bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProtWave-VAE: Integrating autoregressive sampling with latent-based inference for data-driven protein design
Authors: Praljak Niksa , Lian Xinran , Ranganathan Rama , Ferguson Andrew L. 
Published: April 2023

AbstractDeep generative models (DGMs) have shown great success in the understanding of data-driven design of proteins. Variational autoencoders (VAEs) are a popular DGM approach that can learn the correlated patterns of amino acid mutations within a multiple sequence alignment (MSA) of protein sequences and distill this information into a low-dimensional latent space to expose phylogenetic and functional relationships and guide generative protein design. Autoregressive (AR) models are another popular DGM approach that typically lack a low-dimensional latent embedding but do not require training sequences to be aligned into an MSA and enable the design of variable length proteins. In this work, we propose ProtWave-VAE as a novel and lightweight DGM employing an information maximizing VAE with a dilated convolution encoder and autoregressive WaveNet decoder. This architecture blends the strengths of the VAE and AR paradigms in enabling training over unaligned sequence data and the conditional generative design of variable length sequences from an interpretable low-dimensional learned latent space. We evaluate the model’s ability to infer patterns and design rules within alignment-free homologous protein family sequences and to design novel synthetic proteins in four diverse protein families. We show that our model can infer meaningful functional and phylogenetic embeddings within latent spaces and make highly accurate predictions within semi-supervised downstream fitness prediction tasks. In an application to the C-terminal SH3 domain in the Sho1 transmembrane osmosensing receptor in baker’s yeast, we subject ProtWave-VAE designed sequences to experimental gene synthesis and select-seq assays for osmosensing function to show that the model enablesde novogenerative design, conditional C-terminus diversification, and engineering of osmosensing function into SH3 paralogs.
Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor
Authors: Xing Jiawei , Gumerov Vadim M. , Zhulin Igor B. 
Published: April 2023

AbstractSignal perception is a key function in regulating biological activities and adapting to changing environments. PAS domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity remain unknown. Here, we show that using sequence conservation and structural information it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via FAD and FMN cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.TeaserSignaling domains that originated in bacteria hold a potential as drug targets in humans.
Unbiased discovery of natural sequence variants that influence fungal virulence
Authors: Agustinho Daniel Paiva , Brown Holly Leanne , Chen Guohua , Brent Michael Richard , Doering Tamara Lea 
Published: April 2023

SUMMARYIsolates ofCryptococcus neoformans, a fungal pathogen that kills over 120,000 people each year, differ from a 19-megabase reference genome at a few thousand up to almost a million DNA sequence positions. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring sequence variants influence fungal virulence. We identified a region containing such variants, prioritized them, and engineered strains to test our findings in a mouse model of infection. At one locus we identified a 4-nt variant in thePDE2gene, which severely truncates its phosphodiesterase product and significantly alters virulence. Our studies demonstrate a powerful and unbiased strategy for identifying key genomic regions in the absence of prior information, suggest revisions to current assumptions about cAMP levels and about common laboratory strains, and provide significant sequence and strain resources to the community.
DeepComBat: A Statistically Motivated, Hyperparameter-Robust, Deep Learning Approach to Harmonization of Neuroimaging Data
Authors: Hu Fengling , Lucas Alfredo , Chen Andrew A. , Coleman Kyle , Horng Hannah , Ng Raymond W.S. , Tustison Nicholas J. , Davis Kathryn A. , Shou Haochang , Li Mingyao , Shinohara Russell T. ,   The Alzheimer’s Disease Neuroimaging Initiative
Published: April 2023

AbstractNeuroimaging data from multiple batches (i.e. acquisition sites, scanner manufacturer, datasets, etc.) are increasingly necessary to gain new insights into the human brain. However, multi-batch data, as well as extracted radiomic features, exhibit pronounced technical artifacts across batches. These batch effects introduce confounding into the data and can obscure biological effects of interest, decreasing the generalizability and reproducibility of findings. This is especially true when multi-batch data is used alongside complex downstream analysis models, such as machine learning methods. Image harmonization methods seeking to remove these batch effects are important for mitigating these issues; however, significant multivariate batch effects remain in the data following harmonization by current state-of-the-art statistical and deep learning methods. We present DeepCombat, a deep learning harmonization method based on a conditional variational autoencoder architecture and the ComBat harmonization model. DeepCombat learns and removes subject-level batch effects by accounting for the multivariate relationships between features. Additionally, DeepComBat relaxes a number of strong assumptions commonly made by previous deep learning harmonization methods and is empirically robust across a wide range of hyperparameter choices. We apply this method to neuroimaging data from a large cognitive-aging cohort and find that DeepCombat outperforms existing methods, as assessed by a battery of machine learning methods, in removing scanner effects from cortical thickness measurements while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically-motivated deep learning harmonization methods.
Neoliberalism and New Public Management: decision-making and accountability in a public–private partnership
Authors: McDonald-Kerr Lachlan , Boyce Gordon 
Published: April 2023

PurposeThe purpose of this paper is to investigate public disclosures and accountability for government decision-making in the case of a major prison project delivered through a Public–Private Partnership (PPP) in the State of Victoria (Australia).Design/methodology/approachThe study explores a unique case to provide insights into public disclosures for PPPs in a jurisdiction that is a recognised leader in PPP policy and practice. The analysis is theoretically framed by an understanding of neoliberalism and New Public Management, and draws on data from case-specific reporting, media reporting and public policy, to examine interconnections between accounting, public discourse and accountability.FindingsThe analysis shows how publicly available information relating to key government decisions routinely lacked supporting evidence or explanation, even though areas of subjectivity were recognised in public policy. Accounting was deployed numerically and discursively to present potentially contestable decisions as being based on common-sense “facts”. The implied “truth” status of government reporting is problematised by media disclosure of key issues absent from government disclosures.Social implicationsUnder neoliberalism, accountingisation can help depoliticise the public sphere and limit discourse by constructing ostensible “facts” in an inherently contestable arena. By contrast, democratic accountability requires public disclosures that infuse a critical dialogical public sphere.Originality/valueThe paper shows how neoliberalism can be embedded in public policies and institutional practices, and buttressed by the use of accounting. The analysis illuminates the persistence and “failing forward” character of neoliberalism, whereby crises are addressed through further neoliberalisation.
Scuba diving tourism and the challenge of sustainability: evidence from an explorative study in North African-Mediterranean countries
Authors: Cavallini Iacopo , Marzo Daniela , Scaccia Luisa , Scipioni Sara , Niccolini Federico 
Published: April 2023

PurposeScuba diving tourism is reputed to be a potential low-impact recreational activity that allow environmental conservation and socioeconomic benefits for local communities. Few studies have addressed the issue of sustainability of scuba diving tourism through the simultaneously investigation on the economic and socio-cultural aspects and its implications for tourism development. This study aims to examine the scuba diving tourism in three under-explored North African tourism destinations with high ecotourist potential. The authors present an exploratory picture of scuba diving tourist demand, divers' preferences, motivations for recreational diving experiences and their propensity towards conservation.Design/methodology/approachThe authors developed a case study research strategy collecting profile data on 123 divers. Furthermore, regression analysis was performed to investigate the divers' preferences, motivations and propensity towards conservation.FindingsThe divers' limited number, the presence of mainly local seasonal tourists and a moderate propensity towards conservation influence the potential of the diving tourism segment to generate significant socioeconomic benefits for local sustainable development in these destinations. However, establishing a marine protected area (MPA) could foster the development of a long-term strategy for scuba diving tourism, improve conservation awareness and increase divers' satisfaction.Practical implicationsDiverse profiles, preferences and motivations can provide tools to sustainably manage and preserve coastal and marine biodiversity, while also maximising the quality of the recreational experience. One of the most effective site-based strategies to orient the diving sector towards sustainability involves the design and strengthening of MPAs.Originality/valueThe research provides an original contribution to the debate on sustainable tourism strategies by demonstrating how the study of economic and socio-cultural aspects of scuba diving could provide guidelines to orient the tourism development of marine and coastal areas towards the principles of sustainability (also through the establishment of MPAs). The findings present an overview of the sustainability of the scuba diving tourism segment by investigating the preferences, motivations and inclination towards conservation among tourists for whom the diving experience is not a core holiday activity.
Utilizing the push–pull–mooring framework to explore university teachers' intention to switch from traditional classrooms to smart classrooms in China
Authors: Zhu Zhangxiang , Peng Zihui , Yang Kening 
Published: April 2023

PurposeThis study explores the factors that promote university teachers' switching intention from a traditional classroom to a smart classroom based on the push–pull–mooring (PPM) framework to enrich the theoretical research on the smart classroom and provide a reference for smart classroom promotion.Design/methodology/approachThe proposed conceptual framework was developed from a comprehensive review of the related literature. This study tested and validated the proposed framework using a partial least square structural equation model based on 269 valid questionnaires.Findings(1) Perceived inefficiency, inquiry-based learning, future expectation and technical self-efficacy had significant effects on switching intention, while low participation, perceived usefulness and habit had no significant effects on university teachers’ switching intention in the smart classroom. (2) In the process of decision-making, the course category significantly moderates the impact of perceived inefficiency and technical self-efficacy on switching intention, while the user experience of smart classrooms significantly moderates the impact of perceived inefficiency on switching intention.Originality/valueThis study explains university teachers' switching intention from a traditional classroom to the smart classroom, which enriches the application area of the PPM framework.
The effectiveness of the Bisindo-based rational emotive behavior therapy model in reducing social anxiety in deaf women victims of sexual harassment
Authors: Marlina Marlina , Mahdi Arisul , Karneli Yeni 
Published: April 2023

Purpose
Social anxiety disorder is a common phenomenon that occurs in everyone with varying degrees, ranging from mild to severe. One of the causes of social anxiety disorder is a traumatic experience due to sexual harassment that has been experienced. In deaf women, this experience is made more difficult because of the language and speech limitations shared. As a result, irrational thoughts and beliefs arise for the victim. This study aims to examine the effectiveness of the Bisindo-based rational emotive behavior therapy (REBT) model in reducing social anxiety in deaf women who are victims of sexual harassment.

Design/methodology/approach
The research method uses single-subject research with multiple baselines across subjects. The research subjects were deaf women victims of sexual harassment who the National Government Organization Woman Crises Center in West Sumatra and the Association of Indonesian Special Education Professionals identified. Data were collected by observation and social anxiety scale and analyzed by graphical visual analysis.

Findings
The results showed that the Bisindo-based REBT was effective in reducing social anxiety in deaf women who were victims of sexual harassment.

Research limitations/implications
The implementation of therapy in this study involved therapists, teachers and sign language interpreters. It requires extraordinary time and effort for the subjects to be able to reveal the sexual harassment they experienced. Furthermore, the small number of subjects meant that the results of this study could not be generalized widely. Therefore, this study has implications for future researchers to conduct experiments using the Bisindo-based REBT model on more subjects.

Practical implications
Practically, the results of this study have implications for a model for handling cases of sexual harassment in deaf women that can be used by women’s organizations and the Indonesian Association of Women with Disabilities.

Originality/value
It is recommended for counselors, psychologists and therapists to use the Bisindo-based REBT in dealing with cases of sexual harassment in deaf women because therapy that follows the characteristics of the victim’s language can help them to get the expected results.
Service encounter and value co-creation in fundraising activities at the NPO sector
Authors: Klafke Renata , Barrios Andrés , Didonet Simone Regina 
Published: April 2023

PurposeFundraising plays a critical role in the success of non-profit organizations (hereafter NPOs). This study aims to propose to analyze fundraising from a service-dominant logic, specifically from a service ecosystem approach, to understand the different entities and interactions involved in this activity, as well as the types of value that emerge from them.Design/methodology/approachA cross-case study was developed using three health-care Brazilian NPOs. Data collection methods were performed to build each case, including observation of NPOs’ telemarketing staff interaction with donors and long interviews with their marketing managers. Data analysis involved applying the service ecosystem framework to each NPO and contrasting them.FindingsFirst, the findings revealed the way in which religious, political and child-rearing institutions integrate into citizenship ideals that permeate both NPOs’ and donors’ attitudes and behaviors. Second, five different fundraising interactions (emotional, religious, political, influencer and empathetic) in which NPOs and donors pool their resources to co-create value are presented. Third, how the outcomes of fundraising interactions manifest for NPOs in the form of financial (money and time) and social value (social legitimation) and for teleworkers and donors in the form of emotional value (joy and relatedness) are identified.Originality/valueThis paper used a service ecosystem approach to analyze a new service context “fundraising,” which has been scarcely discussed in the literature. The findings show how macro-level institutions work together for fundraising. Five different fundraising interactions were identified, linking the communication with the service experience literature. Finally, the findings identify fundraising’s different value outcomes extending traditional approaches for evaluating this activity.
Make me happy, make it credible – the effect of CSR message framing on online brand engagement
Authors: Cordero-Gutiérrez Rebeca , Aljarah Ahmad , López Manuela , Lahuerta-Otero Eva 
Published: April 2023

PurposeThe objective of this study is to investigate the differential impact of gain versus loss message framing on the effectiveness of corporate social responsibility (CSR) communications in eliciting online brand engagement within the hospitality industry. Furthermore, this research aims to examine the extent to which evoked happiness and message credibility mediate the relationship between CSR message framing and online brand engagement, as these mediating factors have not been thoroughly examined in the existing academic literature.Design/methodology/approachThis study utilizes a between-subjects experimental design to test an integrative research framework, which is grounded in message framing theory and the elaboration likelihood model (ELM), in order to examine the interrelationships among the various constructs of the study within a coffee shop context on Facebook.FindingsThe findings of this study indicate that gain framing is a more powerful predictor of online brand engagement than loss framing. A mediation analysis supports the assertion that the effects of CSR framing communications on online brand engagement are mediated by evoked happiness and message credibility. Specifically, when the CSR message was framed in a positive (gain) manner, it was perceived as more credible and evoked more happiness, leading to increased online brand engagement. Additionally, the study’s results provide empirical evidence for the notion that the happiness elicited by brand messages enhances their credibility, leading to further online brand engagement.Originality/valueThis research makes a novel contribution to the literature by investigating the distinct effects of message framing on online brand advocacy and examining the complex interrelationships that modulate consumer engagement within the context of the hospitality industry.
Contrasting demographic responses to size‐selective harvesting among neighbouring wild fish populations
Authors: Matte Jean‐Michel O. , Glaser Dylan M. , Post John R. , Fraser Dylan J. 
Published: April 2023

Abstract

Sustainable harvesting of wild populations relies on evidence‐based knowledge to predict harvesting outcomes for species and the ecosystems they inhabit. Although harvesting may elicit compensatory density‐dependence, it is generally size‐selective, which induces additional pressures that are challenging to forecast. Furthermore, responses to harvest may be population‐specific and whether generalizable patterns exist remains unclear.

Taking advantage of Parks Canada's mandate to remove introduced brook trout Salvelinus fontinalis to restore alpine lakes in Canadian parks, we experimentally applied standardized size‐selective harvesting rates (the largest ~64% annually) for three consecutive summers in five populations with different initial size structures. Four unharvested populations were used as controls.

At reduced densities, harvested and control populations exhibited similar density‐dependent increases in specific growth, juvenile survival and earlier maturation. However, size‐selective harvesting simultaneously induced changes to size and age structure that contrasted among harvested populations. Average body length decreased in three of five harvested populations, whereas it tended to increase in control populations over the 3 years. We also detected contrasting, population‐specific changes in body length variability and ultimately in length‐ and age‐at‐harvest in harvested populations but not controls.

Overall, populations with smaller, more homogeneous body sizes, and living at high densities were most resilient to size‐selective harvesting, exhibiting the smallest change in size‐at‐age. In contrast, large‐bodied populations exhibited more substantial size‐structure changes following selective harvesting: large‐bodied populations experienced either stabilizing or disruptive pressures, when initial length variability was high or low, respectively.

Synthesis and application. Our results show that within species, size‐selective harvesting inherently leads to more risk and uncertainty when harvesting populations with larger and more varied body sizes than smaller‐bodied populations with less range in body size. Our study supports prioritizing regulations that protect harvested populations with larger and more varied body sizes. Such a management strategy would reduce the likelihood of eliciting unpredictable or undesirable demographic changes to fish populations with these attributes.
‘Tearing Off the Bonds’: Suffrage Visual Culture in Australia, New Zealand and the USA, 1890–1920
Authors: Stevenson Ana 
Published: April 2023

AbstractThis article will examine how transpacific suffrage visual culture imagined and reimagined an artistic tradition centred around the figure of the bound woman. White suffragists and anti‐suffragists in Australia, New Zealand and the United States used the iconography of bonds, chains and whips to mediate the possibility of women’s enfranchisement. Haunted by the legacies of settler colonialism, suffrage cartoons directly and obliquely evoked the spectre of chattel slavery, convict transportation and incarceration alongside the elusive ideals of humanitarian reform. While anti‐suffrage cartoons lamented the prospect of women’s enfranchisement, pro‐suffrage cartoons appropriated this iconography primarily for the benefit of white women.