bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants
Authors: Wang Chonghao , Zhang Jing , Zhou Xin , Zhang Lu 
Published: May 2022

AbstractBackgroundQuantifying an individual’s risk for common diseases is an important goal of precision health. The polygenic risk score (PRS), which aggregates multiple risk alleles of candidate diseases, has emerged as a standard approach for identifying high-risk individuals. A variety of tools have been developed to implement PRS. However, benchmarks for comparatively evaluating the performance of these different methods and for assessing their potential to guide future clinical applications are lacking.ResultsWe systematically validated and compared thirteen statistical methods, five machine learning models and two ensemble models using simulated data, twenty-two common diseases with internal training sets and four diseases with external summary statistics from the UK Biobank resource. The effects of disease heritability, single nucleotide polymorphism (SNP) effect size and sample size are evaluated using simulated data. We also investigated the correlations between methods and their standard deviations of different diseases.ConclusionsIn general, statistical methods outperform machine learning models, and ensemble models, such as Super Learner, generally perform the best for most situations. We observed the correlations were relatively high if the methods were from the same category and the external summary statistics from large cohort GWAS could decrease the standard deviation of method correlations. By varying three factors in the simulated data, we also identified that disease heritability had a strong effect on the predictive performance of individual methods. Both the number and effect sizes of risk SNPs are important; and while sample size strongly influences the performance of machine learning models, but not statistical methods.
A key role of the WEE1-CDK1 axis in mediating TKI-therapy resistance in FLT3-ITD positive acute myeloid leukemia patients
Authors: Massacci Giorgia , Venafra Veronica , Latini Sara , Bica Valeria , Pugliese Giusj Monia , Klingelhuber Felix , Krahmer Natalie , Fischer Thomas , Mougiakakos Dimitrios , Boettcher Martin , Perfetto Livia , Sacco Francesca 
Published: May 2022

SummaryInternal tandem duplications (ITDs) in the FLT3 gene are frequently identified and confer a poor prognosis in patient affected by acute myeloid leukemia (AML). The insertion site of the ITDs in FLT3 significantly impacts the sensitivity to tyrosine kinase inhibitors (TKIs) therapy, affecting patient’s clinical outcome. To decipher the molecular mechanisms driving the different sensitivity to TKIs therapy of FLT3-ITD mutation, we used high-sensitive mass spectrometry-based (phospho)proteomics and deep sequencing. Here, we present a novel generally-applicable strategy that supports the integration of unbiased large-scale datasets with literature-derived signaling networks. The approach produced FLT3-ITDs specific predictive models and revealed a crucial and conserved role of the WEE1-CDK1 axis in TKIs resistance. Remarkably, we found that pharmacological inhibition of the WEE1 kinase synergizes and strengthens the pro-apoptotic effect of TKIs therapy in cell lines and patient-derived primary blasts. In conclusion, this work proposes a new molecular mechanism of TKIs resistance in AML and suggests a combination therapy as option to improve therapeutic efficacy.
The time course of categorical and perceptual similarity effects in visual search
Authors: Yeh Lu-Chun , Peelen Marius V. 
Published: May 2022

AbstractDuring visual search for objects (e.g., an apple), the surrounding distractor objects may share perceptual (tennis ball), categorical (banana), or both (peach) properties with the target. Previous studies showed that the perceptual similarity between target and distractor objects influences visual search. Here, we tested whether categorical target-distractor similarity also influences visual search, and how this influence depends on perceptual similarity. By orthogonally manipulating categorical and perceptual target-distractor similarity, we could investigate how and when the two similarities interactively affect search performance and neural correlates of spatial attention (N2pc) using electroencephalography (EEG). Behavioral results showed that categorical target-distractor similarity interacted with perceptual target-distractor similarity, such that the effect of categorical similarity was strongest when target and distractor objects were perceptually similar. EEG results showed that perceptual similarity influenced the early part of the N2pc (200-250 ms after stimulus onset), while categorical similarity influenced the later part (250-300 ms). Mirroring the behavioral results, categorical similarity interacted with perceptual similarity during this later time window, with categorical effects only observed for perceptually similar target-distractor pairs. Together, these results provide evidence for hierarchical processing in visual search: categorical properties influence spatial attention only when perceptual properties are insufficient to guide attention to the target.Public significance statementSearching for a target object among perceptually similar distractor objects (e.g., looking for an apple among peaches) is relatively difficult. In daily life, target and distractor objects may not only share perceptual but also non-perceptual properties, such as category membership (e.g., fruit). Here, we show that categorical similarity between target and distractor objects influences search performance, particularly when target and distractor objects are perceptually similar. Using electrophysiological recordings, we demonstrate that attentional selection is first influenced by perceptual and then by categorical information. This later categorical influence depended on perceptual similarity, being strongest for perceptually similar objects. These findings provide evidence for hierarchical processing in visual search, with categorical properties extracted after perceptual properties.
AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing’s sarcoma cells
Authors: Kitagawa Takao , Kobayashi Daiki , Baron Byron , Okita Hajime , Miyamoto Tatsuo , Takai Rie , Paudel Durga , Ohta Tohru , Asaoka Yoichi , Tokunaga Masayuki , Nakagawa Koji , Furutani-Seiki Makoto , Araki Norie , Kuramitsu Yasuhiro , Kobayashi Masanobu 
Published: May 2022

AbstractEwing’s sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing’s sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. In addition, AHDC1 co-localized with BRD4. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.
In-vivo detection of cyclic-di-AMP in Staphylococcus aureus
Authors: Mukkayyan Nagaraja , Poon Raymond , Sander Philipp N. , Lai Li-Yin , Zubair-Nizami Zahra , Hammond Ming C. , Chatterjee Som S. 
Published: May 2022

ABSTRACTCyclic-di-AMP (CDA) is a signaling molecule that controls various cellular functions including antibiotic tolerance and osmoregulation in Staphylococcus aureus. In this study, we developed a novel biosensor (bsuO P6-4) for in-vivo detection of CDA in S. aureus. Our study showed that bsuO P6-4 could detect a wide concentration range of CDA in both laboratory and clinical strains making it suitable for use in both basic and clinical research applications.
High-fidelity optical diffraction tomography of live organisms using non-toxic tunable refractive index media
Authors: Lee Dohyeon , Lee Moosung , Kwak Haechan , Kim Youngseo , Shim Jaehyu , Jung Jik Han , Park Wei-Sun , Park Ji-Ho , Lee Sumin , Park Yongkeun 
Published: May 2022

AbstractOptical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, includingC. albicansandC. elegans.Abstract Figure
Acquisition of the Spindle Assembly Checkpoint and its modulation by cell fate and cell size in a chordate embryo
Authors: Roca Marianne , Besnardeau Lydia , Christians Elisabeth , McDougall Alex , Chenevert Janet , Castagnetti Stefania 
Published: May 2022

AbstractThe spindle assembly checkpoint (SAC) is a surveillance system which preserves genome integrity by delaying anaphase onset until all chromosomes are correctly attached to spindle microtubules. Recruitment of SAC proteins to unattached kinetochores generates an inhibitory signal that prolongs mitotic duration. Chordate embryos are atypical in that spindle defects do not delay mitotic progression during early development, implying that either the SAC is inactive or the cell-cycle target machinery unresponsive. Here we show that in embryos of the chordate Phallusia mammillata the SAC delays mitotic progression from the 8th cleavage divisions. Unattached kinetochores are not recognized by the SAC machinery until the 7th cell cycle when the SAC is acquired. Following acquisition, SAC strength, manifest as the degree of mitotic lengthening induced by spindle perturbations, is specific to different cell types and is modulated by cell size showing similarity to SAC control in early Caenorhabditis elegans embryos. We conclude that SAC acquisition is a process likely specific to chordate embryos, while modulation of SAC efficiency in SAC proficient stages depends on cell fate and cell size similarly to non-chordate embryos.
The moderating role of board diversity in the nexus between the quality of financial disclosure and dividends in Jordanian-listed banks
Authors: Karajeh Ahmad Ibrahim 
Published: May 2022

PurposeThis study covers all banks listed on the Amman Stock Exchange. It used (1) dividend-paying status, dividend changes and dividend persistence to measure dividend quality, (2) a checklist instrument consisting of 40 items to measure financial disclosure quality, (3) nationality and (4) the percentage of females and males on the board of directors to measure board diversity. Hierarchical regression analysis was employed to investigate the influence of the board diversity on the relationship between financial disclosure quality and dividend quality.Design/methodology/approachThis study investigates the relationship between financial disclosure quality and dividend quality among Jordanian-listed banks. Moreover, it examines the moderating effect of board diversity on the relationship between financial disclosure quality and dividend quality.FindingsThe results in this work imply that banks with high financial disclosure quality have high-quality dividends. Furthermore, nationality and females on the board of directors play a main role as moderators that influence managers' motivations toward the quality of financial disclosure practices and bank dividends. This paper shows that the boards in Jordanian banks have not changed dividend policies and tend to follow a long-term fixed strategy for paying earnings.Originality/valueBecause of the limited number of practical research on the nexus between financial disclosure quality and dividends quality, this study fills a gap in the literature by examining the relationship between them. In addition, a lack of research exists on the effects of board diversity on the nexus of financial disclosure quality and dividends quality. Therefore, this study makes an original contribution to the literature by using nationality and females and males on the board of directors as moderating variables to investigate the effects of board diversity on the relationship between financial disclosure quality and dividend quality among Jordanian banks.
Political regimes and its influence on the diversity–performance relationship in Malaysia
Authors: Cheong Calvin W.H. 
Published: May 2022

PurposeThe purpose of this study is to investigate the gender and ethnic diversity–performance relationship in Malaysia from two angles: (1) the impact of political regimes; and (2) a possible nonlinear relationship – at the boardroom and employee level.Design/methodology/approachThis study uses a sample of firms listed in Bursa Malaysia during a sample period that spans two political regimes. Two-stage least squares controlling for firm-specific effects, corporate governance and lagged variables to account for endogeneity issues is used to test the relationship.FindingsFindings show that the political alignment of the ruling government affects the significance of the gender/ethnic diversity–performance relationship. The relationship between board gender/ethnic diversity and firm performance is curvilinear while the relationship between employee gender/ethnic diversity is linear and positive.Research limitations/implicationsFirst, promoting gender/ethnic diversity not only requires strong policy but also political will to lead by example. Political regimes that provide lip-service without effective implementation threaten to derail any efforts in furthering the diversity agenda. Second, the presumption of a linear diversity–performance relationship is fallacious. Further studies, especially in pluralistic societies, must not discount the subtleties of intergroup conflicts. Third, in light of allegations of prejudicial hiring policies, Malaysian firms should embrace diversity, not only in the boardroom, but also among its workforce as employee diversity improves firm performance.Originality/valuePrior studies on gender/ethnic diversity in Malaysia have returned mixed results but thus far, there has been no satisfactory explanation for this phenomenon. This study attributes it to lack of political will and cultural subgroup conflicts – two pertinent issues that were never considered in the literature. Prior studies have also exclusively focused on boardroom diversity. This study goes further by examining employee diversity – particularly important since most empowerment and diversity initiatives are targeted at lower level employees. This study is also the first to provide an objective benchmark for gender diversity (30–35% female directors) and ethnic diversity (less than 40% from one ethnicity) to achieve optimal performance.
Evaluating performance of an untargeted urban food security scheme in India
Authors: Nagarajan Magesh , Selvaraj Patturaja 
Published: May 2022

PurposeThe purpose of this study is to evaluate the efficiency of the relative performances of Mother’s canteen across the regions of Tamil Nadu and find out the determinants of inefficiencies in the scheme.Design/methodology/approachAn untargeted food security scheme called Amma (Mother's) canteen was started in Tamil Nadu, India, with an aim to provide the urban poor with hygienic and healthy food at an affordable price. Along with secondary data, interviews were conducted to understand the operational details of Mother's canteen. Data envelopment analysis (DEA) was used to find the relative efficiency of the scheme operated by nine corporations.FindingsBased on the daily expenditure, number of meals served and revenue, seven of nine corporations were found to be inefficient. Further, sensitivity analyses found that among six procurement variables, procurement (quantity and price) of black gram and cooking oil were determinants of inefficiency.Research limitations/implicationsAs an untargeted scheme, the cost of delivering service-based evaluation was used for performance evaluation. Policymakers could use centralized procurement instead of open market procurement at the corporation level and standardized ingredients' usage (quantity) to further reduce the cost of the food security scheme.Practical implicationsThe proposed DEA model may be used by policymakers to empirically evaluate the food security scheme's delivery effectiveness across various corporations in a region. Inefficient branches are identified here with empirical support for further performance improvement changes.Originality/valueThere are limited number of studies evaluating untargeted schemes. This paper presents the challenges of evaluating an untargeted scheme which allows self-selection of beneficiaries. The outcome of this study will help in identifying inefficient corporations, and further, improve the performance and cost of delivering untargeted food security scheme.
A semi-analytical benchmark for the Stefan problem in arbitrary dimension – assessing accuracy of enthalpy-based methods
Authors: Malík Jiří , Souček Ondřej 
Published: May 2022

Purpose
This paper aims to propose a semi-analytical benchmarking framework for enthalpy-based methods used in problems involving phase change with latent heat. The benchmark is based on a class of semi-analytical solutions of spatially symmetric Stefan problems in an arbitrary spatial dimension. Via a public repository this study provides a finite element numerical code based on the FEniCS computational platform, which can be used to test and compare any method of choice with the (semi-)analytical solutions. As a particular demonstration, this paper uses the benchmark to test several standard temperature-based implementations of the enthalpy method and assesses their accuracy and stability with respect to the discretization parameters.

Design/methodology/approach
The class of spatially symmetric semi-analytical self-similar solutions to the Stefan problem is found for an arbitrary spatial dimension, connecting some of the known results in a unified manner, while providing the solutions’ existence and uniqueness. For two chosen standard semi-implicit temperature-based enthalpy methods, the numerical error assessment of the implementations is carried out in the finite element formulation of the problem. This paper compares the numerical approximations to the semi-analytical solutions and analyzes the influence of discretization parameters, as well as their interdependence. This study also compares accuracy of these methods with other traditional approach based on time-explicit treatment of the effective heat capacity with and without iterative correction.

Findings
This study shows that the quantitative comparison between the semi-analytical and numerical solutions of the symmetric Stefan problems can serve as a robust tool for identifying the optimal values of discretization parameters, both in terms of accuracy and stability. Moreover, this study concludes that, from the performance point of view, both of the semi-implicit implementations studied are equivalent, for optimal choice of discretization parameters, they outperform the effective heat capacity method with iterative correction in terms of accuracy, but, by contrast, they lose stability for subcritical thickness of the mushy region.

Practical implications
The proposed benchmark provides a versatile, accessible test bed for computational methods approximating multidimensional phase change problems. The supplemented numerical code can be directly used to test any method of choice against the semi-analytical solutions.

Originality/value
While the solutions of the symmetric Stefan problems for individual spatial dimensions can be found scattered across the literature, the unifying perspective on their derivation presented here has, to the best of the authors’ knowledge, been missing. The unified formulation in a general dimension can be used for the systematic construction of well-posed, reliable and genuinely multidimensional benchmark experiments.
Impact of export diversification on economic growth: a system GMM approach
Authors: Markakkaran Swathi , Sridharan Perumal 
Published: May 2022

Purpose
This paper aims to empirically analyze the impact of export diversification on gross domestic product (GDP) per capita growth.

Design/methodology/approach
Using system generalized method of moments (GMM), a nonlinear model in a dynamic panel data growth framework for 101 countries between 1995 and 2019 was estimated.

Findings
Results evidenced that export concentration, measured by the Herfindahl–Hirschman Index (HHI), is negatively associated with GDP per capita growth after controlling for the effects of other explanatory variables. Further, the squared term of HHI used in the model to measure the nonlinear relationship between export concentration and economic growth indicated that the low-income and lower-middle-income countries benefited from export diversification. At the same time, high-income and upper-middle-income countries perform well with their export specialization. The results of the robustness check validate the findings of nonlinear estimation.

Research limitations/implications
The findings recommend that low-income and lower-middle-income countries diversify their export basket to improve economic growth by generating stable export earnings. Similarly, high-income and upper-middle-income countries should focus on measures to close the product lines which no longer belong to their factor endowments and rebalance their export basket.

Originality/value
This study contributes to the existing literature by using the system GMM method, which is most appropriate for a dynamic panel data growth framework with up-to-date data. Further, this study segregates a large panel into 43 concentrated and 58 diversified countries to test the robustness of the empirical results.
A green supply chain taxonomy in healthcare: critical factors for a proactive approach
Authors: Bentahar Omar , Benzidia Smaïl , Bourlakis Michael 
Published: May 2022

PurposeThe aim of this study is to identify the critical factors of green supply chain (GSC) and to adapt these factors to the taxonomy of green practices in healthcare.Design/methodology/approachA qualitative multiple-case study approach was followed based on 60 interviews with nine French hospitals. An intra-case and a cross-case analysis were implemented.FindingsThe findings provide a taxonomy of healthcare GSC and show that regulation, cost reduction, top management commitment, employee training, information technology and measures of environmental performance are critical factors for GSC implementation. The study also underlines a few emergent critical factors including the purchasing group, environmental champion, building construction, combining safety and green approaches.Research limitations/implicationsThis study was conducted in France following a qualitative methodological approach. Future research can consider other national and cross-national investigations and other quantitative or mixed methods approaches.Practical implicationsThe research provides managers and policy makers numerous invaluable suggestions for the implementation of GSC practices in healthcare facilities. To accelerate GSC implementation, managers can invest in the construction of new buildings, in information technology, and in the automation of flows.Originality/valueTo the authors’ knowledge, this is the first paper identifying the critical factors of GSC implementation in the healthcare sector. It is also the first attempt to provide a taxonomy of hospitals according to their green approaches (reactive, receptive, and proactive).