bluuebunny/crossref_metadata_2025_split huggingface dataset:
An investigation into the critical role of fibre orientation in the ultimate tensile strength and stiffness of human carotid plaque caps
Authors: Johnston R.D. , Gaul R.T. , Lally C. 
Published: August 2020

AbstractThe development and subsequent rupture of atherosclerotic plaques in human carotid arteries is a major cause of ischemic stroke. Mechanical characterization of atherosclerotic plaques can aid our understanding of this rupture risk. Despite this however, experimental studies on human atherosclerotic carotid plaques, and fibrous plaque caps in particular, are very limited. This study aims to provide further insights into atherosclerotic plaque rupture by mechanically testing human fibrous plaque caps, the region of the atherosclerotic lesion most often attributed the highest risk of rupture. The results obtained highlight the variability in the ultimate tensile stress, strain and stiffness experienced in atherosclerotic plaque caps. By pre-screening all samples using small angle light scattering (SALS) to determine the dominant fibre direction in the tissue, along with supporting histological analysis, this work suggests that the collagen fibre alignment in the circumferential direction plays the most dominant role for determining plaque structural stability. The work presented in this study could provide the basis for new diagnostic approaches to be developed, which non-invasively identify carotid plaques at greatest risk of rupture.Graphical Abstract
CAS-LiveFISH: Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos
Authors: Geng Yongtao , Pertsinidis Alexandros 
Published: August 2020

SUMMARYVisualizing the 4D genome in live cells is essential for understanding its regulation. Programmable DNA-binding probes, such as fluorescent clustered regularly interspaced short palindromic repeats (CRISPR) and transcription activator-like effector (TALE) proteins have recently emerged as powerful tools for imaging specific genomic loci in live cells. However, many such systems rely on genetically-encoded components, often requiring multiple constructs that each must be separately optimized, thus limiting their use. Here we develop efficient and versatile systems, based onin vitrotranscribed single-guide-RNAs (sgRNAs) and fluorescently-tagged recombinant, catalytically-inactivated Cas9 (dCas9) proteins. Controlled cell delivery of pre-assembled dCas9-sgRNA ribonucleoprotein (RNP) complexes enables robust genomic imaging in live cells and in early mouse embryos. We further demonstrate multiplex tagging of up to 3 genes, tracking detailed movements of chromatin segments and imaging spatial relationships between a distal enhancer and a target gene, with nanometer resolution in live cells. This simple and effective approach should facilitate visualizing chromatin dynamics and nuclear architecture in various living systems.
Antigen Presentation-Independent Reciprocal Immune Modulation byHLA-DRB1Allelic Epitopes that Associate with Autoimmune Disease Risk or Protection
Authors: van Drongelen Vincent , Scavuzzi Bruna Miglioranza , Nogueira Sarah Veloso , Miller Frederick W. , Sawalha Amr H. , Holoshitz Joseph 
Published: August 2020

AbstractStatistical associations between particular human leukocyte antigen (HLA) alleles and susceptibility to - or protection from - autoimmune diseases have been long observed. Allele-specific antigen presentation (AP) has been widely proposed as a culprit mechanism; however, direct evidence to substantiate that hypothesis is scant. Here we demonstrate AP-independent differential macrophage activation byHLA-DRB1alleles known to associate with autoimmune disease risk or protection with resultant polarization of pro-inflammatory (“M1”) versus anti-inflammatory (“M2”) macrophages, respectively. RNA-sequencing analyses ofin vitro-polarized macrophages in the presence of AP-incompetent short synthetic peptides corresponding to the third allelic hypervariable regions coded by those twoHLA-DRB1alleles showed reciprocal activation of pro- versus anti-inflammatory transcriptomes, with implication of corresponding gene ontologies and upstream regulators. These results identify a previously unrecognized mechanism of differential immune modulation by shortHLA-DRB1-coded allelic epitopes independent of AP, and could shed new light on the mechanistic basis of HLA-disease association.
SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients
Authors: Pérez-Bermejo Juan A. , Kang Serah , Rockwood Sarah J. , Simoneau Camille R. , Joy David A. , Ramadoss Gokul N. , Silva Ana C. , Flanigan Will R. , Li Huihui , Nakamura Ken , Whitman Jeffrey D. , Ott Melanie , Conklin Bruce R. , McDevitt Todd C. 
Published: August 2020

ABSTRACTAlthough COVID-19 causes cardiac dysfunction in up to 25% of patients, its pathogenesis remains unclear. Exposure of human iPSC-derived heart cells to SARS-CoV-2 revealed productive infection and robust transcriptomic and morphological signatures of damage, particularly in cardiomyocytes. Transcriptomic disruption of structural proteins corroborated adverse morphologic features, which included a distinct pattern of myofibrillar fragmentation and numerous iPSC-cardiomyocytes lacking nuclear DNA. Human autopsy specimens from COVID-19 patients displayed similar sarcomeric disruption, as well as cardiomyocytes without DNA staining. These striking cytopathic features provide new insights into SARS-CoV-2 induced cardiac damage, offer a platform for discovery of potential therapeutics, and raise serious concerns about the long-term consequences of COVID-19.
PFRED: A computational platform for siRNA and antisense oligonucleotides design
Authors: Sciabola Simone , Xi Hualin , Cruz Dario , Cao Qing , Lawrence Christine , Zhang Tianhong , Rotstein Sergio , Hughes Jason D , Caffrey Daniel R , Stanton Robert 
Published: August 2020

AbstractPFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading athttps://github.com/pfred/pfred-gui/releasesas a java Jar file. The source code and the links for downloading the precompiled version can be found athttps://github.com/pfred.
Soil nutrient availability alters tree carbon allocation dynamics during drought
Authors: Schönbeck Leonie , Li Mai-He , Lehmann Marco M. , Rigling Andreas , Schaub Marcus , Hoch Günter , Kahmen Ansgar , Gessler Arthur 
Published: August 2020

AbstractDrought alters allocation patterns of carbon (C) and nutrients in trees and eventually impairs tree functioning. Elevated soil nutrient availability might alter the response of trees to drought. We hypothesize that increased soil nutrient availability stimulates root metabolism and carbon allocation to belowground tissues under drought stress. To test this hypothesis, we subjected three-year-oldPinus sylvestrissaplings in open-top cambers during two subsequent years to drought using three different water treatments (100%, 20% and 0% plant available water in the soil) and two soil nutrient regimes (ambient and nitrogen-phosphorus-potassium (N-P-K) fertilization corresponding to 5 g N/m2/yr) and released drought thereafter. We conducted a15N and13C labelling experiment during the peak of the first-year drought by injecting15N labelled fertilizer in the soil and exposing the tree canopies to13C labelled CO2. The abundance of the N and C isotopes in the roots, stem and needles was assessed during the following year. C uptake was slightly lower in drought stressed trees, and extreme drought inhibited largely the N uptake and transport. Carbon allocation to belowground tissues was decreased under drought, but not in combination with fertilization. Our results indicate a potential positive feedback loop, where fertilization improved the metabolism and functioning of the roots, stimulating the source activity and hence C allocation to belowground tissues. This way, soil nutrients compensated for drought-induced loss of root functioning, mitigating drought stress of trees.
Novel cryo-electron tomography structure of Arp2/3 complex in cells reveals mechanisms of branch formation
Authors: Fäßler Florian , Dimchev Georgi , Hodirnau Victor-Valentin , Wan William , Schur Florian KM 
Published: August 2020

AbstractThe actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Our structure indicates a central role for the ArpC3 subunit in stabilizing the active conformation and suggests that in the branch junction relocation of the ArpC5 N-terminus and the C-terminal tail of Arp3 is important to fix Arp2 and Arp3 in an actin dimer-like conformation. Notably, our model of the branch junction in cells significantly differs from the previousin vitrobranch junction model.
Confocal Laser-Scanning Fluorescence-Lifetime Single-Molecule Localisation Microscopy
Authors: Thiele Jan Christoph , Helmerich Dominic , Oleksiievets Nazar , Tsukanov Roman , Butkevich Eugenia , Sauer Markus , Nevskyi Oleksii , Enderlein Jörg 
Published: August 2020

AbstractFluorescence lifetime imaging microscopy (FLIM) is an important technique that adds another dimension to the intensity and colour information of conventional microscopy. In particular, it allows for multiplexing fluorescent labels that have otherwise similar spectral properties. Currently, the only super-resolution technique that is capable of recording super-resolved images with lifetime information is STimulated Emission Depletion (STED) microscopy. In contrast, all Single-Molecule Localisation Microscopy (SMLM) techniques that employ wide-field cameras completely lack the lifetime dimension. Here, we combine Fluorescence-Lifetime Confocal Laser-Scanning Microscopy (FL-CLSM) with SMLM for realising single-molecule localisation-based fluorescence-lifetime super-resolution imaging (FL-SMLM). Besides yielding images with a spatial resolution much beyond the diffraction limit, it determines the fluorescence lifetime of all localised molecules. We validate our technique by applying it to direct STochastic Optical Reconstruction Microscopy (dSTORM) and Points Accumulation for Imaging in Nanoscale Topography (PAINT) imaging of fixed cells, and we demonstrate its multiplexing capability on samples with two different labels that differ only by fluorescence lifetime but not by their spectral properties.
Occurrence of extended spectrum β-lactamase and AmpC-producingEscherichia coliin retail meat products from the Maritime Provinces, Canada
Authors: Awosile Babafela , Eisnor Jessica , Saab Matthew E. , Heider Luke , McClure J T. 
Published: August 2020

AbstractThis study was conducted to determine the occurrence of antimicrobial resistance to the extended-spectrum cephalosporins (ESC) inEscherichia coliisolates recovered from retail meat products collected in the Maritime Provinces of Canada using both selective and traditional culture methods, and genotypically using multiplex polymerase chain reactions.ESC-RE. coliwas detected in 33/559 (5.9%) samples using the traditional culture compared to 151/557 (27.1%) samples using the selective culture method. The recovery of ESC-RE. coliisolates was more common in poultry compared to beef and pork (P<0.001). Multi-drug resistance, ESBL, and AmpC phenotypes were more common in chicken-derived isolates than other retail meat products (P<0.001). From the 98 isolates selected, 76 (77.6%) isolates were positive for either ESBL and AmpC β-lactamases or both. Among the 76 isolates,blaCMY-2(78.9%),blaCTXM(46.1%),blaTEM(21.1%), andblaSHV(1.3%) were detected. Among theblaCTXM-producing isolates;blaCTXM-1,blaCTXM-2, andblaCTXM-9phylogenetic groups were detected. β-lactamase genes were detected more in chicken-derived isolates compared to other meat types (P<0.01). This study demonstrated the occurrence of ESBL and AmpC resistance genes in retail meat products in Maritime Provinces of Canada. Also, selective culture significantly improved the recovery of ESC-RE. coliisolates from retail meat samples.
Stellate cell computational modelling predicts signal filtering in the molecular layer circuit of cerebellum
Authors: Rizza Martina Francesca , Locatelli Francesca , Masoli Stefano , Sánchez Ponce Diana , Muñoz Alberto , Prestori Francesca , D’Angelo Egidio 
Published: August 2020

AbstractThe functional properties of cerebellar stellate cells and the way they regulate molecular layer activity are still unclear. We have measured stellate cells electroresponsiveness and their activation by parallel fiber bursts. Stellate cells showed intrinsic pacemaking, along with characteristic responses to depolarization and hyperpolarization, and showed a marked short-term facilitation during repetitive parallel fiber transmission. Spikes were emitted after a lag and only at high frequency, making stellate cells to operate as delay-high-pass filters. A detailed computational model summarizing these physiological properties allowed to explore different functional configurations of the parallel fiber – stellate cell – Purkinje cell circuit. Simulations showed that, following parallel fiber stimulation, Purkinje cells almost linearly increased their response with input frequency but such an increase was inhibited by stellate cells, which leveled the Purkinje cell gain curve to its 4 Hz value. When reciprocal inhibitory connections between stellate cells were activated, the control of stellate cells over Purkinje cell discharge was maintained only at very high frequencies. These simulations thus predict a new role for stellate cells, which could endow the molecular layer with low-pass and band-pass filtering properties regulating Purkinje cell gain and, along with this, also burst delay and the burst-pause responses pattern.
Synchronization and resilience in the Kuramoto white matter network model with adaptive state-dependent delays
Authors: Park Seong Hyun , Lefebvre Jeremie 
Published: August 2020

AbstractWhite matter pathways form a complex network of myelinated axons that regulate signal transmission in the nervous system and play a key role in behaviour and cognition. Recent evidence reveals that white matter networks are adaptive and that myelin remodels itself in an activity-dependent way, during both developmental stages and later on through behaviour and learning. As a result, axonal conduction delays continuously adjust in order to regulate the timing of neural signals propagating between different brain areas. This delay plasticity mechanism has yet to be integrated in computational neural models, where conduction delays are oftentimes constant or simply ignored. As a first approach to adaptive white matter remodelling, we modified the canonical Kuramoto model by enabling all connections with adaptive, phase-dependent delays. We analyzed the equilibria and stability of this system, and applied our results to two oscillator and large dimensional networks. Our joint mathematical and numerical analysis demonstrates that plastic delays act as a stabilizing mechanism promoting the network’s ability to maintain synchronous activity. Our work also shows that global synchronization is more resilient to perturbations and injury towards network architecture. Our results provide key insights about the analysis and potential significance of activity-dependent myelination in large-scale brain synchrony.
Collegiate athlete brain data for white matter mapping and network neuroscience
Authors: Caron Bradley , Stuck Ricardo , McPherson Brent , Bullock Daniel , Kitchell Lindsey , Faskowitz Joshua , Kellar Derek , Cheng Hu , Newman Sharlene , Port Nicholas , Pestilli Franco 
Published: August 2020

AbstractWe describe a dataset of processed data with associated reproducible preprocessing pipeline collected from two collegiate athlete groups and one non-athlete group. The dataset shares minimally processed diffusion-weighted magnetic resonance imaging (dMRI) data, three models of the diffusion signal in the voxel, full-brain tractograms, segmentation of the major white matter tracts as well as structural connectivity matrices. There is currently a paucity of similar datasets openly shared. Furthermore, major challenges are associated with collecting this type of data. The data and derivatives shared here can be used as a reference to study the effects of long-term exposure to collegiate athletics, such as the effects of repetitive head impacts. We use advanced anatomical and dMRI data processing methods publicly available as reproducible web services at brainlife.io.
A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries inHoxClusters
Authors: Ortabozkoyun-Kara Havva , Huang Pin-Yao , Cho Hyunwoo , Narendra Varun , Leroy Gary , Skok Jane A. , Tsirigos Aristotelis , Mazzoni Esteban O. , Reinberg Danny 
Published: August 2020

AbstractThe essential CCCTC-binding factor (CTCF) is critical to three-dimensional (3D) genome organization. CTCF binding insulates active and repressed genes within theHoxclusters upon differentiation, but such binding does not participate in boundary formation in all cell types, such as embryonic stem cells. We conducted a genome-wide CRISPR knockout screen to identify genes required for CTCF boundary activity at theHoxAcluster, complemented by novel biochemical approaches. This screen identified Myc-associated zinc finger protein (MAZ) as a CTCF insulator co-factor, among other candidates listed herein. MAZ depletion or specific deletion of MAZ motifs within theHoxclusters led to de-repression of posteriorHoxgenes immediately after CTCF boundaries upon differentiation, which phenocopied deletion of the proximal CTCF motifs. Similar to CTCF, MAZ interacted with the cohesin subunit, RAD21. Upon loss of MAZ, local contacts within topologically associated domains (TADs) were disrupted, as evidenced by HiC analysis. Thus, MAZ is a novel factor sharing insulation properties with CTCF and contributing to the genomic architectural organization.One Sentence SummaryMAZ is identified as an insulator functioning at CTCF boundaries delimiting active and repressed genes atHoxclusters
Roles of lysosomotropic agents on LRRK2 activation and Rab10 phosphorylation
Authors: Kuwahara Tomoki , Funakawa Kai , Komori Tadayuki , Sakurai Maria , Yoshii Gen , Eguchi Tomoya , Fukuda Mitsunori , Iwatsubo Takeshi 
Published: August 2020

AbstractLeucine-rich repeat kinase 2 (LRRK2), the major causative gene product of autosomal-dominant Parkinson’s disease, is a protein kinase that phosphorylates a subset of Rab GTPases. Since pathogenic LRRK2 mutations increase its ability to phosphorylate Rab GTPases, elucidating the mechanisms of how Rab phosphorylation is regulated by LRRK2 is of great importance. We have previously reported that chloroquine-induced lysosomal stress facilitates LRRK2 phosphorylation of Rab10 to maintain lysosomal homeostasis. Here we reveal that Rab10 phosphorylation by LRRK2 is potently stimulated by treatment of cells with a set of lysosome stressors and clinically used lysosomotropic drugs. These agents commonly promoted the formation of LRRK2-coated enlarged lysosomes and extracellular release of lysosomal enzyme cathepsin B, the latter being dependent on LRRK2 kinase activity. In contrast to the increase in Rab10 phosphorylation, treatment with lysosomotropic drugs did not increase the enzymatic activity of LRRK2, as monitored by its autophosphorylation at Ser1292 residue, but rather enhanced the molecular proximity between LRRK2 and its substrate Rab GTPases on the cytosolic surface of lysosomes. Lysosomotropic drug-induced upregulation of Rab10 phosphorylation was likely a downstream event of Rab29 (Rab7L1)-mediated enzymatic activation of LRRK2. These results suggest a regulated process of Rab10 phosphorylation by LRRK2 that is associated with lysosomal overload stress, and provide insights into the novel strategies to halt the aberrant upregulation of LRRK2 kinase activity.
Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering
Authors: Shen Cuicui , Liu Haiyang , Guan Zeyuan , Yan Junjie , Zheng Ting , Yan Wenhao , Wu Changyin , Zhang Qifa , Yin Ping , Xing Yongzhong 
Published: August 2020

AbstractCONSTANS, CONSTANS-LIKE, and TIMING OF CAB EXPRESSION1 (CCT) domain-containing proteins are a large family unique to plants. They transcriptionally regulate photoperiodic flowering, circadian rhythms, vernalization, and other related processes. Through their CCT domains, CONSTANS and HEADING DATE1 (HD1) coordinate with the NUCLEAR FACTOR Y (NF-Y) B/C dimer to specifically target a conserved ‘CCACA’ motif within the promoters of their target genes. However, the mechanism underlying DNA recognition by the CCT domain remains unclear. Here we determined the crystal structures of the rice (Oryza sativa) NF-YB/YC dimer and the florigen gene Heading date 3a (Hd3a)-bound HD1CCT/NF-YB/YC trimer with resolutions of 2.0 Å and 2.55 Å, respectively. The CCT domain of HD1 displays an elongated structure containing two α-helices and two loops, tethering Hd3a to the NF-YB/YC dimer. Helix α2 and loop 2 are anchored into the minor groove of the ‘CCACA’ motif, which determines the specific base recognition. Our structures reveal the interaction mechanism among the CCT domain, NF-YB/YC dimer, and the target DNA. These results not only provide insight into the network between the CCT proteins and NF-Y subunits, but also offer potential approaches for improving productivity and global adaptability of crops by manipulating florigen expression.
The relationship between food heritage and clan culture: is “familiness” the missing link in SMEs?
Authors: Khatami Fahimeh , Ferraris Alberto , De Bernardi Paola , Cantino Valter 
Published: August 2020

PurposeThis paper empirically tests the relationship between food heritage, familiness, and clan culture, thus, highlighting the pivotal role of familiness in building robustly competitive food firms based on clan culture and food heritage.Design/methodology/approachThe methodological approach adopted is based on a quantitative analysis with data from one eco-tourist city in Iran (Torqabeh). In this regard, we developed a structured questionnaire surveying 98 small- and medium-sized enterprises (SMEs) operating in the food industry. We then used partial least squares structural equation modeling (PLS-SEM) to carry out the analysis.FindingsThe results indicate the significant positive relationship between food heritage and clan culture, and highlight the role of familiness as a strong mediator, which is also associated with a strong relationship between food heritage and clan culture.Research limitations/implicationsIn the present study, the main limitation was linked to the small sample size and data collection, which took place in only a single city; however, further research could overcome this limitation by investigating SMEs from a heterogeneous geographical context.Originality/valueThe value of this research relates to studies that have examined food heritage as a possible antecedent of familiness. Moreover, the novelty of this research is to study the concept of familiness in improving resource-based views and organizational theories.