bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIX‐01294 enhanced chemotherapy effect in gastric cancer by inducing GSDME‐mediated pyroptosis
Authors: Deng Bei‐Bei , Jiao Bao‐Ping , Liu Yang‐Jun , Li Yan‐Rong , Wang Gui‐Jun 
Published: May 2020

AbstractAdjuvant chemotherapy in combination with surgery is expected to be a curative strategy for gastric cancer. However, drug resistance remains an obstacle in effective chemotherapy. Therefore, understanding the potential mechanisms of chemotherapy induced gastric cancer cell death is of great importance. We demonstrated that BIX‐01294 (BIX) at low concentration could induce autophagic flux by converting LC3B‐I to LC3B‐II and directly activate autophagy associated cell death in gastric cancer cell lines at high concentration. BIX at low concentration could help obtain sensitivity of gastric cancer cells to chemotherapy with significantly reduced cell viability. Interestingly, BIX combined Cis (BIX + Cis) treated SGC‐7901 cells display pyroptosis related cell death with large bubbles blown around the membrane, significantly decreased cell viability, elevated lactate dehydrogenase release and increased percentage of propidium iodide and Annexin‐V double positive cells. Furthermore, the cleavage of gasdermin E (GSDME) and caspase‐3 but not GSDMD was detected by immunoblotting and the knockout of GSDME switched pyroptosis into apoptosis in the BIX + Cis combined treated group. Furthermore, the deficiency of Beclin‐1 to inhibit BIX induced autophagic flux completely blocked BIX + Cis combined treated induced cell pyroptosis related cell death. Additionally, BIX + Cis in vivo treatment could inhibit tumor growth, which could be reversed by the deficiency of Beclin‐1 and be delayed by the deficiency of GSDME. In conclusion, our data was the first to reveal that BIX enhanced the anticancer chemotherapy effect by induced GSDME‐mediated pyroptosis through the activation of autophagic flux in gastric cancer cells.
Anticarcinogenic effects of halofuginone on lung‐derived cancer cells
Authors: Demiroglu‐Zergeroglu Asuman , Turhal Gulseren , Topal Halime , Ceylan Hurmuz , Donbaloglu Fadime , Karadeniz Cerit Kivilcim , Odongo Ronald R. 
Published: May 2020

AbstractMalignant mesothelioma is a rare but aggressive form of malignancy, which is difficult to diagnose and is resistant to current chemotherapeutic treatment options. Molecular techniques have been used to investigate the mechanisms of action and the beneficial therapeutic effects of halofuginone (HF) in several cancers but not malignant mesotheliomas. In this study, the antiproliferative and apoptotic effects of HF were investigated through its ability to deregulate EGFR downstream signalling cascade proteins in the pathologically aggressive malignant mesothelioma and non‐small‐cell lung cancer cells. We showed that administration of HF at nanomolar concentrations induced a dose‐dependent reduction in the viability of cancer cells, made cell cycle arrest, inhibited proliferation of cancer cells via STAT3 and ERK1/2 pathways and triggered the apoptotic cascade via p38MAPK. We demonstrated that the apoptotic cell death mechanism was mediated by enhanced activation of caspase‐3 and concomitant PARP cleavage, downregulation of Bcl‐2 and upregulation of Bax in both malignant mesothelioma and lung cancer cells. In particular, we demonstrated that cancer cells were more sensitive to HF treatment than normal mesothelial cells. Taken together, this study suggests that HF exerts its anticancer effects in lung‐derived cancers by targeting signal transduction pathways mainly through deregulation of ERK1/2, STAT3 and p38MAPK to reduce cancer cell viability, induce cell cycle arrest and apoptotic cell death. Thus, HF might be considered as a potential agent against malignant mesothelioma and/or lung cancer cells.
Bleeding from pancreatic arteriovenous malformation with duodenal ulcer penetration. Case report and literature review
Authors: Takayama Hiroshi , Shimodate Yuichi , Nomura Satoshi , Kitagawa Hirohisa , Akaike Yoko , Uchino Kaori , Watanabe Tetsuo , Mizuno Motowo 
Published: May 2020

AbstractDilated vessels at the ulcer floor of the second part of the duodenum can be signs of pancreatic arteriovenous malformation; contrast‐enhanced computed tomography should be performed, and surgical treatment should be considered.
Scalable approach to high coverages on oxides via iterative training of a machine‐learning algorithm
Authors: Liu Fuzhu , Yang Shengchun , Medford Andrew J. 
Published: May 2020

AbstractUnderstanding the interaction of multiple types of adsorbate molecules on solid surfaces is crucial to establishing the stability of catalysts under various chemical environments. Computational studies on the high coverage and mixed coverages of reaction intermediates are still challenging, especially for transition‐metal compounds. In this work, we present a framework to predict differential adsorption energies and identify low‐energy structures under high‐ and mixed‐adsorbate coverages on oxide materials. The approach uses Gaussian process machine‐learning models with quantified uncertainty in conjunction with an iterative training algorithm to actively identify the training set. The framework is demonstrated for the mixed adsorption of CHx, NHx and OHx species on the oxygen vacancy and pristine rutile TiO2(110) surface sites. The results indicate that the proposed algorithm is highly efficient at identifying the most valuable training data, and is able to predict differential adsorption energies with a mean absolute error of ∼0.3 eV based on <25 % of the total DFT data. The algorithm is also used to identify 76 % of the low‐energy structures based on <30 % of the total DFT data, enabling construction of surface phase diagrams that account for high and mixed coverage as a function of the chemical potential of C, H, O, and N. Furthermore, the computational scaling indicates the algorithm scales nearly linearly (N1.12) as the number of adsorbates increases. This framework can be directly extended to metals, metal oxides, and other materials, providing a practical route toward the investigation of the behavior of catalysts under high‐coverage conditions.
Morphology and Composition Regulation of FeCoNi Prussian Blue Analogues to Advance in the Catalytic Performances of the Derivative Ternary Transition‐Metal Phosphides for OER
Authors: Du Yuanxin , Ding Xin , Han Meng , Zhu Manzhou 
Published: May 2020

AbstractPrussian blue analogues (PBAs) are mostly binary metallic compounds with a cubic structure, which greatly limits the structure and component of derived transition‐metal phosphides (TMPs) and affects their catalytic activities. This work focuses on regulating the morphology and composition of the PBA at the front‐end to optimize the OER performance of the derived TMP. By temperature control surfactant desorption ability, we obtain a series of ternary FeCoNi (FCN‐PBAs). With the increase of temperature, their morphologies change from truncated octahedrons to cubic octahedrons and truncated cubes, in which the Fe content basically remains unchanged and the Co/Ni ratio gradually decreased. Due to the synergistic effect among ternary TMPs, all phosphidation products (FCN‐P) exhibit better OER activities than RuO2, among which FCN‐40‐P shows the best performance. As confirmed by XPS analyses, the appropriate chemical composition enhances the oxidizabilityof TM species, promotes the chemical adsorption of OH−, and accelerates OER kinetics.
Detection of LC3‐Associated Phagocytosis (LAP)
Authors: Martinez Jennifer 
Published: May 2020

AbstractPhagocytes, notably macrophages, are critical sentinels of their environment, patrolling for and eradicating unwanted components. The ability of cells to process extracellular cargo in an appropriate manner is important for both clearance of the cargo and eventual return to homeostasis. Although the evolutionarily conserved pathway of autophagy involves the degradation and recycling of unnecessary or dysfunctional cellular components during starvation, we now appreciate that the reach of autophagy extends beyond nutrient deprivation, notably including cellular quality control (e.g., mitophagy) and host defense against internalized pathogens (i.e., xenophagy). Despite being seemingly disparate, autophagic functions are unified as conserved mechanisms for containment and immunosuppression, suggesting an original immune function for autophagy. A recently described pathway called LC3‐associated phagocytosis (LAP) marries the ancient concepts of phagocytosis and autophagy, revealing new ways in which the autophagy machinery, in a molecularly distinct pathway, contributes to the inflammatory response. In this article, protocols to detect LAP by electron microscopy, immunofluorescence, flow cytometry, and phagosome purification are described, allowing the user to detect multiple characteristics of LAP in both qualitative and quantitative manners. Published 2020. U.S. Government.Basic Protocol 1: Detection of LAP by electron microscopyBasic Protocol 2: Detection of LAP by confocal microscopy of LC3‐GFP‐expressing cellsAlternate Protocol 1: Detection of LAP by confocal microscopy using immunofluorescenceBasic Protocol 3: Detection of LAP using flow cytometry of LC3‐GFP‐expressing cellsAlternate Protocol 2: Detection of LAP using antibody staining and flow cytometryBasic Protocol 4: Detection of LAP by western blot of purified LAPosomes
Mary, Hugo, and Hugo*: Learning to schedule distributed data‐parallel processing jobs on shared clusters
Authors: Thamsen Lauritz , Beilharz Jossekin , Tran Vinh Thuy , Nedelkoski Sasho , Kao Odej 
Published: May 2020

SummaryDistributed data‐parallel processing systems like MapReduce, Spark, and Flink are popular for analyzing large datasets using cluster resources. Resource management systems like YARN or Mesos in turn allow multiple data‐parallel processing jobs to share cluster resources in temporary containers. Often, the containers do not isolate resource usage to achieve high degrees of overall resource utilization despite overprovisioning and the often fluctuating utilization of specific jobs. However, some combinations of jobs utilize resources better and interfere less with each other when running on the same shared nodes than others. This article presents an approach for improving the resource utilization and job throughput when scheduling recurring distributed data‐parallel processing jobs in shared clusters. The approach is based on reinforcement learning and a measure of co‐location goodness to have cluster schedulers learn over time which jobs are best executed together on shared resources. We evaluated this approach over the last years with three prototype schedulers that build on each other: Mary, Hugo, and Hugo*. For the evaluation we used exemplary Flink and Spark jobs from different application domains and clusters of commodity nodes managed by YARN. The results of these experiments show that our approach can increase resource utilization and job throughput significantly.
Whole‐Mount In Situ Hybridization in Post‐Implantation Staged Mouse Embryos
Authors: Barratt Kristen S. , Arkell Ruth M. 
Published: May 2020

AbstractUnderstanding RNA expression in space and time is a key initial step in dissecting gene function. The ability to visualize gene expression in whole‐tissue or whole‐specimen preparations, called in situ hybridization (ISH), was first developed 50 years ago. Two decades later, these protocols were adapted to establish robust methods for whole‐mount ISH to murine embryos. The precise protocols vary somewhat between early‐gestation and mid‐gestation mouse embryos; the protocol presented here is optimal for use with post‐implantation stage mouse embryos (stages 5.5–9.5 dpc). Routine uses of whole‐mount ISH include documenting the wild‐type expression pattern of individual genes and comparison of the expression pattern of signature genes (i.e., those that identify particular cells and tissues within an embryo) between wild‐type and mutant embryos as part of a phenotyping experiment. This technique remains a mainstay of developmental biology studies and complements the massively parallel assessment of gene expression from dissociated tissues and cells via RNA‐sequencing techniques. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Dissection of post‐implantation (5.5‐9.5 dpc) murine embryosBasic Protocol 2: Whole‐mount in situ hybridization in post‐implantation embryosBasic Protocol 3: Visualization of post‐WMISH embryosSupport Protocol 1: Creation of siliconized glass pipettesSupport Protocol 2: Creation of embryo powder
Break Up to Make Up: Utilization of Photocleavable Groups in Biolabeling of Hydrogel Scaffolds
Authors: Truong Vinh X. 
Published: May 2020

AbstractUnderstanding cell behavior within the extracellular matrix is essential for the implementation of biomaterials in medical applications. Conjugation of bioactive molecules to hydrogel scaffolds imparts the materials with biological cues necessary for controlling cell behavior such as adhesion, growth and migration. Photo‐induced ligation is a powerful tool to precisely control when and where such bioactivity can be initiated. Over the past decade, advances in light‐regulated technology have emerged to address the stringent demands for photochemical ligation in biological environments, including high sensitivity, fast reaction kinetics, longer wavelength absorption and site‐selectivity. Here, the utilization of contemporary photolabile groups for light‐mediated bioconjugation of hydrogels are highlighted. In this approach, reactive groups such as thiol, amine and aldehyde are masked with photolabile moieties, which can be photo‐released to participate in click reactions, such as Michael addition and oxime ligation. New chromophores with long wavelength visible light absorption are also examined for potential employment in light‐induced bioconjugation.
Generating Bacterial Foods in Toxicology Studies with Caenorhabditis elegans
Authors: Ke Tao , Santamaría Abel , Tinkov Alexey A. , Bornhorst Julia , Aschner Michael 
Published: May 2020

AbstractCaenorhabditis elegans is a free‐living animal that is used as a powerful experimental model in biological sciences. The natural habitat of the animal are areas rich in material from rotting plants or fruits being decomposed by a growing number of microorganisms. The ecology of the natural habitat of C. elegans is a complex interactive network involving many species, including numerous types of bacteria, viruses, fungi, slugs, snails, and isopods, among which bacteria play multifaceted roles in the natural history of C. elegans. Under laboratory conditions, C. elegans is routinely cultured in a petri dish filled with solidified agar and seeded with Escherichia coli strain OP50, the latter offering an alternative model to study the interaction between bacteria and host. Because of the clear advantages of generating specific bacterial foods for mechanistic studies in C. elegans, it is important to develop a robust protocol to generate high‐quality bacterial foods commensurate with experimental requirements. Based on previous work by us and others, herein we present a protocol on how to generate these optimal bacterial food–based research tools. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Preparing concentrated E. coli OP50Basic Protocol 2: Titrating bacteria concentrationBasic Protocol 3: Generating dead bacterial food by heatingBasic Protocol 4: Generating dead bacterial food by antibioticsBasic Protocol 5: Feeding C. elegans with bacterial foods in liquid
In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses
Authors: Tournayre Orianne , Leuchtmann Maxime , Filippi‐Codaccioni Ondine , Trillat Marine , Piry Sylvain , Pontier Dominique , Charbonnel Nathalie , Galan Maxime 
Published: May 2020

AbstractDuring the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.
Telemonitoring versus standard care in heart failure: a randomised multicentre trial
Authors: Galinier Michel , Roubille François , Berdague Philippe , Brierre Gilles , Cantie Philippe , Dary Patrick , Ferradou Jean‐Marc , Fondard Olivier , Labarre Jean Philippe , Mansourati Jacques , Picard François , Ricci Jean‐Etienne , Salvat Muriel , Tartière Lamia , Ruidavets Jean‐Bernard , Bongard Vanina , Delval Cécile , Lancman Guila , Pasche Hélène , Ramirez‐Gil Juan Fernando , Pathak Atul ,   on behalf of the OSICAT Investigators
Published: May 2020

AimsThe aim was to assess the effect of a telemonitoring programme vs. standard care (SC) in preventing all‐cause deaths or unplanned hospitalisations in heart failure (HF) at 18 months.Methods and resultsOSICAT was a randomised, multicentre, open‐label French study in 937 patients hospitalised for acute HF ≤12 months before inclusion. Patients were randomised to telemonitoring (daily body weight measurement, daily recording of HF symptoms, and personalised education) (n = 482) or to SC (n = 455). Mean ± standard deviation number of events for the primary outcome was 1.30 ± 1.85 for telemonitoring and 1.46 ± 1.98 for SC [rate ratio 0.97, 95% confidence interval (CI) 0.77–1.23; P = 0.80]. In New York Heart Association (NYHA) class III or IV HF, median time to all‐cause death or first unplanned hospitalisation was 82 days in the telemonitoring group and 67 days in the SC group (P = 0.03). After adjustment for known predictive factors, telemonitoring was associated with a 21% relative risk reduction in first unplanned hospitalisation for HF [hazard ratio (HR) 0.79, 95% CI 0.62–0.99; P = 0.044); the relative risk reduction was 29% in patients with NYHA class III or IV HF (HR 0.71, 95% CI 0.53–0.95; P = 0.02), 38% in socially isolated patients (HR 0.62, 95% CI 0.39–0.98; P = 0.043), and 37% in patients who were ≥70% adherent to body weight measurement (HR 0.63, 95% CI 0.45–0.88; P = 0.006).ConclusionTelemonitoring did not result in a significantly lower rate of all‐cause deaths or unplanned hospitalisations in HF patients. The pre‐specified subgroup results suggest the telemonitoring approach improves clinical outcomes in selected populations but need further confirmation.
SIRPα on CD11c+ cells induces Th17 cell differentiation and subsequent inflammation in the CNS in experimental autoimmune encephalomyelitis
Authors: Nishimura Taichi , Saito Yasuyuki , Washio Ken , Komori Satomi , Respatika Datu , Kotani Takenori , Murata Yoji , Ohnishi Hiroshi , Mizobuchi Satoshi , Matozaki Takashi 
Published: May 2020

AbstractSignal regulatory protein α (SIRPα) is expressed predominantly on type 2 conventional dendritic cells (cDC2s) and macrophages. We previously showed that mice systemically lacking SIRPα were resistant to experimental autoimmune encephalomyelitis (EAE). Here, we showed that deletion of SIRPα in CD11c+ cells of mice (SirpaΔDC mice) also markedly ameliorated the development of EAE. The frequency of cDCs and migratory DCs (mDCs), as well as that of Th17 cells, were significantly reduced in draining lymph nodes of SirpaΔDC mice at the onset of EAE. In addition, we found the marked reduction in the number of Th17 cells and DCs in the CNS of SirpaΔDC mice at the peak of EAE. Whereas inducible systemic ablation of SIRPα before the induction of EAE prevented disease development, that after EAE onset did not ameliorate the clinical signs of disease. We also found that EAE development was partially attenuated in mice with CD11c+ cell‐specific ablation of CD47, a ligand of SIRPα. Collectively, our results suggest that SIRPα expressed on CD11c+ cells, such as cDC2s and mDCs, is indispensable for the development of EAE, being required for the priming of self‐reactive Th17 cells in the periphery as well as for the inflammation in the CNS.
COVID‐19 vaccines: Knowing the unknown
Authors: Lv Huibin , Wu Nicholas C. , Mok Chris K. P. 
Published: May 2020

AbstractVaccine development against SARS‐CoV‐2 has drawn attention around the globe due to the exploding pandemic. Although COVID‐19 is caused by a new coronavirus, SARS‐CoV‐2, previous research on other coronavirus vaccines, such as FIPV, SARS, and MERS, has provided valuable information for the rapid development of COVID‐19 vaccine. However, important knowledge gaps remain — some are specific to SARS‐CoV‐2, others are fundamental to immunology and vaccinology. Here, we discuss areas that need to be addressed for COVID‐19 vaccine development, and what can be learned from examples of vaccine development in the past. Since the beginning of the outbreak, the research progress on COVID‐19 has been remarkable. We are therefore optimistic about the rapid development of COVID‐19 vaccine.