bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Deep Convolutional Neural Network for SARS-CoV-2 Variants Classification
Authors: Mwanga Mike J. , Obura Hesborn O. , Evans Mudibo , Awe Olaitan I. 
Published: August 2023

AbstractHigh-throughput sequencing techniques and sequence analysis have enabled the taxonomic classification of pathogens present in clinical samples. Sequencing provides an unbiased identification and systematic classification of pathogens and this is generally achieved by comparing novel sequences to pre-existing annotated reference databases. However, this approach is limited by large-scale reference databases which require considerable computational resources and skills to compare against. Alternative robust methods such as machine learning are currently employed in genome sequence analysis and classification, and it can be applied in classifying SARS-CoV-2 variants, whose continued evolution has resulted in the emergence of multiple variants.We developed a deep learning Convolutional Neural Networks-Long Short Term Memory (CNN-LSTM) model to classify dominant SARS-CoV-2 variants (omicron, delta, beta, gamma and alpha) based on gene sequences from the surface glycoprotein (spike gene). We trained and validated the model using > 26,000 SARS-CoV-2 sequences from the GISAID database. The model was evaluated using unseen 3,057 SARS-CoV-2 sequences. The model was compared to existing molecular epidemiology tool, nextclade.Our model achieved an accuracy of 98.55% on training, 99.19% on the validation and 98.41% on the test dataset. Comparing the proposed model to nextclade, the model achieved significant accuracy in classifying SARS-CoV-2 variants from unseen data. Nextclade identified the presence of recombinant strains in the evaluation data, a mechanism that the proposed model did not detect.This study provides an alternative approach to pre-existing methods employed in the classification of SARS-CoV-2 variants. Timely classification will enable effective monitoring and tracking of SARS-CoV-2 variants and inform public health policies in the control and management of the COVID-19 pandemic.
Structural basis of archaeal FttA-dependent transcription termination
Authors: Wang Chengyuan , Molodtsov Vadim , Sanders Travis J. , Marshall Craig J. , Firlar Emre , Kaelber Jason T. , Santangelo Thomas J. , Ebright Richard H. 
Published: August 2023

AbstractThe ribonuclease FttA mediates factor-dependent transcription termination in archaea1–3. Here, we report the structure of aThermococcus kodakarensistranscription pre-termination complex comprising FttA, Spt4, Spt5, and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic center and that enables endonucleolytic cleavage of RNA by FttA, followed by 5’→3’ exonucleolytic cleavage of RNA by FttA and concomitant 5’→3’ translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, reveal functional homology between archaeal and eukaryotic factor-dependent termination, and reveal fundamental mechanistic similarities in factor-dependent termination in the three domains of life: bacterial, archaeal, and eukaryotic.One sentence summaryCryo-EM reveals the structure of the archaeal FttA pre-termination complex
Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors
Authors: Carreira Raquel , Aguado F. Javier , Crugeiras Maria , Sebesta Marek , Krejci Lumir , Blanco Miguel G. 
Published: August 2023

AbstractHomologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication/recombination intermediates. Here, we employed a biochemical approach to demonstrate that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we confirm that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursorin vitro.Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.
BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes
Authors: Dokaneheifard Sadat , Gomes Dos Santos Helena , Valencia Monica Guiselle , Arigela Harikumar , Shiekhattar Ramin 
Published: August 2023

AbstractIntegrator is a multi-subunits protein complex involved in regulation of gene expression. Several Integrator subunits have been found to be mutated in human neurodevelopmental disorders, suggesting a key role for the complex in the development of nervous system.BRAT1is similarly linked with neurodegenerative diseases and neurodevelopmental disorders such as rigidity and multifocal-seizure syndrome. Here, we show that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 and form a trimeric complex in human HEK293T cells as well as in pluripotent human embryonal carcinoma cell line (NT2). We find thatBRAT1depletion disrupts the differentiation of NT2 cells into astrocytes and neural cells. Loss ofBRAT1results in inability to activate many neuronal genes that are targets of REST, a neuronal silencer. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations inBRAT1diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex.HighlightsIntegrator subunits INTS9 and INTS11 tightly interact with BRAT1Depletion ofBRAT1causes a dramatic delay in human neural differentiationBRAT1 and INTS11 module targets the promoters of neural marker genes and co-regulates their expression. The recruitment of INTS11 to these sites is BRAT1-dependent.Pathogenic E522K mutation inBRAT1disrupts its interaction with INTS11/INTS9 heterodimer.
Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains
Authors: Gu Yajie , Li Huan , Deep Amar , Enustun Eray , Zhang Dapeng , Corbett Kevin D. 
Published: August 2023

SummaryProkaryotes encode diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here we reveal the structural basis for activation ofBacillus cereusShedu. In the inactive homotetramer, a key catalytic residue in Shedu’s nuclease domain is sequestered away from the catalytic site. Activation involves a conformational change that completes the active site and promotes assembly of a homo-octamer for coordinated double-strand DNA cleavage. Removal of Shedu’s N-terminal domain ectopically activates the enzyme, suggesting that this domain allosterically inhibits Shedu in the absence of infection. Bioinformatic analysis of nearly 8,000 Shedu homologs reveals remarkable diversity in their N-terminal regulatory domains: we identify 79 domain families falling into eight functional classes, including diverse nucleic acid binding, enzymatic, and other domains. Together, these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse N-terminal domains that likely respond to a range of infection-related signals.
Microbiome Analysis of the Eastern Oyster As a Function of Ploidy and Seasons
Authors: Pathak Ashish , Marquez Mario , Stothard Paul , Chukwujindu Christian , Su Jian-Qiang , Zhou Yanyan , Zhou Xin-Yuan , Jagoe Charles H. , Chauhan Ashvini 
Published: August 2023

AbstractShellfish, such as the eastern oysters (Crassostrea virginica) are not only valued as seafood but also for the ecosystem services they provide, including improving water quality and reducing eutrophication. Excess N causes eutrophication, harmful algal blooms, fish kills and overall decline of estuarine ecosystems resulting in economic losses. Oyster reefs sequester N and enhance denitrification processes, however, information on the N cycling oyster microbiome is scarce with most studies focusing on random grab samples or on pathogens, such asVibrio spp. Further, triploid oysters are often used for aquaculture, as they grow faster than diploids, but there is little information on potential microbiome differences with ploidy. To address these knowledge gaps, diploid and triploid farmed oysters were collected at monthly intervals over one year and analyzed using a coupled approach encompassing shotgun metagenomics and quantitative microbial elemental cycling (QMEC) qPCR assays. Overall, the genusPsychrobacterdominated the core microbiome across all samples, regardless of season or ploidy, followed bySynechococcus,Pseudomonas,PseudoalteromonasandClostridium.Psychrobacterabundances increased significantly in the colder months; the same trend was also observed in the alpha and beta diversity. However, warmer months had increased bacterial diversity relative to colder months. Gene functional profiles were similar among seasons and ploidy, with respiration and metabolism of carbohydrates, RNA, and proteins as dominant functions. There were strong positive correlations between abundance of the “core” microbiome taxa and gene functions associated with central metabolism, DNA and carbohydrate metabolism, strongly suggesting the functional role ofPsychrobacterin the microbiome. Metagenome assembly was performed to characterize dominant species, followed by phylogenetic analysis of select MAGs (metagenome-assembled genomes), further supporting the presence of multiplePsychrobacterspp. Sequence-based identification of denitrification genes in thePyschrobacterMAGs indicated the presence ofnorB,narH,narI,nirK, andnorB. QMEC analysis indicated C and N cycling genes were most abundant, with no discernable patterns due to seasons or ploidy. Among N cycling genes, the nosZII clade was dominant, which is likely responsible for the eastern oysters potential for bioextraction and enhancing water quality via denitrification.
Structural basis for IL-33 recognition and its antagonism by the helminth effector protein HpARI
Authors: Jamwal Abhishek , Colomb Florent , McSorley Henry J. , Higgins Matthew K. 
Published: August 2023

AbstractInterleukin 33 (IL-33) plays a significant role in inflammation, allergy, and host defence against parasitic helminths. The model gastrointestinal nematodeHeligmosomoides polygyrus bakeri(Hp) secretes the Alarmin Release Inhibitor (HpARI), a potent effector protein which suppresses protective immune responses and asthma in its host by inhibiting IL-33 signalling. Here we reveal the structure of HpARI bound to mouse IL-33. HpARI contains three CCP-like domains, and we show that it contacts IL-33 primarily through the second and third of these. A large loop which emerges from CCP3 directly contacts IL-33 and structural comparison shows that this overlaps with the binding site on IL-33 for its receptor, ST2, preventing formation of a signalling complex. Truncations of HpARI which lack the large loop from CCP3 are not able to block IL-33-mediated signalling in a cell-based assay and in anin vivomodel of asthma. This shows that direct competition between HpARI and ST2 is responsible for suppression of IL-33-dependent responses. This first structure of IL-33 bound to a pathogen-based inhibitor will guide future approaches to design therapeutics blocking IL-33-mediated allergic and inflammatory conditions.
Foxg1bimodally tunesL1-mRNA and -DNA dynamics in the developing murine neocortex
Authors: Liuzzi Gabriele , Mallamaci Antonello 
Published: August 2023

ABSTRACTFoxg1masters telencephalic development via a pleiotropic control of its articulation.L1is a large retrotransposon family expressed within CNS and suggested to contribute to its genomic plasticity. Foxg1 represses gene transcription, andL1elements share putative Foxg1 binding motifs, suggesting the former might limit telencephalic expression (and activity) of the latter. We tested such prediction, in vivo as well as in engineered primary neural cultures, by loss- and gain-of-function approaches. We showed thatFoxg1-dependent, transcriptionalL1repression specifically occurs in neopallial neuronogenic progenitors and post-mitotic neurons, where it is supported by specific changes in theL1epigenetic landscape. Unexpectedly, we also found that Foxg1 physically interacts withL1-mRNA and positively impacts on neonatal neopalliumL1-DNA content, antagonizing the retrotranscription-suppressing activity exerted by Mov10 and Ddx39a helicases. To our knowledge,Foxg1is the first CNS patterning gene acting as a bimodal retrotransposon modulator, limiting and promotingL1transcription and amplification, respectively, within a specific domain of the developing mouse brain.
Mitigating teleworkers' perceived technological complexity and work strains through supportive team communication
Authors: Wahl Ingrid , Wolfgruber Daniel , Einwiller Sabine 
Published: August 2023

PurposeTeleworkers need to use information and communication technology (ICT) to communicate and collaborate with their team members, however, when new and complicated information systems should be used, this can lead to stress. Receiving adequate information and emotional support from team members could reduce the stress caused by technological complexity and subsequent work and occupational strains.Design/methodology/approachParticipants (N = 400) teleworked at least half of their working hours and were employed in organizations with a minimum of 250 employees. Data from the online survey were analyzed using structural equation modeling.FindingsResults demonstrate that aspects of informational and emotional communication contribute to perceived social support from team members, with emotional communication explaining more variance. Stress from technological complexity is mitigated by both supportive team communication and the extent of telework. Perceived stress from technological complexity, however, still increases work and occupational strains.Practical implicationsThe findings emphasize the importance of supportive internal communication to foster a collaborative telework environment. Practitioners in internal communication need to encourage teleworkers to help each other with adequate information and provide also emotional support to overcome the negative effects of complex ICT.Originality/valueThe study shows that supportive communication among team members is important for teleworkers to reduce work and occupational strains, especially when facing difficulties with complex ICT.
A game theory-based analysis of merchants’ mobile payment adoption using hybrid SEM-neural network approach
Authors: Naysary Babak 
Published: August 2023

Purpose
Driven by the evidence from the literature on the significance of mobile (m-)payment in economic growth and productivity and at the same time the relative dismal adoption of this service, the purpose of present paper is to elucidate the merchants’ m-payment adoption from the perspective of trust, drawing upon the game theory framework, in the Malaysian context.

Design/methodology/approach
An online survey consisting of 302 respondents was carried out to investigate the impact of trust and opportunism on merchants’ perceived trustworthiness using a two-staged structural equation modeling–neural network approach to determine the significance and relative importance of variables. This study also applies a game-theoretic approach to analyze the impact of trust on the relationship between merchants and m-payment service providers.

Findings
The results indicate a positive and statistically significant relationship between merchant trust, merchant opportunism and perceived trustworthiness, and a statistically significant negative relationship was found between m-payment provider opportunism and perceived trustworthiness. The findings from the prisoner’s dilemma two-player model indicate that the scenarios of mutual trust and mutual opportunism as paradigmatic of cooperation and defection produce the best and worse outcomes, respectively. An intriguing result was the positive impact of merchant opportunism on perceived trustworthiness, which indicates a very calculative orientation of merchants in m-payment contracting.

Originality/value
To the best of the authors’ knowledge, this is among the first attempts to propose a game theory approach to the interaction between merchants and m-payment providers under the framework of trust and opportunism. A game theory study in the context of m-payment adoption can contribute to the theoretical literature by providing insights into the decision-making processes of merchants. By incorporating trust and opportunism into the game theory model, we can gain a better understanding of how they affect the decision-making process and overall adoption rates. The conclusions and implications provide useful insights for managers of both m-payment platforms and merchants in this relational exchange. The results of the present research can provide insights into the factors that influence merchant decisions and guide them toward suitable partnerships for successful adoption and can guide authorities for policy interventions and supporting adoption efforts.
Pandemic lockdown as policy window for street-level innovation of health and substitution treatment services for people who use drugs
Authors: Nygaard-Christensen Maj , Houborg Esben 
Published: August 2023

Purpose
This paper aims to examine policy innovation among street-level bureaucrats at low-threshold services to people who use drugs during the COVID-19 pandemic in Denmark.

Design/methodology/approach
This paper builds on two research projects conducted during the first pandemic lockdown in Denmark. The first is a case study of how COVID-19 impacted on people who use drugs (PWUD) and services for PWUD at the open drug scene in the neighborhood of Vesterbro in Copenhagen. The second is an ethnographic study of how users of services at the intersection of drug use and homelessness were impacted by lockdown.

Findings
Drawing on Kingdon’s “multiple policy streams” approach, this study shows how lockdown opened a “policy window” for innovating services to people who use drugs. This paper further shows how the pandemic crisis afforded street-level bureaucrats new possibilities for acting as “policy entrepreneurs” in a context where vertical bureaucratic barriers and horizontal cross-sectoral silos temporarily collapsed. Finally, the authors show how this had more lasting effects through the initiation of outreach opioid substitution treatment.

Social implications
In Denmark, the emergence of a “policy window” for street-level bureaucrats to act as street-level “entrepreneurs” occurred in a context of rapid government response to the pandemic. For crises to act as “policy windows” for innovation depends on strong, preexisting institutional landscapes.

Originality/value
This paper adds to existing literature on policy innovation during COVID-19 in two ways: methodologically by contributing an ethnographically grounded approach to studying policy innovation and theoretically by examining the conditions that allowed policy innovation to occur.
Asian Paints Company Limited: post-merger and acculturation challenges
Authors: Sinha Subhashis , Jain Nikunj Kumar , Singh Sachin , Nambudiri Ranjeet 
Published: August 2023

Learning outcomes
The case has the following learning objectives: to understand the dilemmas that an emerging market MNC faces during pre-and post-acquisition scenarios; understand and appreciate the basic tensions that arise when two different companies with different cultural setups are integrated; understand the importance of creating a culture integration road map to leverage the synergies of two successful companies; and understand the role of leadership in leading and managing change.

Case overview/synopsis
Asian Paints Ltd. has been a market leader in the Indian paint market for over five decades (since 1967). Over the years, starting in 1978, the company has steadily spread its footprint in the international arena as well. As of 2017, Asian Paints was a leader in 10 overseas markets, one of the top 3 paint companies in the Middle East, the largest paint manufacturing company in South Asia, and served 60 markets across the world. The international business contributed to around 12% of the company’s group turnover. In line with its long-term vision and to consolidate its presence in emerging markets, the company acquired Causeway Paints, a leading paint company in Sri Lanka, in April 2017. Asian Paints had a presence in Sri Lanka since 1999. Mr. Jatin Upadhyay, International Business Unit Head for Asian Paints, had played significant roles in the past in such acquisitions and was well aware of the impending challenges that came with such acquisitions. How would the integration of the two distinct entities be made possible without losing the overarching objective? How would the transition be managed? How would the cultural transition take place? What and how would the role be handled by the General Manager (GM) of Causeway Lanka? How would the new organisational structure support the transition? The case illustrates the complex management challenges that arise when a leading enterprise from a different country (Asian Paints) acquires a leading company in a different country, in this case, Causeway Paints, Sri Lanka.

Complexity academic level
The target audience for this case study is the students pursuing a post-graduate programme in management or an executive post-graduate programme in management. The case can also be used for management development programmes for experienced participants who are interested in understanding the possible scenarios that may arise after an acquisition when managing an international subsidiary in a different cultural setting.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 6: Human Resource Management.