bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatiotemporal complexity architecture of human brain activity
Authors: Krohn Stephan , von Schwanenflug Nina , Waschke Leonhard , Romanello Amy , Gell Martin , Garrett Douglas D. , Finke Carsten 
Published: June 2021

AbstractThe human brain operates in large-scale functional networks. These networks are thought to arise from neural variability, yet the principles behind this link remain unknown. Here we report a mechanism by which the brain’s network architecture is tightly linked to critical episodes of neural regularity, visible as spontaneous ‘complexity drops’ in functional MRI signals. These episodes support the formation of functional connections between brain regions, subserve the propagation of neural activity, and reflect inter-individual differences in age and behavior. Furthermore, complexity drops define neural states that dynamically shape the coupling strength, topological structure, and hierarchy of brain networks and comprehensively explain known structure-function relationships within the brain. These findings delineate a unifying complexity architecture of neural activity – a human ‘complexome’ that underpins the brain’s functional network organization.
Rapid and Visible RPA-Cas12a fluorescence Assay for Accurate Detection of Zoonotic Dermatophytes
Authors: Wang Liyang , Fu Jinyu , Cai Guang , Zhang Di , Shi Shuobo , Zhang Yueping 
Published: June 2021

AbstractBackgroundDermatophytosis is an infectious disease of global significance caused by several fungal species, which affects the hair, nails, or superficial layers of the skin. The most common zoonotic dermatophytes are Microsporum canis, Nannizzia gypsea and Trichophyton mentagrophytes. Wood’s lamp examination, microscopic identification and fungal culture are the main conventional diagnostic methods used in clinics. Less common methods are dermatophyte PCR and biopsy/histopathology. However, these methods also have limitations for providing both accuracy and timely on-site detection. The recent development of CRISPR-based diagnostic platform provides the possibility of a rapid, accurate, and portable diagnostic tool, which has huge potential for clinical applications.ObjectivesThe purpose of this study is to establish a molecular method for rapid and accurate diagnosis of clinical dermatophytes, which can accelerate clinical diagnostic testing and help timely treatment.MethodsIn this paper, we design a Cas12a-based assay combined with recombinase polymerase amplification (RPA) to differentiate three main zoonotic dermatophytes. The limit of detection (LOD) is determined by using standard strains. A total of 25 clinical samples (hair and scurf) are identified to evaluate the sensitivity and specificity of this assay.ResultsThe RPA-Cas12a method showed high sensitivity and specificity (100% and 100%, respectively). The results could be observed directly by naked-eyes, and all tested samples were consistent with fungal culture and sequencing results.ConclusionsCompared with other methods, the RPA-Cas12a-fluorescence assay requires less time (30 minutes) and less complicated equipment, and visible changes can be clearly observed, which is suitable for on-site clinical diagnosis.
DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells
Authors: Waldrip Zachary J , Burdine Lyle , Harrison David K , Azevedo-Pouly Ana Clara , Storey Aaron J. , Moffett Olivia G. , Mackintosh Samuel G. , Burdine Marie Schluterman 
Published: June 2021

AbstractDNA-dependent protein kinase catalytic subunit (DNA-PKcs) is known primarily for its function in DNA double-stranded break repair and non-homologous end joining (NHEJ). However, DNA-PKcs also has a critical yet undefined role in immunity impacting both myeloid and lymphoid cell lineages spurring interest in targeting DNA-PKcs for therapeutic strategies in immune-related diseases. To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify first order phosphorylation targets of DNA-PKcs. Results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1) at S301. Expression of Egr1 is induced early upon T cell activation and dictates T cell response by modulating expression of cytokines and key costimulatory molecules. Mutation of serine 301 to alanine via CRISPR-Cas9 resulted in increased proteasomal degradation of Egr1 and a decrease in Egr1-dependent transcription of IL2 (interleukin-2) in activated T cells. Our findings identify DNA-PKcs as a critical intermediary link between T cell activation and T cell fate and a novel phosphosite involved in regulating Egr1 activity.
Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation
Authors: Bechon Nathalie , Mihajlovic Jovana , Lopes Anne-Aurélie , Vendrell-Fernández Sol , Deschamps Julien , Briandet Romain , Sismeiro Odile , Martin-Verstraete Isabelle , Dupuy Bruno , Ghigo Jean-Marc 
Published: June 2021

ABSTRACTBacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Whereas adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We identified the genetic determinants of this bile-dependent biofilm formation and showed that it involves the production of the DNase BT3563, degrading extracellular DNA, in biofilms formed in the presence of bile. Our study therefore identifies a physiologically relevant condition inducing B. thetaiotaomicron biofilm and shows that, in contrast to the biofilm-promoting role played by bacterial eDNA scaffold in Firmicutes and Proteobacteria models, degradation of eDNA by BT3563 DNAse and its widespread homologs is required to achieve B. thetaiotaomicron bile-dependent biofilm formation.
The Rab GTPase activating protein TBC-2 regulates endosomal localization of DAF-16 FOXO and lifespan
Authors: Meraş İçten , Chotard Laëtitia , Liontis Thomas , Ratemi Zakaria , Wiles Benjamin , Seo Jung Hwa , Van Raamsdonk Jeremy M. , Rocheleau Christian E. 
Published: June 2021

ABSTRACTFOXO transcription factors have been shown to regulate longevity in model organisms and are associated with longevity in humans. To gain insight into how FOXO functions to increase lifespan, we examined the subcellular localization of DAF-16 in C. elegans. We show that DAF-16 is localized to endosomes and that this endosomal localization is increased by the insulin-IGF signaling (IIS) pathway. Endosomal localization of DAF-16 is modulated by endosomal trafficking proteins. Disruption of the Rab GTPase activating protein TBC-2 increases endosomal localization of DAF-16, while inhibition of TBC-2 targets, RAB-5 or RAB-7 GTPases, decreases endosomal localization of DAF-16. Importantly, the amount of DAF-16 that is localized to endosomes has functional consequences as increasing endosomal localization through mutations in tbc-2 reduced the lifespan of long-lived daf-2 IGFR mutants, depleted their fat stores, and DAF-16 target gene expression. Overall, this work identifies endosomal localization as a mechanism regulating DAF-16 FOXO, which is important for its functions in metabolism and aging.
Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay
Authors: Mule Simon Ngao , Rosa-Fernandes Livia , Coutinho João V. P. , De Morais Vinícius , Macedo da Silva Janaina , Santiago Verônica Feijoli , Quina Daniel , Santos de Oliveira Gilberto , Thaysen-Andersen Morten , Larsen Martin R. , Labriola Letícia , Palmisano Giuseppe 
Published: June 2021

AbstractA new method to probe the conformational changes of glycoproteins on a systems-wide scale, termed limited deglycosylation assay (LDA), is described. The method measures the differential rate of deglycosylation of N-glycans on natively folded proteins by the common peptide:N-glycosidase F (PNGase F) enzyme which in turn informs on their spatial presentation and solvent exposure on the protein surface hence ultimately the glycoprotein conformation. LDA involves 1) protein-level N-deglycosylation under native conditions, 2) trypsin digestion under denaturing conditions, 3) glycopeptide enrichment, 4) peptide-level N-deglycosylation and 5) quantitative MS-based analysis of the formerly N-glycosylated peptides. LDA was initially developed and the experimental conditions optimized using bovine RNase B and fetuin. The method was then applied to glycoprotein extracts from LLC-MK2 epithelial cells upon treatment with dithiothreitol to induce endoplasmic reticulum stress and promote protein misfolding. Data from the LDA and 3D structure analysis showed that glycoproteins predominantly undergo structural changes in loops/turns upon ER stress as exemplified with detailed analysis of ephrin-A5, GALNT10, PVR and BCAM. These results show that LDA accurately reports on systems-wide conformational changes of glycoproteins induced under controlled treatment regimes. Thus, LDA opens avenues to study glycoprotein structural changes in a range of other physiological and pathophysiological conditions relevant to acute and chronic diseases.
The enteric pathogen Cryptosporidium parvum exports proteins into the cytoplasm of the infected host cell
Authors: Dumaine Jennifer E. , Sateriale Adam , Gibson Alexis R. , Reddy Amita G. , Gullicksrud Jodi A. , Hunter Emma N. , Clark Joseph T. , Striepen Boris 
Published: June 2021

ABSTRACTThe parasite Cryptosporidium is responsible for diarrheal disease in young children causing death, malnutrition, and growth delay. Cryptosporidium invades enterocytes where it develops in a unique intracellular niche. Infected cells exhibit profound changes in morphology, physiology and transcriptional activity. How the parasite effects these changes is poorly understood. We explored the localization of highly polymorphic proteins and found members of the C. parvum MEDLE protein family to be translocated into the cytoplasm of infected cells. All intracellular life stages engage in this export, which occurs after completion of invasion. Mutational studies defined an N-terminal host-targeting motif and demonstrated proteolytic processing at a specific leucine residue. Direct expression of MEDLE2 in mammalian cells triggered an ER stress response that was also observed during infection. Taken together, our studies reveal the presence of a Cryptosporidium secretion system capable of delivering pathogenesis factors into the infected enterocyte.
A tumor suppressive long noncoding RNA, DRAIC, inhibits protein translation and induces autophagy by activating AMPK
Authors: Saha Shekhar , Zhang Ying , Wilson Briana , Abounader Roger , Dutta Anindya 
Published: June 2021

AbstractLncRNAs are long RNA transcripts that do not code for proteins and that have been shown to play a major role in cellular processes through diverse mechanisms. DRAIC, a lncRNA which is downregulated in castration-resistant advanced prostate cancer, inhibits the NF-kB pathway by inhibiting the IκBα kinase. Decreased DRAIC expression predicted poor patient outcome in gliomas and seven other cancers. We now report that DRAIC suppresses invasion, migration, colony formation and xenograft growth of glioblastoma derived cell lines. DRAIC activates AMPK by downregulating the NF-κB target gene GLUT1, and thus represses mTOR, leading to downstream effects such as decrease in protein translation and increase in autophagy. DRAIC, therefore, has an effect on multiple signal transduction pathways that are important for oncogenesis: the NF-κB pathway and AMPK-mTOR-S6K/ULK1 pathway. The regulation of NF-κB, protein translation and autophagy by the same lncRNA explains the tumor suppressive role of DRAIC in different cancers and reinforces the importance of lncRNAs as emerging regulators of signal transduction pathways.
Learning ‘The Knowledge’: How London Taxi Drivers Build Their Cognitive Map of London
Authors: Griesbauer Eva-Maria , Manley Ed , Wiener Jan M. , Spiers Hugo J. 
Published: June 2021

AbstractLicenced London taxi drivers have been found to show changes in the grey matter density of their hippocampus over the course of training and decades of navigation in London (UK). This has been linked to their learning and using of the ‘Knowledge of London’, the names and layout of over 26,000 streets and thousands of points of interest in London. Here we examined the process of how this knowledge is acquired and we detail key steps that include: systematic study of maps, travel on selected overlapping routes, the mental visualisation of places and the optimal use of subgoals. We provide the first map of the street network covered by the routes used to learn, allowing insight into where gaps in the network exist. The methods could be widely applied to aid spatial learning in the general population and may provide insights for artificial intelligence (AI) systems to efficiently learn new environments.
Functional Recovery of the Germ Line Following Splicing Collapse
Authors: Cao Wei , Tran Christopher , Archer Stuart K. , Gopal Sandeep , Pocock Roger 
Published: June 2021

ABSTRACTSplicing introns from precursor-messenger RNA (pre-mRNA) transcripts is essential for translating functional proteins. Here, we report that the previously uncharacterized Caenorhabditis elegans protein MOG-7, acts as a pre-mRNA splicing factor. Depleting MOG-7 from the C. elegans germ line causes intron retention in the majority of germline-expressed genes, impeding the germ cell cycle, and causing defects in nuclear morphology, germ cell identity and sterility. Despite the deleterious consequences caused by MOG-7 loss, the adult germ line can functionally recover to produce viable and fertile progeny when MOG-7 is restored. Germline recovery is dependent on a burst of apoptosis that likely clears defective germ cells, and viable gametes generated from the proliferation of germ cells in the progenitor zone. Together, these findings reveal that MOG-7 is essential for germ cell development, and that the germ line is able to functionally recover after a collapse in RNA splicing.
LITE SABR M1: a Phase I Trial of Lattice Stereotactic Body Radiotherapy for Large Tumors
Authors: Duriseti Sai , Kavanaugh James , Szymanski Jeff , Huang Yi , Basarabescu Franco , Chaudhuri Aadel , Henke Lauren , Samson Pamela , Lin Alexander , Robinson Clifford , Spraker Matthew B 
Published: June 2021

AbstractPurposeStereotactic body radiotherapy (SBRT) is an attractive treatment option for patients with metastatic and/or unresectable tumors, however its use is limited to smaller tumors. Lattice is a form of spatially fractionated radiotherapy that may offer safe delivery of SBRT for bulky tumors. We previously described Lattice SBRT, which delivers 20 Gy in 5 fractions with a simultaneous Lattice boost to 66.7 Gy. The goal of this study was to prospectively evaluate the acute toxicity and quality of life (QoL) of patients with large tumors (> 5 cm) treated with Lattice SBRT.MethodsThis was a single-arm phase I trial conducted between October 2019 and August 2020. Patients with tumors >4.5 cm were eligible. Lattice SBRT was delivered every other day.. The primary outcome was the rate of 90-day treatment-associated (probably or definitely attributable) grade 3+ acute toxicity by Common Terminology Criteria for Adverse Events (CTCAE) version 5.0 criteria. Other outcomes included changes in patient reported toxicity and QoL inventories, GTV, and peripheral blood cytokines.ResultsTwenty patients (22 tumors) were enrolled. Median GTV was 783 cc (range: 64-3713 cc). Fifty percent of tumors were in the thorax, 45% abdomen/pelvis, and 5% extremity. There was no treatment-associated grade 3+ toxicity.. There was one case of grade 4 toxicity possibly associated with Lattice SBRT.ConclusionsThis phase I study met its primary endpoint of physician reported safety. An ongoing phase II clinical trial of Lattice SBRT will evaluate late safety and efficacy of this novel technique.
Teachers' digital technology access to motivation, skills and use: a structural equation modeling study
Authors: Habibi Akhmad , Yaakob Mohd Faiz Mohd , Mukminin Amirul , Muhaimin Muhaimin , Prasojo Lantip Diat , Yusop Farrah Dina , Muzakkir Muzakkir 
Published: June 2021

PurposeThe current study aimed to develop and validate a scale to model factors affecting digital technology access for instructional use. The scale was mainly used to assess the structural model. Besides, tests of difference were addressed regarding digital technology access for instructional use based on gender, teaching experience and school location.Design/methodology/approachThe authors implemented a survey design in this study. A scale based on prior studies was developed, validated and piloted. The pilot study data were computed for an exploratory factor analysis. Further, partial least squares structural equation modeling (PLS-SEM) and t-test procedures were used for the main data analysis (n.2677). The authors also included the importance-performance map analysis to extend of the results of the PLS-SEM.FindingsThe findings of the study successfully assessed the validity and reliability of the scale. All hypothetical relationships in the structural model were positively significant. The t-test results show that teaching experience and school location were significantly different regarding instructional use access; however, an insignificant difference emerged based on gender.Practical implicationsFailure in technology integration is possible if policies have not been carefully prepared. Therefore, users' perception is an essential factor in determining technology integration, including access to digital technology.Originality/valueThis research has the potential to enhance the understanding of access to digital technology in the context of developing countries by the elaboration of the proposed model's instrument development and validation, path analysis assessment and difference test examination with a large sample size. Also, the current study emphasizes the importance of raising awareness about digital technology access that the model can facilitate a valid and reliable foundation for future researchers interested in conducting similar types of research.
Links of socio-emotional context on performance in categorization task of adults with moderate to severe intellectual disabilities
Authors: Igier Suzanne , Pennequin Valérie 
Published: June 2021

Purpose
Studies on intellectual disabilities describe difficulties at the cognitive level but little about the other factors that can impact the individual’s performance. The aim of this research was thus to assess the effects of the socio-emotional context on the performance of adults with intellectual disabilities in a cognitive task. The main hypothesis was that people with intellectual disabilities will not have the cognitive ability to see the socioemotional environment as a potential resource, and that they could not use it to mobilize their cognitive resources to try and improve their performance and adopt more positive behavior.

Design/methodology/approach
A total of 32 people with moderate to severe intellectual disabilities were recruited. They performed a categorization task and were then given their results. Throughout the test, the psychologist observed the participants’ behavior and, more specifically, their emotional expressions, their pro-social behavior and their respect for social rules.

Findings
The results support the hypotheses, with better performance among participants who adopted pro-social behaviors, respected the rules and displayed positive emotional expressions. These results highlight the central role played by others in the ability of adults with intellectual disabilities to adapt to a given situation.

Research limitations/implications
This study was conducted by a psychologist, which could have biased the relationship with the participants. A complementary study is in progress to measure the effects.

Practical implications
These findings have implications for cognitive remediation tasks aimed at mobilizing the cognitive resources of adults with intellectual disabilities.

Originality/value
To the best of the authors’ knowledge, this is the only study to evaluate the role of the socio-emotional environment on the performance of adults with intellectual disabilities.
Determination of soil water hydraulic parameters from infiltration data
Authors: Gao Yan , Chang Kai , Xing Xuguang , Liang Jiaping , He Nian , Ma Xiaoyi 
Published: June 2021

PurposeTraditional laboratory measurements of soil water diffusivity (D) and soil water retention curve (SWRC) are always time-consuming and labor-intensive. Therefore, this paper aims to present a simple and robust test method for determiningDand SWRC without reducing accuracy.Design/methodology/approachIn this study, aDmodel of unsaturated soil was established based on Gardner–Russo model and then a combination of Gardner–Russo model with one-dimensional horizontal absorption method to obtainnand a parameters of Gardner–Russo model. One-dimensional horizontal absorption experiments on loam, silt loam and sandy clay loam were conducted to obtain the relationships between measured infiltration rate and cumulative infiltration with wetting front distance. Based on the obtained relationships, the measured infiltration data from the one-dimensional horizontal absorption tests were used to calculatenand a parameters and further constructingDand SWRC.FindingsBoth the calculatedDand SWRC inversed from the infiltration data were in good agreement with the measured ones that obtained from the traditional horizontal absorption method and the centrifuge method, respectively. Error analysis indicated that only the infiltration data are enough to reliably synchronously determineDand SWRC.Originality/valueA simple and robust method is proposed for synchronous determination of soil water diffusivity and water retention curve.
Analysis of supply chain’s resilience in crowd networks
Authors: Meng Shihan , Dong Wenxiang , Hu Hong , Li Yuejiang 
Published: June 2021

Purpose
The purpose of this paper is to analyze the supply chain's resilience in crowd networks from both static and dynamic perspectives.

Design/methodology/approach
This paper first defines the supply chain’s resilience, then proposes a graphical and game-theoretic framework to evaluate the resilience.

Findings
In this framework, an equilibrium with high resilience will be achieved after the iterated prisoner's dilemma in the supply chain. The two-stage update mechanism contributes to higher profits, higher stability and stronger risk resistance capability. The reputation-based tit-for-tat strategy in the second stage helps to realize society cooperation.

Originality/value
This work pays more attention to the dynamic evolution of interactions between organizations in the supply chain. It provides an important theoretical basis for future work such as how to effectively control and guide the evolution of events in the intelligence network and how to stand sudden changes and avoid collapse.