bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemokine CXCL4 interactions with extracellular matrix proteoglycans mediate wide-spread non-receptor mediated immune cell recruitment
Authors: Gray Anna L , Karlsson Richard , Roberts Abigail RE , Ridley Amanda JL , Pun Nabina , Hughes Catherine , Medina-Ruiz Laura , Birchenough Holly L , Salanga Catherina L , Yates Edwin A , Turnbull Jeremy E , Handel Tracy M , Graham Gerard J , Jowitt Thomas A , Schiessl Ingo , Richter Ralf P , Miller Rebecca L , Dyer Douglas P 
Published: July 2022

AbstractLeukocyte recruitment from the vasculature into tissues is a crucial component of the immune system, but is also key to inflammatory disease. Chemokines are central to this process but have yet to be therapeutically targeted during inflammation, due to a lack of mechanistic understanding. Specifically, CXCL4 (PF4) has no established receptor that explains its function. Here we use biophysical, in vitro and in vivo techniques to determine the mechanism underlying CXCL4 mediated leukocyte recruitment. We demonstrate that CXCL4 binds to glycosaminoglycan (GAG) sugars within the endothelial extracellular matrix resulting in increased vascular permeability and non-specific recruitment of a range of leukocytes. Furthermore, GAG sulphation confers selectivity onto chemokine localisation. These findings represent a new understanding of chemokine biology, providing novel mechanisms for future therapeutic targeting.One sentence summaryCXCL4 binds to extracellular matrix proteoglycans resulting in increased vascular permeability and recruitment of a wide range of different leukocytes via a non-canonical mechanism.
Latent Transforming Growth Factor β Binding Protein 3 Controls Adipogenesis
Authors: Singh Karan , Sachan Nalani , Ene Taylor , Dabovic Branka , Rifkin Daniel 
Published: July 2022

AbstractTransforming growth factor-beta (TGFβ) is released from cells as part of a trimeric latent complex consisting of TGFβ, the TGFβ propeptides, and either a latent TGFβ binding protein (LTBP) or glycoprotein-A repetitions predominant (GARP) protein. LTBP1 and 3 modulate latent TGFβ function with respect to secretion, matrix localization, and activation and, therefore, are vital for the proper function of the cytokine in a number of tissues. TGFβ modulates stem cell differentiation into adipocytes (adipogenesis), but the potential role of LTBPs in this process has not been studied. We observed that 72 h post adipogenesis initiation Ltbp1, 2, and 4 expression levels decrease by 74-84%, whereas Ltbp3 expression levels remain constant during adipogenesis. We found that LTBP3 silencing in C3H/10T1/2 cells reduced adipogenesis, as measured by the percentage of cells with lipid vesicles and the expression of the transcription factor peroxisome proliferator-activated receptor gamma (PPARγ). Lentiviral mediated expression of an Ltbp3 mRNA resistant to siRNA targeting rescued the phenotype, validating siRNA specificity. Knockdown (KD) of Ltbp3 expression in 3T3-L1, M2, and primary bone marrow stromal cells (BMSC) indicated a similar requirement for Ltbp3. Epididymal and inguinal white adipose tissue fat pad weights of Ltbp3-/- mice were reduced by 62% and 57%, respectively, compared to wild-type mice. Inhibition of adipogenic differentiation upon LTBP3 loss is mediated by TGFβ, as TGFβ neutralizing antibody and TGFβ receptor I kinase blockade rescue the LTBP3 KD phenotype. These results indicate that LTBP3 has a TGFβ-dependent function in adipogenesis both in vitro and in vivo.SignificanceUnderstanding the control of mesenchymal stem cell fate is crucial for the potential use of these cells for regenerative medicine.HighlightsLatent TGFβ binding protein 3 (LTBP3) is required for adipogenesisLTBP3 mediates TGFβ levels in adipogenesisLoss of LTBP3 results in enhanced rather than decreased levels of active TGFβ
Dynamics of Borrelia Burgdorferi Invasion and Intravasation in a Tissue Engineered Dermal Microvessel Model
Authors: Guo Zhaobin , Zhao Nan , Chung Tracy D. , Singh Anjan , Pandey Ikshu , Wang Linus , Gu Xinyue , Ademola Aisha , Linville Raleigh M. , Pal Utpal , Dumler J. Stephen , Searson Peter C. 
Published: July 2022

AbstractLyme disease is a tick-borne disease prevalent in North America, Europe, and Asia. Dissemination of vector-borne pathogens, such as Borrelia burgdorferi (Bb), results in infection of distant tissues and is the main contributor to poor outcomes. Despite the accumulated knowledge from epidemiological, in vitro, and in animal studies, the understanding of dissemination remains incomplete with several important knowledge gaps, especially related to invasion and intravasation at the site of a tick bite, which cannot be readily studied in animal models or humans. To elucidate the mechanistic details of these processes we developed a tissue-engineered human dermal microvessel model. Fluorescently-labeled Bb (B31 strain) were injected into the extracellular matrix (ECM) of the model to mimic tick inoculation. High resolution, confocal imaging was performed to visualize Bb migration in the ECM and intravasation into circulation. From analysis of migration paths we found no evidence to support adhesin-mediated interactions between Bb and components of the ECM or basement membrane, suggesting that collagen fibers serve as inert obstacles to migration. Transendothelial migration occurred at cell-cell junctions and was relatively fast, consistent with Bb swimming in ECM. In addition, we found that Bb alone can induce endothelium activation, resulting in increased immune cell adhesion but no changes in global or local permeability. Together these results provide new insight into the minimum requirements for dissemination of Bb at the site of a tick bite, and highlight how tissue-engineered models are complementary to animal models in visualizing dynamic processes associated with vector-borne pathogens.Significance StatementUsing a tissue-engineered human dermal microvessel model we reveal new insight into the invasion and intravasation of Borrelia burgdorferi (Bb), a causative agent of Lyme disease in North America, following a tick bite. These results show how tissue-engineered models enable imaging of dynamic processes that are challenging in animal models or human subjects.
metascreen: A modular tool for the design and analysis of drug combination screens
Authors: Hanes Robert , Ayuda-Durán Pilar , Rønneberg Leiv , Zucknick Manuela , Enserink Jorrit 
Published: July 2022

AbstractThere is a rapidly growing interest in high-throughput drug combination screening to identify synergizing drug interactions for treatment of various maladies, such as cancer and infectious disease. This creates the need for pipelines that can be used to design such screens, perform quality control on the data, and generate data files that can be analyzed by synergy-finding bioinformatics applications. metascreen is an open source, end-to-end modular tool available as an R-package for the design and analysis of drug combination screens. The tool allows for a customized build of pipelines through its modularity and provides a flexible approach to quality control and data analysis. metascreen is adaptable to various experimental requirements with an emphasis on precision medicine. It can be coupled to other R packages, such as bayesynergy, to identify synergistic and antagonistic drug interactions in cell lines or patient samples. metascreen is scalable and provides a complete solution for setting up drug sensitivity screens, read raw measurements and consolidate different datasets, perform various types of quality control, and analyze, report and visualize the results of drug sensitivity screens.Availability and implementationThe R-package and technical documentation is available at https://github.com/Enserink-lab; the R source code is publicly available at https://github.com/Enserink-lab/metascreen under GNU General Public License v3.0; bayesynergy is accessible at https://github.com/ocbe-uio/bayesynergy/Selected modules will be available through Galaxy, an open-source platform for FAIR data analysis, Norway: https://usegalaxy.no
Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii based on WGCNA in R-Shiny
Authors: Auger Sandrine , Mournetas Virginie , Chiapello Hélène , Loux Valentin , Langella Philippe , Chatel Jean-Marc 
Published: July 2022

AbstractFaecalibacterium prausnitzii is abundant in the healthy human intestinal microbiota, and the absence or scarcity of this bacterium has been linked with inflammatory diseases and metabolic disorders. F. prausnitzii thus shows promise as a next-generation probiotic for use in restoring the balance of the gut microbial flora and, due to its strong anti-inflammatory properties, for the treatment of certain pathological conditions. However, very little information is available about gene function and regulation in this species. Here, we utilized a systems biology approach - weighted gene co-expression network analysis (WGCNA) – to analyze gene expression in three publicly available RNAseq datasets from F. prausnitzii strain A2-165, all obtained in different laboratory conditions. The co-expression network was then subdivided into 24 co-expression gene modules. A subsequent enrichment analysis revealed that these modules are associated with different kinds of biological processes, such as arginine, histidine, cobalamin, or fatty acid metabolism as well as bacteriophage function, molecular chaperones, stress response, or SOS response. Some genes appeared to be associated with mechanisms of protection against oxidative stress and could be essential for F. prausnitzii’s adaptation and survival under anaerobic laboratory conditions. Hub and bottleneck genes were identified by analyses of intramodular connectivity and betweenness, respectively; this highlighted the high connectivity of genes located on mobile genetic elements, which could promote the genetic evolution of F. prausnitzii within its ecological niche. This study provides the first exploration of the complex regulatory networks in F. prausnitzii, and all of the “omics” data are available online for exploration through a graphical interface at https://feaprau.omics.ovh/.
Transgenerational effects of alcohol on intoxication sensitivity in Caenorhabditis elegans
Authors: Guzman Dawn M. , Chakka Keerthana , Shi Ted , Marron Alyssa , Fiorito Ansley E. , Rahman Nima S. , Ro Stephanie , Sucich Dylan G. , Pierce Jonathan T. 
Published: July 2022

ABSTRACTAlcohol abuse and dependence have a substantial heritable component. Although the genome has been considered the sole vehicle of heritable phenotypes, recent studies suggest that drug or alcohol exposure may induce alterations in gene expression that are transmitted across generations. Still, the transgenerational impact of alcohol use (and abuse) remains largely unexplored in part because multigenerational studies using rodent models present challenges for time, sample size, and genetic heterogeneity. Here, we took advantage of the extremely short generation time, large broods, and clonal form of reproduction of the nematode Caenorhabditis elegans. We developed a model of preconception parental alcohol exposure to test alterations in behavioral responses to acute alcohol treatment (intoxication) in subsequent F1, F2 and F3 generations. We found that a chronic alcohol-treatment paradigm in the parental generation resulted in alcohol-naïve F3 progeny displaying moderate resistance to intoxication. To compare the treatment duration and timing on this transgenerational effect, we repeated the study using an intermittent treatment paradigm. We found that intermittent treatment resulted in alcohol-naïve F3 progeny displaying moderate hypersensitivity to intoxication. Further study of this phenomena using this new C. elegans model may yield mechanistic insights into how transgenerational effects may occur in other animals.
Paving the way for synthetic C1- metabolism in Pseudomonas putida through the reductive glycine pathway
Authors: Bruinsma Lyon , Wenk Sebastian , Claassens Nico J. , Martins dos Santos Vitor A.P. 
Published: July 2022

ABSTRACTOne-carbon (C1) compounds such as methanol, formate, and CO2 are alternative, sustainable microbial feedstocks for the biobased production of chemicals and fuels. In this study, we engineered the carbon metabolism of the industrially important bacterium Pseudomonas putida to assimilate these three substrates through the reductive glycine pathway. First, we demonstrated the functionality of the C1-assimilation module by coupling the growth of auxotrophic strains to formate assimilation. Next, we extended the module from formate to methanol using both NAD and PQQ – dependent methanol dehydrogenases. Finally, we demonstrated CO2-dependent growth through CO2 reduction to formate by the native formate dehydrogenase, which required short-term evolution to rebalance the cellular NADH/NAD+ ratio. This research paves the way to engineer P. putida towards growth on formate, methanol, and CO2 as sole feedstocks, thereby substantially expanding its potential as a sustainable and versatile cell factory.
Machine learning approaches to quantitively predict selectivity of compounds against hDAC1 and hDAC6 isoforms
Authors: Dogan Berna 
Published: July 2022

AbstractThe design of compounds selectively binding to specific isoforms of histone deacetylases (hDAC) is an ongoing research to prevent adverse side effects. Two of the most studied isoforms are hDAC1 and hDAC6 that are important targets to inhibit in various disease conditions. Here, various machine learning approaches were tested with the aim of developing models to predict the bioactivity and selectivity towards specific isoforms. Selectivity models were developed by directly training on the bioactivity differences of tested compounds against hDAC1 and hDAC6. Both classification and regression models were developed and compared to each other by using traditional evaluation metrics.
Dimerization of iLID Optogenetic Proteins Observed Using 3D Single-Molecule Tracking in Live Bacterial Cells
Authors: Achimovich Alecia M. , Yan Ting , Gahlmann Andreas 
Published: July 2022

ABSTRACT3D single molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments. When investigating cellular processes, transient perturbation to protein spatial distributions is preferable to permanent genetic deletion of an essential protein. In this context, optogenetic dimerization systems can be used to manipulate protein spatial distributions which could offer a means to deplete specific diffusive states observed in single molecule tracking experiments. Here, we evaluate the performance of the iLID optogenetic system in living E. coli cells using diffraction-limited microscopy and 3D single-molecule tracking. We observed a robust optogenetic response in protein spatial distributions after 488 nm laser activation. Surprisingly, 3D single-molecule tracking results indicate activation of the optogenetic response when illuminating with high intensity light with wavelengths at which there is minimal photon absorbance by the LOV2 domain. The pre-activation can be minimized through the use of iLID system mutants, and titration of protein expression levels.SIGNIFICANCE STATEMENTWe describe the combination of 3D single-molecule tracking microscopy and optogenetic manipulation of protein spatial distributions in living cells. Such a combination is impactful, because optogenetic systems enable sample perturbation in real time using light, which provides more flexibility than gene deletion and gene editing approaches that result in permanent changes to the specimen. We specifically investigate the performance of the iLID optogenetic system in a knocksideways experiment, in which cytosolic prey proteins (SspB) are sequestered to the membrane by interacting with membrane-anchored bait proteins (iLID). We quantified the magnitude of the optogenetic effect using both diffraction-limited imaging and 3D single-molecule tracking microscopy. We found, surprisingly, that the iLID optogenetic response is activated substantially by high intensity light at wavelengths for which there is negligible photon absorption by the iLID protein. Quantification of this alternative activation mechanism is a necessary component before optogenetic tools, such as iLIDs, are employed in single-molecule knocksideways experiment that are designed to provide new biological insights.
Impact of gradient scheme and shimming on out-of-voxel echo artifacts in edited MRS
Authors: Song Yulu , Zöllner Helge J. , Hui Steve C.N. , Hupfeld Kathleen , Oeltzschner Georg , Edden Richard A.E. 
Published: July 2022

AbstractOut-of-voxel (OOV) signals are common spurious echo artifacts in magnetic resonance spectroscopy (MRS). These signals often manifest in the spectrum as very strong ‘ripples’ which interfere with spectral quantification by overlapping with targeted metabolite resonances. Dephasing Optimization Through Coherence Order Pathway Selection (DOTCOPS) gradient schemes are algorithmically optimized to suppress all potential alternative coherence transfer pathways (CTPs), and should suppress unwanted OOV echoes. In addition, second-order shimming uses non-linear gradient fields to maximize field homogeneity inside the voxel, which unfortunately increases the diversity of local gradient fields outside of the voxel. Given that strong local spatial B0 gradients can refocus unintended CTPs, it is possible that OOVs are less prevalent when only linear first-order shimming is applied. Here we compare the size of unwanted OOV signals in Hadamard-edited (HERMES) data acquired with either a local gradient scheme (which we refer to here as “Shared”) or DOTCOPS, and with first or second-order shimming. We collected data from 15 healthy volunteers in two brain regions (voxel size 30×26×26mm3) from which it is challenging to acquire MRS data: medial prefrontal cortex (MPFC) and left temporal cortex (LTC). Characteristic OOV echoes were seen in both GABA- and GSH-edited spectra for both brain regions, gradient schemes, and shimming approaches. A linear mixed-effect (LME) model revealed a statistically significant difference in the average residual based on gradient scheme in both GABA-(p < 0.001) and GSH-edited (p < 0.001) spectra; that is, the DOTCOPS gradient scheme resulted in smaller OOV artifacts compared with the Shared scheme. There were no significant differences in OOV artifacts associated with shimming method. Thus, these results suggest that the DOTCOPS gradient scheme for J-difference-edited PRESS acquisitions yields spectra with smaller OOV echo artifacts than the Shared gradient scheme implemented in a widely disseminated editing sequence.
Katdetectr: An R/Bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection
Authors: Hazelaar Daan M. , van Riet Job , Hoogstrate Youri , van de Werken Harmen J. G. 
Published: July 2022

AbstractBackgroundKataegis refers to the occurrence of regional genomic hypermutation in cancer and is a phenomenon that has been observed in a wide range of malignancies. A kataegis locus constitutes a genomic region with a high mutation rate, i.e., a higher frequency of closely interspersed somatic variants than the overall mutational background. It has been shown that kataegis is of biological significance and possibly clinically relevant. Therefore, an accurate and robust workflow for kataegis detection is paramount.FindingsHere we presentKatdetectr, an open-source R/Bioconductor-based package for the robust yet flexible and fast detection of kataegis loci in genomic data. In addition,Katdetectrhouses functionalities to characterize and visualize kataegis and provides results in a standardized format useful for subsequent analysis. In brief,Katdetectrimports industry-standard formats (MAF, VCF, and VRanges), determines the intermutation distance of the genomic variants and performs unsupervised changepoint analysis utilizing the Pruned Exact Linear Time search algorithm followed by kataegis calling according to user-defined parameters.We used synthetic data and ana priorilabeled pan-cancer dataset of Whole Genome Sequenced malignancies for the performance evaluation of Katdetectr and five publicly available kataegis detection packages. Our performance evaluation shows that Katdetectr is robust regarding tumor mutational burden (TMB) and shows the fastest mean computation time. Additionally, Katdetectr reveals the highest accuracy (0.99, 0.99) and normalized Matthews Correlation Coefficient (0.98, 0.92) of all evaluated tools for both datasets.ConclusionsKatdetectris a robust workflow for the detection, characterization, and visualization of kataegis and is available on Bioconductor:https://doi.org/doi:10.18129/B9.bioc.katdetectr
Digital artefacts of rural tourism: the case study of Poland
Authors: Król Karol , Zdonek Dariusz 
Published: July 2022

Purpose
Rural tourism facilities in Poland were very keen on amateur websites to promote their hospitality services from 2000 to 2018. In most cases, the websites were nonprofessional, hosted on free servers and made by family members or friends of the holding. After search engine algorithms changed in 2015–2019, the websites started to go extinct on a large scale; they were deleted and often replaced with a more modern design and a commercial domain. These resources offered a rare opportunity to gain insight into rural tourism, rural changes and socioeconomic and cultural phenomena.

Design/methodology/approach
The paper’s objective is to demonstrate with an analysis of archived Polish rural tourism websites that digital cultural artefacts are generated in rural areas. The study was an analysis of selected development attributes of rural tourism websites found in the Internet Archive. The analysis involved those attributes that are important for determining whether a website or content can be considered digital cultural heritage assets.

Findings
The conclusions demonstrate that rural digital cultural heritage is a set of digital artefacts created in rural areas with their characteristics. Rural digital artefacts are records of ICT, infrastructure, environmental, cultural and socioeconomic changes.

Originality/value
The “digital assets” of rural areas are yet to be discussed in the context of rural cultural heritage, as a set of artefacts created in these areas and characteristic of them.