bluuebunny/crossref_metadata_2025_split huggingface dataset:
GOProFormer: A Multi-modal Transformer Method for Gene Ontology Protein Function Prediction
Authors: Kabir Anowarul , Shehu Amarda 
Published: October 2022

AbstractProtein Language Models (PLMs) are shown capable of learning sequence representations useful for various prediction tasks, from subcellular localization, evolutionary relationships, family membership, and more. They have yet to be demonstrated useful for protein function prediction. In particular, the problem of automatic annotation of proteins under the Gene Ontology (GO) framework remains open. This paper makes two key contributions. It debuts a novel method that leverages the transformer architecture in two ways. A sequence transformer encodes protein sequences in a task-agnostic feature space. A graph transformer learns a representation of GO terms while respecting their hierarchical relationships. The learned sequence and GO terms representations are combined and utilized for multi-label classification, with the labels corresponding to GO terms. The method is shown superior over recent representative GO prediction methods. The second major contribution in this paper is a deep investigation of different ways of constructing training and testing datasets. The paper shows that existing approaches under- or over-estimate the generalization power of a model. A novel approach is proposed to address these issues, resulting a new benchmark dataset to rigorously evaluate and compare methods and advance the state-of-the-art.
Inference of Presynaptic Connectivity from Temporally Blurry Spike Trains by Supervised Learning
Authors: Vareberg Adam D. , Eizadi Jenna , Ren Xiaoxuan , Hai Aviad 
Published: October 2022

ABSTRACTReconstruction of neural network connectivity is a central focus of neuroscience. The ability to use neuronal connection information to predict activity at single unit resolution and decipher its effect on whole systems can provide critical information about behavior and cognitive processing. Neuronal sensing modalities come in varying forms, but there is yet to exist a modality that can deliver readouts that sufficiently address the spatiotemporal constraints of biological nervous systems. This necessitates supplementary approaches that rely on mathematical models to mitigate physical limitations and decode network features. Here, we introduce a simple proof-of-concept model that addresses temporal constraints by reconstructing presynaptic connections from temporally blurry data. We use a variation of the perceptron algorithm to process firing rate information at multiple time constraints for a heterogenous feed-forward network of excitatory, inhibitory, and unconnected presynaptic units. We evaluate the performance of the algorithm under these conditions and determine the optimal learning rate, firing rate, and the ability to reconstruct single unit spikes for a given degree of temporal blur. We then test our method on a physiologically relevant configuration by sampling network subpopulations of leaky integrate-and-fire neuronal models displaying bursting firing patterns and find comparable learning rates for optimized reconstruction of network connectivity. Our method provides a recipe for reverse engineering neural networks based on limited data quality that can be extended to more complicated readouts and connectivity distributions relevant to multiple brain circuits.
Molecular basis ofFAAH-OUT-associated human pain insensitivity
Authors: Mikaeili Hajar , Habib Abdella M. , Yeung Charlix , Santana-Varela Sonia , Luiz Ana P. , Panteleeva Kseniia , Zuberi Sana , Athanasiou-Fragkouli Alkyoni , Houlden Henry , Wood John N. , Okorokov Andrei L. , Cox James J. 
Published: October 2022

AbstractChronic pain affects millions of people worldwide. Studying pain insensitive individuals helps to identify novel analgesic strategies. Here we report how the recently discoveredFAAH-OUTlncRNA-encoding gene, which was found from studying a pain insensitive patient with reduced anxiety and fast wound healing, regulates the adjacent key endocannabinoid system geneFAAH, which encodes the anandamide-degrading fatty acid amide hydrolase enzyme. We demonstrate that the disruption inFAAH-OUTlncRNA transcription leads to DNMT1-dependent DNA methylation within theFAAHpromoter. In addition,FAAH-OUTcontains a conserved regulatory element, FAAH-AMP, that acts as an enhancer forFAAHexpression. Furthermore, using transcriptomic analyses we have uncovered a network of genes that are dysregulated from disruption of theFAAH-FAAH-OUTaxis, thus providing a coherent mechanistic basis to understand the human phenotype observed and a platform for development of future gene and small molecule therapies.
Constructed Synchronized Multimodal Signalling in Great Bowerbirds
Authors: Endler John A. , Meehan Selina , Rodrigues Aida 
Published: October 2022

AbstractGreat bowerbird males build bowers for attracting females for mating. Bowers consist of a thatched twig tunnel (avenue) which opens onto two flat courts covered with objects. Male displays on a court are seen by a female from within the avenue. She sees and hears displays through the avenue entrance but can only see the male’s head and objects in his bill as it passes repeatedly across the entrance. We investigated bower acoustic properties by playing standard sounds from multiple court positions and recorded the resulting sounds at the female’s typical avenue head position within the avenue. Bower geometry significantly affects both his acoustic and visual display components and physically synchronizes them as he repeatedly moves in and out of the female’s view. Consequently, complex neural circuitry is unnecessary for linking sound to vision. Experimentally removing bower objects shows that objects significantly increase higher frequencies, hence bandwidth and loudness received inside the avenue. Great Bowerbird bowers produce a synchronized multimodal signal to females which may increase male attractiveness more than if a single sensory mode were used. This multimodal signal is unusual in that it is constructed rather than being part of the body and synchronized as a result of physics rather than neurons.Summary StatementBowerbird bower geometry jointly effects both visual and auditory signal components and synchronizes them without the need for additional neural circuitry.
Managerial ability and informative earnings management: the role of CEO-commissioner relationship and board independence
Authors: Putra Adhitya Agri 
Published: October 2022

Purpose
The purpose of this study is to examine the effect of managerial ability on informative earnings management (hereafter IEM) and to examine the moderating role of the chief executive officer and board of commissioner relationship (hereafter CEO-commissioner relationship) and board independence between managerial ability and IEM.

Design/methodology/approach
Sample consists of 864 firm-years listed on the Indonesian Stock Exchange. Informative earnings management is measured by the relationship between discretionary accruals and earnings growth. Managerial ability is measured by data envelopment analysis. This research uses firm-effect logistic regression to perform the data analysis.

Findings
Based on firm-effect logistic regression, managerial ability increases IEM. It confirms the managers’ stewardship behavior where managers tend to engage in IEM and provide higher quality information for shareholders. The result also shows that the absence of a CEO-commissioner relationship and higher board independence leads higher ability managers to engage more in IEM. It confirms the role of corporate governance to reduce managers-shareholders conflict (in the context of agency theory) or to facilitate higher ability managers to act as both controlling and minority shareholders’ stewards (in the context of stewardship theory) by engaging more in IEM and providing higher-quality information.

Originality/value
This research contributes to filling the previous studies gap that provides conflicting results on managerial ability and earnings management by considering earnings management motivations, CEO-commissioner relationship and board independence. This research also contributes to providing new evidence of managerial ability, IEM, CEO-commissioner relationship and board independence, especially in Indonesia.
Unions' role in intersectional age discrimination litigation cases
Authors: Katz Marsha , LaVan Helen 
Published: October 2022

PurposeHow older workers pursue their employment discrimination claims is the focus of this study. This is part of the broader question of how older, unionized employees pursuing their statutory rights fare in litigation and how unions might organize and subsequently better protect older workers who have been discriminated against.Design/methodology/approachThis study is a random sample of 1889 litigated age discrimination cases in Federal courts using NVivo to conduct a content analysis on unionization, individual, organizational and legal variables.FindingsAn analysis of case characteristics and outcomes in cases filed under the Age Discrimination in Employment Act indicated that older unionized workers pursuing their claims are more likely to have rulings in their favor. Other demographic characteristics of the cases in which unionized workers prevailed include seniority, disability, filing under Title VII and cases involving retaliation.Research limitations/implicationsImportantly, empirical legal scholarship, using the case as the unit of analysis, will significantly add to the understanding of how age discrimination might be reduced through litigation. Empirical legal scholarship strategies would also suggest identifying labor tribunal or arbitration cases. Using content analysis would allow for a deep understanding at the micro level of the context that led to the charges of age (or other types) of discrimination.Practical implicationsThis study offers evidence that union representation can add value when older employees are pursuing their rights in litigation.Originality/valueThis research focuses on individuals who have actually been discriminated against using empirical legal scholarship, content analysis and big data analytics.
Measuring consumer perception of overall brand equity drivers for m-payments
Authors: Sankaran Raja , Chakraborty Shibashish 
Published: October 2022

PurposeThe objective of this study was to investigate the relationship between various drivers of consumer-based brand equity (CBBE) for m-payments and to demonstrate practical relevance. The study examined the indirect relationship between m-payment drivers and satisfaction and their subsequent association with brand equity drivers in the context of m-payments.Design/methodology/approachA survey was administered to a total of 725 respondents. Structural equation modeling, SPSS AMOS and a multi-mediation model using process macros were used to analyze the primary data.FindingsThe results of this study corroborate the post-use driver (satisfaction) and trust mediates drivers of m-payments (perceived usefulness and perceived ease of use) with overall brand equity. Satisfaction and trust exert a positive influence on overall brand equity, and this research will help organizations devise strategies to retain consumers, offer loyalty schemes and brand effectively to bundle services.Originality/valueNovelty was achieved in this study by extending the technology acceptance model to determine the association between m-payment drivers and satisfaction and their subsequent association with overall brand equity, thus providing practical implications.
Big data and big disaster: a mechanism of supply chain risk management in global logistics industry
Authors: Li Lixu , Gong Yeming , Wang Zhiqiang , Liu Shan 
Published: October 2022

PurposeAlthough big data may enhance the visibility, transparency, and responsiveness of supply chains, whether it is effective for improving supply chain performance in a turbulent environment, especially in mitigating the impact of COVID-19, is unclear. The research question the authors addressed is: How do logistics firms improve the supply chain performance in COVID-19 through big data and supply chain integration (SCI)?Design/methodology/approachThe authors used a mixed-method approach with four rounds of data collection. A three-round survey of 323 logistics firms in 26 countries in Europe, America, and Asia was first conducted. The authors then conducted in-depth interviews with 55 logistics firms.FindingsIn the first quantitative study, the authors find mediational mechanisms through which big data analytics technology capability (BDATC) and SCI influence supply chain performance. In particular, BDATC and SCI are two second-order capabilities that help firms develop three first-order capabilities (i.e. proactive capabilities, reactive capabilities, and resource reconfiguration) and eventually lead to innovation capability and disaster immunity that allow firms to survive in COVID-19 and improve supply chain performance. The results of the follow-up qualitative analysis not only confirm the inferences from the quantitative analysis but also provide complementary insights into organizational culture and the institutional environment.Originality/valueThe authors contribute to supply chain risk management by developing a three-level hierarchy of capabilities framework and finding a mechanism with the links between big data and big disaster. The authors also provide managerial implications for logistics firms to address the new management challenges posed by COVID-19.
State of care for EU mobile workers' rights in the Dutch meat sector in times of, and beyond, COVID-19
Authors: Berntsen Lisa , Böcker Anita , De Lange Tesseltje , Mantu Sandra , Skowronek Natalia 
Published: October 2022

PurposeWith a focus on the position of EU mobile workers in the Dutch meat industry, this article discusses the multi-level State efforts to enhance protection of workers who experienced limited protection of existing State and private enforcement institutions. The COVID-19 pandemic, with virus outbreaks at Dutch meat plants, fuelled public and political will to structurally improve these workers' precarious work and living conditions. Yet, the process of policy change is slow. The authors show it is the gradual transformation in the institutional environment that the State needs to counter to become more protective for EU mobile workers.Design/methodology/approachUsing the gradual institutional change approach and the concept of State ignorance, the authors examine State responses drawing on interviews with expert stakeholders in the public and private domain, public administration records and newspaper articles.FindingsThrough knowledge creation, boosted social dialogue mechanisms, enhanced enforcement capacity and new housing legislation, the Dutch State focuses on countering gradual institutional change through which existing institutions lost their effectiveness as protectors of EU mobile workers. The organization of work is, nevertheless, not (yet) fundamentally addressed with tighter public legislation.Originality/valueThe findings contribute to a more nuanced understanding of the role of the State as multifaceted actor in institutional change processes towards increased protection for EU mobile workers.
Serendipity in management studies: a literature review and future research directions
Authors: Balzano Marco 
Published: October 2022

PurposeManagement research on serendipity, which is defined as a search that leads to an unintended discovery, has increased considerably over the last three decades. In this article, management research on serendipity (up to the end of 2021) is reviewed and synthesised.Design/methodology/approachA bibliometric analysis was conducted on 85 peer-reviewed articles extracted from the Scopus database, which was then integrated with a systematic literature review.FindingsThe bibliometric analysis revealed that management literature on serendipity is framed around four main thematic areas: conceptual boundaries, conditions favouring serendipity and outcomes, foreign market entry and the relationship between serendipity, networks and assets. A systematic literature review was then conducted on each of the identified clusters.Originality/valueThe present article offers a systematised view of the extant body of research on serendipity in management studies. Based on the findings, the main implications and future research agendas are discussed.
Modeling and analysis of a sustainable supply chain with fairness concerns and green-sensitive consumer demand
Authors: Shi Ping , Han Kun , Hou Rui 
Published: October 2022

PurposeWith the global spread of environmental education, environmental awareness is becoming increasingly important in daily life and economic activities. Sustainable development, as the most effective development approach to address global climate change, has gradually become a research hotspot in countries around the world. The authors combine sustainable development with supply chain management and incorporate into the study the objective issue of corporate fairness preferences in real society to explore the pricing and product greenness decision problem of a secondary sustainable supply chain consisting of a manufacturer producing green products and a retailer selling green products. In particular, the authors explore how supply chain decisions change when both the manufacturer and the retailer focus on fairness and how this fairness behavior affects pricing and product greenness decisions in sustainable supply chains.Design/methodology/approachThe authors consider that the manufacturers' greening efforts lead to expanded demand at the retail end. Upstream and downstream firms in the supply chain have preferences for the fairness of transactions. The impact of the fairness behavior of upstream and downstream firms in the supply chain on supply chain decisions is explored by building a Stackelberg game model.FindingsThe results of this study show that the fairness concern behavior of manufacturers and retailers in the supply chain has an impact on product greenness, product pricing and corporate profits.Originality/valueThis study on the fairness concern behavior of supply chain firms integrates behavioral economics and supply chain management. First, the authors consider the equilibrium problem of supply chain members in the centralized channel when there are no fairness preferences. Second, the decision problem of firms in the decentralized channel when fairness is considered and when fairness preferences are not considered is explored. The authors compare these three cases to derive the corresponding propositions. Finally, the authors verify the previous conclusions and draw other conclusions using arithmetic analysis.
Plant species biogeographic origin shapes their current and future distribution on the world's highest island mountain
Authors: Trethowan Liam A. , Walker Barnaby E. , Bachman Steven P. , Heatubun Charlie , Puradyatmika Pratita , Rustiami Himmah , Utteridge Timothy M. A. 
Published: October 2022

Abstract

In New Guinea, low elevations are thought to be dominated by plant species with biogeographic origins in Sunda (Borneo, Sumatra, Java, Mainland Asia) and high elevations by species from Sahul (Australia and New Guinea).

In regions where frequent surveys of the flora are unfeasible, herbarium specimens collected over time offer an opportunity to study the co‐occurrence of species. Over 7000 collections have been made on New Guinea's Mount Jaya allowing us to examine species presence under current and future temperatures.

Applying a Bayesian phylogenetic mixed effects model to the Mount Jaya elevation gradient, we show that species of Sunda origin are more likely to occupy warmer lowlands and Sahul species cooler higher elevations.

Using the model to predict species distributions under a 2°C increase, we find that Sahul species are less likely to tolerate future temperatures, especially below 1000 m. Predictions also show a potential increase in species richness across the gradient. It is unclear if these increases are possible due to limits imposed by the species area relationship.

Synthesis. These results emphasise how biogeographic origin influences current and future species distributions on tropical mountains. It remains to be seen how our results link to traits that dictate species' ability to tolerate increasing temperatures.
The role of stakeholder engagement in sustainable water resource management in South Africa
Authors: Adom Richard Kwame , Simatele Mulala Danny 
Published: October 2022

AbstractThe effort to promote participation in decision and policy making, as well as programmes in water management is designed to give everyone who has a stake an opportunity to express an opinion or a preference. Although stakeholder engagements are welcomed initiatives, which lead to public participation, they are often embraced in ideological strife and political propaganda. Nevertheless, stakeholder engagement and participation are prerequisites for any innovative sustainable system of water resource management in post‐independence South Africa. Additionally, stakeholder engagement is an essential component of reforms and a bedrock in developing comprehensive pieces of legislation and policies for sustainable water resource management. It has been a legal requirement for adopting environmental legislation, such as the National Environmental Management Act of 1998, the 1996 Constitution, the National Water Act and the legal instrument for its implementation— the National Water Resource Strategy. In spite of these legislative requirements, the country is yet to realize an inclusive and practical way to engage stakeholders in the water management at the local level. This paper explores the structural and systematic constraints that hinder effective participation of stakeholders in water management. A purposive sampling technique to survey 60 participants from the water sector is used in the study. The findings identified lack of community empowerment and capacity building, inconsistencies in regard to roles and responsibilities of stakeholders, and apathy towards public engagements as fundamental barriers to their effective participation. It is observed that unless efforts are made to enable marginal voices to be raised and heard, claims to inclusiveness and transformation in the water sector will remain only a theory.