bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of previous COVID-19 infection on postoperative complications and functional recovery: a 1-year follow-up ambispective cohort study
Authors: Che Lu , Yu Jiawen , Jin Di , Bai Xue , Wang Yi , Zhang Yuelun , Xu Li , Shen Le , Huang Yuguang 
Published: June 2024

Background:
It’s necessary to reassess the patients’ short-term and long-term postoperative outcomes in the post-COVID-19 era. This study aims to provide more comprehensive evidence regarding the timing of surgery after COVID-19 infection among the vaccinated population upon Omicron variant, considering the duration after acute COVID-19 infection, the severity of COVID-19, patients’ comorbidities, and the full course quality of postoperative recovery.

Materials and methods:
This is a single-center cohort study. Patients diagnosed with preoperative COVID-19 infection were consecutively included before surgery. Patients’ demographics, surgical characteristics, and COVID-19-related factors were documented. Exposure was the time interval from COVID-19 infection to surgery. The primary outcome was postoperative complications within 30 days. The secondary outcomes included postoperative mortality within 30 days, functional disability at 6 and 12 months after surgery.

Results:
A total of 4953 patients were included, and postoperative complications occurred in 353 patients (7.1%) within 30 days after surgery. Time interval from COVID-19 infection to surgery was associated with postoperative complications within 30 days after surgery [adjusted odds ratio (aOR) per day: 0.99; 95% CI, 0.99–1.00; P<0.01], as well as postoperative 6- and 12-month functional disability [(aOR): 1.00; 95% CI, 0.99–1.00; P<0.01; and (aOR) 0.99; 95% CI, 0.98–1.00; P=0.01, respectively). Delaying surgery beyond a time interval of 2 weeks was associated with reduced postoperative 30-day complications [(aOR): 0.63; 95% CI, 0.43–0.91; P=0.01] and mortality [(aOR): 0.07; 95% CI, 0.01–0.38; P<0.01]. Meanwhile, delaying surgery beyond a time interval of 7 weeks was associated with reduced functional disability at both 6-month [(aOR): 0.67; 95% CI, 0.58–0.79; P<0.01] and 12-month postoperatively [(aOR): 0.71; 95% CI, 0.53–0.95; P=0.02].

Conclusion:
A 2 weeks delay after COVID-19 infection is necessary for decreasing short-term postoperative risks, and a longer waiting period could be beneficial for long-term functional recovery.
Comprehensive analysis of cuproptosis-related genes involved in immune infiltration and their use in the diagnosis of hepatic ischemia-reperfusion injury: an experimental study
Authors: Cai Xiaopeng , Deng Jingwen , Zhou Xiaohu , Wang Kaiyue , Cai Huiqiang , Yan Yingcai , Jiang Jun , Yang Jia , Gu Jin , Zhang Yuan , Ding Yuan , Sun Qiang , Wang Weilin 
Published: June 2024

Background:
Hepatic ischemia-reperfusion injury (HIRI) is a common injury not only during liver transplantation but also during major hepatic surgery. HIRI causes severe complications and affects the prognosis and survival of patients. Cuproptosis, a newly identified form of cell death, plays an important role in a variety of illnesses. However, its role in HIRI remains unknown.

Materials and methods:
The GSE151648 dataset was mined from the Gene Expression Omnibus (GEO) database, and differences were analyzed for intersections. Based on the differentially expressed genes (DEGs), functional annotation, differentially expressed cuproptosis-related genes (DE-CRGs) identification and lasso logistic regression were conducted. Correlation analysis of DE-CRGs and immune infiltration was further conducted, and DE-CRGs were applied to construct an HIRI diagnostic model. The hierarchical clustering method was used to classify the specimens of HIRI, and functional annotation was conducted to verify the accuracy of these DE-CRGs in predicting HIRI progression. The GSE14951 microarray dataset and GSE171539 single-cell sequencing dataset were chosen as validation datasets. At the same time, the significance of DE-CRGs was verified using a mouse model of HIRI with cuproptosis inhibitors and inducers. Finally, a network of transcription-factor-DE-CRGs and miRNA-DE-CRGs was constructed to reveal the regulation mechanisms. And potential drugs for DE-CRGs were predicted using Drug-Gene Interaction Database (DGIdb).

Results:
Overall, 2390 DEGs and 19 DE-CRGs were identified. Through machine learning algorithms, 8 featured DE-CRGs (GNL3, ALAS1, TSC22D2, KLF5, GTF2B, DNTTIP2, SLFN11 and HNRNPU) were screened, and 2 cuproptosis-related subclusters were defined. Based on the 8 DE-CRGs obtained from the HIRI model [area under the curve (AUC)=0.97], the nomogram model demonstrated accuracy in predicting HIRI. Eight DE-CRGs were highly expressed in HIRI samples and were negatively related to immune cell infiltration. A higher level of immune infiltration and expression of CRG group B was found in the HIRI population. Differences in cell death and immune regulation were found between the 2 groups. The diagnostic value of the 8 DE-CRGs was confirmed in the validation of two datasets. The identification of 7 DE-CRGs (SLFN11 excluded) by HIRI animal model experiments was also confirmed. Using hTFtarget, miRWalk and DGIDB database, we predicted that 17 transcription factors, 192 miRNAs and 10 drugs might interact with the DE-CRGs.

Conclusion:
This study shows that cuproptosis may occur in HIRI and is correlated with immune infiltration. Additionally, a cuproptosis-related predictive model was constructed for studying the causes of HIRI and developing targeted treatment options for HIRI.
Genotype–phenotype characteristics of 57 patients with Prader–Willi syndrome: a single-center experience from Turkey
Authors: Torun Deniz , Akin Onur 
Published: June 2024

Objectives
Prader–Willi syndrome (PWS) is a rare and complex genetic disorder caused by the loss of expression of the paternal copy of the imprinted genes on chromosome 15q11-q13. A variety of findings have been reported on the phenotypic differences between the genetic subtypes of PWS. This article compares the clinical findings of 57 PWS patients by genetic subtype and explores possible associations in this context.

Methods
Methylation‑specific multiplex ligation–dependent probe amplification and single nucleotide polymorphism microarrays were used to diagnose deletion and uniparental disomy (UPD). For phenotype–genotype correlation, clinical data were collected and genetic subgroups were compared statistically, and P < 0.05 was considered to indicate statistical significance.

Results
These 57 patients consisted of 15 type I deletions, 20 type II deletions, six atypic deletions, 11 heterodisomy UPD, four isodisomy UPD, and one translocation-type PWS. All patients had hypotonia, poor neonatal sucking, and feeding difficulties during infancy. Other PWS-related clinical findings, such as speech articulation problems (85.9%), sleep apnea (77.2%), normal birth length (71.9%), small hands/feet (71.9%), childhood polyphagia (57.9%), clinodactyly (56.1%), thick viscous saliva (54.4%), and behavioral problems (50.9%) were observed at varying rates with no statistical difference between genetic subtypes in general.

Conclusion
This study highlights the phenotype–genotype associations on PWS from a cohort of Turkish pediatric patients as a single-center experience.
Gastroduodenal injury and repair mechanisms
Authors: Hagen Susan J. 
Published: June 2024

Purpose of reviewAlthough the mucosal barrier serves as a primary interface between the environment and host, little is known about the repair of acute, superficial lesions or deeper, persistent lesions that if not healed, can be the site of increased permeability to luminal antigens, inflammation, and/or neoplasia development.Recent findingsStudies on acute superficial lesions have been sparse in the past year, with more focus given to novel mechanisms of mucosal protection, and the way in which mature epithelial cells or committed stem cells dedifferentiate, reprogram, proliferate, and then regenerate the gastroduodenal mucosa after injury. For this, adenoviral therapy showed organ specific targeting with mRNA and protein expression of effectors to protect against mucosal injury and ulceration. A large database of plant-based agents known to protect against injury and ulceration was published, along with studies using plant-based compounds delivered with alginates, polysaccharide/gel floating rafts, or incorporated into nanoparticles or green carbon dots to improve targeting and retention at the ulcerated lesion. With RNA technology developing rapidly, particularly single-cell RNA sequencing, important and novel data was forthcoming on mucosal regeneration. In particular, the role of interleukin-17 hub proteins in mucosal healing was highlighted. The presence and role of injury reserve cells was determined, as was the composition of ligand gradients for cell differentiation in both stomach and duodenum. The role of amphiregulin in parietal cell differentiation from lineage-restricted stem cells and the Yap1 gene signature in metaplasia vs. healing ulcers were of particular importance. Additionally, studies unveiled the important role of mesenchymal stromal cells in differentiation and repair mechanisms, in Muse cells as an exciting new therapy for mucosal repair after injury, and the role of sympathetic neurons in activating the immune system to regulate mucosal repair mechanisms.SummaryRecent studies highlight novel mechanisms that promote mucosal regeneration after injury of the gastroduodenal mucosa.
Accuracy and Interpretation of Transcutaneous Carbon Dioxide Monitoring in Critically Ill Children
Authors: Setar Leah , Lee Jessica G. , Sanchez-Pinto L. Nelson , Coates Bria M. 
Published: June 2024

OBJECTIVES:
Transcutaneous carbon dioxide (Tcco
2) monitoring can noninvasively assess ventilation by estimating carbon dioxide (CO
2) levels in the blood. We aimed to evaluate the accuracy of Tcco
2 monitoring in critically ill children by comparing it to the partial pressure of arterial carbon dioxide (Paco
2). In addition, we sought to determine the variation between Tcco
2 and Paco
2 acceptable to clinicians to modify patient care and to determine which patient-level factors may affect the accuracy of Tcco
2 measurements.

DESIGN:
Retrospective observational cohort study.

SETTING:
Single, quaternary care PICU from July 1, 2012, to August 1, 2020.

PATIENTS:
Included participants were admitted to the PICU and received noninvasive ventilation support (i.e., continuous or bilevel positive airway pressure), conventional mechanical ventilation, or high-frequency oscillatory or percussive ventilation with Tcco
2 measurements obtained within 15 minutes of Paco
2 measurement.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Three thousand four hundred seven paired arterial blood gas and Tcco
2 measurements were obtained from 264 patients. Bland-Altman analysis revealed a bias of –4.4 mm Hg (95% CI, –27 to 18.3 mm Hg) for Tcco
2 levels against Paco
2 levels on the first measurement pair for each patient, which fell within the acceptable range of ±5 mm Hg stated by surveyed clinicians, albeit with wide limits of agreement. The sensitivity and specificity of Tcco
2 to diagnose hypercarbia were 93% and 71%, respectively. Vasoactive-Infusion Score (VIS), age, and self-identified Black/African American race confounded the relationship between Tcco
2 with Paco
2 but percent fluid overload, weight-for-age, probe location, and severity of illness were not significantly associated with Tcco
2 accuracy.

CONCLUSIONS:
Tcco
2 monitoring may be a useful adjunct to monitor ventilation in children with respiratory failure, but providers must be aware of the limitations to its accuracy.
The Development of Social Determinants of Health Outcome Measures: The Role of Multisector Partnerships and Community Validation
Authors: Hacker Karen , Thomas Craig , Sheridan Juliet , Glasgow LaShawn 
Published: June 2024

Purpose
To develop a set of social determinants of health (SDOH) measurements.

Problem
Despite burgeoning interest in addressing both SDOH and health-related social needs, the evidence on what works is limited due in part to the lack of standardized measures for evaluation.

Methods
In 2020, the Centers for Disease Control and Prevention (CDC) National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) identified 5 SDOH domains related to chronic disease for future programmatic work. These included built environment, community connections to clinical care, tobacco-free policies, social connectedness, and food and nutrition security. Subsequently, NCCDPHP launched an effort to develop a set of SDOH measures for evaluating funded programs in these domains. The approach involved a literature scan and a rating process based on 5 criteria relevant to NCCDPHP’s SDOH priorities. A complementary community review by 13 multisector community partnerships (MCPs) applied a real-world public health practice lens to measure development. MCPs’ ratings were analyzed to create summary scores for each measure, and open-ended feedback was synthesized using rapid qualitative analysis.

Results
The internal workgroup identified 59 measures from the initial 200 measures. Feedback from the MCPs identified issues of relevancy and burden of measures. Their high scores narrowed the 59 measures to 22 covering all 5 domains. In response, CDC is honing the original measures review criteria to include community perspectives.

Conclusion
Public health measures development is often an academic pursuit. Engaging MCPs lends real-world credibility to the development of common SDOH measures.
Massive Hepatocellular Carcinoma Combined With Giant Uterine Fibroid on 18F-FDG PET/CT
Authors: Chen Bo-Lin , Huang Wen-Shan , Yu Jie-Qun , Yan Chu-Shan , Xu Jie-Hua 
Published: June 2024

Abstract
A 50-year-old woman was admitted due to a liver mass discovered by ultrasound in routine physical examination. MRI demonstrated a large hepatocellular carcinoma. It also discovered an abdominal mass simultaneously. 18F-FDG PET/CT was performed for staging. PET/CT showed mixed and mild metabolism of the hepatic lesion and giant abdominopelvic mass, respectively. Hepatocellular carcinoma combined with a benign mass in abdominopelvic cavity from uterine was considered and finally proved pathologically. We present a rare case of woman with large liver cancer accompanied by giant uterine fibroid where 18F-FDG PET/CT helped in making the right diagnosis.
Revised Diagnosis From Histiocytic Neoplasm to Optic Chiasm Glioblastoma After Genetic Analysis
Authors: Magharious Mark M. , Pekmezci Melike , Mamlouk Mark D. , Horton Jonathan C. , Levin Marc H. 
Published: June 2024

Abstract:
A 46-year-old man presented with left eye blurring. Automated visual field testing showed an incongruous right hemianopia, with sparing of the lower temporal quadrant in the right eye. MRI revealed foci of gadolinium enhancement in the optic chiasm and optic tracts. Serologic testing (including myelin oligodendrocyte glycoprotein and neuromyelitis optica antibodies) and cerebrospinal fluid analysis were negative. Whole-body PET/CT scan found no malignancy. Biopsy of the optic chiasm revealed a moderately cellular neoplasm composed of atypical, discohesive cells with enlarged nuclei, prominent eosinophilic nucleoli, and abundant vacuolated cytoplasm. Immunohistochemical stains for CD68 and S100 were positive, whereas those for GFAP, OLIG2, SOX10, and multiple others were negative, supporting a diagnosis of histiocytic neoplasm. Five weeks later, results became available from next-generation sequencing targeting the coding regions of hundreds of malignancy-associated genes and select introns. Alterations associated with histiocytic neoplasms (i.e. BRAF and MAP2K1 mutations) were absent. However, there was a nonsense mutation in the PTEN gene, a hotspot mutation in the TERT gene promotor, and focal amplifications of the CDK4 and MDM2 genes. Additionally, there was chromosome 6q loss, 7 gain, and 10q loss. Based on these findings, the diagnosis was revised to glioblastoma, IDH-wildtype, CNS WHO grade 4. The patient began treatment with temozolomide while continuing radiation therapy. This case illustrates how next-generation sequencing can at times provide more accurate diagnostic information than standard tissue histopathology.
Beyond Stereo-EEG: Is It Worth Combining Stereo-EEG With Other Diagnostic Methods?
Authors: Jacobs Julia , Klotz Kerstin Alexandra , Pizzo Francesca , Federico Paolo 
Published: June 2024

Summary:
Stereo-EEG is a widely used method to improve the diagnostic precision of presurgical workup in patients with refractory epilepsy. Its ability to detect epileptic activity and identify epileptic networks largely depends on the chosen implantation strategy. Even in an ideal situation, electrodes record activity generated in <10% of the brain and contacts only record from brain tissue in their immediate proximity. In this article, the authors discuss how recording stereo-EEG simultaneously with other diagnostic methods can improve its diagnostic value in clinical and research settings. It can help overcome the limited spatial coverage of intracranial recording and better understand the sources of epileptic activity. Simultaneous scalp EEG is the most widely available method, often used to understand large epileptic networks, seizure propagation, and EEG activity occurring on the contralateral hemisphere. Simultaneous magnetoencephalography allows for more precise source localization and identification of deep sources outside the stereo-EEG coverage. Finally, simultaneous functional MRI can highlight metabolic changes following epileptic activity and help understand the widespread network changes associated with interictal activity. This overview highlights advantages and methodological challenges for all these methods. Clinical use and research applications are presented for each approach.
Funmap: integrating high-dimensional functional annotations to improve fine-mapping
Authors: Li Yuekai , Xiao Jiashun , Ming Jingsi , Zeng Yicheng , Cai Mingxuan 
Published: June 2024

AbstractFine-mapping aims to prioritize causal variants underlying complex traits by accounting for the linkage disequilibrium of GWAS risk locus. The expanding resources of functional annotations serve as auxiliary evidence to improve the power of fine-mapping. However, existing fine-mapping methods tend to generate many false positive results when integrating a large number of annotations. In this study, we propose a unified method to integrate high-dimensional functional annotations with fine-mapping (Funmap). Funmap can effectively improve the power of fine-mapping by borrowing information from hundreds of functional annotations. Meanwhile, it relates the annotation to the causal probability with a random effects model that avoids the over-fitting issue, thereby producing a well-controlled false positive rate. Paired with a fast algorithm, Funmap enables scalable integration of a large number of annotations to facilitate prioritizing multiple causal SNPs. Our simulations demonstrate that Funmap is the only method that produces well-calibrated FDR under the setting of high-dimensional annotations while achieving better or comparable power gains as compared to existing methods. By integrating GWASs of 4 lipid traits with 187 functional annotations, Funmap consistently identified more variants that can be replicated in an independent cohort, achieving 15.5% − 26.2% improvement over the runner-up in terms of replication rate.
Exploiting multivariate network meta-analysis: A calibrated Bayesian composite likelihood inference
Authors: Wang Yifei , Lin Lifeng , Liu Yu-Lun 
Published: June 2024

SummaryMultivariate network meta-analysis has emerged as a powerful tool in evidence synthesis by incorporating multiple outcomes and treatments. Despite its advantages, this method comes with methodological challenges, such as the issue of unreported within-study correlations among treatments and outcomes, which potentially lead to misleading conclusions. In this paper, we proposed a calibrated Bayesian composite likelihood approach to overcome this limitation. The proposed method eliminated the need to specify a full likelihood function while allowing for the unavailability of within-study correlations among treatments and outcomes. Additionally, we developed a hybrid Gibbs sampler algorithm along with the Open-Faced Sandwich post-sampling adjustment to enable robust posterior inference. Through comprehensive simulation studies, we demonstrated that the proposed approach yielded unbiased estimates while maintaining coverage probabilities close to the nominal level. Furthermore, we implemented the proposed method on two real-world network meta-analysis datasets; one comparing treatment procedures for the root coverage and another comparing treatments for anaemia in chronic kidney disease patients.
Preliminary X-ray diffraction and ligand-binding analyses of the N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv
Authors: Park Jihyun , Cheon Yu Jeong , Jeong Yoon Chae , Lee Ki Seog 
Published: June 2024

Mycobacterium tuberculosis can reside and persist in deep tissues; latent tuberculosis can evade immune detection and has a unique mechanism to convert it into active disease through reactivation. M. tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that has been proposed to be involved in nucleotide binding-related metabolism in cell-growth and cell-division processes. However, due to a lack of structural information, the detailed function of MtRv1421 remains unclear. In this study, a truncated N-terminal domain (NTD) of MtRv1421, which contains a Walker A/B-like motif, was purified and crystallized using PEG 400 as a precipitant. The crystal of MtRv1421-NTD diffracted to a resolution of 1.7 Å and was considered to belong to either the C-centered monoclinic space group C2 or the I-centered orthorhombic space group I222, with unit-cell parameters a = 124.01, b = 58.55, c = 84.87 Å, β = 133.12° or a = 58.53, b = 84.86, c = 90.52 Å, respectively. The asymmetric units of the C2 or I222 crystals contained two or one monomers, respectively. In terms of the binding ability of MtRv1421-NTD to various ligands, uridine diphosphate (UDP) and UDP-N-acetylglucosamine significantly increased the melting temperature of MtRv1421-NTD, which indicates structural stabilization through the binding of these ligands. Altogether, the results reveal that a UDP moiety may be required for the interaction of MtRv1421-NTD as a nucleotide-binding protein with its ligand.
Synergistic corrosion behavior of Cl− and oxalic acid on ADC12 aluminum alloy
Authors: Liu Sudan , Huang Hualiang , He Jinbei 
Published: June 2024

Purpose
As a commonly engine coolant, ethylene glycol can produce corrosive acid byproducts at high temperatures when the car is running, specifically oxalic acid (OA), which can shorten the service life of engine. At the same time, chloride ions can also be introduced during coolant preparation processes. Therefore, this paper aims to investigate the synergistic corrosion behavior of Cl− and OA on ADC12 aluminum alloy.

Design/methodology/approach
The electrochemical tests, scanning electron microscopy, energy dispersive spectrometer, X-ray diffraction and X-ray photoelectron spectroscopy) were used.

Findings
The results showed that the corrosion rate of the aluminum alloy increased with the increase of OA and Cl− concentrations. After adding Cl−, the surface film of the aluminum alloy was further damaged, Cl− has a synergistic effect with OA and their interaction further accelerated the corrosion of the aluminum alloy. Nevertheless, as the immersion time increased, the corrosion rate of the aluminum alloy gradually diminished due to the formation of aluminum oxalate.

Originality/value
The corrosion of ADC12 aluminum alloy was studied in OA, Cl− and their mixed solutions; the synergistic effect of OA and Cl− on the corrosion of ADC12 aluminum alloy was discussed, and aluminum oxalate formed inhibited its corrosion.