bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum Phosphorus and Hypophosphatemia During Therapy of Diabetic Ketoacidosis in Children: Single-Center, Retrospective Cohort 2016–2022
Authors: Hasan Rashed A. , Hesen Jacob Z. , Millican Nicklaus , Pederson John M. , Agus Michael S. D. 
Published: November 2024

OBJECTIVES:
To assess factors associated with serum phosphorus (P) and hypophosphatemia in children with type 1 diabetes mellitus (T1DM) treated for diabetic ketoacidosis (DKA).

DESIGN:
Retrospective cohort.

SETTING:
Community-based PICU in a university-affiliated hospital.

PATIENTS:
Patients 1–20 years old with T1DM hospitalized for DKA from July 1, 2016, to July 31, 2022.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
We collected age, sex, duration of T1DM, conscious state at presentation, and most recent glycohemoglobin level. P was tested initially and then every 4 hours. Probability of hypophosphatemia and time to hypophosphatemia and hospital length of stay (LOS) were analyzed via binomial and linear mixed-effects regression analyses, respectively. A total of 852 DKA episodes occurred in 365 patients (46.3% female, median age 14.7 yr), of which 158 (18.5%) episodes were new-onset T1DM. Hypophosphatemia developed during 656 of 852 (77%) episodes, including 49 of 852 (5.8%) episodes of severe hypophosphatemia with median (interquartile range) onset 8.0 hours (4.7–11.9 hr) and 12.0 hours (8.1–17.6 hr), respectively, following initiation of therapy. Higher glycohemoglobin was associated with greater odds of hypophosphatemia (odds ratio [OR], 1.22; p < 0.001). However, lower odds of hypophosphatemia were associated with older age (OR, 0.89; p < 0.01), male (OR, 0.11; p = 0.01), longer T1DM duration (OR, 0.87; p < 0.001), and having initial normal conscious state (OR, 0.18; p < 0.01). Older age (3.0%/yr; p = 0.02), T1DM duration (4.1%/yr; p = 0.01), and initial serum P (23.4%/mg/dL; p < 0.001) were associated with later hypophosphatemia. LOS was shorter with increased T1DM duration (3.6%/yr; p < 0.001) and normal conscious state (33.1% shorter; p < 0.001), but longer with increasing glycohemoglobin (4.0%; p < 0.001). All patients survived with normal neurologic function.

CONCLUSIONS:
Higher glycohemoglobin was associated with greater odds of hypophosphatemia and longer LOS. Older male, longer duration of T1DM, and conscious at admission were factors associated with lower odds of developing hypophosphatemia and with later onset when it occurred. Hypophosphatemia was associated with longer LOS.
Dementia and Emergency Department Use in Older Adults With Systemic Lupus Erythematosus
Authors: Lieber Sarah B. , Nahid Musarrat , Navarro-Millán Iris , Rajan Mangala , Sattui Sebastian E. , Reid M. Carrington , Mandl Lisa A. 
Published: November 2024

Background/Objective
Systemic lupus erythematosus (SLE) is associated with increased dementia risk. Whether this association is present among older adults with SLE is unclear. Further, whether individuals with concomitant SLE and dementia are at increased risk of emergency department (ED) use has not been explored. Using US Centers for Medicare & Medicaid Services (2006–2015) administrative claims data, we (1) quantified long-term all-cause dementia prevalence in adults with SLE ≥65 years of age and (2) determined whether dementia duration is associated with risk of ED visits in a cohort of older adults with SLE relative to comparators.

Methods
Medicare beneficiaries ≥65 years of age with SLE and age- and sex-matched comparators (1:4) with osteoarthritis were identified at baseline (2006). Dementia was considered a time-varying exposure, updated annually. Mixed-effect Poisson regression was used to estimate the effect of dementia duration on risk of multiple ED visits for the study period (January 2006 to September 2015), adjusting for relevant covariates.

Results
Baseline dementia prevalence was similar among beneficiaries with SLE (n = 1338 [4.6%]) and non–systemic rheumatic disease (non-SRD) comparators (n = 5352 [5.7%]). Stronger association between dementia duration and ED use was observed in older adults with SLE, including after adjustment for covariates (SLE: incidence rate ratio, 1.10; 95% confidence interval, 1.07–1.13; non-SRD: incidence rate ratio, 1.05; 95% confidence interval, 1.03–1.06).

Conclusions
Although dementia prevalence was similar between older adults with SLE and non-SRD comparators, dementia duration had a greater impact on ED use in aging adults with SLE versus non-SRD comparators. Geriatric assessment may be especially important in older adults with SLE.
An Unexpected Mediastinal Fibrosis Case Detected and Evaluated of Treatment Response With 18F-FDG PET/CT
Authors: Akgun Elife , Kaya Meryem 
Published: November 2024

Abstract
IgG4-releated disease is systemic fibroinflammatory disease characterized by infiltration of IgG4-positive plasma cells in the affected tissue. Mediastinal fibrosis, which is also known as fibrosing mediastinitis, is a rare form of IgG4-releated disease. We present a case of mediastinal and retroperitoneal fibrosis in 52-year-old man who was detected with increased radiopharmaceutical uptake in 18F-FDG PET/CT imaging.
FDG PET/CT in a Case of Metastasizing Pleomorphic Adenoma in the Ilium
Authors: Xiao Zhengguang , Dong Aisheng , Wang Yang , Yao Weiwu , Bai Yushu 
Published: November 2024

Abstract
Although pleomorphic adenomas of the salivary glands are benign tumors, they can metastasize to distant organs without evidence of malignant transformation. We describe FDG PET/CT finding in a case of metastasizing pleomorphic adenoma in the right ilium occurring 22 years after initial surgical resection of a lip pleomorphic adenoma. On FDG PET/CT, the iliac metastasis appeared as an expansile osteolytic lesion with heterogeneous activity. This case indicates that metastasizing pleomorphic adenoma, although rare, should be included in the differential diagnosis of FDG-avid osteolytic bone lesions in patients with a history of salivary gland pleomorphic adenoma.
Re-Rechallenge 177Lu-PSMA-617 Radioligand Therapy in Metastatic Castration-Resistant Prostate Cancer
Authors: Aggarwal Piyush , Gunasekaran Vinisha , Sood Ashwani , Kumar Narendra , Rathore Yogesh , Kumar Rajender , Mittal Bhagwant Rai 
Published: November 2024

Abstract

177Lu-PSMA-617 radioligand therapy has been US Food and Drug Administration–approved safe and effective treatment modality for metastatic castration-resistant prostate cancer, usually administered in 4 to 6 cycles at 6 to 8 weeks apart. Many patients achieve partial response or stable disease with biochemical response after treatment. However, these effects are usually short-lived, and patients ultimately show disease progression after a median period of 6 to 9 months. Rechallenge therapy appears to be safe and effective treatment modality in such patients. We show the clinical efficacy and safety of re-rechallenge 177Lu-PSMA radioligand therapy in a 64-year-old man with metastatic castration-resistant prostate cancer with disease progression on multiple lines of hormonal and chemotherapy treatment.
11C-Methionine PET/CT in Cryptococcus Meningoencephalitis
Authors: Otomi Yoichi , Teshima Natsumi , Shinya Takayoshi , Otsuka Hideki , Harada Masafumi 
Published: November 2024

Abstract
A 70-year-old man experienced an epileptic seizure. Subsequent MRI performed on close examination revealed high signal in the left occipital cortex on fluid-attenuated inversion recovery. Gadolinium contrast indicated enhancement along the cortex. 11C-Methionine PET/CT scan, performed to differentiate from a brain tumor, showed high uptake mainly along the left occipital lobe cortex. Spinal fluid examination revealed Cryptococcus neoformans, leading to a diagnosis of Cryptococcus meningoencephalitis.
Bilateral Glomus Caroticum With Rare Metastatic Sites Demonstrated on 68Ga-DOTATATE PET/CT
Authors: Aydinbelge-Dizdar Nur , Cinar Alev , Inanir Ayberk , Ozmen Ozlem 
Published: November 2024

Abstract
A 39-year-old woman with bilateral carotid body tumors was referred to 68Ga-DOTATATE PET/CT for further evaluation. Unknown metastatic sites with increased 68Ga-DOTATATE uptake were detected in the left cervical lymph node, liver, and bone. Carotid body paragangliomas (CBPs) represent less than 0.5% of all head and neck tumors and are rarely seen as metastatic disease. 68Ga-DOTATATE PET/CT is a substantial imaging method for primary staging of CBPs, revealing unknown lesions, changing the treatment approaches and determining prognosis. We aimed to present the contribution of 68Ga-DOTATATE PET/CT to patient management in a rare case of bilateral CBPs with rare metastatic sites.
Lupus Nephritis Revealed by FAPI PET/CT
Authors: Zhang Wenjie , Qi Zhongzhi , Shen Guohua 
Published: November 2024

Abstract
A 38-year-old woman received a 68Ga-FAPI-04 PET/CT scan for the evaluation of systemic lupus erythematosus. Diffuse uptake in both kidney parenchyma indicated the presence of lupus nephritis. In addition, an incidental carotid body tumor with increased FAPI uptake was also observed. Our case described the imaging features of lupus nephritis coexistent with a carotid body tumor on FAPI PET/CT.
Implementation of Electronic Medical Record Interventions to Maximize Opioid Disposal after Surgery in Routine Clinical Practice
Authors: Deshmukh Yash , Amezcua Mateo L , Barth Brendan W , Cotter Robin R , Barth Richard J 
Published: November 2024

Background:
Despite guideline directed opioid prescribing after surgery, many patients retain excess opioids. Leftover pills increase the risk for misuse, diversion, and dependency. It is unclear whether interventions applied in routine clinical practice can increase excess opioid disposal rates.

Study Design:
All adult patients at our institution with postoperative opioid prescriptions were identified in general surgery, otolaryngology, plastic surgery, neurosurgery, urology and transplant surgery. Disposal rates for 453 pre-intervention patients (surgery between 3/1/23—6/30/23) were compared with 545 intervention patients (surgery between 10/1/23—1/31/24). Pre- and post-intervention patients were called 1-3 months after surgery and asked about excess opioids.
Interventions:
1. Opioid disposal information sheets provided after surgery.
2. Opioid disposal reminder delivered via patient portal in electronic medical record (EMR).
3. Best practice alert (BPA) triggered in EMR at post operative visit reminded providers to discuss opioid disposal.

Results:
Opioid disposal outcomes were obtained from 70% (699/998) of patients. 54% (375/699) had excess opioids. The percentage of patients disposing of their excess opioids increased from 30% (39/130) pre-intervention to 83% (204/245) post-intervention, p<0.00001. Forty-seven percent (247/545) of post-intervention patients had discussions with their providers after a BPA fired at their post-operative visits. Patients who had a provider discussion were more likely to dispose of excess opioids than those who only received an information sheet and patient portal reminder (92% vs 70%, p < 0.00001).

Conclusions:
Interventions easily incorporated into the EMR as part of routine clinical practice can markedly increase excess opioid disposal rates after surgery. When information on opioid disposal and patient portal reminders are combined with disposal discussions with providers at the postoperative visit, opioid disposal rates of >90% can be achieved.
Speech motor cortex enables BCI cursor control and click
Authors: Singer-Clark Tyler , Hou Xianda , Card Nicholas S. , Wairagkar Maitreyee , Iacobacci Carrina , Peracha Hamza , Hochberg Leigh R. , Stavisky Sergey D. , Brandman David M. 
Published: November 2024

AbstractDecoding neural activity from ventral (speech) motor cortex is known to enable high-performance speech brain-computer interface (BCI) control. It was previously unknown whether this brain area could also enable computer control via neural cursor and click, as is typically associated with dorsal (arm and hand) motor cortex. We recruited a clinical trial participant with ALS and implanted intracortical microelectrode arrays in ventral precentral gyrus (vPCG), which the participant used to operate a speech BCI in a prior study. We developed a cursor BCI driven by the participant’s vPCG neural activity, and evaluated performance on a series of target selection tasks. The reported vPCG cursor BCI enabled rapidly-calibrating (40 seconds), accurate (2.90 bits per second) cursor control and click. The participant also used the BCI to control his own personal computer independently. These results suggest that placing electrodes in vPCG to optimize for speech decoding may also be a viable strategy for building a multi-modal BCI which enables both speech-based communication and computer control via cursor and click.
Timing of decompressive craniectomy and in-hospital mortality in children following severe traumatic brain injury using the German Hospital Database
Authors: Hojeij Rayan , Brensing Pia , Kowall Bernd , Stang Andreas , Nonnemacher Michael , Felderhoff-Müser Ursula , Dammann Philipp , Dudda Marcel , Dohna-Schwake Christian , Bruns Nora 
Published: November 2024

AbstractIntroductionDecompressive craniectomy (DC) is a last tier to control refractory intracranial pressure elevation in children with severe traumatic brain injury (sTBI), but the optimal timing is unknown. This study aimed to describe the association between timing of DC and in-hospital mortality in children with sTBI in Germany.MethodsA retrospective cohort study of the German national hospital discharge database (2016-2022) was conducted for cases < 18 years. Children undergoing DC following sTBI were extracted. Time from admission to DC were calculated as complete hours and data were compared between early (time to DC ≤ 2 hours) and late DC (> 2 hours). Hierarchical logistic regression models evaluated the association of DC timing with in-hospital mortality, functional outcomes (Pediatric Complex Chronic Conditions (PCCC) ≥2)), poor outcome (composite outcome of death or PCCC≥2), length of hospital stay, days on mechanical ventilation (MV) and coding of seizures.ResultsAmong 13,492,821 children hospitalized, 9,495 had sTBI. DC was performed in 598 cases with time to decompression ranging from 0 to 27 days. More than half of DCs (54.8%) were performed within the first two hours after admission. 164 (27.6%) deaths occurred, with a median time from admission to death of 2 days. Early DC had a higher case-fatality (37.4%) compared to late DC (15.8%), with higher odds of death (adjusted odds ratio [OR] 2.89; 95% confidence interval [95%CI] 1.43-5.85) and poor outcome (OR 1.22; 95% CI 0.71-2.21). However, in survivors, early DC was associated with a shorter duration of MV. No differences in functional outcomes were associated with the timing of DC.ConclusionChildren undergoing early DC exhibited a higher risk of case fatality and poor outcome, alongside with less days on MV in survivors.Key pointsQuestionIs there an association between the timing of decompressive craniectomy (DC) and in-hospital mortality in children with severe traumatic brain injury (sTBI)?FindingEarly DC (≤ 2 hours after admission) was associated with higher case fatality and poor outcomes but fewer days on mechanical ventilation in survivors compared to late DC (> 2 hours).MeaningThe timing of DC may impact survival and recovery outcomes in pediatric sTBI, suggesting the need to balance early intervention with potential risks.
High δ15N values in Predynastic Egyptian archeological remains: A potential indicator for localised soil fertilisation practices in extreme conditions
Authors: Poulallion Eve , Perraud Annie , Besson David , Berthet Didier , Richardin Pascale , Vinçon-Laugier Arnauld , Fourel François , Flandrois Jean-Pierre , Maureille Bruno , Lécuyer Christophe 
Published: November 2024

AbstractPredynastic Egypt arose around 5700 BC when nomadic people settled in the Nile Valley. Without voluntary practice related to anthropic mummification, as will be seen with the Egyptian Dynastic empires, human remains from this period were naturally mummified because of the natural environmental conditions, possibly enveloped in plant mats and animal skins. This study focuses on four mummies from the Natural History Museum of Musée des Confluences in Lyon (France). The geographic origin of the mummies and climatic conditions at that time were deduced from ο18O measurements on teeth and bones. These measurements confirm that the primary source of drinking water was the Nile, and that one mummy of unknown origin also originated from Upper Egypt like the other three. The diet and life habits of these individuals were inferred from carbon (ο13C), nitrogen (ο15N) and sulfur (ο34S) isotope compositions of their skins and bone collagens. Our study is of particular interest as we were able to analyse the animal skins and plant material enveloping the mummies using the same isotopic systems. The mean ο15N values obtained in human skins (17.9±2.4‰, AIR) were found to be high, and consistent with the values measured in animal skins (16.0±2.9‰, AIR). The analysed plants have even higher values, with an average of 22.1±2.2‰, AIR. The most probable explanation for the markedly elevated δ15N values observed in all the materials investigated is localised soil amendment practices. This is corroborated by the consistent nitrogen isotopic signatures across all the examined tissues, with a notable prevalence in plant tissues.
Beyond Integration: SuperGLUE Facilitates Explainable Training Framework for Multi-modal Data Analysis
Authors: Liu Tianyu , Zhao Jia , Zhao Hongyu 
Published: November 2024

AbstractSingle-cell Multi-modal Data Integration has been an area of active research in recent years. However, it is difficult to unify the integration process of different omics in a pipeline, and evaluate the contributions of data integration. In this manuscript, we revisit the definition and contributions of multi-modal data integration, and propose a novel and scalable method based on probabilistic deep learning with an explainable framework powered by statistical modeling to extract meaningful information after data integration. Our proposed method is capable of integrating different types of omic and sensing data. It offers an approach to discovering important relationships among biological features or cell states. We demonstrate that our method outperforms other baseline models in preserving both local and global structures and perform a comprehensive analysis for mining structural relationships in complex biological systems, including inference of gene regulatory networks, extraction of significant biological linkages, and analysis of differentially regulatory relationships.
RobustCell: Exploring the Model Attack-Defense Framework for Robust Transcriptomic Data Analysis
Authors: Liu Tianyu , Xiao Yijia , Luo Xiao , Zhao Hongyu 
Published: November 2024

AbstractComputational methods should be accurate and robust for tasks in biology and medicine, especially when facing different types of attacks, defined as perturbations of benign data that can cause a significant drop in method performance. Therefore, there is a need for robust models that can defend attacks. In this manuscript, we propose a novel framework named RobustCell to analyze attack-defense methods in single-cell and spatial transcriptomic data analysis. In this biological context, we consider three types of attacks as well as two types of defenses in our framework and systemically evaluate the performances of the existing methods on their performance of both clustering and annotating single cells and spatial transcriptomic data. Our evaluations show that successful attacks can impair the performances of various methods, including single-cell foundation models. A good defense policy can protect the models from performance drops. Finally, we analyze the contributions of specific genes toward the cell-type annotation task by running the single-gene and group-genes attack methods. Overall, RobustCell is a user-friendly and extension-flexible framework for analyzing the risks and safety of analyzing transcriptomic data under different attacks.
MCC: Automated Mass and Charge Curation at Genome-Scale Applied toC. tuberculostearicum
Authors: Mostolizadeh Reihaneh , Mier Finn , Dräger Andreas 
Published: November 2024

ABSTRACTBackgroundFor many years, antibiotics reliably protected mankind against bacterial infections, including the respiratory tract colonizerCorynebacterium tuberculostearicum. However, the spread of antimicrobial resistance necessitates the search for new treatment options, where the microbiota may play a crucial role. One way to investigate the complex nature of bacteria and their interactions with human hosts or microbiota is through genome-scale metabolic models (GEMs). Constructing GEMs is labor-intensive and time-consuming.ResultsWe introduce the Python package Mass and Charge Curation (MCC), which implements a new automated algorithm to facilitate mass and charge balancing—one of the most time-consuming reconstruction steps. This package manipulates reconstructions by consolidating data from multiple resources and updating thenotes-field with relevant changes. It also generates a visual comparison between draft and curated models, ensuring high-quality metabolic reconstructions. Using MCC, we developed a metabolic reconstruction ofC. tuberculostearicumstrain DSM 44922. The model was improved based on standardization policies, resulting in a functional, well-annotated, high-quality product. We also simulated the organism’s growth in synthetic nasal medium 3 (SNM3).ConclusionsThe high-quality modeliCTUB2024RM consistently resembles growth behavior under realistic conditions in an artificial human nasal environment, enhancing understanding ofC. tuberculostearicumand its potential impact on health and disease. The curation process of this model led to the development of the MCC package, which facilitates the mass and charge balancing of arbitrary flux balance constraints (fbc) models in SBML format.AvailabilityMCC is freely available via PIP, fromhttps://github.com/draeger-lab/MassChargeCuration/. The modeliCTUB2024RM can be obtained as an SBML file wrapped in an OMEX archive from BioModels Database, accessionMODEL2407310001.ImportanceThe rise of antibiotic resistance has made it essential to explore alternative treatments for bacterial infections, particularly those caused by respiratory tract colonizers likeCorynebacterium tuberculostearicum. Understanding the metabolic behavior of these bacteria and their interactions with the human host or microbiota is crucial. genome-scale metabolic models (GEMs) are powerful tools for investigating these interactions, but they are time-consuming to build. Our new Python package, Mass and Charge Curation (MCC), automates a crucial step in the GEM reconstruction process-mass and charge balancing-making it more efficient and reliable. By applying this tool, we developed a high-quality, functional metabolic model forC. tuberculostearicum(iCTUB2024RM), which provides deeper insights into the organism’s growth in a simulated human nasal environment. This work offers a foundation for future research into microbial communities and their role in human health.