bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Human Point of View
Authors: Costa Emanuele 
Published: February 2025

Abstract
Spinoza’s philosophy of emotions is often credited with creating the notion of affect, thanks to its refusal to separate mind and body, and to its insistence on the reciprocity of casual and effectual roles in interrelation between individuals. Beginning with Spinoza’s conatus theory and its focus on power dynamics, this chapter is dedicated to understanding how Spinoza’s concept of action, passion, and affect can guide his epistemology as well as his philosophical anthropology, ultimately leading him to establish a possibility for ethical acting through intuition, also known as intellectual love of God, or third kind of knowledge.
Big Stories and Local Weaves: Al-Ghazālī’s Ethics and Psychology of Godlikeness
Authors: Vasalou Sophia 
Published: February 2025

Abstract
This chapter introduces al-Ghazālī’s ethics of virtue as mediated by a variety of works and draws out some of the interpretive questions that concern their relations. In The Revival of the Religious Sciences, the idea of imitating God weaves itself through al-Ghazālī’s reflections on ethics and psychology in a number of important ways. It comes into focus more fully in a shorter work, The Most Exalted Aim in Expounding God’s Most Beautiful Names, where he builds on both philosophical and Sufi precedents to articulate the thought that human happiness lies in the assumption of God’s character traits. He supports this with a psychological model of emulation in which cognition, emotion, and conation are clearly ordered.
Feelings, For and Against: Patience, Compassion, and God’s Emotionless Virtues
Authors: Vasalou Sophia 
Published: February 2025

Abstract
This chapter explores al-Ghazālī’s negotiation of the conceptual challenges posed by the idea of God’s exemplarity by focusing on two key traits: patience and compassion. A key feature of al-Ghazālī’s analysis of God’s patience is that it decouples it from the experience of psychological conflict. A key feature of his analysis of God’s compassion is that it decouples it from the experience of emotional states such as sympathy or pity. This reflects a principled theological view about God’s insusceptibility to emotion. Yet in the ordinary human context, the psychological experiences that al-Ghazālī’s analysis elides are linked to the intelligibility but also the admirability of these virtues.
Nanomedicine-based immunotherapy for tissue regeneration
Authors: Li Song , Lu Li , Xiong Yuan , Xiao Jun 
Published: February 2025

Abstract
Tissue regeneration is essential for repairing and restoring damaged tissues, which has significant implications for clinical outcomes. Understanding the cellular mechanisms and the role of the immune system in this process provides a basis for improved regenerative techniques. The emergence of nanomedicine has advanced this field by introducing nanoscale technology that offer precise control over therapeutic delivery and cellular interactions. By modulating immune responses, various immunotherapeutic approaches, including cytokine therapy and immune checkpoint inhibitors, can establish an optimal environment for tissue repair. This review summarizes recent findings and applications of nanomedicine-based immunotherapy in tissue regeneration. It highlights the properties and advantages of nanomedicine in immunotherapy, discusses recent progress in using nanocomposite biomaterials for tissue engineering, and addresses the challenges and future directions in this evolving field. This review aims to emphasize the promising potential of nanomedicine-based immunotherapy in tissue engineering, thereby contributing to the functional design and strategic development of next-generation nanomedicine for regenerative medicine.
SCN5A variant type-dependent risk prediction in Brugada syndrome
Authors: Aizawa Takanori , Makiyama Takeru , Huang Hai , Imamura Tomohiko , Fukuyama Megumi , Sonoda Keiko , Kato Koichi , Hisamatsu Takashi , Nakamura Yuko , Hoshino Kenji , Ozawa Junichi , Suzuki Hiroshi , Yasuda Kazushi , Aoki Hisaaki , Kurita Takashi , Yoshida Yoko , Suzuki Tsugutoshi , Nakamura Yoshihide , Ogawa Yoshiharu , Yamagami Shintaro , Morita Hiroshi , Yuasa Shinsuke , Fukuda Masakazu , Ono Makoto , Kondo Hidekazu , Takahashi Naohiko , Ohno Seiko , Nakagawa Yoshihisa , Ono Koh , Horie Minoru 
Published: February 2025

Abstract

Aims
The variant in SCN5A with the loss of function (LOF) effect in the cardiac Na+ channel (Nav1.5) is the definitive cause for Brugada syndrome (BrS), and the functional analysis data revealed that LOF variants are associated with poor prognosis. However, which variant types (e.g. missense or non-missense) affect the prognoses of those variant carriers remain unelucidated.

Methods and results
We defined SCN5A LOF variants as all non-missense and missense variants that produce peak INa &lt; 65% of wild-type previously confirmed by patch-clamp studies. The study population consisted of 76 Japanese BrS patients (74% patients were male and the median age [IQR] at diagnosis was 28 [14–45] years) with LOF type of SCN5A variants: 40 with missense and 36 with non-missense variants. Non-missense variant carriers presented significantly more severe cardiac conduction disorder compared to the missense variant carriers. During follow-up periods of 9.0 [5.0–14.0] years, compared to missense variants, non-missense variants were significant risk factors of lifetime lethal arrhythmia events (LAEs) (P = 0.023). When focusing only on the missense variants that produce no peak INa, these missense variant carriers exhibited the same clinical outcomes as those with non-missense (log-rank P = 0.325). After diagnosis, however, both variant types were comparable in risk of LAEs (P = 0.155).

Conclusion
We identified, for the first time, that SCN5A non-missense variants were associated with higher probability of LAE than missense variants in BrS patients though it did not change significantly after diagnosis.
War Trauma and Strength: A Qualitative Study of Participants in the Vietnamese Insights into Cognitive Aging Program (VIP)
Authors: Vu Uyen T M , Farias Sarah Tomaszewski , Hinton Ladson , Park Van T , Tiet Quyen Q , Whitmer Rachel A , Heuer Sierra , Nguyen Boi-san , Meyer Oanh L 
Published: February 2025

Abstract

Objectives
Vietnamese Americans are the fourth-largest Asian subgroup in the United States (US), but little qualitative work has been done on their war and migration experiences. In this study, we delineated the war-related traumas and strength in participants of the Vietnamese Insights into Cognitive Aging Program (VIP).

Methods
VIP is a longitudinal study of 548 Vietnamese Americans aged 65+ years living in Northern California. During visit 1, a semi-structured interview was conducted on participants’ life and experiences in Vietnam and immigration to the US. Using data at one of the recruitment sites, interviews of participants having the highest total self-reported traumas were transcribed in Vietnamese (N=43) for coding and analysis following a thematic approach.

Results
Participants were 73.2 years old on average (SD=5.48). Most were male (67.4%) and had attempted to escape Vietnam by boat at least once (67%). Two major themes were found: (1) experiences of adversity and suffering, which included subthemes on tough life experiences during the war, imprisonment and hard life after the war, escaping by boat and living in the refugee camps, witnessing or hearing about others’ traumas during the war and escape, and experiences of loss; and, (2) personal fortitude and gratitude, which included subthemes on fortitude and endurance, personal skills to cope and navigate, and perceived “luck and blessings.”

Discussion
Results from this study revealed various traumas and aspects of strength. These findings can contribute to future VIP research on cognitive aging and inform research and practice on health disparities.
The Effect of Heat and Fermentation Treatments of Soybean Meal on Performance, Immune System, Microbial Population, Intestinal Morphology, and PepT1 Gene Expression in Broiler Chickens
Authors: Miraalami Nariman , Mousavi Seyed Naser , Abedini Mohammad Reza , Asgari Jafarabadi Ghobad 
Published: February 2025

Abstract
We investigated the effects of replacing raw soybean meal (RSM) with autoclaved soybean meal (ASBM) and fermented soybean meal by Lactobacillus plantarum (FSBMLP) and Bacillus pumilus (FSBMBP) on the performance, microbial population, intestinal morphology, immune system, and PepT1 gene expression in broiler chickens. One-day-old male Ross 308 broiler chicks (n=800) were utilized in a fully randomized design featuring eight treatments and five replicates, and each replicate consisted of 20 chicks. The experimental treatments included: 1) a control group ((RSM)-based diet), 2) a basal diet + ASBM, 3) a basal diet + 2% FSBMLP, 4) basal diet + 4% FSBMLP, 5) basal diet + 6% FSBMLP, 6) basal diet + 2% FSBMBP, 7) basal diet + 4% FSBMBP, and 8) basal diet + 6% FSBMBP. The results showed significant improvements in feed conversion ratio and body weight gain throughout the experiment for broiler chickens receiving various FSBMLP levels and 4% and 6% FSBMBP compared to the controls (P&lt;0.05). The group receiving 6% FSBMLP also demonstrated significantly higher antibody titers against Newcastle disease virus and Gumboro disease, along with increased IgG and total immunoglobulin levels in response to sheep red blood cells (SRBCs), compared to the controls (P&lt;0.05). Additionally, the Lactobacillus population in the ileum and villus height in the jejunum were significantly higher in chickens fed FSBMLP than in the control group (P&lt;0.01). Furthermore, chickens fed 6% FSBMLP showed a significant increase in PepT1 gene expression compared to the control group (P&lt;0.05). Overall, the results suggested that replacing 6% of RSM with FSBMLP in broiler chicken diets improved growth performance, immune function, intestinal health, and PepT1 gene expression compared to ASBM and FSBMBP.
Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery
Authors: Werner Marcel , Trauner Manuel , Schauer Tamas , Ummethum Henning , Márquez-Gómez Elizabeth , Lalonde Maxime , Lee Clare S K , Tsirkas Ioannis , Sajid Atiqa , Murriello Augusto C , Längst Gernot , Hamperl Stephan 
Published: February 2025

Abstract
Progressing transcription and replication machineries profoundly impact their underlying chromatin template. Consequently, transcription-replication conflict (TRC) sites are vulnerable to chromatin and epigenome alterations, provoking genome instability. Here, we engineered an inducible TRC reporter system using a genome-integrated R-loop-prone sequence and characterized the dynamic changes of the local chromatin structure inflicted by TRCs, leading to reduced nucleosome occupancy and replication fork blockage. Strikingly, inducing a small number of TRCs on the genome results in a measurable global replication stress response. Furthermore, we find a TRC-dependent increase in H3K79 methylation specifically at the R-loop forming TRC site. Accordingly, inhibition of the H3K79 methyltransferase DOT1L leads to reduced transcriptional output and an exacerbated DNA damage response, suggesting that deposition of this mark is required for effective transcription recovery and resolution of TRCs. Our work shows the molecular dynamics and reveals a specific epigenetic modifier bookmarking TRC sites, relevant to cancer and other diseases.
Evaluating short-term survivors of glioblastoma: A proposal based on SEER registry data
Authors: Tomita Yusuke , Otani Yoshihiro , Omae Ryo , Mizuta Ryo , Ishida Joji , Hirotsune Nobuyuki , Tanaka Shota 
Published: February 2025

Abstract

Background
Glioblastomas (GBMs) are central nervous system tumors with a poor prognosis and limited treatment options. Although small subsets of GBM patients survive longer than 3 years, there is little evidence regarding the prognostic factors of GBM. Therefore, we conducted a thorough characterization of GBM in the United States.

Methods
We queried the Surveillance, Epidemiology and End Results database between 2000 and 2021 to extract age-adjusted incidence rates (AAIR), age-adjusted mortality rates (AAMR), and survival data for GBM. We compared trends in AAIR, AAMR, and survival time across age groups 0–14, 15–39, 40–69, and 70+ years. Also, we employed the Fine-Gray competing risk model among short-term survivors (STSs), defined as those with a survival time of 6 months or less, and long-term survivors (LTSs), defined as those with a survival time of 3 years or more.

Results
This study included 60,615 incident GBM cases, 54,998 GBM-specific deaths, and 47,207 GBM patients with available survival time between 2000 and 2021. The mortality-to-incidence ratio was constant among STSs, whereas it increased with age among LTSs. Higher age and male sex were significantly associated with GBM-specific death among LTSs, whereas non-Hispanic White and less intensive treatments were associated with GBM-specific deaths among STSs. Interestingly, higher age was significantly associated with other causes of death among STSs.

Conclusions
STSs partially consist of populations who died from causes other than GBM. It is important to include only GBM-specific deaths in STS groups to conduct reproducible research comparing STSs and LTSs.
Dogs fed a high protein, low carbohydrate diet have elevated postprandial plasma glucagon and amino acid concentrations and tend to have lower glucose concentrations compared to two different moderate protein, moderate carbohydrate diets
Authors: Banton Sydney , Raheb Shari , Singh Pawanpreet , Cant John P , Shoveller Anna K 
Published: February 2025

Abstract
As dog owners continue to seek to feed their dogs similarly to themselves, there is demand for high protein, low carbohydrate (HPLC) diets. The consumption of HPLC diets can improve glycemic control, similarly to high fiber diets. However, the effects of HPLC and high fiber diets on cardiac function have yet to be evaluated in healthy dogs. The objective of the present study was to investigate the glucose, insulin, glucagon and amino acid (AA) postprandial response and echocardiographic measurements in laboratory-housed, adult large breed dogs fed a commercially available HPLC, a moderate protein, moderate carbohydrate (MPMC), or a commercially available MPMC, high fiber, ‘metabolic’ diet for 42 days. This study was conducted as a 3x3 Latin Square where dogs received: 1) a commercial HPLC diet (48% of metabolizable energy (ME) from protein, 10% of ME from nitrogen-free extract; NFE), 2) a MPMC diet (28% of ME from protein, 39% of ME from NFE) formulated with the same ingredients as HPLC or 3) a MPMC, high fiber, ‘metabolic’ (MET) diet (30% of ME from protein, 37% of ME from NFE) as a commercial control. An echocardiogram and a 12-h glucose, insulin and glucagon response and 6-h AA meal response were performed on day 42 of feeding. Data were analyzed using proc glimmix in SAS (version 9.4). All echocardiographic parameters remained within a healthy reference range for dogs of this size. Dogs fed HPLC had a larger net area under the curve (NetAUC) for plasma glucagon (P &lt; 0.001) compared to dogs fed MPMC and MET, a smaller NetAUC for glucose: insulin (P = 0.039) compared to dogs fed MPMC but MET was similar to both. Glucose NetAUC tended to be different among treatments (P = 0.057), where dogs fed MPMC had a greater netAUC than dogs fed HPLC and dogs fed MET tended to have a greater netAUC than HPLC. Dogs fed HPLC had greater concentrations of Ile, Leu, Lys, Thr, Tyr and Val over time compared to dogs fed MPMC and MET, and dogs fed MET had greater concentrations of Gln and Met over time compared to dogs fed HPLC and MPMC (P &lt; 0.05). Dogs fed a HPLC diet may have improved glucose uptake compared to dogs fed a MPMC diet. This research provides the first insight into the cardiometabolic health of dogs consuming three diets differing in their protein, carbohydrate and fiber content.
Preoperative Iron Supplementation Mitigates the Risk Of Postoperative Complications Associated with Iron Deficiency Anemia Following Lumbar Spinal Fusion
Authors: Jain Rishubh , Farias Michael J. , Singh Manjot , Pisani Claire , Nassar Joseph E. , Diebo Bassel G. , Daniels Alan H. 
Published: February 2025

Study Design.
Retrospective cohort study.

Objective.
Evaluate postoperative outcomes in lumbar fusion patients with preoperative iron deficiency anemia (IDA) on iron supplementation.

Background.
IDA has been associated with impaired cognition, compromised immune response, and increased risk of morbidity and mortality following surgery. However, little is known about the relationship between IDA and postoperative complications among patients undergoing lumbar fusion, as well as about the impact of preoperative iron supplementation on these outcomes.

Methods.
A national all-payer claims database was queried for adult patients who underwent lumbar spinal fusion between 2010 to 2022. Patients were initially stratified by a preoperative diagnosis of IDA and matched 1:1 based on age, sex, and medical comorbidities. IDA patients were further stratified by preoperative iron supplementation use and similarly matched. Postoperative complications and hospital costs were compared using chi-square, t-test, and multivariate logistic regressions.

Results.
The matched cohorts consisted of 27,669 patients, with mean age of 59 years and 89% female sex. IDA patients had higher rates of pulmonary embolism, acute kidney infection, deep venous thromboembolism, surgical site infection, urinary tract infection, blood transfusion, 90-day readmission rates, and hospital length of stay (all P<0.001). IDA patients on preoperative iron supplementation had lower rates of acute kidney injury, hematoma, pulmonary embolism, surgical site infection, urinary tract infection, stroke, 90-day readmission rates, and 90-day total hospital costs (all P<0.001). Non-IDA patients on preoperative iron supplementation similarly had lower rates of many of these complications as well.

Conclusion.
IDA was associated with increased risk of 90-day postoperative medical complications and hospital resource utilization. However, preoperative oral iron supplementation mitigated these risks. Further research is critical to understand how pre- or peri-operative iron supplementation can be used to optimize patients’ hematologic status before lumbar fusion to maximize clinical outcomes.

Level of Evidence.
IV
IGD: A simple, efficient genotype data format
Authors: DeHaas Drew , Wei Xinzhu 
Published: February 2025

AbstractMotivationWhile there are a variety of file formats for storing reference-sequence-aligned genotype data, many are complex or inefficient. Programming language support for such formats is often limited. A file format that is simple to understand and implement – yet fast and small – is helpful for research on highly scalable bioinformatics.ResultsWe present the Indexable Genotype Data (IGD) file format, a simple uncompressed binary format that can be more than 100 times faster and 3.5 times smaller thanvcf.gzon Biobank-scale whole-genome sequence data. The implementation for reading and writing IGD in Python is under 350 lines of code, which reflects the simplicity of the format.AvailabilityA C++ library reading and writing IGD, and tooling to convert .vcf.gzfiles, can be found athttps://github.com/aprilweilab/picovcf. A Python library is athttps://github.com/aprilweilab/pyigd
Primitive steroidogenesis in mast cells: A novel regulatory mechanism for mast cell function
Authors: Pramanik Jhuma , Zhao Qiuchen , Yamashita-Kanemaru Yumi , Hussein Hosni , Homer Natalie Z. M. , Chakraborty Soura , Shaji Sanu K. , Okkenhaug Klaus , Roychoudhuri Rahul , Mahata Bidesh 
Published: February 2025

SUMMARYMast cells, ancient immune sentinels, are crucial in immune responses, tissue homeostasis and inflammatory pathologies. This study unveils a previously unknown regulatory mechanism in mast cell biology:de novosteroidogenesis. Through comprehensive multi-omics analysis and functional assays, we demonstrate that mast cells express Cyp11a1 and produce pregnenolone, representing a primitive form of steroidogenesis. This cell-intrinsic steroidogenic pathway is essential for mast cell development, survival, and functional regulation. Genetic abrogation of mast cell steroidogenesis leads to exaggerated inflammatory and anaphylactic responsesin vivo. Our integrative approach reveals extensive transcriptional and proteomic remodelling during mast cell regranulation, with steroidogenesis playing a pivotal role in coordinating recovery and tissue repair processes. We uncover significant sexual dimorphism in mast cell proteomes and a global uncoupling of transcriptional and translational programmes. These findings advance our understanding of mast cell physiology and provide a foundation for developing targeted therapies for mast cell-associated pathologies.
Cardiac-specific deletion of GCN5L1 promotes fatty liver disease in HFpEF
Authors: Bugga Paramesha , Mushala Bellina A.S. , Stoner Michael W. , Manning Janet R. , Bhattarai Nisha , Sharifi-Sanjani Maryam , Vandevender Amber , Mooli Raja G.R. , Ramakrishnan Sadeesh K. , Kaufman Brett A. , Shiva Sruti S. , Happe Cassandra L. , Mullet Steven J. , Gelhaus Stacy L. , Jurczak Michael J. , Scott Iain 
Published: February 2025

ABSTRACTThe prevalence of cardiometabolic heart failure with preserved ejection fraction (HFpEF) continues to grow, representing over half of heart failure cases in the United States. As no specific medication for HFpEF exists, treatment guidelines focus on the management of comorbidities related to metabolic syndrome (e.g. obesity, diabetes, hypertension) that promote the disease. These same comorbidities also drive pathology in non-cardiac tissues, and the links between cardiometabolic disease presentations in different organs are increasingly being recognized. Preclinical studies on the potential crosstalk between HFpEF and metabolic disease in the liver (e.g. metabolic-associated fatty liver disease; MAFLD) have focused on how liver dysfunction may affect the heart, particularly through the release of secreted liver proteins. This may reflect the situation in the clinic, where incident MAFLD is a risk factor for future HFpEF development. Here, in contrast to this developing paradigm of liver-initiated cardiac disease, we report for the first time a defect in cardiac metabolism related to the mitochondrial metabolic protein GCN5L1 that drives hepatic steatosis and MAFLD in HFpEF.