bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of earthquake fault rupture kinematics on tsunami generation: a numerical study of real events
Authors: Sementsov K A , Baba T , Kolesov S V , Tanioka Y , Nosov M A 
Published: November 2024

SUMMARY
The study is devoted to the effect of the fault rupture kinematics in the earthquake source on tsunami generation. Sixteen events of years 1992–2021 are investigated. For each event, the kinematic tsunami source (bottom motion during the earthquake) and the static tsunami source (permanent bottom deformation) were calculated using the Finite Fault Models provided by the U.S. Geological Survey. For both sources, numerical tsunami simulations were carried out within the framework of linear long-wave theory. Comparison of the simulation results showed that in 10 out of 16 events, the energy of tsunami excited by the kinematic source is greater than that excited by the static source. The maximum energy amplification (9.1 per cent) is observed at the minimum ratio of average rupture velocity to long-wave velocity. The Illapel 2015 event has been investigated more thoroughly using dispersive tsunami models jagurs and cptm. This investigation showed that the kinematic source causes a spatial redistribution of tsunami amplitudes and a notable amplification of the high-frequency component in the time-series of tsunami height. At some points along the Chilean coast, the difference between the kinematic and static calculations is more than 2 m.
Pharmacologic Inhibition of Macrophage Triglyceride Biosynthesis Pathways Does Not Improve Mycobacterium tuberculosis Control in Infected Mice
Authors: Ruelas Castillo Jennie , Guerrini Valentina , Quijada Darla , Karanika Styliani , Neupane Pranita , Urbanowski Michael E , Shenkoya Babajide , Harris Harley , Garcia Andrew , Yilma Addis , Annunziata Hannah , Khan Rehan , Gopalakrishnan Mathangi , Gennaro Maria L , Karakousis Petros C 
Published: November 2024

Abstract
Tuberculosis necrotic granulomas contain triglyceride-rich macrophages (foam cells) with reduced antimicrobial functions. We assessed the ability of 2 compounds to reduce the triglyceride content and Mycobacterium tuberculosis (Mtb) burden in infected human monocyte-derived macrophages and in the lungs of Mtb-infected C3HeB/FeJ mice: A-922500 (DGATi), an inhibitor of diacylglycerol O-acyltransferase 1, and LY2584702 (p70S6Ki), an inhibitor of p70 S6 kinase. DGATi and p70S6Ki significantly reduced the lipid content and bacillary burden in Mtb-infected macrophages. Each inhibitor reduced the cellular triglyceride content in bronchoalveolar lavage samples of Mtb-infected mice. After 6 weeks of treatment, p70S6Ki alone reduced the lung bacterial burden in Mtb-infected mice. However, DGATi alone and DGATi or p70S6Ki in combination with isoniazid did not reduce lung bacterial burden or alter lung inflammation. These findings provide further insight into the role of foam cells in tuberculosis pathogenesis and the utility of interventions targeting these cell populations as adjunctive host-directed therapies.
Gravity with History: on Incumbency Effects in International Trade
Authors: Egger Peter , Foellmi Reto , Schetter Ulrich , Torun David 
Published: November 2024

Abstract
Countries trade more if they liberalized their trade relationship earlier. We derive a gravity equation featuring this path dependence due to sunk market-access costs that generate incumbency effects. We provide supporting evidence for the underlying mechanism and derive an augmented ACR (Arkolakis, Costinot, and Rodríguez-Clare 2012) formula for the gains from trade that accounts for incumbency effects. A quantification suggests our mechanism explains up to 25% of countries’ home shares, and the gains from trade are, on average, 10% larger when allowing for incumbency effects. The analysis further reveals novel distributional effects of trade, boosting real wages but reducing profits.
The professional profile, competence, and responsiveness of senior bureaucrats: a paired survey experiment with citizens and elite respondents
Authors: Askim Jostein , Bach Tobias , Kolltveit Kristoffer 
Published: November 2024

Abstract
How do the professional backgrounds of senior bureaucrats affect their competence and political responsiveness? This article fills a gap by examining these questions in a meritocratic context that accommodates nuanced but potentially consequential variations in the recruitment of senior bureaucrats. Using a paired survey experiment with citizens, representatives, and administrators in Norway, the article demonstrates that agency heads are perceived as less competent and—to a lesser extent—more politically responsive if their profile deviates from the meritocratic ideal of the career civil servant with mission-specific expertise. The article also compares perceptions between groups of stakeholders, filling another gap in the literature. Treatment effects go in the same direction across groups, but the results reveal a mismatch between popular and insider perceptions of bureaucracy: whereas citizens are practically indifferent, administrators are deeply concerned about the competence of an agency head who is a former politician rather than a career bureaucrat. Perceptions of substantive expertise are more aligned: all stakeholder groups view agency heads with mission-specific expertise as more competent and less politically responsive than generalists. Overall, the results demonstrate that variations in who is recruited to senior bureaucrat positions may either strengthen or undermine stakeholders’ views on good governance.
Five flaps or four? Z-plasty for the release of first webspace burn contractures of the hand
Authors: Rogers Alan D , Moltaji Syena , Wallace David 
Published: November 2024

Abstract
First webspace contractures are common indications for reconstructive burn surgery. Commonly performed procedures for this indication include either the four- or five-flap variations of the z-plasty, which involves the transposition of flaps about a central limb in order to obtain greater length, and thus, improve the thumb’s important contribution to coordinated and precise hand function. This paper outlines the predominant reason for favouring the five-flap variation for this indication. This conclusion is derived from the notion that although the gain in length may be greater for the four flap, to make the comparison it assumes that the length of the central limbs are the same for the two techniques. For most cases, however, the central limb cannot exceed much &gt;3 cm for a four-flap z-plasty, while 4 cm may be utilized for a ‘jumping man’ procedure.
Concerts and Cures at the Crichton Royal Institution, 1840–1860
Authors: Golding Rosemary 
Published: November 2024

ABSTRACT
The Crichton Royal Institution in Dumfries, founded in 1839, was renowned for its programme of educational and recreative activities, firmly part of the system of ‘moral management’ embedded by its founding physician, W. A. F. Browne. Music played a key part in this system, with a series of concerts at the core. This article summarizes Browne’s approach to music as a therapeutic agent before examining the rich body of extant concert programmes and associated material. It draws out key elements such as the inclusion of sacred music, early music, Scottish repertory, and music for education, using these to frame a close study of a defined musical community. Unlike examples of music used in English asylums, Browne’s use of ‘national’ music (namely Scottish traditional music) represents the application of a specific musical repertory in a way that directly linked it to health benefits.
Deep learning insights into distinct patterns of polygenic adaptation across human populations
Authors: Tripathi Devashish , Bhattacharyya Chandrika , Basu Analabha 
Published: November 2024

Abstract
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter tuning before performing feature selection and prediction tasks. We tested RAISING on published and newly designed simulations that incorporate the complex interplay between demographic history and selection gradients. RAISING outperformed Phylogenetic Generalized Least Squares (PGLS), ridge regression and DeepGenomeScan, with significantly higher true positive rates (TPR) in detecting genetic adaptation. It reduced computational time by 60-fold and increased TPR by up to 28% compared to DeepGenomeScan on published data. In more complex demographic simulations, RAISING showed lower false discoveries and significantly higher TPR, up to 17-fold, compared to other methods. RAISING demonstrated robustness with least sensitivity to demographic history, selection gradient and their interactions. We developed a sliding window method for genome-wide implementation of RAISING to overcome the computational challenges of high-dimensional genomic data. Applied to African, European, South Asian and East Asian populations, we identified multiple genomic regions undergoing polygenic selection. Notably, ∼70% of the regions identified in Africans are unique, with broad patterns distinguishing them from non-Africans, corroborating the Out of Africa dispersal model.
Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs
Authors: Awawdeh Aya , Tapia Alejandro , Alshawi Sarah A , Dawodu Olabode , Gaier Sarah A , Specht Caitlin , Beaudoin Jean-Denis , Tharp Jeffery M , Vargas-Rodriguez Oscar 
Published: November 2024

Abstract
Mutations that introduce premature termination codons (PTCs) within protein-coding genes are associated with incurable and severe genetic diseases. Many PTC-associated disorders are life-threatening and have no approved medical treatment options. Suppressor transfer RNAs (sup-tRNAs) with the capacity to translate PTCs represent a promising therapeutic strategy to treat these conditions; however, developing novel sup-tRNAs with high efficiency and specificity often requires extensive engineering and screening. Moreover, these efforts are not always successful at producing more efficient sup-tRNAs. Here we show that a pyrrolysine (Pyl) tRNA (tRNAPyl), which naturally translates the UAG stop codon, offers a favorable scaffold for developing sup-tRNAs that restore protein synthesis from PTC-containing genes. We created a series of rationally designed Pyl tRNAScaffold Suppressor-tRNAs (PASS-tRNAs) that are substrates of bacterial and human alanyl-tRNA synthetase. Using a PTC-containing fluorescent reporter gene, PASS-tRNAs restore protein synthesis to wild-type levels in bacterial cells. In human cells, PASS-tRNAs display robust and consistent PTC suppression in multiple reporter genes, including pathogenic mutations in the tumor suppressor gene BRCA1 associated with breast and ovarian cancer. Moreover, PTC suppression occurred with high codon specificity and no observed cellular dysregulation. Collectively, these results unveil a new class of sup-tRNAs with encouraging potential for tRNA-based therapeutic applications.
scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human pan-cancer
Authors: Huang Changzhi , Liu Zekai , Guo Yunlei , Wang Wanchu , Yuan Zhen , Guan Yusheng , Pan Deng , Hu Zhibin , Sun Linhua , Fu Zan , Bian Shuhui 
Published: November 2024

Abstract
Genomic, epigenomic and transcriptomic alterations are hallmarks of cancer cells, and are closely connected. Especially, epigenetic regulation plays a critical role in tumorigenesis and progression. The growing single-cell epigenome data in cancer research provide new opportunities for data mining from a more comprehensive perspective. However, there is still a lack of databases designed for interactively exploring the single-cell multi-omics data of human pan-cancer, especially for the single-cell epigenome data. To fill in the gap, we developed scCancerExplorer, a comprehensive and user-friendly database to facilitate the exploration of the single-cell genome, epigenome (chromatin accessibility and DNA methylation), and transcriptome data of 50 cancer types. Five major modules were provided to explore those data interactively, including ‘Integrated multi-omics analysis’, ‘Single-cell transcriptome’, ‘Single-cell epigenome’, ‘Single-cell genome’ and ‘TCGA analysis’. By simple clicking, users can easily investigate gene expression features, chromatin accessibility patterns, transcription factor activities, DNA methylation states, copy number variations and TCGA survival analysis results. Taken together, scCancerExplorer is distinguished from previous databases with rich and interactive functions for exploring the single-cell multi-omics data of human pan-cancer. It bridges the gap between single-cell multi-omics data and the end-users, and will facilitate progress in the field of cancer research. scCancerExplorer is freely accessible via https://bianlab.cn/scCancerExplorer.
Long-term outcomes of IgA nephropathy in China
Authors: Shen Xue , Chen Pei , Liu Muqing , Liu Lijun , Shi Sufang , Zhou Xujie , Lv Jicheng , Zhang Hong 
Published: November 2024

ABSTRACT

Background
The long-term prognosis of immunoglobulin A nephropathy (IgAN) and the optimal target for proteinuria treatment remain controversial. This study, utilizing a large prospective cohort from China, aims to assess the long-term outcomes of IgAN and to explore the definition of proteinuria remission.

Methods
We enrolled 2141 patients with biopsy-proven IgAN, all with at least 12 months of follow-up, from a prospective IgAN cohort at Peking University First Hospital. We utilized Kaplan–Meier analysis, Cox regression and an estimated glomerular filtration rate (eGFR) slope calculated via a linear mixed model to investigate kidney outcomes.

Results
The median (Q1, Q3) baseline proteinuria was 1.26 (0.65, 2.40) g/day, and the eGFR was 80 (52, 103) mL/min/1.73 m2. After a mean follow-up of 5.8 (±4.4) years, 509 (24%) patients progressed to end-stage kidney disease (ESKD). The median kidney survival time was 12.4 years, the annual event rate of ESKD was 41.1 per 1000 person-years and the 15-year kidney survival rate was 40%. Time-averaged proteinuria level was strongly associated with kidney failure (adjusted hazard ratio 1.76, 95% confidence interval 1.65 to 1.88). Restriction cubic spline analysis indicated that the risk of ESKD increases rapidly when time-average proteinuria exceeded 0.5 g/day. There was no significant difference in long-term kidney survival between patients with proteinuria &lt;0.3 g/day and those with 0.3–0.5 g/day, with both groups demonstrating a better prognosis.

Conclusion
The long-term outcomes for patients with IgAN under current treatment strategies remain poor, with most progressing to ESKD within 15 years. Patients with time-averaged proteinuria ≥0.5 g/day experience worse kidney outcomes, challenging the previous view that proteinuria &lt;1.0 g/day was associated with a low risk of kidney failure.
Ion channel modulator DPI-201-106 significantly enhances antitumor activity of DNA damage response inhibitors in glioblastoma
Authors: Dewdney Brittany , Miranda Panimaya Jeffreena , Kuchibhotla Mani , Palanisamy Ranjith , Richworth Caitlyn , Milligan Carol J , Ng Zi Ying , Ursich Lauren , Petrou Steve , Fletcher Emily V , Daly Roger J , Lim Kam Sian Terry C C , Valvi Santosh , Endersby Raelene , Johns Terrance G 
Published: November 2024

Abstract

Background
Glioblastoma, a lethal high-grade glioma, has not seen improvements in clinical outcomes in nearly 30 years. Ion channels are increasingly associated with tumorigenesis, and there are hundreds of brain-penetrant drugs that inhibit ion channels, representing an untapped therapeutic resource. The aim of this exploratory drug study was to screen an ion channel drug library against patient-derived glioblastoma cells to identify new treatments for brain cancer.

Methods
Seventy-two ion channel inhibitors were screened in patient-derived glioblastoma cells, and cell viability was determined using the ViaLight Assay. Cell cycle and apoptosis analysis were determined with flow cytometry using PI and Annexin V staining, respectively. Protein and phosphoprotein expression was determined using mass spectrometry and analyzed using gene set enrichment analysis. Kaplan-Meier survival analyses were performed using intracranial xenograft models of GBM6 and WK1 cells.

Results
The voltage-gated sodium channel modulator, DPI-201-106, was revealed to reduce glioblastoma cell viability in vitro by inducing cell cycle arrest and apoptosis. Phosphoproteomics indicated that DPI-201-106 may impact DNA damage response (DDR) pathways. Combination treatment of DPI-201-106 with the CHK1 inhibitor prexasertib or the PARP inhibitor niraparib demonstrated synergistic effects in multiple patient-derived glioblastoma cells both in vitro and in intracranial xenograft mouse models, extending survival of glioblastoma-bearing mice.

Conclusions
DPI-201-106 enhances the efficacy of DDR inhibitors to reduce glioblastoma growth. As these drugs have already been clinically tested in humans, repurposing DPI-201-106 in novel combinatorial approaches will allow for rapid translation into the clinic.
Real Clinical Effectiveness of Molnupiravir Against 30-day Mortality Among 74 541 SARS-CoV-2–Positive Patients: A Nationwide Cohort Study From the Czech Republic
Authors: Pavlík Tomáš , Jarkovský Jiří , Šanca Ondřej , Koziar Vašáková Martina , Dlouhý Pavel , Černý Vladimír , Štourač Petr , Válek Vlastimil , Dušek Ladislav 
Published: November 2024

Abstract

Background
We examined the clinical effectiveness of molnupiravir in reducing deaths in a real-world cohort of adult patients with COVID-19 during the Omicron outbreak.

Methods
This was a population-wide retrospective cohort study in the Czech Republic. We analyzed all 74 541 patients with an officially registered diagnosis of SARS-CoV-2 infection between 1 January and 31 December 2022, aged 18 years or older, treated with molnupiravir. The primary outcome was 30-day all-cause mortality; the secondary outcome was 30-day COVID-19-related mortality. Hazard ratios (HRs) were estimated using stratified Cox regression and the Fine-Gray model.

Results
The use of molnupiravir in adult SARS-CoV-2 positive patients was associated with a lower risk of both 30-day all-cause mortality: adjusted HR 0.58 (95% confidence interval, 0.53–0.64; P &lt; .001) and 30-day COVID-19–related mortality: adjusted HR 0.50 (95% confidence interval, 0.42–0.58; P &lt; .001). The effect of molnupiravir was highly significant regardless of sex, Deyo-Charlson Comorbidity Index score, hospitalization status, COVID-19 vaccination status, and patients older than age 65 years.

Conclusions
In this cohort study, early initiation of molnupiravir was associated with a significant reduction in 30-day all-cause and COVID-19–related mortality in adult SARS-CoV-2 positive patients.
Community Approaches to Archaeology, Heritage, and Museums
Authors: Apaydin Veysel 
Published: November 2024

AbstractThis chapter explores the ways in which the fields of archaeology, heritage, and museums developed in relation to communities from a historical perspective. On the one hand, the emergence and development of these fields was based on colonialist and nationalist perspectives that not only excluded communities from heritage, archaeological, and museum research and work through their top-down approaches, but also appropriated the material culture and intellectual property of the local and Indigenous communities. On the other hand, the last quarter of the twentieth century witnessed an emergence of ethical and people-centered approaches and methods that aim to include communities in research, heritage, and museum work and decision-making processes. This chapter critically examines the changing attitudes of archaeology, heritage, and museums towards communities from a historical perspective.
A Mean Value Theorem for General Dirichlet Series
Authors: Broucke Frederik , Hilberdink Titus 
Published: November 2024

ABSTRACT
In this paper we obtain a mean value theorem for a general Dirichlet series $f(s)= \sum_{j=1}^\infty a_j n_j^{-s}$ with positive coefficients for which the counting function $A(x) = \sum_{n_{j}\le x}a_{j}$ satisfies $A(x)=\rho x + O(x^\beta)$ for some ρ &gt; 0 and β &lt; 1. We prove that $\frac1T\int_0^T |\,f(\sigma+it)|^2\, dt \to \sum_{j=1}^\infty a_j^2n_j^{-2\sigma}$ for $\sigma\gt\frac{1+\beta}{2}$ and obtain an upper bound for this moment for $\beta\lt\sigma\le \frac{1+\beta}{2}$. We provide a number of examples indicating the sharpness of our results.
Development of equivalent dose assessment methodology for the lens of the eye at nuclear power plant workers
Authors: Kim Siyoung , Son Jungkwon , Kim Cheon-Woo 
Published: November 2024

Abstract
As the International Commission on Radiological Protection lowers the equivalent dose limit for lens of the eye of radiation workers, the importance of radiation protection for the lens of the eye has been increased. In the case of poor working condition, such as high temperatures and humid environments at nuclear power plants, wearing an eye dosemeter near the worker’s eye may interfere with work. In addition, it would not be reasonable for all workers to wear an eye dosemeter to evaluate the lens equivalent dose even in areas with an expected low exposure dose in the NPPs. Therefore, it is necessary to develop an indirect assessment method for lens equivalent dose. The purpose of this study is to develop an indirect assessment method for a lens equivalent dose using correlation factors between whole-body dose and eye. The correlation factors are calculated by MCNP simulation results.
Psychotic Experiences and Risk of Suicidal Thoughts and Behaviors: A Systematic Review and Meta-Analysis of Longitudinal Population Studies
Authors: O’Hare Kirstie , Fadiloglu Kubra , Lång Ulla , Healy Colm , Cannon Mary , DeVylder Jordan , Kelleher Ian 
Published: November 2024

Abstract

Background and Hypothesis
Since a prior systematic review and meta-analysis reported an association between psychotic experiences (PEs) and suicidal thoughts and behaviors, a large number of new studies have been published on the topic, including several novel studies on the association between PEs and transition from suicidal ideation to attempt.

Study Design
Two authors independently searched PubMed, Embase, CINAHL, and PsycINFO databases from inception until July 2023, conducted data extraction, and assessed study quality using the Newcastle-Ottawa Quality Assessment Scale. Random-effects models were used to calculate pooled odds ratios (ORs) for the association of PEs and subsequent suicide ideation, suicide attempts, suicide death, and transition from suicidal ideation to attempt, first for the total population, and second stratified by age group. Secondary analyses assessed the mediating role of co-occurring psychopathology.

Study Results
Twenty studies from 18 different samples (n = 81,861) were identified. Individuals who reported PEs had increased odds of subsequent suicidal ideation (k = 12, OR = 1.90, 95% CI = 1.65-2.19), suicide attempt (k = 13, OR = 2.95, 95% CI = 2.21-3.94), transition from suicidal ideation to suicide attempt (k = 3, OR = 2.83, 95% CI = 1.60-4.99), and suicide death (k = 1, OR = 4.39, 95% CI = 1.63-11.80). This heightened risk was stable across childhood, adolescence, and adulthood. PEs predicted suicide attempts over and above co-occurring psychopathology (k = 8, OR = 2.85, 95% CI = 2.06-3.95).

Conclusions
Individuals reporting PEs are at increased risk of all types of suicidal thoughts and behaviors. In addition, PEs are particularly important risk markers for future suicidal behaviors, including in individuals already reporting suicidal ideation. This risk is in excess of what is explained by co-occurring psychopathology.