bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide ChIPseq analysis of AhR, COUP-TF, and HNF4 enrichment in TCDD-treated mouse liver
Authors: Cholico Giovan N. , Nault Rance , Zacharewski Timothy R. 
Published: June 2021

ABSTRACTThe aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor known for mediating the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. Although the canonical mechanism of AhR activation involves heterodimerization with the aryl hydrocarbon receptor nuclear translocator, other transcriptional regulators that interact with AhR have been identified. Enrichment analysis of motifs in AhR-bound genomic regions implicated co-operation with COUP transcription factor (COUP-TF) and hepatocyte nuclear factor 4 (HNF4). The present study investigated AhR, HNF4α and COUP-TFII genomic binding and effects on gene expression associated with liver-specific function and cell differentiation in response to TCDD. Hepatic ChIPseq data from male C57BL/6 mice at 2 hrs after oral gavage with 30 µg/kg TCDD were integrated with bulk RNA-sequencing (RNAseq) time-course (2 - 72 hrs) and dose-response (0.01 - 30 µg/kg) datasets to assess putative AhR, HNF4α and COUP-TFII interactions associated with differential gene expression. TCDD treatment resulted in the genomic enrichment of 23,701, 11,688, and 9,547 binding regions for AhR, COUP-TFII and HNF4α, respectively, throughout the genome. Functional enrichment analysis of differentially expressed genes (DEGs) identified differential binding enrichment for AhR, COUP-TFII, and HNF4a to regions within liver-specific genes suggesting intersections associated with the loss of liver-specific functions and hepatocyte differentiation. Analysis found that the repression of liver-specific, HNF4α target and hepatocyte differentiation genes, involved increased AhR and HNF4α binding with decreased COUP-TFII binding. Collectively, these results suggested TCDD-elicited loss of liver-specific functions and markers of hepatocyte differentiation involved interactions between AhR, COUP-TFII and HNF4α.
The Promise of Deep Learning for BCIs: Classification of Motor Imagery EEG using Convolutional Neural Network
Authors: Tibrewal Navneet , Leeuwis Nikki , Alimardani Maryam 
Published: June 2021

AbstractMotor Imagery (MI) is a mental process by which an individual rehearses body movements without actually performing physical actions. Motor Imagery Brain-Computer Interfaces (MI-BCIs) are AI-driven systems that capture brain activity patterns associated with this mental process and convert them into commands for external devices. Traditionally, MI-BCIs operate on Machine Learning (ML) algorithms, which require extensive signal processing and feature engineering to extract changes in sensorimotor rhythms (SMR). However, in recent years, Deep Learning (DL) models have gained popularity for EEG classification as they provide a solution for automatic extraction of spatio-temporal features in the signals. In this study, EEG signals from 54 subjects who performed a MI task of left-or right-hand grasp was employed to compare the performance of two MI-BCI classifiers; a ML approach vs. a DL approach. In the ML approach, Common Spatial Patterns (CSP) was used for feature extraction and then Linear Discriminant Analysis (LDA) model was employed for binary classification of the MI task. In the DL approach, a Convolutional Neural Network (CNN) model was constructed on the raw EEG signals. The mean classification accuracies achieved by the CNN and CSP+LDA models were 69.42% and 52.56%, respectively. Further analysis showed that the DL approach improved the classification accuracy for all subjects within the range of 2.37 to 28.28% and that the improvement was significantly stronger for low performers. Our findings show promise for employment of DL models in future MI-BCI systems, particularly for BCI inefficient users who are unable to produce desired sensorimotor patterns for conventional ML approaches.
BioProfiling.jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations
Authors: Vulliard Loan , Hancock Joel , Kamnev Anton , Fell Christopher W. , da Silva Joana Ferreira , Loizou Joanna , Nagy Vanja , Dupré Loïc , Menche Jörg 
Published: June 2021

AbstractMotivationHigh-content imaging screens provide a cost-effective and scalable way to assess cell states across diverse experimental conditions. The analysis of the acquired microscopy images involves assembling and curating morphological measurements of individual cells into morphological profiles suitable for testing biological hypotheses. Despite being a critical step, there is currently no standard approach to morphological profiling and no solution is available for the high-performance Julia programming language.ResultsHere, we introduce BioProfiling.jl, an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. The package contains all the necessary data structures to curate morphological measurements and helper functions to transform, normalize and visualize profiles. Robust statistical distances and permutation tests enable quantification of the significance of the observed changes despite the high fraction of outliers inherent to high-content screens. This package also simplifies visual artifact diagnostics, thus streamlining a bottleneck of morphological analyses. We showcase the features of the package by analyzing a chemical imaging screen, in which the morphological profiles prove to be informative about the compounds’ mechanisms of action and can be conveniently integrated with the network localization of molecular targets.AvailabilityThe Julia package is available on GitHub:https://github.com/menchelab/BioProfiling.jlWe also provide Jupyter notebooks reproducing our analyses:https://github.com/menchelab/BioProfilingNotebooksContactjoerg.menche@univie.ac.at
A gate and clamp regulate sequential DNA strand cleavage by CRISPR-Cas12a
Authors: Naqvi Mohsin M. , Lee Laura , Torres Montaguth Oscar E. , Szczelkun Mark D. 
Published: June 2021

AbstractCRISPR-Cas12a has been widely used for genome editing and diagnostic applications, yet it is not fully understood how RNA-guided DNA recognition activates the sequential cleavage of the non-target strand (NTS) followed by the target strand (TS). Here we used single-molecule magnetic tweezers microscopy, ensemble gel-based assays and nanopore sequencing to explore the coupling of DNA unwinding and cleavage. In addition to dynamic R-loop formation, we also directly observed transient dsDNA unwinding downstream of the 20 bp DNA:RNA hybrid and, following NTS cleavage and prior to TS cleavage, formation of a hyperstable “clamped” Cas12a-DNA intermediate resistant to DNA twisting. Alanine substitution of a conserved aromatic amino acid “gate” in the REC2 domain that normally caps the heteroduplex produced more frequent and extended downstream DNA breathing, a longer-lived twist-resistant state, and a 16-fold faster rate of TS cleavage. We suggest that both breathing and clamping events, regulated by the gate and by NTS cleavage, deliver the unwound TS to the RuvC nuclease and result from previously described REC2 and NUC domain motions.
Does habitat restoration disturb? A case study of a shallow urban water reservoir in western India using cladoceran zooplankton
Authors: Kulkarni Mihir R. , Padhye Sameer M. 
Published: June 2021

ABSTRACTAnthropogenic stressors, including restoration activities, can have ecosystem wide impacts, reflecting in various biotic components, particularly the basal levels in the trophic webs. Functional traits link taxonomic diversity to ecosystem function, thereby enabling a better ecological assessment of ecosystem health. We studied the effects of restoration activities on the community structure and functional diversity of freshwater cladoceran zooplankton in an urban water reservoir. Samples were taken in the early and late phases of the restoration work. Cladoceran species community and functional composition was significantly different between the two phases. There was a considerable reduction in taxonomic richness, functional richness and redundancy in the late phase. Taxonomic beta diversity between the two phases was explained more by nestedness. Habitat degradation due to haphazard restoration measures such as destruction of littoral zone and arbitrary desilting in addition to the dumping of untreated sewage could have contributed to the decrease in species and functional richness within the reservoir.
Lysosomal proteolysis of amyloid beta is impeded by fibrils grown in both acidic and neutral pH environments
Authors: Lambeth Tyler R. , Julian Ryan R. 
Published: June 2021

AbstractAggregation of amyloid-beta (Aβ) into extracellular plaques is a well-known hallmark of Alzheimer’s disease (AD). Similarly, autophagic vacuoles, autophagosomes, and other residual bodies within dystrophic neurites, though more difficult to detect, are characteristic features of AD. To explore the potential intersection between these observations, we conducted experiments to assess whether Aβ fibril formation disrupts lysosomal proteolysis. Fibrils constituted from either Aβ 1-40 or Aβ 1-42 were grown under both neutral and acidic pH. The extent of proteolysis by individual cathepsins (L, D, B, and H) was monitored by both thioflavin T fluorescence and liquid-chromatography combined with mass spectrometry. The results show that all Aβ fibrils are resistant to cathepsin digestion, with significant amounts of undigested material remaining for samples of fibrils grown in both neutral and acidic pH. Further analysis revealed that the neutral-grown fibrils are proteolytically resistant throughout the sequence, while the acid-grown fibrils prevented digestion primarily in the C-terminal portion of the sequence. Fibrils grown from Aβ 1-42 are generally more resistant to degradation compared to Aβ 1-40. Overall, the results indicate that Aβ fibrils formed in the neutral pH environments found in intracellular or extracellular spaces may pose the greatest difficulty for complete digestion by the lysosome, particularly when the fibrils are comprised of Aβ 1-42.
BioCPPNet: Automatic Bioacoustic Source Separation with Deep Neural Networks
Authors: Bermant Peter C 
Published: June 2021

ABSTRACTWe introduce the Bioacoustic Cocktail Party Problem Network (BioCPPNet), a lightweight, modular, and robust UNet-based machine learning architecture optimized for bioacoustic source separation across diverse biological taxa. Employing learnable or handcrafted encoders, BioCPPNet operates directly on the raw acoustic mixture waveform containing overlapping vocalizations and separates the input waveform into estimates corresponding to the sources in the mixture. Predictions are compared to the reference ground truth waveforms by searching over the space of (output, target) source order permutations, and we train using an objective function motivated by perceptual audio quality. We apply BioCPPNet to several species with unique vocal behavior, including macaques, bottlenose dolphins, and Egyptian fruit bats, and we evaluate reconstruction quality of separated waveforms using the scale-invariant signal-to-distortion ratio (SI-SDR) and downstream identity classification accuracy. We consider mixtures with two or three concurrent conspecific vocalizers, and we examine separation performance in open and closed speaker scenarios. To our knowledge, this paper redefines the state-of-the-art in end-to-end single-channel bioacoustic source separation in a permutation-invariant regime across a heterogeneous set of non-human species. This study serves as a major step toward the deployment of bioacoustic source separation systems for processing substantial volumes of previously unusable data containing overlapping bioacoustic signals.
Century plus journeys: using career crafting to explore the career success of pioneer women accountants
Authors: Vidwans Mohini P. , Whiting Rosalind H. 
Published: June 2021

PurposeThe purpose of this study is to explore the struggle for entry and career success of the early pioneer women accountants in Great Britain and its former colonies the USA, Canada, Australia and New Zealand.Design/methodology/approachA career crafting matrix guides the analysis of historical information available on five pioneer women accountants in order to understand their success in gaining entry into the profession and their subsequent careers.FindingsDespite an exclusionary environment, career crafting efforts coupled with family and organizational support enabled these women to become one of the first female accountants in their respective countries. Their struggles were not personal but much broader—seeking social, political, economic and professional empowerment for women.Originality/valueThis is the first paper to utilize the career crafting matrix developed from current female accountants' careers to explore careers of pioneering female accountants. It adds to the limited literature on women actors in accounting and may provide insight into approaching current forms of difference and discrimination.
Perceived food safety and food defense responsibility for farmers, transporters, retailers and consumers
Authors: Larson Ronald B. 
Published: June 2021

PurposeContaminated food is a major source of illnesses around the world. This research seeks to learn how people assign responsibility for two food contamination risks and how they allocate costs to reduce these risks to four members of the food supply chain. The aims are to identify differences between countries and test options to control for cultural differences.Design/methodology/approachA random sample of online panellists from six countries (N = 6,090) was surveyed on how they assigned responsibility for controlling natural and accidental food contamination (traditional food safety) and for controlling intentional contamination (food defense) to farmers, transporters/distributors, retailer grocery stores/restaurants and consumers. They were also asked how they would allocate food safety and defense costs to the four groups. Differences between countries were tested with dummy variables and cultural measures.FindingsIn nearly every country, respondents assigned the least responsibility and allocated the smallest cost shares to consumers. In multivariate models, responsibility and cost-share results differed, suggesting that preferences varied by country and that respondents did not allocate costs the same way they assessed responsibility. The food safety and defense models also differed, implying that the respondents believed the two sources of contamination represented different risks.Originality/valueThis is the first study to examine how adults allocate the responsibility and costs for food safety and defense to farmers, transporters/distributors, retailer grocery stores/restaurants and consumers. Other research did not differentiate between these two food risks. This study also compared Hofstede's cultural measures with the recently developed Minkov's cultural measures.
Board processes revisited: an exploration of the relationship between board processes, board role performance and board effectiveness in comparable European listed companies
Authors: Jansen Peter AM 
Published: June 2021

Purpose
This study aims to analyse the relationships between board processes, board role performance and board effectiveness for a cross-country (UK and Romania) sample of comparable European listed companies.

Design/methodology/approach
The research design is quantitative in nature and based on the survey method, a self-administered questionnaire which was send to 342 chairmen of selected Romanian and British listed companies and which contains validated statements measured through a seven-point Likert-type scale and grouped in validated constructs.

Findings
This study found further empirical evidence that board processes are stronger determinants of board effectiveness than board characteristics and that board roles mediate the relationship between board processes and board effectiveness. It further confirmed the relevance of the three board processes mentioned by Forbes and Milliken (1999) in their seminal work on board decision-making.

Research limitations/implications
The main limitation of this study is the relatively small number of responses (55), which indicates a reduced reliability and generalizability of the results. However, several steps were taken to assure the homogeneity of the sample, starting with a unique data set of firms of comparable size and industry representation.

Practical implications
This study is useful to board directors and chairmen of listed companies, as it can help them to better understand and manage board behaviour.

Originality/value
This study contributes to the limited body of research that investigates specific board process constructs derived from the small team literature and their effect on board effectiveness.
HPC in business: the impact of corporate digital responsibility on building digital trust and responsible corporate digital governance
Authors: Jelovac Dejan , Ljubojević Čedomir , Ljubojević Ljubomir 
Published: June 2021

Purpose
The implementation of high performance computing (HPC) in business (especially small and medium-sized enterprises) is accompanied with mistrust to a certain extent, which has imposed the need for building of digital trust (DTrust) among stakeholders. The purpose of the present paper is to find out the ways on how to build and maintain such trust.

Design/methodology/approach
Analysis and critical reflection on previous research dealing with phenomena of digital transformation (DT), HPC, corporate digital responsibility (CDR) and DTrust have enabled the authors to design their own conceptual model as the answer to the research questions of how, and in what way, CDR influences DTrust.

Findings
The authors have determined that the previous researches pointed to the existence of the correlation between CDR and DTrust although they did not elaborate on this explicitly. It was shown that the DT itself directly influences trust and sustainability. The indirect influence DT has via CDR was the task the authors undertook through designing a new conceptual model within whose frame the authors separately presented the influence of total CDR on DTrust as well as of the specific CDR dimensions on the particular dimensions of DTrust.

Originality/value
The authors tried to offer the conceptual model that exactly determines the relation of individual dimensions of the processed phenomena by analyzing theoretical and empirical researches carried out so far, and eo ipso shed more light on their mutual relation. The authors firmly believe that this paper offers a useful frame for further empirical researches.
Sounds like a broken record: preservation and access of audio-visual records at the South African broadcasting corporation radio
Authors: Ngoasheng Cyril , Ngoepe Mpho , Marutha Ngoako Solomon 
Published: June 2021

Purpose
Audio-visual records produced by public broadcasters play a role in preserving the history, culture and language of a country. The records are used by broadcasters to repeat and support programmes on air. The formats that carry these records such as tapes and compact discs are fragile and have a short life span. This is compounded by evolving technologies and results in obsolete playback equipment, which can result in records not being accessible. This study aims to explore the preservation and access of audio-visual records at the South African Broadcasting Corporation (SABC) radio in Limpopo regional offices.

Design/methodology/approach
Qualitative data were collected through interviews from purposively selected participants in three radio stations of the SABC in the Limpopo province which are Munghana Lonene FM, Phalaphala FM and Thobela FM. The interview data were augmented through participant observation.

Findings
The findings revealed that the SABC radio archive was preserving audio-visual records in obsolete formats such as long plays and cassettes, which also lacked playback equipment. These formats were not properly arranged and were kept in a storage area that was not monitored for decaying and security. It was further established that the radio stations were using IONA technology for retrieval of and access to records while the news division within the radio stations were relying on Electronic News Production System. As audio-visual materials were not catalogued, it proved difficult for users to access these records.

Practical implications
This study adds value to the existing theoretical and conceptual issues that form the ongoing discourse on the preservation of and access to audio-visual records which are often neglected in the developing countries. The study also laid the groundwork for further investigation of the audio-visual records at broadcasting corporations. This is prompted by the findings which established that valuable information has been lost and continues to be lost due to poor management of audio-visual records. Therefore, a further study on migration of content from analogue to digital for the purpose of continuous preservation is recommended.

Originality/value
The study triangulated data collection tools including interviews and participant observation. The context was on the national broadcaster and the focus was on the preservation of and access to audio-visual records for the radio.
Factors affecting organizational adoption and acceptance of computer-based security awareness training tools
Authors: Dahabiyeh Laila 
Published: June 2021

Purpose
As insiders remain to be a main reason behind security breaches, effective information security awareness campaigns become critical in protecting organizations from security incidents. The purpose of this paper is to identify factors that influence organizational adoption and acceptance of computer-based security awareness training tools.

Design/methodology/approach
The paper uses content analysis of online reviews of the top ten computer-based security awareness training tools that received Gartner peer insights Customers’ Choice 2019 award.

Findings
This study identifies nine critical adoption and success factors. These are synthesized into a conceptual framework based on the technology–organization–environment framework. The findings reveal that technological, organizational and environmental factors come into play in adoption decisions but with varying degrees of importance.

Practical implications
This study highlights key factors that technology vendors should take into consideration when designing computer-based security awareness training tools to increase adoption rates.

Originality/value
This research offers a novel contribution to the literature on information security awareness delivery methods by identifying key factors that influence organizational adoption and acceptance of computer-based security awareness training tools. Those factors were identified using content analysis of online reviews, which is a new methodological approach to the information security awareness literature.