bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality and Safety in Nursing: Recommendations From a Systematic Review
Authors: Patrician Patricia A. , Campbell Caitlin M. , Javed Mariyam , Williams Kathy M. , Foots Lozay , Hamilton Wendy M. , House Sherita , Swiger Pauline A. 
Published: May 2024

ABSTRACT
As a consistent 24-hour presence in hospitals, nurses play a pivotal role in ensuring the quality and safety (Q&S) of patient care. However, a comprehensive review of evidence-based recommendations to guide nursing interventions that enhance the Q&S of patient care is lacking. Therefore, the purpose of our systematic review was to create evidence-based recommendations for the Q&S component of a nursing professional practice model for military hospitals. To accomplish this, a triservice military nursing team used Covidence software to conduct a systematic review of the literature across five databases. Two hundred forty-nine articles met inclusion criteria. From these articles, we created 94 recommendations for practice and identified eight focus areas from the literature: (1) communication; (2) adverse events; (3) leadership; (4) patient experience; (5) quality improvement; (6) safety culture/committees; (7) staffing/workload/work environment; and (8) technology/electronic health record. These findings provide suggestions for implementing Q&S practices that could be adapted to many healthcare delivery systems.
Liver transplantation for tumor entities
Authors: Patrono Damiano , De Stefano Nicola , Romagnoli Renato 
Published: May 2024

Purpose of review
Tumor entities represent an increasing indication for liver transplantation (LT). This review addresses the most contentious indications of LT in transplant oncology.

Recent findings
Patient selection based on tumor biology in LT for colorectal cancer liver metastases (CRLM) demonstrated promising long-term outcomes and preserved quality of life despite high recurrence rates. In selected cases, LT for intrahepatic cholangiocarcinoma (iCCA) is feasible, with acceptable survival even in high-burden cases responsive to chemotherapy. LT following a strict neoadjuvant protocol for perihilar cholangiocarcinoma (pCCA) resulted in long-term outcomes consistently surpassing benchmark values, and potentially outperforming liver resection.

Summary
While preliminary results are promising, prospective trials are crucial to define applications in routine clinical practice. Molecular profiling and targeted therapies pave the way for personalized approaches, requiring evolving allocation systems for equitable LT access.
Optimizing Triage
Authors: Levkowitz Eilan , Gibson Robert , Xu Hongyan , Zhang Li Fang , Eskine Katherine , Buck Brian , Bruno Michael , Seeyave Desiree 
Published: May 2024

Objective
We investigated the diagnostic value of shock index, pediatric age-adjusted (SIPA) in predicting Emergency Severity Index level 3 patients' outcomes. Secondary objectives included exploring the impact of fever and participant variables on SIPA's predictive ability.

Methods
A retrospective chart review identified children aged 1 to 15 years triaged as a level 3 in the emergency department between January 2018 and December 2021. Shock index, pediatric age-adjusted thresholds based on age, 1 to 6 years (>1.2), 7 to 12 years (>1.0), and 13 to 17 years (>0.9), were used. We assessed elevated SIPA and SIPA corrected for fever to evaluate associations with outcomes and interventions.

Results
Our findings, involving 192 patients, revealed that elevated SIPA demonstrated enhanced discrimination relative to nonelevated SIPA. Patients with elevated SIPA had more average interventions: 1.14 versus 0.74, P < 0.016; average interventions using SIPA corrected for fever: 1.14 versus 0.77, P < 0.006; average interventions controlling for race and sex: 1.15 versus 0.71, P < 0.001; hospital admission: 64.4% versus 42.9%, P = 0.004; hospital length of stay (LOS): 3.06 days (SE, 0.42) versus 1.46 days (SE, 0.23); hospital LOS using SIPA corrected for fever: 2.75 days (SE, 0.44) versus 1.72 days (SE, 0.24); ventilatory support: 16.44% versus 3.36%, P < 0.002; fluid bolus: 28.77% versus 14.29%, P < 0.015; intravenous medications (antibiotics, antiepileptics, immune globulin, albumin): 45.21% versus 30.25%, P < 0.036. There was no difference between other interventions, pediatric intensive care admission, and LOS between the 2 groups. Importantly, SIPA was unaffected by fever, race, or sex.

Conclusions
Shock index, pediatric age-adjusted identifies level 3 Emergency Severity Index pediatric patients more likely to require hospital admission, longer LOS, and a lifesaving intervention especially ventilatory support, intravenous fluids, or specific intravenous medications. Shock index, pediatric age-adjusted's predictive ability remained unaffected by fever, race, or sex, making it a valuable tool in preventing mistriage and justifying inclusion in the Emergency Severity Index danger zone vitals criteria for up-triage.
Unnecessary Explantation of IDEAL IMPLANT Structured Saline Breast Implants Prompted byRadiologic Misdiagnosis of Rupture
Authors: Boston Rebecca S. , Hamas Robert S. , Mango Victoria L. , Nichter Larry S. 
Published: May 2024

Abstract
The unique dual-lumen and baffle design of the IDEAL IMPLANT Structured Saline breast implant gives it specific advantages over both silicone gel–filled and the original saline-filled implants. This internal baffle structure also gives it an appearance on various radiologic imaging studies that may be misinterpreted as a rupture because of similarities to the well-known radiologic appearance of a ruptured silicone gel implant. Patients may present with various misinterpreted imaging studies, highlighting the need for plastic surgeons and radiologists to be familiar with the normal appearance of the intact IDEAL IMPLANT and be able to distinguish it from a ruptured IDEAL IMPLANT. The radiology findings must be correlated with the clinical findings, or an intact IDEAL IMPLANT misdiagnosed as ruptured, may cause unnecessary patient worry, and may prompt unnecessary surgery for removal or replacement.
Coraliomargarita algicola sp. nov., isolated from a marine green alga
Authors: Lee Jae Kyeong , Choi Dae Gyu , Choi Byeong Jun , Kim Jeong Min , Jeon Che Ok 
Published: May 2024

A Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, non-motile, non-flagellated, and coccus-shaped bacterium, strain J2-16T, isolated from a marine green alga, was characterized taxonomically. Strain J2-16T grew at 20–40 °C (optimum, 30 °C), pH 6.0–10.0 (optimum, pH 7.0), and 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). Menaquinone-7 was identified as the sole respiratory quinone, and major fatty acids (>5 %) were C18 : 1
ω9c, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, C18 : 0, C16 : 0, and C17 : 1
ω8c. The polar lipids of strain J2-16T consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and three unidentified lipids. The genome size of strain J2-16T was 5384 kb with a G+C content of 52.0 mol%. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strain J2-16T formed a distinct phyletic lineage within the genus Coraliomargarita, closely related to Coraliomargarita sinensis WN38T and Coraliomargarita akajimensis DSM 45221T with 16S rRNA gene sequence similarities of 95.7 and 94.4 %, respectively. Average nucleotide identity and digital DNA–DNA hybridization values between strain J2-16T and Coraliomargarita species were lower than 71.2 and 20.0 %, respectively. The phenotypic, chemotaxonomic, and molecular features support that strain J2-16T represents a novel species of the genus Coraliomargarita, for which the name Coraliomargarita algicola sp. nov. is proposed. The type strain is J2-16T (=KACC 22590T=JCM 35407T).
Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling
Authors: Giamundo Giuliana , Intartaglia Daniela , Prete Eugenio Del , Polishchuk Elena , Andreone Fabrizio , Ognibene Marzia , Buonocore Sara , Mele Bruno Hay , Salierno Francesco Giuseppe , Monfregola Jlenia , Antonini Dario , Grumati Paolo , Eva Alessandra , de Cegli Rossella , Conte Ivan 
Published: May 2024

AbstractEndosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events. Ezrin, a major membrane-actin linker that assembles and coordinates macromolecular signaling complexes at membranes, has emerged recently as an important regulator of lysosomal function. Here, we report that endosomal-localized EGFR/Ezrin complex interacts with and triggers the inhibition of the Tuberous Sclerosis Complex (TSC complex) in response to EGF stimuli. This is regulated through activation of the AKT signaling pathway. Loss of Ezrin was not sufficient to repress TSC complex by EGF and culminated in translocation of TSC complex to lysosomes triggering suppression of mTORC1 signaling. Overexpression of constitutively active EZRINT567Dis sufficient to relocalize TSC complex to the endosomes and reactivate mTORC1. Our findings identify EZRIN as a critical regulator of autophagy via TSC complex in response to EGF stimuli and establish the central role of early endosomal signaling in the regulation of mTORC1. Consistently, Medaka fish deficient for Ezrin exhibit defective endo-lysosomal pathway, attributable to the compromised EGFR/AKT signaling, ultimately leading to retinal degeneration. Our data identify a pivotal mechanism of endo-lysosomal signaling involving Ezrin and its associated EGFR/TSC complex, which are essential for retinal function.
Multi-omics Reveals Immune Response and Metabolic Profiles during High-Altitude Mountaineering
Authors: Yin Jianhua , Lv Jingzhi , Yang Shichen , Wang Yang , Huang Zhuoli , Wang Xue , Hou Guixue , Zhou Wenwen , Liu Ying , Wang Weikai , Lin Xiumei , Huang Yunting , Zheng Yuhui , Wei Chen , Yuan Yue , Huang Yaling , Liu Chang , Tao Haoran , Liu Huanhuan , Liu Ruquan , Zhang Yan , Zeng Guodan , Gao Peng , Liu Longqi , Cao Jun , Liu Chuanyu , Jin Xin , Wang Jian 
Published: May 2024

SUMMARYThe physiological perturbations induced by high-altitude exposure in mountain climbers, manifesting as metabolic and immunologic deviations, have been previously reported but are not fully understood. In this study, we obtained longitudinal multi-omic profiles of blood samples for healthy mountain climbers during two mountaineering stages (acclimatization and extreme altitude mountaineering). Our integrative assay included metabolomics and lipidomics profiling of plasma coupled with single-cell transcriptomic analysis of 375,722 immune cells. Longitudinal analysis revealed dynamic immune response profiles, during the acclimatization period, characterized by the downregulation of inflammatory responses in monocytes and classical dendritic cells (cDCs) and an increase in the proportion of cytotoxic CD8+T cells with enhanced immune effector processes. In contrast, during extreme altitude mountaineering, the activation of inflammatory responses and impairment of T cell effector function were observed, concomitant with an increased cellular response to hypoxia and oxidative stress pathways. Furthermore, we found upregulated glycolysis and antioxidant gene expression during extreme altitude mountaineering, which was primarily orchestrated byHIF1AandNFE2L2, while decreased expression of these genes was observed in dysregulated plasmacytoid dendritic cells (pDCs). Finally, high-resolution plasma metabolic analysis revealed significant alterations in the metabolism of climbers, involving enhanced glutamine and fatty acid metabolism.
Neutrophil percentages in bronchoalveolar lavage fluid: Implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia
Authors: Grudzinski Kevin M. , Fenske Samuel , Peltekian Alec , Markov Nikolay S. , Pawlowski Anna , Kang Mengjia , Walter James M. , Pickens Chiagozie I. , Nadig Nandita R. , Agrawal Ankit , Singer Benjamin D. , Wunderink Richard G. , Gao Catherine A. 
Published: May 2024

AbstractRationalePneumonia is the most common infection in ICU patients and a leading cause for death. Assessment of bronchoalveolar lavage fluid (BALF) cellularity can aid in pneumonia diagnosis. Low percentages (<50%) of BALF neutrophils have a high negative predictive value for bacterial pneumonia in a general medical ICU population. The operating characteristics in patients with immunocompromise and neutropenia are less clear.ObjectiveTo compare BALF % neutrophils operating characteristics in patients with and without immunocompromise or neutropenia.MethodsThis was a single center observational cohort study. Patients were categorized into three groups: (1) patients with neutropenia, (2) patients with underlying immunocompromise, and (3) patients with neither. BAL-level analysis reflected neutropenia and immunocompromise state on day of BAL sampling. Operating characteristics of BALF % neutrophils were calculated using varying thresholds of alveolar neutrophilia. Median [Q1,Q3] are reported for nonparametric data and compared using Mann-Whitney U tests.Results688 mechanically ventilated patients had 1736 BAL samples. Among bacterial pneumonia episodes, no difference was found in BALF % neutrophils between patients with underlying immunocompromise and patients with neither neutropenia nor immunocompromise on day of sampling: 82.0% [61.0, 91.0] vs 81.0% [66.0, 91.0], p=0.859. However, when neutropenic on day of sampling, the median BALF % neutrophils was 35.0% [8.8, 67.5] (p<0.001 compared with other categories). In patients with neutropenia, a BALF % neutrophil threshold of 7% had a sensitivity of 90% for excluding bacterial pneumonia.ConclusionsWe found that among patients with bacterial pneumonia, BALF % neutrophil was not significantly lower in patients with a broad spectrum of immunocompromised states but was significantly lower when measured during acute neutropenia. We found varying thresholds of BALF % neutrophils across the three groups. Patients with neutropenia who mount even a low percent of alveolar neutrophils should raise concern for bacterial pneumonia.
Prediction of antibiotic resistance mechanisms using a protein language model
Authors: Yagimoto Kanami , Hosoda Shion , Sato Miwa , Hamada Michiaki 
Published: May 2024

AbstractMotivationAntibiotic resistance has emerged as a major global health threat, with an increasing number of bacterial infections becoming difficult to treat. Predicting the underlying resistance mechanisms of antibiotic resistance genes (ARGs) is crucial for understanding and combating this problem. However, existing methods struggle to accurately predict resistance mechanisms for ARGs with low similarity to known sequences and lack sufficient interpretability of the prediction models.ResultsIn this study, we present a novel approach for predicting ARG resistance mechanisms using Protein-BERT, a protein language model based on deep learning. Our method outperforms state-of-the-art techniques on diverse ARG datasets, including those with low homology to the training data, highlighting its potential for predicting the resistance mechanisms of unknown ARGs. Attention analysis of the model reveals that it considers biologically relevant features, such as conserved amino acid residues and antibiotic target binding sites, when making predictions. These findings provide valuable insights into the molecular basis of antibiotic resistance and demonstrate the interpretability of protein language models, offering a new perspective on their application in bioinformatics.AvailabilityThe source code is available for free athttps://github.com/hmdlab/ARG-BERT. The output results of the model are published athttps://waseda.box.com/v/ARG-BERT-suppl.Contactmhamada@waseda.jp
Singular Odorant Receptor Expression Orchestrated by Promoter Activation Specificity inApis MelliferaOlfactory Sensory Neurons
Authors: Zhang Weixing , Nie Yage , Li Yiheng , Xu Yicong , Xu Tao , Shi Peiyu , Liu Fang , Zhao Hongxia , Ma Qing , Xu Jin 
Published: May 2024

AbstractHoneybee, positioned as an outgroup of flies and mosquitos, have exhibited intriguing duplications and expansions of OR genes in genomic studies. However, little is known about how the OR genes are expressed and regulated in honeybee olfactory sensory neurons (OSNs). In this study, we utilized a single-cell multi-omics approach to profile the transcriptome and chromatin accessibility inApis melliferaantennal nuclei, aiming to elucidate OR gene expression and its underlying regulatory mechanisms. Our systematical analysis unveiled a similar singular expression pattern of ligand-specific receptors inApis melliferaOSNs, parallel with those observed inDrosophila melanogaster. Mechanistically, we discovered that promoter activation of OR genes orchestrates receptor expression patterns. For instance, although multiple adjacent OR genes are co-expressed with a single active promoter through polycistronic transcription, only the first OR gene could produce functional receptor protein, as supported by transcriptome quantification in OSNs. Additionally, we found that co-expression of receptor proteins might occur only when co-expressed OR genes possess multiple accessible promoters. This scenario is less common than expected, considering the number and evolutionary age of OR genes inApis mellifera, suggesting a selection favoring the specialization of rapidly expanded OR genes inApis mellifera. Overall, our study provides significant insights into the insect olfaction system and the regulatory mechanisms of OR genes expression.
Linking intercontinental biogeographic events to decipher how European vineyards escaped Pierce’s disease
Authors: Moralejo Eduardo , Giménez-Romero Àlex , Matías Manuel A. 
Published: May 2024

AbstractUnlike most grapevine diseases of American origin, the vector-borne bacteriumXylella fastidiosa(Xf) responsible for Pierce’s disease (PD) has not yet spread to continental Europe. The reasons for this lack of invasiveness remain unclear. Here, we present phylogenetic, epidemiological and historical evidence to explain how European vineyards escaped Xf. Using Bayesian temporal reconstruction, we show that the export of American grapevines to France as rootstocks to combat phylloxera (∼1872-1895) preceded the spread of the Xf grapevine lineage in the US. In the dated tree, the time of the most recent common ancestor places the introduction of Xf into California around 1875, which agrees with the emergence of the main PD outbreak and the onset of its expansion into the southeastern US around 1895. We also show that between 1870 and 1990, climatic conditions in continental Europe were mostly below the threshold for PD epidemics. This lack of spatiotemporal concurrence between factors that could facilitate the establishment of the Xf grapevine lineage would explain the historical absence of PD in continental Europe. However, our model indicates that there has been an inadvertent expansion of risk in southern European vineyards since the 1990s, which is accelerating with global warming. Our temporal approach identifies the biogeographic conditions that have so far prevented PD, and gives continuity to predictions of increased risk in important southern European wine-producing areas under a forthcoming scenario of +2 and +3°C temperature increases.
Mechanism, and treatment of anti-CV2/CRMP5 autoimmune pain
Authors: Martin Laurent , Stratton Harrison J. , Gomez Kimberly , Do Le Duy , Loya-Lopez Santiago , Tang Cheng , Calderon-Rivera Aida , Ran Dongzhi , Nunna Venkatrao , Bellampalli Shreya S. , François-Moutal Liberty , Dumaire Nicolas , Salih Lyuba , Luo Shizhen , Porreca Frank , Ibrahim Mohab , Rogemond Véronique , Honnorat Jérôme , Khanna Rajesh , Moutal Aubin 
Published: May 2024

AbstractParaneoplastic neurological syndromes arise from autoimmune reactions against nervous system antigens due to a maladaptive immune response to a peripheral cancer. Patients with small cell lung carcinoma or malignant thymoma can develop an autoimmune response against the CV2/collapsin response mediator protein 5 (CRMP5) antigen. For reasons that are not understood, approximately 80% of patients experience painful neuropathies. Here, we investigated the mechanisms underlying anti-CV2/CRMP5 autoantibodies (CV2/CRMP5-Abs)-related pain. We found that patient-derived CV2/CRMP5-Abs can bind to their target in rodent dorsal root ganglia (DRG) and superficial laminae of the spinal cord. CV2/CRMP5-Abs induced DRG neuron hyperexcitability and mechanical hypersensitivity in rats that were abolished by preventing binding to their cognate autoantigen CRMP5. The effect of CV2/CRMP5-Abs on sensory neuron hyperexcitability and mechanical hypersensitivity observed in patients was recapitulated in rats using genetic immunization providing an approach to rapidly identify possible therapeutic choices for treating autoantibody-induced pain including the repurposing of a monoclonal anti-CD20 antibody that selectively deplete B-lymphocytes. These data reveal a previously unknown neuronal mechanism of neuropathic pain in patients with paraneoplastic neurological syndromes resulting directly from CV2/CRMP5-Abs-induced nociceptor excitability. CV2/CRMP5-Abs directly sensitize pain responses by increasing sensory neuron excitability and strategies aiming at either blocking or reducing CV2/CRMP5-Abs can treat pain as a comorbidity in patients with paraneoplastic neurological syndromes.
Disentangling associations between complex traits and cell types withseismic
Authors: Lai Qiliang , Dannenfelser Ruth , Roussarie Jean-Pierre , Yao Vicky 
Published: May 2024

AbstractIntegrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific biological processes underlying complex traits and disease. However, current methods have technical limitations that hinder them from making systematic, scalable, interpretable disease-cell-type associations. In order to rapidly and accurately pinpoint associations, we develop a novel framework,seismic, which characterizes cell types using a new specificity score. We compareseismicwith alternative methods across over 1,000 cell type characterizations at different granularities and 28 traits, demonstrating thatseismicboth corroborates findings and identifies trait-relevant cell groups which are not apparent through other methodologies. Furthermore, as part of theseismicframework, the specific genes driving cell type-trait associations can easily be accessed and analyzed, enabling further biological insights. The advantages ofseismicare particularly salient in neurodegenerative diseases such as Parkinson’s and Alzheimer’s, where disease pathology has not only cell-specific manifestations, but also brain region-specific differences. Interestingly, a case study of Alzheimer’s disease reveals the importance of considering GWAS endpoints, as studies relying on clinical diagnoses consistently identify microglial associations, while GWAS with a tau biomarker endpoint reveals neuronal associations. In general,seismicis a computationally efficient, powerful, and interpretable approach for identifying associations between complex traits and cell type-specific expression.