bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence, Predictors, and Adverse Outcomes of Extubation Failure in Young Children with Isolated Traumatic Brain Injury: A Prospective Observational Study
Authors: Hazarika Amarjyoti , Gupta Aakriti , Jain Kajal , Kajal Kamal 
Published: February 2020

Abstract
Background Mechanical ventilation is a life-saving mainstay of therapy in pediatric patients with isolated traumatic brain injury (iTBI). Because of the numerous complications and side effects associated with tracheal intubation, it is prudent to remove it as early as possible. Extubation failure and reintubation, however, are also associated with significant risks. Till date, there has been no comprehensive study on extubation failure in pediatric patients less than 5 years with iTBI.
Materials and Methods A prospective observational study was conducted in the trauma intensive care unit (TICU) of a tertiary care center. All the children with iTBI, aged 0 to 5 years, on mechanical ventilation for more than 24 hours, admitted to the TICU were included. Extubation failure was defined as the need for reintubation occurring within 24 hours of extubation. Only the first attempt at extubation was included in the analysis.
Results Pre-extubation paO2/FiO2 ratio < 310 mm Hg is a predictor for extubation failure. Mean base deficit postextubation were found to be 2 ± 0.9 and –0.2 ± 1 (p = 0.00) between success and failure groups, respectively. Similarly, postextubation systolic blood pressure was also high in the failure group than in the success group (113.8 ± 10.4 vs. 100.5 ± 7.4; p = 0.00).
Conclusions The incidence of first attempt extubation failure was 62.5%. Lower values of pre-extubation paO2/FiO2 ratio (ratio < 310 mm Hg) are a predictor for extubation failure. Developing predictive tools and optimizing extubation decisions lead to timely identification of patients at elevated risk of extubation failure.
Pre-expanded bipedicled visor flap: an ideal option for the reconstruction of upper and lower lip defects postburn in Asian males
Authors: Min Peiru , Li Jie , Brunetti Beniamino , Pu Zheming , Su Weijie , Xi Wenjing , Zhang Zheng , Salzillo Rosa , Feng Shaoqing , Zhang Yixin 
Published: February 2020

AbstractBackgroundReconstruction of upper and lower lip subunits is a complicated and elusive challenge. For patients affected by defects involving upper and lower lip subunits, a technique able to reconstruct both aesthetic units with matched colour, sufficient contours and similar texture would be ideal. In this study, we present our experience with upper and lower lip reconstruction using the pre-expanded bipedicled visor flap.MethodsFrom January 2014 to January 2017, 12 male patients presenting with defects of the upper and lower lip subunits were treated using this surgical technique. After a period of expansion of the scalp flap of over 6 months, the bipedicled visor flap was raised from both the parietal regions and rotated to resurface the defect. Delay and section of the pedicle were then performed.ResultsTwelve male patients with postburn scars aged 22 to 48 years (mean: 34 years) were successfully treated with no major complications. The donor site was closed primarily in all cases. Subsequent flap debulking and minor revisions were performed under local anaesthesia between 6 and 12 months postoperatively.ConclusionsThe pre-expanded bipedicled visor flap provides an effective and reliable option for upper and lower lip reconstruction with excellent colour and texture. It is feasible to achieve these results simultaneously from a single donor site by using a pre-expanded bipedicled visor flap.
Moho depth of the British Isles: a probabilistic perspective
Authors: Licciardi A , England R W , Piana Agostinetti N , Gallagher K 
Published: February 2020

SUMMARYWe present a new Moho depth model of the British Isles and surrounding areas from the most up-to-date compilation of Moho depth estimates obtained from refraction, reflection and receiver function data. We use a probabilistic, trans-dimensional and hierarchical approach for the surface reconstruction of Moho topography. This fully data-driven approach allows for adaptive parametrization, assessment of relative importance between different data-types and uncertainties quantification on the reconstructed surface. Our results confirm the first order features of the Moho topography obtained in previous work such as deeper Moho (29–36 km) in continental areas (e.g. Ireland and Great Britain) and shallower Moho (12–22 km) offshore (e.g. in the Atlantic Ocean, west of Ireland). Resolution is improved by including recent available data, especially around the Porcupine Basin, onshore Ireland and Great Britain. NE trending features in Moho topography are highlighted above the Rockall High (about 28 km) and the Rockall Trough (with a NE directed deepening from 12 to about 20 km). A perpendicular SE oriented feature (Moho depth 26–28 km) is located between the Orkney and the Shetland, extending further SW in the North Sea. Onshore, our results highlight the crustal thinning towards the N in Ireland and an E–W oriented transition between deep (34 km) and shallow (about 28 km) Moho in Scotland. Our probabilistic results are compared with previous models showing overall differences around ±2 km, within the posterior uncertainties calculated with our approach. Bigger differences are located where different data are used between models or in less constrained areas where posterior uncertainties are high.
Silicon influences the localization and expression ofPhytophthora sojaeeffectors in interaction with soybean
Authors: Rasoolizadeh Aliyeh , Santhanam Parthasarathy , Labbé Caroline , Shivaraj Sheelavanta Matha , Germain Hugo , Bélanger Richard R 
Published: February 2020

AbstractIn plant–pathogen interactions, expression and localization of effectors in the aqueous apoplastic region play a crucial role in the establishment or suppression of pathogen development. Silicon (Si) has been shown to protect plants in several host–pathogen interactions, but its mode of action remains a source of debate. Its deposition in the apoplastic area of plant cells suggests that it might interfere with receptor–effector recognition. In this study, soybean plants treated or not with Si were inoculated with Phytophthora sojae and differences in the ensuing infection process were assessed through different microscopy techniques, transcript analysis of effector and defense genes, and effector (Avr6) localization through immunolocalization and fluorescence labeling. In plants grown without Si, the results showed the rapid (4 d post-inoculation) host recognition by P. sojae through the development of haustorium-like bodies, followed by expression and release of effectors into the apoplastic region. In contrast, Si treatment resulted in limited pathogen development, and significantly lower expression and presence of Avr6 in the apoplastic region. Based on immunolocalization and quantification of Avr6 through fluorescence labeling, our results suggest that the presence of Si in the apoplast interferes with host recognition and/or limits receptor–effector interactions, which leads to an incompatible interaction.
Segmenting the Universe into dynamically coherent basins
Authors: Dupuy Alexandra , Courtois Hélène M , Libeskind Noam I , Guinet Daniel 
Published: February 2020

ABSTRACT
This paper explores in depth a watershed concept to partition the Universe, introduced in a previous Letter and applied to the Cosmicflows-3 observational data set. We present a series of tests conducted with cosmological dark matter simulations. In particular, we are interested in quantifying the evolution with redshift of large-scale structures when defined as segmented basins of attraction. This new dynamical definition in the field of measuring standard rulers demonstrates robustness since all basins show a density contrast δ above 1 (mean Universe density) independently of the simulation spatial resolution or the redshift. Another major finding is that density profiles of the basins show universality in slope. Consequently, there is a unique definition of what is a gravitational watershed at a large scale, which can be further used as a probe for cosmology studies.
Conceptual Aspects of Global Value Chains
Authors: Antràs Pol 
Published: February 2020

AbstractThis article offers an overview of some key conceptual aspects associated with the rise of global value chains (GVCs). It outlines a series of alternative interpretations and definitions of what the rise of GVCs entails, and it traces the implications of these alternative conceptualizations for the measurement of the phenomenon, as well as for elucidating the key determinants and implications of GVC participation, both at the country level and at the firm level. In the process, it offers some speculative thoughts about the future of GVCs in light of the advent of an array of new technologies.
Predicting and Visualizing STK11 Mutation in Lung Adenocarcinoma Histopathology Slides Using Deep Learning
Authors: Hong Runyu , Liu Wenke , Fenyö David 
Published: February 2020

AbstractStudies have shown that STK11 mutation plays a critical role in affecting the lung adenocarcinoma (LUAD) tumor immune environment. By training an Inception-Resnet-v2 deep convolutional neural network model, we were able to classify STK11-mutated and wild type LUAD tumor histopathology images with a promising accuracy (per slide AUROC=0.795). Dimensional reduction of the activation maps before the output layer of the test set images revealed that fewer immune cells were accumulated around cancer cells in STK11-mutation cases. Our study demonstrated that deep convolutional network model can automatically identify STK11 mutations based on histopathology slides and confirmed that the immune cell density was the main feature used by the model to distinguish STK11-mutated cases.
Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation
Authors: Choudry Fizzah A , Bagger Frederik Otzen , Macaulay Iain C , Farrow Samantha , Burden Frances , Kempster Carly , McKinney Harriet , Olsen Lars R , Huang Ni , Downes Kate , Voet Thierry , Uppal Rakesh , Martin John F , Mathur Anthony , Ouwehand Willem H , Laurenti Elisa , Teichmann Sarah A , Frontini Mattia 
Published: February 2020

AbstractIn the current understanding of adult bone marrow hematopoiesis, megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. Here, we use single cell RNA sequencing to characterize HSCs and MKs from human bone marrow, to investigate MK lineage commitment and maturation. We identify two MK primed HSC clusters exhibiting unique differentiation kinetics, at least one of which is used in steady state and stress thrombopoiesis. By analyzing transcriptional signatures we show that human bone marrow MKs originate from MK primed HSC subpopulations, supporting the notion that these display exclusive priming for MK differentiation. We show that transcriptional programs change with increasing MK ploidy, where genes upregulated in high ploidy states may have functional relevance in platelet production. Finally, we highlight the presence of a specific transcriptional signature in MKs from individuals with myocardial infarction, supporting the aberration of MK differentiation in this thrombotic state.
Stomatal density affects gas diffusion and CO2assimilation dynamics in Arabidopsis under fluctuating light
Authors: Sakoda Kazuma , Yamori Wataru , Shimada Tomoo , Sugano Shigeo S. , Hara-Nishimura Ikuko , Tanaka Yu 
Published: February 2020

AbstractStomatal density (SD) is closely associated with photosynthetic and growth characteristics in plants. In the field, light intensity can fluctuate drastically throughout a day. The objective of the present study is to examine how the change inSDaffects stomatal conductance (gs) and CO2assimilation rate (A) dynamics, biomass production, and water use under fluctuating light. Here, we compared the photosynthetic and growth characteristics under constant and fluctuating light among four lines ofArabidopsis thaliana(L.): a wild-type (WT), aSTOMAGEN/EPFL9-overexpressing line,STOMAGEN/EPFL9-silencing line, and anEPIDERMAL PATTERNING FACTOR 1knockout line (epf1). LowerSDresulted in faster response ofAowing to the faster response ofgsto fluctuating light and higher water use efficiency without decreasingA. HigherSDresulted in a faster response ofAbecause of the higher initialgs.epf1, with a moderate increase inSD, showed the larger carbon gain, attributable to the high capacity and fast response ofA, yielding higher biomass production than WT under fluctuating light. The present study suggests that higherSDcan be beneficial to improve biomass production in the plant under field conditions.
HOW TO MEASURE THE INFLUENCE OF LANDSCAPE ON POPULATION GENETIC STRUCTURE: DEVELOPING RESISTANCE SURFACES USING A PATTERN-ORIENTED MODELING APPROACH
Authors: Souza Kelly , Pinto-Ledezma Jesús N. , de Campos Telles Mariana Pires , Soares Thannya Nascimento , Chaves Lazaro José , Ruas Clarissa Bonafé Gaspar , Dobrovolski Ricardo , Diniz-Filho José Alexandre Felizola 
Published: February 2020

AbstractThere are several approaches to understand how a landscape, with its several components, affects the genetic population structure by imposing resistance to gene flow. Here we propose the creation of resistance surfaces using a Pattern-Oriented Modeling approach to explain genetic differentiation, estimated by pairwise FST, among “Baruzeiro” populations (Dipteryx alata), a tree species widely distributed in Brazilian Cerrado. To establish the resistance surface, we used land use layers from the area in which the 25 “Baruzeiro” populations were sampled, generating 10000 resistance surfaces. To establish the resistance surface, we used land use layers from the area in which the 25 “Baru” populations were sampled, generating 10000 resistance surfaces. We randomized the cost values for each landscape component between 0 and 100. We use these surfaces to calculate pairwise matrices of the effective resistance among populations. Mantel test revealed a correlation of pairwise FST with a geographical distance equal to r = 0.48 (P < 0.001), whereas the Mantel correlations between pairwise FST and the generated resistance matrices ranged between r = −0.2019 and r= 0.6736. Partial regression on distance matrices was used to select the resistance matrix that provided the highest correlation with pairwise FST, based on the AIC criterion. The selected models suggest that the areas with lower resistance are characterized as natural savanna habitats of different forms, mainly arboreal dense savannas. In contrast, roads, big rivers, and agricultural lands cause higher resistance to gene flow.
Genome-wide analysis ofEscherichia colifitness determinants in a cross-feeding mutualism withRhodopseudomonas palustris
Authors: LaSarre Breah , Deutschbauer Adam M. , Love Crystal E. , McKinlay James B. 
Published: February 2020

ABSTRACTMicrobial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairingEscherichia coliandRhodopseudomonas palustris, whereinE. coliprovides carbon toR. palustrisin the form of glucose fermentation products andR. palustrisfixes N2gas and provides nitrogen toE. coliin the form of NH4+. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search forE. coligenes that influence fitness during cooperative growth withR. palustris. RB-TnSeq revealed hundreds of genes that increased or decreasedE. colifitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. Additionally, we discovered unexpected purine cross-feeding fromR. palustristoE. coli, with coculture rescuing growth of anE. colipurine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictablea priori.IMPORTANCEMicrobial communities impact life on earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influencedEscherichia colifitness during cooperative growth with a mutualistic partner,Rhodospeudomonas palustris. Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen,E. colifitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.
Inactivating porcine coronavirus before nuclei acid isolation with the temperature higher than 56 °C damages its genome integrity seriously
Authors: Zhang Qingxin , Zhao Qingshun 
Published: February 2020

Abstract2019-Novel Coronavirus (2019-nCoV) is the pathogen of Corona Virus Disease 2019. Nucleic acid detection of 2019-nCoV is one of the key indicators for clinical diagnosis. However, the positive rate is only 30-50%. Currently, fluorescent quantitative RT-PCR technology is mainly used to detect 2019-nCoV. According to “The Laboratory Technical Guidelines for Detection 2019-nCoV (Fourth Edition)” issued by National Health and Commission of China and “The Experts’ Consensus on Nucleic Acid Detection of 2019-nCoV” released by Chinese Society of Laboratory Medicine, the human samples must be placed under 56°C or higher to inactivate the viruses in order to keep the inspectors from virus infection before the nucleic acids were isolated as the template of qRT-PCR. In this study, we demonstrated that the virus inactivation treatment disrupts its genome integrity seriously when using porcine epidemic diarrhea virus (vaccine), a kind of coronavirus, as a model. Our results showed that only 50.11% of the detectable viral templates left after the inactivation of 56 °C for 30 minutes and only 3.36% left after the inactivation of 92 °C for 5 minutes when the samples were preserved by Hank’s solution, one of an isotonic salt solutions currently suggested. However, the detectable templates of viral nucleic acids can be unchanged after the samples were incubated at 56 °C or higher if the samples were preserved with an optimized solution to protect the RNA from being disrupted. We therefore highly recommend to carry out systematic investigation on the impact of high temperature inactivation on the integrity of 2019-nCoV genome and develop a sample preservation solution to protect the detectable templates of 2019-nCoV nucleic acids from high temperature inactivation damage.
A stronger transcription regulatory circuit of HIV-1C drives the rapid establishment of latency with implications for the direct involvement of Tat
Authors: Chakraborty Sutanuka , Kabi Manisha , Ranga Udaykumar 
Published: February 2020

AbstractThe magnitude of transcription factor binding site variation emerging in HIV-1C, especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong LTR? We constructed panels of sub-genomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. We found surprisingly that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.ImportanceOver the past 10-15 years, HIV-1C has been evolving rapidly towards gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive for HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and a concomitant strong, positive transcriptional feedback is the primary question we attempted to address in the present manuscript. The role Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype C (HIV-1C) offers crucial leads towards Tat possessing a dual-role in serving both as transcriptional activator and repressor at different phases of the viral infection of the cell. The leads we offer through the present work have significant implications for HIV-1 cure research.