bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)
Authors: Paudel Dev , Parrish S Brooks , Peng Ze , Parajuli Saroj , Deng Zhanao 
Published: February 2025

Abstract
Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the cultivated primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers &gt;92% of the genome length and contains over 98% of complete BUSCOs. Approximately 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87 968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.
Integrating State-Space Modeling, Parameter Estimation, Deep Learning, and Docking Techniques in Drug Repurposing: A Case Study on COVID-19 Cytokine Storm
Authors: Bakshi Abhisek , Gangopadhyay Kaustav , Basak Sujit , De Rajat K , Sengupta Souvik , Dasgupta Abhijit 
Published: February 2025

Abstract

Objective
This study addresses the significant challenges posed by emerging SARS-CoV-2 variants, particularly in developing diagnostics and therapeutics. Drug repurposing is investigated by identifying critical regulatory proteins impacted by the virus, providing rapid and effective therapeutic solutions for better disease management.

Materials and Methods
We employed a comprehensive approach combining mathematical modeling and efficient parameter estimation to study the transient responses of regulatory proteins in both normal and virus-infected cells. Proportional-integral-derivative (PID) controllers were used to pinpoint specific protein targets for therapeutic intervention. Additionally, advanced deep learning models and molecular docking techniques were applied to analyze drug-target and drug-drug interactions, ensuring both efficacy and safety of the proposed treatments. This approach was applied to a case study focused on the cytokine storm in COVID-19, centering on Angiotensin-converting enzyme 2 (ACE2), which plays a key role in SARS-CoV-2 infection.

Results
Our findings suggest that activating ACE2 presents a promising therapeutic strategy, whereas inhibiting AT1R seems less effective. Deep learning models, combined with molecular docking, identified Lomefloxacin and Fostamatinib as stable drugs with no significant thermodynamic interactions, suggesting their safe concurrent use in managing COVID-19-induced cytokine storms.

Discussion
The results highlight the potential of ACE2 activation in mitigating lung injury and severe inflammation caused by SARS-CoV-2. This integrated approach accelerates the identification of safe and effective treatment options for emerging viral variants.

Conclusion
This framework provides an efficient method for identifying critical regulatory proteins and advancing drug repurposing, contributing to the rapid development of therapeutic strategies for COVID-19 and future global pandemics.
Effects of Cocoa Extract Supplementation and Multivitamin/Multimineral Supplements on Self-Reported Fractures in the Cocoa Supplement and Multivitamins Outcomes Study (COSMOS) Randomized Clinical Trial
Authors: Crandall Carolyn J , Chou Sharon , Kim Eunjung , Ratnarajah Dana , Cook Nancy R , Clar Allison , Sesso Howard D , Manson JoAnn E , LeBoff Meryl S 
Published: February 2025

Abstract
Osteoporosis is a major public health problem among older adults. Forty percent of older U.S. adults take multivitamin/multimineral (MVM) supplementation. The effects of MVM supplementation on fractures is unclear. Preclinical and observational studies suggest that MVM and flavanols may have beneficial effects on bone. We conducted an ancillary study to COcoa Supplement and Multivitamin Outcomes Study (COSMOS; NCT05232669) designed to investigate incident fracture and injurious falls in 21 442 COSMOS participants (12 666 females aged ≥65 years and 8776 males aged ≥60 years) randomized in a 2x2 factorial design to 1 of 4 intervention groups: cocoa extract + MVM, cocoa extract + MVM placebo, cocoa extract placebo + MVM, or double placebo. The daily cocoa extract supplement contained 500 mg/d flavanols and 80 mg/d (–)-epicatechin (Mars Edge); the daily MVM supplement was Centrum Silver® (Haleon). The median (interquartile range) duration of the intervention was 3.6 (3.2-4.2) years. Annually, participants self-reported incident fractures. In intention-to-treat analyses, we examined the effects of cocoa extract and MVM on the primary outcomes of total clinical fracture (hip, upper leg, forearm/wrist, pelvis, upper arm/shoulder, spine, knee, or other), hip fracture, and nonvertebral fracture, and secondary outcomes of clinical spine, forearm/wrist, major osteoporotic, and pelvic fracture using Cox proportional hazards models. During the intervention period, 2083 incident clinical fractures occurred. Compared with placebo, cocoa extract was not significantly associated with lower risk of incident clinical fracture (adjusted hazard ratio [aHR] 1.03, 95% CI 0.95-1.12) or nonvertebral fracture (aHR 1.05, 95% CI 0.96-1.14). MVM supplementation was not associated with lower risk of total clinical fracture (aHR 1.09, 95% CI 1.00-1.19), hip fracture (aHR 1.06, 95% CI 0.80-1.42), or nonvertebral fracture (aHR 1.10, 95% CI 1.00-1.20). These findings do not support the use of cocoa extract or MVM to decrease fracture risk in older individuals not selected for pre-existing osteoporosis.
The distribution of galaxy rotation in JWST Advanced Deep Extragalactic Survey
Authors: Shamir Lior 
Published: February 2025

Abstract
JWST provides a view of the Universe never seen before, and specifically fine details of galaxies in deep space. JWST Advanced Deep Extragalactic Survey (JADES) is a deep field survey, providing unprecedentedly detailed view of galaxies in the early Universe. The field is also in relatively close proximity to the Galactic pole. Analysis of spiral galaxies by their direction of rotation in JADES shows that the number of galaxies in that field that rotate in the opposite direction relative to the Milky Way galaxy is ∼50 % higher than the number of galaxies that rotate in the same direction relative to the Milky Way. The analysis is done using a computer-aided quantitative method, but the difference is so extreme that it can be noticed and inspected even by the unaided human eye. These observations are in excellent agreement with deep fields taken at around the same footprint by HST and JWST. The reason for the difference may be related to the structure of the early Universe, but it can also be related to the physics of galaxy rotation and the internal structure of galaxies. In that case the observation can provide possible explanations to other puzzling anomalies such as the Ho tension and the observation of massive mature galaxies at very high redshifts.
New Red Supergiant Stars in the other side of our Galaxy
Authors: Zhang Lin , Chen Bingqiu , Ren Yi , Zhang Zehao , Gao Jian , Jiang Biwei 
Published: February 2025

Abstract
Red supergiant stars (RSGs) are massive stars in a late stage of evolution, crucial for understanding stellar life cycles and Galactic structure. However, RSGs on the far side of our Galaxy have been underexplored due to observational challenges. In this study, we introduce a novel method and present a new catalogue comprising 474 RSGs situated on the far side of the Milky Way, sourced from the OGLE-III catalogue of Variable Stars (OIII-CVS). The identification of these RSGs was made possible by analyzing the granulation parameters extracted from OGLE I-band time-series data and the stellar parameters from Gaia DR3. Additionally, we estimate the distances to these RSGs using an empirical relation between their characteristic amplitude, absolute magnitude, and intrinsic color, achieving a distance uncertainty of 13 %. These newly identified RSGs are distributed at Galactocentric distances between 0 and 30 kpc, and reside roughly 1 to 4 kpc above and below the Galactic plane. This distribution provides new insights into the structure of the Milky Way, particularly at its outer boundaries. Our results reveal that the vertical distribution of these RSGs is consistent with the flare structure of the Galactic disk, confirming that the far side of the Milky Way exhibits a similar flaring pattern to the near side. This catalogue offers a valuable resource for future detailed studies of RSGs and contributes to a more comprehensive understanding of the Galactic structure and stellar evolution.
Time-resolved proteomic profiling of Cupriavidus metallidurans CH34 in the copper-induced viable-but-non-culturable state
Authors: Patocka Timothej , Gupta Surya , Mastroleo Felice , Leys Natalie , Matroule Jean-Yves , Van Houdt Rob 
Published: February 2025

Abstract
Copper-based materials are actively explored for their potential as antimicrobial agents. However, recent studies show that sublethal concentrations of Cu ions can induce the viable-but-non-culturable (VBNC) cell state in certain bacteria, hampering contamination control and monitoring. In this study we contribute to the unravelling of this largely enigmatic phenomenon by determining the time-resolved proteome of Cu-treated Cupriavidus metallidurans CH34 during VBNC induction and resuscitation. High-throughput quantitative LC-MS/MS analysis was performed at multiple sample time points, revealing the cellular adaptations that trigger VBNC formation and the characteristic spontaneous recovery of culturability. Entry into the VBNC state correlated with a widespread response to oxidative stress as well as downregulated pyruvate metabolism. The expression of specific metal resistance determinants changed with Cu exposure time and culminated in the strong upregulation of proteins linked to periplasmic Cu ion detoxification during the resuscitation phase. We suggest that this delayed induction of Cu resistance proteins is paralleled by the gradual reconstitution of energy reserves through metabolization of intracellular polyhydroxybutyrate, as supported by flow cytometric fluorescence measurements. Furthermore, Cu-treated cells showed upregulation of several motility and chemotaxis proteins, and increased cell motility was observed phenotypically. Our results reveal a highly dynamic proteomic response, provide fundamental insights into the VBNC state and emphasize the advantages of time-resolved proteomic analysis.
Tensor renormalization group study of the three-dimensional SU(2) and SU(3) gauge theories with the reduced tensor network formulation
Authors: Yosprakob Atis , Okunishi Kouichi 
Published: February 2025

Abstract
We perform a tensor renormalization group simulation of non-Abelian gauge theory in three dimensions using a formulation based on the ‘armillary sphere.’ In this formulation, matrix indices are completely traced out, eliminating the degeneracy in the singular value spectrum of the initial tensor. We demonstrate the usefulness of this technique by computing the average plaquette at zero temperature and the Polyakov loop susceptibility at finite temperatures for 2+1D SU(2) and SU(3) gauge theories. The deconfinement transition is identified for both gauge groups, with the SU(2) case being consistent with previous Monte Carlo results.
52 THE INFLUENCE OF FOLK MUSIC ON SOCIAL FUNCTION AND SOCIAL DISORDER IN PATIENTS WITH SCHIZOPHRENIA
Authors: Wang Haicheng 
Published: February 2025

Abstract

Background
Social dysfunction and social withdrawal are common in schizophrenia patients, affecting the quality of life and social adaptability. Improving social function is the key goal of treatment. Folk music can express emotions and trigger cultural resonance, and is considered to be an effective non-drug intervention that can promote emotional communication and social interaction of patients. However, there are few systematic studies on the effects of folk music on social function and disorder in patients with schizophrenia. The aim of this study was to evaluate the effect of folk music intervention on improving patients’ social function and alleviating social disorders, and to provide evidence for its application in the field of mental health.

Methods
A randomized controlled trial design was used to include 100 patients with schizophrenia, who were randomly divided into a folk music intervention group (n=50) and a control group (n=50). The intervention group received 12 weeks of ethnic music therapy twice a week for 60 minutes, including instrumental experience, song singing, and musical social activities. The control group received only conventional medication and psychological support. The Social Functioning Scale (SFS) and Social Disability Assessment Scale (SDAS) were measured at baseline, every 3 weeks, and at the end of the intervention.

Results
Baseline assessment showed no significant difference in SFS and SDAS scores between the intervention group and the control group (P&gt;0.05). After the intervention, the SFS score in the intervention group gradually increased from 48.3±8.6 at baseline to 68.7±9.4 at week 12, which was significantly higher than 55.4±8.9 in the control group (P&lt;0.05). SDAS scores in the intervention group decreased progressively from 12.7±3.1 at baseline to 6.3±2.5 at week 12, while those in the control group only decreased from 12.5±3.2 to 10.4±2.9 (P&lt;0.05). The details are shown in Table 1.

Discussion
Folk music therapy can significantly improve the social function of schizophrenia patients and reduce their social barriers, and promote the recovery of social ability through cultural resonance and emotional expression, which has important psychological treatment value. This study provides scientific basis for the application of folk music in the treatment of schizophrenia, and demonstrates its unique advantages as a means of cultural intervention. Future studies may further explore the specific mechanisms of different ethnic music forms.
97 THE EFFECT OF NON-HERITAGE CULTURE ON STRESS RELIEF OF SCHIZOPHRENIC PATIENTS UNDER THE CONCEPT OF STEAM EDUCATION ANALYZED
Authors: Sun* Yanhu , Majid Nuriah Abd , Halim Sharina Abdul , Li Haoze , Zhang Qi 
Published: February 2025

Abstract

Background
Schizophrenia patients often face high levels of psychological stress, which not only affects their daily life and social functions, but may also aggravate the severity of symptoms. Traditional treatment methods mainly focus on medication and psychotherapy, but rarely involve cultural and artistic interventions. As a comprehensive cultural resource, intangible cultural heritage (ICH) under the educational concept of Science, Technology, Engineering, Arts, and Mathematics Education (STEAM) has the potential to relieve stress and improve mental health. By integrating ICH into the STEAM education framework and exploring its stress relief effect on schizophrenia patients, it is helpful to provide new ideas and methods for mental treatment.

Methods
Fifty schizophrenia patients were selected and randomly divided into an ICH intervention group and a control group, with 25 patients in each group. The ICH intervention group participated in a 12-week training by participating in an ICH course with traditional crafts, folk music and dance as the content. The course combined the STEAM education concept and emphasized hands-on operation and artistic creation. The control group continued to receive conventional drug treatment and psychological intervention. Before and after the study, the stress level and symptom changes were evaluated by the Stress Assessment Scale (SAS) and the Positive and Negative Syndrome Scale (PANSS).

Results
The results showed that the intangible cultural heritage intervention significantly reduced the psychological stress of patients with schizophrenia and improved the patients’ positive symptoms and overall symptom performance. See Table 1 for specific data. As can be seen from Table 1, the improvement in the stress score of the intangible cultural heritage intervention group was 13.7 points, from 42.3 points to 28.6 points (P &lt; 0.05), and the positive symptom score dropped from 16.4 points to 12.3 points (P &lt; 0.05). In the control group, the improvement in stress scores and positive symptom scores was smaller, 2.6 points and 0.3 points respectively. It can be seen that the improvement effect of the intangible cultural heritage intervention group was significantly better than that of the control group (P &lt; 0.05).

Discussion
Research shows that intangible cultural heritage intervention under the STEAM education concept can significantly alleviate the psychological stress of patients with schizophrenia and effectively improve the positive symptoms of patients. By combining the unique charm of intangible cultural heritage and the diversified teaching methods of STEAM education, a new and effective stress relief method can be provided for patients with schizophrenia. This intervention method has good clinical application prospects and provides a new direction for the rehabilitation treatment of schizophrenia.
105 THE EFFECT OF INK PAINTING ART THERAPY ON EMOTIONAL AND SOCIAL COGNITION INTERVENTION IN PATIENTS WITH SCHIZOPHRENIA
Authors: Feng Momo , Bai* Ying 
Published: February 2025

Abstract

Background
Schizophrenia is a chronic mental disorder characterized by cognitive impairments, emotional dysregulation, and social cognition deficits, severely affecting patients’ quality of life. Non-pharmacological therapies, especially art therapy, have gained attention for their creativity and psychological intervention. Ink painting therapy, part of Chinese culture, may positively impact emotional control and social cognition in patients through the expression and regulation of emotions in painting. Research on its therapeutic effects is scarce; this study aims to explore its impact on schizophrenia patients’ emotional stability and social cognition, offering new clinical treatment approaches.

Methods
The study included 120 patients meeting the diagnostic criteria for schizophrenia and were randomly divided into the experimental group (n=60) and the control group (n=60). The experimental group received 12 weeks for 90 minutes; the control group was maintained with conventional treatment. Ink painting art therapy includes the teaching of basic painting skills, free subject painting, and group discussion. Intervention effects were assessed by emotional stability on the Emotional Stability Scale (Emotional Stability Scale, ESS), social cognition measured by the Social cognitive Questionnaire (Social Cognition Questionnaire, SCQ), and P300 component changes related to emotional processing and social cognition were analyzed by event-related potentials (Event-Related Potentials, ERP). Data analysis used SPSS 26.0 software.

Results
The changes in emotional and social cognitive indicators between the experimental group and the control group before and after the intervention are shown in Table 1. As shown in Table 1, the experimental group showed significant improvements in ESS, SCQ, and P300 amplitudes. After intervention, the amplitudes increased from 48.5±6.2 to 67.3±5.8, 58.9±7.1 to 74.6±6.3, and 8.3±1.2 to 10.6±1.1, respectively. The control group showed no significant changes, ranging from 49.2±6.4 to 52.1± 6.5, 59.3±7.5 to 61.2±7.0, and 8.2±1.3 to 8.4±1.3, respectively. The inter group differences and time effects were significant (P&lt;0.001), indicating that the intervention had a significant positive effect on emotional stability, social cognition, and P300 amplitude.

Discussion
The results indicate that ink painting art therapy can significantly improve the emotional stability and social cognitive ability of patients with schizophrenia, and its mechanism of action may be related to enhancing P300 amplitude. This suggests that ink painting art therapy may indirectly enhance patients’ social cognitive function by improving their attention allocation and emotional processing abilities. Future research should further explore its intervention mechanisms and optimal implementation strategies, while considering the impact of different cultural backgrounds on intervention effectiveness.
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels
Authors: Abreu Edson F , Prado Joyce R , Maldonado Jesús E , Wilson Don E , Percequillo Alexandre R , Pavan Silvia E 
Published: February 2025

Abstract
Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlying processes of speciation are also central components of systematic biology that frame our comprehension of the evolutionary mechanisms generating biodiversity. The South American tree squirrels (genus Guerlinguetus) are keystone mammals, widely distributed, that are critical in tree-seed predation and dispersal in one of the most fragile and threated ecosystems of the world, the tropical rainforests of South America. We obtained genomic data (ultraconserved elements and single nucleotide polymorphisms) to explore alternative hypotheses on species limits of this genus and to clarify recent and rapid speciation on continental-scale and dynamically evolving landscapes. Using a multilayered genomic approach that integrates fine-scale population genetic analyses with quantitative molecular species delimitation methods, we observed that (i) the most likely number of species within Guerlinguetus is six, contrasting with both classic morphological revision and mitochondrial species delimitation; (ii) incongruencies in species relationships still persist, which might be a response to population migration and gene flow taking place in the lowlands of eastern Amazonia and/or to the extremely rapid successive speciation events; and (iii) effective migration surfaces detected important geographic barriers associated with the major Amazonian riverine systems and the mountain ranges of the Guiana Shield. In conclusion, we uncovered unexpected and higher species diversity on Guerlinguetus and corroborate recent findings suggesting that much of the extant species-level diversity in Amazonia is young, dating back to the Quaternary. We also reinforce long-established hypotheses on the role of rivers and climate-driven forest dynamics in triggering Amazonian speciation. [gene flow; Guerlinguetus; migration; mito-nuclear discordance; Neotropics; quantitative species delimitation; Sciuridae; ultraconserved elements]