bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socioeconomic Resources are Associated with Distributed Alterations of the Brain’s Intrinsic Functional Architecture in Youth
Authors: Sripada Chandra , Gard Arianna , Angstadt Mike , Taxali Aman , Greathouse Tristan , McCurry Katherine , Hyde Luke W. , Weigard Alexander , Walczyk Peter , Heitzeg Mary 
Published: June 2022

ABSTRACTLittle is known about how exposure to limited socioeconomic resources (SER) in childhood gets “under the skin” to shape brain development, especially using rigorous whole-brain multivariate methods in large, adequately powered samples. The present study examined resting state functional connectivity patterns from 5,821 youth in the Adolescent Brain Cognitive Development (ABCD) study, employing multivariate methods across three levels: whole-brain, network-wise, and connection-wise. Across all three levels, SER was associated with widespread alterations across the connectome. However, critically, we found that parental education was the primary driver of neural associations of SER. These parental education associations were robust to additional tests for confounding by head motion, and they exhibited notable concentrations in somatosensory and subcortical regions. Moreover, parental education associations with the developing connectome were partially accounted for by home enrichment activities, child’s cognitive abilities, and child’s grades, indicating interwoven links between parental education, child stimulation, and child cognitive performance. These results add a new data-driven, multivariate perspective on links between household SER and the child’s developing functional connectome.
Docking-based long timescale simulation of cell-size protein systems at atomic resolution
Authors: Vakser Ilya A. , Grudinin Sergei , Jenkins Nathan W. , Kundrotas Petras J. , Deeds Eric J. 
Published: June 2022

ABSTRACTComputational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, so far, have included protein docking and molecular simulation. The latter approaches account for the dynamics of the interactions, but are relatively slow, if carried out at all-atom resolution, or are significantly coarse-grained. Protein docking algorithms are far more efficient in sampling spatial coordinates. However, they do not account for the kinetics of the association (i.e., they do not involve the time coordinate). Our proof-of-concept study bridges the two modeling approaches, developing an approach that can reach unprecedented simulation timescales at all-atom resolution. The global intermolecular energy landscape of a large system of proteins was mapped by the pairwise Fast Fourier Transform docking and sampled in space and time by Monte Carlo simulations. The simulation protocol was parametrized on existing data and validated on a number of observations from experiments and molecular dynamics simulations. The simulation protocol performed consistently across very different systems of proteins at different protein concentrations. It recapitulated data on the previously observed protein diffusion rates and aggregation. The speed of calculation allows reaching second-long trajectories of protein systems that approach the size of the cells, at atomic resolution.
Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities
Authors: Brisson Vanessa , Swink Courtney , Kimbrel Jeffrey , Mayali Xavier , Samo Ty , Kosina Suzanne M. , Thelen Michael , Northen Trent R. , Stuart Rhona K. 
Published: June 2022

ABSTRACTThe roles of exometabolites in mediating algal-bacterial interactions and regulating microbial community composition are not well understood. Here, we identified specific exometabolites from the model diatom Phaeodactylum tricornutum affecting abundance of specific bacterial taxa in isolation and in a community setting. We examined the response of a P. tricornutum-adapted enrichment community and found that both algal exudates and algal presence drove similar changes in community composition compared to controls. Using LC-MS/MS, we identified 50 metabolites produced by axenic P. tricornutum and found that different exometabolites accumulated during different algal growth phases. Profiling growth of 12 bacterial isolates representative of the enrichment community uncovered two algal exometabolites (out of 12 tested) which supported growth of a subset of isolates as a primary carbon source. We compared enrichment community response with and without the addition of two contrasting metabolites: 4-hydroxybenzoic acid, which supported isolate growth, and lumichrome, which did not. Exogenous metabolite additions did promote increased abundances of taxa that were able to utilize the metabolite in the isolate study, but also revealed the importance of factors relating to algal presence in regulating community composition. Collectively, this work demonstrates the influence of specific algal exometabolites in driving microbial community composition.
A genomic platform for epidemiological surveillance and vaccine antigen discovery using long-read amplicon sequencing
Authors: Plaza David Fernando , Zerebinski Julia , Broumou Ioanna , Lautenbach Maximilian Julius , Ngasala Billy , Sundling Christopher , Färnert Anna 
Published: June 2022

AbstractMany vaccine candidate proteins are under strong selective pressure to diversify in terms of antigenicity. We present a sequencing and data analysis platform for epidemiological surveillance and discovery of indel-rich vaccine antigens by long-read circular consensus sequencing (CCS) in multiclonal pathogen isolates. Our platform uses 40 PCR primers to asymmetrically barcode and identify multiclonal infections in pools of up to 384 samples. We validated the method using 235 mock infections combining 10 synthetic variants of the indel-rich gene merozoite surface protein 2 of Plasmodium falciparum at different concentrations and infection complexities, as well as 95 isolates from P. falciparum-infected residents of Nyamisati, Tanzania. We also constructed a fully automated analysis pipeline that streamlines the processing and interpretation of epidemiological and antigenic diversity data from demultiplexed FASTQ files. This platform can be easily adapted to other polymorphic antigens of interest in Plasmodium and other human pathogens.
Fine tuning of CpG spatial distribution with DNA origami for improved therapeutic cancer vaccination
Authors: Zeng Yang C. , Young Olivia J. , Wintersinger Christopher M. , Anastassacos Frances M. , MacDonald James I. , Isinelli Giorgia , Dellacherie Maxence O. , Sobral Miguel , Bai Haiqing , Graveline Amanda R. , Vernet Andyna , Sanchez Melinda , Mulligan Kathleen , Choi Youngjin , Ferrante Thomas C. , Keskin Derin B. , Fell Geoffrey G. , Neuberg Donna , Wu Catherine J. , Mooney David J. , Kwon Ick Chan , Ryu Ju Hee , Shih William M. 
Published: June 2022

AbstractMultivalent presentation of ligands often enhances receptor activation and downstream signaling. DNA origami offers precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here we introduce a “square block” DNA origami platform to explore the importance of spacing of CpG oligonucleotides, which engage Toll-like receptors and thereby act as danger signals for dendritic cells. Throughin vitrocell-culture studies andin vivotumor-treatment models, we demonstrate that square blocks induce Th1 immune polarization when CpG is spaced at 3.5 nm. We observe that this DNA origami vaccine enhances DC activation, antigen cross-presentation, CD8 T cell activation, Th1-polarized CD4 activation and NK cell activation. The vaccine also synergizes effectively with anti-PD-L1 for improved cancer immunotherapy in melanoma and lymphoma models and induces long-term T cell memory. Our results suggest that DNA origami may serve as an advanced vaccine platform for controlling adjuvant spacing and co-delivering antigens.One Sentence SummaryThis study developed a DNA origami-based cancer vaccine (DoriVac) that co-delivers antigen and CpG immune adjuvant with an optimal nanospacing for Th1 immune polarization.
Highly accurate isoform identification for the human transcriptome
Authors: Sommer Markus J. , Cha Sooyoung , Varabyou Ales , Rincon Natalia , Park Sukhwan , Minkin Ilia , Pertea Mihaela , Steinegger Martin , Salzberg Steven L. 
Published: June 2022

AbstractWe explore a new hypothesis in genome annotation, namely whether computationally predicted protein structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by structure predictions, we evaluated over 140,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly-curated catalog of human proteins.One-Sentence SummaryWe describe the use of 3D protein structures on a genome-wide scale to evaluate human protein isoforms for biological functionality.
Stress-relief function of migrasomal autophagosome formed by inhibition of autophagosome/lysosome fusion
Authors: Lee Seon Yong , Choi Sang-Hun , Ahn Hee-Sung , Ko Young-Gyu , Kim Kyunggon , Chi Sung Wook , Kim Hyunggee 
Published: June 2022

AbstractGlioblastoma (GBM) is more difficult to treat than other intractable adult tumors. Here, we describe the composition and function of migrasomes generated along with GBM cell migration. Proteomic analysis revealed that LC3B-positive autophagosomes were abundant in the migrasomes of GBM cells. An increased number of migrasomes was observed following treatment with chloroquine (CQ) or inhibition of the expression of STX17 and SNAP29, which are involved in autophagosome/lysosome fusion. Although ATG7 ablation, which is involved in LC3B lipidation, did not suppress migrasome formation, it was confirmed that migrasome formation could be diminished by blocking the alternative autophagy pathway through double knockout of ATG7/BECN1. Furthermore, depletion of ITGA5 or TSPAN4 did not relieve endoplasmic reticulum (ER) stress in cells, resulting in cell death. Taken together, our study suggests that increasing the number of autophagosomes, through inhibition of autophagosome/lysosome fusion, generates migrasomes that have the capacity to alleviate cellular stress.Summary statementThis study demonstrates that glioblastoma cells contain autophagosomes within their migrasomes. Under stress conditions, the formation of migrasomes serves as a stress-relief mechanism to alleviate cell death.
Cell-free synthesis and reconstitution of Bax in nanodiscs: comparison between wild-type Bax and a constitutively active mutant
Authors: Eyitayo Akandé Rouchidane , Giraud Marie-France , Daury Laetitia , Lambert Olivier , Gonzalez Cécile , Manon Stéphen 
Published: June 2022

AbstractBax is a major player in the mitochondrial pathway of apoptosis, by permeabilizing the Outer Mitochondrial Membrane (OMM) to various apoptogenic factors, including cytochrome c. In order to get further insight into the structure and function of Bax when it is inserted in the OMM, we attempted to reconstitute Bax in nanodiscs. Cell-free protein synthesis in the presence of nanodiscs did not allow to obtain Bax-containing nanodiscs, but it provided a simple way to purify full-length Bax without any tag. Purified wild-type Bax (BaxWT) and a constitutively active mutant (BaxP168A) displayed biochemical properties that were in line with previous characterizations following their expression in yeast and human cells followed by their reconstitution into liposomes. Both Bax variants were then reconstituted in nanodiscs. Size exclusion chromatography, dynamic light scattering and transmission electron microscopy showed that nanodiscs formed with BaxP168A were larger than nanodiscs formed with BaxWT. This was consistent with the hypothesis that BaxP168A was reconstituted in nanodiscs as an active oligomer.
Simultaneous swept anhedral helicopter blade tip shape and control-system design
Authors: Sal Firat 
Published: June 2022

Purpose
This paper aims to offer a simultaneous design approach for helicopter having swept anhedral blade tip shape and helicopter flight control system (HFCS) to minimize controller cost.

Design/methodology/approach
By considering previously stated offer, control-oriented models and a stochastic optimization method are applied to minimize controller cost of the HFCS.

Findings
Using simultaneous design approach for helicopters having blade tip swept and blade tip anhedral causes considerably less control effort than the helicopters not benefiting this related design approach.

Practical implications
Simultaneous design approach for helicopters having blade tip swept and blade tip anhedral is applicable to consider fuel economy.

Originality/value
One important novelty of this paper is using simultaneous approach for determining optimum shape of blade tip swept and anhedral. Another considerable novelty of this paper is also using a stochastic optimization method called simultaneous perturbation stochastic approximation for previously mentioned purpose. In this paper, it is also reached that using simultaneous design approach for swept anhedral helicopter blade tip shape and HFCS causes less control effort than the helicopters not using this approach. This leads to less fuel consumption and green environment.
Synthesis cascade estimation for aircraft system identification
Authors: Jianhong Wang , Ramirez-Mendoza Ricardo A. 
Published: June 2022

Purpose
The purpose of this paper extends the authors’ previous contributions on aircraft system identification, such as open loop identification or closed loop identification, to cascade system identification. Because the cascade system is one special network system, existing in lots of practical engineers, more unknown systems are needed to identify simultaneously within the statistical environment with the probabilistic noises. Consider this problem of cascade system identification, prediction error method is proposed to identify three unknown systems, which are parameterized by three unknown parameter vectors. Then the cascade system identification is transferred as one parameter identification problem, being solved by the online subgradient descent algorithm. Furthermore, the nonparametric estimation is proposed to consider the general case without any parameterized process. To make up the identification mission, model validation process is given to show the asymptotic interval of the identified parameter. Finally, simulation example confirms the proposed theoretical results.

Design/methodology/approach
Firstly, aircraft system identification is reviewed through the understanding about system identification and advances in control theory, then cascade system identification is introduced to be one special network system. Secondly, for the problem of cascade system identification, prediction error method and online subgradient decent algorithm are combined together to identify the cascade system with the parameterized systems. Thirdly from the point of more general completeness, another way is proposed to identify the nonparametric estimation, then model validation process is added to complete the whole identification mission.

Findings
This cascade system corresponds to one network system, existing in lots of practice, such as aircraft, ship and robot, so it is necessary to identify this cascade system, paving a way for latter network system identification. Parametric and nonparametric estimations are all studied within the statistical environment. Then research on bounded noise is an ongoing work.

Originality/value
To the best of the authors’ knowledge, research on aircraft system identification only concern on open loop and closed loop system identification, no any identification results about network system identification. This paper considers cascade system identification, being one special case on network system identification, so this paper paves a basic way for latter more advanced system identification and control theory.
A comprehensive examination of psychological capital research using bibliometric, TCCM and content analysis
Authors: Goswami Meghna , Goswami Anil Kumar 
Published: June 2022

PurposeIn today's dynamic business environment and crisis and pandemic like situations, psychological capital has become very significant for sustainable competitive advantage. Due to its importance in organizational context, researchers are investigating it from various perspectives, making it a burgeoning research area. Hence, this study aims to review the literature, provide identity in terms of various patterns and trends, and build the intellectual structure (academic structure) of psychological capital research by presenting a big picture. It further provides the theories, characteristics, context and methodologies (TCCM) analysis and potential avenues for possible future research to facilitate the growth of the field.Design/methodology/approachThis study compiles, evaluates and synthesizes the extant literature of psychological capital, consisting of 954 journal articles collected from Web of Science (WOS) database, using bibliometric techniques, content analysis, and TCCM analysis.FindingsThe study identifies various patterns and trends of psychological capital research and unfolds four major themes, namely psychological capital theoretical concept development, psychological capital relationship building with organizational variables, psychological capital as an underlying mechanism for linkage between organizational variables and psychological capital interventions. It also identifies TCCM outcome and potential avenues for possible future research. The study reveals that psychological capital research area is progressing and has enormous potential to advance in the future.Research limitations/implicationsThis study is pivotal to past–future orientation wherein past is being investigated for developing new pathways of psychological capital research. It has used research articles published in the WOS database, and future studies may further enhance the understanding of psychological research using other databases.Practical implicationsIn addition to advance a comprehensive understanding of psychological capital research, this study will be a quick reference and notable and profound resource for researchers venturing into this marked research area. Further, it will facilitate to leaders and managers to look into various possible avenues to enhance psychological capital of their subordinates for greater organizational good.Originality/valueTo the best of authors' knowledge, this is first study to advance a comprehensive and systematic understanding of psychological capital by integrating bibliometric, TCCM and content analysis.
Talent management practices on employee performance: a mediating role of employee engagement in institution of higher learning: quantitative analysis
Authors: Abdullahi Mohammed Sani , Adeiza Adams , Abdelfattah Fadi , Fatma Mobin , Fawehinmi Olawole , Aigbogun Osaro 
Published: June 2022

PurposeThe purpose of this paper is to investigate the effect of talent management (TM) practices on employee performance (EP) and to explore the mediating role of employee engagement (EE) on the relationship between TM practices and EP in Malaysian private universities (MPUs).Design/methodology/approachThe paper used both descriptive and quantitative approaches, and the unit of analysis of this research consists of MPUs academic staff. The research sample consists of 314 MPUs academic staff, and a questionnaire was used to collect data from the target respondents, while partial least squares-structural equation modelling was used to evaluate the study hypotheses through bootstrapping approach.FindingsThe research outcome revealed that TM practices that comprise of talent recruitment practice (TRP), training and development practice (T&DP), compensation practice (CP) have a significant effect on EP. Furthermore, EE partially mediates the relationship between T&DP, CP and EP, while EE does not mediate the relationship between TRP and EP in MPUs.Practical implicationsThe research suggests that universities management should focus on TM practices as a tool to achieve and maintain EE and positive attitudes (EP) in relation to work.Originality/valueThe research makes substantial contributions to the literature by investigating the effect of TM practices on EP through the role of EE as mediation in MPUs. The research is one of the very few studies undertaken in MPUs. Therefore, the results of this research serve as a guide for the universities management to develop their institutional strategies and policies in a manner in which their employees’ success can be achieved and encouraged.International Journal of Business and Society.
Building a thematic framework of identity research in hospitality organizations: a systematic literature review approach
Authors: Ponting Sandra Sun-Ah , Lee Lindsey 
Published: June 2022

Purpose
The purpose of this study is to systematically review and synthesize identity research in the hospitality management literature. A critical revision of identity research in hospitality organizations, built on major identity constructs in the general management literature, is conducted to create thematic frameworks. This framework yields theoretical and practical future hospitality research agendas.

Design/methodology/approach
The current study adopted a systematic literature review approach to analyze and synthesize identity research in hospitality organizations. A total of 55 articles published since 2000 are included in this review.

Findings
Stemming from general management conceptualizations, identity research in hospitality organizations are categorized into four overarching themes. This review also points to research gaps in epistemological conceptualizations, definitional frameworks and methodology.

Originality/value
The study reviews identity research in hospitality organizations, builds an integrative thematic framework of identity research in hospitality and proposes directions for future research.