bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Associated With Survival Following Extracorporeal Cardiopulmonary Resuscitation in Children
Authors: Melvan John Nicholas , Davis Joel , Heard Micheal , Trivedi Jaimin R. , Wolf Michael , Kanter Kirk R. , Deshpande Shriprasad R. , Alsoufi Bahaaldin 
Published: April 2020

Objectives: We examined a large single-institution experience in extracorporeal cardiopulmonary resuscitation (ECPR) in children having cardiac arrest refractory to conventional resuscitation measures with focus on factors affecting survival. Methods: Between 2002 and 2017, 184 children underwent ECPR at our institution. We entered demographic, anatomic, clinical, surgical, and ECPR support details into a multivariable logistic regression models to determine factors associated with mortality. Results: Median age was 54 days (interquartile range [IQR]: 11-272). In all, 157 (85%) patients had primary cardiac disease, including 136 (74%) with congenital heart disease (71 with single ventricle). Extracorporeal cardiopulmonary resuscitation occurred following cardiac surgery in 124 (67%) patients. Median cardiopulmonary resuscitation (CPR) duration was 27 minutes (IQR: 18-40) and median support duration was 3.0 days (IQR: 1.6-5.3). Overall, ECPR was weaned in 115 (63%), with 79 (43%) surviving to hospital discharge. Survival for patients with congenital heart disease, noncongenital cardiac, and noncardiac pathologies was 44%, 71%, and 15%, respectively. On multivariable regression analysis, risk factors associated with mortality were presupport pH <7.1 (odds ratio [OR] = 3.7, 95% confidence interval [CI]: 1.11-12.41, P = .033), mechanical complications (OR = 8.33, 95% CI: 1.91-36.25, P = .005), neurologic complications (OR = 6.27, 95% CI: 1.40-28.10, P = .017), and renal replacement therapy (OR = 3.31, 95% CI: 1.03-10.66, P = .045). Conclusions: Extracorporeal cardiopulmonary resuscitation plays a valuable role salvaging children with refractory cardiac arrest. Survival varies with underlying pathology and can be expected even with relatively longer CPR durations. Efforts to improve systemic output before and after institution of ECPR might mitigate some of the significant risk factors for mortality.
Pediatric Ventricular Assist Device Support in the Netherlands
Authors: Rohde Sofie , Antonides Christiaan F. J. , Muslem Rahatullah , de Woestijne Pieter C. van , der Meulen Marijke H. van , Kraemer Ulrike S. , Dalinghaus Michiel , Bogers Ad J. J. C. 
Published: April 2020

Background: This study aimed to evaluate the changes in heart transplantation (HTx) waiting list mortality following the introduction of the Berlin Heart EXCOR (BH EXCOR) in the Netherlands, as well as the occurrence of adverse events in these children. Methods: A retrospective, single-center study was conducted including all pediatric patients (≤18 years) awaiting HTx. Patients were grouped in two eras based on availability of the BH EXCOR in our center, era I (1998-2006; not available) and era II (2007 to July 31, 2018; available). Results: In total, 87 patients were included, 15 in era I and 72 in era II. Extracorporeal membrane oxygenator support was required in 1 (7%) patient in era I and in 13 (18%) patients in era II. Overall mortality (7/15 in era I vs 16/72 in era II; 47% vs 22%, P = .06) and transplantation rates (8/15 in era I vs 47/72 in era II; 53% vs 65%, P = .39) did not differ significantly. Eleven (39%) patients of the pediatric ventricular assist device (VAD) population died, with the predominant cause being cerebrovascular accidents (CVAs) in eight (29%) patients. Furthermore, 14 (50%) of the pediatric VAD patients survived to transplantation. Adverse events most frequently occurring in VAD patients included CVA in 14 (50%), mostly (68%) within 30 days after VAD implantation, and bleeding requiring rethoracotomy in 14 (50%), all within 30 days after VAD implantation. Conclusions: The introduction of the BH EXCOR has positively impacted the survival of pediatric patients with end-stage heart failure in our center. The predominant cause of death changed from end-stage heart failure in era I to CVA in era II. We emphasize the need for large prospective registry–based studies.
Promoting Human Security: Planned Relocation as a Protection Tool in a Time of Climate Change
Authors: Ferris Elizabeth , Weerasinghe Sanjula 
Published: April 2020

Executive Summary In light of the science and evidence on hazards and climate risk, and the scale and breadth of large-scale disasters witnessed around the world, it is time for states and other actors to begin developing national and local frameworks on planned relocation. While planned relocations have had a poor record in terms of their socioeconomic effects, it is precisely for these reasons that proactive action is necessary. Planned relocation has the potential to save lives and assets, and consequently to safeguard or augment the human security of populations living in areas at high risk for disasters and the effects of climate change. Among the challenges hampering better outcomes for people, however, are the lack of national and local frameworks, community-driven decision making, and sufficient lead times to plan and implement appropriate interventions that promote human security. Relocation of populations is referenced in global frameworks on disaster risk reduction (DRR) and climate change adaptation (CCA) because it is a tool that will become increasingly important as a preventive and responsive measure to reduce the risks of disasters and displacement. This article recommends that national and local DRR and CCA strategies and development plans begin to incorporate planned relocation among the options under consideration to protect people and their human security. It argues that planning for relocations is an expression of a government’s responsibility to protect the human security of its people.
The gut microbial metabolite trimethylamine N-oxide aggravates GVHD by inducing M1 macrophage polarization in mice
Authors: Wu Kunpeng , Yuan Yan , Yu Huihui , Dai Xin , Wang Shu , Sun Zhengxu , Wang Fen , Fei He , Lin Qiwang , Jiang Hua , Chen Tong 
Published: April 2020

Abstract
The diversity of the human microbiome heralds the difference of the impact that gut microbial metabolites exert on allogenic graft-versus-host (GVH) disease (GVHD), even though short-chain fatty acids and indole were demonstrated to reduce its severity. In this study, we dissected the role of choline-metabolized trimethylamine N-oxide (TMAO) in the GVHD process. Either TMAO or a high-choline diet enhanced the allogenic GVH reaction, whereas the analog of choline, 3,3-dimethyl-1-butanol reversed TMAO-induced GVHD severity. Interestingly, TMAO-induced alloreactive T-cell proliferation and differentiation into T-helper (Th) subtypes was seen in GVHD mice but not in in vitro cultures. We thus investigated the role of macrophage polarization, which was absent from the in vitro culture system. F4/80+CD11b+CD16/32+ M1 macrophage and signature genes, IL-1β, IL-6, TNF-α, CXCL9, and CXCL10, were increased in TMAO-induced GVHD tissues and in TMAO-cultured bone marrow–derived macrophages (BMDMs). Inhibition of the NLRP3 inflammasome reversed TMAO-stimulated M1 features, indicating that NLRP3 is the key proteolytic activator involved in the macrophage’s response to TMAO stimulation. Consistently, mitochondrial reactive oxygen species and enhanced NF-κB nuclear relocalization were investigated in TMAO-stimulated BMDMs. In vivo depletion of NLRP3 in GVHD recipients not only blocked M1 polarization but also reversed GVHD severity in the presence of TMAO treatment. In conclusion, our data revealed that TMAO-induced GVHD progression resulted from Th1 and Th17 differentiation, which is mediated by the polarized M1 macrophage requiring NLRP3 inflammasome activation. It provides the link among the host choline diet, microbial metabolites, and GVH reaction, shedding light on alleviating GVHD by controlling choline intake.
Co/CoP Nanoparticles Encapsulated Within N, P-Doped Carbon Nanotubes on Nanoporous Metal-Organic Framework Nanosheets for Oxygen Reduction and Oxygen Evolution Reactions
Authors: Yang Xinxin , Mi Hongwei , Ren Xiangzhong , Zhang Peixin , Li Yongliang 
Published: April 2020

AbstractHerein, Co/CoP nanoparticles encapsulated with N, P-doped carbon nanotubes derived from the atomic layer deposited hexagonal metal-organic frameworks (MOFs) are obtained by calcinations and subsequent phosphating and are employed as electrocatalyst. The electrocatalytic performance evaluations show that the as-prepared electrocatalyst exhibits an overpotential of 342 mV at current density of 10 mA cm−2 and the Tafel slope of 74 mV dec−1 for oxygen evolution reaction (OER), which is superior to the most advanced ruthenium oxide electrocatalyst. The electrocatalyst also shows better stability than the benchmark RuO2. After 9 h, the current density is only decreased by 10%, which is far less than the loss of RuO2. Moreover, its onset potential for oxygen reduction reaction (ORR) is 0.93 V and follows the ideal 4-electron approach. After the stability test, the current density of the electrocatalyst retains 94% of the initial value, which is better than Pt/C. The above results indicate that the electrocatalyst has bifunctional activity and excellent stability both for OER and ORR. It is believed that this strategy provides guidance for the synthesis of cobalt phosphide/carbon-based electrocatalysts.
Sparse multiple co-Inertia analysis with application to integrative analysis of multi -Omics data
Authors: Min Eun Jeong , Long Qi 
Published: April 2020

Abstract
Background
Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensional -omics datasets. However, its estimated loading vectors are non-sparse, which presents challenges for identifying important features and interpreting analysis results. We propose two new mCIA methods: 1) a sparse mCIA method that produces sparse loading estimates and 2) a structured sparse mCIA method that further enables incorporation of structural information among variables such as those from functional genomics.

Results
Our extensive simulation studies demonstrate the superior performance of the sparse mCIA and structured sparse mCIA methods compared to the existing mCIA in terms of feature selection and estimation accuracy. Application to the integrative analysis of transcriptomics data and proteomics data from a cancer study identified biomarkers that are suggested in the literature related with cancer disease.

Conclusion
Proposed sparse mCIA achieves simultaneous model estimation and feature selection and yields analysis results that are more interpretable than the existing mCIA. Furthermore, proposed structured sparse mCIA can effectively incorporate prior network information among genes, resulting in improved feature selection and enhanced interpretability.
Brick plots: an intuitive platform for visualizing multiparametric immunophenotyped cell clusters
Authors: Norton Samuel E. , Leman Julia K. H. , Khong Tiffany , Spencer Andrew , Fazekas de St Groth Barbara , McGuire Helen M. , Kemp Roslyn A. 
Published: April 2020

Abstract
Background
The advent of mass cytometry has dramatically increased the parameter limit for immunological analysis. New approaches to analysing high parameter cytometry data have been developed to ease analysis of these complex datasets. Many of these methods assign cells into population clusters based on protein expression similarity.

Results
Here we introduce an additional method, termed Brick plots, to visualize these cluster phenotypes in a simplified and intuitive manner. The Brick plot method generates a two-dimensional barcode that displays the phenotype of each cluster in relation to the entire dataset. We show that Brick plots can be used to visualize complex mass cytometry data, both from fundamental research and clinical trials, as well as flow cytometry data.

Conclusion
Brick plots represent a new approach to visualize complex immunological data in an intuitive manner.
microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation
Authors: Penso-Dolfin Luca , Haerty Wilfried , Hindle Allyson , Di Palma Federica 
Published: April 2020

AbstractBackgroundThe Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving > 900 m deep and remaining underwater for more than 60 min. A number of key physiological specializations have been identified, including the low levels of aerobic, lipid-based metabolism under hypoxia, significant increase in oxygen storage in blood and muscle; high blood volume and extreme cardiovascular control. These adaptations have been linked to increased abundance of key proteins, suggesting an important, yet still understudied role for gene reprogramming.In this study, we investigate the possibility that post-transcriptional gene regulation by microRNAs (miRNAs) has contributed to the adaptive evolution of diving capacities in the Weddell Seal.ResultsUsing small RNA data across 4 tissues (brain, heart, muscle and plasma), in 3 biological replicates, we generate the first miRNA annotation in this species, consisting of 559 high confidence, manually curated miRNA loci. Evolutionary analyses of miRNA gain and loss highlight a high number of Weddell seal specific miRNAs.Four hundred sixteen miRNAs were differentially expressed (DE) among tissues, whereas 80 miRNAs were differentially expressed (DE) across all tissues between pups and adults and age differences for specific tissues were detected in 188 miRNAs. mRNA targets of these altered miRNAs identify possible protective mechanisms in individual tissues, particularly relevant to hypoxia tolerance, anti-apoptotic pathways, and nitric oxide signal transduction. Novel, lineage-specific miRNAs associated with developmental changes target genes with roles in angiogenesis and vasoregulatory signaling.ConclusionsAltogether, we provide an overview of miRNA composition and evolution in the Weddell seal, and the first insights into their possible role in the specialization to diving.
Protein–protein interaction of Rv0148 with Htdy and its predicted role towards drug resistance in Mycobacterium tuberculosis
Authors: Bhargavi Gunapati , Hassan Sameer , Balaji Subramanyam , Tripathy Srikanth Prasad , Palaniyandi Kannan 
Published: April 2020

Abstract
Background
Mycobacterium tuberculosis resides inside host macrophages during infection and adapts to resilient stresses generated by the host immune system. As a response, M. tuberculosis codes for short-chain dehydrogenases/reductases (SDRs). These SDRs are nicotinamide adenine dinucleotide-reliant oxidoreductases involved in cell homeostasis. The precise function of oxidoreductases in bacteria especially M. tuberculosis were not fully explored. This study aimed to know the detail functional role of one of the oxidoreductase Rv0148 in M. tuberculosis.

Results
In silico analysis revealed that Rv0148 interacts with Htdy (Rv3389) and the protein interactions were confirmed using far western blot. Gene knockout mutant of Rv0148 in M. tuberculosis was constructed by specialized transduction. Macrophage cell line infection with this knockout mutant showed increased expression of pro-inflammatory cytokines. This knockout mutant is sensitive to oxidative, nitrogen, redox and electron transport inhibitor stress agents. Drug susceptibility testing of the deletion mutant showed resistance to first-line drugs such as streptomycin and ethambutol and second-line aminoglycosides such as amikacin and kanamycin. Based on interactorme analysis for Rv0148 using STRING database, we identified 220 most probable interacting partners for Htdy protein. In the Rv0148 knockout mutants, high expression of htdy was observed and we hypothesize that this would have perturbed the interactome thus resulting in drug resistance. Finally, we propose that Rv0148 and Htdy are functionally interconnected and involved in drug resistance and cell homeostasis of M. tuberculosis.

Conclusions
Our study suggests that Rv0148 plays a significant role in various functional aspects such as intermediatory metabolism, stress, homeostasis and also in drug resistance.
Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate
Authors: Kim Eiseul , Yang Seung-Min , Lim Bora , Park Si Hong , Rackerby Bryna , Kim Hae-Yeong 
Published: April 2020

Abstract
Background
Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods.

Results
To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label.

Conclusions
The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus, and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.
Wide crossing diversify mitogenomes of rice
Authors: Yang Weilong , Zou Jianing , Wang Jiajia , Li Nengwu , Luo Xiaoyun , Jiang Xiaofen , Li Shaoqing 
Published: April 2020

AbstractBackgroundIn most angiosperms, the inheritance of the mitochondria takes place in a typical maternal manner. However, very less information is available about if the existence of structural variations or not in mitochondrial genomes (mitogenomes) between maternal parents and their progenies.ResultsIn order to find the answer, a stable rice backcross inbred line (BIL) population was derived from the crosses ofOryza glaberrima/Oryza sativa//Oryza sativa.The current study presents a comparative analysis of the mitogenomes between maternal parents and five BILs. There were recorded universal structural variations such as reversal, translocation, fusion, and fission among the BILs. The repeat-mediated recombination and non-homologous end-joining contributed virtually equal to the rearrangement of mitogenomes. Similarly, the relative order, copy-number, expression level, and RNA-editing rate of mitochondrial genes were also extensively varied among BILs.ConclusionsThese novel findings unraveled an unusual mystery of the maternal inheritance and possible cause for heterogeneity of mitogenomes in rice population. The current piece of work will greatly develop our understanding of the plant nucleo-cytoplasmic interaction and their potential role in plant growth and developmental processes.
Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant
Authors: Wan Liyun , Lei Yong , Yan Liying , Liu Yue , Pandey Manish K. , Wan Xia , Varshney Rajeev K. , Fang Jiahai , Liao Boshou 
Published: April 2020

Abstract
Background
Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil. An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation.

Result
Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced plant hormones synthesis and signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and DFR by controlling hormone synthesis and signaling as well as the MBW complex.

Conclusions
The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.
Crystal structure of DRIK1, a stress-responsive receptor-like pseudokinase, reveals the molecular basis for the absence of ATP binding
Authors: Aquino Bruno , da Silva Viviane C. H. , Massirer Katlin B. , Arruda Paulo 
Published: April 2020

Abstract
Background
Plants reprogram metabolism and development to rapidly adapt to biotic and abiotic stress. Protein kinases play a significant role in this process by phosphorylating protein substrates that activate or inactivate signaling cascades that regulate cellular and metabolic adaptations. Despite their importance in plant biology, a notably small fraction of the plant kinomes has been studied to date.

Results
In this report, we describe ZmDRIK1, a stress-responsive receptor-like pseudokinase whose expression is downregulated under water restriction. We show the structural features and molecular basis of the absence of ATP binding exhibited by ZmDRIK1. The ZmDRIK1 kinase domain lacks conserved amino acids that are essential for phosphorylation activity. The crystal structure of the ZmDRIK1 kinase domain revealed the presence of a spine formed by the side chain of the triad Leu240, Tyr363, and Leu375 that occludes the ATP binding pocket. Although ZmDRIK1 is unable to bind nucleotides, it does bind the small molecule ENMD-2076 which, in a cocrystal structure, revealed the potential to serve as a ZmDRIK1 inhibitor.

Conclusion
ZmDRIK1 is a novel receptor-like pseudokinase responsive to biotic and abiotic stress. The absence of ATP binding and consequently, the absence of phosphorylation activity, was proven by the crystal structure of the apo form of the protein kinase domain. The expression profiling of the gene encoding ZmDRIK1 suggests this kinase may play a role in downregulating the expression of stress responsive genes that are not necessary under normal conditions. Under biotic and abiotic stress, ZmDRIK1 is down-regulated to release the expression of these stress-responsive genes.