bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance
Authors: Salovska Barbora , Li Wenxue , Bernhardt Oliver M. , Germain Pierre-Luc , Gandhi Tejas , Reiter Lukas , Liu Yansheng
Published: November 2024

Measuring protein turnover is essential for understanding cellular biological processes and advancing drug discovery. The multiplex DIA mass spectrometry (DIA-MS) approach, combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC), has proven to be a reliable method for analyzing protein turnover and degradation kinetics. Previous multiplex DIA-MS workflows have employed various strategies, including leveraging the highest isotopic labeling channels of peptides to enhance the detection of isotopic MS signal pairs or clusters. In this study, we introduce an improved and robust workflow that integrates a novel machine learning strategy and channel-specific statistical filtering, enabling dynamic adaptation to systematic or temporal variations in channel ratios. This allows comprehensive profiling of protein turnover throughout the pSILAC experiment without relying solely on the highest channel signals. Additionally, we developedKdeggeR, a data processing and analysis package optimized for pSILAC-DIA experiments, which estimates and visualizes peptide and protein degradation rates and dynamic profiles. Our integrative workflow was benchmarked on both 2-channel and 3-channel standard DIA datasets and workflow to an aneuploid cancer cell model before and after cisplatin resistance development demonstrated a strong negative correlation between transcript regulation and protein degradation for major protein complex subunits. We also identified specific protein turnover signatures associated with cisplatin resistance.
APOBEC3A, not APOBEC3B, drives deaminase mutagenesis in human gastric epithelium
Authors: An Yohan , Lee Ji-Hyun , Lim Joonoh , Youk Jeonghwan , Park Seongyeol , Park Ji-Hyung , Yi Kijong , Kim Taewoo , Nam Chang Hyun , Lee Won Hee , Oh Soo A , Bae Yoo Jin , Lee Junehwak , Park Jung Woo , Kim Jie-Hyun , Kim Hyunki , Snippert Hugo , Koo Bon-Kyoung , Ju Young Seok
Published: November 2024

Cancer genomes frequently carry APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like)-associated DNA mutations, suggesting APOBEC enzymes as innate mutagens during cancer initiation and/or evolution. However, the pure mutagenic impacts of the specific enzymes among this family that are responsible for APOBEC-associated mutagenesis remain unclear, particularly the comparative mutagenic activities ofAPOBEC3AandAPOBEC3B. Here, we investigated the mutagenic contributions of these enzymes through whole-genome sequencing of human normal gastric organoid lines carrying doxycycline-inducibleAPOBEC3AorAPOBEC3Bcassettes. Our findings demonstrated that transcriptionalAPOBEC3Aupregulation led to the acquisition of a massive number of genomic mutations in a few cell cycles. By contrast,APOBEC3Bupregulation did not generate a substantial number of mutations in gastric epithelium.APOBEC3B-associated mutagenesis remained insignificant even after a combined inactivation ofTP53. Based on the spectrum of acquired mutations afterAPOBEC3Aupregulation, we further analyzedAPOBEC3A-associated mutational signatures, encompassing indels mainly composed of 1bp deletions, characteristics of clustered mutations, and selective pressures operative on cells carrying the mutations. Our observations provide a clear foundation for understanding the mutational impact of APOBEC enzymes in human cells.
Potential impact of a population-based screening program on the increased burden of prostate cancer in Thailand: A simulation study
Authors: Alvarez Christian S. , Mondul Alison M. , Rozek Laura S. , Sriplung Hutcha , Meza Rafael , Jeon Jihyoun
Published: November 2024

Background

Prostate cancer incidence and mortality are expected to increase considerably in the near future in Thailand. There is thus an urgent need to establish prevention measures, such as screening, to reduce the increasing burden of prostate cancer in Thailand.

Methods

Using data from several sources including the Songkhla Cancer Registry and the census data from Thailand, we conducted a simulation analysis to assess the potential impact of screening on the incidence and mortality of prostate cancer among 10 million males aged 50 to 70 of 1960 birth cohort from Songkhla, Thailand. We assumed 4 different scenarios, including no screening, 15%, 60% and 100% screening uptakes of the prostate-specific antigen test. Furthermore, stage distribution of prostate cancer was assumed based on two major prostate cancer screening trials: European Randomized Study of Screening for Prostate Cancer (ERSPC) and Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. The number of prostate cancer cases was projected using an age-period-cohort model approach, accounting for the expected excess of cases due to screening. Deaths from prostate cancer were then projected using survival probabilities from Songkhla and the United States. Case fatality ratios (CFRs) were also computed.

Results

Prostate cancer incidence increased with screening, as expected, with a shift of the stage distribution toward earlier stages, but mortality from prostate cancer decreased with higher screening uptake. Assuming 1.71 excess risk of cases due to screening and stage distribution from the ERSPC trial, we projected an increase of over 7,000 localized cases under 100% screening uptake, while the cases in advanced stages decreased from 4,046 (no screening) to 96 under 100% screening uptake. The number of deaths were reduced by 82% under 100% screening uptake compared to no screening. The CFR also decreased from 0.42 (no screening) to 0.05 (100% screening).

Conclusion

Screening for prostate cancer could substantially reduce the number of prostate cancer cases in advanced stages and prostate cancer deaths. Although the net benefit depends on the assumed survival rates under screening, which could vary depending on the quality of the implementation, screening would contribute to reducing the escalating burden of prostate cancer in Thai population.
REDD1 is a determinant of the sensitivity of renal cell carcinoma cells to autophagy inhibition that can be therapeutically exploited by targeting PIM kinase activity
Authors: Carew Jennifer S. , Espitia Claudia M. , Sureshkumar Sruthi , Espinoza Maria Janina Carrera , Gamble Madison E. , Wang Wei , Lee Benjamin R. , Nawrocki Steffan T.
Published: November 2024

Purpose

Repurposing FDA approved drugs with off-target autophagy inhibition such as chloroquine/hydroxychloroquine (CQ, HCQ) has produced modest anticancer activity in clinical trials, due in part, to a failure to define predictive biomarkers that enable the selection of patients that best respond to this treatment strategy. We identified a new role for REDD1 as a determinant of sensitivity to autophagy inhibition in renal cell carcinoma (RCC).

Experimental Design

RNA sequencing, qRT-PCR, immunoblotting, gene silencing, knockout and overexpression studies revealed that REDD1 expression is a key regulator of cell death stimulated by autophagy inhibitors. Comprehensivein vitroandin vivostudies were conducted to evaluate the selectivity, tolerability, and efficacy of the PIM kinase inhibitor TP-3654 and CQ in preclinical models of renal cell carcinoma (RCC). Markers of autophagy inhibition and cell death were evaluated in tumor specimens.

Results

Transcriptomic analyses identified REDD1 (DDIT4) as a highly induced gene in RCC cells treated with the PIM kinase inhibitor TP-3654. Focused studies confirmed that PIM1 inhibition was sufficient to induce REDD1 and stimulate autophagy through the AMPK cascade.DDIT4knockout and overexpression studies established its mechanistic role as a regulator of sensitivity to autophagy inhibition. Inhibition of autophagy with CQ synergistically enhanced the in vitroandin vivoanticancer activity of TP-3654.

Conclusions

Our findings identify REDD1 as a novel determinant of the sensitivity of RCC cells to autophagy inhibition and support further investigation of PIM kinase inhibition as a precision strategy to drive sensitivity to autophagy-targeted therapies through REDD1 upregulation.

Translational Relevance

PIM kinases are overexpressed in renal cell carcinoma (RCC) and other malignancies. Here we show that targeting PIM1 significantly upregulates REDD1/DDIT4expression, resulting in inhibition of mTOR and autophagy activation. REDD1 induction was determined to be a major factor that regulates the sensitivity of RCC cells to autophagy inhibition. Comprehensivein vitroandin vivostudies in preclinical models of RCC demonstrated that the PIM kinase inhibitor TP-3654 induced REDD1-mediated autophagy and synergistically sensitized cells to autophagy inhibition. Our findings define a new role for REDD1 as a determinant of the sensitivity of RCC cells to autophagy inhibition and demonstrate that antagonizing PIM kinase activity is a precision approach to augment REDD1 levels and potentiate the therapeutic benefit of targeting the autophagy pathway.
The limited capacity of bioaerosols to serve as cloud-condensation nuclei may restrict their potential to initiate ice formation in mixed-phase clouds
Authors: Šantl-Temkiv Tina , Živec Miha , Lund Marie Braad , Benčina Mojca , Bohn Anja Bille , Stanič Samo , Močnik Griša
Published: November 2024

Bioaerosols are gaining prominence due to their ability to nucleate ice in clouds at high subzero temperatures, thereby impacting cloud characteristics, and longevity. Acting first as cloud condensation nuclei (CCN) and second as ice nucleating particles, bioaerosols induce ice formation through immersion freezing. Nevertheless, insights into bioaerosol ability to act as CCNin situare currently lacking. We simultaneously collected bioaerosols from the condensed and interstitial phase of clouds using size selective inlets during autumn 2020 from the Otlica observatory (Slovenia). With a polarization Raman Lidar, we confirmed the coexistence of ice particles and liquid droplets during one of the three sampling campaigns. Using spectral flow cytometers, the PINGUIN cold-stage setup and MiSeq-facilitated amplicon sequencing to assess bacterial and fungal communities, we found that both bioaerosols and biogenic ice-nucleating particles were significantly more abundant in the interstitial phase compared to the condensed phase, suggesting that they were poor CCN, unable to compete with more hygroscopic particles. Most taxa did not exhibit preferential partitioning, suggesting that surface properties generally did not significantly influence their behaviour as CCN. Our results underline the need to systematically investigate the relation between hygroscopicity and ice-nucleating activity of bioaerosols to understand theirin-situeffects on cloud formation.

Synopsis

The relationship between the ability of bioaerosols to nucleate cloud droplets and ice particles has not been determined. This study found that bioaerosols are poor cloud condensation nuclei which may impair their ability to nucleate ice and affect cloud formation and climate.
Physical-aware model accuracy estimation for protein complex using deep learning method
Authors: Wang Haodong , Sun Meng , Xie Lei , Liu Dong , Zhang Guijun
Published: November 2024

With the breakthrough of AlphaFold2 on monomers, the research focus of structure prediction has shifted to protein complexes, driving the continued development of new methods for multimer structure prediction. Therefore, it is crucial to accurately estimate quality scores for the multimer model independent of the used prediction methods. In this work, we propose a physical-aware deep learning method, DeepUMQA-PA, to evaluate the residue-wise quality of protein complex models. For the input complex model, the residue-based contact area and orientation features were first constructed using Voronoi tessellation, representing the potential physical interactions and hydrophobic properties. Then, the relationship between local residues and the overall complex topology as well as the inter-residue evolutionary information are characterized by geometry-based features, protein language model embedding representation, and knowledge-based statistical potential features. Finally, these features are fed into a fused network architecture employing equivalent graph neural network and ResNet network to estimate residue-wise model accuracy. Experimental results on the CASP15 test set demonstrate that our method outperforms the state-of-the-art method DeepUMQA3 by 3.69% and 3.49% on Pearson and Spearman, respectively. Notably, our method achieved 16.8% and 15.5% improvement in Pearson and Spearman, respectively, for the evaluation of nanobody-antigens. In addition, DeepUMQA-PA achieved better MAE scores than AlphaFold-Multimer and AlphaFold3 self-assessment methods on 43% and 50% of the targets, respectively. All these results suggest that physical-aware information based on the area and orientation of atom-atom and atom-solvent contacts has the potential to capture sequence-structure-quality relationships of proteins, especially in the case of flexible proteins. The DeepUMQA-PA server is freely available athttp://zhanglab-bioinf.com/DeepUMQA-PA/.
Transmembrane domains of H1 and H3 hemagglutinin contribute to membrane fusion in a different manner
Authors: Borkowska Paulina , Kubiszewski-Jakubiak Szymon , Bykowski Michał , Kowalewska Łucja , Michalski Michał , Setny Piotr , Worch Remigiusz
Published: November 2024

Hemagglutinin (HA), a fusion protein of influenza virus, has been extensively researched as a model fusion viral protein. However, most of the efforts focus on the fusion peptide (FP) and the ectodomain, while relatively little is known about the “membrane anchor”, a transmembrane domain (TMD). While the structural insights on H1 subtype full-length HA underlay the influence of TMD on the ectodomain orientations, the structures representing the other phylogenetic group are still unavailable. Inspired by the sequential varieties of TMDs in both groups, we performed a series of experiments on full-length HA proteins with H1and H3-swapped TMD domains in virus-like particles (VLP). In parallel, we studied the behaviour an and interplay of FP and TMD-corresponding fragments with the use of artificial membrane systems and molecular dynamics simulations. We detect clearly a distinct interplay between FP and TMDs in the two phylogenetic groups. We observe that TMD-dependent fusion activity originates from TMD-lipid interactions, but not direct FP:TMD complexing.
Parallel cases of ring speciation within a rapid adaptive radiation of cichlid fishes
Authors: Gautier Grégoire , Mahulu Anna , Seehausen Ole , Singh Pooja
Published: November 2024

Ring species provide a valuable framework for studying intermediate steps of speciation resulting in two new species. Classic examples of ring species have involved large spatial and temporal scales – and this is partly why few idealised cases exist. In contrast, we focus on two species complexes of cichlid fishes from Southern Lake Victoria that evolved rapidly within the last 15,000 years across relatively small geographic space. We reconstruct the path to speciation between two forms ofPundamiliaandNeochromisspecies that exist in a ring-like distribution around deep water, which acts as a dispersal barrier for these shallow water adapted fishes. We test key predictions of ring-like biogeography, population connectivity, terminal overlap and differentiation in mating and ecological traits. Our results indicate that both species complexes show a gradual change in craniofacial morphology along a ring-like distribution, corresponding to diet shifts. This phenotypic change is correlated with geographical distance in both rings, although they appear to have spatially different evolutionary trajectories. Sympatric species at the ends of both rings exhibit signs of convergent and divergent ecological character displacement in several craniofacial traits, potentially explaining their coexistence. In contrast to craniofacial morphology, male nuptial colouration changes abruptly in both rings, with the change occurring at the end of the ring inPundamiliaand early inNeochromis. We discuss the influence of environmental factors on the observed phenotypic variation and how resistance to connectivity might alter the isolation-by-distance pattern. Our study provides compelling evidence of how concerted changes in mating and ecological traits during isolation by distance can lead to new species and highlights the importance of parapatric speciation in adaptive radiation.
Eigenstate plateau transition and equilibration in one-dimensional quantum lattice models
Authors: Li Wei-Han , Saberi Abbas Ali
Published: November 2024

We report a remarkable spectral phenomenon in a generic quantum lattice gas model. As the interaction strength increases, eigenstates spontaneously reorganize, leading to plateaus in the interaction energy. Gaps between plateaus can emerge similarly to continuous phase transitions. Our perturbation analysis indicates that, aside from these gaps, the plateau structure of the spectrum remains stable in the thermodynamic limit. The structured spectrum naturally manifests in far-from-equilibrium dynamics, exhibiting multiple stages. Our findings reveal a connection between emergent properties in high-energy states and equilibration dynamics in closed quantum systems, offering insights into the impact of interactions across the entire energy spectrum. These results directly relate to experiments probing equilibration in quantum spin systems and lattice gases.

Published by the American Physical Society
2024
A systematic review on mediators and moderators of job insecurity–health relation before and after COVID-19 pandemic
Authors: Charkhabi Morteza , Radi Afsouran Naghi , Johnson Laura K. , Dutheil Frédéric
Published: November 2024

Purpose

Job insecurity is one of the most hazardous work stressors in the twenty-first century, placing employees between employment and unemployment may threaten employees’ health in the workplaces. Using a systematic review, the first aim of this study is to list the mediators and moderators of the link between job insecurity and health-related outcomes, and second, to explain and discuss the mechanisms that could explain the mediating and moderating effects.

Design/methodology/approach

We searched four databases (Science Direct, PubMed, Springer Link and Google Scholar) from 2008 to 2018 to detect these mediators and moderators. Also, as the study was conducted during COVID-19 pandemic, we particularly searched and reported the same associations over this period (2019–2022).

Findings

The results of the review suggest that job insecurity negatively influences a wide range of both health- and safety-related outcomes in the workplace. The results also showed that the most studied mediator and moderator of the job insecurity-health link over the past 10 years has been workload and employability. During COVID-19, the number of studies on mediators were more than moderators and coping strategies appeared to gain more research attention. Additionally, this review suggests that, to explain the mediation and moderation effects, a combination of cognitive appraisal theory and the conservation of resources theory can be used.

Originality/value

Although this review suggests that job insecurity detrimentally influences employee health, the severity of this impact on health-related outcomes may vary by the effects of various moderators.
A review of ex ante and ex post materiality measures, and consequences and determinants of material disclosures in sustainability reporting
Authors: Huq Asif M. , Mohammadrezaei Mahsa
Published: November 2024

Purpose

The purpose of the review is to synthesize the research on materiality measures of sustainability reporting and highlight how preparers, users, auditors, regulators and other stakeholders assess or determine the materiality in sustainability reporting. The review further summarizes the findings on consequences and determinants of material disclosures in sustainability reporting. Several directions for future research are also discussed.

Design/methodology/approach

This study provides a systematic review of materiality measures developed in the context of sustainability reporting. This synthesis of the literature summarizes the existing methodologies of measuring materiality. It also evaluates the strength and limitations of existing methods and approaches of measuring materiality in sustainability disclosures.

Findings

We find that the ex post materiality measures are simplistic and unidirectional in nature and ex ante materiality measures lack external validity and are generally narrow in focus – for example, focused on single firms or industries. Another major limitation in the current literature is the absence of robust empirical investigation of double materiality in sustainability reporting and a vast majority of the measures are developed without stakeholder engagement. Lastly, we document that the findings on determinants of material disclosure are fragmented and inconclusive and that the literature on consequences of material disclosure is rather un-explored.

Originality/value

The study explains the connections and differences between the various materiality measures. We document that materiality is measured in two distinct ways, ex ante and ex post and often times without stakeholder engagement. Moreover, given that a vast majority of the measures rely on manual content analysis, we find that they suffer from reproducibility and scalability.
Cognitive bias undermining intellectual capital development in the scientific contexts: a study to understand origins, effects and solutions
Authors: Palmucci Dario Natale , Ključnikov Aleksandr , Ferraris Alberto
Published: November 2024

Purpose

This article identifies and discusses the most common cognitive biases affecting reviewers and editors when they deal with papers, books or any kind of scientific research/project and how they can undermine intellectual capital (IC) in scientific contexts (SCs) as universities and research institutions.

Design/methodology/approach

As we posit that certain biases prevent from publishing original and relevant scientific works, literature research and semi-structured interviews with experts have been conducted to identify these biases undermining IC of SCs.

Findings

This contribution identifies biases undermining IC in SCs distinguishing the ones influencing editors only (representativeness heuristic, group polarization, country/language and affinity bias) and the ones influencing both editors and reviewers (framing and halo effects, overconfidence/overoptimism, confirmation, adjustment, status quo, bias bias and single-action biases). Also, it provides practical examples on how to overcome them.

Research limitations/implications

This work is based on a limited number of interviews (and most of them to researchers of the economic field). Then, future quantitative researches are needed to increase the generalizability of the data. With regard to implications, the results of this study can be adopted by academies and their components in order to preserve their IC and in particular their knowledge-based resources of human capital.

Practical implications

As this piece of research provides practical examples and it concludes with tips that come from scholars’ experience, it is useful for a wide audience of scholars (in particular for less experienced researchers) pursuing scientific career upgrades and for reviewers looking for useful guidelines.

Originality/value

This study offers a more comprehensive analysis on the factors influencing IC of SCs both mixing literature findings with practical experts’ experience and including different areas of knowledge (e.g. behavioral theories on decision making) as scarcely done in previous studies.
Can ultrasonography be used to detect root perforation? An in vitro study
Authors: Sariyilmaz Öznur , Eren İrem , Sariyilmaz Evren , Eren Hakan , Uslu Gulşah
Published: November 2024

This study assessed the usability of ultrasonography in detecting root canal perforations. The buccal side of incisor root were perforated. The actual lengths up to the perforation site were measured by visualisation of the tip of a file. Specimens were embedded in gypsum, and it was scraped to simulate bone resorption. Resorption cavities were filled with ultrasound gel. Measurements were taken by advancing a file through the canal until the tip became visible in the ultrasound image. 3D scans were obtained using cone‐beam computed tomography (CBCT) and the distance between the coronal point of the resorption cavity and the reference point was measured. The actual distance of the resorption cavity from the reference point varied 6–10.6 mm. The same distances were measured via ultrasound as 5.7–10.9 mm, while measured using CBCT 6–10.5 mm. No significant differences were found. Ultrasonography shows promise for detecting root perforations, however further research is needed.
Cognitive behavioral therapy combined with selective serotonin reuptake inhibitors for premature ejaculation: A systematic review and meta‐analysis
Authors: Li Liang , Geng Hao , Chen Meng , Hu Wei , Ye Qinglin
Published: November 2024

Background

Premature ejaculation (PE) remains one of the most common male disorders. Many clinical trials have shown that cognitive behavioral therapy (CBT) has significant efficacy in the treatment of PE. The purpose of this article is to review the current evidence regarding the efficacy and safety of CBT combined with selective serotonin reuptake inhibitors (SSRIs) for treating PE.

Methods

We selected eligible randomized controlled trials (RCTs) from databases including Chinese National Knowledge Infrastructure (CNKI), Wanfang, VIP, China Biology Medicine (CBM), Pubmed, Embase, and Cochrane Library. All data in this paper were analyzed using STATA 17.1 software. Cochrane Evaluator's Manual 5.3 was used to assess the quality of the included literature. Data collection was conducted up until May 2024.

Results

Finally, 15 high‐quality randomized controlled trials were included, with 1243 patients, 653 experimental groups and 590 control groups. The meta‐analysis showed that, compared with SSRIs alone, behavioral therapy combined with SSRIs can significantly prolong the IELT of PE patients, and improve perceived control over ejaculation, Chinese Index of Premature ejaculation‐5 (CIPE‐5), sexual life satisfaction, and spouses' sexual life satisfaction. Furthermore, there were no significant differences in side effects between the two groups. In addition, the published bias test results showed no significant bias.

Conclusion

CBT combined with SSRIs could be a viable alternative for the treatment of PE. Both cognitive and behavioral training or behavioral training alone as a supplement to SSRIs are effective, with no significant increase in adverse reactions.
A luminal non‐coding RNA‐based genomic classifier confirms favourable outcomes in patients with clinically organ‐confined bladder cancer treated with radical cystectomy
Authors: de Jong Joep J. , Proudfoot James A. , Daneshmand Siamak , Svatek Robert S. , Narayan Vikram , Gibb Ewan A. , Davicioni Elai , Joshi Shreyas , Dahmen Aaron , Li Roger , Inman Brant A. , Shah Paras , Chaplin Iftach , Wright Jonathan , Lotan Yair
Published: November 2024

Objective

To further evaluate a genomic classifier (GC) in a cohort of patients undergoing radical cystectomy (RC), as long non‐coding RNA (lncRNA)‐based genomic profiling has suggested utility in identifying a distinct tumour subgroup corresponding to a favourable prognosis in patients with bladder cancer.

Patients and Methods

Transcriptome‐wide expression profiling using Decipher Bladder was performed on transurethral resection of bladder tumour samples from a cohort of patients with high‐grade, clinically organ‐confined (cTa–T2N0M0) urothelial carcinoma (UC) who subsequently underwent RC without any neoadjuvant therapy (n = 226). The lncRNA‐based luminal favourable status was determined using a previously developed GC. The primary endpoint was overall survival (OS) after RC. Secondary endpoints included cancer‐specific mortality and upstaging at RC.

Results

In the study, 134 patients were clinical non‐muscle‐invasive bladder cancer (cTa/Tis/T1) and 92 patients were cT2. We identified 60 patients with luminal favourable subtype, all of which showed robust gene expression patterns associated with less aggressive bladder cancer biology. On multivariate analysis, patients with the luminal favourable subtype (vs without) were significantly associated with lower odds of upstaging to pathological (p)T3+ disease (odds ratio [OR] 0.32, 95% confidence interval [CI] 0.12–0.82; P = 0.02), any upstaging (OR 0.41, 95% CI 0.20–0.83; P = 0.01), and any upstaging and/or pN+ (OR 0.50, 95% CI 0.25–1.00; P = 0.05). Luminal favourable bladder cancer was significantly associated with better OS (hazard ratio 0.33, 95% CI 0.15–0.74; P = 0.007).

Conclusions

This study validates the performance of the GC for identifying UCs with a luminal favourable subtype, harbouring less aggressive tumour biology.
Have plastic culture models prevented the discovery of effective cancer therapeutics?
Authors: Tharp Kevin M.
Published: November 2024

Conventional cell culture techniques generally fail to recapitulate the expression profiles or functional phenotypes of the in vivo equivalents they are meant to model. These cell culture models are indispensable for preclinical drug discovery and mechanistic studies. However, if our goal is to develop effective therapies that work as intended in the human body, we must revise our cell culture models to recapitulate normal and disease physiology to ensure that we identify compounds that are useful and effective beyond our in vitro models.
ENTRY ORDER, PERFORMANCE, AND GEOGRAPHY: THE CASE OF THE CONVENIENCE‐STORE INDUSTRY IN JAPAN
Authors: Nishida Mitsukuni
Published: November 2024

Entry‐order effects on economic profits have not been extensively studied due to data limitations. This article empirically examines these effects on revenues and costs using a structural approach without requiring information on accounting profits and costs. Utilizing panel data from Japan's convenience‐store industry, I apply a two‐step estimator for many geographic markets. The results reveal that whereas early entrants gain 4.8% more revenue at the outlet level, subsequent entrants benefit from a 7.6% and 5.8% reduction in variable and expansion costs. Simulations suggest initial benefits from delayed entry, but these may dissipate over time, particularly in rapidly growing markets.
Experiences of Turkish nurses volunteering in the disaster zone following the 2023 Türkiye–Syria earthquake
Authors: Mercan Annak İnci , Erdoğan Birgül , Yıldız Emre Nihal
Published: November 2024

Aim

The study aimed to determine the experiences of Turkish nurses who volunteered in the disaster zone following the 2023 Türkiye–Syria earthquake.

Background

The earthquake devastated 11 cities in Türkiye, which required a comprehensive humanitarian response. Despite the crucial role of nurses in crisis management, limited research exists on their experiences in earthquake zones.

Introduction

Nurses experience difficulties in disaster areas, such as physical conditions, lack of disaster plans, and inadequate disaster training before being deployed to earthquake areas.

Methods

This study used a qualitative research model and case study design. Data were collected through in‐depth qualitative interviews. Nine participants who had worked in earthquake zones for at least 5 days were included in the study. The discussions were recorded, transcribed verbatim, and analyzed thematically. The purposive sampling method was used, and the Consolidated Criteria for Reporting Qualitative Research guidelines were followed.

Results

As a result, 4 themes, namely physical conditions, psychosocial conditions, professional conditions, and organization, and their 14 subthemes were determined. This study revealed that nurses encountered difficulties related to physical conditions in earthquake zones. Moreover, the emotional burden expressed by the nurses highlighted the profound psychological impact of disaster response.

Conclusion

This study determines that disaster preparedness and support for nurses should be enhanced to improve the arrangement of health services in future calamities.

Implications for nursing policy

The results of this study can be used by nurse managers and healthcare policymakers to create nursing training programs that focus on disaster‐related competencies.
A Man's World? The Descriptive Representation of Women Inside Europarties
Authors: Hertner Isabelle , Wolfs Wouter
Published: November 2024

Men are over‐represented in the majority of national political parties. This article makes a significant contribution to the analysis of women's representation inside ‘Europarties’ that operate at the European level. It draws on new data, including interviews with Europarties' representatives. We focus on women's representation in party leadership positions, including Spitzenkandidat:innen. We show that more women have become part of Europarties' leaderships in recent years, but that overall, men remain over‐represented, especially in right‐wing parties. We explain this development by focusing on the role of gender quotas and women's organisations in enhancing women's representation. Whereas gender quotas have increased women's presence in leadership bodies, women's organisations have not. Drawing on feminist institutionalism, we also analyse some of the informal norms and practices that have (dis)empowered women. We argue that without statutory gender quotas for governing bodies, as well as formal and transparent decision‐making processes, women risk being excluded from leadership positions.
Editorial on: Protection against influenza hospitalizations from enhanced influenza vaccines among older adults: A systematic review and network meta‐analysis
Authors: Andrew Melissa K. , McGeer Allison
Published: November 2024

See related articles by Ferdinands et al.
Second Language Sentence Stress Assignment: Self‐ and Other‐Assessment
Authors: Teló Cesar , Kivistö de Souza Hanna , O'Brien Mary Grantham , Carlet Angélica
Published: November 2024

Research on second language (L2) pronunciation self‐assessment reports a general misalignment between self‐ and other‐assessment. This has been attributed to the object of self‐assessment, the self‐assessment task, the measures to which self‐assessment is compared, and speakers’ characteristics. Here, we examined self‐assessment of a discrete phonological feature—sentence stress—by L2 English speakers as compared to the assessment of first language English listeners through a timed, forced‐choice judgment task with low‐pass filtered stimuli, which contained only suprasegmental cues. Additionally, we explored how individual differences among speakers predict self‐assessment. Speakers generally overestimated their accuracy in sentence stress assignment in a pattern resembling the Dunning‐Kruger effect despite the controlled nature of the task. Speakers with larger vocabulary size judged their sentence stress assignment as correct more often and showed greater overconfidence and miscalibration. Finally, the assessments of speakers with a background in applied linguistics and/or language teaching were more aligned with listeners’ assessments.
Coronary Spasm Due to Pulsed Field Ablation: A State‐of‐the‐Art Review
Authors: Ramirez David A. , Garrott Kara , Garlitski Ann , Koop Brendan
Published: November 2024

With the ever‐growing population of patients undergoing cardiac ablation with pulsed electric fields, there is a need to understand secondary effects from the therapy. Coronary artery spasm is one such effect that has recently emerged as the subject of further investigation in electrophysiology literature. This review aims to elucidate the basic anatomy underlying vascular spasm due to pulsed electric fields and the effects of irreversible electroporation on coronary arteries. This review also aims to gather the current preclinical and clinical data regarding the physiology and function of coronary arteries following electroporation.
The Study on Risk Assessment Method of Severe Accident Management Strategies in Nuclear Power Plants
Authors: Niu Shipeng , Yu Yun , Wang Gaopeng , Yu Xinli , Liu Yang , Zhang Jiarui , Zhang Yapei
Published: November 2024

In order to provide more convenient and efficient severe accident management tools and improve the ability to cope with severe accident conditions, a risk assessment method of severe accident management strategies is proposed based on severe accident analysis, big data and neural network intelligent learning technology. In this method, the critical state parameters of nuclear power plant are selected as the research object, and different severe accident management strategies are adopted at different accident process states for typical severe accident conditions, and a large amount of calculation and analysis are carried out to obtain the changes of critical state parameters after implementing different strategies, and the risk database of severe accident management strategies is developed. Based on the database, the risk assessment model is developed by using neural network intelligent learning, and the model is verified. The results show that the risk assessment model of severe accident management strategies can quickly evaluate the state changes after different severe accident management strategies are adopted under different severe accident conditions, and the error is low, which meets the needs to evaluate the implementation effect of severe accident management strategy. The evaluation results for the critical state parameters will be compared with the setting values, and then the risks of different severe accident management strategies can be evaluated under the severe accident conditions, which can provide technical support for the severe accident management personnel.
Research on Pressure Suppression and Against Hydrogen Risk of the SMR in Floating Nuclear Power Plants
Authors: Chen Jialei , Lyu Xuefeng , Zhang Jiayu , Wang Shengfei , Zhao Houjian , Liu Fang , Yu Yu
Published: November 2024

In the event of loss of coolant accident (LOCA) in small modular reactors (SMRs) in floating nuclear power plants (FNPP), appropriate pressure suppression and hydrogen elimination measures must be taken to ensure small modular reactors’ safety. This paper utilizes GASFLOW to analyze the environmental conditions and gas behavior following the implementation of pressure suppression and hydrogen elimination measures in SMRs. The results indicate that: 1) The suppression effect is optimal when the capacity of the suppression pool is 200m3. 2) In cases where the cross-sectional area of the suppression pipeline is either excessively large or small, adverse effects on suppression effectiveness are observed. The study shows that there is an optimal cross-sectional area of suppression pipeline to achieve the best suppression effect of suppression pool. 3) The combination of passive autocatalytic recombiners (PARs) and igniters can safely and efficiently eliminate the risk of hydrogen and have a good hydrogen mitigation effect.
Two Phase Flow Interface Dynamic Behavior During CHF Transient
Authors: Liu Haidong , Zeng Qiao , Chen Deqi
Published: November 2024

Due to the absence of detailed two-phase flow interface dynamic behavior in the vicinity of the heated wall during CHF transient, a deep understanding of the boiling crisis phenomenon is not achieved. In this paper, a flow boiling heat transfer facility is designed and constructed. Meanwhile, a transparent test section, which can withstand high temperatures and pressures, is designed and machined. Flow visualization experiments have been conducted in a vertical rod channel with water as the working fluid. Based on visualization experiments of flow boiling crisis, the two phase flow interface dynamic behavior during the CHF transient is analyzed utilizing self-developed image processing programs. The vapor-liquid interface variations characteristics in various operating conditions can be directly extracted through the processed raw images. The two-phase flow interface morphology under different operating conditions exhibits significantly different behavioral characteristics. For vapor layer thickness, the thickness becomes thinner as the inlet subcooling increases, mainly due to the increased condensation effect as the subcooling increases. Furthermore, the mass flux has an extremely pronounced effect on the vapor layer thickness, mainly since the mass flux directly affects the meso-interfacial heat and mass transfer behavior, leading to an increase in the interfacial perturbation, which results in the presentation of smaller vapor layer thickness. In addition, the results show that as the heat flux approaches the CHF, the liquid film thickness is zero in several places, which means that several dry spots appear. The results presented in this paper have important implications for a more in-depth understanding of CHF phenomenon and further support in the development of a mechanistic model for flow boiling.
Internal Nitridation of Ni-Based Superalloy IN617 During Aging at 950 °C
Authors: Wang Yue , Zhao Hongsheng , Wang Haitao , Shi Li , Li Kejian
Published: November 2024

Aging experiments were performed on Ni-based superalloy IN617 at 950 °C in air (containing 78.8 wt.% N2) for three different durations (50 h, 500 h, and 3000 h). Internal nitridation was found. The layered distribution structures of oxides, nitrides, and carbides were investigated. The formation of oxides and nitrides and the evolution of carbides during aging were analyzed. Results showed that oxidation only occurred in the nearest-surface vicinity, forming an external Cr2O3 layer and an internal Al2O3 layer as well as a Cr-depleted zone. With increasing aging duration, the oxide layer became continuous, and the thickness of the Cr-depleted zone was increased. Nitridation occurred in the sub-surface vicinity below the oxide zones. As aging duration was increased, there were increases in both the thickness of nitride zone and the nitride type. Specifically, only TiN was formed after aging for 50 h. When the aging duration was increased to 500 h, TiN and AlN both precipitated. TiN, AlN, and Cr3.25Ni1.75N all precipitated for the aging duration of 3000 h. At the zones far away from the external surface, the carbides including Cr-rich M23C6 and Mo-rich M6C were coarsened and transformed to discontinuous large blocks from the continuous thin film of the as-received condition under the effect of high temperature.
Research on Fuel Pebble Modeling Methods Comparison and Eigenvalue Analysis of the Running-in Phase of HTR-PM
Authors: Yang Qianye , Gui Nan , Tu Jiyuan , Jiang Shengyao
Published: November 2024

The High-Temperature Gas-Cooled Pebble bed Reactor (HTR) utilizes fuel pebbles that consist of an outer graphite shell and a fuel region with thousands of TRi-structural ISOtropic (TRISO) particles dispersing in a graphite matrix, causing the double heterogeneity effect, and presenting computational challenges for neutronics simulations. The Monte Carlo (MC) method is considered a powerful tool for neutronics analysis of complicated reactor design, but it is computationally expensive and inefficient for large-scale systems. This study calculates and compares different fuel pebble modeling methods to balance accuracy and efficiency. Models ranging from high-fidelity to various homogenized approaches are assessed. Results indicate the Reactivity-equivalent Physical Transformation (RPT) model optimally captures heterogeneous effects while reducing the computational cost. Based on RPT, eigenvalue analysis is performed to simulate the running-in phase of the HTR-PM. A linear correlation is observed between the descending surface height and keff, which is consistent with the phenomenon in reactors of smaller scales like HTR-10. This comparative modeling and analysis provide insights into fuel pebble homogenization and support the feasibility of applying proper fuel pebble modeling to full-core HTR design and simulation.
Core Design and Neutronic Analysis of the European Sodium Fast Reactor With Metallic Fuel
Authors: Jiménez-Carrascosa Antonio , Mikityuk Konstantin , Stauff Nicolas , Karahan Aydin , Fridman Emil , Ponomarev Alexander
Published: November 2024

The current ESFR (European Sodium Fast Reactor) design was proposed and in-depth evaluated in the frame of the past ESFR-SMART project. As a follow-up project, the ESFR-SIMPLE has been launched with the aim of challenging the current commercial-size ESFR design in terms of safety features and economic performance. Among the new safety measures to be developed and assessed in ESFR-SIMPLE, the current oxide fuel ESFR design will be challenged by a modified version of the core with metallic fuel. This intends to conclude on what types of benefits can be obtained with high-density fuel, under similar safety and design constraints. In this paper, the designing approach for enabling the use of metallic fuel in the current ESFR core is described and a preliminary neutronic evaluation is carried out. The optimal configuration is established through the optimization of key neutronic parameters aiming at the potential reduction of the plutonium inventory. The resulting core configuration serves as a basis for further safety assessment analyses, which will provide insight into the advantages and drawbacks of the two types of fuels.
Preliminary Investigation of THFR Passive Residual Heat Removal System
Authors: Huang Yuan , Xu Wei , Xie Heng , Shi Lei
Published: November 2024

The RELAP5 code was employed to study the natural circulation characteristics and core thermal-hydraulic parameters of THFR (Tsinghua High Flux Reactor) under the condition that only the passive residual heat removal system was used when the emergency cooling pump powered by the battery bank shut down due to power exhaustion. To achieve a higher neutron flux, high flux reactor possesses several distinctive properties, including high power density, narrow coolant channels, and low coolant pressure., so the loss of heat sinks under accident conditions can be catastrophic, Therefore, it is necessary to establish a passive residual heat removal system. This study compared the two-loop and three-loop schemes, The results showed that both schemes can reliably establish natural circulation and efficiently remove core residual heat. Throughout the process, the maximum temperatures of the coolant, cladding surface, and fuel meat were below the design limits. Because the maximum temperature of the cladding surface was lower than the saturation temperature, the DNB phenomenon did not appear in the core. The three-loop scheme, with lower total resistance and higher coolant flow rate, is more favorable for improving the thermal safety of the reactor. It also has a lower overall heat transfer area, which helps reduce the cost of heat exchangers.