bluuebunny/crossref_metadata_2025_split huggingface dataset:
Susceptibility to Xylella fastidiosa and functional xylem anatomy in Olea europaea: revisiting a tale of plant–pathogen interaction
Authors: Petit Giai , Bleve Gianluca , Gallo Antonia , Mita Giovanni , Montanaro Giuseppe , Nuzzo Vitale , Zambonini Dario , Pitacco Andrea 
Published: May 2021

Abstract
Xylella fastidiosa is a xylem-limited bacterium causing the Olive Quick Decline Syndrome, which is currently devastating the agricultural landscape of Southern Italy. The bacterium is injected into the xylem vessels of leaf petioles after the penetration of the insect vector’s stylet. From here, it is supposed to colonize the xylem vasculature moving against water flow inside conductive vessels. Widespread vessel clogging following the bacterial infection and causing the failure of water transport seemed not to fully supported by the recent empirical xylem anatomical observations in infected olive trees. We tested the hypothesis that the higher susceptibility to the X. fastidiosa’s infection in Cellina di Nardò compared with Leccino is associated to the higher vulnerability to air embolism of its larger vessels. Such hypothesis is motivated by the recognized ability of X. fastidiosa in degrading pit membranes and also because air embolism would possibly provide microenvironmental conditions more favourable to its more efficient aerobic metabolism. We revised the relevant literature on bacterium growth and xylem physiology, and carried out empirical field, mid-summer measurements of xylem anatomy and native embolism in olive cultivars with high (Cellina di Nardò) and low susceptibility (Leccino) to the infection by X. fastidiosa. Both cultivars had similar shoot mass traits and vessel length (~80 cm), but the highly susceptible one had larger vessels and a lower number of vessels supplying a given leaf mass. Native air embolism reduced mean xylem hydraulic conductance by ~58 % (Cellina di Nardò) and ~38 % (Leccino). The higher air-embolism vulnerability of the larger vessels in Cellina di Nardò possibly facilitates the X. fastidiosa’s infection compared to Leccino. Some important characteristics of the vector–pathogen–plant interactions still require deep investigations acknowledging both the pathogen metabolic pathways and the biophysical principles of xylem hydraulics.
3DBionotes COVID-19 edition
Authors: Macias Jose Ramon , Sanchez-Garcia Ruben , Conesa Pablo , Ramirez-Aportela Erney , Martinez Gonzalez Marta , Wert-Carvajal Carlos , Parra-Perez Alberto M , Segura Mora Joan , Horrell Sam , Thorn Andrea , Sorzano Carlos O S , Carazo Jose Maria 
Published: May 2021

Abstract

Summary
The web platform 3DBionotes-WS integrates multiple web services and an interactive web viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic electron microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context, we have developed 3DBionotes-COVID-19 as an answer to: (i) the need to explore multiomics data in a unified context with a special focus on structural information and (ii) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryo-EM.

Availability and implementation
https://3dbionotes.cnb.csic.es/ws/covid19.

Supplementary information
Supplementary data are available at Bioinformatics online.
Loss of Mafb and Maf distorts myeloid cell ratios and disrupts fetal mouse testis vascularization and organogenesis†
Authors: Li Shu-Yun , Gu Xiaowei , Heinrich Anna , Hurley Emily G , Capel Blanche , DeFalco Tony 
Published: May 2021

Abstract
Testis differentiation is initiated when Sry in pre-Sertoli cells directs the gonad toward a male-specific fate. Sertoli cells are essential for testis development, but cell types within the interstitial compartment, such as immune and endothelial cells, are also critical for organ formation. Our previous work implicated macrophages in fetal testis morphogenesis, but little is known about genes underlying immune cell development during organogenesis. Here, we examine the role of the immune-associated genes Mafb and Maf in mouse fetal gonad development, and we demonstrate that deletion of these genes leads to aberrant hematopoiesis manifested by supernumerary gonadal monocytes. Mafb; Maf double knockout embryos underwent initial gonadal sex determination normally, but exhibited testicular hypervascularization, testis cord formation defects, Leydig cell deficit, and a reduced number of germ cells. In general, Mafb and Maf alone were dispensable for gonad development; however, when both genes were deleted, we observed significant defects in testicular morphogenesis, indicating that Mafb and Maf work redundantly during testis differentiation. These results demonstrate previously unappreciated roles for Mafb and Maf in immune and vascular development and highlight the importance of interstitial cells in gonadal differentiation.
The tree of participation: a new model for inclusive decision-making
Authors: Bell Karen , Reed Mark 
Published: May 2021

Abstract
Community development often involves organizing participatory decision-making processes. The challenge is for this to be meaningful. Participatory decision-making has the potential to increase the transparency, accountability, equity and efficiency with which public administration serves the least privileged in society. However, in practice, it often fails to bring about these outcomes. A number of academics and practitioners have, therefore, theorized how participatory decision-making processes can better empower marginalized groups. By critically reviewing this body of work and empirically grounding the debate in recent practice, we aimed to develop a theoretically rigorous, easily applicable and holistic model of an inclusive participatory decision-making process that can work across a range of contexts. The empirical strand included surveying public engagement practitioners and participants about the participatory events they had organized or attended. These empirical findings were combined with insights from the theoretical literature to devise a new conceptual model of emancipatory, inclusive and empowering participatory decision-making – the ‘Tree of Participation’. The model can be useful to both organizers of participatory processes, as a check for empowering and inclusive practice, and to disadvantaged groups, as a set of expectations and demands when engaging in public decision-making.
Micro grid for All India Institute of Medical Sciences, Madurai
Authors: Palanichamy C , Naveen P 
Published: May 2021

Abstract
In 2018, the Government of India approved the establishment of the New All India Institute of Medical Sciences (AIIMS) in Thoppur, Madurai, Tamil Nadu, India. As the most important amenity for continuing primary care and rescue response is a healthcare facility, a secure electricity supply becomes an imperative necessity. Hence, as the energy supplier for the new AIIMS, Madurai, this paper proposes a microgrid combined with the utility grid. The microgrid consists of a 4-MW photovoltaic system, a 1.8-MW wind-turbine energy-conversion system, a backup diesel generator capable of meeting the forecasted maximum demand and a 1-MW battery energy-storage system. The AIIMS Microgrid will have a service providing a capacity of 20 MVA following integration with the utility grid. The proposed microgrid would be the first attempt at healthcare facilities in India since its first day of work to ensure the availability of electricity. It would have a 9.8% return on investment, a 13.6% internal rate of return and a payback period of 6.75 years once it is operational, as well as an attractive levelized cost of energy (LCOE) of USD 0.07547/kWh. It would provide an environmentally friendly atmosphere by avoiding an annual emission of 6 261 132 kg of carbon dioxide, 27 362 kg of sulphur dioxide and 12 838 kg of nitrogen oxides as compared to power supplied entirely from the utility grid.
Simultaneous Determination of Five Coumarins in Peucedanum Decursivum Radix by UPLC
Authors: Ma Sinan , Li Qian , Feng Yanmei , Chen Yuying , Yu Ping , Ding Xiaoqin 
Published: May 2021

Abstract

Objective
To establish an ultra-high performance liquid chromatography (UPLC) method for simultaneous determination of umbelliferonel, nodakenin, psoralen, xanthotoxin and bergapten contents in Peucedanum decursivum Radix.

Methods
The analysis was achieved on a Symmetry®C18 column (4.6 mm × 250 mm, 5 μm), with acetonitrile and water as the mobile phase in gradient elution mode. The column temperature was maintained at 30°C, with flow rate 1.0 mL·min−1. The injection volume of sample was 10 μL. The ultraviolet detection wavelength was set at the maximum absorption wavelength 325 nm for umbelliferonel and nodakenin, 259 nm for psoralen, xanthotoxin and bergapten, respectively.

Results
The five kinds of coumarins in Peucedanum decursivum Radix were separated well and the linear relation was obtained (R2 ≥ 0.9998). The average recoveries were 101.31, 105.27, 90.85, 106.42 and 90.19%, respectively, with Relative standard deviation (RSD) 3.07, 3.17, 1.62, 2.53 and 4.54%, respectively.

Conclusions
The established method was accurate and feasible, which could be used as the basis of quality control of Peucedanum decursivum Radix.
How Does the Application ofBeauveria bassianaand Compost on Corn Crops Affect the Survival and Genetic Diversity ofPhyllophaga obsoleta(Coleoptera: Melolonthinae)?
Authors: Dávila-Orozco Guillermo , Cruz-Salazar Bárbara , Ruiz-Montoya Lorena 
Published: May 2021

AbstractThe knowledge of the diversity and genetic structure of pest insects under management contributes to the improvement of control strategies. An experiment was run to investigate whether the addition of the fungus Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Cordycipitaceae) (BB) and compost to soil affects the presence and genetic diversity of adults and larvae of Phyllophaga obsoleta Blanch (Coleoptera: Melolonthinae) larvae in maize crops. We collected adults in and used mating pairs under four treatments (BB, compost, soil, blank). Genetic diversity and structure were determined through five allo/iso-enzymatic loci. Beauveria bassiana affected the presence and mortality of P. obsoleta in the laboratory but not under field conditions. The genetic diversity of P. obsoleta ranged from moderate to high (Ho = 0.26–0.31), with a low genetic differentiation among localities or treatments (Phi &lt; 0.05), indicating high levels of gene flow. Our results showed a weak effect of B. bassiana on P. obsoleta in the field. Still, our laboratory observations suggest that the fungus may be a suitable alternative for biological control.
Direct comparison of high-sensitivity cardiac troponin T and I in the early differentiation of type 1 vs. type 2 myocardial infarction
Authors: Nestelberger Thomas , Boeddinghaus Jasper , Giménez Maria Rubini , Lopez-Ayala Pedro , Ratmann Paul David , Badertscher Patrick , Wildi Karin , Wussler Desiree , Koechlin Luca , Arslani Ketina , Zimmermann Tobias , Freese Michael , Rinderknecht Therese , Miró Òscar , Martin-Sanchez F Javier , Kawecki Damian , Geigy Nicolas , Keller Dagmar , Twerenbold Raphael , Müller Christian ,   for the APACE investigators
Published: May 2021

Abstract

Aims
To directly compare the diagnostic accuracy of high-sensitivity cardiac troponin (hs-cTn) T vs. hs-cTnI in the early non-invasive differentiation of Type 1 myocardial infarction (T1MI) due to plaque rupture and atherothrombosis from Type 2 myocardial infarction (T2MI) due to supply–demand mismatch.

Methods and results
In a prospective multicentre diagnostic study, two independent cardiologists centrally adjudicated the final diagnosis of T1MI vs. T2MI according to the fourth universal definition of myocardial infarction (MI), using all available clinical information including cardiac imaging in patients presenting with acute chest pain. Diagnostic accuracy was quantified by the area under the receiver operating characteristics curve (AUC). The most extensively validated hs-cTnT-Elecsys and hs-cTnI-Architect assays were measured at presentation, 1 h, and 2 h. Among 5887 patients, 1106 (19%) had a final diagnosis of MI, including 860 (78%) T1MI and 246 (22%) T2MI. The AUC of hs-cTnT-Elecsys to differentiate T1MI from T2MI was moderate and comparable to that provided by hs-cTnI-Architect: hs-cTnT-Elecsys AUC-presentation 0.67 [95% confidence interval (CI) 0.64–0.71], AUC-1 h 0.70 (95% CI 0.66–0.74), and AUC-2 h 0.71 (95% CI 0.66–0.75) vs. hs-cTnI-Architect AUC-presentation 0.71 (95% CI 0.67–0.74), AUC-1 h 0.72 (95% CI 0.68–0.76), and AUC-2 h 0.74 (95% CI 0.69–0.78), all P = not significant (NS). Similarly, the AUC of absolute changes was moderate and comparable for hs-cTnT-Elecsys and hs-cTnI-Architect (all P = NS). Cut-off concentrations achieving at least 90% specificity for the differentiation of T1MI vs. T2MI were &gt;114 ng/L for hs-cTnT-Elecsys [odds ratio (OR) 4.2, 95% CI 2.7–6.6] and &gt;371 ng/L for hs-cTnI-Architect (OR 4.0, 95% CI 2.6–6.2).

Conclusion
hs-cTnT-Elecsys and hs-cTnI-Architect provided comparable, albeit only moderate, diagnostic accuracy for the early differentiation of T1MI vs. T2MI.

Clinical trial registration
ClinicalTrials.gov number, NCT00470587, https://clinicaltrials.gov/ct2/show/NCT00470587.
Right ventricle assessment in patients with pulmonary embolism at low risk for death based on clinical models: an individual patient data meta-analysis
Authors: Becattini Cecilia , Maraziti Giorgio , Vinson David R , Ng Austin C C , den Exter Paul L , Côté Benoit , Vanni Simone , Doukky Rami , Khemasuwan Danai , Weekes Anthony J , Soares Thiago Horta , Ozsu Savas , Polo Friz Hernan , Erol Serhat , Agnelli Giancarlo , Jiménez David 
Published: May 2021

AbstractAims Patients with acute pulmonary embolism (PE) at low risk for short-term death are candidates for home treatment or short-hospital stay. We aimed at determining whether the assessment of right ventricle dysfunction (RVD) or elevated troponin improves identification of low-risk patients over clinical models alone.Methods and results Individual patient data meta-analysis of studies assessing the relationship between RVD or elevated troponin and short-term mortality in patients with acute PE at low risk for death based on clinical models (Pulmonary Embolism Severity Index, simplified Pulmonary Embolism Severity Index or Hestia). The primary study outcome was short-term death defined as death occurring in hospital or within 30 days. Individual data of 5010 low-risk patients from 18 studies were pooled. Short-term mortality was 0.7% [95% confidence interval (CI) 0.4–1.3]. RVD at echocardiography, computed tomography or B-type natriuretic peptide (BNP)/N-terminal pro BNP (NT-proBNP) was associated with increased risk for short-term death (1.5 vs. 0.3%; OR 4.81, 95% CI 1.98–11.68), death within 3 months (1.6 vs. 0.4%; OR 4.03, 95% CI 2.01–8.08), and PE-related death (1.1 vs. 0.04%; OR 22.9, 95% CI 2.89–181). Elevated troponin was associated with short-term death (OR 2.78, 95% CI 1.06–7.26) and death within 3 months (OR 3.68, 95% CI 1.75–7.74).Conclusion  RVD assessed by echocardiography, computed tomography, or elevated BNP/NT-proBNP levels and increased troponin are associated with short-term death in patients with acute PE at low risk based on clinical models. RVD assessment, mainly by BNP/NT-proBNP or echocardiography, should be considered to improve identification of low-risk patients that may be candidates for outpatient management or short hospital stay.
Identification of the MuRF1 Skeletal Muscle Ubiquitylome Through Quantitative Proteomics
Authors: Baehr Leslie M , Hughes David C , Lynch Sarah A , Van Haver Delphi , Maia Teresa Mendes , Marshall Andrea G , Radoshevich Lilliana , Impens Francis , Waddell David S , Bodine Sue C 
Published: May 2021

Abstract
MuRF1 (TRIM63) is a muscle-specific E3 ubiquitin ligase and component of the ubiquitin proteasome system. MuRF1 is transcriptionally upregulated under conditions that cause muscle loss, in both rodents and humans, and is a recognized marker of muscle atrophy. In this study, we used in vivo electroporation to determine whether MuRF1 overexpression alone can cause muscle atrophy and, in combination with ubiquitin proteomics, identify the endogenous MuRF1 substrates in skeletal muscle. Overexpression of MuRF1 in adult mice increases ubiquitination of myofibrillar and sarcoplasmic proteins, increases expression of genes associated with neuromuscular junction instability, and causes muscle atrophy. A total of 169 ubiquitination sites on 56 proteins were found to be regulated by MuRF1. MuRF1-mediated ubiquitination targeted both thick and thin filament contractile proteins, as well as, glycolytic enzymes, deubiquitinases, p62, and VCP. These data reveal a potential role for MuRF1 in not only the breakdown of the sarcomere but also the regulation of metabolism and other proteolytic pathways in skeletal muscle.
Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas
Authors: Wu Weisheng , Lovett Jennie L , Shedden Kerby , Strassmann Beverly I , Vincenz Claudius 
Published: May 2021

AbstractGenomic imprinting is an epigenetic mechanism that results in allele-specific expression (ASE) based on the parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze imprinted genes using reciprocal crosses in mice to generate large numbers of informative SNPs. Studies in humans are more challenging due to the paucity of SNPs and the poor preservation of RNA in term placentas and other tissues. Targeted RNA-seq (tar-RNAseq) can potentially mitigate these challenges by focusing sequencing resources on the regions of interest in the transcriptome. Here, we compared tar-RNAseq and wht-RNAseq in a study of ASE in known imprinted genes in placental tissue collected from a healthy human cohort in Mali, West Africa. As expected, tar-RNAseq substantially improved the coverage of SNPs. Compared to wht-RNAseq, tar-RNAseq produced on average four times more SNPs in twice as many genes per sample and read depth at the SNPs increased fourfold. In previous research on humans, discordant ASE values for SNPs of the same gene have limited the ability to accurately quantify ASE. We show that tar-RNAseq reduces this limitation as it unexpectedly increased the concordance of ASE between SNPs of the same gene, even in cases of degraded RNA. Studies aimed at discovering associations between individual variation in ASE and phenotypes in mammals and flowering plants will benefit from the improved power and accuracy of tar-RNAseq.
An 11-gene signature for the prediction of systemic recurrences in colon adenocarcinoma
Authors: Cai Jia-Wei , Huang Xiao-Ming , Li Xiao-Lan , Qin Si , Rong Yu-Ming , Chen Xi , Weng Jing-Rong , Zou Yi-Feng , Lin Xu-Tao 
Published: May 2021

AbstractBackgroundPrognosis varies among patients within the same colon adenocarcinoma (COAD) stage, indicating the need for reliable molecular markers to enable individualized treatment. This study aimed to investigate gene signatures that can be used for better prognostic prediction of COAD.MethodsGene-expression profiles of COAD patients were obtained from the Gene Expression Omnibus database (n = 332) and The Cancer Genome Atlas database (n = 431). The relationship between gene signature and relapse-free survival was analysed in the training set (n = 93) and validated in the internal validation set (n = 94) and external validation sets (n = 145 and 431).ResultsOverall, 11 genes (N-myc downstream regulated gene 1 [NDRG1], fms-like tyrosine kinase 1 [FLT1], lipopolysaccharide binding protein [LBP], fatty acid binding protein 4 [FABP4], adiponectin gene [ADIPOQ], angiotensinogen gene [AGT], activin A receptor, type II-like kinase 1 [ACVRL1], CC chemokine ligand 11 [CCL11], cell division cycle 42 [CDC42], T-cell receptor alpha variable 9_2 [TRAV9_2], and proopiomelanocortin [POMC]) were identified by univariable and least absolute shrinkage and selection operator (LASSO) Cox regression analyses. Based on the risk-score model, the patients were grouped into the high-risk or low-risk groups using the median risk score as the cut-off. The area under the curve (AUC) values for 1-, 3-, and 5-year recurrence were 0.970, 0.849, and 0.859, respectively. Patients in the high-risk group had significantly poorer relapse-free survival than did those in the low-risk group. The predictive accuracy of the 11-gene signature was proven in the validation sets. Our gene signature showed better predictive performance for 1-, 3-, and 5-year recurrence than did the other four models.ConclusionsThe 11-gene signature showed good performance in predicting recurrence in COAD. The accuracy of the signature for prognostic classification requires further confirmation.
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae)
Authors: Yan Bin , Ou Houding , Wei Lan , Wang Xiuqin , Yu Xiaofei , Liu Jianfeng , Yang Maofa 
Published: May 2021

Abstract
The moth Ephestia elutella (Hübner), is a storage pest that feeds on tobacco, cacao beans, cereals, dried fruits, and nuts. We generated a chromosome-level genome assembly containing 576.94 Mb using Nanopore long reads (approximately 130×) and Hi-C data (approximately 134×). The final assembly contained 804 scaffolds, with an N50 length of 19.00 Mb, and 94.96% (547.89 Mb) of the assembly was anchored into 31 pseudochromosomes. We masked 58.12% (335.32 Mb) of the genome as repetitive elements, identified 727 noncoding RNAs, and predicted 15,637 protein-coding genes. Gene family evolution and functional enrichment analyses revealed significantly expanded gene families primarily involved in digestion, detoxification, and chemosensation. Strong chromosomal syntenic relationships were also observed among E. elutella, silkworm, and tobacco cutworm. This study could provide a valuable genomic basis for better understanding the biology of E. elutella.