bluuebunny/crossref_metadata_2025_split huggingface dataset:
TUSX: an accessible toolbox for transcranial ultrasound simulation
Authors: Heimbuch Ian S. , Faas Guido C. , Iacoboni Marco , Charles Andrew C. 
Published: June 2021

AbstractNormally, the complicated nature of acoustic simulation makes it infeasible for most research groups doing individual transcranial ultrasound studies, hindering interpretation of results and complicating the determination of safety limits. We present here an open-source MATLAB toolbox to perform acoustic simulations using subject-specific medical images for transcranial ultrasound experiments. This toolbox, Transcranial Ultrasound Simulation Toolbox (TUSX), consists of an integrated processing pipeline that takes in structural MR or CT images, processes them for accurate simulation, and runs the simulations using k-Wave, an existing open-source acoustics package. We describe here the processing TUSX performs, along with its reasoning. We also validate its output using real-world pressure measurements in a water tank.
SALARECON connects the Atlantic salmon genome to growth and feed efficiency
Authors: Zakhartsev Maksim , Rotnes Filip , Gulla Marie , Øyås Ove , van Dam Jesse C. J. , Suarez-Diez Maria , Grammes Fabian , Hafþórsson Róbert Anton , van Helvoirt Wout , Koehorst Jasper J. , Schaap Peter J. , Jin Yang , Mydland Liv Torunn , Gjuvsland Arne B. , Sandve Simen R. , Martins dos Santos Vitor A. P. , Vik Jon Olav 
Published: June 2021

AbstractAtlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds.Author summaryAtlantic salmon aquaculture generates billions of euros annually, but faces challenges of sustainability. Salmon are carnivores by nature, and fish oil and fish meal have become scarce resources in fish feed production. Novel, sustainable feedstuffs are being trialed hand in hand with studies of the genetics of growth and feed efficiency. This calls for a mathematical-biological framework to integrate data with understanding of the effects of novel feeds on salmon physiology and its interplay with genetics. We have developed the SALARECON model of the core salmon metabolic reaction network, linking its genome to metabolic fluxes and growth. Computational analyses show good agreement with observed growth, amino acid limitations, and feed efficiencies, illustrating the potential for in silico studies of potential feed mixtures. In particular, in silico screening of possible diets will enable more efficient animal experiments with improved knowledge gain. We have adopted best practices for test-driven development, virtual experiments to assay metabolic capabilities, revision control, and FAIR data and model management. This facilitates fast, collaborative, reliable development of the model for future applications in sustainable production biology.
Characterization of the MIRO-independent mitochondrial association activity of TRAK proteins
Authors: Mitchell Lili , Reda Kathryn E. , Fatima Hijab , Vasquez Claudia E. , Quintero-Carmona Omar A. 
Published: June 2021

AbstractCurrent models suggest that MIRO GTPases anchor cytoskeletal motors to the mitochondrial outer membrane (MOM). However, our previous findings indicate that the unconventional myosin, MYO19, interacts with MIRO weakly but that a MIRO-independent MOM-localizing domain interacts more tightly with the MOM. To test the model that MIRO proteins serve as weaker, initial recruiters of cytoskeletal motors to mitochondria, we examined interactions between TRAK proteins (microtubule motor-mitochondria adapter proteins) and the MOM via quantitative fluorescence microscopy and steady-state kinetic approaches. Using GFP-TRAK truncations expressed in MIRO1-2 double knockout mouse embryonic fibroblasts, we identified a MIRO-independent mitochondrial binding domain in the C-terminus of TRAK1 and TRAK2, sufficient for localization to the MOM--similar to what we observed for full length GFP-TRAK proteins. The MIRO-binding domains (MBD) of the TRAK proteins were only able to localize to mitochondria in the presence of ectopic expression of MIRO. Importantly, fluorescence recovery after photobleaching (FRAP) demonstrated that the steady-state kinetics of TRAKMBD/MIRO2 interaction were faster-exchanging than for either full-length TRAK or the TRAK C-terminal MOM-binding domain expressed alone. These data support the model that MIRO supports weak associations of cytoskeletal motors to the MOM, while MIRO-independent binding contributes significantly to tighter association of such motors to the MOM.
Digital PCR quantification of DNA, RNA and extracellular microRNA of mouse oocytes
Authors: Yang Joan Xiaohui , Zhao Xin Yuan , Bi Dexi , Wei Qing , Mattar Citra , Ling Pang Joy Yan , Lee Yie Hou 
Published: June 2021

ABSTRACTDespite numerous advances in in vitro fertilization (IVF) techniques since its first success in 1978, almost half of the patients treated remain childless. The multifactorial nature of IVF treatment means that success is dependent on variables, including the quality of oocytes. Therefore, new technologies are needed to objectively and quantitatively examine how each oocyte can be selected or optimized to achieve for the best possible outcomes for patients. Here, we report an optimized digital polymerase chain reaction (dPCR) for direct absolute quantification of nucleic acids within 3.5 h without the need for sample extraction or purification. Using individual oocytes, the developed method demonstrated absolute quantification with a linear dynamic range of 0.65 – 33 copies/µL (r2=0.999), high accuracy and excellent reproducibility of <10% relative standard deviation. The method then identified the variable expression of Gapdh (0.72-16.95 copies/oocyte), Hprt1 (1.05-19.05 copies/oocyte) and ATPase 6, (5.55-32358.15 copies/oocyte) in ovaries even from the same mouse. Finally, dPCR was used to validate extracellular microRNAs from oocytes incubated with a toxic unsaturated very-long chained ceramide. This study therefore shows the feasibility of dPCR for the rapid and sensitive absolute quantification of DNA/RNA and extracellular miRNA for the study of oocytes.
Panx1 channels promote both anti- and pro-seizure-like activities in the zebrafish via p2rx7 receptors and ATP signaling
Authors: Whyte-Fagundes Paige , Taskina Daria , Safarian Nickie , Zoidl Christiane , Carlen Peter L , Donaldson Logan W , Zoidl Georg R 
Published: June 2021

AbstractThe molecular mechanisms of excitation-inhibition imbalances promoting seizure generation in epilepsy patients are not fully understood. Experimental evidence suggests that Pannexin1 (Panx1), an ATP release channel, modulates excitability of the brain. In this report, we have performed behavioral and molecular phenotyping experiments on zebrafish larvae bearing genetic or pharmacological knockouts of panx1a or panx1b channels, each highly homologous to human PANX1. When Panx1a function is lost or both channels are under pharmacological blockage, treatment with pentylenetetrazol to induce seizures causes reduced ictal-like events and seizure-like locomotion. These observations were extended by transcriptome profiling, where a spectrum of distinct metabolic and cell signaling states correlates with the loss of panx1a. The pro- and anticonvulsant activities of both Panx1 channels affects ATP release and involves the purinergic receptor p2rx7. We propose that Panx1 zebrafish models offer opportunities to explore the molecular and physiological basis of seizures and assist anticonvulsant drug discovery.
Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow
Authors: Acar Omer , Zhang She , Bahar Ivet , Carvunis Anne-Ruxandra 
Published: June 2021

AbstractThe high-level organization of the cell is embedded in long-range interactions that connect distinct cellular processes. Existing approaches for detecting long-range interactions consist of propagating information from source nodes through cellular networks, but the selection of source nodes is inherently biased by prior knowledge. Here, we sought to derive an unbiased view of long-range interactions by adapting a perturbation-response scanning strategy initially developed for identifying allosteric interactions within proteins. We deployed this strategy onto an elastic network model of the yeast genetic network. The genetic network revealed a superior propensity for long-range interactions relative to simulated networks with similar topology. Long-range interactions were detected systematically throughout the network and found to be enriched in specific biological processes. Furthermore, perturbation-response scanning identified the major sources and receivers of information in the network, named effector and sensor genes, respectively. Effectors formed dense clusters centrally integrated into the network, whereas sensors formed loosely connected antenna-shaped clusters. Long-range interactions between effector and sensor clusters represent the major paths of information in the network. Our results demonstrate that elastic network modeling of cellular networks constitutes a promising strategy to probe the high-level organization of the cell.
An alignment free approach confirms semantic properties of species proteomes
Authors: Starcevic Antonio , Melvan Ena , Cvrljak Toni , Diminic Janko , Zucko Jurica , Long Paul F. 
Published: June 2021

AbstractAlignment-based methods dominate molecular biology. However, by primarily allowing one-to-one comparisons, these methods are focused on a gene-centered viewpoint and lack the broad context essential to analyze how complex biological systems function and evolve. In actuality, a gene is part of genome where more than one sequence contributes to the functional network and evolutionary trajectory of the cell. The need for conservation of established interactions, is arguably more important to the evolutionary success of species than conservation of individual function. To test whether such contextual information exists, a distributional semantics method - Latent Semantic Analysis (LSA), was applied to thousands of species proteomes. Using natural language processing, Latent Taxonomic Signatures (LTSs) were identified that outperformed existing alignment-based BLAST methods when random protein sequences were being mapped to annotated taxonomy according to GenBank. LTSs are a novel proteome distributed feature, suggesting the existence of evolutionary constraints imposed on individual proteins by their proteome context. Even orphan proteins are exhibiting LTSs, which makes their uniqueness linked to a specific taxonomic level questionable. Unlike more simple bias, LTSs represent a self-similarity pattern, where random sets of species proteins show the same statistical properties of a complete proteome at many scales. Natural language processing and machine learning provide insights not easily discernable using alignment based methods suggestive there is more to species related differences than just translational optimization.
Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection
Authors: Grodzki Marco , Bluhm Andrew P. , Schäfer Moritz , Tagmount Abderrahmane , Russo Max , Sobh Amin , Rafiee Roya , Vulpe Chris D. , Karst Stephanie M. , Norris Michael H. 
Published: June 2021

AbstractThe COVID-19 pandemic has resulted in 153 million infections and 3.2 million deaths as of May 2021. While effective vaccines are being administered globally, there is still a great need for antiviral therapies as potentially antigenically distinct SARS-CoV-2 variants continue to emerge across the globe. Viruses require host factors at every step in their life cycle, representing a rich pool of candidate targets for antiviral drug design. To identify host factors that promote SARS-CoV-2 infection with potential for broad-spectrum activity across the coronavirus family, we performed genome-scale CRISPR knockout screens in two cell lines (Vero E6 and HEK293T ectopically expressing ACE2) with SARS-CoV-2 and the common cold-causing human coronavirus OC43. While we identified multiple genes and functional pathways that have been previously reported to promote human coronavirus replication, we also identified a substantial number of novel genes and pathways. Of note, host factors involved in cell cycle regulation were enriched in our screens as were several key components of the programmed mRNA decay pathway. Finally, we identified novel candidate antiviral compounds targeting a number of factors revealed by our screens. Overall, our studies substantiate and expand the growing body of literature focused on understanding key human coronavirus-host cell interactions and exploit that knowledge for rational antiviral drug development.One Sentence SummaryGenome-wide CRISPR screens identified host factors that promote human coronavirus infection, revealing novel antiviral drug targets.
Analysing and evaluating environmental information disclosure in universities: the role of corporate governance, stakeholders and culture
Authors: Flórez-Parra Jesús Mauricio , Lopez-Perez Maria Victoria , López Hernández Antonio M. , Garde Sánchez Raquel 
Published: June 2021

Purpose
The purpose of this paper is to analyse the internal and external factors related to the disclosure of environmental information in universities which reflect the actions carried out in these universities.

Design/methodology/approach
Taking as reference the first 200 universities in the Shanghai ranking, several factors associated with the degree of environmental information disclosure in universities – governance dimension, the relationship and participation of stakeholders, position and prestige as signs of the quality of the institution and cultural concern in the university’s country for the environment – are analysed.

Findings
The results obtained show that the size of the leadership team, stakeholder participation, the position of the university in rankings and cultural concern in the university’s country for the environment are determining factors in the university’s environmental actions and, consequently, in their disclosure. Other factors – such as the size of the university, the level of self-financing and financial autonomy – do not affect the disclosure of environmental information.

Originality/value
Scant research exists on the environmental commitments of universities; this paper aims to fill that gap. Their role as the main channel of research and as instructors of future professionals makes them points of reference in society. Research on university ranking has traditionally focussed on teaching and research results, but environmental issues are becoming increasingly important. This paper enumerates the factors that influence the dissemination of environmental information in the most prestigious universities. This research also provides an original approach by considering not only top-down but also bottom-up strategies through communication channels and the incidence of cultural factors.
Investigating the impact of personality traits on perceived usability evaluation of e-learning platforms
Authors: Vlachogianni Prokopia , Tselios Nikolaos 
Published: June 2021

Purpose
The purpose of this paper is to investigate the impact of personality traits on the perceived usability evaluation of e-learning platforms. In specific, perceived usability levels of the educational platforms and tools used in primary and secondary education in Greece are demonstrated. The impact which personality traits and other individual-related factors have on the perceived usability were also examined.

Design/methodology/approach
In total, 2,239 Greek primary and secondary education teachers participated in the study through an online survey. The system usability scale (SUS) and Big 5 personality test questionnaires were adopted, as well as a demographics questionnaire and nine platforms were examined: e-me, eclass, Google Classroom, Microsoft Teams, Cisco Webex, Edmodo, Padlet, Skype and Zoom.

Findings
Most platforms were rated as satisfactory in terms of perceived usability as measured by SUS. SUS scores were not found to be significantly related with participants’ age, gender, private/public school, working relationship. Furthermore, openness to new experience and extraversion demonstrated the strongest positive correlation with perceived usability evaluation.

Research limitations/implications
The current study used a sample of Greek teachers as participants, so the generalizability of results without considering cultural or organizational issues is of questionable validity. The Big 5 personality test is widely adopted; however, it seems that it does not capture comprehensively all possible dimensions of personality.

Practical implications
Acknowledging the correlations between personality traits and perceived usability for each platform, teachers may now choose the most user-friendly one depending on the personality traits. Designers can adapt their systems to meet users’ needs accordingly. Moreover, the reported results provide a frame of reference for the respective organizations and companies to compare the quality of user experience of their products and services. Thus, development costs of an e-learning platform/tool can be reduced accordingly.

Social implications
Text.

Originality/value
Perceived usability of a technological system affects the way users interact with it and consequently the whole learning experience. Thus, factors which may affect perceived usability and, in turn, the learning outcomes are of paramount importance and should be exhaustively examined. Giving that personality affects or is related to, other parameters related with technology (technology adoption, perceived and actual use, acceptance, interaction, perceived ease of use), this study addresses a significant research gap and sheds light to the before-mentioned issues.
The effects of green brand equity on green word of mouth: the mediating roles of three green factors
Authors: Mehdikhani Rasoul , Valmohammadi Changiz 
Published: June 2021

Purpose
This study aims to investigate the effects of green brand equity (GBE) on green brand attachment (GBA), green self-brand connection (GSBC), green brand attitude (GBAT) and green word of mouth (GWOM). Moreover, the mediating role of three main factors, namely, GBA, GSBC and GBAT.

Design/methodology/approach
Through an in-depth review of the relevant literature, a conceptual model was developed and a questionnaire was designed. Out of 600 distributed questionnaires among customers of disposable tableware brands in Tehran, 265 questionnaires were returned. Data were analyzed for measuring the proposed model using the structural equation modeling technique.

Findings
The obtained results showed that GBE has positive impacts on GBA, GSBC, GBAT and GWOM. GBA, GSBC and GBAT have positive impacts on GWOM. Also, GBA, GSBC and GBA partially mediate the relationship between GBE and GWOM.

Research limitations
This study has been done in the context of Iran, so caution should be taken to generalize the results.

Practical implications
This study provides a clear insight for brand managers and marketers about the mechanism of enhancing green signals, which a brand can transfer to consumers through GBE. Also, the study suggests that companies should design their advertisement in a way that demonstrates the environmental responsibility of the brand and environmentally friendly features of products to increase consumer awareness of environmental concerns.

Social implications
The obtained results might increase green awareness among the people which is hoped other industries, particularly manufacturing ones make necessary efforts toward promoting the implementation of green manufacturing.

Originality/value
The results provide important environmental concepts in the field of green marketing and use sustainable development and signaling theories to enhance the attraction of disposable tableware in both business-to-business and business-to-consumer contexts. This study also adds a new concept of GSBC to the marketing literature.
Investigating key dimensions for the development of women-owned enterprises: interpretive structural modeling and MICMAC approach
Authors: Agarwal Sucheta , Agrawal Vivek , Srivastava Anugamini Priya 
Published: June 2021

Purpose
Women-owned enterprises (WOEs) are one of the fastest-growing entrepreneurial sectors in the world. Therefore, this study aims to identify and develop the structural cause and effect relationship among the various strategic dimensions that affect the performance of WOEs in the Indian context.

Design/methodology/approach
With the help of the questionnaire survey, the data has been gathered. Further, the experts’ opinions are considered, which is followed by interpretative structural modeling and the impact matrix cross-reference multiplication applied to a classification (MICMAC) approach to explore the 13 dimensions associated with the development of WOEs such as work–life balance (WLB), entrepreneurial learning (EL), competencies, social identity (SI) and culture.

Findings
WLB and support of financial institutions are the dominant independent dimensions and EL and competencies have emerged as dominant dependent dimensions, which impact the development of WOEs. The other linkage dimensions are experience, entrepreneurship education and training, SI, government, non-government organizations, family, friends, culture, role models, etc.

Research limitations/implications
This conceptual model can be validated for any type of WOEs in India and in other countries.

Practical implications
Through this study, the academicians, decision-makers and policymakers must become aware of the importance of each dimension and their relatedness with each other, which provides the direction for designing and implementing appropriate policies to enhance the growth of WOEs.

Originality/value
This is the foremost research that provides an interpretive structural conceptual model to develop a map of the complex relationships and magnitude among the identified dimensions of WOEs.