bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digging roots is easier with AI
Authors: Han Eusun , Smith Abraham George , Kemper Roman , White Rosemary , Kirkegaard John , Thorup-Kristensen Kristian , Athmann Miriam 
Published: December 2020

AbstractThe scale of root quantification in research is often limited by the time required for sampling, measurement and processing samples. Recent developments in Convolutional Neural Networks (CNN) have made faster and more accurate plant image analysis possible which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of Machine Learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN-software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model, i.e., learning from labeled examples, can effectively exclude the debris by comparing the end-results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training and the derived measurements were compared with manual measurements. After 200 minutes of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R2=0.99), profile wall (R2=0.76) and core-break (R2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.
ramr: an R package for detection of rare aberrantly methylated regions
Authors: Nikolaienko Oleksii , Lønning Per Eystein , Knappskog Stian 
Published: December 2020

AbstractMotivationWith recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyse such events.ResultsWe have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs).ramrcan be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics oframrand confirmed its applicability for analysis of large public data sets. Usingramrwe identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.Availability and implementationThe R package is freely available athttps://github.com/BBCG/ramr
Histone H4K20 methylation synchronizes cytoskeletal dynamics with cell cycle phases during epidermal differentiation
Authors: Angerilli Alessandro , Tait Janet , Berges Julian , Shcherbakova Irina , Schauer Tamas , Smialowski Pawel , Hsam Ohnmar , Mentele Edith , Nicetto Dario , Rupp Ralph A.W. 
Published: December 2020

SUMMARYHistone tails are subject to various post-translational modifications, which play a fundamental role in altering chromatin accessibility. Although they are thought to regulate progression through development, the impact of the most abundant histone modification in vertebrates, i.e., histone H4 lysine 20 dimethylation (H4K20m2), has remained largely elusive. H4K20m2 arises from sequential methylation of new, unmodified histone H4 proteins, incorporated into chromatin during DNA replication, by the mono-methylating enzyme PR-SET7/KMT5A during G2/M phases, followed by conversion to the dimethylated state by SUV4-20H1 enzymes in the following G1/G0 phase. To address its function, we have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases, which convert H4K20 monomethylated to di- and tri-methylated states, respectively In the frog larval epidermis this results in a severe loss of cilia in multiciliated cells (MCC), a key component of all mucociliary epithelia. MCC precursor cells are correctly specified and amplify centrioles, but ultimately fail in ciliogenesis due to perturbation of cytoplasmic processes. Genome wide transcriptome profiling reveals that SUV4-20H1/H2 depleted ectodermal Animal Cap explants preferentially down-regulate the expression of several hundred cytoskeleton and cilium related genes as a consequence of persistent H4K20 monomethyl marks on postmitotic chromatin. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that overexpression of the H4K20m1-specific histone demethylase PHF8 rescues the ciliogenic defect in significant, although partial, manner. Taken together, this indicates that the conversion of H4K20m1 to H4K20m2 by SUV4-20H1 is critical to synchronize cytoskeletal dynamics in concert with the cell cycle.
Cryptic β-lactamase evolution is driven by low β-lactam concentrations
Authors: Fröhlich Christopher , Gama João Alves , Harms Klaus , Hirvonen Viivi H.A. , Lund Bjarte Aarmo , van der Kamp Marc W. , Johnsen Pål Jarle , Samuelsen Ørjan , Leiros Hanna-Kirsti S. 
Published: December 2020

ABSTRACTOur current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the wide-spread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to develop clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-minimum inhibitory concentrations (sub-MIC) of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MIC of ceftazidime, they showed strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies towards ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones towards clinical resistance.
Combining Two Classes of Epigenetic Modifiers and Their Effect on Prostate Cancer Cells
Authors: Lodi Mudassir K. , Goliadze Ekaterine , Manjili Masoud H. , Guruli Georgi 
Published: December 2020

AbstractThe main objective of this experiment was to determine and study the effects of combining two epigenetic modifiers, 5-azacyticidine (5-AzaC) and SB939, on a RM-1 murine prostate cancer cell model. The effectiveness of this combination on prostate cancer cells has not been previously studied. The study was implemented on ex vivo cell models to gain a better understanding of the true effects of the combination therapy on prostate cancer cells. Two variations of the combination therapy were tested in this study, each with different concentrations of SB939 (100nm and 200nm).To determine the effectivity of the combination therapy on prostate cancer cells, three factors were measured: cell proliferation, cancer testis antigen (CTA) expression, and apoptosis rate. To measure cell proliferation, a cell proliferation assay was conducted, and absorption rate was measured through a 450 nm wavelength. CTA expression was measured through a quantitative polymerase chain reaction (quant-PCR). For this study, the expression rates of five CTAs were measured (TEX15, CEP55, CCNA1, P1A, SPA17). Apoptosis rate was measured through an Annexin-V assay, in which two markers, Annexin-V and 7-AAD, were used.We found that SB939 combined with 5-AzaC show highest efficacy compare to each drug alone in terms of inhibiting tumor cell proliferation, as well as inducing tumor cells apoptosis and enhancing tumor cell immunogenicity by the induction of the expression of CTAs. This combination proved to be effective in combating murine prostate cancer cells, and can potentially be effective within in vivo models due to its high toxicity to these cancer cells, and its ability to render prostate cancer more immunogenic.
Deep immune profiling reveals targetable mechanisms of immune evasion in checkpoint blockade-refractory glioblastoma
Authors: Simonds Erin F. , Lu Edbert D. , Liu Eric V. , Tamaki Whitney , Rancan Chiara , Stultz Jacob , Sinha Meenal , McHenry Lauren K. , Nasholm Nicole M. , Chuntova Pavlina , Sundström Anders , Genoud Vassilis , Shahani Shilpa A. , Wang Leo D. , Brown Christine E. , Walker Paul R. , Swartling Fredrik J. , Fong Lawrence , Okada Hideho , Weiss William A. , Hellström Mats 
Published: December 2020

ABSTRACTBackgroundGlioblastoma (GBM) is refractory to checkpoint blockade immunotherapy (CPI). We sought to determine to what extent this immune evasion is due to intrinsic properties of the tumor cells versus the specialized immune context of the brain, and if it can be reversed.MethodsWe used CyTOF mass cytometry to compare the tumor immune microenvironments (TIME) of human tumors that are generally CPI-refractory (GBM and sarcoma) or CPI-responsive (renal cell carcinoma), as well as mouse models of GBM that are CPI-responsive (GL261) or CPI-refractory (SB28). We further compared SB28 tumors grown intracerebrally versus subcutaneously to determine how tumor site affects TIME and responsiveness to dual CTLA-4/PD-1 blockade. Informed by these data, we explored rational immunotherapeutic combinations.ResultsCPI-sensitivity in human and mouse tumors was associated with increased T cells and dendritic cells, and fewer myeloid cells, in particular PD-L1+ tumor associated macrophages. The SB28 mouse model of GBM responded to CPI when grown subcutaneously but not intracerebrally, providing a system to explore mechanisms underlying CPI resistance in GBM. The response to CPI in the subcutaneous SB28 model required CD4 T cells and NK cells, but not CD8 T cells. Recombinant FLT3L expanded dendritic cells, improved antigen-specific T cell priming, and prolonged survival of mice with intracerebral SB28 tumors, but at the cost of increased Tregs. Targeting PD-L1 also prolonged survival, especially when combined with stereotactic radiation.ConclusionsOur data suggest that a major obstacle for effective immunotherapy of GBM is the low antigenicity of the tumor cells coupled with poor antigen presentation in the brain, rather than intrinsic immunosuppressive properties of GBM tumor cells. Deep immune profiling identified dendritic cells and PD-L1+ tumor-associated macrophages as promising targetable cell populations, which was confirmed using therapeutic interventionsin vivo.Graphical AbstractIn BriefIn mice and humans, tumors that were sensitive to checkpoint blockade had consistent immunological features. A mouse model of glioma that is refractory to checkpoint blockade was sensitized by increasing antigen presentation through a variety of approaches.
Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose
Authors: Qian Cheng , Wu Zhaofa , Sun Rongbo , Yu Huasheng , Zeng Jianzhi , Rao Yi , Li Yulong 
Published: December 2020

AbstractVesicular neurotransmitter transporters (VNTs) mediate the selective uptake and enrichment of small molecule neurotransmitters into synaptic vesicles (SVs) and are therefore a major determinant of the synaptic output of specific neurons. To identify novel VNTs expressed on SVs (thus identifying new neurotransmitters and/or neuromodulators), we conducted localization profiling of 361 solute carrier (SLC) transporters tagging with a fluorescent protein in neurons, which revealed 40 possible candidates through comparison with a known SV marker. We parallelly performed proteomics analysis of immunoisolated SVs and identified 7 transporters in overlap. Ultrastructural analysis confirmed one of the transporters, SLC35D3, localized to SVs. Finally, by combining metabolite profiling with a radiolabeled substrate transport assay, we identified UDP-glucose as the principal substrate for SLC35D3. These results provide new insights into the functional role of SLC transporters in neurotransmission and improve our understanding of the molecular diversity of chemical transmitters.
Multimodal-Multisensory Experiments: Design and Implementation
Authors: Razavi Moein , Yamauchi Takashi , Janfaza Vahid , Leontyev Anton , Longmire-Monford Shanle , Orr Joseph 
Published: December 2020

AbstractThe human mind is multimodal. Yet most behavioral studies rely on century-old measures of behavior - task accuracy and latency (response time). Multimodal and multisensory analysis of human behavior creates a better understanding of how the mind works. The problem is that designing and implementing these experiments is technically complex and costly. This paper introduces versatile and economical means of developing multimodal-multisensory human experiments. We provide an experimental design framework that automatically integrates and synchronizes measures including electroencephalogram (EEG), galvanic skin response (GSR), eye-tracking, virtual reality (VR), body movement, mouse/cursor motion and response time. Unlike proprietary systems (e.g., iMotions), our system is free and open-source; it integratesPsychoPy, Unityand Lab Streaming Layer (LSL). The system embeds LSL insidePsychoPy/Unityfor the synchronization of multiple sensory signals - gaze motion, electroencephalogram (EEG), galvanic skin response (GSR), mouse/cursor movement, and body motion - with low-cost consumer-grade devices in a simple behavioral task designed byPsychoPyand a virtual reality environment designed byUnity. This tutorial shows a step-by-step process by which a complex multimodal-multisensory experiment can be designed and implemented in a few hours. When conducting the experiment, all of the data synchronization and recoding of the data to disk will be done automatically.
Acetylcholine as a trigger of the somatic exocytosis in Retzius neurons
Authors: Kazakova Tatiana A. , Suchalko Oleg N. , Ivanov Alexey D. , Alova Anna V. , Maksimov George V. 
Published: December 2020

AbstractThe redistribution of vesicles containing serotonin in leech neurons was studied using the fluorescent, scanning ion-conductance, and laser phase microscopy methods. During acetylcholine receptor (AChR) activation in Retzius neurons, the changes of Ca2+desorption, cellular stiffness and the cell optical phase difference (OPD) were established. It was found that the amplitude of OPD changes in the near-membrane area (membrane and near-membrane of the cytoplasm layers) increases upon AChR activation and this is, possibly, associated with the neurons vesicle redistribution. The decrease in the cell stiffness upon AChR activation suggests the crucial role of cytoskeleton for vesicle transport and release. Ca2+rise in the cytoplasm during AChR activation may regulate the mitochondrial recruitment to regions with high energy demand for vesicle trafficking.
Aspergillus fumigatusversus GenusAspergillus: Conservation, adaptive evolution and specific virulence genes
Authors: Gupta Shishir K , Srivastava Mugdha , Osmanoglu Özge , Xu Zhuofei , Brakhage Axel A , Dandekar Thomas 
Published: December 2020

AbstractAspergillusis an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genusAspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows to investigate the selection pressure driving the adaptive evolution in the pathogenic speciesA. fumigatus.Among single-copy orthologs (SCOs) forA. fumigatusand the closely related speciesA. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be clearly positively selected and thus important for adaption.A. fumigatusPSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory, and virulence related pathways such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal of GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives ofA. fumigatusas ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution ofA. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, for antimycotic targeting and understanding fundamental processes of virulence.
Construction and Analysis of Protein-Protein Interaction Network of Non-Alcoholic Fatty Liver Disease
Authors: Amanatidou Athina I. , Dedoussis George V. 
Published: December 2020

AbstractNon-alcoholic fatty liver disease (NAFLD) is a disease with multidimensional complexities. Many attempts have been made over the years to treat this disease but its incidence is rising. For this reason, the need to identify and study new candidate proteins that may be associated with NAFLD is of utmost importance. Systems-based approaches such as the analysis of protein-protein interaction (PPI) network could lead to the discovery of new proteins associated with a disease that can then be translated into clinical practice. The aim of this study is to analyze the interaction network of human proteins associated with NAFLD as well as their experimentally verified interactors and to identify novel associations with other human proteins that may be involved in this disease. Computational analysis made it feasible to detect 77 candidate proteins associated with NAFLD, having high network scores. Furthemore, clustering analysis was performed to identify densely connected regions with biological significance in this network. Additionally, gene expression analysis was conducted to validate part of the findings of this research work. We believe that our research will be helpful in extending experimental efforts to address the pathogenesis and progression of NAFLD.
Lysosomal positioning regulates Rab10 phosphorylation at LRRK2-positive lysosomes
Authors: Kluss Jillian H. , Beilina Alexandra , Williamson Chad D. , Lewis Patrick A. , Cookson Mark R. , Bonet-Ponce Luis 
Published: December 2020

ABSTRACTGenetic variation at theLeucine-rich repeat kinase 2 (LRRK2)locus contributes to enhanced lifetime risk of familial and sporadic Parkinson’s disease. Previous data have demonstrated that recruitment to various membranes of the endolysosomal system results in LRRK2 activation. However, the mechanism(s) underlying LRRK2 activation at endolysosomal membranes and the cellular consequences of these events are still poorly understood. Here, we directed LRRK2 to lysosomes and early endosomes, triggering both LRRK2 autophosphorylation and phosphorylation of the direct LRRK2 substrates Rab10 and Rab12. However, when directed to the lysosomal membrane, pRab10 was restricted to perinuclear lysosomes, whereas pRab12 was visualized on both peripheral and perinuclear LRRK2-positive lysosomes, suggesting that lysosomal positioning provides additional regulation of LRRK2-dependent Rab phosphorylation. Anterograde transport of lysosomes to the cell periphery by increasing expression of ARL8B and SKIP or by knockdown of the motor adaptor protein JIP4 blocked recruitment and phosphorylation of Rab10 by LRRK2. Conversely, overexpression of the Rab7 effector protein RILP resulted in lysosomal clustering within the perinuclear area and increased LRRK2-dependent Rab10 recruitment and phosphorylation. The regulation of Rab10 phosphorylation in the perinuclear area depends on counteracting phosphatases, as knockdown of phosphatase PPM1H significantly increased pRab10 signal and lysosomal tubulation in the perinuclear region. Our novel findings suggest LRRK2 can be activated at multiple cellular membranes including lysosomes, and that lysosomal positioning further provides regulation of some Rab substrates likely via differential phosphatase activity in nearby cellular compartments.
Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor
Authors: Godsel Lisa M , Roth-Carter Quinn R , Koetsier Jennifer L , Tsoi Lam C , Broussard Joshua A , Fitz Gillian N , Lloyd Sarah M , Kweon Junghun , Huffine Amber L , Burks Hope E , Hegazy Marihan , Amagai Saki , Harms Paul W. , Johnson Jodi L , Urciuoli Gloria , Doglio Lynn T. , Swindell William R , Awatramani Rajeshwar , Sprecher Eli , Bao Xiaomin , Cohen-Barak Eran , Missero Caterina , Gudjonsson Johann E , Green Kathleen J 
Published: December 2020

AbstractDesmoglein 1 (Dsg1) is a cadherin restricted to stratified tissues of terrestrial vertebrates, which serve as essential physical and immune barriers. Dsg1’s importance in epidermal integrity is underscored by genetic, autoimmune and bacterial toxin-mediated disorders interfering with Dsg1 function. Dsg1 loss-of-function mutations in humans result not only in skin lesions, but also multiple allergies, and isolated patient keratinocytes exhibit increased pro-allergic cytokine expression. However, the mechanism by which genetic deficiency of Dsg1 causes chronic inflammation is unknown. To determine the systemic response to Dsg1 loss, we deleted the three tandem Dsg1 genes in mice using CRISPR/Cas9. Whole transcriptome analysis of E18.5Dsg1−/−skin showed changes consistent with the observed aberrant differentiation and barrier impairment. Comparing epidermal transcriptomes from E18.5 Dsg1-deficient mice and humans with Dsg1 mutations revealed a shared psoriatic-like IL-17-skewed inflammatory signature and less so a pro-allergic IL-4/13 signature. Although the impaired intercellular adhesion observed inDsg1−/−mice resembles that resulting from autoimmune anti-Dsg1 pemphigus foliaceus antibodies, transcriptomic analysis of pemphigus skin lesions lacks a prominent IL-17 signature. Thus, beyond impairing the physical barrier, chronic loss of Dsg1 function through gene mutation results in a psoriatic-like inflammatory signature before birth, possibly predisposing to skin inflammation.