bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons
Authors: Bell Andrew M. , Utting Charlotte , Dickie Allen C. , Kucharczyk Mateusz W. , Quillet Raphaëlle , Gutierrez-Mecinas Maria , Razlan Aimi N.B. , Cooper Andrew H. , Lan Yuxuan , Hachisuka Junichi , Weir Greg A. , Bannister Kirsty , Watanabe Masahiko , Kania Artur , Hoon Mark A. , Macaulay Iain C. , Denk Franziska , Todd Andrew J. 
Published: August 2023

AbstractThe anterolateral system (ALS) is a major ascending pathway from the spinal cord that projects to multiple brain areas and underlies the perception of pain, itch and skin temperature. Despite its importance, our understanding of this system has been hampered by the considerable functional and molecular diversity of its constituent cells. Here we use fluorescence-activated cell sorting to isolate ALS neurons belonging to the Phox2a-lineage for single-nucleus RNA sequencing. We reveal five distinct clusters of ALS neurons (ALS1-5) and document their laminar distribution in the spinal cord usingin situhybridization. We identify 3 clusters of neurons located predominantly in laminae I-III of the dorsal horn (ALS1-3) and two clusters with cell bodies located in deeper laminae (ALS4 & ALS5). Our findings reveal the transcriptional logic that underlies ALS neuronal diversity in the adult mouse and uncover the molecular identity of two previously identified classes of projection neurons. We also show that these molecular signatures can be used to target groups of ALS neurons using retrograde viral tracing. Overall, our findings provide a valuable resource for studying somatosensory biology and targeting subclasses of ALS neurons.Significance StatementThe anterolateral system (ALS) is a major ascending pathway from the spinal cord that underlies perception of pain, itch and skin temperature. It is therefore an important target for the development of new treatments for chronic pain. Our understanding of this system has been hampered by the considerable diversity of its constituent cells. Here we dissect the complex heterogeneity of these cells by using high-resolution RNA sequencing. We reveal five distinct types of ALS neurons, which are differentially distributed within the spinal cord, and probably represent functional populations. Our data provide novel insights into the molecular architecture of the ALS, and will be important for future studies to define the roles of different ALS cell types in sensory processing.
Expression-based machine learning models for predicting plant tissue identity
Authors: Palande Sourabh , Arsenault Jeremy , Basurto-Lozada Patricia , Bleich Andrew , Brown Brianna N. I. , Buysse Sophia F. , Connors Noelle A. , Adhikari Sikta Das , Dobson Kara C. , Guerra-Castillo Francisco Xavier , Guerrero-Carrillo Maria F. , Harlow Sophia , Herrera-Orozco Héctor , Hightower Asia T. , Izquierdo Paulo , Jacobs MacKenzie , Johnson Nicholas A. , Leuenberger Wendy , Lopez-Hernandez Alessandro , Luckie-Duque Alicia , Martínez-Avila Camila , Mendoza-Galindo Eddy J. , Plancarte David , Schuster Jenny M. , Shomer Harry , Sitar Sidney C. , Steensma Anne K. , Thomson Joanne Elise , Villaseñor-Amador Damián , Waterman Robin , Webster Brandon M. , Whyte Madison , Zorilla-Azcué Sofía , Montgomery Beronda L. , Husbands Aman Y. , Krishnan Arjun , Percival Sarah , Munch Elizabeth , VanBuren Robert , Chitwood Daniel H. , Rougon-Cardoso Alejandra 
Published: August 2023

ABSTRACTThe selection ofArabidopsisas a model organism played a pivotal role in advancing genomic science, firmly establishing the cornerstone of today ‘s plant molecular biology. Competing frameworks to select an agricultural- or ecological-based model species, or to decentralize plant science and study a multitude of diverse species, were selected against in favor of building core knowledge in a species that would facilitate genome-enabled research that could assumedly be transferred to other plants. Here, we examine the ability of models based onArabidopsisgene expression data to predict tissue identity in other flowering plant species. Comparing different machine learning algorithms, models trained and tested onArabidopsisdata achieved near perfect precision and recall values using the K-Nearest Neighbor method, whereas when tissue identity is predicted across the flowering plants using models trained onArabidopsisdata, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64, depending on the algorithm used. Below-ground tissue is more predictable than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance fromArabidopsis. This suggests that gene expression signatures rather than marker genes are more valuable to create models for tissue and cell type prediction in plants. Our data-driven results highlight that, in hindsight, the assertion that knowledge fromArabidopsisis translatable to other plants is not always true. Considering the current landscape of abundant sequencing data and computational resources, it may be prudent to reevaluate the scientific emphasis onArabidopsisand to prioritize the exploration of plant diversity.
XRE Transcription Factors Conserved inCaulobacterand φCbK Modulate Adhesin Development and Phage Production
Authors: McLaughlin Maeve , Fiebig Aretha , Crosson Sean 
Published: August 2023

AbstractUpon infection, transcriptional shifts in both a host bacterium and its invading phage determine host and viral fitness. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis ofCaulobacterspecies isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation inC. crescentus. We further discovered related XRE TFs across the classAlphaproteobacteriaand its phages, including the φCbK Caulophage, suggesting that members of this gene cluster impact host-phage interactions. Here we show that that a closely related group of XRE proteins, encoded by bothC. crescentusand φCbK, can form heteromeric associations and control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK XRE paralog,tgrL, is highly expressed at the earliest stages of infection and can directly repress transcription ofhfiA, a potent holdfast inhibitor, andgafYZ, a transcriptional activator of prophage-like gene transfer agents (GTAs) encoded on theC. crescentuschromosome. XRE proteins encoded from theC. crescentuschromosome also directly repressgafYZtranscription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting host XRE transcription factors reduced φCbK burst size, while overexpressing these genes or φCbKtgrLrescued this burst defect. We conclude that an XRE TF gene cluster, shared byC. crescentusand φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.
The focal adhesion protein talin is a mechanically-gated A-kinase anchoring protein (AKAP)
Authors: Kang Mingu , Otani Yasumi , Guo Yanyu , Yan Jie , Goult Benjamin T. , Howe Alan K. 
Published: August 2023

AbstractThe cAMP-dependent protein kinase (Protein Kinase A; PKA) is a ubiquitous, promiscuous kinase whose activity is focused and specified through subcellular localization mediated by A-kinase anchoring proteins (AKAPs). PKA has complex roles as both an effector and a regulator of integrin-mediated cell adhesion to the extracellular matrix (ECM). Recent observations demonstrate that PKA is an active component of focal adhesions (FA), intracellular complexes coupling ECM-bound integrins to the actin cytoskeleton, suggesting the existence of one or more FA AKAPs. Using a combination of a promiscuous biotin ligase fused to PKA type-IIα regulatory (RIIα) subunits and subcellular fractionation, we identify the archetypal FA protein talin1 as an AKAP. Talin is a large, mechanosensitive scaffold that directly links integrins to actin filaments and promotes FA assembly by recruiting additional components in a force-dependent manner. The rod region of talin1 consists of 62 α-helices bundled into 13 rod domains, R1-R13. Direct binding assays and nuclear magnetic resonance spectroscopy identify helix41 in the R9 subdomain of talin as the PKA binding site. PKA binding to helix41 requires unfolding of the R9 domain, which requires the linker region between R9 and R10. Finally, single-molecule experiments with talin1 and PKA, and experiments in cells manipulated to alter actomyosin contractility demonstrate that the PKA-talin interaction is regulated by mechanical force across the talin molecule. These observations identify the first mechanically-gated anchoring protein for PKA, a new force-dependent binding partner for talin1, and thus a new mechanism for coupling cellular tension and signal transduction.
Acquired stress resilience through bacteria-to-nematode horizontal gene transfer
Authors: Pandey Taruna , Kalluraya Chinmay , Wang Bingying , Xu Ting , Huang Xinya , Guang Shouhong , Daugherty Matthew D. , Ma Dengke K. 
Published: August 2023

AbstractNatural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode generml-3, which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins inC. elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides.C. elegans rml-3is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly,rml-3deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterialrml-3homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.
What drives small and medium enterprises to establish and terminate banking relationships?
Authors: Afridi Muhammad Asim , Tahir Muhammad 
Published: August 2023

PurposeThis paper investigates the factors crucial for small and medium enterprises (SMEs) in establishing business relationships with banks in Pakistan.Design/methodology/approachTo investigate how SMEs select banking relationships using criteria, such as decision factors, decision-makers, and decision processes, a comprehensive literature review was used to classify SMEs' decision factors for bank selection. A survey questionnaire was distributed to 200 SMEs, randomly selected from the Small and Medium Enterprise Development Authority database in Pakistan. Probit/Tobit model is estimated to explain the behavior of SMEs.FindingsThe results reveal that SMEs consider a bank's Reputation, Price, and Location essential while establishing bank relationships. SMEs tend to terminate relationships with banks when the Price and Location of the bank are considered essential factors in the relationship with the banks. Price and Location are necessary for SMEs to reduce banking relationships. The SMEs also tend to reduce if they get attractive offers, or the SMEs are recommended to make a banking relationship. This study also provides intuitions for bank policymakers to design policies to retain SME customers and attract new business relationships.Practical implicationsThe research emphasizes the importance of competitive and transparent pricing strategies in designing products for SMEs. Banks must prioritize their Reputation and credibility to attract and retain relationships with SMEs.Originality/valueThe study attempts to provide evidence on the SME-Bank relationship focusing on the factors that are crucial for SMEs to decide while establishing business relationships with banks. Also, most of the related literature focuses on developed countries; this research adds to the literature on SMEs' behavior, particularly in a developing country's context.
Reading the Tulsa Race Massacre: a study exploring a white reader’s shifts in stance across genres of historical text
Authors: Bene Emma , Robillard Stephanie M. 
Published: August 2023

PurposeUsing a discourse analytic approach, the purpose of this paper is to examine how genre impacts white readers when reading about historic acts of racial violence. Specifically, this study explores one white high school student’s stance-taking as she read an informational text and an eyewitness narrative about the Tulsa Race Massacre.Design/methodology/approachThis study used discourse analysis (Gee, 1999) and the think-aloud method (Pressley and Afflerbach, 1996) to explore the white student’s interactions with genres of historical texts. The authors coupled iterative coding and memoing with discourse analysis to analyze the stances she adopted while reading.FindingsThe findings illustrate that the informational text allowed for a distancing from the racialized violence in the text, whereas the narrative created an opportunity for more connection to those who experienced the violence.Originality/valueWhile genre and reader response has long been explored in English Education research, little research has examined the impact of genre on reading historical texts. This study demonstrates the influence that genre may have on white readers’ emotional responses and stance-taking practices when reading about historic acts of racial violence.
Determinants of housing affordability in the USA
Authors: Iqbal Javed , Brdedthauer Jeff , Decker Christopher S. 
Published: August 2023

Purpose
This study aims to identify the determinants of housing affordability in an effort to inform policy.

Design/methodology/approach
The authors use econometric analysis to determine variables that impact housing affordability in the USA.

Findings
The authors find that affordability depends on a number of demographic factors as well as physical characteristics of properties, including average age of homeowner, family size and average dwelling square footage. The authors also find that vacancy rates, increase in house price and median family income also have a significant impact on housing affordability. Additionally, the authors find that households with high-cost burdens are more vulnerable to mortgage rates and property taxes than those with moderate-cost burdens. As a result, changes in economic or policy variables tend to have a disproportionate impact on high-cost-burdened households, and they are more vulnerable to economic and policy shocks.

Originality/value
To date, the literature has not done a systematic investigation of housing affordability using detailed census data.
Toward a common humanitarian supply chain process model: the Frontline Humanitarian Logistics Initiative
Authors: Saïah Félicia , Vega Diego , Kovács Gyöngyi 
Published: August 2023

PurposeThis study focuses to develop a common humanitarian supply chain process model (HSCPM) that enables effective enterprise resource planning (ERP) systems for NGOs, and the study also investigates the role of modularity as a dynamic capability that supports creating such model.Design/methodology/approachA multifocus group study was performed as part of a larger project, the Frontline Humanitarian Logistics Initiative, aiming to establish a common data model that would serve as the backbone of humanitarian ERP systems. Fourteen international humanitarian organizations (IHOs) participated in the process, reaching a consensus on the structure of the process model.FindingsAn HSCPM was proposed based on the consensus reached across IHOs. Four degrees of customization differentiating between “generic,” “tailored,” “specific,” and “unique” processes are presented and discussed.Research limitations/implicationsThe findings show modularity applied to process as a mean to create dynamic efficiencies and position the modular process model within the dynamic capabilities framework, supporting supply chain responsiveness and expanding the literature on supply chain management (SCM), dynamic capabilities, and humanitarian logistics.Practical implicationsThis research proposes a consensus-based data model, facilitating the advancement of ERP systems in the humanitarian context and lays a foundation for interoperability among ERP systems across diverse IHOs.Originality/valueFirst attempt to elucidate the specific characteristics and unique processes defining an HSCPM, this study reached an unprecedented consensus for the humanitarian sector, setting the base toward an industry standard.
A bibliometric and content analysis discourse on business application of blockchain technology
Authors: Chandel Ajay , Bhanot Neeraj , Sharma Rahul 
Published: August 2023

PurposeThe article aims to provide a bibliometric and content analysis of the business application of blockchain technology.Design/methodology/approachBibliometric analysis and content analysis were undertaken to accomplish the stated objectives of the study.FindingsThe results revealed publication and country collaboration trends, declining, emerging, and niche research areas, the topmost influential articles, authors, and most relevant journals.Originality/valueAs researchers have been myopic towards some mainstream research agendas studying the specific contexts of blockchain applications, this research believes a holistic approach to understanding blockchain technology's versatility to disrupt different business processes across a myriad of industries is lacking. In addition, to strengthen the research's conclusions, a content analysis of the most significant articles is conducted as part of the study.
Semantic web and machine learning techniques addressing semantic interoperability in Industry 4.0
Authors: Hafidi Mohamed Madani , Djezzar Meriem , Hemam Mounir , Amara Fatima Zahra , Maimour Moufida 
Published: August 2023

Purpose
This paper aims to offer a comprehensive examination of the various solutions currently accessible for addressing the challenge of semantic interoperability in cyber physical systems (CPS). CPS is a new generation of systems composed of physical assets with computation capabilities, connected with software systems in a network, exchanging data collected from the physical asset, models (physics-based, data-driven, . . .) and services (reconfiguration, monitoring, . . .). The physical asset and its software system are connected, and they exchange data to be interpreted in a certain context. The heterogeneous nature of the collected data together with different types of models rise interoperability problems. Modeling the digital space of the CPS and integrating information models that support cyber physical interoperability together are required.

Design/methodology/approach
This paper aims to identify the most relevant points in the development of semantic models and machine learning solutions to the interoperability problem, and how these solutions are implemented in CPS. The research analyzes recent papers related to the topic of semantic interoperability in Industry 4.0 (I4.0) systems.

Findings
Semantic models are key enabler technologies that provide a common understanding of data, and they can be used to solve interoperability problems in Industry by using a common vocabulary when defining these models.

Originality/value
This paper provides an overview of the different available solutions to the semantic interoperability problem in CPS.
The non-linear impact of financial development on income inequality: evidence from dynamic panel threshold model
Authors: Sikhawal Shobhana 
Published: August 2023

PurposeThis study examines the non-linear impact of financial development on income inequality and analyses the mediators through which financial development affects income inequality.Design/methodology/approachThe study uses a dynamic panel threshold method with an endogeneous threshold variable on a comprehensive sample of 85 countries over the period of 1996-2015.FindingsThe author finds that financial development activities increase income inequality in developed countries. However, financial development promotes income equality in developing countries. Further, the study finds that education and institutional quality are the channels through which financial development has non-linear impacts on income inequality.Originality/valueThe study explores relatively new method to examine the nonlinear impact of financial development and also considers new dataset for the main explanatory variable.
Linking supply chain resilience with knowledge management for achieving supply chain performance
Authors: Mukherjee Subhodeep , Nagariya Ramji , Mathiyazhagan K. , Scuotto Veronica 
Published: August 2023

Purpose
Supply chain (SC) and knowledge management (KM) have been studied; still, there is a need to understand how KM can be used for SC resilience and improving the firm’s performance. The purpose of the paper is to study and analyze SC resilience strategies based on KM processes to enhance SC performance considering six SC strategies: SC reengineering, collaboration, SC innovation, SC integration, SC agility and SC risk management.

Design/methodology/approach
By adopting the dynamic capability theory, the empirical research is conducted on a sample of 312 Indian micro, small to medium enterprises. To evaluate 312 samples, the structural equation modeling approach is adopted.

Findings
The study found a is a positive relationship between SC reengineering, SC collaboration, SC integration, SC agility, SC risk management and KM. Nevertheless, the relationship between SC innovation and KM is not significant. This study also found the mediating effect of KM on SC performance, and the results shows that SC reengineering, SC collaboration, SC agility and SC risk management are having complementary mediation, while SC innovation and SC integration did not show any mediation.

Originality/value
This is the only research that integrates resilience strategies and KM for improving SC performance. Using KM, SC reengineering will improve SC performance by enhancing readiness and recovery strategies to avoid SC disruption. KM will improve SC collaboration. It will enhance the SC process’ overall visibility, transparency and so on. Agility leads to increased speed, visibility and flexibility, which aids in dealing with uncertainty in the environment. SCRM entails investments and additional resources (such as equipment and labor) to navigate uncertainty and risks in the SC and improve SC performance.