bluuebunny/crossref_metadata_2025_split huggingface dataset:
CbpD crystal structure adds intrigue to substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases
Authors: Dade Christopher M. , Douzi Badreddine , Cambillau Cristian , Ball Genevieve , Voulhoux Romé , Forest Katrina T. 
Published: April 2022

AbstractPseudomonas aeruginosa secretes diverse proteins via its Type 2 Secretion System, including a 39 KDa Chitin-Binding Protein, CbpD. CbpD was recently shown to be a lytic polysaccharide monooxygenase active on chitin, and to contribute substantially to virulence. To-date no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the Cellvibrio japonicus CjLPMO10A CBM73 domain. We report the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement, which required ab initio models of each CbpD domain generated by the artificial intelligence deep learning structure prediction algorithm RoseTTAFold. The structure of CbpD confirms previously postulated chitin-specific motifs in the AA10 domain while challenging the deterministic effects of other postulated substrate specificity motifs. Additionally, the structure of CbpD shows that post translational modifications occur on the chitin binding surface. Moreover, the structure raises interesting possibilities about how Type 2 Secretion System substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure prediction algorithms in making challenging structural targets tractable.
Defensiveness measurement in honey bees (Apis mellifera) and brain expression of associated genes after noxious stimulus
Authors: Acevedo-Gonzalez Jenny P. , Galindo-Cardona Alberto , Fuenzalida-Uribe Nicolas L. , Ghezzi Alfredo , Giray Tugrul 
Published: April 2022

AbstractHoney bee (Apis mellifera sp.) colonies and individuals respond variably to disturbances. In this study, we examined the role of neural modulation and metabolism in constitutive and experience-dependent differences in defensive response. We compared brain gene expression in bees of identified gentle and defensive colonies in a standard assay. For neuromodulation, we examined membrane receptor genes for the biogenic amines dopamine (DOPR2), octopamine (OAR), and serotonin (5HT2a), and the enzyme gene in the synthesis pathway (THR). To examine neural metabolism, we assessed the Oxidative Phosphorylation Pathway “OXPHOS” gene expression (i.e., ND51 and ND20-LIKE). Bees of defensive colonies had a significantly lower expression of amine receptor, synthesis genes, and OXPHOS genes. Experience differences or exposure to nociceptive neurons activated by nocive stimuli (electric shock) led to differences in the expression of all genes except 5HT2a. The same target genes demonstrated an increase in expression levels after electric shock and sting response. We discuss the convergence of neuromodulation, neural metabolism
Cadmium is detrimental to Caenorhabditis elegans via a network involving circRNA, lncRNA and phosphorylated protein
Authors: Qu Zhi , Guo Peisen , Zheng Shanqing , Yu Zengli , Liu Limin , Wang Panpan , Zheng Fengjiao , Lin Guimiao , Wang Peixi , Liu Nan 
Published: April 2022

AbstractCadmium (Cd) as a heavy metal causes serious environmental pollution and multiple organ and system damage in human. However, little is known about the specific molecular mechanisms of the associated regulatory networks. In this study, we selected Caenorhabditis elegans (C. elegans) to investigate the effects of Cd exposure as it acts as an acknowledged and established genetic model organism. A total of 26 differentially-expressed circular RNA (DEcircRNAs), 143 lncRNAs (DElncRNAs), 69 microRNAs (DEmiRNAs) and 6209 mRNAs (DEmRNAs) were found and identified, which might influence reproductive function, aging processes and nervous system functions through regulating the levels of circRNAs and lncRNAs and the controlling of regulatory networks of circRNA/lncRNA-miRNA-mRNA. Based on quantitative PCR, four DEcircRNAs and three DElncRNAs were confirmed to have different expression levels between the Cd-treated and control group. Further, 5 protein-coding genes might be regulated by DElnRNAs through cis-acting and 114 by trans-acting elements. Additionally, 42 differentially regulative phosphopeptides were detected and 4 novel pairs of transcription factors (TFs)-kinase-substrate that might be influenced by Cd exposure were constructed by phosphoproteomics. Our findings suggest that Cd might influence multi-functions and the aging process of C. elegans and may inhibit the expression of TFs to reduce phosphorylated levels of the corresponding protein.SynopsisCadmium exists widely in soil, water and air. This study manifested the regulatory network involving circRNA, lncRNA and phosphorylated protein in C.elegans after Cd exposure, which revealing the potential molecular mechanism underlying the toxic effect caused by Cd.Graphic Abstract
Quantitative MHC class-I/-II gene expression levels inCDK12mutated prostate cancer reveal intratumorally T cell adaptive immune response in tumors
Authors: Lautert-Dutra William , Melo Camila M. , Chaves Luiz P. , Crozier Cheryl , Saggioro Fabiano P. , dos Reis Rodolfo B. , Bayani Jane , Bonatto Sandro L. , Squire Jeremy A. 
Published: April 2022

AbstractBackgroundCDK12 inactivation is a predictive biomarker for immune checkpoint blockers (ICB) treatment response in advanced prostate cancer (PCa), but some CDK12-altered patients fail to respond to ICB. Downregulation of MHC expression has been described as a mechanism of intrinsic and acquired resistance to ICB in various cancers, but there is little information on whether MHC expression levels are altered in CDK12 defective PCa that fails to respond to ICB treatments.MethodsUsing genomics data of primary and metastatic prostate cancer from two public domain cohorts and a retrospective cohort, we investigated variation in the expression of the MHC genes and associated downstream changes inCDK12mutated patients. The findings of public domain data were validated using transcriptomic data from a 53-patient retrospective cohort from our Institute.ResultsBased on the analysis of gene expression quartiles, we divided the tumors into “High” and “Low” expression levels of MHC-I and -II.CDK12defective tumors with increased MHC levels showed the activation of several pathways associated with the immune system and elevatedPD-L1,IDO1, andTIM3expression. These transcriptomic findings were confirmed using expression analyses of our cohort of 53 primary PCa. There was an increased composition of CD8+ T cells, B cells, γδ T cells, and M1 Macrophages inCDK12mutated tumors with elevated MHC levels based on digital cytometric analyses. In contrast,CDK12defective tumors with decreased MHC expression were often subject to loss of heterozygosity (LOH) genomic events affecting MHC-I/-II and theHLAgene cluster on chromosome 6.CDK12defective PCa expresses higher levels of classical MHC, has an active and inflamed tumor microenvironment, and increases the presence of effector T cells.ConclusionsReduced MHC expression may be caused by the acquisition of specific somatic genomic events that reduce the expression of antigen presentation genes. Combining CDK12 mutation, MHC expression levels, and LOH status may better predict outcomes for ICB-eligible PCa. In addition, these findings draw attention to the need to investigate therapeutic approaches for enhancing MHC expression inCDK12defective PCa to improve ICB responses.
Structural and Dynamic Effects of PTEN C-terminal Tail Phosphorylation
Authors: Smith Iris N. , Dawson Jennifer E. , Krieger James , Thacker Stetson , Bahar Ivet , Eng Charis 
Published: April 2022

ABSTRACTThe phosphatase and tensin homolog deleted on chromosome ten (PTEN) tumor suppressor gene encodes a tightly regulated dual-specificity phosphatase that serves as the master regulator of PI3K/AKT/mTOR signaling. The carboxy-terminal tail (CTT) is key to regulation and harbors multiple phosphorylation sites (Ser/Thr residues 380-385). CTT phosphorylation suppresses the phosphatase activity by inducing a stable, closed conformation. However, little is known about the mechanisms of phosphorylation-induced CTT-deactivation dynamics. Using explicit solvent microsecond molecular dynamics simulations, we show that CTT phosphorylation leads to a partially collapsed conformation, which alters the secondary structure of PTEN and induces long-range conformational rearrangements that encompass the active site. The active site rearrangements prevent localization of PTEN to the membrane, precluding lipid phosphatase activity. Notably, we have identified phosphorylation-induced allosteric coupling between the interdomain region and a hydrophobic site neighboring the active site in the phosphatase domain. Collectively, the results provide a mechanistic understanding of CTT phosphorylation dynamics and reveal potential druggable allosteric sites in a previously believed clinically undruggable protein.
Analysis of chemical and mechanical behaviors in living cells by continuum mechanics-based FRAP
Authors: Saito Takumi , Matsunaga Daiki , Deguchi Shinji 
Published: April 2022

AbstractFluorescence recovery after photobleaching (FRAP) is a common technique to analyze the turnover of molecules in living cells. Numerous physicochemical models have been developed to quantitatively evaluate the rate of turnover driven by chemical reaction and diffusion that occurs in a few seconds to minutes. On the other hand, they have limitations in interpreting long-term FRAP responses where intracellular active movement inevitably provides target molecular architectures with additional effects other than chemical reaction and diffusion, namely directed transport and structural deformation. To overcome the limitations, we develop a continuum mechanics-based model that allows for decoupling FRAP response into the intrinsic turnover rate and subcellular mechanical characteristics such as displacement vector and strain tensor. Our approach was validated using fluorescently-labeled beta-actin in an actomyosin-mediated contractile apparatus called stress fibers, revealing spatially distinct patterns of the multi-physicochemical events, in which the turnover rate of beta-actin was significantly higher at the center of the cell. We also found that the turnover rate is negatively correlated with the strain rate along stress fibers but, interestingly, not with the absolute strain magnitude. Moreover, stress fibers are subjected to centripetal flow as well as both contractile and tensile strains along them. Taken together, this novel framework for long-term FRAP analysis allows for unveiling the contribution of overlooked microscopic mechanics to molecular turnover in living cells.
Enabling sustainable food transitions in schools: a systemic approach
Authors: Graça João , Roque Lisa , Guedes David , Campos Lúcia , Truninger Monica , Godinho Cristina , Vinnari Markus 
Published: April 2022

PurposeRecent reviews and reports have highlighted the need for integrated, context-specific efforts to enable sustainable food transitions. This study aimed to identify pathways to promote healthier and more environmentally friendly food practices in school contexts, with a focus on increased plant-based eating.Design/methodology/approachThe study used a systemic approach with data collected from relevant stakeholders in an EU country (Portugal) at diverse levels of influence in the school meals system (i.e. proximal, intermediate, distal; from end-consumers to food providers, market actors, civil society organizations, and policy and decision-makers). Data from individual interviews (N = 33) were subjected to thematic analysis.FindingsMeat-centric cultural perceptions of a ‘proper meal’ can be a socio-emotional barrier for sustainable food transitions in schools. Main pathways identified to unlock these transitions included: (1) Levering orientations toward ethical and environmentally beneficial consumption; (2) Improving and increasing the offer of plant-based meals; and (3) Mobilizing local communities and society.Originality/valueThe current findings suggest that promoting healthier and more environmentally friendly food practices in schools requires systemic, integrated approaches which focus on food consumption, food provision, and the broader political and sociocultural environment.
How do the technological capability and strategic flexibility of an organization impact its successful implementation of Industry 4.0? A qualitative viewpoint
Authors: Sony Michael , Antony Jiju , Mc Dermott Olivia 
Published: April 2022

PurposeIndustry 4.0 (I 4.0) consists of numerous digital technologies applied in organizations strategically to add value to the customer. Different organizations have varying degrees of technological capability and strategic flexibility. This paper aims to explore the relationship between technological capability and strategic flexibility on successful implementation of I 4.0.Design/methodology/approachA qualitative study using a grounded theory approach is conducted on 34 senior managers from Europe and North America who have implemented I 4.0 participated in this study through a theoretical sampling frame.FindingsThis study finds that technological capability and strategic flexibility have an impact on the successful implementation of I 4.0. The study also finds that different dimensions of technological capability also impact I 4.0. The interactive effect of strategic flexibility and technological capability is also noted. The study also develops a framework for successful implementation of I 4.0.Practical implicationsThis study can be used by managers while implementing I 4.0 to devise a strategic roadmap for acquiring technological capability with I 4.0 technologies. Besides, it will help the managers to consider the bidirectional relationship between technological capability and strategic flexibility while formulating I 4.0 strategy for successful implementation of I 4.0 in their organizations.Originality/valuePrevious studies have examined the importance of I 4.0 technologies. However, this study extends the previous works by suggesting how technological capability and strategic flexibility can help in the successful implementation of I 4.0.
Cross-cultural differences in information processing of chatbot journalism: chatbot news service as a cultural artifact
Authors: Shin Donghee , Al-Imamy Saifeddin , Hwang Yujong 
Published: April 2022

PurposeHow does algorithmic information processing affect the thoughts and behavior of artificial intelligence (AI) users? In this study, the authors address this question by focusing on algorithm-based chatbots and examine the influence of culture on algorithms as a form of digital intermediation.Design/methodology/approachThe authors conducted a study comparing the United States (US) and Japan to examine how users in the two countries perceive the features of chatbot services and how the perceived features affect user trust and emotion.FindingsClear differences emerged after comparing algorithmic information processes involved in using and interacting with chatbots. Major attitudes toward chatbots are similar between the two cultures, although the weights placed on qualities differ. Japanese users put more weight on the functional qualities of chatbots, and US users place greater emphasis on non-functional qualities of algorithms in chatbots. US users appear more likely to anthropomorphize and accept explanations of algorithmic features than Japanese users.Research limitations/implicationsDifferent patterns of chatbot news adoption reveal that the acceptance of chatbots involves a cultural dimension as the algorithms reflect the values and interests of their constituencies. How users perceive chatbots and how they consume and interact with the chatbots depends on the cultural context in which the experience is situated.Originality/valueA comparative juxtaposition of cultural-algorithmic interactions offers a useful way to examine how cultural values influence user behaviors and identify factors that influence attitude and user acceptance. Results imply that chatbots can be a cultural artifact, and chatbot journalism (CJ) can be a socially contextualized practice that is driven by the user's input and behavior, which are reflections of cultural values and practices.
Person-environment fit: a luxury good for those who can afford it?
Authors: Renz Franziska M. 
Published: April 2022

PurposeThe study integrates organizational demography theory into person-environment fit theories to question the assumption that all employees can afford to strive for person-environment fit. The ethnic/racial diversity in organizations is investigated as a boundary condition in order to develop implications to mitigate the challenges of employees with precarious jobs, especially persons of color (POCs), in the society.Design/methodology/approachPublicly accessible and objective data from organizations in the S&P 1500 index were collected through Compustat, ExecuComp, the Bloomberg Terminal and the websites of Fortune, the United States Census Bureau and the U.S. Department of Labor. A path analysis of time-lagged data was performed to support causal relationships between the examined constructs while controlling for alternative explanations.FindingsUnsafe working conditions moderate the U-shaped relationship between ethnic/racial diversity and turnover and turn it into an inverted U-shaped relationship because employees in precarious jobs, especially POCs, cannot afford to leave unsafe working conditions. Organizations with unsafe working conditions are more likely to invest in sustainability initiatives. However, organizations' financial performance does not benefit from this investment.Originality/valueThe circumstance that not all employees can afford person-environment fit and its organizational outcomes are identified and empirically tested. Scholars can integrate this boundary condition in future research. Implications for practice and policy are also derived.
Mapping the research status and dynamic frontiers of functional clothing: a review via bibliometric and knowledge visualization
Authors: Li Shuyang , Jiang Shu , Tian Miao , Su Yun , Li Jun 
Published: April 2022

PurposeThe purpose of this paper is to gain an in-depth understanding of the research progress, hotspots and future trends in the field of functional clothing.Design/methodology/approachThe records of 4,153 pieces of literature related to functional clothing were retrieved from Web of Science by using a comprehensive retrieval strategy. A piece of software, CiteSpace was used as a tool to visualize the results of specific terms, such as author, institution and keyword. By analyzing the knowledge maps with several indicators, the intellectual basis and research fronts for the functional clothing domain could then be demonstrated.FindingsThe result indicated that functional clothing was a popular research field, with approximately 500 papers published worldwide in 2020. Its main research area was material science and involved public environmental and occupational health, engineering, etc. showing the characteristic of multi-interdisciplinary. Textile Research Journal and International Journal of Clothing Science and Technology were the top two journals in this field. The USA, China, Australia, England and Germany have been active and frequently cooperating with each other. Donghua University, the Hong Kong Polytechnic University and NASA, with the largest number of publications, were identified as the main research drivers. According to the co-citation analysis, thermal stress, nanogenerator and electrospinning were the topics of most cited articles during the past 20 years.Practical implicationsThe findings identified smart clothing and protective clothing to be the research frontiers in the field of functional clothing, which deserved further study in the future.Originality/valueThe outcomes offered an overview of the research status and future trends of the functional clothing field. It could not only provide scholars with convenience in identifying research hotspots and building potential cooperation in the follow-up research, but also assist beginners in searching core scholars and literature of great significance.
Design and development of new spiral head projectiles undergoing ballistics impact
Authors: Pranay V. , Panigrahi S.K. 
Published: April 2022

PurposeThe purpose of this study is to design and develop new spiral head projectiles undergoing ballistics impact.Design/methodology/approachThe introduction of the rifled barrel in firearms made projectile spin during its flight path. The central translational velocity (impact velocity) is one parameter to defeat/penetrate the target in the penetration process. Another important parameter considered to be the shape of the projectile. Many types of projectile shapes have been designed to defeat the target. In the recent years, ogival nose shape is one of the well-known projectile shapes in use abundantly. The present research is made to design the nose shape so as to use the spin during the penetration of target effectively. In this study, a new spiral head projectile shape is proposed and designed, which uses the rotation of projectile (spin) for penetrating the Al7075-T6 target. When the ogive and new spiral head projectile is impacted on Al 7075-T6 target of 12.5 mm, 18 mm thicknesses at ordnance velocities, the residual velocity is evaluated numerically using ANSYS/Explicit Dynamics at normal impact condition. Two projectile materials, steel 4340 and tungsten alloy, are used as projectile materials. Along with the translational velocity, rotation velocities (spin rate) 13,000, 26,000 and 52,000 rad/s also provided to projectile. The residual velocities verses spin rate are plotted for different spiral angle projectiles for impact velocities 1,000–1,500 m/s, at normal impact conditions on the Al 7075-T6 target. Compared with the ogive nose projectile, the proposed new spiral head projectile made of tungsten alloy is significantly effective.FindingsSpiral head projectile having tungsten alloy material gives encouraging results at 12.5 mm target thickness. The new spiral head projectile is damaged partially. At 18 mm target thickness impact conditions, it is observed that the projectile head is completely damaged. The effectiveness of spiral head projectile on a target plate thickness of 18 mm is considered to study the impact condition.Research limitations/implicationsAll the above results need to be experimentally verified. However, the basic numerical model used in the present study, i.e. the basic ogive nose numerical model with only translational energy, is well validated with penetration theory available in literatures.Practical implicationsThe designed new spiral head projectile is only effective with tungsten alloy material within considered design parameters. For steel 4340 material, the spiral head projectile is less effective than the ogive nose projectile. In tungsten alloy projectiles, by observing all considered spiral angles, 30-degree spiral angle projectile gives the best performance at most of the considered impact velocity conditions.Originality/valueThe proposed research outputs are original, innovative and, have lot of importance in defence applications particularly in arms and ammunitions.