bluuebunny/crossref_metadata_2025_split huggingface dataset:
PHB2 Promotes SHIP2 Ubiquitination via the E3 ligase NEDD4 to Regulate AKT Signaling in Gastric Cancer
Authors: Xu Liang , Xiang Wanying , Yang Jiezhen , Gao Jing , Wang Xinyue , Meng Li , Ye Kaihong , Zhao Xiao Hong , Zhang Xu Dong , Jin Lei , Ye Yan 
Published: October 2023

Abstract
Background:
Prohibitin 2 (PHB2) exhibits opposite functions of promoting or inhibiting tumour across various cancer types; nevertheless, its involvement in gastric cancer (GC) remains predominantly unexplored.
Method:
PHB2 protein expression levels in GC and normal tissues were examined using western blot and Immunohistochemistry. PHB2 expression level associations with patient outcomes were examined through Kaplan-Meier plotter analysis utilizing GEO datasets (GSE14210 and GSE29272). The biological role of PHB2 and its subsequent regulatory mechanisms were elucidated in vitro and in vivo. GC cell proliferation was assessed using MTT cell viability analysis, clonogenic assays, and BrdU incorporation assays, while the growth of GC xenografted tumors was measured via IHC staining of Ki-67. The interaction among PHB2 and SHIP2, as well as between SHIP2 and NEDD4, was identified through co-immunoprecipitation, GST pull-down assays, and deletion-mapping experiments. SHIP2 ubiquitination and degradation were assessed using Cycloheximide treatment, plasmid transfection and co-immunoprecipitation, followed by western blot analysis.
Results:
Our analysis revealed a substantial increase in PHB2 expression in GC tissues compared to adjacent normal tissues. Notably, higher PHB2 levels correlated with poorer patient outcomes, suggesting its clinical relevance. Functionally, silencing PHB2 in GC cells significantly reduced cell proliferation and retarded GC tumour growth, whereas overexpression of PHB2 further enhanced GC cell proliferation. Mechanistically, PHB2 physically interacted with Src homology 2-containing inositol 5-phosphatase 2 (SHIP2) in the cytoplasm of GC cells, thus leading to SHIP2 degradation via its novel E3 ligase NEDD4. It subsequently activated the PI3K/Akt signaling pathway and thus promoted GC cell proliferation.
Conclusion:
Our findings highlight the importance of PHB2 upregulation in driving GC progression and its association with adverse patient outcomes. Understanding the functional impact of PHB2 on GC growth contributes valuable insights into the molecular underpinnings of GC and may pave the way for the development of targeted therapies to improve patient outcomes.
Factors associated with medical students’ career choice in different specialties: a multiple cross-sectional questionnaire study at a German medical school
Authors: Leutritz Tobias , Krauthausen Maike , Simmenroth Anne , König Sarah 
Published: October 2023

Abstract

Background: Given the shortage and unequal distribution of physicians across specialties, we aimed to evaluate factors associated with medical students’ career choices, including background, personality traits, educational experience, personal interests, lifestyle considerations, and the awareness of work requirements.
Methods: We conducted multiple cross-sectional surveys of students; a 159-item online questionnaire was designed and students from three different stages of the six-year medical degree course (outset, clinical phase, and on graduation) were invited to complete the survey. Data were collected between May 2021 and April 2023.
Results: The questionnaire was sent to 1406 students, of whom 683 replied (49%); 481 respondents were female (70%). The top specialty choices across the respondents were internal medicine, surgery, and general practice, with anaesthesiology, paediatric and adolescent medicine (ranging 11-15%), and obstetrics and gynaecology also receiving interest, with 6% undecided. In particular, female students lost interest in surgery during the course of study in favour of the other options. The choice of general practice was associated with more vocational training, prior positive experiences with the specialty, and lower grades in the university entry examination. Clinical clerkships in a specific (freely chosen) specialty aligned with career choice, while the final practical year did not have an impact on career decision-making. All students highly desired regulated working hours and work-life-balance; however, students choosing surgery rated these items as less important. Willingness to work in a hospital environment was highly associated with choosing anaesthesiology and surgery, whereas rural areas and practices were associated with general practice. Higher scores at agreeableness were associated with choosing paediatric and adolescent medicine by more female students, whereas lower neuroticism values were associated with the choice of anaesthesiology.
Conclusions: The results highlight the intricate nature of decision-making and shed light on various aspects that contribute to the process of selecting a specialty. By identifying and addressing influencing factors, we can develop targeted interventions and policies to enhance diversity and distribution across medical specialisations and to aim for high-quality and equitable healthcare that matches the specific needs of both individuals and the population as a whole.
Reproducible Method for 1-methylcylopropene (1-MCP) Application and Quantitation for Post-harvest Research
Authors: Stowe Evan , Mattinson D. Scott , Blauer Jacob , Dhingra Amit 
Published: October 2023

Abstract
Background: Actively combating post-harvest food spoilage and waste can dramatically increase the efficiency of food utilization worldwide. In climacteric fruits, treatment with 1-MCP effectively reduces post-harvest spoilage and waste by inhibiting the fruit’s ability to perceive ethylene. 1-MCP treatment is increasingly being used to explore the complex nature of ripening physiology at a fundamental level; however, differences in application and quantitation methods create difficulties in comparing conclusions across studies.
Results Here, we report an effective and reproducible 1-MCP application and quantitation method to enable research investigations. The highly volatile and elusive 1-MCP molecule can be identified and quantified by gas chromatography by using surrogate alkenes 1-butene and cis-2-butene to develop standard curves.
Conclusions. It is hoped that the methodology outlined here can help standardize consistent 1-MCP application for post-harvest research without excessive investment in specialized equipment.
Electrocardiogram Prediction Based on Variational Modal Decomposition and Convolutional Recurrent Gate Unit
Authors: Wang Hongbo , Wang Yizhe , Liu Yu , Yao Yuejuan 
Published: October 2023

Abstract
Electrocardiogram (ECG) prediction is of great significance in compressing and storing heart signals and reminding of potential health hazards. In order to improve the duration and accuracy of ECG prediction on the basis of noise filtering, a new algorithm based on Variational Mode Decomposition (VMD) and Convolutional Recurrent Gate Unit (ConvGRU) was proposed, named VMD-ConvGRU. VMD can directly remove noise such as the baseline drift without manual interventions, which greatly improves the usability of the model, and the combination with ConvGRU improves the prediction time and accuracy. The proposed algorithm was compared with three related algorithms (PSR-NN, VMD-NN and TS Fuzzy) on MIT-BIH, an internationally recognized arrhythmia database. Experiments show that VMD-ConvGRU not only has better prediction accuracy than the above three algorithms, but also has a considerable advantage in the prediction time. In addition, the prediction experiments on both MIT-BIH and EDB have shown better generalization performance of VMD-ConvGRU.
A Novel Signature Model Based on Ferroptosis-Related Genes for Predicting the Prognosis of Colorectal Carcinoma.
Authors: Wei Jingjing , Deng Cini , Zeng Zhiwu , Fu Dongmei , Han Jianglong , Fu Zhenming , Liu Li 
Published: October 2023

Abstract
Colorectal carcinoma (CRC) is a prevalent malignant tumour worldwide, and understanding its prognosis is crucial for effective treatment. The purpose of this work was to use genes linked to ferroptosis to create a prognostic prediction model for CRC. The GEO and TCGA databases were used to obtain data from CRC patients, and the Ferroptosis Gene Database was used to gather information on genes associated with ferroptosis. To discover prognostic markers and build the prognostic model, LASSO regression analysis was utilized. We assessed the prognostic significance of the model by employing Kaplan-Meier analysis and ROC curve evaluation. We utilised the CIBERSORT tool to investigate the possible link between ferroptosis-related genes and immune cells. In this research, a prognostic model comprising 11 ferroptosis-related genes was developed. This model demonstrates a high level of accuracy in predicting outcomes and assessing immune responses in CRC. Based on the analysis of the receiver operating characteristic curve, patients belonging to the high-risk group exhibited an unfavourable prognosis. The model achieved area under the curve values of 0.756, 0.774, and 0.782 at 1-, 3-, and 5-years, respectively. The ferroptosis-related gene biomarkers identified in this study may serve as independent predictors of CRC. The examination of differentially expressed genes in enrichment showed significant immune function differences between high-risk and low-risk groups. This suggests that immune-related mechanisms affect CRC prognosis. This research proposes a prediction model employing 11 ferroptosis-related genes that may help personalise treatment and evaluate CRC patients' prognoses.
The mechanism underlying correlation of particulate matter-induced ferroptosis with inflammasome activation and iron accumulation in macrophages
Authors: Lee Seon-Jin , Park Minkyung , Park Sujeong , Choi Yumin , Cho Young-Lai , Kim Min Jeong , Park Young-Jun , Chung Su Wol , Lee Heedoo 
Published: October 2023

Abstract
Particulate matter (PM) is a global environmental hazard, which affects human health through free radical production, cell death induction, and immune responses. PM activates inflammasomes leading to an excessive inflammatory response, and induces ferroptosis, a type of cell death. Despite ongoing research on the correlation among PM-induced ferroptosis, immune response, and inflammasomes, the underlying mechanism of this relationship has not been elucidated. In this study, we demonstrated the levels of PM-induced cell death and immune responses in murine macrophages, J774A.1 and RAW264.7, depending on the size and composition of particulate matter. PM2.5, with extraction ions, induced significant levels of cell death and immune responses; it induces lipid peroxidation, iron accumulation, and reactive oxygen species (ROS) production, which characterize ferroptosis. In addition, inflammasome-mediated cell death occurred owing to the excessive activation of inflammatory responses. PM-induced iron accumulation activates ferroptosis and inflammasome formation through ROS production; similar results were observed in vivo. These results suggest that the link between ferroptosis and inflammasome formation induced by PM, especially PM2.5 with extraction ions, is established through the iron-ROS axis. Moreover, this study can effectively facilitate the development of a new therapeutic strategy for PM-induced immune and respiratory diseases.
On multifaceted inhibitory control in betel-quid-dependent chewers
Authors: Chang Tzu-Yi , Ho Ming-Chou 
Published: October 2023

Abstract
Background: Betel-quid (BQ) is regarded as a human carcinogen by the World Health Organization. We asked whether BQ chewers have worse inhibitory control, in terms of three separate inhibitory control functions: propotent response inhibition, resistance to distractor interference, and resistance to proactive interference (PI).
Methods: The antisaccade task, the flanler task and the recent-probe task are employed to measure the three inhibition functions, respectively. BQ dependent chewers with concurrent use of tobacco and alcohol (BQD), tobacco and alcohol user controls (TAC), and healthy controls (HC) were included.
Results: We found that the BQD group did not differ from TAC and HC in prepotent response inhibition, measured by the antisaccade task, and resistance to distractor interference, measured by the flanker task. Finally, the BQD group had a worse resistance to PI than the two control groups, measured by the recent-probe task.
Conclusions: When discussing from the perspective of multifacted inhibitory control, we can fully understand the inhibitory control ability of BQ chewers.
Structure elucidation of a human melanocortin-4 receptor specific orthosteric nanobody agonist
Authors: Menet Christel , Laeremans Toon , Fontaine Thomas , Busch Andreas , De Cesco Stéphane , Triest Sarah , Dekeyzer Lies , Samyn Noor , Loeys Nicolas , Perneel Lisa , Debaere Melanie , virmani richa , skieterska kamila , staelens stephanie , Roy maarten Van , Liang Yi-Lynn , Jaakola Veli-Pekka , Sands Zara , Masiulis Simonas , Martini Murielle , Barroco Rosa 
Published: October 2023

Abstract

The melanocortin receptor 4 (MC4R) belongs to the melanocortin receptor family of G-protein coupled receptors and is a key switch in the leptin-melanocortin molecular axis that controls hunger and satiety. Brain-produced hormones such as α-melanocyte-stimulating hormone (agonist) and agouti-related peptide (inverse agonist) regulate the molecular communication of the MC4R axis but are promiscuous for melanocortin receptor subtypes and induce a wide array of biological effects. Using a conformation-selective ConfoBody, the use of active state-stabilized MC4R facilitated efficient de novo discovery of a sequence diverse panel of MC4R-specific, potent and full agonistic nanobodies. We solved the active state MC4R structure in complex with the full agonistic nanobody pN162 at 3.4 Å resolution. The structure shows a unique interaction with pN162 binding deeply in the orthosteric pocket of MC4R and lacking the structural interactions of MC4R agonists reported to date. MC4R peptide agonists, such as the marketed setmelanotide, lack receptor selectivity and show off-target effects. In contrast, the agonistic nanobody is highly specific and hence can be a more suitable agent for anti-obesity therapeutic intervention via MC4R.
Midregional pro atrial naturetic peptide (MRproANP) and copeptin (COPAVP) as predictors of all- cause mortality in early COPD – Results from COSYCONET
Authors: Fähndrich Sebastian , Herr Christian , Teuteberg Sebastian , Alter Peter , Söhler Sandra , Soriano Daniel , Classen Johanna , Adams Julia , Weinhold Victoria , Watz Henrik , Waschki Benjamin , Zeller Tanja , Eichenlaub Martin , Trudzinski Franziska C , Michels Julia D , Omlor Albert , Seiler Frederik , Moneke Isabelle , Biertz Frank , Stolz Daiana , Welte Tobias , Kauczor Hans-Ulrich , Kahnert Kathrin , Jörres Rudolf A , vogelmeier claus , bals robert , group COSYCONET study 
Published: October 2023

Abstract
Background: A number of prognostic markers of mortality are known in chronic obstructive pulmonary disease (COPD) but less so for early and mild stages of the disease. We thus analyzed several biomarkers as potential predictors of mortality in early COPD.
Methods: The blood biomarkers considered were copeptin (COPAVP), midregional adrenomedullin (MRproADM), midregional pro atrial naturetic peptide (MRproANP), and fibrinogen. Analyses were performed in patients with stable “early COPD” defined by GOLD grades 0-2 and diagnosis of COPD ≤5 years prior to inclusion into the COSYCONET cohort (COPD and Systemic Consequences - Comorbidities Network), using Cox regression analysis with stepwise adjustment for multiple COPD characteristics, comorbidities, troponin and NT-proBNP.
Results: 655 patients with early COPD were included. In the initial regression model, 43 of 655 patients died during the 6-year follow-up, in the final model 27 of 487. Regression analyses with adjustment for confounders identified COPAVP and MRproANP as statistically robust biomarkers (p<0.05 each) of all-cause mortality, while MRproADM and fibrinogen were not. The fourth quartile of MRproANP (97 pmol/L) was associated with a hazard ratio of 4.5 (95%CI: 1.6; 12.8), and the fourth quartile of COPAVP (9.2 pmol/L) with 3.0 (1.1; 8.0). The results for MRproANP were confirmed in the total cohort of grade 0-4 (n=1470 finally).
Conclusion: In patients with early COPD, elevated values of COPVP and in particular MRproANP were robust, independent biomarkers for all-cause mortality risk after adjustment for multiple other factors. This suggests that these markers might be considered in the risk assessment of early COPD.
Machine Intelligence Accelerated Design of Conductive MXene Aerogels with Programmable Properties
Authors: Chen Po-Yen , Shrestha Snehi , Barvenik Kieran , Chen Tianle , Yang Haochen , Li Yang , Kesavan Meera , Little Joshua , Tubaldi Eleonora 
Published: October 2023

Abstract

Designing ultralight conductive aerogels with tailored electrical and mechanical properties is critical for various applications. Conventional approaches rely on iterative optimization experiments, which are time-consuming when exploring a vast parameter space. Herein, an integrated workflow is developed to combine collaborative robotics with machine learning to accelerate the design of conductive aerogels with programmable electrical and mechanical properties. First, an automated pipetting robot is operated to prepare 264 mixtures using four building blocks at different ratios/loadings (including Ti3C2Tx MXene, cellulose nanofibers, gelatin, glutaraldehyde). After freeze-drying, the structural integrity of conductive aerogels is evaluated to train a support vector machine classifier. Through 8 active learning cycles with data augmentation, 162 kinds of conductive aerogels are fabricated/characterized via robotics-automated platforms, enabling the construction of an artificial neural network prediction model. The prediction model can conduct two-way design tasks: (1) predicting the physicochemical properties of conductive aerogels from fabrication parameters and (2) automating the inverse design of conductive aerogels for specific property requirements. The combined use of model interpretation and finite element simulations validates a pronounced correlation between aerogel density and its compressive strength. The model-suggested conductive aerogels with high electrical conductivity, customized compression resilience, and pressure insensitivity allow for compression-stable Joule heating for wearable thermal management. The fusion of robotics-accelerated experimentation, machine intelligence, and simulation tools expedites the tailored design and scalable production of conductive aerogels.
Head-to-tail plume shrinking contributes to the Hawaiian-Emperor Bend and plume zonation
Authors: Wang Zhensheng , Wang Qin , He Xiaobo , Wen Bin , Kusky Timothy 
Published: October 2023

Abstract
The Hawaiian-Emperor Bend (HEB) is traditionally attributed to the motion of the Pacific plate over a fixed or drifting mantle plume. Yet, the role of the plume's evolving radius in this process remains unexplored. We incorporate a shrinking plume head into plate reconstructions to investigate the formation of the HEB. Initially, the plume transported magma near the Kula-Pacific plate boundary, ~1500 km away from the plume axis. During 80-47 Ma, the shrinking plume head compelled newly formed craters to move from the mid-ocean ridge toward the mantle plume axis, forming an age-progressive volcanic chain on the moving plate and with decreased asthenospheric material signatures. After 47 Ma, seamounts approached the plume axis, causing the later island chain to align more parallel to the plate motion and exhibit more distinct plume signatures. Our model thus provides a new mechanism that contributed to the migration and compositional change of the Hawaiian-Emperor seamounts during the plume-plate interaction.
PM2.5 Source apportionment and health effects in urban districts of Hanoi: inter-comparison of source apportionment results
Authors: Bui Thi Hieu , Nguyen Thi Phuong Mai 
Published: October 2023

Abstract
Comparison results obtained by different models with different physical assumptions and constraints for source apportionment is important for better understanding the sources of the pollutants. Source apportionment of PM2.5 measured at three sites located in inner urban districts of Hanoi was performed using two receptor models, UNMIX and principal component analysis with absolute principle component score (PCA/APCS). A total of 78 daily samples were collected consecutively during the dry and wet seasons in 2019 and 2020. Both UNMIX and PCA/APCS expressed comparable ability to reproduce measured PM2.5 concentrations. Additionally, both models distinguished 4 potential sources of PM2.5 including traffic-related emission, scrap metal recycling villages, crustal mixed with construction sources, coal combustion mixed with industry, and biomass burning. Both UNMIX and PCA/APCS confirmed that traffic-related emission was the most influential PM2.5 with a high percentage contribution (59% and 55.97%, respectively). All the HQ and Cr values for both children and adults of toxic elements apportioned by both UNMIX and PCA/APCS in every source were within the acceptable range.
Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes
Authors: Boyd Joseph , Nadeau Emily A.W. , Kogut Sophie , Rodriguez Princess , Munteneau Daniel , O’Leary Thomas , Filler Sara , Lockwood Brent , Cahan Sara Helms , Frietze Seth 
Published: October 2023

Abstract
Background
RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms.
Results
In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in Drosophila melanogaster under thermal stress conditions. To achieve this, we conducted a comparative analysis of two RNA-seq library protocols: polyA + RNA capture and rRNA-depletion. Our approach involved the development and application of a Transcriptome Analysis Pipeline (TAP) designed to systematically assess both the technical and functional dimensions of RNA-seq, facilitating a robust comparison of these library protocols. Our findings underscore the efficacy of the polyA + protocol in capturing the majority of expressed lncRNAs within the Drosophila melanogaster transcriptome. In contrast, rRNA-depletion exhibited limited advantages in the context of D. melanogaster studies. Notably, the polyA + protocol demonstrated superior performance in terms of usable read yield and the accurate detection of splice junctions.
Conclusions
Our study introduces a versatile transcriptomic analysis pipeline, TAP, designed to uniformly process RNA-seq data from any organism with a reference genome. It also highlights the significance of selecting an appropriate RNA-seq library protocol tailored to the specific research context.