bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cnidarian phylogenomic tree fitted with hundreds of 18S leaves
Authors: DeBiasse Melissa B. , Buckenmeyer Ariane , Macrander Jason , Babonis Leslie S. , Bentlage Bastian , Cartwright Paulyn , Prada Carlos , Reitzel Adam M. , Stampar Sergio N. , Collins Allen G. , Daly Marymegan , Ryan Joseph F. 
Published: October 2022

AbstractCnidarians are critical members of aquatic communities and have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet we still lack a well-resolved, taxonomically balanced, cnidarian tree of life to place this research in appropriate phylogenetic context. To move towards this goal, we combined data from 26 new anthozoan transcriptomes with 86 previously published cnidarian and outgroup datasets to generate two 748-locus alignments containing 123,051 (trimmed) and 449,935 (untrimmed) amino acids. We estimated maximum likelihood phylogenies for both matrices under partitioned and unpartitioned site-homogeneous and site-heterogenous models of substitution. We used the resulting topology to constrain a phylogenetic analysis of 1,814 small subunit ribosomal (18S) gene sequences from GenBank. Our results confirm the position of Ceriantharia (tube-dwelling anemones), a historically recalcitrant group, as sister to the rest of Hexacorallia across all phylogenies regardless of data matrix or model choice. We also find unanimous support for the sister relationship of Endocnidozoa and Medusozoa and propose the name Operculozoa for the clade uniting these taxa. Our 18S hybrid phylogeny provides insight into relationships of 15% of extant taxa. Together these data are an invaluable resource for comparative cnidarian research and provide perspective to guide future refinement of cnidarian systematics.
MarR-Dependent Transcriptional Regulation of mmpSL5 induces Ethionamide Resistance in Mycobacterium abscessus
Authors: Rodriguez Ronald , Campbell-Kruger Nick , Camba Jesus Gonzalez , Berude John , Fetterman Rachel , Stanley Sarah 
Published: October 2022

AbstractMycobacterium abscessus (Mabs) is an emerging non-tuberculosis mycobacterial (NTM) pathogen responsible for a wide variety of respiratory and cutaneous infections that are difficult to treat with standard antibacterial therapy. Mabs has a high degree of both innate and acquired antibiotic resistance to most clinically relevant drugs, including standard anti-mycobacterial agents. Ethionamide (ETH), an inhibitor of mycolic acid biosynthesis is currently utilized as a second-line agent for treating multidrug resistant tuberculosis (MDR-TB) infections. Here, we show that ETH has activity against clinical strains of Mabs in vitro at concentrations that are therapeutically achievable. Using transposon mutagenesis and whole genome sequencing of spontaneous drug-resistant mutants, we identified marR (MAB_2648c) as a genetic determinant of ETH sensitivity in Mabs. The gene marR encodes a transcriptional regulator of the TetR family of regulators. We show that MarR represses expression of MAB_2649 (mmpS5) and MAB_2650 (mmpL5). Further, we show that de-repression of these genes in marR mutants confers resistance to ETH, but not other antibiotics. To identify determinants of resistance that may be shared across antibiotics, we also performed Tn-Seq during treatment with amikacin and clarithromycin, drugs currently used clinically to treat Mabs. We found very little overlap in genes that modulate the sensitivity of Mabs to all three antibiotics, suggesting a high degree of specificity for resistance mechanisms in this emerging pathogen.ImportanceAntibiotic resistant infections caused by Mycobacterium abscessus (Mabs) have been increasing in prevalence and treatment is often unsuccessful. Success rates range from 30-50%, primarily due to the high intrinsic resistance of Mabs to most clinically useful antibiotics. New therapeutic strategies, including repurposing of existing antibiotics, are urgently needed to improve treatment success rates. Here, we show that the anti-TB antibiotic ethionamide (ETH) has repurposing potential against Mabs, displaying bacteriostatic activity and delaying emergence of drug resistance when combined with clinically relevant antibiotics currently used against Mabs in vitro. We identified genes that modulated susceptibility of Mabs to ETH. marR encodes a transcriptional regulator that when deleted, confers ETH resistance. Our collective findings can be used to further explore the function of other genes that contribute to ETH susceptibility and help design the next generation of antibacterial regimens against Mabs that may potentially include ETH.
Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing
Authors: Iwakiri Junichi , Tanaka Kumiko , Chujo Takeshi , Yamazaki Tomohiro , Terai Goro , Asai Kiyoshi , Hirose Tetsuro 
Published: October 2022

AbstractThe mammalian cell nucleus contains dozens of membrane-less nuclear bodies that play significant roles in various aspects of gene expression. Several nuclear bodies are nucleated by specific architectural noncoding RNAs (arcRNAs) acting as structural scaffolds. We have reported that a minor population of cellular RNAs exhibits an unusual semi-extractable feature upon using the conventional procedure of RNA preparation and that needle shearing or heating of cell lysates remarkably improves extraction of dozens of RNAs. Because semi-extractable RNAs, including known arcRNAs, commonly localize in nuclear bodies, this feature may be a hallmark of arcRNAs. Using the semi-extractability of RNA, we performed genome-wide screening of semi-extractable long non-coding RNAs to identify new candidate arcRNAs for arcRNA under hyperosmotic and heat stress conditions. After screening stress-inducible and semi-extractable RNAs, hundreds of readthrough downstream-of-gene (DoG) transcripts over several hundreds of kilobases, many of which were not detected among RNAs prepared by the conventional extraction procedure, were found to be stress-inducible and semi-extractable. We further characterized some of the abundant DoGs and found that stress-inducible transient extension of the 3’-UTR made DoGs semi-extractable. Furthermore, they were localized in distinct nuclear foci that were sensitive to 1,6-hexanediol. These data suggest that semi-extractable DoGs exhibit arcRNA-like features and our semi-extractable RNA-seq is a powerful tool to extensively monitor DoGs that are induced under specific physiological conditions.
142 telomere-to-telomere assemblies reveal the genome structural landscape inSaccharomyces cerevisiae
Authors: O’Donnell Samuel , Yue Jia-Xing , Saada Omar Abou , Agier Nicolas , Caradec Claudia , Cokelaer Thomas , Chiara Matteo De , Delmas Stéphane , Dutreux Fabien , Fournier Téo , Friedrich Anne , Kornobis Etienne , Li Jing , Miao Zepu , Tattini Lorenzo , Schacherer Joseph , Liti Gianni , Fischer Gilles 
Published: October 2022

SUMMARYAs population genomics is transitioning from single reference genomes to pangenomes, major improvements in terms of genome contiguity, phylogenetic sampling, haplotype phasing and structural variant (SV) calling are required. Here, we generated theSaccharomyces cerevisiaeReference Assembly Panel (ScRAP) comprising 142 reference-quality genomes from strains of various geographic and ecological origins that faithfully represent the genomic diversity and complexity of the species. The ca. 4,800 non-redundant SVs we identified impact the expression of genes near the breakpoints and contribute to gene repertoire evolution through disruptions, duplications, fusions and horizontal transfers. We discovered frequent cases of complex aneuploidies, preferentially involving large chromosomes that underwent large SVs. We also characterized the evolutionary dynamics of complex genomic regions that classically remain unassembled in short read-based projects, including the 5 Ty families and the 32 individual telomeres. Overall, the ScRAP represents a crucial step towards establishing a high-quality, unified and complete S. cerevisiae pangenome.
Molecular basis of the TRAP complex function in ER protein biogenesis
Authors: Jaskolowski Mateusz , Jomaa Ahmad , Gamerdinger Martin , Shrestha Sandeep , Leibundgut Marc , Deuerling Elke , Ban Nenad 
Published: October 2022

ABSTRACTThe Translocon Associated Protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the translating ribosome to facilitate biogenesis of secretory and membrane proteins1–4. TRAP is essential for the secretion of many hormones, and its key role in the production of the hormone peptide insulin has been particularly well established5,6. The mechanism by which TRAP engages ribosomes and the translocon to facilitate translocation of protein clients in the secretory pathway is not clear. Here, we reveal the molecular architecture of the mammalian TRAP complex and how it engages the translating ribosome associated with Sec61 translocon on the ER membrane. The TRAP complex is anchored to the ribosome via a long tether and its position relative to the ribosome and the translocon is further stabilized by a finger-like loop. This spatial arrangement positions a cradle-like lumenal domain of TRAP below the protein conducting pore of the translocon for interactions with translocated nascent chains. The biological importance of these key interactions is evident by structure-guided TRAP mutations in C. elegans that lead to growth deficits associated with increased ER stress and defects in insulin secretion. Our findings elucidate the molecular basis of the TRAP complex in the biogenesis and translocation of proteins at the ER.
A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection
Authors: Kulsuptrakul Jessie , Turcotte Elizabeth A. , Emerman Michael , Mitchell Patrick S. 
Published: October 2022

SummaryInflammasomes are cytosolic innate immune complexes that play a critical role in host defense against pathogens but can also contribute to inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 senses HIV-1 infection via site-specific cleavage of the CARD8 N-terminus by the HIV protease (HIV-1PR). HIV-1PR cleavage of CARD8 induces pyroptotic cell death and the release of pro-inflammatory cytokines from infected cells, processes that we find are dependent on Toll-like receptor stimulation prior to viral infection. Our evolutionary analyses reveal that the HIV-1PR cleavage site in CARD8 is unique to humans, and that chimpanzee CARD8 does not recognize proteases from HIV or simian immunodeficiency viruses from chimpanzees (SIVcpz). In contrast, SIVcpz does cleave human CARD8, suggesting that SIVcpz was poised to activate the human CARD8 inflammasome prior to its cross-species transmission into humans and implicating the CARD8 inflammasome as a potential driver of HIV pathogenesis.
Discovery of novel papillomaviruses in the critically-endangered Malayan and Chinese pangolins
Authors: Barreat Jose Gabriel Nino , Kamada Anselmo Jiro , de Souza Charles Reuben , Katzourakis Aris 
Published: October 2022

AbstractPangolins are scaly and toothless mammals which are distributed across Africa and Asia. Currently, the Malayan, Chinese and Philippine pangolins are all designated as critically-endangered species. Although few pangolin viruses have been described, their viromes have received more attention following the discovery that they harbour sarbecoviruses related to SARS-CoV-2. Using a large-scale genome mining strategy, we discovered novel lineages of papillomaviruses infecting the Malayan and Chinese pangolins. We were able to assemble 3 complete circular papillomavirus genomes with an intact coding capacity, and 5 additional L1 genes encoding the major capsid protein. Phylogenetic analysis revealed that 7 out of 8 L1 sequences formed a monophyletic group which is the sister lineage to the Tree shrew papillomavirus 1, isolated from Yunnan province in China. Additionally, a single L1 sequence assembled from a Chinese pangolin was placed in a clade closer to alpha- and omegapapillomaviruses. Examination of the SRA data from 95 re-sequenced genomes revealed that 49.3% Malayan pangolins and 50% Chinese pangolins, were positive for papillomavirus reads. Our results indicate that pangolins in South East Asia are the hosts to diverse and highly prevalent papillomaviruses, which may have implications for pangolin health and conservation.
NuMA deficiency causes micronuclei via checkpoint-insensitive k-fiber minus-end detachment from mitotic spindle poles
Authors: van Toorn Marvin , Gooch Amy , Boerner Susan , Kiyomitsu Tomomi 
Published: October 2022

AbstractMicronuclei resulting from improper chromosome segregation foster chromosomal instability in somatic cell division cycles. To prevent micronuclei formation, bundled kinetochore-microtubules called k-fibers must be properly connected to all sister kinetochores on chromosomes via their plus-ends, whereas k-fiber minus-ends must be clustered at the two opposing spindle poles throughout mitosis. The bipolar attachment between sister kinetochores and k-fiber plus-ends is carefully monitored by the spindle assembly checkpoint and further promoted by error-correction mechanisms. However, how k-fiber minus-end clustering is maintained and monitored remains poorly understood. Here, we show that degradation of the Nuclear Mitotic Apparatus (NuMA) protein by auxin-inducible degron technologies in human cells results in micronuclei formation through k-fiber minus-end detachment from focused spindle poles during metaphase. Importantly, this k-fiber minus-end detachment creates misaligned chromosomes that maintain chromosome biorientation and do not activate the mitotic checkpoint, resulting in lagging chromosomes in anaphase. Moreover, we find that NuMA depletion causes centrosome clustering defects in tetraploid cells, leading to an increased frequency of multipolar divisions. Together, our data indicate that NuMA-mediated minus-end clustering of k-fibers and spindle microtubules is critical for faithful chromosome segregation. Similar to erroneous merotelic kinetochore attachments, detachment of k-fiber minus-ends from metaphase spindle poles evades spindle checkpoint surveillance and may therefore be a source of genomic instability in dividing cells.
Huntingtin is essential for synaptic plasticity in the adult hippocampus
Authors: Barron Jessica C. , Nafar Firoozeh , Parsons Matthew P. 
Published: October 2022

AbstractHuntingtin (HTT), an exceptionally large protein with hundreds of interacting partners within the central nervous system, has been extensively studied due to its role in Huntington’s disease (HD) pathology. HD is a monogenic disorder caused by a polyglutamine repeat expansion in the HTT gene, which results in the production of a pathogenic mutant huntingtin (mHTT) protein, and toxic effects of this mutant protein in the context of HD have been well-established. Less-established, however, is the role of wild type HTT (wtHTT) in the adult brain, particularly in areas outside the corticostriatal pathway. wtHTT has previously been suggested to play a vital role in cellular functions that promote synapse homeostasis, such as fast axonal transport of synaptic cargo, vesicle replenishment and receptor localization and stability. Synaptic dysfunction precedes and predicts cell death in many neurodegenerative diseases including HD (termed synaptopathies) and whether proper synaptic transmission can be maintained without wtHTT in extrastriatal brain areas such as the hippocampus remains unknown. Consequences of wtHTT reduction in the adult brain are of particular importance as clinical trials for many non-selective HTT-lowering therapies for HD are underway, which are unable to distinguish between mHTT and wtHTT, and therefore reduce levels of both proteins. We investigated the consequences of wtHTT loss of function in the CA3-CA1 pathway of the adult hippocampus using a conditional knockout mouse model and found that 1-2 month deletion of wtHTT in excitatory hippocampal neurons inhibits post-tetanic potentiation and completely abolishes NMDA receptor-dependent long-term potentiation in these animals. These data reveal a novel role of wtHTT as an essential regulator of short- and long-term plasticity in the adult hippocampus.
Securing ADS-B data transmissions using blockchain: a comprehensive survey and analysis
Authors: Pennapareddy Swathi , Natarajan K. 
Published: October 2022

Purpose
The purpose of this paper is to study the various solutions and recommendations provided by researchers in applying the blockchain concept to different problems in aviation industry. It will discuss and highlight the specific approaches that leverages blockchain to mitigate the automatic dependent surveillance-broadcast (ADS-B) security issues. Furthermore, it introduces an innovative design and method to secure ADS-B data using a tamper-resistant distributed public ledger of authenticated flight plans and validates the position and other parameters of the associated aircraft identifier against the flight paths/routes that are stored in the blockchain ledger.

Design/methodology/approach
ADS-B is the key technology that is mandated by Federal Aviation Administration in USA by 2020. However, ADS-B data is neither encrypted nor authenticated. This paper proposes a novel solution using blockchain to secure the ADS-B data communications and in-depth analysis of existing solutions covering the following aspects: classification of various possible attacks on ADS-B. Presents various solutions proposed by different researchers regarding use of blockchain in aviation industry. Discuss a new solution to secure ADS-B using blockchain. Discuss the high-level architectural framework of the proposed and patented solution. Finally, presents the conclusions and future work scope.

Findings
While the main intention of this paper is to bring together all the existing solutions using blockchain to secure aviation and ADS-B data at one place, the proposed novel solution could contribute to maintaining security and privacy for aircrafts flying in the airspace at any point in time. Continuously securing the ADS-B data transmissions based upon the filed flight plans in real time can provide a mechanism to identify spoofed aircraft messages and communicate the same to ground stations for authentication of existence of such a malicious aircraft. Thus, this solution also differs from all the existing ones.

Practical implications
As aviation industry is in its infancy stage in implementing blockchain-based solutions, practical implementation of the proposed concept might take longer.

Originality/value
This paper is a comprehensive survey and review paper. To the best of the authors’ knowledge, this is the first of its kind that presents various use cases for usage of blockchain in aviation industry along with a detailed review of existing proposed or implemented solutions using blockchain to secure ADS-B data. This can serve as an invaluable reference for the future researchers on this topic in both industry and academia.
On the micro-foundations of corporate social responsibility: a perspective based on dynamic managerial capabilities
Authors: Chen Yantai , Guo Yanlin , Hu Xuhui 
Published: October 2022

PurposeThis study proposes that the three core underpinnings of dynamic managerial capabilities (DMCs) – managerial cognition, managerial human capital and managerial social capital – represent individual-level micro-foundations that influence corporate social responsibility (CSR). It further explores the interaction mechanism between the three underpinnings in influencing CSR, and their influence depends on the technological turbulence caused by big-data-related technologies.Design/methodology/approachThis study uses a quantitative research method and partial least squares structural equation modelling (PLS-SEM) to test the relationship between latent factors based on a sample of 270 Chinese top managers.FindingsThe three core underpinnings of DMCs are positively related to CSR. Managerial human capital and managerial social capital mediate the relationship between managerial cognition and CSR. Technological turbulence's moderating effects are also tested. Specifically, technological turbulence amplifies the positive relationship between managerial cognition, managerial human capital and CSR but negatively moderates the relationship between managerial social capital and CSR.Originality/valueWhy are some firms more willing to participate in CSR than others mainly depend on the fact that the actual participants of CSR are the top managers who formulate strategies and implement CSR plans. This study, grounded in the DMCs framework and the upper echelons perspective, is arguably the first to link DMCs' three core underpinnings and CSR, and further explore the multiple drivers' mechanisms and boundary conditions. This study contributes to individual micro-foundation of CSR literature, and advances the understanding of whether and how top managers influence CSR engagement.
Preparation and tribological performance of MoS2 nanoparticles supported on fly ash microparticles
Authors: Hu Kunhong , Miao Yan , Lu Ziyan 
Published: October 2022

Purpose
This paper aims to explore the preparation and tribological performance of MoS2 nanoparticles supported on fly ash (FA) microparticles.

Design/methodology/approach
FA was activated by NaOH, oleic acid and HCl to obtain three modified FA samples. Nano-MoS2 was deposited on them to form MoS2/FA additives for poly-α-olefin (PAO) modification. Tribological tests were conducted on a reciprocating rig through the ball-on-disk friction manner. Using X-ray diffraction, scanning electron microscope, energy dispersive spectrometer, Raman spectrometer and element analyzers, the products and their lubrication mechanisms were characterized.

Findings
At 1.5 Wt.%, nano-MoS2 and MoS2/FA could remarkably improve the tribological properties of PAO. The nano-MoS2 deposited on the HCl-activated FA presented better lubrication performance than nano-MoS2. It could reduce friction and wear by approximately 27% and approximately 66%, respectively. The lubrication of MoS2/FA can be attributed to the formation of MoS2 and carbon containing lubricating film.

Originality/value
FA was applied as a supporter to prepare MoS2/FA lubricants. The reuse of FA, a solid waste, is important for environmental protection. Moreover, MoS2/FA is more economical than nano-MoS2 as a lubricant, because it contains approximately 71% of low-cost FA.