bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporally transcriptomic analyses of floral buds reveal the high-resolution landscape of flower development and dormancy regulation in peach
Authors: Zhao Ya-lin , Li Yong , Guo Dan-dan , Chen Xue-jia , Cao Ke , Wu Jin-long , Fang Wei-chao , Chen Chang-wen , Wang Xin-wei , Wang Li-rong 
Published: February 2025

Abstract
The spatiotemporal transcriptome dataset reported here provides the peach flower bud’s gene expression atlas at spatiotemporal resolution level by 10x genomics Visium platform. This dataset can be used to define the transcript accumulation for any interesting genes across several flower bud cells by three peach flower bud samples during the activity-dormancy period, providing valuable insight into gene expression profiling and developmental stages under different environmental contexts or conditions. Importantly, we found that different cell types are related to specific regulatory programs, including signal transduction, environment and stress responses, and flower development. Our research provides insight into the transcriptomic landscape of the key cell types for flower buds and opens new avenues to study cell-type specification, function, and differentiation in Rosaceae fruit trees. A series of pivotal genes (e.g., AMS, MS188, MS1) for flower bud development were identified, these works provided a valuable reference for activity-dormancy transition in perennial deciduous fruit trees.
Photocontrol of the small GTPase Ras using its regulatory factor, GTPase-activating protein, modified with photochromic nanodevices
Authors: Ahmed Rajib , Nishibe Nobuyuki , Zhang Ziyun , Maruta Shinsaku 
Published: February 2025

Abstract
Ras, a small GTPase, is central to the regulation of diverse cellular processes including transcription, cell cycle progression, growth, migration, cytoskeletal reorganization, apoptosis, cell survival, and senescence. Ras activation is mediated by GTP binding, whereas its inactivation occurs via GDP binding, which is tightly controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs). GAPs accelerate GTP hydrolysis, playing a crucial role in modulating Ras signaling to prevent excessive or prolonged activation. Here, we investigated monofunctional azobenzene derivatives as photochromic modulators to control the function of Ras in a light-dependent and reversible manner. Three thiol-reactive azobenzene derivatives with distinct electrostatic properties were synthesized and incorporated into GAP functional sites to modulate Ras activity. GAP mutants containing a single cysteine residue at the functional site were generated using an Escherichia coli expression system. Our results showed that modifications near the GAP “arginine finger,” a critical region for stabilizing the GTP hydrolysis transition state of Ras, induced significant light-dependent changes in GTPase activity. We achieved photoreversible control of the interaction between Ras and its effector Raf using these azobenzene derivatives. These findings suggest that Ras function can be precisely modulated using photochromic molecules, providing a novel light-based approach for controlling Ras activity.
An investigation of Haemaphysalis longicornis (Ixodida:Ixodidae) habitat and pathogen overlap with resident tick species in Southeastern Pennsylvania forests
Authors: Phillips Payton M , Fahey Jackson , Behm Jocelyn E 
Published: February 2025

Abstract
The long-horned tick, Haemaphysalis longicornis Neumann (Ixodida: Ixodidae) was recently introduced to the United States from its native range in Asia. Although H. longicornis transmits numerous disease-causing pathogens in its native range, it is unclear to what extent H. longicornis will act as a disease vector in the United States. The ability of H. longicornis to acquire pathogens likely depends on overlap with resident tick species in both habitat and pathogens transmitted within its introduced range. To assess the potential overlap in habitat and pathogens between invasive H. longicornis and resident tick species, we field-collected ticks across southeastern Pennsylvania and tested them for pathogens. We then contextualized the risk of pathogen transmission to and by H. longicornis at sites where it overlaps with the current vector species using a network of vectored pathogens. None of the collected H. longicornis individuals tested positive for any pathogens. However, we found significant overlap in habitat use among H. longicornis and resident tick nymphs, as well as several overlaps in the pathogens vectored by resident ticks and those carried by H. longicornis in Asia. These findings indicate a high but yet-to-be-realized potential for H. longicornis to acquire North American tick-borne pathogens.
Clinical characteristics and quality of life in children with PFAPA syndrome and Behçet’s disease
Authors: Gürel Bedir Asli , Kilic Sara Sebnem 
Published: February 2025

Abstract

Objective
Periodic fever, aphthous stomatitis, pharyngitis, cervical adenitis (PFAPA) syndrome and Behçet’s disease (BD) are non-monogenic autoinflammatory disorders with common clinical characteristics and genetic features. We aimed to review both patients’ clinical characteristics and quality of life.

Methods
Retrospective data were collected on patients’ clinical and laboratory characteristics with PFAPA and BD between 2019 and 2022. The quality of life questionnaire (Pediatric Quality of Life Inventory) form was completed by the parents of all patients and the control group.

Results
The study included 150 cases aged between 2 and 18, including 60 with PFAPA, 30 BD patients and 60 healthy volunteers. The duration of attacks in males with PFAPA was longer than that in females (P = 0.015). During attacks, the mean acute phase reactants of PFAPA patients were higher than those of BD (P = 0.010). In addition, there was a statistically significant relationship between the use of colchicine and a decrease in attack frequency in BD patients at 89.29% (P = 0.001 &lt; 0.05) and in PFAPA patients at 88% (P = 0.001 &lt; 0.05). Precisely, 61.67% of PFAPA (n = 37) and 73.33% of BD patients (n = 22) exhibited poor quality of life regarding daily activities and school attendance.

Conclusion
Limited data on the quality of life of paediatric BD and PFAPA syndrome are available. During the attacks of patients with PFAPA and BD, acute-phase reactants were higher in PFAPA patients. Colchicine is an effective medication in reducing attacks in both groups. Effective and timely treatment is indispensable to improve quality of life.
Profiles of gut microbiota and metabolites for high risk of transgenerational depression‐like behavior by paternal methamphetamine exposure
Authors: Zhang Yuanyuan , Hu Tao , Wang Xinyu , Sun Nongyuan , Cai Qinglong , Kim Hee Young , Fan Yu , Liu Dekang , Guan Xiaowei 
Published: February 2025

AbstractParental substance abuse increases the risk of neurological and psychiatric disorders in offsprings. However, its underlying mechanism remains elusive. Our previous study demonstrated that long‐term exposure to methamphetamine (Meth), a psychostimulant drug with high addiction potential, remarkably alters the gut microbiome and metabolites in male mice, which contribute to Meth‐induced anxiety‐like behaviors. The current study aimed to investigate whether gut microbiota and metabolism serve as potential peripheral targets for transgenerational mental problems by paternal Meth exposure. We found that paternal Meth exposure induced depression‐like behaviors both in the first (F1) and the second (F2) generations of male mice. Further, the depletion of gut bacteria through antibiotic treatments normalized the depression‐like behaviors to normal levels in both F1 and F2 male mice. Then, alterations in gut bacterial composition were observed in both F1 and F2 male mice. Specifically, Eubacterium_ruminantium_group, Enterorhabdus, Alloprevotella, and Parabacteroides were the commonly affected bacterial taxa in F1 and F2 male mice. In addition, the results of alterations in gut metabolism showed that LPC 14:1‐SN1 emerged as the consistently altered metabolite in the colons of F1 and F2 male mice. Taken together, our findings provide the first evidence that paternal Meth exposure enhances depression‐like behaviors in F1 and F2 male mice, potentially mediated by the gut microbiome and metabolism.
Dysregulated fatty acid metabolism in pericardiac adipose tissue of pulmonary hypertension due to left heart disease mice
Authors: Qiu Haihua , Chen Jingyuan , Mei Zhang , Chen Wenjie , Jun Luo , Chen Yusi , Tan Yingjie , Wang Tianyu , Chen Yaqin , Li Jiang 
Published: February 2025

AbstractPulmonary hypertension associated with left heart disease (PH‐LHD) represents the most prevalent form of pulmonary hypertension; however, being lacks precise and effective treatment strategies. Recent clinical studies have indicated a positive correlation between the volume of pericardiac adipose tissue (PAT) and the severity of PH‐LHD. Nonetheless, there is a paucity of research characterizing PAT phenotypes in PH‐LHD disease models. This study aimed to elucidate the gene‐level characteristics of PAT in PH‐LHD through RNA sequencing and targeted metabolomic analysis of PAT in order to identify potential therapeutic targets for PH‐LHD by modulating PAT. This study developed a mouse model of PH‐LHD through cardiac overload combined with metabolic syndrome and verified that PAT volume and adipocyte size were significantly increased in PH‐LHD mice. We used RNA sequencing to reveal that DEGs in PAT were primarily enriched in fatty acid metabolism pathways. Then, real‐time PCR showed no significant differences in the mRNA expression of inflammatory markers or adipocytokines; however, genes of fatty acid synthesis (Fasn, Acaca, and Scd1) and fatty acid decomposition (Ehhadh, Acot4, and Pdk1) significantly changed between the two groups. Consistently, targeted metabolomic analysis showed levels of most types of medium‐ and long‐chain fatty acids substantially reduced in PAT, suggesting that PAT in PH‐LHD mice exhibits suppressed fatty acid de novo synthesis and enhanced fatty acid breakdown, resulting in impaired fatty acid storage. These findings highlight the potential of targeting PAT fatty acid synthesis and metabolism pathways as a novel therapeutic approach for PH‐LHD.
UBE2D3 functions in mouse oocyte meiotic maturation
Authors: Zhang Guorui , Zhang Na , Zhang Bin , Zhao Yilong , Wang Qiang , Han Longsen 
Published: February 2025

AbstractUbiquitin‐mediated proteolysis plays a critical role in meiotic cell‐cycle regulation and must be tightly controlled to achieve correct chromosome segregation. While the role of E2 ubiquitin‐conjugating enzymes in mitosis is well‐documented, their functions in oocyte meiosis remain largely unexplored. In this study, we identified UBE2D3 as the most highly expressed E2 enzyme in mouse oocytes, which is essential for proper meiotic division. UBE2D3 depletion caused (metaphase I) MI arrest and Cyclin B1 accumulation, whereas its overexpression led to reduced Cyclin B1 levels, kinetochore‐microtubule (K‐MT) mis‐attachments, spindle assembly checkpoint (SAC) dysfunction, and increased aneuploidy. Notably, UBE2D3 upregulation in oocytes from aged mice contributed to age‐related meiotic defects, which were partially reversed by UBE2D3 knockdown or Cyclin B1 overexpression. This study underscores the importance of the UBE2D3‐Cyclin B1 axis in maintaining meiotic fidelity and highlights its potential as a therapeutic target for improving oocyte quality and fertility in aged females.
Incidence of Shared Clinical Instruction in Physical Therapy Clinical Education in the United States
Authors: Silberman Nicki , Hochman Lori , Rachwani Jaya 
Published: February 2025

Introduction.
Physical therapy clinical education experiences (CEE) typically involve a 1:1 or 2:1 student:instructor ratio. Students may also be supervised by more than 1 clinical instructor (CI), referred to as shared clinical instruction. The purpose of this study was to examine the incidence and implementation of shared clinical instruction in the United States.

Review of Literature.
Burnout and moral distress, along with the growing number of physical therapist (PT) education programs, contribute to limitations in clinical education capacity. Shared clinical instruction may benefit both educators and students, warranting further investigation.

Subjects.
Deidentified data were extracted from 178 PT education programs using Exxat in September 2023.

Methods.
This study analyzed CEE data between January 2014 and September 2023 (placement setting, state, dates, length of the CEE, number of assigned CIs, CI years of clinical experience and as a CI, credentialed instructor status, and specialization status) using descriptive and inferential statistics.

Results.
Almost all, 175 (98.3%) of the 178 programs, and 16,356 (12.5%) of the 131,184 CEEs in the data set had students who participated in shared clinical instruction, representing all 50 states, and every clinical setting. Shared clinical instruction occurred in longer CEEs compared with 1:1 experiences; binary logistic regression indicated that longer CEEs predicted higher rates of shared clinical instruction. Independent t-tests indicate that primary CIs in shared clinical instruction had slightly more years of clinical and instructional experience.

Discussion and Conclusion.
Shared clinical instruction is occurring in most PT education programs and clinical settings in the United States. Further investigation should explore the rationale behind the use of shared clinical instruction in various practice settings, and the selection and pairing of CIs in this model, along with the efficacy of shared clinical instruction, including benefits, challenges, and best practices.
Use of a Knowledge Translation Approach to Promote Implementation of Clinical Practice Guidelines in an Experiential Learning Course Within an Entry-Level Doctor of Physical Therapy Program: A Qualitative Study
Authors: Romney Wendy , Rodis Marco , Spiro Alicia L. , Roberts Kylie E. , Hemmer Mary Claire , Deutsch Judith E. 
Published: February 2025

Introduction.
Teaching health sciences students how to evaluate and implement clinical practice guidelines (CPGs) is challenging.

Review of Literature.
Physical therapist education offers experiential learning opportunities to teach students how to evaluate and implement CPGs. Knowledge translation (KT) guides the process of moving research evidence into practice. Experiential learning using KT principles can teach students to assess barriers to evidence use and overcome implementation challenges. The purpose of this retrospective phenomenological qualitative study was to explore the beliefs, perceptions, and experiences of former physical therapist students' who completed a neurologic elective course implementing 2 CPGs. Furthermore, how the course impacted their clinical experiences is also described.

Subjects.
Nine third-year physical therapist students.

Methods.
Students who participated in an elective experiential learning course developed using KT principles were recruited. Focus groups were held to determine the students' perceptions and experiences with implementing CPGs in the classroom and during their clinical experiences. Content analysis was used to identify codes and categories, and they were aligned with the Consolidated Framework of Implementation Research. Trustworthiness was established through member checking, peer debriefing, and an external audit.

Results.
Students reported individual and contextual facilitators during the elective that supported CPG use. Students identified improved knowledge, confidence, and skill to perform the CPGs that facilitated their transfer of knowledge from the classroom to the clinic. During their clinical experiences, students discussed contextual factors, such as culture, environment, and patient population, which served as both facilitators and barriers to CPG use.

Discussion and Conclusion.
Experiential learning enhanced knowledge, confidence, and skill with using CPGs and facilitated students' integration of evidence-based practice into their clinical experiences. Where possible, physical therapy curricula should incorporate experiential learning with KT principles to help students identify barriers to CPG use and develop strategies to enhance future evidence-based practice implementation.
Recognizing and responding to human trafficking in clinical care environments: A pediatric primary care case study
Authors: Peck Jessica L. , King Kelcey Y. , Hettenhaus Katherine P. , Rigby Kelley B. , McMichael Tami 
Published: February 2025

ABSTRACT
Human trafficking is a proliferating abuse within the United States in which persons who are victimized frequently interface with clinical environments across the care continuum with a variety of presentations for health needs. However, in the absence of uniform standards for evidence-based training among the health professions, recognition and response in these scenarios remains low. This case study presents a young adolescent female accessing primary care with a chief complaint of commercial sexual exploitation. The Core Competencies for Human Trafficking Response in Health Systems is used as a guiding lens for practical applications in clinical practice in provision of pediatric primary care. Health care providers in a direct service role should be prepared to respond with evidence-based, trauma-informed, culturally responsive procedures and protocols used within their scope of practice.
Performance of Clinical Risk Prediction Models for Post-ERCP Pancreatitis: A Systematic Review
Authors: Sabrie Nasruddin , Minhas Gurjot , Vaska Marcus , Meng Zhao Wu , Brenner Darren R. , Forbes Nauzer 
Published: February 2025

Objectives:
Pancreatitis is common following endoscopic retrograde cholangiopancreatography (ERCP). Despite increased vigilance of post-ERCP pancreatitis (PEP), both its incidence and associated mortality are rising. Risk prediction models may provide more accurate stratification of patient risk and proactive mitigation of PEP incidence and/or severe associated outcomes.

Methods:
We conducted an electronic search of MEDLINE, PubMEd, Cochrane, and CINAHL from inception through April 9, 2024 for studies evaluating the details and performances of available PEP prediction models. Studies were eligible if they used statistical measures to quantify their model’s predictive ability. Risk of bias was determined using the PROBAST tool.

Results:
Nineteen studies met eligibility criteria and were included. Logistic regression models were used in 15 studies, with machine learning models representing the second most commonly employed approach. Ten studies reported the performance of their risk prediction models using derivation data, with areas under the receiver operating curve (AUC) ranging from 0.68 to 0.86. Fifteen studies reported the performance of their risk prediction models on internally validated data, with AUCs ranging from 0.66 to 0.97. Eight studies reported on the performance of their risk prediction models on external validation data, with AUCs ranging from 0.67 to 0.98.

Discussion:
Numerous PEP clinical prediction models exist with variable performances. The use of PEP prediction tools can support the management of patients following ERCP. Implementation studies assessing the optimal usability of these tools, followed by prospective evaluations, are needed to evaluate their potential impacts on reducing PEP in real-world practice.
Opioid Prescribing Disparity in Traumatically Injured Patients
Authors: Smith Sophia M , Adams Rachel , Ha Emily , Chan Wang Pong , Jenkins Kendall , Michael Cara , Saillant Noelle N , Franks Jeffrey A , Sanchez Sabrina E 
Published: February 2025

Background:
Opioid prescribing is understudied in trauma patients, where disadvantaged communities are overrepresented. In this study, we evaluated disparities in opioid administration after trauma.

Study Design:
We conducted a retrospective cohort study of injured adults at a level I trauma center, 2018-2021. Opioids were quantified in milligram morphine equivalents (MME). Primary outcomes were receipt of opioids inpatient and at discharge, MMEs per hospital day, and, for patients prescribed opioids at discharge, MMEs and discharge pain control days. Multivariable logistic regression identified factors associated with overall receipt of opioids after injury, general linear modeling identified factors associated with MMEs received inpatient and at discharge, and negative binomial regression evaluated pain control days prescribed at discharge.

Results:
Of 3,032 patients, 2,514 (82.92%) required opioids as an inpatient and 1,803 (71.72%) still required opioids the day of discharge. Of these, 1,310 (72.66%) were discharged with opioids. Black (β-24.94, 95%CI -37.25, -12.62, p<0.001) and Hispanic (β -21.96, 95%CI -39.21, -4.71, p=0.01) patients received lower MMEs while inpatient. Factors associated with lower odds of discharge with opioids included non-English language (OR 0.56, 95%CI 0.38, 0.82, p=0.003), substance use disorder (SUD) (OR 0.69, 95%CI 0.49, 0.97, p=0.03), neuropsychiatric comorbidities (OR 0.58, 95%CI 0.39, 0.87, p=0.008), and violent injury (OR 0.61, 95%CI 0.45, 0.85, p=0.003). On discharge, Black individuals (β -130.71, 95%CI -251.26, -10.17, p=0.03) received lower MMEs and patients with SUD (IRR 0.65, 95%CI 0.53, 0.80, p<0.001) received fewer pain control days.

Conclusions:
Trauma patients experienced disparities in opioid prescribing throughout hospitalization. Lower opioid doses were administered to non-white patients, while language, mental health comorbidities, and mechanism influenced discharge opioid prescriptions.
Unveiling Sleep Dysregulation in Chronic Fatigue Syndrome with and without Fibromyalgia Through Bayesian Networks
Authors: Bechny Michal , Scutari Marco , van der Meer Julia , Faraci Francesca , Natelson Benjamin H. , Kishi Akifumi 
Published: February 2025

AbstractChronic Fatigue Syndrome (CFS) and Fibromyalgia (FM) often co-occur as medically unexplained conditions linked to disrupted physiological regulation, including altered sleep. Building on the work of Kishi et al. [7], who identified differences in sleep-stage transitions in CFS and CFS+FM females, we exploited the same strictly controlled clinical cohort using a Bayesian Network (BN) to quantify detailed patterns of sleep and its dynamics. Our BN confirmed that sleep transitions are best described as a second-order process [14], achieving a next-stage predictive accuracy of 70.6%, validated on two independent data sets with domain shifts (60.1–69.8% accuracy). Notably, we demonstrated that sleep dynamics can reveal the actual diagnoses. Our BN successfully differentiated healthy, CFS, and CFS+FM individuals, achieving an AUROC of 75.4%. Using interventions, we quantified sleep alterations attributable specifically to CFS and CFS+FM, identifying changes in stage prevalence, durations, and first- and second-order transitions. These findings reveal novel markers for CFS and CFS+FM in early-to-mid-adulthood females, offering insights into their physiological mechanisms and supporting their clinical differentiation.