bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water volume, biological and PCR replicates influence the characterization of deep-sea pelagic fish communities
Authors: Peres Pedro A. , Bracken-Grissom Heather 
Published: August 2024

ABSTRACTThe pelagic deep sea is challenging to investigate due to logistical constraints regarding access and collection of samples, however environmental DNA (eDNA) can potentially revolutionize our understanding of this ecosystem. Although recent advancements are being made regarding eDNA technology and autonomous underwater vehicles, no investigation has been performed to assess the impact of different experimental designs using gear found on many research vessels (i.e., CTD mounted with Niskin bottles). Here, we investigated the effects of sampled water volume, biological and PCR replicates in characterizing deep-sea pelagic biodiversity at the level of species and exact sequence variants (ESVs, representing intraspecific variation). Samples were collected at 450m depth at night in the northern Gulf of Mexico using Niskin bottles, and we targeted the fish community using the MiFish primer (12S rRNA). Our results show that 1L is insufficient to characterize deep-sea pelagic fish communities. The 5L and 10L treatments detected similar community structure (i.e., the combination of number of species and relative occurrence) and numbers of species per biological replicate, but the 10L treatment detected a higher total number of species, more ESVs, and a different community structure when considering ESVs. We found that five biological replicates can detect up to 80% of the species detected in this study in the water collected in both 5L and 10L treatments. PCR replicates also had an important role in species and ESV detection, which implies increasing PCR replicates if water volume is limited. We suggest that future studies collect at least 5L, 5 or more field replicates, and 5-10 PCR replicates to adequately investigate deep-sea pelagic biodiversity using eDNA, considering resource limitations. Our study provides guidance for future eDNA studies and a potential route to expand eDNA studies at a global scale.
Prewetting couples membrane and protein phase transitions to greatly enhance coexistence in models and cells
Authors: Bagheri Yousef , Rouches Mason , Machta Benjamin , Veatch Sarah L. 
Published: August 2024

ABSTRACTBoth membranes and biopolymers can individually separate into coexisting liquid phases. Here we explore biopolymer prewetting at membranes, a phase transition that emerges when these two thermodynamic systems are coupled. In reconstitution, we couple short poly-L-Lysine and poly-L-Glutamic Acid polyelectrolytes to membranes of saturated lipids, unsaturated lipids, and cholesterol, and detect coexisting prewet and dry surface phases well outside of the region of coexistence for each individual system. Notability, polyelectrolyte prewetting is highly sensitive to membrane lipid composition, occurring at 10 fold lower polymer concentration in a membrane close to its phase transition compared to one without a phase transition. In cells, protein prewetting is achieved using an optogenetic tool that enables titration of condensing proteins and tethering to the plasma membrane inner leaflet. Here we show that protein prewetting occurs for conditions well outside those where proteins condense in the cytoplasm, and that the stability of prewet domains is sensitive to perturbations of plasma membrane composition and structure. Our work presents an example of how thermodynamic phase transitions can impact cellular structure outside their individual coexistence regions, suggesting new possible roles for phase-separation-prone systems in cell biology.
Microbial Weathering Analysis of Anshun Tunbao Artifacts
Authors: Abudureyimu Paierzhati , Luo Xiaoyan , Gui Chu , Liu Manchun , Su Xining , Lan Dingsong , Chen Zhi , Lon Jerome Rumdon , Luo Jianfei 
Published: August 2024

AbstractsCultural heritages are the crystallization of human technology, culture and embody the efforts of many craftsmen in ancient times. Wooden cultural heritages are affected by their own materials, and are very susceptible to microbial invasion under suitable temperature and humidity conditions. This project mainly studies the microbial weathering of the core wood carving masks and wooden ancient stage in Anshun Tunpu cultural heritage, and uses scanning electron microscopy, high-throughput sequencing and traditional culture methods to analyze the characteristics of their microbial communities, and finds that the bacteria represented by Pseudomonas, Paenibacillus and Stenotrophomonas, and the fungi represented by Cladosporium, Alternaria and Aspergillus, are the core microorganisms shared by indoor and outdoor cultural heritage. The dominant genera such as Pseudomonas, Stenotrophomonas, and Cladosporium showed lignocellulose deradation ability. By cultivating insect eggs extracted from sampled specimens and analyzing the correlation with surface microbiota, we verified the role of insect eggs as vectors in dispersing key microbial communities. We speculate that these insects are likely to be Anobiidae family. Furthermore, by comparing the microbial compositions under different climatic conditions, we validated the influence of temperature, humidity, vegetation diversity, and microbial intrinsic structures on microbial growth. Therefore, monitoring the surrounding environment is crucial in microbial weathering studies and cultural heritage preservation efforts. This study pioneered the investigation of microbial weathering aspects on unique heritage of the Tuenbao culture, emphasizing the importance of preserving distinctive ethnic cultures. Additionally, it presented a case study on the microbial weathering of wooden artifacts in karst landscape environments.
Understanding the roles of secondary shell hotspots in protein-protein complexes
Authors: Jayadevan Parvathy , Arangasamy Yazhini , Srinivasan Narayanaswamy , Sowdhamini Ramanathan 
Published: August 2024

AbstractHotspots are interfacial residues in protein-protein complexes that contribute significantly to complex stability. Methods for identifying interfacial residues in protein-protein complexes are based on two approaches, namely, (a) distance-based methods, which identify residues that form direct interactions with the partner protein and (b) Accessibility Surface Area (ASA)-based methods, which identify those residues which are solvent-exposed in the isolated form of the protein and become buried upon complex formation. In this study, we introduce the concept of secondary shell hotspots, which are hotspots uniquely identified by the distance-based approach, staying buried in both the bound and isolated forms of the protein and yet forming direct interactions with the partner protein. From the analysis of the dataset curated from Docking Benchmark 5.5, comprising of 94 protein-protein complexes, we find that secondary shell hotspots are more evolutionarily conserved and have distinct Chou-Fasman propensities and interaction patterns compared to other hotspots. Finally, we present detailed case studies to show that the interaction network formed by the secondary shell hotspots is crucial for complex stability and activity. Further, they act as potentially allosteric propagators and bridge interfacial and non-interfacial sites in the protein. Their mutations to any other amino acid types cause significant destabilization. Overall, this study sheds light on the uniqueness and importance of secondary shell hotspots in protein-protein complexes.
rpcFold: residual parallel convolutional neural network to decipher RNA folding from RNA sequence
Authors: Sharma Nandita , Mitra Pralay 
Published: August 2024

AbstractThe complex and versatile structures of the RNA molecules allow them to exhibit a wide range of functionalities in a cell. Precise secondary structure information offers deeper insights into the functionality of many RNA molecules. Earlier approaches primarily relying on the concept of free-energy minimization proved inadequate, as RNA often adopts complex folds that do not adhere strictly to free energy rules, especially with increasing length. Subsequently, learning-based models were introduced, but they struggled with handling cross-family data and tended to avoid longer sequences to mitigate computational overhead and the risk of overfitting or underfitting due to limited data availability. Here, we propose a residual parallel convolutional neural network-based RNA secondary structure prediction model, called rpcFold, which can effectively accommodate RNAs of varying lengths by integrating the sliding window method. Further, we consider all the 16 possible base pairs, including canonical and noncanonical pairs, and compute the base-pairing possibility score for each nucleotide in the sequence using a locally weighted Gaussian function. This helps to gain intricate base pairing information and better understand the long- and short-range interactions. We pass these input features as an image-like representation to our model rpcFold. The rpcFold outperforms the existing works and shows a significant improvement of 15% in the F1-score over the previous best score on the benchmark cross-family dataset. We observe a 7% and 5% enhancement in F1-score and accuracy respectively over the last best score, for within family dataset. Our precise prediction of RNA structures will help in revealing the roles of functional RNAs and advancing the development of biomedical applications based on RNA.
Camouflage in autism: a bibliometric perspective
Authors: Hernández Osvaldo , Durán Leila Regina , Fresno Andrés , Chamorro María Fernanda 
Published: August 2024

Purpose
In response to the challenges posed by the social environment, numerous individuals with autism use coping strategies, engaging in a phenomenon known as “camouflaging” to mask their distinctive traits. Despite the growing attention directed toward this area of study, to date, there are no bibliometric studies delineating the evolution of this research theme. This study aims to analyze scientific research on camouflage and the autistic spectrum published in Web of Science (WoS).

Design/methodology/approach
Articles on camouflage and autism were retrieved from the WoS. The advanced search interface used was “Title, Abstract, Keywords (autistic OR asperger syndrome OR Autism OR ASD AND camouflage OR camouflaging AND Masking).” The analysis and visualization of the selected records and their data were carried out using MS Excel (v16.0) and Biblioshiny (v2.0, R package).

Findings
Following the selection process, a total of 70 articles were included. Notably, the UK emerged as the leading contributor in terms of the number of published articles. Prominent authors in this domain included William Mandy, Laura Hull and Meng-Chuan Lai, who exhibited the highest number of published articles and citations. The Journal of Autism and Developmental Disorders stood out as the most prolific journal. Predominant research themes encompassed camouflage (and its synonyms, masking or compensation), gender differences and mental health.

Originality/value
This study contributes to existing knowledge on this topic, as well as identifying new areas of research related to autism and camouflage. Moreover, it serves as a valuable resource for health-care professionals, including physicians and clinical psychologists, who may seek to augment their understanding and proficiency in the field.
Heuristics and biases in human–algorithm interaction and hotel revenue management override decision-making
Authors: Mohammed Ibrahim , Denizci Guillet Basak 
Published: August 2024

Purpose
This study aims to provide insights into human–algorithm interaction in revenue management (RM) decision-making and to uncover the underlying heuristics and biases of overriding systems’ recommendations.

Design/methodology/approach
Following constructivist traditions, 20 in-depth interviews were conducted with revenue optimisers, analysts, managers and directors with vast experience in over 25 markets and working with different RM systems (RMSs) at the property and corporate levels. The hermeneutics approach was used to interpret and make meaning of the participants’ lived experiences and interactions with RMSs.

Findings
The findings explain the nature of the interaction between RM professionals and RMSs, the cognitive mechanism by which the system users judgementally adjust or override its recommendations and the heuristics and biases behind override decisions. Additionally, the findings reveal the individual decision-maker characteristics and organisational factors influencing human–algorithm interactions.

Research limitations/implications
Although the study focused on human–system interaction in hotel RM, it has larger implications for integrating human judgement into computerised systems for optimal decision-making.

Practical implications
The study findings expose human biases in working with RMSs and highlight the influencing factors that can be addressed to achieve effective human–algorithm interactions.

Originality/value
The study offers a holistic framework underpinned by the organisational role and expectation confirmation theories to explain the cognitive mechanisms of human–system interaction in managerial decision-making.
Critical issues of online learning management in higher educational institutions in a developing country context: examples from Ghana
Authors: Mahama Patrick Yin , Amankwah-Sarfo Fred , Gyedu Francis 
Published: August 2024

PurposeOnline learning has come to stay in a technologically advancing world with increasing populations. The search for ways to make online learning more efficient and effective in some developing countries continues as the accompanying issues in developing country contexts abound. This paper explores the issues that underlie online learning management in a developing country context, focusing on the Moodle, Sakai and Zoom platforms used in some selected public universities in Ghana.Design/methodology/approachThe study relied on the qualitative approach to data collection and a descriptive design for analysis. Using the social constructivism theory, the paper discussed the critical issues students, and to a lesser extent, instructors encounter in their engagement on these platforms for academic learning.FindingsThe study found that the inefficient use of these platforms is due to several factors including the high cost of data, poor perception of the quality of online learning compared to traditional in-person contacts, poor attitude of students, low participation in online learning, lack of computers and poor internet connectivity among others.Research limitations/implicationsIt is important to mention that this study was limited to some selected public universities in Ghana. Data could have been collected from a wider sample including other Ghanaian tertiary institutions or some other developing countries. The similarity of study outcomes in other developing countries, however, suggests that similar results would have been obtained in an international sample.Practical implicationsDespite the robustness of the Learning Management systems in place, the evidence suggests that their utilisation is far less than optimal. However, with relevant policies and the provision of needed technical support, training, provision of equipment like computers for use by both students and instructors and efficient internet connectivity, the LMS platforms could be more efficient for online learning.Originality/valueThe authors conducted this research using original data from interviews in the selected public universities in Ghana. The data was meant to inform the discussion on some of the critical issues that underlie online learning in a developing country context. Although the study relied on data from selected public universities in a single country, its outcomes reflect fundamental issues of online learning in a developing country context which find relevance in available study outcomes.
Achieving project performance goals in extreme resource-constrained environments: the role of bricolage in social enterprise projects
Authors: Jewer Jennifer , Pourasgari Pedram , Jugdev Kam 
Published: August 2024

PurposeAchieving project performance goals in extremely resource-constrained environments, such as those of social enterprises, is challenging. These organizations often employ bricolage – making the most of available resources – to navigate challenging landscapes. This study aims to understand how bricolage capabilities enhance or attenuate organizational project outcomes in resource-constrained social enterprises.Design/methodology/approachAn exploratory survey was conducted to understand project management practices in Canadian social enterprises. Established scales were used to measure constructs with confirmatory factor analysis, and linear regression was employed to analyze relationships.FindingsThe study provides empirical evidence of the positive influence of bricolage on organizational project performance, with a crossover interaction observed for moderators – entrepreneurial leadership and project management capabilities. While project capabilities strengthen the positive impact of bricolage capabilities on project performance, entrepreneurial leadership has the opposite effect.Practical implicationsThe insights from this study offer an initial roadmap for project managers for effective resource acquisition and utilization through bricolage, ultimately enhancing project management effectiveness in resource-constrained environments.Originality/valueDespite the crucial role of bricolage capabilities in resource-constrained environments, the project management literature has largely neglected this concept. It is unclear how organizations use bricolage to manage projects. This lack of understanding challenges organizations, hindering their ability to apply bricolage consistently and thoughtfully in managing projects. Our study provides a deeper understanding of how bricolage facilitates project performance and enriches our understanding of it as an effective resource mobilization strategy within social enterprises.
Beyond the new normal for sustainability: transformative operations and supply chain management for negative emissions
Authors: Matos Stelvia V. , Schleper Martin C. , Hall Jeremy K. , Baum Chad M. , Low Sean , Sovacool Benjamin K. 
Published: August 2024

PurposeThis paper aims to explore three operations and supply chain management (OSCM) approaches for meeting the 2 °C targets to counteract climate change: adaptation (adjusting to climatic impacts); mitigation (innovating towards low-carbon practices); and carbon-removing negative emissions technologies (NETs). We suggest that adaptation nor mitigation may be enough to meet the current climate targets, thus calling for NETs, resulting in the following question: How can operations and supply chains be reconceptualized for NETs?Design/methodology/approachWe draw on the sustainable supply chain and transitions discourses along with interview data involving 125 experts gathered from a broad research project focused on geoengineering and NETs. We analyze three case studies of emerging NETs (biochar, direct air carbon capture and storage and ocean alkalinity enhancement), leading to propositions on the link between OSCM and NETs.FindingsAlthough some NETs are promising, there remains considerable variance and uncertainty over supply chain configurations, efficacy, social acceptability and potential risks of unintended detrimental consequences. We introduce the concept of transformative OSCM, which encompasses policy interventions to foster the emergence of new technologies in industry sectors driven by social mandates but lack clear commercial incentives.Originality/valueTo the best of the authors’ knowledge, this paper is among the first that studies NETs from an OSCM perspective. It suggests a pathway toward new industry structures and policy support to effectively tackle climate change through carbon removal.
How and when does digitalization influence export performance? A meta-analysis of its consequences and contingencies
Authors: Dong Yuge , He Xinming , Blut Markus 
Published: August 2024

PurposeThis study aims to clarify the direct impact of digitalization on export performance (EP) by synthesizing previous research and testing this relationship empirically. Furthermore, the study investigates digitalization types, contextual moderators and method moderators affecting the impact of digitalization on EP.Design/methodology/approachThe study uses meta-analysis to test the digitalization–EP relationship (k = 81) using data from 106 independent samples involving 62,082 respondents across nearly 30 countries.FindingsThe study finds digitalization’s positive and significant effect on EP (r = 0.36). The impact of digitalization on EP is also subject to different moderators, including digitalization type (i.e. digital capabilities), contextual factors (i.e. institutions, export experience, development of the region and industry) and method factors (i.e. back translation and strategy measurement).Originality/valueScholars have initiated studies on the impacts of diverse digitalization types on EP, while empirical findings on these effects remain inconclusive. Based on resource-based theory, the study develops and validates a comprehensive meta-analytic framework, revealing the important influence of digitalization on EP. The moderator findings further highlight the impact of internal and external contingencies on the outcomes of exporting firms’ digitalization.
Cultural dynamics and tenure trajectories: how auditor tenure and culture influence key audit matters in the GCC
Authors: Al-Asmakh Sara , Elamer Ahmed A. , Uadiale Olayinka 
Published: August 2024

PurposeThis study examines the impact of audit partner tenure on Key Audit Matters (KAM) disclosures within Gulf Cooperation Council (GCC) countries. It explores how Hofstede’s cultural dimensions influence this relationship, elucidating the effect of cultural context on auditing practices.Design/methodology/approachUtilizing a sample of 456 non-financial firms in the GCC from 2016 to 2021, the study employs regression analyses to explore audit partner tenure's influence on KAM disclosures and the moderating effects of Hofstede's dimensions of power distance, individualism, masculinity and uncertainty avoidance. This affords a detailed examination of individual and cultural impacts on audit quality.FindingsResults reveal a positive relationship between audit partner tenure and KAM disclosures, suggesting that firm-specific knowledge and industry expertise acquired over a long tenure may enhance auditors' ability to identify and report significant matters. Power distance and uncertainty avoidance amplify this effect, whereas individualism diminishes it. Masculinity does not yield significant results.Research limitations/implicationsThis study underscores the need for auditing standards to reflect the complex interplay of auditor tenure and cultural dynamics in the profession's global landscape.Originality/valueThis research contributes to the literature on audit quality by highlighting the formative role of individual auditors and cultural characteristics in KAM disclosure practices. It is among the first to quantitatively analyse the intersection of audit partner tenure and culture in the GCC. It provides valuable insights for regulators, practitioners and policymakers seeking to enhance audit practices across diverse cultural environments.