bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virus-encoded Shemin pathway highlights the importance of tetrapyrrole metabolism during host infection
Authors: Wegner Helen , Roitman Sheila , Kupczok Anne , Braun Vanessa , Woodhouse Jason , Grossart Hans-Peter , Zehner Susanne , Béjà Oded , Frankenberg-Dinkel Nicole 
Published: December 2023

ABSTRACTTetrapyrroles such as heme, chlorophyll, or vitamin B12are among the most complex molecules synthesised by nature and play a crucial role in many vital processes such as respiration, photosynthesis, methanogenesis, and catalysis. All modified tetrapyrroles are derived from the common precursor molecule 5-aminolevulinic acid (5-ALA). However, 5-ALA can be synthesised in two different ways. While alphaproteobacteria, mammals, and birds use the so-called Shemin pathway, all other bacteria, archaea, and plants use the C5 pathway. Here, we present evidence for the presence of 5-ALA synthase genes of the Shemin pathway in the genomes of viruses (valaS) that infect bacteria (bacteriophages) in marine and freshwater environments. These genes either occur in a three-gene cassette with two heme catabolising enzymes involved in linear tetrapyrrole biosynthesis, as broken cassettes or as individual genes. valaSencodes a functional enzyme, as shown by the enzymatic turnover of the co-substrates succinyl-Coenzyme A and glycine in anEscherichia colistrain overexpressing valaS. Phylogenetic analysis in combination with three-dimensional structure prediction supported our data that the viral sequences encode active enzymes. Interestingly, the viral valaSsequence is capable of functionally complementing a 5-ALA-auxotrophicEscherichia colistrain, which lacks one of the two enzymes of the C5 pathway. Host prediction suggests that different valaScarrying phages might infect bacteria that either utilise the Shemin or the C5 pathway for 5-ALA biosynthesis. Our results thus support the hypothesis that metabolic reprogramming and maintenance of the host bacterium’s energy metabolism are crucial during bacteriophage infection and that tetrapyrroles play a key role in this process.
LncRNA Bigheart trans-activates gene expression in a feed forward mechanism that facilitates calcineurin-NFAT signaling in myocardial hypertrophy
Authors: Mangraviti Nicolò , Rühle Frank , Kinet Virginie , Hegenbarth Jana-Charlotte , Dirkx Ellen , Spanò Giulia , De Majo Federica , Peppas Panagiotis , Martens Leonie , Gandhi Shrey , Colpaert Robin , Rupérez Celia , Olieslagers Servé , Falcao-Pires Inês , Calore Martina , Witten Anika , da Costa Martins Paula , Mayr Manuel , Müller Oliver , Stoll Monika , De Windt Leon J. 
Published: December 2023

ABSTRACTTerminally differentiated cardiomyocytes exhibit hypertrophy as a default response to injury by translating biomechanical stress into a complex network of intracellular signaling events. The molecular intricacies how calcium-dependent signaling engage molecular circuits and epigenetic modifications to activate deleterious gene programs remain enigmatic. Here we report on the re-activation of the evolutionarily conserved lncRNA “Bigheart”, which is repressed in the postnatal myocardium and quickly re-activated in a calcineurin-NFAT-dependent fashion in the diseased myocardium in man and mouse. In line, AAV9-mediated overexpression of lncRNABigheartin otherwise healthy primary cardiomyocytes or mouse hearts suffices to drive maladapative hypertrophy. Conversely, mice receiving a “Gapmer” antisense oligonucleotide designed to specifically silence endogenous lncRNABigheartdisplay resistance to biomechanical stress-induced myocardial remodeling, indicating its requirement in left ventricular hypertrophy. Mechanistically, lncRNABigheartrecruits the RNA binding proteins hnRNP-F1 and HMGB1 to modulate the local chromatin environment andtrans-activateBighearttarget genes includingRcan1to stimulate calcineurin-NFAT coupling. Our observations confirm that human heart failure arises from specific susceptibilities in gene regulatory circuits that are amenable for therapeutic intervention using RNA-based therapeutics.
Chemical mutagenesis ofListeria monocytogenesfor increased tolerance to benzalkonium chloride shows independent genetic underpinnings and off-target antibiotic resistance
Authors: Bechtel Tyler D. , Hershelman Julia , Ghoshal Mrinalini , McLandsborough Lynne , Gibbons John G. 
Published: December 2023

AbstractListeria monocytogenes, a potentially fatal foodborne pathogen commonly found in food processing facilities, creates a significant economic burden that totals more than $2 billion annually in the United States due to outbreaks. Quaternary ammonium compounds (QACs), including benzalkonium chloride (BAC), are among the most widely used sanitizers to inhibit the growth and spread ofL. monocytogenesfrom food processing facilities. However, resistance to QACs has been increasing inL. monocytogenesand different genetic mechanisms conferring resistance have been discovered. Here, we used ethyl methanesulfonate (EMS) to chemically mutagenize the BAC-susceptible strain,L. monocytogenesFSL-N1-304. We isolated two mutants with increased tolerance to BAC compared to the parental strain. Next, we assessed the off-target effect of increased tolerance to BAC by measuring the minimum inhibitory concentrations (MICs) of a diverse set of antibiotics, revealing thatmut-1andmut-2displayed significantly increased resistance to fluoroquinolone antibiotics compared to the parental strain. We then sequenced the genomes of the parental strain and both mutants to identify mutations that may be involved in the increased resistance to BAC. We identified 3 and 29 mutations inmut-1andmut-2, respectively.mut-1contained nonsynonymous mutations indagK(a diacylglycerol kinase), lmo2768 (a permease-encoding gene), andlmo0186(resuscitation promoting factor).mut-2contained a nonsense mutation in the nucleotide excision repair enzyme UvrABC system protein B encoding gene,uvrB, which likely accounts for the higher number of mutations observed. Transcriptome analysis in the presence of BAC revealed that genes related to the phosphotransferase system and internalins were upregulated in both mutants, suggesting their significance in the BAC stress response. These two mutants provide insights into alternative mechanisms for increased BAC tolerance and could further our understanding of howL. monocytogenespersists in the food processing environment.
Role of two modules controlling the interaction between SKAP1 and SRC kinases Comparison with SKAP2 architecture and consequences for evolution
Authors: Levillayer Laurine , Brighelli Camille , Demeret Caroline , Sakuntabhai Anavaj , Bureau Jean-François 
Published: December 2023

AbstractSRC kinase associated phosphoprotein 1 (SKAP1), an adaptor for protein assembly, plays an important role in the immune system such as stabilizing immune synapses. Understanding how these functions are controlled at the level of the protein-protein interactions is necessary to describe these processes and to develop therapeutics. Here, we dissected the SKAP1 modular organization to recognize SRC kinases and compared it to that of its paralog SRC kinase associated phosphoprotein 2 (SKAP2). Different conserved motifs common to either both proteins or specific to SKAP2 were found using this comparison. Two modules harboring different binding properties between SKAP1 and SKAP2 were identified: one composed of two conserved motifs located in the second interdomain interacting at least with the SH2 domain of SRC kinases and a second one composed of the DIM domain modulated by the SH3 domain and the activation of SRC kinases. This work suggests a convergent evolution of the binding properties of some SRC kinases interacting specifically with either SKAP1 or SKAP2.
Modeling the Depth of Cellular Dormancy from RNA-sequencing data
Authors: Wei Michelle Yuchen , Yao Guang 
Published: December 2023

AbstractHigh-throughput transcriptome RNA sequencing is a powerful tool for understanding dynamic biological processes. Here, we present a computational framework, implemented in an R package QDSWorkflow, to characterize heterogeneous cellular dormancy depth using RNA-sequencing data from bulk samples and single cells.
Restoration of the FunctionalnifGene Cluster by Seven Excision and Two Inversion Events during Heterocyst Development in the Nitrogen-Fixing CyanobacteriumCalothrixsp. NIES-4101
Authors: Uesaka Kazuma , Banba Mari , Chiba Sotaro , Fujita Yuichi 
Published: December 2023

AbstractIn the genome of the heterocystous cyanobacteriumCalothrixsp. NIES-4101 (NIES-4101), the four genes essential for nitrogen fixation (nifB,nifH,nifD, andnifK) are highly fragmented into 13 parts in a 350-kb chromosomal region, and four of these parts are encoded in the reverse strand. Such a complex fragmentation feature makes it difficult to restore the intactnifBHDKgenes by the excision mechanism found in thenifDgene of theAnabaenasp. PCC 7120 heterocyst. To examine the nitrogen-fixing ability of NIES-4101, we confirmed that NIES-4101 grew well on combined nitrogen-free medium and showed high nitrogenase activity, which strongly suggested that the completenifBHDKgenes are restored by a complex recombination process in heterocysts. Next, we resequenced the genome prepared from cells grown under nitrogen-fixing conditions. Two contigs covering the completenifHDKandnifBgenes were found byde novoassembly of the sequencing reads. In addition, DNA fragments covering thenifBHDKoperon were successfully amplified by PCR. We propose that the process ofnifBHDKrestoration occurs as follows. First, thenifD-nifKgenes are restored by four excision events. Then the completenifHandnifBgenes are restored by two excision events followed by two successive inversion events between the inverted repeat sequences and one excision event, forming the functionalnifgene cluster,nifB-fdxN-nifS-nifU-nifH-nifD-nifK. All genes coding recombinases responsible for these nine recombination events are located close to the terminal repeat sequences. The restoration of thenifBHDKgenes in NIES-4101 is the most complex genome reorganization reported in heterocystous cyanobacteria.
Glioma Cells Secrete Collagen VI to Facilitate Invasion
Authors: Cha Junghwa , Ding Erika A. , Carvalho Emily M. , Fowler Annabelle , Aghi Manish K. , Kumar Sanjay 
Published: December 2023

AbstractWhile glioblastoma (GBM) progression is associated with extensive extracellular matrix (ECM) secretion, the causal contributions of ECM secretion to invasion remain unclear. Here we investigate these contributions by combining engineered materials, proteomics, analysis of patient data, and a model of bevacizumab-resistant GBM. We find that GBM cells cultured in engineered 3D hyaluronic acid hydrogels secrete ECM prior to invasion, particularly in the absence of exogenous ECM ligands. Proteomic measurements reveal extensive secretion of collagen VI, and collagen VI-associated transcripts are correspondingly enriched in microvascular proliferation regions of human GBMs. We further show that bevacizumab-resistant GBM cells deposit more collagen VI than their responsive counterparts, which is associated with marked cell-ECM stiffening. COL6A3 deletion in GBM cells reduces invasion, β-catenin signaling, and expression of mesenchymal markers, and these effects are amplified in hypoxia. Our studies strongly implicate GBM cell-derived collagen VI in microenvironmental remodeling to facilitate invasion.
Corporate sustainability reporting and information infrastructure
Authors: Troshani Indrit , Rowbottom Nick 
Published: December 2023

PurposeInformation infrastructures can enable or constrain how companies pursue their visions of sustainability reporting and help address the urgent need to understand how corporate activity affects sustainability outcomes and how socio-ecological challenges affect corporate activity. The paper examines the relationship between sustainability reporting information infrastructures and sustainability reporting practice.Design/methodology/approachThe paper mobilises a socio-technical perspective and the conception of infrastructure, the socio-technical arrangement of technical artifacts and social routines, to engage with a qualitative dataset comprised of interview and documentary evidence on the development and construction of sustainability reporting information.FindingsThe results detail how sustainability reporting information infrastructures are used by companies and depict the difficulties faced in generating reliable sustainability data. The findings illustrate the challenges and measures undertaken by entities to embed automation and integration, and to enhance sustainability data quality. The findings provide insight into how infrastructures constrain and support sustainability reporting practices.Originality/valueThe paper explains how infrastructures shape sustainability reporting practices, and how infrastructures are shaped by regulatory demands and costs. Companies have developed “uneven” infrastructures supporting legislative requirements, whilst infrastructures supporting non-legislative sustainability reporting remain underdeveloped. Consequently, infrastructures supporting specific legislation have developed along unitary pathways and are often poorly integrated with infrastructures supporting other sustainability reporting areas. Infrastructures developed around legislative requirements are not necessarily constrained by financial reporting norms and do not preclude specific sustainability reporting visions. On the contrary, due to regulation, infrastructure supporting disclosures that offer an “inside out” perspective on sustainability reporting is often comparatively well developed.
Design and aerodynamic characteristics analysis of propellers for a novel rescue unmanned aerial vehicle
Authors: Guan Ying-Jie , Li Yong-Ping 
Published: December 2023

Purpose
To solve the shortcomings of existed search and rescue drones, search and rescue the trapped people trapped in earthquake ruins, underwater and avalanches quickly and accurately, this paper aims to propose a four-axis eight-rotor rescue unmanned aerial vehicle (UAV) which can carry a radar life detector. As the design of propeller is the key to the design of UAV, this paper mainly designs the propeller of the UAV at the present stage.

Design/methodology/approach
Based on the actual working conditions of UAVs, this paper preliminarily estimated the load of UAVs and the diameters of propellers and designed the main parameters of propellers according to the leaf element theory and momentum theory. Based on the low Reynolds number airfoil, this paper selected the airfoil with high lift drag ratio from the commonly used low Reynolds number airfoils. The chord length and twist angle of propeller blades were calculated according to the Wilson method and the maximum wind energy utilization coefficient and were optimized by the Asymptotic exponential function. The aerodynamic characteristics of the designed single propeller and coaxial propeller under different installation pitch angles and different installation distances were analyzed.

Findings
The results showed that the design of coaxial twin propellers can increase the load capacity by about 1.5 times without increasing the propeller diameter. When the installation distance between the two propellers was 8 cm and the tilt angle was 15° counterclockwise, the aerodynamic characteristics of the coaxial propeller were optimal.

Originality/value
The novelty of this work came from the conceptual design of the new rescue UAV and its numerical optimization using the Wilson method combined with the maximum wind energy utilization factor and the exponential function. The aerodynamic characteristics of the common shaft propeller were analyzed under different mounting angles and different mounting distances.
Osteoconductive properties of synthetic eggshell hydroxyapatite: an experimental study in rats
Authors: Al Bayaty Fouad , Al-Obaidi Mazen M. Jamil , Lokman Anissa , Yazid Suhaila , Ibrahim Omar Emad 
Published: December 2023

PurposeThis study examines the osteoconductive and healing capabilities of locally implanted synthetic hydroxyapatite (sHAp) derived from eggshells in the central incisor sockets of rats.Design/methodology/approachToxicity experiments were conducted in vitro and in vivo, to testify the safety dosage of sHAp. Around 24 mature male Sprague–Dawley (SD) rats had their upper central incisors extracted. The rats were placed into three groups of eight rats each: Group 1: the sockets of extracted central incisors were left unfilled (control), Group 2: filled up with commercially available hydroxyapatite (HAp) and Group 3: implanted with sHAp locally retrieved from eggshells. After extraction, four rats from each group were sacrificed at 2nd and 4th weeks. Maxillary tissue sections were obtained and stained with hematoxylin and eosin (H&E) and Masson’s trichome (MT) staining. Anti-osteocalcin (OCN) and proliferating cell nuclear antigen (PCNA) were used primary antibodies for immunohistochemistry (IHC) special labeling.FindingsThe results showed that the locally implanted sHAp was non-toxic and safe in cell lines (human osteoblast and fibroblast) and animals. Histological analysis of H&E, MT and IHC showed that the sockets treated with locally implanted sHAp from eggshells were filled with new bone tissue of comparable thickness to other groups.Originality/valueThis unique technique uses locally implanted eggshell-derived sHAp with osteoconductive characteristics. In an in vivo model, sHAps increased OCN and PCNA expression to improve bone repair.
Exploring the critical success factors for adopting gamification in the Nigerian construction sector
Authors: Aliu John , Oke Ayodeji Emmanuel , Abayomi Timilehin , Aigbavboa Clinton , Makanjuola Sina 
Published: December 2023

PurposeWith a view to ensuring the effective and efficient delivery of construction projects, this study evaluates the critical success factors (CSFs) for the adoption of gamification principles by construction professionals in developing countries, with an emphasis on Nigeria.Design/methodology/approachThis study adopted a post-positivism philosophical approach, using a questionnaire survey to obtain quantitative data from 126 construction professionals in Lagos State. The data obtained were analyzed using frequencies, percentages, mean item scores (MIS), Kruskal–Wallis H-test and principal component analysis (PCA) as part of the exploratory factor analysis (EFA).FindingsThe findings indicated that the most significant factors for the adoption of gamification principles in the construction industry were “clear game mechanics and rules,” “incentives and rewards for users,” “secure and reliable technology infrastructure,” “real-time progress tracking and feedback” and “clear and measurable objectives.” Employing factor analysis, these CSFs were subsequently grouped into three primary clusters, namely “relevance and user experience,” “technology and support” and “integration and process.”Practical implicationsThese findings not only enrich the existing theoretical framework but also provide a solid foundation upon which researchers can build for further theoretical development. This study also offers valuable insights that can inform and improve practical applications of gamification within the construction industry.Originality/valueWhile prior research has explored gamification in various contexts, the unique contribution of this study is the thorough investigation of CSFs for gamification adoption specifically within the construction industry. In essence, this study fills a critical gap in the literature by offering fresh perspectives and tailored solutions for the construction industry's specific gamification needs.
Integrated Lean Six Sigma and Kotter change management framework for emergency healthcare services in Saudi Arabia
Authors: Al Owad Ali , Yadav Neeraj , Kumar Vimal , Swarnakar Vikas , Jayakrishna K. , Haridy Salah , Yadav Vishwas 
Published: December 2023

PurposeLean Six Sigma (LSS) implementation follows a structured approach called define-measure-analyze-improve-control (DMAIC). Earlier research about its application in emergency healthcare services shows that it requires organizational transformation, which many healthcare setups find difficult. The Kotter change management model facilitates organizational transformation but has not been attempted in LSS settings till now. This study aims to integrate the LSS framework with the Kotter change management model to come up with an integrated framework that will facilitate LSS deployment in emergency health services.Design/methodology/approachTwo-stage Delphi method was conducted by using a literature review. First, the success factors and barriers of LSS are investigated, especially from an emergency healthcare point of view. The features and benefits of Kotter's change management models are then reviewed. Subsequently, they are integrated to form a framework specific to LSS deployment in an emergency healthcare set-up. The elements of this framework are analyzed using expert opinion ratings. A new framework for LSS deployment in emergency healthcare has been developed, which can prevent failures due to challenges faced by organizations in overcoming resistance to changes.FindingsThe eight steps of the Kotter model such as establishing a sense of urgency, forming a powerful guiding coalition, creating a vision, communicating the vision, empowering others to act on the vision, planning for and creating short-term wins, consolidating improvements and producing still more change, institutionalizing new approaches are derived from the eight common errors that managers make while implementing change in the institution. The study integrated LSS principles and Kotter’s change management model to apply in emergency care units in order to reduce waste and raise the level of service quality provided by healthcare companies.Research limitations/implicationsThe present study could contribute knowledge to the literature by providing a framework to integrate lean management and Kotter's change management model for the emergency care unit of the healthcare organization. This framework guides decision-makers and organizations as proper strategies are required for applying lean management practices in any system.Originality/valueThe proposed framework is unique and no other study has prescribed any integrated framework for LSS implementation in emergency healthcare that overcomes resistance to change.