized due to COVID-19
Authors: Chatys-Bogacka Żaneta , Mazurkiewicz Iwona , Słowik Joanna , Słowik Agnieszka , Drabik Leszek , Wnuk Marcin 
Published: January 2025

Cel pracyOcena częstości występowania zaburzenia emocjonalnych i snu (ESD) wśród pacjentów po COVID-19 wymagającym hospitalizacji, identyfikacja czynników predykcyjnych i poznanie ich wpływu na symptomy mgły mózgowej (BFS) oraz jakość życia w pracy (QWL).MetodaPacjenci ≥18 lat retrospektywnie raportowali obecność objawów z zakresu ESD (smutek, lęk, niepokój, bezsenność, nadmierna senność w ciągu dnia, koszmary senne) i BFS oraz oceniali QWL przed COVID-19 i w ciągu 0-4, 4-12 i >12 tygodni po infekcji za pomocą poddanego walidacji kwestionariusza w wersji papierowej lub internetowej. Zebrano dane dotyczące wieku, płci, chorób współistniejących, leczenia przed przyjęciem oraz wyników badań laboratoryjnych. Do badania ostatecznie włączono 181 pacjentów (średni wiek 56,02+-13,02 lat, kobiety 37,02%).WynikiCOVID-19 zwiększał 1,6 do 2,2-krotnie zapadalność na ESD w ciągu 0-4, 4-12 i >12 tygodni od infekcji (odpowiednio 66,85%, 60,77% i 50,28%). W analizie wieloczynnikowej, predyktorem nowo powstałych ESD po COVID-19 było stężenie hemoglobiny w ostrej fazie infekcji (OR 0,64, 95%CI: 0,50-0,80 na 1g/L, p=0.001). U pacjentów z istniejącymi wcześniej i nowopowstałymi ESD, COVID-19 zwiększał ryzyko występowania BFS odpowiednio 1,9 i 3,9-krotnie >12 tygodni od infekcji. Pogorszenie QWL >12 tygodni po COVID-19 było związane z wiekiem (OR 0,62, 95%CI:0,37-0,73 na 10 lat, p<0,001), płcią żeńską (OR 3,47, 95%CI:1,40-8,56, p=0,007), występującymi wcześniej (OR 21,58, 95%CI:2,57-181,30, p=0,005) i nowopowstałymi ESD (OR 30,88, 95%CI:3,85-247,90, p=0,001).WnioskiWiększość pacjentów po COVID-19 cierpi na objawy z kręgu ESD, których predyktorem jest stężenie hemoglobiny. ESD zwiększają ryzyko współistnienia BFS. ESD, szczególnie smutek, niepokój, bezsenność i nadmierna senność w ciągu dnia, silnie wpływają na QWL >12 tygodni po COVID-19.
Cultural Homophily and Collaboration in Superstar Teams
Authors: Békés Gábor , Ottaviano Gianmarco I. P. 
Published: January 2025

One may reasonably think that cultural homophily, defined as the tendency to associate with others of similar culture, affects collaboration in multinational teams in general but not in superstar teams of professionals at the top of their industry. The analysis of an exhaustive data set on the passes made by professional European football players in the top five men’s leagues reveals that on the contrary, cultural homophily is persistent, pervasive, and consequential, even in superstar multinational teams of very-high-skill individuals with clear common objectives and aligned incentives who are involved in interactive tasks that are well defined and not particularly culture intensive. This paper was accepted by Olav Sorenson, organizations. Funding: G. Békés thanks the Hungarian Academy of Sciences [Grant “Firms, Strategy and Performance” Lendület] for support. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2022.01799 .
Revealed Wisdom of the Crowd: Bids Predict Loan Quality
Authors: Yao Jiayu , Lin Mingfeng , Wu D. J. 
Published: January 2025

Despite the popularity of the phrase “wisdom of the crowd,” not all crowds are wise because not everyone in them acts in an informed, rational manner. Identifying informative actions, therefore, can help to isolate the truly wise part of a crowd. Motivated by this idea, we evaluate the informational value of investors’ bids using data from online, debt-based crowdfunding, in which we were able to track both investment decisions and ultimate repayment statuses for individual loans. We propose several easily scalable variables derived from the heterogeneity of investors’ bids in terms of size and timing. We first show that loans funded with larger bids relative to the typical bid amount in the market or to the bidder’s historical baseline, particularly early in the bidding period, are less likely to default. More importantly, we perform theory-driven feature engineering and find that these variables improve the predictive performance of state-of-the-art models that have been proposed in this context. Even during the fundraising process, these variables improve predictions of both funding likelihood and loan quality. We discuss the implications of these variables, including loan pricing in secondary markets, crowd wisdom in different market mechanisms, and financial inclusion. Crowdfunding platforms can easily implement these variables to improve market efficiency without compromising investor privacy. This paper was accepted by David Simchi-Levi, information systems. Funding: We gratefully acknowledge the financial support of the Business Analytics Center in the Scheller College of Business and the Ewing Marion Kauffman Foundation. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2022.02575 .
Can Socially Minded Governance Control the Artificial General Intelligence Beast?
Authors: Gans Joshua S. 
Published: January 2025

This paper robustly concludes that it cannot. A model is constructed under idealized conditions that presume that the risks associated with artificial general intelligence (AGI) are real, that safe AGI products are possible, and that there exist socially minded funders who are interested in funding safe AGI, even if this does not maximize profits. It is demonstrated that a socially minded entity formed by such funders would not be able to minimize harm from AGI that unrestricted products released by for-profit firms might create. The reason is that a socially minded entity can only minimize the use of unrestricted AGI products in ex post competition with for-profit firms at a prohibitive financial cost and so, does not preempt the AGI developed by for-profit firms ex ante. This paper was accepted by Maria Guadalupe, business strategy.
Grey areas in restorative dentistry: Part 3. clinical decision making and care planning
Authors: Caplin Robert L 
Published: January 2025

Much of clinical dentistry is subjective rather than objective, and every dental practitioner must make decisions about how to manage the various clinical and ethical challenges that patients present. These clinical decisions are ultimately idiosyncratic and are, therefore, the reason that there can be wide variation between dentists as to how each would manage a particular situation. There is a need to balance the demands of the patient with the ethical requirements of the profession and the moral position of the practitioner. CPD/Clinical Relevance: Whereas some aspects of dentistry are supported by science and the evidence base, many are not, especially in the realm of clinical decision making.
Football and Fascism: The Politics of Popular Culture in Portugal, Rahul Kumar (2023)
Authors: Serapiglia Daniele 
Published: January 2025

Review of: Football and Fascism: The Politics of Popular Culture in Portugal, Rahul Kumar (2023)
Berlin and Boston, MA: De Gruyter, 265 pp.,
ISBN 978-3-11072-122-5, h/bk, €129.00
ISBN 978-3-11072-150-8, e-book, €129.00
Encounters with Jazz on Television in Cold War Era Portugal, Pedro Cravinho (2022)
Authors: Lopes Sofia Vieira 
Published: January 2025

Review of: Encounters with Jazz on Television in Cold War Era Portugal, Pedro Cravinho (2022)
New York and Milton Park: Routledge, 202 pp.,
ISBN 978-0-36748-904-5, p/bk, £39.99
ISBN 978-0-36748-904-5, h/bk, £135.00
ISBN 978-0-36748-904-5, e-book, £35.99
Ilian, I. y Šabec, M. (2024). "Pablo Neruda en el espejo del socialismo". Bruselas: Peter Lang Verlag.
Authors: Sánchez Pablo 
Published: January 2025

Reseña del libro Ilian, I. y Šabec, M. (2024). Pablo Neruda en el espejo del socialismo. Bruselas: Peter Lang Verlag, 432 pp, ISBN: 9783034349055