bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ascertainment bias in the genomic test of positive selection on regulatory sequences
Authors: Jiang Daohan , Zhang Jianzhi 
Published: August 2023

ABSTRACTEvolution of gene expression mediated bycis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptivecis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former atnsites, one can predict the TF binding affinities of manyn-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of three TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
ATP Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks
Authors: Kota Divya , Prasad Ramesh , Zhou Huan-Xiang 
Published: August 2023

AbstractATP is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients at 200-5000) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (∼25 pN/μm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (∼1 μm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.
Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold
Authors: Kosugi Takatsugu , Ohue Masahito 
Published: August 2023

AbstractMore than 930,000 protein-protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting protein-protein interactions (PPIs), but it is difficult to predict the structure of a target protein-cyclic peptide complex or to design a cyclic peptide sequence that binds to the target protein using computational methods. Recently, AlphaFold with a cyclic offset has enabled predicting the structure of cyclic peptides, thereby enabling de novo cyclic peptide designs. We developed a cyclic peptide complex offset to enable the structural prediction of target proteins and cyclic peptide complexes and found AlphaFold2 with a cyclic peptide complex offset can predict structures with high accuracy. We also applied the cyclic peptide complex offset to the binder hallucination protocol of AfDesign, a de novo protein design method using AlphaFold, and we could design a high predicted local-distance difference test and lower separated binding energy per unit interface area than the native MDM2/p53 structure. Furthermore, the method was applied to 12 other protein-peptide complexes and one protein-protein complex. Our approach shows that it is possible to design putative cyclic peptide sequences targeting PPI.
NPR1 protects young leaves from systemic salicylic acid-induced damage during bacterial infection
Authors: Hõrak Hanna , Rolfe Stephen A. , Ton Jurriaan , Gray Julie E. 
Published: August 2023

AbstractThe phytohormone salicylic acid (SA) is an important molecular signal that mediates pathogen defence mechanisms, including triggering Arabidopsis immune responses to the hemi-biotrophPseudomonas syringaepv.tomato(Pst). SA induces the expression of a myriad of defence genes via its receptor and transcriptional regulator NONEXPRESSER OF PR GENES 1 (NPR1). Here, we used chlorophyll fluorescence imaging of Fv/Fm, to detect damage to photosystem II beforePst-induced disease symptoms were visible. We observed that the pathogen only induced damage, and subsequent cell death, in mature leaves while developing leaves in the center of the rosette appeared to be protected. However, in thenpr1-1mutant,Pst-infected mature leaves were able to systemically transmit a signal that caused damage to the photosynthetic machinery in uninfected young leaves. Reductions in Fv/Fmcould also be induced systemically in developingnpr1-1leaves by high levels of SA in mature leaves, and rescued by SA biosynthesis deficiency innpr1-1sid2-2mutants. Together, these results indicate that, in addition to its well-known role as a positive regulator of SA responses, NPR1 also acts to suppress SA-dependent immune responses and thereby protects developing leaves from autoimmune damage.
Developing an interactive pile training module for construction risk management and gaging users’ intentions
Authors: Du Wei , M.E. Sepasgozar Samad , Khan Ayaz , Shirowzhan Sara , Garzon Romero Juan 
Published: August 2023

Purpose
This study aims to develop a novel theoretical model for predicting the users’ intention to use virtual tools designed for construction risk evaluation. Risk evaluation is a vital objective for construction managers. This paper intends to examine critical factors such as potential benefits, motivation, performance expectancy and rich sources of information that may affect users’ intention to use virtual technology.

Design/methodology/approach
A pile training module (PTM) was developed in a virtual environment to analyze the proposed virtual reality-technology acceptance model (VR-TAM) factors. Further, a questionnaire survey was conducted with the participation of 102 construction professionals in China to validate the proposed VR-TAM model and PTM tool. The retrieved data was computed to test the proposed model by using partial least squares structural equation modeling and the significance of the PTM tool in a virtual environment.

Findings
The results of this study reveal that high-significance paths represent five relationships between crucial factors affecting users’ intention to use a selected virtual reality (VR) module. Five of seven hypothesis paths were significant with acceptable t-values. By quantitative measurement of high-significance paths, this research has found that each factor under VR-TAM has received significant loadings, with many above the 0.7 threshold mark and others around 0.6. The top factors include “motivation” and “benefits” and have multiplier effects on “intention to use” as the source factors.

Practical implications
The finding of this study presents crucial factors for VR adoption, and the proposed VR-TAM model contributes to the body of knowledge toward managing construction risk using pre-optimization and understanding in a virtual environment. This study supports Chinese construction company managers in effectively using VR technology in their construction projects for risk assessment and management.

Originality/value
This study offered the development of a novel VR-TAM integrated with risk assessment techniques for piling processes. Further, the developed model was analyzed by using a survey of Chinese construction professionals to collect perceptions about the modified theoretical model of VR-TAM.
Poverty, population growth and agglomeration effects in all Brazil cities
Authors: M. Marques André 
Published: August 2023

PurposeThis paper aims to test three hypotheses in city growth literature documenting the poverty reduction observed in Brazil and exploring a rich spatial dataset for 5,564 Brazilian cities observed between 1991 and 2010. The large sample and the author's improved econometric methods allows one to better understand and measure how important income growth is for poverty reduction, the patterns of agglomeration and population growth in all Brazilian cities.Design/methodology/approachThe author identifies literature gaps and use a sizeable spatial dataset for 5,564 Brazilian cities observed in 1991, 2000 and 2010 applying instrumental variables methods. The bias-corrected accelerated bootstrap percentile interval supports the author's point estimates.FindingsThis manuscript finds that Brazilian data for cities does not support Gibrat's law, raising the scope for urban planning and associated policies. Second, economic growth on a sustainable basis is still a vital source of poverty reduction (The author estimates the poverty elasticity at four percentage points). Lastly, agglomeration effects positively affect the city's productivity, while negative externalities underlie the city's development patterns.Originality/valueData for cities in Brazil possess unique characteristics such as spatial autocorrelation and endogeneity. Applying proper methods to find more reliable answers to the above three questions is a desirable procedure that must be encouraged. As the author points out in the manuscript, dealing with endogenous regressors in regional economics is still a developing matter that regional scientists could more generally apply to many regional issues.
Semantic technology for cultural heritage: a bibliometric-based review
Authors: Desul Sudarsan , Mahapatra Rabindra Kumar , Patra Raj Kishore , Sethy Mrutyunjay , Pandey Neha 
Published: August 2023

Purpose
The purpose of this study is to review the application of semantic technologies in cultural heritage (STCH) to achieve interoperability and enable advanced applications like 3D modeling and augmented reality by enhancing the understanding and appreciation of CH. The study aims to identify the trends and patterns in using STCH and provide insights for scholars and policymakers on future research directions.

Design/methodology/approach
This research paper uses a bibliometric study to analyze the articles published in Scopus and Web of Science (WoS)-indexed journals from 1999 to 2022 on STCH. A total of 580 articles were analyzed using the Biblioshiny package in RStudio.

Findings
The study reveals a substantial increase in STCH publications since 2008, with Italy leading in contributions. Key research areas such as ontologies, semantic Web, linked data and digital humanities are extensively explored, highlighting their significance and characteristics within the STCH research domain.

Research limitations/implications
This study only analyzed articles published in Scopus and WoS-indexed journals in the English language. Further research could include articles published in other languages and non-indexed journals.

Originality/value
This study extensively analyses the research published on STCH over the past 23 years, identifying the leading authors, institutions, countries and top research topics. The findings provide guidelines for future research direction and contribute to the literature on promoting, preserving and managing the CH globally.
Cyberattacks in the context of international law enforcement
Authors: Alweqyan Deymah 
Published: August 2023

Purpose
This paper aims to manage the dilemma of cyberspace operations, as the incidence of cybercrimes has increased tremendously in the past few decades, turning cyberspace into a field of war in which all nations must fight. For many countries, cyberattacks and conflicts, and even the basic operation of cyberspace in general, are new territories. Furthermore, international law today does not address many aspects of cyber warfare, as it typically has dealt with only traditional warfare.

Design/methodology/approach
This study examined this crime whether it is a domestic or an international crime and whether cyber wars are under international law or domestic law to address these issues.

Findings
Although many attempts to criminalize these actions occurred, the findings suggest that the world has failed to frame the legal instruments against cyberattacks. The findings also suggest recommendations to solve this issue.

Originality/value
To the best of the author’s knowledge, this study analyzed the comparison between the same crime in the perspective of domestic and international law, highlighting an unsolved dilemma in the world, suggesting some unprecedented solutions to solve.
Integrating forensic accounting in education and practices to detect and prevent fraud and misstatement: case study of Jordanian public sector
Authors: Alharasis Esraa Esam , Haddad Hossam , Alhadab Mohammad , Shehadeh Maha , Hasan Elina F. 
Published: August 2023

Purpose
This study aims to examine the degree of consciousness of forensic accounting (FA) in Jordan. This study surveys practitioners and academicians about their views and thoughts toward the expected role of using FA techniques to detecting and preventing fraud practices and shedding more light on advantages and obstacles of using the FA techniques.

Design/methodology/approach
To collect the data, a questionnaire was constructed and distributed to the study population which consists of accounting academics, students and accounting practitioners.

Findings
The results of this study show evidence that both students and professionals have a lower level of awareness on the FA concept and its importance. The results also confirm there is a significant correlation between, fraud prevention and detection, advantages of the application of FA, the training courses toward the application of FA and the application of FA in the context of Jordan. It has also been confirmed that there is a number of significant factors hinders this implementation in Jordan.

Research limitations/implications
The findings of this study offer many policy implications for regulators and policymakers on the needed relevant information to address and implement FA in education and practice, thereby activating the FA concept in Jordan.

Originality/value
The primary motivation of this study is driven by the limited and inconclusive research on the FA as a monitoring tool, notably there is a high possibility of fraud and misstatement practices due to the agency conflict. This study is the first of its kind to discuss this topic in the context of Jordan. The need to integrating the accounting education within accounting profession regarding FA becomes an urgent need to develop the awareness level of practitioners when it comes to practice of FA.
The Recovering Citizenship Learning Collaborative: a system-wide intervention to increase citizenship practices and outcomes
Authors: Flanagan Elizabeth , Tondora Janis , Harper Annie , Benedict Patricia , Giard Julienne , Bromage Billy , Williamson Bridgett , Acker Paul , Bragg Cheri , Adams Virginia , Rowe Michael 
Published: August 2023

Purpose
This paper aims to describe the Recovering Citizenship Learning Collaborative (RCLC), a training, consultation and implementation effort for 13 local mental health authorities and two state hospitals.

Design/methodology/approach
The learning collaborative used a Recovering Citizenship approach, which holds that recovery occurs in the context of people’s lives in their communities and society, that is, their citizenship. The RCLC was implemented by the Connecticut Department of Mental Health and Addiction Services (DMHAS) in the USA and the Yale Program for Recovery and Community Health along with lived experience leaders. The RCLC supported system change through training DMHAS staff on concepts of recovery and citizenship and developing agency action plans, with the long-term goal of improving citizenship-oriented care at the agency-level and recovery and citizenship-related outcomes for people receiving services.

Findings
Lessons learned include the importance of assessing organizational readiness for change, addressing leadership investment and attention to systemic barrier, and offering tools to promote structure and accountability. Next steps are supporting agency action plans through technical assistance, state-wide educational offerings and a resource library.

Research limitations/implications
Systemic barriers are considerable and must be addressed before system transformation is possible.

Practical implications
The authors are hopeful that the RCLC has been part of overcoming those challenges and can be a tool for building foundations for improving citizen practices and people’s citizenship-related outcomes.

Social implications
Next steps are sustaining agency action plans, ongoing agency-specific technical assistance, ongoing state-wide educational offerings and a resource library.

Originality/value
The RCLC has provided tools and supports to build the foundation for improved citizenship practices and client outcomes at the multiagency system level.
Revolutionizing libraries: leveraging the deep Web as a lasting solution for displacement and replacement challenges
Authors: Bashorun Musediq Tunji , Ajani Yusuf Ayodeji , Fagbola Olaronke Oyinlola 
Published: August 2023

PurposeThis paper aims to explore the deep Web as a solution for displacement and replacement challenges in libraries, addressing the challenges, benefits, strategies and case studies.Design/methodology/approachThe paper synthesizes existing literature on deep Web integration in libraries, providing a comprehensive analysis of insights from scholarly articles, case studies and expert opinions.FindingsThe deep Web grants libraries access to unique content, improving information access, fostering collaboration and enabling personalized content. However, security, privacy, ethics and data protection must be considered.Originality/valueThis paper contributes to the literature by providing a comprehensive examination of deep Web integration in libraries, offering valuable recommendations for navigating the changing landscape and leveraging the deep Web’s potential.
The impact of job loss on mental health during the COVID-19 crisis in Tunisia: analysis based on counterfactual decomposition approach
Authors: Nasri Khaled , Ben Abdallah Mohamed Anis , Amri Fethi 
Published: August 2023

Purpose
This study aims to investigate the impact of job loss on the mental health of individuals in Tunisia during the COVID-19 crisis.

Design/methodology/approach
In this research, the authors use the counterfactual decomposition technique and the potential outcome approach. In the first part, the authors calculated mental health indicators for all individuals included in the sample based on the World Health Organization-5 items. The individuals were then grouped into two subpopulations: the first group included those who had lost their jobs and the second group included individuals whose status in the labor market had remained unchanged. In the second part, the authors used the Blinder and Oaxaca decomposition to explain the mean difference in the mental health scores between the two groups and determine the factors contributing to this difference.

Findings
The empirical results identified symptoms of depressed mood, decreased energy and loss of interest in several individuals. Based on these three symptoms, the authors were able to classify individuals into three types of depression: mild, moderate and severe. In addition, it appeared that job loss had significantly contributed to the worsening mental health of the individuals.

Originality/value
Although the psychological impact of the COVID-19 outbreak among health-care professionals has been the subject of other studies in health literature on Tunisia, to the best of the authors’ knowledge, no research has addressed the impact of job loss on the mental health of Tunisian workers. Thus, this study fills this gap in the literature.
Quality indicators of effective teacher-created summative assessment
Authors: Brownlie Nicole , Burke Katie , van der Laan Luke 
Published: August 2023

Purpose
The current literature on school teacher-created summative assessment lacks a clear consensus regarding its definition and key principles. The purpose of this research was therefore to arrive at a cohesive understanding of what constitutes effective summative assessment.

Design/methodology/approach
Conducting a systematic literature review of 95 studies, this research adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The objective was to identify the core principles governing effective teacher-created summative assessments.

Findings
The study identified five key principles defining effective summative assessment creation: validity, reliability, fairness, authenticity and flexibility.

Research limitations/implications
The expansiveness of education research is such that not all relevant studies may have been identified, particularly outside of mainstream databases. This study considered only the school environment, so contextual limitations will exist.

Originality/value
To the best of the authors’ knowledge, this study contributes original insights by proposing a holistic definition that can facilitate consensus-building in further research. The assimilation of core principles guided the development of quality indicators beneficial for teacher practice. The comprehensive definition, key principles and quality indicators offer a unique perspective on summative assessment discourse.