bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scaphocapitate Arthrodesis for Wrist Deformities: A Systematic Review
Authors: Deptula Peter , McCullough Meghan , Brown Theodore , Singh Dylan , Kuschner Stuart , Kulber David 
Published: October 2024

Background:
Scaphocapitate arthrodesis (SCA) is a described technique for chronic wrist pathology such as Kienbock disease and carpal instability. The technique aims to preserve motion, while maintaining carpal height, preserving the radioscaphoid articulation, and offloading the lunate. Limited case series evaluate the outcomes of this previously described technique. We aim to determine if the collective, updated literature on outcomes of SCA support its continued application by the wrist surgeon. Furthermore, we investigated if any technical variations offer an advantage in improving patient-reported outcomes after SCA.

Methods:
A literature search was performed using Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Articles selected for critical review were examined for patient demographic data, functional outcomes, radiographic outcomes, and complications. A qualitative analysis was then performed to synthesize the available date.

Results:
A total of 18 unique articles published between 1991 and 2022 were identified, representing a total of 285 individual cases of SCA. Nonunion rate ranged 0%–22%. Preoperative visual analog scale pain scores ranged from 3.2 to 10, whereas postoperative visual analog scale pain scores ranged from 0 to 4. Patient-reported outcomes are reported by validated instruments, including the Disabilities of the Arm, Shoulder, and Hand, QuickDASH, Patient-rated Wrist Evaluation, and Mayo Wrist Score.

Conclusions:
SCA is a viable treatment option for patients with Kienbock disease. SCA offers reliable improvements in patient pain, grip strength, and patient-reported outcomes.
Accelerated Agony
Authors: Kattamuri Lakshmi Prasanna Vaishnavi , Senapati Sidhartha Gautam , Vulisha Abhinav , Rao Sheldon 
Published: October 2024

Abstract
This case report discusses a 39-year-old male with advanced HIV infection presenting with fever, weight loss, and respiratory symptoms, ultimately succumbing to fulminant pulmonary coccidioidomycosis. Despite initial empirical treatment for bacterial pneumonia and Pneumocystis jirovecii, the patient's condition rapidly deteriorated, highlighting the diagnostic challenges posed by this fungal infection, especially in immunocompromised individuals. Diagnostic confirmation was complicated by nonspecific clinical features, overlapping symptoms with other opportunistic infections, and unreliable serological tests. Radiological findings resembled those of other pulmonary infections, further complicating timely diagnosis. Delayed recognition of disseminated coccidioidomycosis contributed to the patient's poor prognosis. Antifungal therapy, primarily azoles, remains the cornerstone of management, with prognosis worsening with additional dissemination sites and advanced HIV illness. This case underscores the importance of considering pulmonary coccidioidomycosis in immunocompromised patients presenting with respiratory symptoms, particularly in endemic regions.
Mobility Loss in Hospitalized Adults Predicts Poor Clinical Outcomes
Authors: Rogers Stephanie E. , Mulvey Jade , Turingan Roniela , Coco L. Maurine , Hubbard Colin C. , Binford Sasha , Harrison James D. 
Published: October 2024

Background:
The Johns Hopkins Activity and Mobility Program is a systematic approach to measure and improve patient mobility.

Purpose:
The purpose of this study was to evaluate the relationship between mobility loss and quality outcomes.

Methods:
A retrospective cohort study design was used. Patients were categorized into 3 groups (gain, loss, no change in mobility) using the Johns Hopkins Highest Level of Mobility (JH-HLM) scores. The association between mobility loss and falls risk, in-hospital mortality, delirium, discharge to a facility, length of stay, and 30 day readmissions were assessed.

Results:
Those who lost mobility were more at risk of being a high fall risk, in-hospital mortality, delirium, discharging to a facility, and had 48% longer lengths of stay. There was no association between mobility loss and 30-day readmissions.

Conclusions:
Loss of mobility assessed using JH-HLM scores is associated with worse patient outcomes.
Precise Localization of the Posterior Clinoid Process in the Fetal Skull Base
Authors: Öztürk Cansu , Şencan Zeynep , İnce Rümeysa , Çalişir Ebru Sena , Cihan Ömer Faruk , Beger Orhan 
Published: October 2024

Objective:
To determine the precise position of the posterior clinoid process (PCP) in fetuses.

Materials and Methods:
Skull bases of 32 fetuses (11 males/21 females) aged 17 to 32 weeks in utero were included in the study. The distances of PCP to certain reference points were measured.

Results:
The distances of PCP to the foramen ovale, foramen rotundum, superior orbital fissure, anterior clinoid process, foramen magnum, and crista galli were measured as 7.70±1.86 mm, 6.99±1.65 mm, 6.07±1.85 mm, 3.85±1.10 mm, 15.34±3.38 mm, and 14.49±2.65 mm, respectively. All parameters were similar for both sides (P>0.05). Apart from the distance of PCP to the foramen magnum, the remaining parameters were similar for both genders. This parameter was greater in males than females (P=0.001). All parameters were greater in the third-trimester fetuses than the second-trimester fetuses. All parameters increased with advancing gestational weeks (P<0.001). Linear functions were calculated for the distances of PCP to the crista galli (y = 1.311 + 0.551 × age), to the foramen magnum (y = 0.086 + 0.638 × age), to the anterior clinoid process (y = −0.303 + 0.174 × age), to the superior orbital fissure (y = − 2.013 + 0.338 × age), to the foramen rotundum (y = 1.803 + 0.217 × age), and to the foramen ovale (y = 0.760 + 0.290 × age).

Conclusion:
The measured distances increased with growth. The linear functions displaying the growth dynamics of PCP-related parameters may be used to estimate the distances.
Correct patient identification and matching of adults in an ambulatory care setting: a best practice implementation project
Authors: Tran Louise Dung , Neil Bronwyn , Taylor Christine 
Published: October 2024

ABSTRACT

Introduction:
Ambulatory care settings are at high risk for errors when identifying patients and matching them to their intended care.

Objective:
The objective of this project was to improve correct and consistent patient identification and matching to their intended care by nurses in ambulatory care settings.

Methods:
The seven-phase JBI Evidence Implementation Framework was used to guide this project. JBI tools were used to audit current practices and implement best practices in four ambulatory care units. The implementation plan included a baseline audit and two follow-up audits. Feedback was obtained through interviews with ambulatory care nursing staff, educational sessions were conducted for nursing staff, and unit guidelines were developed.

Results:
In the baseline audit, compliance with best practice criteria for patient matching and identification was below 62% for 7/13 criteria. After conducting education sessions and other strategies, 1/3 pre- and post-clinical intervention criteria improved in compliance, while 2 were unchanged. For blood product administration criteria, 2/5 improved, 1 was unchanged, and 2 were lower than baseline. Nurses’ education in patient identification procedures improved (1/1) and knowing where to access relevant policies remained unchanged at 100%. Criteria for patients knowing the importance of patient identification (2/2) and the identification band following national standards (1/1) improved from baseline.

Conclusions:
The results support the use of education sessions and infrastructure changes to promote and sustain change in evidence-based practice in ambulatory care units. Not all criteria improved, and the audit team identified strategies to improve the implementation of evidence-based practice in ambulatory care units.

Spanish abstract:

http://links.lww.com/IJEBH/A275
Ultrastructural Organization of the Honeybee Blood-Brain Barrier and Comparison with Age
Authors: Quigley Tyler , Amdam Gro 
Published: October 2024

AbstractThe blood-brain barrier is an essential feature of the most animal nervous systems, adapted to maintain brain homeostasis across species occupying unique and dynamic environments. Understanding the structural and functional diversity of animal blood-brain barriers can aid our understanding of how this structure contributes to important areas of neuroscience such as behavior, health, and disease. The honeybee worker is a well-established model for exploring these dimensions of brain function, however, the honeybee worker blood-brain barrier has yet to be described. Here, we present the first global anatomic analysis and description of the honeybee worker blood-brain barrier and compare key ultrastructural features between two age groups. We describe the cellular makeup of the honeybee worker blood-brain barrier, patterns of heterogeneity in barrier structure throughout the brain, and highlight important areas of further study.
Prenatal exposure to genocide accelerates epigenetic aging as measured in second-generation clocks among young adults
Authors: Uwizeye Glorieuse , Rivera Luisa M. , Stolrow Hannah G. , Christensen Brock C. , Rutherford Julienne N. , Thayer Zaneta M. 
Published: October 2024

AbstractPrenatal exposure to trauma, including genocide and maternal rape, and adverse childhood experiences (ACEs), are associated with lifespan reduction. We evaluated whether prenatal exposure to genocide or genocidal rape, and ACEs among individuals conceived during the 1994 genocide against Tutsi in Rwanda were associated with differences in age acceleration in three first-generation (Horvath, Hannum, PhenoAge) and four second-generation epigenetic aging clocks (GrimAge, DunedinPace, YingDamAge, YingAdaptAge), given the association between biological aging and mortality. No differences in age acceleration were observed with first-generation age clocks. However, age acceleration was associated with prenatal exposure to extreme stress for all second-generation clocks, with the greatest acceleration observed in the genocidal rape conception group. For YingDamAge clock, acceleration effects were strengthened after inclusion of ACEs. We suggest that prenatal trauma exposure is associated with epigenetic age acceleration. Second-generation clocks may more accurately capture these relationships.
Role of MicroRNAs in Autosomal Dominant Polycystic Kidney Disease: Expression Profiles and Pathway Analysis
Authors: Devi Chandra , Ranjan Prashant , Mishra Jitendra Kumar , Singh Shivendra , Das Parimal 
Published: October 2024

ABSTRACTThis study investigates the role of specific microRNAs (miRNAs) in autosomal dominant polycystic kidney disease (ADPKD). Network analysis using Cytoscape 3.10.1 revealed 28 miRNAs that target two or more PKD related genes, while 14 miRNAs interacted with three or more genes. Pathway analysis of these 14 miRNAs, conducted via the miRPath V4.0 tool, utilized various resources such as KEGG, GO terms, Pfam, and MSigDB, highlighting their functional roles in ADPKD. Among these 14 miRNAs, four were prioritized for further analysis based on the higher number of target genes and existing evidence of their expression in blood. These miRNAs were analyzed for fold change expression levels using qRT-PCR on blood-derived RNA samples from ADPKD patients (n=19) and healthy controls (n=5). These four miRNAs—hsa-miR20a-5p, hsa-miR27b-3p, hsa-miR3613-3p, and hsa-miR181a-5p— showed significant upregulation with p-values of 0.0179, 0.0002, 0.0166, and 0.0402 respectively. The functional enrichment of miRNAs involved in PKD evidently suggests that these play diverse roles in regulating key processes such as cell cycle progression, mTOR signaling, autophagy, EMT, and cellular responses to hypoxia thus playing crucial role in the pathogenesis of ADPKD and could serve as potential biomarkers or therapeutic targets.
Knowledge, Attitude, and Practice of Vasoactive Agents Infusions : Development and Psychometric Properties of a Questionnaire with Chinese Clinical Nurses
Authors: Huang Yanfang , Chen Yi , Fang Yaping , Mou Junjie , Li Shiqin , Lei Xianying , Li Yuxin , Ai Zhongping 
Published: October 2024

AbstractBackgroundInconsistencies with guidelines or standards regarding nurses’ practice of vasoactive agent infusion have been documented. Adequate knowledge and positive attitudes are critical for compliance. However, there are currently no validated tools specifically designed to measure the knowledge and attitudes related to vasoactive agent infusions among nurses.ObjectiveThe aim of this study was to develop and test the validity and reliability of the Chinese mainland version of Knowledge, Attitude, and Practice of Vasoactive Agents Infusions Questionnaire among nurses.MethodsThe initial questionnaire items were developed through a comprehensive literature review, expert consultation, and pilot study. From February to June 2024, cross-sectional data were collected using convenience sampling from 538 nurses across 9 hospitals in Sichuan Province, China. The reliability and validity of the scale were evaluated through internal consistency reliability, inter-rater reliability, exploratory factor analysis, and confirmatory factor analysis.ResultsThe final version of the questionnaire included 33 items across 3 dimensions, explaining 78.04% of the variance, with item loadings ranging from 0.56 to 0.89. The content validity index ranged from 0.91 to 1.00, and the scale-level content validity index was 0.98. The overall Cronbach’s α for the questionnaire was 0.96, with Cronbach’s α for each dimension ranging from 0.96 to 0.98. The test-retest reliability for the entire questionnaire was 0.90, and for each dimension, it ranged from 0.90 to 0.94 (p < 0.05). The confirmatory factor analysis demonstrated acceptable fit indices for the three-dimensional model: χ²/(df) = 1.135, p = 0.200, RMSEA = 0.024, CFI = 0.986, TLI = 0.985, GFI = 0.884, and NFI = 0.895.ConclusionThe Knowledge, Attitude, and Practice of Vasoactive Agents Infusions Questionnaire demonstrates good reliability and validity, making it a reliable measurement tool for assessing nurses’ attitudes and knowledge related to vasoactive agents’ infusions. This version will facilitate further research and advancements in this specific field of study.
Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data
Authors: Seidel Sophie , Zwaans Antoine , Regalado Samuel , Choi Junhong , Shendure Jay , Stadler Tanja 
Published: October 2024

AbstractCRISPR-based lineage tracing offers a promising avenue to decipher single cell lineage trees, especially in organisms that are challenging for microscopy. A recent advancement in this domain is lineage tracing based on sequential genome editing, which not only records genetic edits but also the order in which they occur. To capitalize on this enriched data, we introduce SciPhy, a simulation and inference tool integrated within the BEAST 2 framework. SciPhy utilizes a Bayesian phylogenetic approach to estimate time-scaled phylogenies and cell population parameters. After validating SciPhy using simulations, we apply it to lineage tracing data obtained from a monoclonal culture of HEK293T cells for which we estimate time-scaled trees together with cell proliferation rates. We compare SciPhy to the lineage reconstruction based on a widely used clustering method, UPGMA, and find that the UPGMA-reconstructed lineage trees differ from SciPhy trees in some key aspects of tree structure; in particular, SciPhy trees stand out for their later estimated cell division times. In addition, SciPhy reports uncertainty as well as proliferation rates, neither of which are available within a UPGMA analysis. This study showcases the application of advanced phylogenetic and phylodynamic tools to explore and quantify cell lineage trees, laying the groundwork for enhanced and confident analyses to decode the complexities of biological development in multicellular organisms. SciPhy’s codebase is publicly available athttps://github.com/azwaans/SciPhy.
IgBlend: Unifying 3D Structures and Sequences in Antibody Language Models
Authors: Malherbe Cedric , Uçar Talip 
Published: October 2024

AbstractLarge language models (LLMs) trained on antibody sequences have shown significant potential in the rapidly advancing field of machine learning-assisted antibody engineering and drug discovery. However, current state-of-the-art antibody LLMs often overlook structural information, which could enable the model to more effectively learn the functional properties of antibodies by providing richer, more informative data. In response to this limitation, we introduce IgBlend, which integrates both the 3D coordinates of backbone atoms (C-alpha, N, and C) and antibody sequences. Our model is trained on a diverse dataset containing over 4 million unique structures and more than 200 million unique sequences, including heavy and light chains as well as nanobodies. We rigorously evaluate IgBlend using established benchmarks such as sequence recovery, complementarity-determining region (CDR) editing and inverse folding and demonstrate that IgBlend consistently outperforms current state-of-the-art models across all benchmarks. Furthermore, experimental validation shows that the model’s log probabilities correlate well with measured binding affinities.
Camera traps unable to determine whether plasticine models of caterpillars reliably measure bird predation
Authors: Schillé Laura , Plat Nattan , Barbaro Luc , Jactel Hervé , Raspail Frédéric , Rivoal Jean-Baptiste , Castagneyrol Bastien , Mrazova Anna 
Published: October 2024

AbstractSampling methods that are both scientifically rigorous and ethical are cornerstones of any experimental biological research. Since its introduction 30 years ago, the method of using plasticine prey to quantify predation pressure has become increasingly popular in biology. However, recent studies have questioned the accuracy of the method, suggesting that misinterpretation of predator bite marks and the artificiality of the models may bias the results. Yet, biasper semight not be a methodological issue as soon as its statistical distribution in the samples is even, quantifiable, and thus correctable in quantitative analyses. In this study, we focus on avian predation of lepidopteran larvae models, which is one of the most extensively studied predator-prey interactions across diverse ecosystems worldwide. We compared bird predation on plasticine caterpillar models to that on dead caterpillars of similar size and color, using camera traps to assess actual predation events and to evaluate observer accuracy in identifying predation marksa posteriori. The question of whether plasticine models reliably measure insectivorous bird predation remained unanswered, for two reasons: (1) even the evaluation of experienced observers in the posterior assessment of predation marks on plasticine models was subjective to some extent, and (2) camera traps failed to reflect predation rates as assessed by observers, partly because they could only record evidence of bird presence rather than actual predation events. Camera traps detected more evidence of bird presence than predation clues on plasticine models, suggesting that fake prey may underestimate the foraging activity of avian insectivores. The evaluation of avian predation on real caterpillar corpses was probably also compromised by losses to other predators, likely ants. Given the uncertainties and limitations revealed by this study, and in the current absence of more effective monitoring methods, it remains simpler, more cost-effective, ethical, and reliable to keep using plasticine models to assess avian predation. However, it is important to continue developing improved monitoring technologies to better evaluate and refine these methods in order to advance research in this field.
Ternary complex formation of VCP, VCPIP1 and p47 facilitates Golgi reassembly
Authors: Shah Binita , Hunkeler Moritz , Bratt Ariana , Yue Hong , Jaen Maisonet Isabella , Fischer Eric S. , Buhrlage Sara J. 
Published: October 2024

AbstractVCP/p97 regulates a wide range of cellular processes, including post-mitotic Golgi reassembly. In this context, VCP is assisted by p47, an adapter protein, and VCPIP1, a deubiquitinase (DUB). However, how they organize into a functionally competent complex and promote reassembly remains unknown. Here, we use cryo-EM to characterize VCP-VCPIP1 and VCP-VCPIP1-p47 complexes. We show that VCPIP1 engages VCP through two interfaces: one involving the N-domain of VCP and the UBX domain of VCPIP1, and the other involving the VCP D2 domains and a region of VCPIP1 we refer to as VCPID. The p47 UBX domain competitively binds to the VCP N-domain, while not affecting VCPID binding. We show that VCPID is critical for VCP-mediated enhancement of DUB activity and Golgi reassembly.
Fully Hyperbolic Neural Networks: A Novel Approach to Studying Aging Trajectories
Authors: Ramirez Hugo , Tabarelli Davide , Brancaccio Arianna , Belardinelli Paolo , Marsh Elisabeth B. , Funke Michael , Mosher John C. , Maestu Fernando , Xu Mengjia , Pantazis Dimitrios 
Published: October 2024

AbstractCharacterizing age-related alterations in brain networks is crucial for understanding aging trajectories and identifying deviations indicative of neurodegenerative disorders, such as Alzheimer’s disease. In this study, we developed a Fully Hyperbolic Neural Network (FHNN) to embed functional brain connectivity graphs derived from magnetoencephalography (MEG) data into low dimensions on a Lorentz model of hyperbolic space. Using this model, we computed hyperbolic embeddings of the MEG brain networks of 587 individuals from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) dataset. Notably, we leveraged a unique metric—the radius of the node embeddings—which effectively captures the hierarchical organization of the brain, to characterize subtle hierarchical organizational changes in various brain subnetworks attributed to the aging process. Our findings revealed that a considerable number of subnetworks exhibited a reduction in hierarchy during aging, with some showing gradual changes and others undergoing rapid transformations in the elderly. Moreover, we demonstrated that hyperbolic features outperform traditional graph-theoretic measures in capturing age-related information in brain networks. Overall, our study represents the first evaluation of hyperbolic embeddings in MEG brain networks for studying aging trajectories, shedding light on critical regions undergoing significant age-related alterations in the large cohort of the Cam-CAN dataset.