bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma proteome association with coronary heart disease and carotid intima media thickness: results from the KORA F4 study
Authors: Elhadad Mohamed A. , del C. Gómez-Alonso Mónica , Chen Chien-Wei , Neumeyer Sonja , Delerue Thomas , Rathmann Wolfgang , Näbauer Michael , Meisinger Christa , Kääb Stefan , Seissler Jochen , Graumann Johannes , Koenig Wolfgang , Suhre Karsten , Gieger Christian , Völker Uwe , Peters Annette , Hammer Elke , Waldenberger Melanie 
Published: May 2024

Abstract
Background and aims
Atherosclerosis is the main cause of stroke and coronary heart disease (CHD), both leading mortality causes worldwide. Proteomics, as a high-throughput method, could provide helpful insights into the pathological mechanisms underlying atherosclerosis. In this study, we characterized the associations of plasma protein levels with CHD and with carotid intima-media thickness (CIMT), as a surrogate measure of atherosclerosis.

Methods
The discovery phase included 1000 participants from the KORA F4 study, whose plasma protein levels were quantified using the aptamer-based SOMAscan proteomics platform. We evaluated the associations of plasma protein levels with CHD using logistic regression, and with CIMT using linear regression. For both outcomes we applied two models: an age-sex adjusted model, and a model additionally adjusted for body mass index, smoking status, physical activity, diabetes status, hypertension status, low density lipoprotein, high density lipoprotein, and triglyceride levels (fully-adjusted model). The replication phase included a matched case-control sample from the independent KORA F3 study, using ELISA-based measurements of galectin-4. Pathway analysis was performed with nominally associated proteins (p-value < 0.05) from the fully-adjusted model.

Results
In the KORA F4 sample, after Bonferroni correction, we found CHD to be associated with five proteins using the age-sex adjusted model: galectin-4 (LGALS4), renin (REN), cathepsin H (CTSH), and coagulation factors X and Xa (F10). The fully-adjusted model yielded only the positive association of galectin-4 (OR = 1.58, 95% CI = 1.30–1.93), which was successfully replicated in the KORA F3 sample (OR = 1.40, 95% CI = 1.09–1.88). For CIMT, we found four proteins to be associated using the age-sex adjusted model namely: cytoplasmic protein NCK1 (NCK1), insulin-like growth factor-binding protein 2 (IGFBP2), growth hormone receptor (GHR), and GDNF family receptor alpha-1 (GFRA1). After assessing the fully-adjusted model, only NCK1 remained significant (β = 0.017, p-value = 1.39e-06). Upstream regulators of galectin-4 and NCK1 identified from pathway analysis were predicted to be involved in inflammation pathways.

Conclusions
Our proteome-wide association study identified galectin-4 to be associated with CHD and NCK1 to be associated with CIMT. Inflammatory pathways underlying the identified associations highlight the importance of inflammation in the development and progression of CHD.
Importance of on-farm research for validating process-based models of climate-smart agriculture
Authors: Ellis Elizabeth , Paustian Keith 
Published: May 2024

AbstractClimate-smart agriculture can be used to build soil carbon stocks, decrease agricultural greenhouse gas (GHG) emissions, and increase agronomic resilience to climate pressures. The US recently declared its commitment to include the agricultural sector as part of an overall climate-mitigation strategy, and with this comes the need for robust, scientifically valid tools for agricultural GHG flux measurements and modeling. If agriculture is to contribute significantly to climate mitigation, practice adoption should be incentivized on as much land area as possible and mitigation benefits should be accurately quantified. Process-based models are parameterized on data from a limited number of long-term agricultural experiments, which may not fully reflect outcomes on working farms. Space-for-time substitution, paired studies, and long-term monitoring of SOC stocks and GHG emissions on commercial farms using a variety of climate-smart management systems can validate findings from long-term agricultural experiments and provide data for process-based model improvements. Here, we describe a project that worked collaboratively with commercial producers in the Midwest to directly measure and model the soil organic carbon (SOC) stocks of their farms at the field scale. We describe this study, and several unexpected challenges encountered, to facilitate further on-farm data collection and the creation of a secure database of on-farm SOC stock measurements.
Lysine-specific methyltransferase Set7/9 in stemness, differentiation, and development
Authors: Daks Alexandra , Parfenyev Sergey , Shuvalov Oleg , Fedorova Olga , Nazarov Alexander , Melino Gerry , Barlev Nickolai A. 
Published: May 2024

AbstractThe enzymes performing protein post-translational modifications (PTMs) form a critical post-translational regulatory circuitry that orchestrates literally all cellular processes in the organism. In particular, the balance between cellular stemness and differentiation is crucial for the development of multicellular organisms. Importantly, the fine-tuning of this balance on the genetic level is largely mediated by specific PTMs of histones including lysine methylation. Lysine methylation is carried out by special enzymes (lysine methyltransferases) that transfer the methyl group from S-adenosyl-L-methionine to the lysine residues of protein substrates. Set7/9 is one of the exemplary protein methyltransferases that however, has not been fully studied yet. It was originally discovered as histone H3 lysine 4-specific methyltransferase, which later was shown to methylate a number of non-histone proteins that are crucial regulators of stemness and differentiation, including p53, pRb, YAP, DNMT1, SOX2, FOXO3, and others. In this review we summarize the information available to date on the role of Set7/9 in cellular differentiation and tissue development during embryogenesis and in adult organisms. Finally, we highlight and discuss the role of Set7/9 in pathological processes associated with aberrant cellular differentiation and self-renewal, including the formation of cancer stem cells.
Hemodynamic instability caused by pneumorrachis and pneumomediastinum following epidural analgesia: a case report
Authors: Fountoulaki Maria , Kapetanakis Emmanouil I. , Kouna Niki , Papagiannis Nikolaos , Sidiropoulou Tatiana 
Published: May 2024

Abstract
Background
Pneumomediastinum and pneumorrachis are rare complications following epidural analgesia, that can either be asymptomatic or rarely can produce mild to moderate severity symptoms. Most reported cases regarding the presentation of these two entities with epidural analgesia concern asymptomatic patients, however there are cases reporting post-dural puncture headache and respiratory manifestations.

Case presentation
We present a case where a combined lumbar epidural and spinal anesthesia was performed using the loss of resistance to air technique (LOR), on a 78-year-old Greek (Caucasian) male undergoing a total hip replacement. Despite being hemodynamically stable throughout the operation, two hours following epidural analgesia the patient manifested a sudden drop in blood pressure and heart rate that required the administration of adrenaline to counter. Pneumomediastinum, pneumorrachis and paravertebral soft tissue emphysema were demonstrated in a Computed Tomography scan. We believe that injected air from the epidural space and surrounding tissues slowly moved towards the mediastinum, stimulating the para-aortic ganglia causing parasympathetic stimulation and therefore hypotension and bradycardia.

Conclusion
Anesthesiologists should be aware that epidural analgesia using the LOR to technique injecting air could produce a pneumomediastinum and pneumorrachis, which in turn could produce hemodynamic instability via parasympathetic stimulation.
Eradication of Klebsiella pneumoniae pulmonary infection by silver oxytetracycline nano-structure
Authors: Mosallam Farag M. , Elshimy Rana 
Published: May 2024

AbstractTargeted bactericidal nanosystems hold significant promise to improve the efficacy of existing antimicrobials for treatment of severe bacterial infections by minimizing the side effects and lowering the risk of antibiotic resistance development. In this work, Silver Oxytetracycline Nano-structure (Ag-OTC-Ns) was developed for selective and effective eradication of Klebsiella pneumoniae pulmonary infection. Ag-OTC-Ns were prepared by simple homogenization-ultrasonication method and were characterized by DLS, Zeta potential, TEM and FT-IR. The antimicrobial activity of Ag-OTC-Ns was evaluated in vitro using broth micro-dilution technique and time-kill methods. Our study showed that MICs of AgNO3, OTC, AgNPs and Ag-OTC-Ns were 100, 100, 50 and 6.25 µg/ml, respectively. Ag-OTC-Ns demonstrated higher bactericidal efficacy against the targeted Klebsiella pneumoniae at 12.5 µg/ml compared to the free Oxytetracycline, AgNO3 and AgNPs. In vivo results confirmed that, Ag-OTC-Ns could significantly eradicate K. pneumoniae from mice lung in compare with free Oxytetracycline, AgNO3 and AgNPs. In addition, Ag-OTC-Ns could effectually diminish the inflammatory biomarkers levels of Interferon Gamma and IL-12, and as a result it could effectively lower lung damage in K. pneumoniae infected mice. Ag-OTC-Ns has no significant toxicity on tested mice along the experimental period, there was no sign of behavioral abnormality in the surviving mice indicating that the Ag-OTC-Ns is safe at the used concentration. Furthermore, capability of 5 kGy Gamma ray to sterilize Ag-OTC-Ns solution without affecting it stability was proven.
BHLHE41 inhibits bladder cancer progression via regulation of PYCR1 stability and thus inactivating PI3K/AKT signaling pathway
Authors: Xiao Shuai , Chen Junjie , Wei Yongbao , Song Wei 
Published: May 2024

Abstract
Background
The basic helix-loop-helix family member e41 (BHLHE41) is frequently dysregulated in tumors and plays a crucial role in malignant progression of various cancers. Nevertheless, its specific function and underlying mechanism in bladder cancer (BCa) remain largely unexplored.

Methods
The expression levels of BHLHE41 in BCa tissues and cells were examined by qRT-PCR and western blot assays. BCa cells stably knocking down or overexpressing BHLHE41 were constructed through lentivirus infection. The changes of cell proliferation, cell cycle distribution, migration, and invasion were detected by CCK-8, flow cytometry, wound healing, transwell invasion assays, respectively. The expression levels of related proteins were detected by western blot assay. The interaction between BHLHE41 and PYCR1 was explored by co-immunoprecipitation analysis.

Results
In this study, we found that BHLHE41 was lowly expressed in bladder cancer tissues and cell lines, and lower expression of BHLHE41 was associated with poor overall survival in bladder cancer patients. Functionally, by manipulating the expression of BHLHE41, we demonstrated that overexpression of BHLHE41 significantly retarded cell proliferation, migration, invasion, and induced cell cycle arrest in bladder cancer through various in vitro and in vivo experiments, while silence of BHLHE41 caused the opposite effect. Mechanistically, we showed that BHLHE41 directly interacted with PYCR1, decreased its stability and resulted in the ubiquitination and degradation of PYCR1, thus inactivating PI3K/AKT signaling pathway. Rescue experiments showed that the effects induced by BHLHE41 overexpression could be attenuated by further upregulating PYCR1.

Conclusion
BHLHE41 might be a useful prognostic biomarker and a tumor suppressor in bladder cancer. The BHLHE41/PYCR1/PI3K/AKT axis might be a potential therapeutic target for bladder cancer intervention.
Applying LASSO logistic regression for the prediction of biliary complications after ex vivo liver resection and autotransplantation in patients with end-stage hepatic alveolar echinococcosis
Authors: Lin Xin , Shao Ying-Mei , Zhang Rui-Qing , Aji Tuerganaili 
Published: May 2024

Abstract
Background
The purpose of this study was to explore the relevant risk factors associated with biliary complications (BCs) in patients with end-stage hepatic alveolar echinococcosis (HAE) following ex vivo liver resection and autotransplantation (ELRA) and to establish and visualize a nomogram model.

Methods
This study retrospectively analysed patients with end-stage HAE who received ELRA treatment at the First Affiliated Hospital of Xinjiang Medical University between August 1, 2010 and May 10, 2023. The least absolute shrinkage and selection operator (LASSO) regression model was applied to optimize the feature variables for predicting the incidence of BCs following ELRA. Multivariate logistic regression analysis was used to develop a prognostic model by incorporating the selected feature variables from the LASSO regression model. The predictive ability, discrimination, consistency with the actual risk, and clinical utility of the candidate prediction model were evaluated using receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). Internal validation was performed by the bootstrapping method.

Results
The candidate prediction nomogram included predictors such as age, hepatic bile duct dilation, portal hypertension, and regular resection based on hepatic segments. The model demonstrated good discrimination ability and a satisfactory calibration curve, with an area under the ROC curve (AUC) of 0.818 (95% CI 0.7417–0.8958). According to DCA, this prediction model can predict the risk of BCs occurrence within a probability threshold range of 9% to 85% to achieve clinical net benefit.

Conclusions
A prognostic nomogram with good discriminative ability and high accuracy was developed and validated to predict BCs after ELRA in patients with end-stage HAE.
Rethinking students’ mental health assessment through GHQ-12: evidence from the IRT approach
Authors: Comotti Anna , Barnini Teresa , Fattori Alice , Paladino Maria Emilia , Riva Michele Augusto , Bonzini Matteo , Belingheri Michael 
Published: May 2024

Abstract
Background
The General Health Questionnaire-12 (GHQ-12) is a widely used screening tool for mental health assessment however its traditional scoring methods and cutoffs may not adequately capture the mental health complexities of younger populations.

Methods
This study explores GHQ-12 responses from a sample of university students. Possible differences in means scores considering gender, age, academic field and degree course were assessed through t-test or one-way ANOVA as appropriate. To deeper understanding different levels of severity and individual item impact on general distress measurement, we applied Item-Response-Theory (IRT) techniques (two-parameters logistic model). We compared students’ population with a population of workers who underwent a similar psychological evaluation.

Results
A total of 3834 university students participated in the study. Results showed that a significant proportion (79%) of students reported psychological distress. Females and younger students obtained significantly higher average scores compared to others. IRT analysis found item-specific variations in mental distress levels, with more indicative items for short-term fluctuations and potential severe mental health concerns. Latent class analysis identified three distinct subgroups among students (including 20%, 37%, 43% of the participants respectively) with different levels of psychological distress severity. Comparison with a population of adults showed that students reported significantly higher scores with differences in the scale behavior.

Conclusion
Our results highlighted the unique mental health challenges faced by students, suggesting a reevaluation of GHQ-12 applicability and cutoff scores for younger populations, emphasizing the need for accurate instruments in mental health evaluation.
Monitoring of ground subsidence using PS-InSAR technique in the Southeast Texas (SETX) Region
Authors: Nur Arip Syaripudin , Nam Boo Hyun , Choi Shinwoo , Kim Yong Je 
Published: May 2024

AbstractThe southeast Texas (SETX) coastal area, owing to its unique geographical location and geological attributes, is facing a spectrum of geological challenges, such as ground subsidence, flooding, and coastal erosion. This study endeavors to evaluate the recent instances of ground subsidence and their associated rates, focusing on comprehending their implications for flooding within SETX. Employing the Persistence Scatterer Interferometric Synthetic Aperture Radar (PS-InSAR) technique, this study employs Sentinel-1 SAR satellite data with descending orbit observations spanning from January 2020 to March 2023. Our findings indicate that both the northwestern and eastern regions of Houston have been settled with rates up to 2 cm/year. This settlement trend is consistent with data derived from GPS and groundwater level measurements. This investigation explicitly shows the substantial temporal and spatial variations in subsidence rates, predominantly influenced by localized groundwater extraction due to urbanization (e.g., population growth, land development, etc.). By advocating for the integration of InSAR, GPS, and groundwater measurements, this research aspires to make valuable contributions toward the mitigation of subsidence and flood-related hazards in the SETX area.
A pediatric case of Burkitt’s lymphoma with bile duct obstruction requiring surgical biliary reconstruction
Authors: Watanabe Shun , Suzuki Kan , Ogino Kei , Irie Sumiko , Kamata Yuko , Matsudera Shotaro , Hatanaka Masahiro , Kurosaki Kazunori , Ishikawa Makoto , Okuya Mayuko , Sato Yuya , Yamamiya Akira , Irisawa Atsushi , Ishida Kazuyuki , Yoshihara Shigemi , Kojima Kazuyuki 
Published: May 2024

Abstract
Background
Biliary obstruction due to compression by a B-cell solid tumor occurs rarely. A few reports have described biliary reconstruction surgery for obstructive jaundice caused by Burkitt’s lymphoma. However, there are no detailed reports on pediatric cases. We report a pediatric case of obstructive jaundice due to malignant lymphoma treated with biliary reconstruction surgery.

Case presentation
A 5-year-old girl presented to our hospital with a massive abdominal tumor that caused biliary stricture. Chemotherapy was initiated after an open tumor biopsy. However, endoscopic biliary stent placement was performed owing to elevated bilirubin levels. We treated the patient with chemotherapy for 9 months while endoscopically replacing the biliary stent every few months. She achieved complete tumor remission. However, sclerotic lymph nodes were persistent on the dorsal side of the cholecystic duct junction, and biliary stricture at the same site had changed to stent-dependent biliary obstruction. Therefore, we performed choledochojejunostomy and retrocolic Roux-en-Y reconstruction 15 months after initial admission. There were no postoperative complications or tumor recurrences, and the bilirubin level remained low. Histopathologically, the resected bile duct wall was fibrotic and thick, and the bile duct lumen narrowed.

Conclusions
Biliary reconstruction is effective to achieve long-term biliary patency in pediatric patients with stent-dependent biliary obstruction due to malignant lymphoma. However, the decision on when to stop biliary stent replacement and proceed to biliary reconstruction surgery is a matter of debate. Further case studies are required to address this issue.
Interpretable machine learning decodes soil microbiome’s response to drought stress
Authors: Hagen Michelle , Dass Rupashree , Westhues Cathy , Blom Jochen , Schultheiss Sebastian J. , Patz Sascha 
Published: May 2024

Abstract
Background
Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota and affect plant health. Early recognition of soil affected by drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential for drought stress classification of soil based on marker taxa.

Results
This study demonstrates that the 16S rRNA-based metagenomic approach of Differential Abundance Analysis methods and machine learning-based Shapley Additive Explanation values provide similar information. They exhibit their potential as complementary approaches for identifying marker taxa and investigating their enrichment or depletion under drought stress in grass lineages. Additionally, the Random Forest Classifier trained on a diverse range of relative abundance data from the soil bacterial micobiome of various plant species achieves a high accuracy of 92.3 % at the genus rank for drought stress prediction. It demonstrates its generalization capacity for the lineages tested.

Conclusions
In the detection of drought stress in soil bacterial microbiota, this study emphasizes the potential of an optimized and generalized location-based ML classifier. By identifying marker taxa, this approach holds promising implications for microbe-assisted plant breeding programs and contributes to the development of sustainable agriculture practices. These findings are crucial for preserving global food security in the face of climate change.
Quality of life in individuals with neurofibromatosis type 1 associated cutaneous neurofibromas: validation of the Dutch cNF-Skindex
Authors: Dhaenens Britt A. E. , van Dijk Sarah A. , Fertitta Laura , Taal Walter , Wolkenstein Pierre , Oostenbrink Rianne 
Published: May 2024

Abstract
Background
Almost all patients with Neurofibromatosis type 1 (NF1) develop cutaneous neurofibroma (cNF), benign dermal tumours that have a large impact on the patient’s Quality of Life (QoL). The French cNF-Skindex is the first questionnaire to specifically assess cNF-related QoL in patients with NF1. We aimed to adapt and validate a Dutch version of the cNF-Skindex.

Methods
The questionnaire was translated using forward and backwards translation, and subsequently administered to a sample of 59 patients on two separate occasions. Feasibility was evaluated by the presence of floor/ceiling effects. Reliability was assessed by evaluating internal consistency and test-retest reliability, by calculating Cronbach’s alpha and Spearman’s rank correlation coefficients. The EQ-5D-5L and SF-36 were used to evaluate convergent validity, using Spearman’s rank correlation coefficients. An exploratory factor analysis was performed to study the data’s internal structure. Multivariable linear regression was used to model the relationship between patient characteristics and the cNF-Skindex.

Results
The Dutch cNF-Skindex demonstrated excellent feasibility and reliability (Cronbach’s alpha 0.96, test-retest correlation coefficient 0.88). Convergent validity was confirmed for the EQ-5D-5L and relevant SF-36 scales. All items and subdomains from the original questionnaire were confirmed following exploratory factor analysis. The patient characteristics included in the multivariable linear regression were not significantly associated with the cNF-Skindex score.

Conclusions
The Dutch cNF-Skindex displayed excellent psychometric properties, enabling use in the Netherlands.