bluuebunny/crossref_metadata_2025_split huggingface dataset:
Karyotype, Male Meiosis, and Pollen Features of Barleria (Acanthaceae): A Wild Ornamental From India
Authors: Patil Suraj S , Lekhak Manoj M 
Published: November 2024

Abstract
Barleria is a palaeotropical genus of herbs, shrubs, and rarely climbers or trees. We investigated the karyotypes and male meiosis of 12 and 13 species, respectively, for the first time. Mitotic metaphases revealed two chromosome counts, 2n = 40 and 2n = 44. Chromosomes had median (m), submedian (sm), and subterminal (st) region centromeres. The total haploid chromosome length (TCL) ranged from 78.95 µm (Barleria sahyadrica) to 37.80 µm (B. nitida). Dispersion index differentiated the species into two groups, one with lower (3.40–4.79) and the other with higher (6.63–12.87) values. Principal component analysis based on six karyological parameters, namely base number (x), 2n, TCL, coefficient of variation of chromosome length, coefficient of variation of centromeric index, and mean centromeric asymmetry, exhibited three clusters. Cluster I included species of the subgenus Barleria. Cluster III had species of the subgenus Prionitis section Somalia. Cluster II comprised species of the subgenus Barleria and the subgenus Prionitis section Prionitis (B. sahyadrica). Pollen grains were oblate spheroidal or distinctly three-lobed, tri-brevicolporate with honey-combed tectum. Our analyses revealed karyological relationships among the investigated species and also provide raw data to breeders interested in horticultural applications of Barleria for accomplishing interspecific hybridization.
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation
Authors: Tiedemann Rochelle L , Hrit Joel , Du Qian , Wiseman Ashley K , Eden Hope E , Dickson Bradley M , Kong Xiangqian , Chomiak Alison A , Vaughan Robert M , Tibben Bailey M , Hebert Jakob M , David Yael , Zhou Wanding , Baylin Stephen B , Jones Peter A , Clark Susan J , Rothbart Scott B 
Published: November 2024

Abstract
The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. The model posits that nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). However, the extent to which DNMT1 relies on ubiquitin signaling through UHRF1 in support of DNA methylation maintenance remains unclear. Here, with integrative epigenomic and biochemical analyses, we reveal that DNA methylation maintenance at low-density cytosine-guanine dinucleotides (CpGs) is particularly vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMDs), a methylation signature observed across human cancers. In contrast, UIM2 disruption completely abolishes the DNA methylation maintenance function of DNMT1 in a CpG density-independent manner. In the context of DNA methylation recovery following acute DNMT1 depletion, we further reveal a ‘bookmarking’ function for UHRF1 ubiquitin ligase activity in support of DNA re-methylation. Collectively, these studies show that DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process that is partially reliant on UHRF1 and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to PMD formation in cancers.
RAD51 recruitment but not replication fork stability associates with PARP inhibitor response in ovarian cancer patient-derived xenograft models
Authors: Talens Francien , Teixeira Vivian Oliviera Nunes , Kok Yannick P , Chen Mengting , Rosenberg Efraim H , Debipersad Rashmie , Duiker Evelien W , van den Tempel Nathalie , Janatova Marketa , Zemankova Petra , Nederlof Petra M , Wisman G Bea A , Kleibl Zdenek , de Jong Steven , van Vugt Marcel A T M 
Published: November 2024

Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) are currently used to treat BRCA1/2 mutant cancers. Although PARPi sensitivity has been attributed to homologous recombination (HR) defects, other roles of HR factors have also been linked to response to PARPi, including replication fork protection. In this study, we investigated PARPi sensitivity in ovarian cancer patient-derived xenograft (PDX) models in relation to HR proficiency and replication fork protection. Analysis of BRCA1/2 status showed that in our cohort of 31 ovarian cancer PDX models 22.6% harbored a BRCA1/2 alteration (7/31), and 48.3% (15/31) were genomically unstable as measured by copy number alteration analysis. In vivo, PARPi olaparib response was measured in 15 selected PDX models. Functional assessment of HR using ex vivo irradiation-induced RAD51 foci formation identified all olaparib-sensitive PDX models, including four models without BRCA1/2 alterations. In contrast, replication fork protection or replication speed in ex vivo tumor tissue did not correlate with olaparib response. Targeted panel sequencing in olaparib-sensitive models lacking BRCA1/2 alterations revealed a MUS81 variant as a possible mechanism underlying PARPi sensitivity. Combined, we show that ex vivo RAD51 analysis effectively predicts in vivo olaparib response and revealed a subset of PARPi-sensitive, HR-deficient ovarian cancer PDX models, lacking a BRCA1/2 alteration.
VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data
Authors: Fuhrmann Lara , Langer Benjamin , Topolsky Ivan , Beerenwinkel Niko 
Published: November 2024

Abstract
RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring diversity from error-prone reads is challenging. Here, we present VILOCA (VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data), a method for mutation calling and reconstruction of local haplotypes from short- and long-read viral sequencing data. Local haplotypes refer to genomic regions that have approximately the length of the input reads. VILOCA recovers local haplotypes by using a Dirichlet process mixture model to cluster reads around their unobserved haplotypes and leveraging quality scores of the sequencing reads. We assessed the performance of VILOCA in terms of mutation calling and haplotype reconstruction accuracy on simulated and experimental Illumina, PacBio and Oxford Nanopore data. On simulated and experimental Illumina data, VILOCA performed better or similar to existing methods. On the simulated long-read data, VILOCA is able to recover on average $82\%$ of the ground truth mutations with perfect precision compared to only $69\%$ recall and $68\%$ precision of the second-best method. In summary, VILOCA provides significantly improved accuracy in mutation and haplotype calling, especially for long-read sequencing data, and therefore facilitates the comprehensive characterization of heterogeneous within-host viral populations.
Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein–protein interaction networks
Authors: Alsaggaf Ibrahim , Freitas Alex A , Wan Cen 
Published: November 2024

Abstract
Ageing is a highly complex and important biological process that plays major roles in many diseases. Therefore, it is essential to better understand the molecular mechanisms of ageing-related genes. In this work, we proposed a novel enhanced Gaussian noise augmentation-based contrastive learning (EGsCL) framework to predict the pro-longevity or anti-longevity effect of four model organisms’ ageing-related genes by exploiting protein–protein interaction (PPI) networks. The experimental results suggest that EGsCL successfully outperformed the conventional Gaussian noise augmentation-based contrastive learning methods and obtained state-of-the-art performance on three model organisms’ predictive tasks when merely relying on PPI network data. In addition, we use EGsCL to predict 10 novel pro-/anti-longevity mouse genes and discuss the support for these predictions in the literature.
Abdominal myosteatosis measured with computed tomography predicts poor outcomes in patients with glioblastoma
Authors: Rahmani Farzaneh , Camps Garrett , Mironchuk Olesya , Atagu Norman , Ballard David H , Benzinger Tammie L S , Chow Vincent Tze Yang , Dahiya Sonika , Evans John , Jaswal Shama , Hosseinzadeh Kassani Sara , Ma Da , Naeem Muhammad , Popuri Karteek , Raji Cyrus A , Siegel Marilyn J , Xu Yifei , Liu Jingxia , Beg Mirza Faisal , Chicoine Michael R , Ippolito Joseph E 
Published: November 2024

Abstract

Background
Alterations in cellular metabolism affect cancer survival and can manifest in metrics of body composition. We investigated the effects of various body composition metrics on survival in patients with glioblastoma (GBM).

Methods
We retrospectively analyzed patients who had an abdominal and pelvic computed tomography (CT) scan performed within 1 month of diagnosis of GBM (178 participants, 102 males, 76 females, median age: 62.1 years). Volumetric body composition metrics were derived using automated CT segmentation of adipose tissue, skeletal muscle, and aortic calcification from L1 to L5. Univariable and multivariable Cox proportional hazards models were performed separately in males and females using known predictors of GBM overall survival (OS) as covariates. A sex-specific composite score of predisposing and protective factors was constructed using the relative importance of each metric in GBM OS.

Results
Higher skeletal muscle volume and lower skeletal muscle fat fraction were associated with better OS in the entire dataset. A robust and independent effect on GBM OS was seen specifically for fraction of inter/intramuscular adipose tissue to total adipose tissue after correction for known survival predictors and comorbidities. Worse OS was observed with increased abdominal aortic calcification volume in both sexes. There was a significant difference in GBM OS among participants stratified into quartiles based on sex-specific composite predisposing and protective scores.

Conclusion
The relationship between body composition and GBM OS provides an actionable advancement toward precision medicine in GBM management, as lifestyle and dietary regimens can alter body composition and metabolism and from there GBM survival.
Hierarchical simplicial manifold learning
Authors: Zhang Wei , Shih Yi-Hsuan , Li Jr-Shin 
Published: November 2024

Abstract
Learning global structures, i.e. topological properties, inherent in complex data is an essential yet challenging task that spans across various scientific and engineering disciplines. A fundamental approach is to extract local data representations and use them to assemble the global structure. This conjunction of local and global operations catalyzes the integration of tools from algebraic and computational topology with machine learning. In this article, we propose a hierarchical simplicial manifold learning algorithm, constituted by nested clustering and topological reduction, for constructing simplicial complexes and decoding their topological properties. We show that the learned complex possesses the same topology as the original embedding manifold from which the data were sampled. We demonstrate applicability, convergence, and computational efficiency of the algorithm on both synthetic and real-world data.
Modeling long-term nutritional behaviors using deep homeostatic reinforcement learning
Authors: Yoshida Naoto , Arikawa Etsushi , Kanazawa Hoshinori , Kuniyoshi Yasuo 
Published: November 2024

Abstract
The continual generation of behaviors that satisfy all conflicting demands that cannot be satisfied simultaneously, is a situation that is seen naturally in autonomous agents such as long-term operating household robots, and in animals in the natural world. Homeostatic reinforcement learning (homeostatic RL) is known as a bio-inspired framework that achieves such multiobjective control through behavioral optimization. Homeostatic RL achieves autonomous behavior optimization using only internal body information in complex environmental systems, including continuous motor control. However, it is still unknown whether the resulting behaviors actually have the similar long-term properties as real animals. To clarify this issue, this study focuses on the balancing of multiple nutrients in animal foraging as a situation in which such multiobjective control is achieved in animals in the natural world. We then focus on the nutritional geometry framework, which can quantitatively handle the long-term characteristics of foraging strategies for multiple nutrients in nutritional biology, and construct a similar verification environment to show experimentally that homeostatic RL agents exhibit long-term foraging characteristics seen in animals in nature. Furthermore, numerical simulation results show that the long-term foraging characteristics of the agent can be controlled by changing the weighting for the agent’s multiobjective motivation. These results show that the long-term behavioral characteristics of homeostatic RL agents that perform behavioral emergence at the motor control level can be predicted and designed based on the internal dynamics of the body and the weighting of motivation, which change in real time.
Towards a Unitary Formulation of Quantum Field Theory in Curved Space-Time: The Case of the Schwarzschild Black Hole
Authors: Kumar K Sravan , Marto João 
Published: November 2024

Abstract
We argue that the origin of unitarity violation and the information loss paradox in our understanding of black holes (BHs) lies in the standard way of doing quantum field theory in curved space-time (QFTCS), which is heavily biased on intuition borrowed from classical general relativity. In this paper, with the quantum-first approach, we formulate a so-called direct-sum QFT (DQFT) in BH space-time based on a novel formulation of discrete space-time transformations in gravity that potentially restores unitarity. By invoking the quantum effects associated with the gravitational backreaction, we show that the Hawking quanta emerging outside of the Schwarzschild radius ($r_S=2GM$) cannot be independent of the quanta that continue to be inside $r_S$. This enables information to be carried by Hawking quanta, but in the BH DQFT formalism, we do not get any firewalls. Furthermore, DQFT leads to the BH evaporation involving only pure states. This means the quantum mechanical effects at the BH horizon produce two components of a maximally entangled pure state in geometric superselection sector Hilbert spaces. This construction enables pure states to evolve into pure states, restoring unitarity and observer complementarity. Finally, we discuss how our framework leaves important clues for formulating a scattering matrix and probing the nature of quantum gravity.
Decellularization of fish tissues for tissue engineering and regenerative medicine applications
Authors: Chen Wenhui , Chen Mengshi , Chen Siyi , Wang Siran , Huang Zijin , Zhang Lining , Wu Jiaming , Peng Weijie , Li Huaqiong , Wen Feng 
Published: November 2024

Abstract
Decellularization is the process of obtaining acellular tissues with low immunogenic cellular components from animals or plants while maximizing the retention of the native extracellular matrix structure, mechanical integrity and bioactivity. The decellularized tissue obtained through the tissue decellularization technique retains the structure and bioactive components of its native tissue; it not only exhibits comparatively strong mechanical properties, low immunogenicity and good biocompatibility but also stimulates in situ neovascularization at the implantation site and regulates the polarization process of recruited macrophages, thereby promoting the regeneration of damaged tissue. Consequently, many commercial products have been developed as promising therapeutic strategies for the treatment of different tissue defects and lesions, such as wounds, dura, bone and cartilage defects, nerve injuries, myocardial infarction, urethral strictures, corneal blindness and other orthopedic applications. Recently, there has been a growing interest in the decellularization of fish tissues because of the abundance of sources, less religious constraints and risks of zoonosis transmission between mammals. In this review, we provide a complete overview of the state-of-the-art decellularization of fish tissues, including the organs and methods used to prepare acellular tissues. We enumerated common decellularized fish tissues from various fish organs, such as skin, scale, bladder, cartilage, heart and brain, and elaborated their different processing methods and tissue engineering applications. Furthermore, we presented the perspectives of (i) the future development direction of fish tissue decellularization technology, (ii) expanding the sources of decellularized tissue and (iii) innovating decellularized tissue bio-inks for 3D bioprinting to unleash the great potential of decellularized tissue in tissue engineering and regenerative medicine applications.
Clinical and Functional Outcomes of Community-Recruited Individuals at Clinical High-Risk for Psychosis: Results From the Youth Mental Health Risk and Resilience Study (YouR-Study)
Authors: Haining Kate , Gajwani Ruchika , Gross Joachim , Gumley Andrew I , Lawrie Stephen M , Schultze-Lutter Frauke , Schwannauer Matthias , Uhlhaas Peter J 
Published: November 2024

Abstract
Clinical high-risk for psychosis (CHR-P) individuals are typically recruited from clinical services but the clinical and functional outcomes of community-recruited CHR-P individuals remain largely unclear. The Youth Mental Health Risk and Resilience Study (YouR-Study) obtained a community sample of CHR-P individuals through an online-screening approach and followed-up these individuals for a period of up to 3 years to determine transition rates, persistence of attenuated psychotic symptoms (APS) and functional outcomes. Baseline data were obtained from n = 144 CHR-P participants, n = 51 participants who met online cutoff criteria but not CHR-P criteria (CHR-Ns), and n = 58 healthy controls. Baseline assessments included clinical measures for assessing CHR-P status, including the Comprehensive Assessment of At-Risk Mental States (CAARMS) and the Schizophrenia Proneness Instrument, Adult version (SPI-A), as well as functioning and cognitive measures. CHR-P and CHR-N groups were followed-up. Results show that 12.1% of CHR-P individuals transitioned to psychosis over 3 years, with no transitions in the CHR-N group. Nearly 60% of CHR-P individuals experienced poor functional outcome (PFO) and over 40% experienced persistent APS. A combination of CAARMS/SPI-A criteria was associated with a higher likelihood of PFO, but not with transition to psychosis nor APS persistence. However, transition risk was generally higher among those meeting both CAARMS/SPI-A criteria (64.3%) vs CAARMS (28.6%) or SPI-A (7.1%) alone. In summary, community-recruited CHR-P individuals are characterized by similar clinical characteristics and longitudinal outcomes to those recruited from clinical services, emphasizing the need to widen the scope of early detection and intervention strategies.
Challenges and strategies for implementing the STAR tool for comprehensive evaluation of guidelines: A qualitative study with Chinese clinicians
Authors: Yang Nan , Wang Xu , He Hongfeng , Zhao Jungang , Qin Yishan , Li Yueyan , Estill Janne , Wei Junmin , Chen Yaolong 
Published: November 2024

Abstract

Background:
The STAR (Scientific, Transparent, and Applicable rankings) working group conducts regular evaluations of Chinese guidelines and consensus statements. This study gathered insights from STAR working group members using qualitative interviews.

Methods:
From March to August 2023, members of the STAR specialist committees were interviewed using semi-structured interview outline. The interviewees were selected through purpose-based sampling. Subject analysis was employed to summarize the findings.

Results:
We conducted interviews with 37 members from 36 committees and summarized the contents into four main themes and 16 specific topics. The value of STAR in enhancing the development and selection of high-quality guidelines in China was commonly mentioned. Challenges identified included the lack of resources and suboptimal organizational structures, collaboration, and evaluation efficiency. Suggestions for the STAR tool included developing extensions for different guideline types, adjusting certain items, and better covering guideline applicability. The promotion of STAR and the consideration of an international committee for global outreach were also highlighted.

Conclusion:
STAR has exerted a substantial influence on the evaluation of Chinese guidelines, and the insights gained from interviews offer valuable directions for its further enhancement.
Preventing the Re-emergence of Deadly Nipah Virus
Authors: Tyagi Satvik , Sahai Sanjeev , Upadhyay Shalini 
Published: November 2024

Abstract
The Indo-Bangladesh region frequently suffers from periodic Nipah virus (NiV) outbreaks. NiV is a zoonotic agent that can be transmitted from animals to humans and also from humans to humans. NiV infections may cause deadly neurological dysfunctions with a fatality rate of up to 75%. Various methods have been developed to diagnose NiV infections at different stages of the disease, but there is currently no specific antiviral treatment or vaccine available. NiV outbreaks are mostly endemic; however, the high susceptibility of the human population, high mutation rates of the viral RNA genome and the possibility of human-to-human transmission in this era of globalization enable NiV to potentially cause a pandemic. To prevent serious consequences of NiV outbreaks, international deliberation on risk assessment, investigation of the molecular and genetic aspects of NiV, pertinent measures of surveillance and framing of general guidelines for its management should be integrated. This review underlines the basic information available in the literature and its application for further research to reach a solution for mitigation of such catastrophic infections.
Food for thought: optimal diet in patients with asthma and chronic obstructive pulmonary disease
Authors: Vameghestahbanati Motahareh , Wang Carolyn J. , Sin Don D. 
Published: November 2024

Purpose of review
Nutritional intake plays a major role in the management of lung health. This review provides the latest perspective on how dietary choices can modulate lung function in patients with chronic obstructive pulmonary disease (COPD) and asthma.

Recent findings
The pathophysiology of COPD and asthma is driven by oxidative stress and inflammation of the airways, which is exacerbated by modifiable risk factors such as cigarette smoking and diet. Various foods can influence patient symptoms; highly processed foods increase the production of reactive oxygen species that augment airway inflammation, whereas foods rich in antioxidants, fiber and protein combat oxidative stress and muscle wastage. Patients with COPD or asthma are at increased risk of developing metabolic comorbidities, including cachexia and obesity that complicate disease phenotypes, leading to greater symptom severity. While clinical findings suggest a role for antioxidant and macronutrient support of lung function, comprehensive translational and clinical studies are necessary to better understand the mechanisms underlying nutrient interaction and lung structure–function.

Summary
Understanding the nutritional requirements that protect lung health and support weight management in COPD and asthma is imperative to providing personalized dietary recommendations and reducing patient morbidity.