bluuebunny/crossref_metadata_2025_split huggingface dataset:
P53 and Parkin co-regulate mitophagy in bone marrow mesenchymal stem cells to promote the repair of early steroid-induced osteonecrosis of the femoral head
Authors: Zhang Fei , Peng Wuxun , Zhang Jian , Dong Wentao , Wu Jianhua , Wang Tao , Xie Zhihong 
Published: January 2020

AbstractSurvival and stemness of bone marrow mesenchymal stem cells (BMSCs) in osteonecrotic areas are especially important in the treatment of early steroid-induced osteonecrosis of the femoral head (ONFH). We had previously used BMSCs to repair early steroid-induced ONFH, but the transplanted BMSCs underwent a great deal of stress-induced apoptosis and aging in the oxidative-stress (OS) microenvironment of the femoral-head necrotic area, which limited their efficacy. Our subsequent studies have shown that under OS, massive accumulation of damaged mitochondria in cells is an important factor leading to stress-induced apoptosis and senescence of BMSCs. The main reason for this accumulation is that OS leads to upregulation of protein 53 (P53), which inhibits mitochondrial translocation of Parkin and activation of Parkin’s E3 ubiquitin ligase, which decreases the level of mitophagy and leads to failure of cells to effectively remove damaged mitochondria. However, P53 downregulation can effectively reverse this process. Therefore, we upregulated Parkin and downregulated P53 in BMSCs. We found that this significantly enhanced mitophagy in BMSCs, decreased the accumulation of damaged mitochondria in cells, effectively resisted stress-induced BMSCs apoptosis and senescence, and improved the effect of BMSCs transplantation on early steroid-induced ONFH.
Non-equilibrium signal integration in hydrogels
Authors: Korevaar Peter A. , Kaplan C. Nadir , Grinthal Alison , Rust Reanne M. , Aizenberg Joanna 
Published: January 2020

AbstractMaterials that perform complex chemical signal processing are ubiquitous in living systems. Their synthetic analogs would transform developments in biomedicine, catalysis, and many other areas. By drawing inspiration from biological signaling dynamics, we show how simple hydrogels have a previously untapped capacity for non-equilibrium chemical signal processing and integration. Using a common polyacrylic acid hydrogel, with divalent cations and acid as representative stimuli, we demonstrate the emergence of non-monotonic osmosis-driven spikes and waves of expansion/contraction, as well as traveling color waves. These distinct responses emerge from different combinations of rates and sequences of arriving stimuli. A non-equilibrium continuum theory we developed quantitatively captures the non-monotonic osmosis-driven deformation waves and determines the onset of their emergence in terms of the input parameters. These results suggest that simple hydrogels, already built into numerous systems, have a much larger sensing space than currently employed.
Time-of-flight resolved light field fluctuations reveal deep human tissue physiology
Authors: Kholiqov Oybek , Zhou Wenjun , Zhang Tingwei , Du Le V. N. , Srinivasan Vivek J. 
Published: January 2020

AbstractRed blood cells (RBCs) transport oxygen to tissues and remove carbon dioxide. Diffuse optical flowmetry (DOF) assesses deep tissue RBC dynamics by measuring coherent fluctuations of multiply scattered near-infrared light intensity. While classical DOF measurements empirically correlate with blood flow, they remain far-removed from light scattering physics and difficult to interpret in layered media. To advance DOF measurements closer to the physics, here we introduce an interferometric technique, surmounting challenges of bulk motion to apply it in awake humans. We reveal two measurement dimensions: optical phase, and time-of-flight (TOF), the latter with 22 picosecond resolution. With this multidimensional data, we directly confirm the unordered, or Brownian, nature of optically probed RBC dynamics typically assumed in classical DOF. We illustrate how incorrect absorption assumptions, anisotropic RBC scattering, and layered tissues may confound classical DOF. By comparison, our direct method enables accurate and comprehensive assessment of blood flow dynamics in humans.
The SUSTech-SYSU dataset for automatically segmenting and classifying corneal ulcers
Authors: Deng Lijie , Lyu Junyan , Huang Haixiang , Deng Yuqing , Yuan Jin , Tang Xiaoying 
Published: January 2020

AbstractCorneal ulcer is a common ophthalmic symptom. Segmentation algorithms are needed to identify and quantify corneal ulcers from ocular staining images. Developments of such algorithms have been obstructed by a lack of high quality datasets (the ocular staining images and the corresponding gold-standard ulcer segmentation labels), especially for supervised learning based segmentation algorithms. In such context, we prepare a dataset containing 712 ocular staining images and the associated segmentation labels of flaky corneal ulcers. In addition to segmentation labels for flaky corneal ulcers, we also provide each image with three-fold class labels: firstly, each image has a label in terms of its general ulcer pattern; secondly, each image has a label in terms of its specific ulcer pattern; thirdly, each image has a label indicating its ulcer severity degree. This dataset not only provides an excellent opportunity for investigating the accuracy and reliability of different segmentation and classification algorithms for corneal ulcers, but also advances the development of new supervised learning based algorithms especially those in the deep learning framework.
Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments
Authors: Gobbi Alex , Kyrkou Ifigeneia , Filippi Elisa , Ellegaard-Jensen Lea , Hansen Lars Hestbjerg 
Published: January 2020

AbstractWinemakers have long used copper as a conventional fungicide treatment on grapevine and only recently, the use of biocontrol agents depicted a promising alternative. Most of the studies that investigate the impact of fungicide treatments, focus on specific pathogenic microbes. In the present work instead, a field experiment conducted in South Africa shows the seasonal microbial change occurring on grapevine leaves, periodically treated with two different fungicide treatments: copper sulphate and Lactobacillus plantarum MW-1. In this work, NGS data were combined with strain-specific and community qPCRs to reveal the shift of the microbial communities throughout the growing season and highlight the impact of fungicides on the microbiota. Only the family of Lactobacillaceae systematically changed between treatments, while the bacterial community remained relatively stable over time. MW-1 was exclusively detected on biocontrol-sprayed leaves. Conversely, the fungal community was largely shaped by sampling time, underlining the succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the fungal load was also comparable. Monitoring the dynamics of the microbial community under different fungicide treatments may advise the best timing to apply treatments to the plants, toward the realization of more sustainable agricultural practices.
Delineation of hypoxia-induced proteome shifts in osteosarcoma cells with different metastatic propensities
Authors: Song Zifeng , Pearce Martin C. , Jiang Yuan , Yang Liping , Goodall Cheri , Miranda Cristobal L. , Milovancev Milan , Bracha Shay , Kolluri Siva K. , Maier Claudia S. 
Published: January 2020

AbstractOsteosarcoma (OS) is the most common bone cancer in children and young adults. Solid tumors are characterized by intratumoral hypoxia, and hypoxic cells are associated with the transformation to aggressive phenotype and metastasis. The proteome needed to support an aggressive osteosarcoma cell phenotype remains largely undefined. To link metastatic propensity to a hypoxia-induced proteotype, we compared the protein profiles of two isogenic canine OS cell lines, POS (low metastatic) and HMPOS (highly metastatic), under normoxia and hypoxia. Label-free shotgun proteomics was applied to comprehensively characterize the hypoxia-responsive proteome profiles in the OS cell phenotypes. Hypothesis-driven parallel reaction monitoring was used to validate the differential proteins observed in the shotgun data and to monitor proteins of which we expected to exhibit hypoxia responsiveness, but which were absent in the label-free shotgun data. We established a “distance” score (|zHMPOS − zPOS|), and “sensitivity” score (|zHypoxia − zNormoxia) to quantitatively evaluate the proteome shifts exhibited by OS cells in response to hypoxia. Evaluation of the sensitivity scores for the proteome shifts observed and principal component analysis of the hypoxia-responsive proteins indicated that both cell types acquire a proteome that supports a Warburg phenotype with enhanced cell migration and proliferation characteristics. Cell migration and glucose uptake assays combined with protein function inhibitor studies provided further support that hypoxia-driven adaption of pathways associated with glycolytic metabolism, collagen biosynthesis and remodeling, redox regulation and immunomodulatory proteins typify a proteotype associated with an aggressive cancer cell phenotype. Our findings further suggest that proteins involved in collagen remodeling and immune editing may warrant further evaluation as potential targets for anti-metastatic treatment strategies in osteosarcoma.
Tempo-spectral multiplexing in flow cytometry with lifetime detection using QD-encoded polymer beads
Authors: Kage Daniel , Hoffmann Katrin , Nifontova Galina , Krivenkov Victor , Sukhanova Alyona , Nabiev Igor , Resch-Genger Ute 
Published: January 2020

AbstractSemiconductor quantum dots (QDs) embedded into polymer microbeads are known to be very attractive emitters for spectral multiplexing and colour encoding. Their luminescence lifetimes or decay kinetics have been, however, rarely exploited as encoding parameter, although they cover time ranges which are not easily accessible with other luminophores. We demonstrate here the potential of QDs made from II/VI semiconductors with luminescence lifetimes of several 10 ns to expand the lifetime range of organic encoding luminophores in multiplexing applications using time-resolved flow cytometry (LT-FCM). For this purpose, two different types of QD-loaded beads were prepared and characterized by photoluminescence measurements on the ensemble level and by single-particle confocal laser scanning microscopy. Subsequently, these lifetime-encoded microbeads were combined with dye-encoded microparticles in systematic studies to demonstrate the potential of these QDs to increase the number of lifetime codes for lifetime multiplexing and combined multiplexing in the time and colour domain (tempo-spectral multiplexing). These studies were done with a recently developed novel luminescence lifetime flow cytometer (LT-FCM setup) operating in the time-domain, that presents an alternative to reports on phase-sensitive lifetime detection in flow cytometry.
The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome
Authors: Hildreth Sherry B. , Foley Evan E. , Muday Gloria K. , Helm Richard F. , Winkel Brenda S. J. 
Published: January 2020

AbstractWhile the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a high-resolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.
Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer
Authors: Hwang Sohyun , Kwon Ah-Young , Jeong Ju-Yeon , Kim Sewha , Kang Haeyoun , Park Joonsuk , Kim Joo-Hang , Han Ok Jin , Lim Sun Min , An Hee Jung 
Published: January 2020

AbstractImmune checkpoint blockade is promising for treating non-small-cell lung cancer (NSCLC). We used multipanel markers to predict the response to immune checkpoint inhibitors (ICIs) by characterizing gene expression signatures or individual genes in patients who showed durable clinical benefit to ICIs. Twenty-one patients with NSCLC treated with single-agent anti-programmed cell death protein (PD)-1 antibody were analyzed and their clinicopathological characteristics and response to ICIs were characterized. Nine (43%) showed a durable clinical benefit (DCB), while the remaining 12 (57%) patients showed non-durable benefit (NDB). The M1 and peripheral T cell signatures showed the best performance for discriminating DCB from NDB (sensitivity, specificity, accuracy = 0.89, 1.0, 0.95, respectively). Progression-free survival (PFS) was significantly longer in patients with high M1 signature or high peripheral T cell signature scores. CD137 and PSMB9 mRNA expression was higher in the DCB group than in the NDB group. Patients with high PSMB9 expression showed longer PFS. M1 signature, peripheral T cell signature and high mRNA expression level of CD137 and PSMB9 showed better predictive performance than known biomarkers, such as PD-L1 immunohistochemistry, tumor mutation burden, or tumor-infiltrating lymphocytes.
Identification of emulsifier potato peptides by bioinformatics: application to omega-3 delivery emulsions and release from potato industry side streams
Authors: García-Moreno Pedro J. , Gregersen Simon , Nedamani Elham R. , Olsen Tobias H. , Marcatili Paolo , Overgaard Michael T. , Andersen Mogens L. , Hansen Egon B. , Jacobsen Charlotte 
Published: January 2020

AbstractIn this work, we developed a novel approach combining bioinformatics, testing of functionality and bottom-up proteomics to obtain peptide emulsifiers from potato side-streams. This is a significant advancement in the process to obtain emulsifier peptides and it is applicable to any type of protein. Our results indicated that structure at the interface is the major determining factor of the emulsifying activity of peptide emulsifiers. Fish oil-in-water emulsions with high physical stability were stabilized with peptides to be predicted to have facial amphiphilicity: (i) peptides with predominantly α-helix conformation at the interface and having 18–29 amino acids, and (ii) peptides with predominantly β-strand conformation at the interface and having 13–15 amino acids. In addition, high physically stable emulsions were obtained with peptides that were predicted to have axial hydrophobic/hydrophilic regions. Peptides containing the sequence FCLKVGV showed high in vitro antioxidant activity and led to emulsions with high oxidative stability. Peptide-level proteomics data and sequence analysis revealed the feasibility to obtain the potent emulsifier peptides found in this study (e.g. γ-1) by trypsin-based hydrolysis of different side streams in the potato industry.
Information Propagation Formalized Representation of Micro-blog Network Based on Petri Nets
Authors: Liang Xun , Zhang Shusen , Liu Yu , Ma Yuefeng 
Published: January 2020

AbstractThe description of user behavior in social networks is an important issue for studying social networks. Given that Petri nets can describe the resource flow problem, this study utilizes the features of Petri nets to portray the user behavior states during the message propagation of a micro-blog network and presents an information propagation formalized representation method of a micro-blog network. On this basis, this study analyzed the proposed formalized representation method in detail. We provide examples of applying formalized representation (e.g., micro-blog network addiction of users, user behavior influence, and public opinion analysis). In addition, we introduce the algorithms of formalized representation. We conduct experiments using Sina micro-blog data. Results show that the information propagation formalized representation method of micro-blog network based on Petri nets can depict user behaviors of micro-blog network intuitively and accurately. This study reveals a new perspective for information transmission of a micro-blog network and provides some tools to support public opinion monitoring and micro-blog marketing applications.
Prolonged production of 14C during the ~660 BCE solar proton event from Japanese tree rings
Authors: Sakurai Hirohisa , Tokanai Fuyuki , Miyake Fusa , Horiuchi Kazuho , Masuda Kimiaki , Miyahara Hiroko , Ohyama Motonari , Sakamoto Minoru , Mitsutani Takumi , Moriya Toru 
Published: January 2020

AbstractAnnual rings record the intensity of cosmic rays (CRs) that had entered into the Earth’s atmosphere. Several rapid 14C increases in the past, such as the 775 CE and 994CE 14C spikes, have been reported to originate from extreme solar proton events (SPEs). Another rapid 14C increase, also known as the ca. 660 BCE event in German oak tree rings as well as increases of 10Be and 36Cl in ice cores, was presumed similar to the 775 CE event; however, as the 14C increase of approximately 10‰ in 660 BCE had taken a rather longer rise time of 3–4 years as compared to that of the 775 CE event, the occurrence could not be simply associated to an extreme SPE. In this study, to elucidate the rapid increase in 14C concentrations in tree rings around 660 BCE, we have precisely measured the 14C concentrations of earlywoods and latewoods inside the annual rings of Japanese cedar for the period 669–633 BCE. Based on the feature of 14C production rate calculated from the fine measured profile of the 14C concentrations, we found that the 14C rapid increase occurred within 665–663.5 BCE, and that duration of 14C production describing the event is distributed from one month to 41 months. The possibility of occurrence of consecutive SPEs over up to three years is offered.
In vitro testing of a funnel-shaped tip catheter model to decrease clot migration during mechanical thrombectomy
Authors: Tanyildizi Yasemin , Payne Emily , Gerber Tiemo , Seidman Larissa , Heimann Axel , Kempski Oliver , Leithner Doris , Garcia-Bardon Andreas , Kloeckner Roman , Hahn Felix , Keric Naureen , Masomi-Bornwasser Julia , Brockmann Marc A. , Kirschner Stefanie 
Published: January 2020

AbstractOne limitation of mechanical thrombectomy (MT) is clot migration during procedure. This might be caused by abruption of the trapped thrombus at the distal access catheter (DAC) tip during stent-retriever retraction due to the cylindrical shaped tip of the DAC. Aiming to solve this problem, this study evaluates the proof-of-concept of a new designed funnel-shaped tip, in an experimental in vitro setting. Two catheter models, one with a funnel-shaped tip and one with a cylindrical-shaped tip, were compared in an experimental setup. For MT a self-made vessel model and thrombi generated from pig’s blood were used. MT was performed 20 times for each device using two different stent-retrievers, 10 times respectively. For the funnel-shaped model: for both stent-retrievers (Trevo XP ProVue 3/20 mm; Trevo XP ProVue 4/20 mm) MT was successful at first pass in 9/10 (90%), respectively. For the cylindrical-shaped model: MT was successful at first pass in 5/10 (50%) with the smaller stent-retriever and in 6/10 (60%) with the larger stent-retriever. The experiments show a better recanalization rate for funnel-shaped tips, than for cylindrical-shaped tips. These results are indicating a good feasibility for this new approach, thus the development of a prototype catheter seems reasonable.
Comparative efficacy and safety of warfarin care bundles and novel oral anticoagulants in patients with atrial fibrillation: a systematic review and network meta-analysis
Authors: Ng Siok Shen , Lai Nai Ming , Nathisuwan Surakit , Jahan Nowrozy Kamar , Dilokthornsakul Piyameth , Kongpakwattana Khachen , Hollingworth William , Chaiyakunapruk Nathorn 
Published: January 2020

AbstractWarfarin care bundles (e.g. genotype-guided warfarin dosing, patient’s self-testing [PST] or patient’s self-management [PSM] and left atrial appendage closure) are based on the concept of combining several interventions to improve anticoagulation care. NOACs are also introduced for stroke prevention in atrial fibrillation (SPAF). However, these interventions have not been compared in head-to-head trials yet. We did a network meta-analysis based on a systematic review of randomized controlled trials comparing anticoagulant interventions for SPAF. Studies comparing these interventions in adults, whether administered alone or as care bundles were included in the analyses. The primary efficacy outcome was stroke and the primary safety outcome was major bleeding. Thirty-seven studies, involving 100,142 patients were assessed. Compared to usual care, PSM significantly reduced the risk of stroke (risk ratio [RR] 0.24, 95% CI 0.08–0.68). For major bleeding, edoxaban 60 mg (0.80, 0.71–0.90), edoxaban 30 mg (0.48, 0.42–0.56), and dabigatran 110 mg (0.81, 0.71–0.94) significantly reduced the risk of major bleeding compared with usual warfarin care. Cluster rank plot incorporating stroke and major bleeding outcomes indicates that some warfarin care bundles perform as well as NOACs. Both interventions are therefore viable options to be considered for SPAF. Additional studies including head-to-head trials and cost-effectiveness evaluation are still warranted.
A Machine Learning Approach to Growth Direction Finding for Automated Planting of Bulbous Plants
Authors: Booth Brian G. , Sijbers Jan , De Beenhouwer Jan 
Published: January 2020

AbstractIn agricultural robotics, a unique challenge exists in the automated planting of bulbous plants: the estimation of the bulb’s growth direction. To date, no existing work addresses this challenge. Therefore, we propose the first robotic vision framework for the estimation of a plant bulb’s growth direction. The framework takes as input three x-ray images of the bulb and extracts shape, edge, and texture features from each image. These features are then fed into a machine learning regression algorithm in order to predict the 2D projection of the bulb’s growth direction. Using the x-ray system’s geometry, these 2D estimates are then mapped to the 3D world coordinate space, where a filtering on the estimate’s variance is used to determine whether the estimate is reliable. We applied our algorithm on 27,200 x-ray simulations from T. Apeldoorn bulbs on a standard desktop workstation. Results indicate that our machine learning framework is fast enough to meet industry standards (<0.1 seconds per bulb) while providing acceptable accuracy (e.g. error < 30° in 98.40% of cases using an artificial 3-layer neural network). The high success rates of the proposed framework indicate that it is worthwhile to proceed with the development and testing of a physical prototype of a robotic bulb planting system.