bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene-by-environment interactions are pervasive among natural genetic variants
Authors: Chen Shi-An A. , Kern Alexander F. , Ang Roy Moh Lik , Xie Yihua , Fraser Hunter B. 
Published: June 2022

SummaryGene-by-Environment (GxE) interactions are fundamental to understanding fitness landscapes and evolution, but have been difficult to identify at the single-nucleotide level, precluding understanding of their prevalence and molecular mechanisms. Most examples involving natural genetic variants exist at the level of entire genomes, e.g. measurement of microbial strain growth across environments, or loci encompassing many variants identified by quantitative trait loci mapping. Here, we introduce CRISPEY- BAR, a high-throughput precision-editing strategy, and use it to map base-pair resolution GxE interactions impacting yeast growth under stress conditions. First, we used CRISPEY-BAR to uncover 338 variants with fitness effects within QTLs previously mapped in different environments. We then measured 1432 ergosterol pathway variants from diverse lineages across six environments, identifying 205 natural variants affecting fitness measured in all six conditions, of which 93.7% showed GxE interactions. Finally, we examine pleiotropic cis-regulatory variants suggesting molecular mechanisms of GxE interaction. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions, while also demonstrating high- throughput genome editing as an effective means for investigating this complexity.
Cross-modal Graph Contrastive Learning with Cellular Images
Authors: Zheng Shuangjia , Rao Jiahua , Zhang Jixian , Cohen Ethan , Li Chengtao , Yang Yuedong 
Published: June 2022

AbstractConstructing discriminative representations of molecules lies at the core of a number of domains such as drug discovery, material science, and chemistry. State-of-the-art methods employ graph neural networks (GNNs) and self-supervised learning (SSL) to learn the structural representations from unlabeled data, which can then be fine-tuned for downstream tasks. Albeit powerful, these methods that are pre-trained solely on molecular structures cannot generalize well to the tasks involved in intricate biological processes. To cope with this challenge, we propose using high-content cell microscopy images to assist in learning molecular representation. The fundamental rationale of our method is to leverage the correspondence between molecular topological structures and the caused perturbations at the phenotypic level. By including cross-modal pre-training with different types of contrastive loss functions in a unified framework, our model can efficiently learn generic and informative representations from cellular images, which are complementary to molecular structures. Empirical experiments demonstrated that the model transfers non-trivially to a variety of downstream tasks and is often competitive with the existing SSL baselines, e.g., a 15.4% absolute Hit@10 gains in graph-image retrieval task and a 4.0% absolute AUC improvements in clinical outcome predictions. Further zero-shot case studies show the potential of the approach to be applied to real-world drug discovery.
Conoid extrusion serves as gatekeeper for entry of glideosome components into the pellicular space to control motility and invasion in Apicomplexa
Authors: Dos Santos Pacheco Nicolas , Brusini Lorenzo , Haase Romuald , Tosetti Nicolò , Maco Bohumil , Brochet Mathieu , Vadas Oscar , Soldati-Favre Dominique 
Published: June 2022

SUMMARYMembers of the Apicomplexa are defined by apical cytoskeletal structures and secretory or-ganelles, tailored for motility and invasion. Gliding is powered by actomyosin-dependent rearward translocation of apically secreted transmembrane adhesins. InToxoplasma gondii, the conoid, composed of a cone of spiraling tubulin fibers and apposed preconoidal rings (PCRs), is an enigmatic, dynamic organelle of undefined function. Here we mapped five new components of the PCRs and deduce that the structure serves as a pivotal hub for actin polymerization and glideosome assembly. F-actin produced by Formin1 on the PCRs is used by Myosin H to generate the force for conoid extrusion. A set of B-box-type zinc finger domain containing proteins conserved in Apicomplexa is indispensable for PCRs formation, conoid extrusion and motility inToxoplasmaandPlasmodium. Conoid dynamics directs the flux of F-actin to the pellicular space, acting as dynamic gatekeeper to tightly control parasite motility during invasion and egress.
Aging and sperm signals alter DNA break formation and repair in theC. elegansgermline
Authors: Toraason Erik , Adler Victoria L. , Libuda Diana E. 
Published: June 2022

AbstractFemale reproductive aging is associated with decreased oocyte quality and fertility. The nematodeCaenorhabditis elegansis a powerful system for understanding the biology of aging and exhibits age-related reproductive defects that are analogous to those observed in many mammals, including dysregulation of DNA repair.C. elegansgermline function is influenced simultaneously by both reproductive aging and signals triggered by limited supplies of sperm, which are depleted over chronological time. To delineate the causes of DNA repair defects in agedC. elegansgermlines, we assessed both DNA double strand break (DSB) induction and repair during meiotic prophase progression in aged germlines which were depleted of self-sperm, mated, or never exposed to sperm. We find that germline DSB induction is dramatically reduced only in hermaphrodites which have exhausted their endogenous sperm, suggesting that a signal due specifically to sperm depletion downregulates DSB formation. We also find that DSB repair is delayed in aged germlines regardless of whether hermaphrodites had either a reduction in sperm supply or an inability to endogenously produce sperm. These results demonstrate that in contrast to DSB induction, DSB repair defects are a feature ofC. elegansreproductive aging independent of sperm presence. Finally, we demonstrate that the ubiquitin E2 ligase variant UEV-2 is required for efficient DSB repair specifically in young germlines, implicating UEV-2 in the regulation of DNA repair during reproductive aging. In summary, our study demonstrates that DNA repair defects are a feature ofC. elegansreproductive aging and uncovers parallel mechanisms regulating efficient DSB formation in the germline.Author SummaryAging leads to a decline in the quality of the female reproductive cells, known as oocytes. Oocytes subjected to reproductive aging experience an increase in both infertility and aneuploidies that cause miscarriages and birth defects. The nematodeCaenorhabditis elegansis a classic model system used to determine the mechanisms of aging. OldC. elegansoocytes accrue many defects which may contribute to their reduced quality, including dysregulation of DNA repair.C. elegansfertility and germline function is also regulated oocyte-independently by sperm-dependent signals. To determine how aging and sperm may independently impact DNA repair in agingC. elegansoocytes, we control oocyte aging and sperm presence independently to evaluate their effects on DNA break formation and repair. We find that running out of sperm reduces the levels of DNA breaks which are produced, but the efficiency of DNA repair declines during aging independent of sperm effects. We also identify a protein which specifically promotes DNA repair in the oocytes of young animals, suggesting that this protein may regulate DNA repair in the germline during aging. Taken together, our research defines aging-specific and aging-independent mechanisms which regulate the genome integrity of oocytes.
Food literacy as a resilience factor in response to health-related uncertainty
Authors: Gianni Maria , Reitano Antonella , Fazio Marco , Gkimperiti Athanasia , Karanasios Nikolaos , Taylor David W. 
Published: June 2022

PurposeDuring the Covid-19 pandemic, people were deprived of their freedom, unable to engage in physical and social activities, and worried about their health. Uncertainty, insecurity, and confinement are all factors that may induce stress, uneasiness, fear, and depression. In this context, this study aims to identify possible relationships of emotions caused by health risks and restrictions to outdoor activities with well-informed decisions about food consumption.Design/methodology/approachThe theoretical framework of this research draws on the stimulus-organism-response paradigm yielding six research hypotheses. An online survey was designated to test these hypotheses. A total of 1,298 responses were gathered from Italy, Greece, and the United Kingdom. Data analyses include demographic group comparisons, moderation, and multiple regression tests.FindingsThe results showed that when people miss their usual activities (including freedom of movement, social contact, travelling, personal care services, leisure activities, and eating at restaurants) and worry about their health and the health of their families, they turn to safer food choices of higher quality, dedicating more of their time and resources to cooking and eating.Research limitations/implicationsThe findings showcase how risk-based thinking is critical for management and marketing strategies. Academics and practitioners may rely on these findings to include extreme conditions within their scope, understanding food literacy as a resilience factor to cope with health risks and stimulated emotions.Originality/valueThis study identified food behavioural patterns under risk-laden conditions. A health risk acted as an opportunity to look at food consumption as a means of resilience.
New business capacity of developed, developing and least developing economies: inspection through state-of-the-art fuzzy clustering and PSO-GBR frameworks
Authors: Ghosh Indranil , Jana Rabin K. , Pramanik Paritosh 
Published: June 2022

PurposeIt is essential to validate whether a nation's economic strength always transpires into new business capacity. The present research strives to identify the key indicators to the proxy new business ecosystem of countries and critically evaluate the similarity through the lens of advanced Fuzzy Clustering Frameworks over the years.Design/methodology/approachThe authors use Fuzzy C Means, Type 2 Fuzzy C Means, Fuzzy Possibilistic C Means and Fuzzy Possibilistic Product Partition C Means Clustering algorithm to discover the inherent groupings of the considered countries in terms of intricate patterns of geospatial new business capacity during 2015–2018. Additionally, the authors propose a Particle Swarm Optimization driven Gradient Boosting Regression methodology to measure the influence of the underlying indicators for the overall surge in new business.FindingsThe Fuzzy Clustering frameworks suggest the existence of two clusters of nations across the years. Several developing countries have emerged to cater praiseworthy state of the new business ecosystem. The ease of running a business has appeared to be the most influential feature that governs the overall New Business Density.Practical implicationsIt is of paramount practical importance to conduct a periodic review of nations' overall new business ecosystem to draw action plans to emphasize and augment the key enablers linked to new business growth. Countries found to lack new business capacity despite enjoying adequate economic strength can focus effectively on weaker dimensions.Originality/valueThe research proposes a robust systematic framework for new business capacity across different economies, indicating that economic strength does not necessarily transpire to equivalent new business capacity.
The relationship between minority directors and earnings management: an empirical analysis in the Italian institutional setting
Authors: Fera Pietro , Moscariello Nicola , Pizzo Michele , Ricciardi Giorgio 
Published: June 2022

Purpose
Although the previous literature considers independent directors as an internal mechanism for good corporate governance and higher financial disclosure quality, in contexts characterized by high ownership concentration, they may lack the mandate, the incentives and the ability to be an effective monitoring mechanism. Therefore, this study aims to focus on minority directors and investigate their impact on the earnings management activities for firms with concentrated ownership structures.

Design/methodology/approach
As the slate voting system is a peculiar feature of Italian corporate governance regulations, which gives minority shareholders the right to appoint at least one member of the board of directors (minority directors), this paper carries out a quantitative empirical analysis based on a sample of non-financial companies listed on the Italian Stock Exchange to test the role played by minority directors in increasing incentives towards higher financial reporting quality.

Findings
Robust to different model specifications, including the endogeneity test, empirical findings show a negative relationship between minority directors and earnings management, while no relationship holds between the latter and independent directors, suggesting that minority directors might promote greater directors’ accountability than independent directors in highly concentrated ownership structures.

Originality/value
Relying on the empirical findings, this paper offers new insights on a peculiar internal corporate governance mechanism related to one of the most debated issues among financial market practitioners and regulators, namely, the protection of minority shareholders. Moreover, this paper offers new insights for academics and practitioners on a peculiar governance mechanism that could soon be widely adopted.
Is technology everywhere? Exploring Generation Z's perceptions of sustainable tourism in developing countries
Authors: Sfodera Fabiola , Cain Lisa Nicole , Di Leo Alessio 
Published: June 2022

PurposeThis study examines the role of technology as a driver of sustainable tourism perceptions among Generation Z.Design/methodology/approachThe work considers the perspective of locals in Pakistan and uses a multi-method, multiphase embedded research design approach.FindingsThe research findings demonstrated that technology has a positive correlation with the environmental, socio-cultural and economic dimensions of sustainable tourism perception among Generation Z. Therefore, technology could be considered a dimension of sustainable tourism perception for locals, but perceptions differ significantly depending on the size of the city of the participant. The results of the experimental design phase that utilized picture stimuli demonstrated a linear relationship between technology and sustainability and enhanced their definition and implementation for developing countries.Originality/valueThis research diverges from most past research on these topics by focusing on Generation Z, for whom digital media and technology play a crucial role and for whom these technologies are positively correlated with sustainability and its overall perception. Implications for policies and practices for emerging country governments are provided.
Hardness measurements as a technique for measuring accumulated fatigue damage
Authors: Bjørheim Fredrik , Pavlou Dimitrios , Siriwardane Sudath C. 
Published: June 2022

PurposeBrinell, Vickers and low-force Vickers hardness measurements are herein adopted to investigate and quantify the fatigue damage evolution in specimens made of S355J2+AR ferritic pearlitic steel. Though nano and microhardness measurements have been well adopted, they require a strict preparation routine, whereas macroscopic hardness measurements are not as stringent.Design/methodology/approachThe feasibility of adopting macroscopic hardness measurements as a means of measuring fatigue damage is investigated through a combination of experimental tests and finite element analyses with both Brinell and Vickers hardness indenter.FindingsIt is found that the Brinell hardness measurements method seems more feasible, regarding finding a continuous and significant change during the fatigue life, in comparison to both Vickers and low-force Vickers. Thereafter, the question regarding the feasibility of the hardness measurements as a method of assessing accumulated fatigue damage in situ is discussed.Originality/valueMuch work has previously been performed towards correlation of the micro and nano hardness indentations, which generally has stringent preparation requirements before testing. Herein, the adoption of macroscopic hardness measurements as a means of assessing accumulated fatigue damage is considered both experimentally and theoretically.
Visualising and calculating the smart city: a dialogue perspective
Authors: Trunova Olga , Khodachek Igor , Khodachek Aleksandr 
Published: June 2022

PurposeThis study addresses the implications of smart city development paths (techno-centric and human-centric) by investigating the evolution of a city strategy, focusing on how different actors in a dialogue centred on strategic planning documents for Saint Petersburg, Russia, visualised the smart city and then made it calculable.Design/methodology/approachThe authors conducted a case study based on a documentary analysis supported by ethnographic elements relying on the smart city conceptual proposals, the approved city strategy and the artifacts of expert discussions leading to the strategy implementation plan.FindingsThrough the lens of dialogue theory, the authors show how government and non-government actors in different organisational settings devised techno-centric smart city calculations, which arose despite an initial human-centric vision.Research limitations/implicationsWhile the case study allowed the study to illustrate the depth and richness of the context of the authoritarian Russian state where the role of citizens in public decision-making is rather limited, different and even contrasting results could be produced in other contexts.Practical implicationsThere is a gap between a smart city vision and its grounding in calculations. Thus, the human-centric elements require special attention, and the organisation of the dialogue on smart city strategy must enable plurality of voices besides those of government actors.Originality/valueThe case suggests viewing the human-centric and techno-centric perspectives not as dichotomous, but rather emerging consecutively throughout the journey from an initial strategic vision to its implementation in the city's calculations.
Micromechanical response of SAC305 solder alloy under gamma radiation via nanoindentation approach
Authors: Wan Yusoff Wan Yusmawati , Ismail Norliza , Mohmad Lehan Nur Farisa Nadia , Amat Azuraida , Ku Ahmad Ku Zarina , Jalar Azman , Abdul Rahman Irman 
Published: June 2022

Purpose
This paper aims to investigate the effect of different doses of gamma radiation on the micromechanical response (hardness properties and creep behaviour) of 96.5Sn-3.0Ag-0.5Cu (SAC305) solder alloys.

Design/methodology/approach
SAC305 solder pastes deposited on printed circuit boards (PCBs) were subjected to a reflow soldering process to form soldered samples. The soldered samples were irradiated with a gamma source at different doses (5–50 Gy). Nanoindentation testing was used to determine the hardness properties and creep behaviour after gamma irradiation.

Findings
The results showed that the hardness of SAC305 solder alloys gradually increased up to 15 Gy and then gradually decreased to 50 Gy of gamma irradiation. The highest hardness value (0.37 GPa) was observed on SAC305 solder alloys exposed to 15 Gy irradiation. Hardening of SAC305 solder alloy was suggested to be due to the high defect density induced by the gamma irradiation. Meanwhile, exposure to 50 Gy irradiation resulted in the lowest hardness value, 0.13 GPa. The softening behaviour of SAC305 solder alloy was probably due to the evolution of defect size in the solder joint. In addition, the creep behaviour of the SAC305 solder alloys changed significantly with different gamma irradiation doses. The creep rates were higher at a dose of 10 Gy up to a dose of 50 Gy. Gamma irradiation caused the SAC305 solder alloy to become more ductile compared to the non-irradiated alloy. The stress exponent also showed different deformation mechanisms with varying gamma doses.

Originality/value
Research into the micromechanical properties of solder alloys subjected to gamma irradiation has rarely been reported, especially for Sn-Ag-Cu lead-free solder. Thus, this research provides a fundamental understanding of the micromechanical response (hardness and creep behaviour) of solder, especially lead-free solder alloy, to gamma irradiation.
Locating skarns with magnetic survey data, Geyer, Erzgebirge: optimizing data acquisition procedures
Authors: Ugalde Hernan , Morris William , Madriz Yuleika , Kirsch Moritz , Gloaguen Richard , Schneider Michael , Schiffler Markus , Siemon Bernhard , Fréville Tristan , Munschy Marc 
Published: June 2022

ABSTRACTMagnetic data can be acquired from a number of different platforms (e.g., ground, drone, helicopter) using a variety of sensors (e.g., caesium vapour‐type optically pumped magnetometers, fluxgate, superconducting quantum interference devices) with different flight line configurations. To detect a magnetic anomaly associated with a mineral commodity that is not exposed but is thought to be associated with the anomalous magnetic mineral content, it is necessary to optimize the survey parameters through a complete data integration process. Prior petrophysical measurements provide insight into the physical contrast that might be expected between adjacent lithologic units and between the ore zone and the encompassing lithology. Oriented rock samples provide access to magnetic remanence data through palaeomagnetic laboratory measurements. Knowing the typical morphology of the ore zone one can compute a forward model of the expected anomalous response and determine which combination of survey parameters provides the highest probability of detecting the commodity being sought. In this study, we analyse magnetic patterns associated with thin dipping skarn bodies from the Geyer mining district in Erzgebirge, Germany. Petrophysical measurements indicate that the skarns are more magnetic than the surrounding host rock. Partially oriented samples from a bore core record a Variscan age metamorphic remanence. Forward modelling indicates that clusters of skarn bodies are required to produce a reliably detectable magnetic signal. Ground, or low elevation drone surveys are needed to detect these anomalies with standard scalar‐type optically pumped magnetometer or fluxgate magnetic surveys. The enhanced spatial resolution and long‐wavelength rejection of a superconducting quantum interference device based full‐tensor magnetic gradiometer provide an improvement over optically pumped magnetometers for an aircraft‐based survey platform.