bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunomodulatory effect of mycobacterial outer membrane vesicles coated nanoparticles
Authors: George Edna , Goswami Avijit , Lodhiya Tejan , Padwal Priyanka , Iyer Shalini , Gauttam Iti , Sethi Lakshay , Jeyasankar Sharumathi , Sharma Pallavi Raj , Dravid Ameya Atul , Mukherjee Raju , Agarwal Rachit 
Published: June 2022

AbstractTuberculosis (TB) is one of the most widely prevalent infectious diseases that cause significant mortality. Bacillus Calmette-Guérin (BCG), the current TB vaccine used in clinics, shows variable efficacy and has safety concerns for immunocompromised patients. There is a need to develop new and more effective TB vaccines. Outer membrane vesicles (OMVs) are vesicles released by Mycobacteria that contain several lipids and membrane proteins and act as a good source of antigens to prime immune response. However, the use of OMVs as vaccines has been hampered by their heterogeneous size and low stability. Here we report that mycobacterial OMVs can be stabilized by coating over uniform-sized 50 nm gold nanoparticles. The OMV-coated gold nanoparticles (OMV-AuNP) show enhanced uptake and activation of macrophages and dendritic cells. Proteinase K and TLR inhibitor studies demonstrated that the enhanced activation was attributed to proteins present on OMVs and was mediated primarily by TLR2 and TLR4. Mass spectrometry analysis revealed several potential membrane proteins that were common in both free OMVs and OMV-AuNP. Such strategies may open up new avenues and the utilization of novel antigens for developing TB vaccines.
Method Comparison for Japanese Encephalitis Virus Detection in Samples Collected from the Indo-Pacific Region
Authors: Crispell Gary , Williams Kelly , Zielinksi Eric , Iwami Akira , Homas Zachary , Thomas Karen 
Published: June 2022

ABSTRACTIntroductionJapanese encephalitis virus (JEV) is a mosquito-borne viral pathogen, which is becoming a growing public health concern throughout the Indo-Pacific. Five genotypes of JEV have been identified. Current vaccines are based on genotype III and provide a high degree of protection for 4 of the 5 known genotypes.MethodsRT-PCR, Magpix, Twist Biosciences Comprehensive Viral Research Panel (CVRP), and SISPA methods were used to detect JEV from mosquito samples collected in South Korea during 2021. These methods were compared to determine which method would be most effective for biosurveillance in the Indo-Pacific region.ResultsOur data showed that RT-PCR, Twist CVRP, and SISPA methods were all able to detect JEV genotype I, however, the proprietary Magpix panel was only able to detect JEV genotype III. Use of minION sequencing for pathogen detection in arthropod samples will require further method development.ConclusionBiosurveillance of vectorborne pathogens remains an area of concern throughout the Indo-Pacific. RT-PCR was the most cost effective method used in the study, but TWIST CVRP allows for the identification of over 3,100 viral genomes. Further research and comparisons will be conducted to ensure optimal methods are used for large scale biosurveillance.
The effect of potential factors on all-cause and cause-specific and mortality: a pre-COVID-19 period review
Authors: Xu Jia , Lin Yunkai , Tong Jianyu , Zhou Ying 
Published: June 2022

AbstractBackgroundAbout 3 million people die every year in USA. In order to provide a general direction and background for subsequent research and development in this field, we reviewed the studies about impact of potential factors associated with the main causes of mortality and all-cause mortality.MethodResearches are selected by PubMed website for last 15 years with published language of English. The leading cause of death were published by CDC in 2020 (excluded COVID-19) including the ten natural mortalities and unnatural mortality. We summarized the potential factors associated with the mortality and sorted them by “positive/negative effect” and “long-term/short-term effect”.ResultAmong risk factors, the factors of depression, unhealthy diet, overweight and obesity and other similar factors increase the mortality of main leading natural causes. Among protective factors, the factors of physical activity, nut intake, chocolate consumption were associated with the reduced mortality of multiple diseases. We also found that some factors possess bidirectional influence on different diseases or even one disease. The gender of female negatively affects mortality of diabetes, but positively affects cardiovascular diseases. The majority of air pollutants are risk factors for respiratory diseases while ozone possibly reduce the mortality.ConclusionOur review summarized various factors which have positive/negative and long-term/short-term effects on the main mortality of cause-specific and all-caused mortality. Further study is required to investigate the contribution of different variable on mortality.
Looking for the mechanism of arsenate respiration in an arsenate-dependent growing culture ofFusibactersp. strain 3D3, independent of ArrAB
Authors: Mauricio Acosta Grinok , Vázquez Susana , Nicolás Guiliani , Marín Sabrina , Cecilia Demergasso 
Published: June 2022

AbstractThe literature has reported the isolation of arsenate-dependent growing (ADG) microorganisms which lack a canonical homolog for respiratory arsenate reductase, ArrAB. We recently isolated an ADG bacterium from arsenic-bearing environments in Northern Chile,Fusibactersp. strain 3D3 (Fas) and studied the arsenic metabolism in this Gram-positive isolate. Features ofFasdeduced from genome analysis and comparative analysis with other arsenic-reducing microorganisms revealed the lack of ArrAB coding genes and the occurrence of twoarsCgenes encoding for putative cytoplasmic arsenate reductases named ArsC-1 and ArsC-2. Interestingly, ArsC-1 and ArsC-2 belong to the thioredoxin-coupled family (because of the redox-active disulfide protein used as reductant), but they conferred differential AsV resistance to theE. coliWC3110 ΔarsCstrain. PCR experiments confirmed the absence ofarrABgenes and results obtained using uncouplers revealed thatFasgrowth is linked to the proton gradient. In addition,Fasharbors ferredoxin-NAD+oxidoreductase (Rnf) coding genes. These are key molecular markers of a recently discovered flavin-based electron bifurcation mechanism involved in energy conservation, mainly in anaerobic metabolisms regulated by the cellular redox state and mostly associated with cytoplasmic enzyme complexes. At least three electron-bifurcating flavoenzyme complexes were evidenced inFas, some of them shared in conserved genomic regions by other members of theFusibactergenus. These physiological and genomic findings permit us to hypothesize the existence of an uncharacterized arsenate-dependent growth metabolism regulated by the cellular redox state inFusibactergenus.
Set1 regulates telomere function via H3K4 methylation-dependent and independent pathways and calibrates the abundance of telomere maintenance factors
Authors: Jezek Meagan , Sun Winny , Negesse Maraki Y. , Smith Zachary M. , Orosz Alexander , Green Erin M. 
Published: June 2022

AbstractSet1 is an H3K4 methyltransferase which comprises the catalytic subunit of the COMPASS complex and has been implicated in transcription, DNA repair, cell cycle control, and numerous other genomic functions. Set1 also promotes proper telomere maintenance, as cells lacking Set1 have short telomeres and disrupted subtelomeric gene repression; however, the precise role for Set1 in these processes has not been fully defined. In this study, we have tested mutants of Set1 and the COMPASS complex which differentially alter H3K4 methylation status and attempt to separate catalytic and non-catalytic functions of Set1. Our data reveal that Set1-dependent subtelomeric gene repression relies on its catalytic activity towards H3K4, whereas telomere length is regulated by Set1 catalytic activity but likely independent of the H3K4 substrate. Furthermore, we uncover a role for Set1 in calibrating the abundance of critical telomere maintenance proteins, including components of the telomerase holoenzyme and members of the telomere capping CST (Cdc13-Stn1-Ten1) complex, through both transcriptional and post-transcriptional pathways. Altogether, our data provide new insights into the H3K4 methylation-dependent and independent roles for Set1 in telomere maintenance in yeast and shed light on possible roles for Set1-related methyltransferases in other systems.
Cryo-EM structure and B-factor refinement with ensemble representation
Authors: Cragnolini Tristan , Beton Joseph , Topf Maya 
Published: June 2022

AbstractCryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. It is common to fit atomic models of the contained molecules to interpret those maps, followed by a density-guided refinement. Here, we propose TEMPy-REFF, a novel method for atomic structure refinement in cryo-EM density maps. By representing the atomic positions as components of a mixture model, their variances as B-factors, and a model ensemble description, we significantly improve the fit to the map compared to what is currently achievable with state-of-the-art methods. We validate our method on a large benchmark of 366 cryo-EM maps from EMDB at 1.8-7.1Å resolution and their corresponding PDB assembly models. We also show that our approach can provide newly-modelled regions in EMDB deposited maps by combining it with AlphaFold-Multimer. Finally, our method provides a natural interpretation of maps into components, allowing us to accurately create composite maps.
A Modular Chemoenzymatic Approach to C14-Functionalized Steroids
Authors: Song Fuzhen , Zheng Mengmeng , Wang Junlin , Liu Huanhuan , Lin Zhi , Liu Benben , Deng Zixin , Zhou Qianghui , Qu Xudong 
Published: June 2022

AbstractC14-functionalized steroids belong to a unique class of steroids with important biological activities. However, the lack of efficient methods to access C14-functionalized steroids impede related steroidal drug discovery. Herein we report a modular chemoenzymatic approach to access diversified C14-functionalized steroids. We first identified a novel C14α-hydroxylase (CYP14A) from Cochliobolus lunatus with high catalytic efficiency and substrate promiscuity. Protein engineering of CYP14A generated three variants I111A, M115K and V124A that greatly improved the C14-hydroxy regioselectivity. Based on this efficient biocatalytic method, a range of C14α-OH steroids with C17 side chain were prepared in good yields, which was then transformed into Δ14 olefins through a facile elimination. The newly formed Δ14 olefin served as a versatile handle to install diversified functional groups (e.g. epoxide, β-OH, F, Cl and N3) at C14 position through hydrofunctionalization. Furthermore, the synthetic utility of this powerful chemoenzymatic methodology was demonstrated by performing a 7-step semisynthesis of periplogenin and the diversity-oriented synthesis of cardenolide (+)-digitoxigenin and its three diastereomers in a concise manner.
Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells
Authors: Doimo Mara , Abrahamsson Sanna , L’Hôte Valentin , Ndi Mama , Das Rabindra Nath , Aasumets Koit , Berner Andreas , Goffart Steffi , Pohjoismäki Jaakko L.O. , López Marcela Dávila , Chorell Erik , Wanrooij Sjoerd 
Published: June 2022

AbstractMitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate.In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrated that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
Systematic analysis of the molecular and biophysical properties of key DNA damage response factors
Authors: Heyza Joshua R. , Mikhova Maria , Bahl Aastha , Broadbent David , Schmidt Jens C. 
Published: June 2022

ABSTRACTRepair of DNA double strand breaks (DSBs) is integral to preserving genomic integrity. Therefore, defining the mechanisms underlying DSB repair will enhance our understanding of how defects in these pathways contribute to human disease and could lead to the discovery of new approaches for therapeutic intervention. Here, we established a panel of HaloTagged DNA damage response factors in U2OS cells which enables concentration-dependent protein labeling. Genomic insertion of the HaloTag at the endogenous loci of the repair factors preserves expression levels and proteins retain proper subcellular localization, foci-forming ability, and functionally support DSB repair. We systematically analyzed total cellular protein abundance, measured recruitment kinetics to DSBs, and defined the diffusion dynamics and chromatin binding by live-cell single-molecule imaging. Our work demonstrates that the Shieldin complex, a critical factor in end joining, does not exist in a preassembled state and Shieldin components are recruited to DSBs with different kinetics. Additionally, live-cell single-molecule imaging revealed the constitutive interaction between MDC1 and chromatin mediated by the PST repeat domain of MDC1. Altogether, our studies demonstrate the utility of single-molecule imaging to provide mechanistic insights into DNA repair, which will serve as a powerful resource for characterizing the biophysical properties of DNA repair factors in living cells.
Wellness programs in times of COVID-19, perceived organizational support and affective commitment: effects on employee innovative behavior
Authors: Muñoz Rosa M. , Andrade Silvia M. , Peña Isidro , Donate Mario J. 
Published: June 2022

PurposeInnovation is one of the most important foundations on which to create and sustain competitive advantages in companies, but at the individual level, employee innovative behavior has recently been jeopardized by the situation caused by the COVID-19 pandemic (e.g. changes in workplaces, employee interaction, motivation). This study analyzes wellness programs and actions through which organizations have tried to adapt to the new situation caused by COVID-19 and their effect on employee innovation behavior.Design/methodology/approachStructural equation modeling by means of the partial least squares technique was used to test the study's hypotheses after collecting survey data from Spanish companies, providing evidence that wellness programs and measures to deal with COVID-19 through perceived organizational support and affective commitment encourage employee innovation behavior.FindingsThe results suggest that efforts developed by firms focused on employee well-being to overcome difficulties caused by the pandemic strengthen innovative behaviors by means of intrinsic motivation based essentially on personal commitment. Theoretical and practical implications of the findings are discussed by the paper's authors.Originality/valueThis paper corroborates and extends previous research regarding wellness programs, perceived organization support and affective commitment. It provides a comprehensive model of relationships that predicts employee innovative behavior. It analyzes the influence of enterprise wellness programs based on protective COVID-19 measures.
Examining predictors of digital library use: an application of the information system success model
Authors: Iqbal Memoona , Rafiq Muhammad , Soroya Saira Hanif 
Published: June 2022

Purpose
Digital libraries are not only an assortment of information assets yet have turned into a digital community for correspondence, searching and electronic learning. Also, economically the investment in terms of money, time, energy and manpower associated with the development of effective digital library (DL) systems demands high utilization of these resources. This study aims to explore the factors that affect the utilization of digital libraries and may lead to users’ satisfaction and finally high exposure to information systems like digital libraries. However, these factors may work differently in different cultures. Considering this fact, DeLone and McLean’s IS success model (ISSM) is tested and expanded in a local academic context.

Design/methodology/approach
Following the quantitative research design, a total of 355 responses were collected through a questionnaire-based survey. Research scholars of the University of Punjab, Lahore, Pakistan were the reviewed population of this study. A two-stage stratified random sampling method was used to choose the sample. Structural equation modelling is used to find out the nature and extent of the relationship among studied variables.

Findings
The findings confirm that service quality is the strong predictor of DL system use, whereas overall users’ satisfaction mediates the relationship between the predictors (content and service quality) and the outcome variable (use).

Originality/value
This work done is the first main endeavour to use the “Information System Success” theories to intervene and mediate the effect of content, IQ, system quality and service quality on the use of DL in the local context.
Team autonomy, information exchange and team innovation performance: the moderating role of team conflict
Authors: Li Bao , Chen Wanming , He Changqing , Zhang Yuwen 
Published: June 2022

PurposeTeam autonomy is thought to be important for team innovation performance. However, the theoretical basis of the relationship between team autonomy and team innovation performance is not well understood, and previous studies have found inconsistent relations between them. Based on motivated information processing in groups (MIP-G) theory, this paper aims to explain how and when team autonomy could influence team innovation performance from a new team-level perspective.Design/methodology/approachUsing a two-wave, time-lagged survey design, the authors collected data from 340 members of 86 teams in China. PROCESS 3.0 for SPSS was used to test hypothesized relationships.FindingsThe results show that team autonomy is positively related to team information exchange. Team information exchange mediates the positive relationship between team autonomy and team innovation performance. Furthermore, the positive relationship between team autonomy and team information exchange is stronger with less task conflict, which runs contrary to the hypothesis. Additionally, relationship conflict does not adjust the impact of team autonomy on team information exchange.Originality/valueThis study provides a new perspective to explain the mechanism between team autonomy and team innovation performance at team level from the information processing approach, specifically, MIP-G theory. It also incorporates team conflicts as important contextual factors to answer the call for a wider study of boundary conditions in the team autonomy research.
A novel federated learning based lightweight sustainable IoT approach to identify abnormal traffic
Authors: Alharbi Yasser 
Published: June 2022

Purpose
This strategy significantly reduces the computational overhead and storage overhead required when using the kernel density estimation method to calculate the abnormal evaluation value of the test sample.

Design/methodology/approach
To effectively deal with the security threats of botnets to the home and personal Internet of Things (IoT), especially for the objective problem of insufficient resources for anomaly detection in the home environment, a novel kernel density estimation-based federated learning-based lightweight Internet of Things anomaly traffic detection based on nuclear density estimation (KDE-LIATD) method. First, the KDE-LIATD method uses Gaussian kernel density estimation method to estimate every normal sample in the training set. The eigenvalue probability density function of the dimensional feature and the corresponding probability density; then, a feature selection algorithm based on kernel density estimation, obtained features that make outstanding contributions to anomaly detection, thereby reducing the feature dimension while improving the accuracy of anomaly detection; finally, the anomaly evaluation value of the test sample is calculated by the cubic spine interpolation method and anomaly detection is performed.

Findings
The simulation experiment results show that the proposed KDE-LIATD method is relatively strong in the detection of abnormal traffic for heterogeneous IoT devices.

Originality/value
With its robustness and compatibility, it can effectively detect abnormal traffic of household and personal IoT botnets.
Management control systems effect on the micro-level processes of product innovation
Authors: Biswas Sharlene Sheetal Narayan , Akroyd Chris , Sawabe Norio 
Published: June 2022

Purpose
Using institutional theory, this study aims to understand how the management control systems (MCSs) designed by top managers influence the micro-level process practices of organization members during product innovation.

Design/methodology/approach
This paper reports on a case study carried out at NZMed to examine the design and use of MCSs and their product innovation practices. Simons’ levers of control was used to understand the ways in which MCSs were designed and used in a product innovation setting.

Findings
The findings indicate that the everyday micro-level processes of organization members encoded MCS when their espoused values aligned with those of top managers. However, when the perspectives within the organization differed, variations to the micro-level processes of organization members emerged. The authors show how this resulted in an increase in innovation capabilities necessary to meet organizational goals.

Practical implications
The misalignment between espoused values and enacted values had a positive effect as it helped the organization maintain their innovation culture, and build long-term trusting relationships with suppliers which enabled the achievement of organizational goals.

Originality/value
By focusing on the relationship between MCS and the micro-level processes of organization members in product innovation, the paper shows how the lack of alignment between the espoused values of top management and the enacted values of project managers explained the variations between the MCS used by top managers and the practices of project teams at our case study company.