bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical validation and clinical utilization of K-4CARETM: a comprehensive genomic profiling assay with personalized MRD detection
Authors: Nguyen Thien-Phuc Hoang , Nguyen Tien Anh , Tran Nam HB , Nguyen Hoang Van-Anh , Dao Hong Thuy Thi , Tran Vu-Uyen , Nguyen Yen Nhi , Nguyen Anh Tuan , Nguyen Thi Cam Tu , Do Thi Thanh Thuy , Nguyen Duy Sinh , Nguyen Hoai-Nghia , Giang Hoa , Tu Lan N 
Published: November 2023

abstractBackgroundBiomarker testing has gradually become standard of care in precision oncology to help physicians select optimal treatment for patients. Compared to single-gene or small gene panel testing, comprehensive genomic profiling (CGP) has emerged as a more time- and tissue-efficient method. This study demonstrated in-depth analytical validation of K-4CARE, a CGP assay that integrates circulating tumor DNA (ctDNA) tracking for residual cancer surveillance.MethodsThe assay utilized a panel of 473 cancer-relevant genes with a total length of 1.7 Mb. Reference standards were used to evaluate limit of detection (LOD), concordance, sensitivity, specificity and precision of the assay to detect single nucleotide variants (SNVs), small insertion/deletions (Indels), gene amplification and fusion, microsatellite instability (MSI) and tumor mutational burden (TMB). The assay was then benchmarked against orthogonal methods using 155 clinical samples from 10 cancer types. In selected cancers, top tumor-derived somatic mutations, as ranked by our proprietary algorithm, were used to detect ctDNA in the plasma.ResultsFor detection of somatic SNVs and Indels, gene fusion and amplification, the assay had sensitivity of >99%, 94% and >99% respectively, and specificity of >99%. Detection of germline variants also achieved sensitivity and specificity of >99%. For TMB measurement, the correlation coefficient between whole-exome sequencing and our targeted panel was 97%. MSI analysis when benchmarked against polymerase chain reaction method showed sensitivity of 94% and specificity of >99%. The concordance between our assay and the TruSight Oncology 500 assay for detection of somatic variants, TMB and MSI measurement was 100%, 89% and 98% respectively. When CGP-informed mutations were used to personalize ctDNA tracking, the detection rate of ctDNA in liquid biopsy was 79%, and clinical utility in cancer surveillance was demonstrated in 2 case studies.ConclusionsK-4CARETMassay provides comprehensive and reliable genomic information that fulfills all guideline-based biomarker testing for both targeted therapy and immunotherapy. Integration of ctDNA tracking helps clinicians to further monitor treatment response and ultimately provide well-rounded care to cancer patients.
Analysis of 245,368 diverse individuals from the NIH All of Us Cohort identifies incomplete penetrance of the VEXAS-defining UBA1 p.M41L somatic mutation
Authors: Corty Robert W. , Byram Kevin , Springer Jason , Grayson Peter C. , Bick Alexander 
Published: November 2023

AbstractObjectiveSomatic mutations inUBA1cause the recently described systemic auto-inflammatory syndrome, VEXAS. Study of this disease has largely been limited to highly symptomatic patients. We sought to determine the prevalence of VEXAS-associated somatic mutations and their disease penetrance in a diverse, unselected population.MethodsWe analyzed clinical-grade whole genome sequencing data from 245,368 individuals in the All of Us Research Program. We compared persons with canonical VEXAS-associated mutations to ten age, sex, and ancestry matched controls across the domains of diagnoses, medications, and laboratory values.Results74 persons were identified with a VEXAS-defining somatic mutation at c.121A>C (p.Met41Leu) inUBA1. The variant allele fraction ranged from 4.5% to 33%. No other canonical VEXAS-associated mutations were identified. Of the 74 persons, 62 (84%) were women, 20 (27%) were African American, and 14 (19%) were American Admixed / Latino. There was no statistically significant association between case/control status and any diagnosis code, medication prescription, or laboratory value.ConclusionWe report the largest cohort to date of persons with the VEXAS-associated p.Met41Leu mutation. This cohort differed substantially from reported cohorts of patients with clinical VEXAS, having a higher proportion of persons who were young, female, and of diverse ancestry. Variant allele fractions of p.Met41Leu mutations were lower than reported in clinical VEXAS and none of the patients had bioinformatically apparent VEXAS syndrome. The p.Met41LeuUBA1variant displayed incomplete penetrance for VEXAS. Further study is needed to determine the natural history of VEXAS-associated mutations in the pre-disease phase.
Structural insights into the RNA maturation of the mitoribosome by GTPBP10
Authors: Nguyen Thu Giang , Ritter Christina , Kummer Eva 
Published: November 2023

AbstractMitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a previously unknown large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require 2 biogenesis factors in contrast to only 1 in bacteria.
Interaction between Solo and PDZ-RhoGEF is involved in actin cytoskeletal remodeling and response to substrate stiffness
Authors: Kunitomi Aoi , Chiba Shuhei , Higashitani Nahoko , Higashitani Atsushi , Sato Shinichi , Mizuno Kensaku , Ohashi Kazumasa 
Published: November 2023

ABSTRACTRecent findings indicate that Solo, a RhoGEF, is involved in cellular mechanical stress responses. However, the mechanism of actin cytoskeletal remodeling via Solo remains unclear. Therefore, this study was aimed at identifying Solo-interacting proteins using the BioID, a proximal-dependent labeling method and elucidating the molecular mechanisms of function of Solo. We identified PDZ-RhoGEF (PRG) as a Solo-interacting protein. PRG co-localized with Solo in the basal area of cells, depending on Solo localization, and enhanced actin polymerization at Solo accumulation sites. Additionally, Solo and PRG interaction was necessary for actin cytoskeletal remodeling and RhoA activation. Moreover, overexpression of the binding domains of Solo and PRG had a dominant-negative effect on actin polymerization and actin stress fiber formation in response to substrate stiffness. Therefore, Solo restricts the localization of PRG and regulates actin cytoskeletal remodeling in synergy with PRG in response to the surrounding mechanical environment.
Effect of post-treated methods on corrosion resistance of MF-DC magnetron sputtering Al coating on TC4
Authors: Li Wensheng , Zhang Yiding , Xu Yanwei , Jiao Guangming , Zuo Dunwen , Lu Wenting , Cheng Quanshi , Yu Jiaqi , Chen Yajun 
Published: November 2023

Purpose
This study aims to investigate the effect of post-treatment on anti-corrosion performance of Al coating on the surface of Ti-6Al-4V (TC4) fastener.

Design/methodology/approach
The Al coatings with different layer structures were prepared on TC4 by middle-frequency and direct-current combined magnetron sputtering. The cross-sectional morphology and surface roughness of coatings were characterized by scanning electron microscope and atomic force microscope. The corrosion resistance was evaluated by electrochemical method. The monolayer coating was post-treated by Alodine chemical conversion, Ar+ bombardment and a combination of two methods above.

Findings
The results show that the interfaces in bilayer and trilayer coatings reduce the defects. Ar+ bombardment reduces the corrosion current density, and Alodine chemical conversion leads to a higher pitting corrosion potential. The combined post-treatment has the highest polarization resistance.

Originality/value
The corrosion resistance of the Al coating is enhanced as the layer quantity increases. The combination of two post-treatments, Ar+ bombardment and Alodine chemical conversion, could achieve an overall improvement in corrosion resistance of Al coating.
Will the “nouveau-riche” (new-rich) waste more food? Evidence from China
Authors: Hao Na , Wang H. Holly , Wang Xinxin , Michael Wetzstein 
Published: November 2023

PurposeThis study aims to test the compensatory consumption theory with the explicit hypothesis that China's new-rich tend to waste relatively more food.Design/methodology/approachIn this study, the authors use Heckman two-step probit model to empirically investigate the new-rich consumption behavior related to food waste.FindingsThe results show that new-rich is associated with restaurant leftovers and less likely to take them home, which supports the compensatory consumption hypothesis.Practical implicationsUnderstanding the empirical evidence supporting compensatory consumption theory may improve forecasts, which feed into early warning systems for food insecurity. And it also avoids unreasonable food policies.Originality/valueThis research is a first attempt to place food waste in a compensatory-consumption perspective, which sheds light on a new theory for explaining increasing food waste in developing countries.
Digitalization and sustainable development goals in emerging Islamic economies
Authors: Tlemsani Issam , Zaman Asif , Mohamed Hashim Mohamed Ashmel , Matthews Robin 
Published: November 2023

Purpose
This study examines the intersection of emerging Islamic economies and the digital economy in the context of the United Nations sustainable development goals (UN SDGs). This study aims to investigate the opportunities, challenges and barriers faced by emerging Islamic economies in the context of the digital economy. It specifically focuses on how these economies can contribute to the achievement of UN SDGs established in 2015. In addition, the study explores the prospects of Islamic digital finance and its potential to facilitate the adoption of the UN SDGs.

Design/methodology/approach
The following components outline the design, methods and approach of this study, identify and select specific UN SDGs that are relevant to the research aims. These selected goals serve as the basis for evaluating the impact of conventional and Islamic digital financial inclusion, gathered data from credible sources such as Bloomberg and Refinitiv Thomson Reuters to support the analysis. These sources provide comprehensive data on global indicators, progress and targets related to the UN SDGs, compare and evaluate the impact of both conventional and Islamic digital financial inclusion strategies on the selected UN SDGs; the study uses qualitative interpretation of the gathered data, which involves identifying patterns, themes and connections within the data to draw meaningful conclusions.

Findings
Results revealed that Islamic digital finance has the potential to contribute significantly to achieving the UN SDGs by promoting financial inclusion, encouraging ethical investments, supporting small and medium enterprises, promoting sustainable investments and leveraging technology to expand access to Islamic financial services and support sustainable investments.

Research limitations/implications
While there are many potential benefits of Islamic digital finance in helping to achieve the UN SDGs, there are also several limitations that should be considered in research, such as limited access to digital infrastructure, regulatory challenges, product offerings, scale, awareness and adoption. Addressing these limitations will be critical to maximizing the potential of Islamic digital finance to contribute to achieving the UN SDGs.

Practical implications
This study points to an important gap in the literature; for practitioners, this study has significant managerial consequences for achieving the UN SDGs in emerging economies by facilitating social impact investments and promoting ethical and sustainable investments.

Originality/value
This study’s uniqueness lies in its exploration of the limited exploration of connecting the implementation of digital financial systems to promote UN SDGs within emerging Islamic economies.
Encouraging prolonged consumption through habit-boosting efforts: conceptualization and research agenda
Authors: Taylor Jennifer F. , Beatty Sharon E. , Roberto Katherine J. 
Published: November 2023

Purpose
This paper aims to provide a better understanding of the prolonged consumption journey and how they are sustained by service providers’ use of habit-boosting strategies. Existing research is critically evaluated, and a research agenda is provided to inspire and guide future research.

Design/methodology/approach
This paper develops a conceptual framework that integrates habit and transformative consumer intervention theories with customer journey literature to explain the role of habit in sustaining prolonged consumption journeys. Habit-boosting strategies are introduced as mechanisms for service providers to facilitate their customers’ prolonged consumption journeys.

Findings
This paper argues that habit strength is a limited operant resource that often lacks resource integration efficiency and hinders customers’ abilities to sustain prolonged consumption journeys. Four distinct habit-boosting strategies are identified that provide the potential for service providers to facilitate their customers’ prolonged consumption journeys.

Originality/value
This study presents a typology of habit-boosting strategies and a research agenda that discusses a range of practically relevant and theoretically insightful contributions.
How do employees maintain their well-being during loneliness? The power of organizational nostalgia
Authors: Tatar Berivan , Müceldili Büşra , Erdil Oya 
Published: November 2023

Purpose
The spread of technology usage and the increasing popularity of network technology have formed a basis for alternative working systems as virtual teams and teleworking in the working environment. However, social relations have weakened in these working systems and loneliness has become a common emotion in the workplace. Hence, the concept of loneliness has attracted significant interest in recent years. Yet, despite this interest, research examining loneliness in the workplace is limited in the literature. This study aims to investigate the role of workplace loneliness on intrinsic motivation and the effect of intrinsic motivation on employee well-being through the moderating role of organizational nostalgia.

Design/methodology/approach
Data were collected from 380 respondents working in different sectors. The hypotheses were tested by using structural equation modeling and PROCESS macro for SPSS.

Findings
Results empirically showed that workplace loneliness negatively relates to intrinsic motivation, intrinsic motivation positively relates to employee well-being, intrinsic motivation mediates the link between workplace loneliness and employee well-being and organizational nostalgia moderates the link between workplace loneliness and intrinsic motivation. Furthermore, organizational nostalgia also moderates the indirect effect of workplace loneliness on employee well-being through intrinsic motivation.

Originality/value
To the best of the authors’ knowledge, this study contributes to the existing literature on workplace loneliness by investigating underlying mechanisms and boundary conditions for loneliness in the workplace.
Drivers for design for deconstruction (DfD) implementation among design professionals
Authors: Pittri Hayford , Agyekum Kofi , Botchway Edward Ayebeng , Alencastro João , Oladinrin Olugbenga Timo , Dompey Annabel Morkporkpor Ami 
Published: November 2023

PurposeThe design for deconstruction (DfD) technique, a contemporaneous solution to demolition by optimizing disassembly activities to enable reuse, has recently emerged with several promises to promote the circular economy. However, little attention has been given to its implementation among design professionals, especially in the Global South. Therefore, this study aims to explore the drivers for DfD implementation among design professionals in the Ghanaian construction industry (GCI).Design/methodology/approachThe study adopted a mixed research approach (explanatory sequential design) with an initial quantitative instrument phase, followed by a qualitative data collection phase. Data from the survey were analyzed using mean, standard deviation, one-sample t-Test, and normalization value (NV) test after a review of pertinent literature. These data were then validated through semistructured interviews with ten design professionals with in-depth knowledge of DfD.FindingsThe findings revealed that although all ten drivers are important, the eight key drivers for the DfD implementation were identified as, in order of importance, “Availability of computer software applications regarding DfD,” “Inclusion of DfD in the formal education of design professionals,” “Increasing public awareness of the concept of DfD,” “Organizing workshops/seminars for design professionals on the concept of DfD,” “Availability of DfD training,” “Regulation regarding DfD,” “Industry guidance regarding DfD” and “Establishing a market for salvaged construction components.”Originality/valueThis study's findings provide insights into an under-investigated topic in Ghana and offer new and additional information and insights into the current state-of-the-art on the factors that drive DfD implementation.
Modelling animal network data in R using STRAND
Authors: Ross Cody T. , McElreath Richard , Redhead Daniel 
Published: November 2023

Abstract

There have been recent calls for wider application of generative modelling approaches in applied social network analysis. At present, however, it remains difficult for typical end users—for example, field researchers—to implement generative network models, as there is a dearth of openly available software packages that make application of such models as simple as other, permutation‐based approaches.

Here, we outline the STRAND R package, which provides a suite of generative models for Bayesian analysis of animal social network data that can be implemented using simple, base R syntax.

To facilitate ease of use, we provide a tutorial demonstrating how STRAND can be used to model proportion, count or binary network data using stochastic block models, social relation models or a combination of the two modelling frameworks.

STRAND facilitates the application of generative network models to a broad range of data found in the animal social networks literature.
Effects of large mammal exclusion on seedling communities depend on plant species traits and landscape protection in human‐modified Costa Rican forests
Authors: Huanca‐Nuñez Nohemi , Chazdon Robin L. , Russo Sabrina E. 
Published: November 2023

Abstract

Large terrestrial herbivorous mammals (LTH‐mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH‐mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH‐mammals influence forest regeneration in human‐modified landscapes.

We tested the hypothesis that the strength of LTH‐mammals' effects on seedling establishment depends on landscape protection, forest successional stage and plant species' traits using a manipulative field experiment in six 1‐ha sites with varying successional age and landscape protection. In each site, we established 40 seedling plot‐pairs, with one plot excluding LTH‐mammals and one not, and monitored seedlings of 116 woody species for 26 months.

We found significant effects of LTH‐mammal exclusion on seedling survival contingent upon the protection of forests at the landscape level and forest stage. After 26 months, survival differences between LTH‐mammal exclusion and non‐exclusion treatments were greater in protected than unprotected landscapes. Additionally, plant species' traits were related to the LTH‐mammals' differential effects, as LTH‐mammals reduced the survival of seedlings of larger‐seeded species the most. Overall, LTH‐mammals' effects translated into significant shifts in community composition as seedling communities inside and outside the exclosures diverged. Moreover, lower density and higher species diversity were found as early as 12 and 18 months outside than inside exclosures.

Synthesis and applications. Insight into the interactions between LTH‐mammals and seedling communities in forest regeneration can be instrumental in planning effective restoration efforts. We highlight the importance of landscape protection in seedling survival and the role of LTH‐mammals in promoting seedling diversity in mature forests but also in secondary successional forests. The findings suggest that conservation efforts and possibly trophic rewilding can be important approaches for preserving diversity and influencing the trajectory of secondary tropical forest succession. However, we also caution that an overabundance of LTH‐mammals may adversely impact the pace of forest succession due to their preference for large‐seeded species. Therefore, a comprehensive wildlife management plan is indispensable. Additionally, longer term studies on LTH‐mammals are necessary to understand the effects of temporal fluctuations that are undetected in short‐term studies.
Relics of an Unwanted Past: Slavery, Polygamy and the Harem at the End of the Ottoman Empire
Authors: Karamursel Ceyda 
Published: November 2023

AbstractThis article traces the ways in which the newly inaugurated Turkish Republic dealt with such institutional and legal ‘relics’ as the imperial harem, slavery and polygamy, that it inherited from its immediate, largely undesirable imperial past, condemned retrospectively as ‘backward’, but nevertheless continued to exist for years to come. Focusing on the immediate aftermath of the abolition of the Caliphate and the exile of the Ottoman dynasty, it examines a set of legal, governmental and discursive weapons that the new regime deployed – from expropriation and disposal of dynastic property to exoticisation and sexualisation of court practices – to severe the imperial harem and its erstwhile powerful actors from the political, social and cultural contexts they had long been closely linked with. It argues that while such measures affected a relatively small number of individuals, particularly women, they had significant implications for the republican government's reconceptualisation of citizenship and state belonging for the wider public.
Are party families in Europe ideologically coherent today?
Authors: DE LA CERDA NICOLÁS , GUNDERSON JACOB R. 
Published: November 2023

AbstractResearchers classify political parties into families by their shared cleavage origins. However, as parties have drifted from the original ideological commitments, it is unclear to what extent party families today can function as effective heuristics for shared positions. We propose an alternative way of classifying parties based solely on their ideological positions as one solution to this challenge. We use model‐based clustering to recast common subjective decisions involved in the process of creating party groups as problems of model selection, thus, providing non‐subjective criteria to define ideological clusters. By comparing canonical families to our ideological clusters, we show that while party families on the right are often too similar to justify categorizing them into different clusters, left‐wing families are weakly internally cohesive. Moreover, we identify two clusters predominantly composed of parties in Eastern Europe, questioning the degree to which categories originally designed to describe Western Europe can generalize to other regions.