bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of Life in elderly ICU survivors: A Rapid Systematic Review and Meta-Analysis of Cohort Studies
Authors: Ariyo Kevin , Canestrini Sergio , David Anthony S. , Keene Alex Ruck , Owen Gareth S. 
Published: August 2020

ABSTRACTBACKGROUNDThe influence of age upon intensive care unit (ICU) decision-making is complex and it is unclear if it is based on expected subjective or objective patient outcomes. To address recent concerns over age-based ICU decision-making we explored patient-assessed quality of life (QoL) in ICU survivors.METHODSWe conducted a rapid database search of cohort studies published between January 2000 to April 2020, of elderly patients admitted to ICUs. We extracted data on self-reported QoL (EQ-5D composite score), study characteristics and demographic and clinical variables. Using a random-effects model, we then compared QoL scores at follow-up to scores either before admission, age-matched population controls or younger ICU survivors. Finally, we conducted follow-up quantitative analyses to explore potential moderators of these effects, and a qualitative synthesis of QoL subscores. A study protocol was registered prospectively on PROSPERO, ID: CRD42020181181.FINDINGSOur database search found 2536 studies and from these we reviewed 376 potentially relevant full texts. 21 of these studies met the inclusion criteria for qualitative synthesis and 18 were also included in the meta-analysis (N= 2090 elderly adults). The follow-up periods ranged between 3-100 months. There was no significant difference in the elderly’s QoL scores between one month before ICU and follow-up, or between follow-up and age-matched community controls. QoL in elderly ICU survivors was significantly worse than younger ICU survivors, with a small-to-medium effect size (d= .33 [.10 to .55]). Mortality rates and length of follow up were possible intermediary factors. The qualitative synthesis suggested that any reductions in QoL were primarily due to reductions in physical health, rather than mental health items.INTERPRETATIONOverall, elderly ICU patients did not experience significantly impaired QoL at follow up, compared to before ICU or their healthy peers. Elderly patients who survive ICU can be expected to have slightly worse QoL compared to younger patients, especially in the longterm. The results suggest that the proportionality of age as a determinant of (population level) ICU resource allocation should be kept under close review and that subjective QoL outcomes (not only objective survival data) should inform person-centred decision making in elderly ICU patients.DECLARATIONS OF INTERESTAlex Ruck Keene is an adviser on the Faculty of Intensive Care Medicine’s Legal and Ethical Policy Unit. We report no other competing interests.
Proteomic signatures of perioperative oxygen delivery in skin after major surgery
Authors: Ackland Gareth L. , Bliss Emily , Bahelil Fatima , Cyrus Trinda , Crescente Marilena , Jones Timothy , Iqbal Sadaf , Paredes Laura Gallego , Toner Andrew J. , Arroyo Ana Gutierrez del , Heywood Wendy E. , O’Toole Edel A. , Mills Kevin 
Published: August 2020

AbstractObjectiveMaintaining adequate oxygen delivery after major surgery is associated with minimizing organ dysfunction, although the precise molecular mechanisms remain unclear.BackgroundSkin, the largest organ in the body, is vulnerable to reduced oxygen delivery. We hypothesized that the skin proteome, assessed before and after surgery, would reveal molecular differences in patients randomized to receive cardiovascular therapy aimed at maintaining preoperative oxygen delivery (DO2).MethodsAbdominal punch skin biopsies were snap frozen or fixed in paraformaldehyde immediately before and 48h after elective esophageal or liver resection. Immediately after surgery, patients were randomized to standard of care or therapy to maintain preoperative DO2. On-line two-dimensional liquid chromatography, followed by ultra-high definition label-free mass spectrometry analysis, and/or immunoblots quantified significant proteomic changes. Selected proteins identified by mass spectrometry were confirmed by immunohistochemistry and immunoblot. In a murine hepatic resection model, confirmation of specific proteomic signatures identified in patients was sought by immunoblotting.ResultsPaired biopsies were analyzed from 35 patients (mean age:68±9y; 31% female). We identified 2096 proteins, of which 157 were differentially expressed after surgery. Similar results for selected proteins were found using immunohistochemistry (n=6 patients), immunoblots (n=12 patients) and murine abdominal skin obtained after liver resection (n=14). After surgery, 14 proteins distinguished esophagectomy patients with normal (n=10) versus low (n=7) DO2.values. Failure to maintain preoperative DO2 was associated with upregulation of proteins counteracting oxidative stress and.ConclusionsSerial skin biopsies afford mechanistic insight into end-organ injury by quantifying proteomic changes associated with impaired oxygen delivery during high-risk surgery.Trial registrationISRCTN76894700FundingAcademy of Medical Sciences/Health Foundation Clinician Scientist Award [GLA]; British Oxygen Company research chair grant in Anesthesia [GLA]; Great Ormond Street Hospital Biomedical Research Centre [EB,WH,KM]; British Heart Foundation:PG/17/40/33028 [MC]; UK NIHR [GLA]; Barts Charity [TJ]Mini-AbstractSkin, one of the largest organs in the body, is vulnerable to reduced oxygen delivery. Proteomic analysis of skin biopsies obtained before and after surgery show distinct metabolic and inflammatory changes related to perioperative oxygen delivery. Mirrored by complementary laboratory data in mice, skin proteomics reveal new insights into perioperative organ dysfunction.
Twitter Interaction to Analyze Covid-19 Impact in Ghana, Africa from March to July
Authors: Chire Saire Josimar E. , Panford-Quainoo Kobby 
Published: August 2020

AbstractPresent pandemic generated by Coronavirus Covid-19 has stopped the world, from Tourism, Business, Education and more. Actually, there are reported cases in every continent from America to Europe, from Europe to Australia. Africa is one continent in process of development with a variety of languages, limitations/problems and of course, abundance of culture. The aim of this paper is to analyze the impact in one country located in the middle-west, named Ghana. The data source for the analysis is Twitter(Social Network) and the analysis is using a Text Mining approach. Besides, a composition of graphics are presented considering Google search, daily reported cases. The study is exploratory to know what topics are most frequent in Great Accra Region. The conclusions are: Twitter is useful to get data for the analysis, and the interest of user from Ghana was high at the beginning but it was decreasing from April until July, probably the people is tired or adapting themselves to the actual situation.
SARS-CoV-2 induces inflammasome-dependent pyroptosis and downmodulation of HLA-DR in human monocytes, which can be prevented by atazanavir
Authors: Ferreira André C. , Soares Vinicius Cardoso , de Azevedo-Quintanilha Isaclaudia G. , Dias Suelen da Silva Gomes , Fintelman-Rodrigues Natalia , Sacramento Carolina Q. , Mattos Mayara , de Freitas Caroline S. , Temerozo Jairo R. , Teixeira Lívia , Hottz Eugenio Damaceno , Barreto Ester A , Pão Camila R. R. , Palhinha Lohanna , Miranda Milene , Bou-Habib Dumith Chequer , Bozza Fernando A. , Bozza Patrícia T. , Souza Thiago Moreno L. 
Published: August 2020

AbstractInfection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been associated with leukopenia and uncontrolled inflammatory response in critically ill patients. A better comprehension of SARS-CoV-2-induced monocytes death is essential for the identification of therapies capable to control the hyper-inflammation and reduce viral replication in patients with COVID-19. Here, we show that SARS-CoV-2 induces inflammasome activation and cell death by pyroptosis in human monocytes, experimentally infected and in patients under intensive care. Pyroptosis was dependent on caspase-1 engagement, prior to IL-1ß production and inflammatory cell death. Monocytes exposed to SARS-CoV-2 downregulate HLA-DR, suggesting a potential limitation to orchestrate the immune response. Our results originally describe the mechanism by which monocytes, a central cellular component recruited from peripheral blood to respiratory tract, succumb in patients with severe 2019 coronavirus disease (COVID-19), and emphasize the need for identifying anti-inflammatory and antiviral strategies to prevent SARS-CoV-2-induced pyroptosis.
Racing against stomatal attenuation: rapid CO2response curves more reliably estimate photosynthetic capacity than steady state curves in a low conductance species
Authors: Vincent C , Pierre MO , Stinziano JR 
Published: August 2020

AbstractA/Cicurves are an important gas-exchange-based approach to understanding the regulation of photosynthesis, describing the response of net CO2assimilation (A) to leaf internal concentration of CO2(Ci). Low stomatal conductance species pose a challenge to the measurement ofA/Cicurves by reducing the signal-to-noise ratio of gas exchange measures. Additionally, the stomatal attenuation effect of elevated ambient CO2leads to further reduction of conductance and may lead to erroneous interpretation of highCiresponses ofA. RapidA/Ciresponse (RACiR) curves offer a potential practice to developA/Cicurves faster than the stomatal closure response to elevated CO2. We used the moderately low conductanceCitrusto compare traditional steady state (SS)A/Cicurves with RACiR curves. SS curves failed more often than RACiR curves. Overall parameter estimates were the same between SS and RACiR curves. When low stomatal conductance values were removed, triose-phosphate utilization (TPU) limitation estimates increased. Overall RACiR stomatal conductance values began and remained higher than SS values. Based on the comparable resulting parameter estimates, higher likelihood of success and reduced measurement time, we propose RACiR as a valuable tool to measureA/Ciresponses in low conductance species.
Genetic diversity analysis of Chinese plum (Prunus salicinaL.) based on whole-genome resequencing
Authors: Wei Xiao , Shen Fei , Zhang Qiuping , Liu Ning , Zhang Yuping , Xu Ming , Liu Shuo , Zhang Yujun , Ma Xiaoxue , Liu Weisheng 
Published: August 2020

AbstractChinese plum (Prunus salicinaL.), also known as Japanese plum, is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we construed high-density haplotype map by whole-genome resequencing of 67Prunusaccessions with a depth of ~20× to evaluate the genome-level diversity and population structure. The phylogenetic analysis, the principal component analysis, and the population structure profiling, indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China were clustered with the other three groups. The genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. The gene flow from the SCG to the FG was detected as well. We concluded that the origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided genetic variation features and population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants for improving Chinese plum varieties.
Nutri rich cattle feed (NuCa feed) supplement with improved fiber content free of anti-nutritional factor Phytic acid
Authors: Makam Shivakiran , Kolla Harish Babu , Golla Daya Mouni , Payal Ananya , Somarowthu Meghanath 
Published: August 2020

AbstractMost of the commercial ruminant feeds comprise Corn meal, Groundnut cake, Maize etc., which contain anti-nutritional factors called Phytates. They have high binding affinity to cationic minerals. This results in decrease in activity of the cattle by making minerals unavailable for absorption in the intestine. Many of the feed industries add Phytase enzyme that degrades the Phytic acid. Addition of Phytase enzyme is very complex method and increases the cost of the feed. If Phytase is not added, Phytic acid enters the ecosystem through the dung and due to microbial degradation, the Phytic acid gets converted into Phosphates. Phosphate abundance in water bodies leads to Eutrophication, which is a serious ecological issue. And also, in many parts of the country, post-harvest Paddy straw is burnt unused. This intentional stubble burning causes air pollution. We combined paddy straw and Azolla along with jaggery to prepare animal feed supplement. The feed pellets were evaluated for their nutritional composition and efficacy. The efficacy of the developed feed was evaluated by feeding it to milch cows and compared with regular feed for a period of 15 days. The Azolla-Hay feed improved the milk yield and also quality of the milk in comparison to the control group. This study revealed that Azolla in combination with paddy straw powder can be low-cost feed alternative especially during the lean period where the availability of feed is scarce.
Full-lengthde novoprotein structure determination from cryo-EM maps using deep learning
Authors: He Jiahua , Huang Sheng-You 
Published: August 2020

AbstractAdvances in microscopy instruments and image processing algorithms have led to an increasing number of cryo-EM maps. However, building accurate models for the EM maps at 3-5 Å resolution remains a challenging and time-consuming process. With the rapid growth of deposited EM maps, there is an increasing gap between the maps and reconstructed/modeled 3-dimensional (3D) structures. Therefore, automatic reconstruction of atomic-accuracy full-atom structures from EM maps is pressingly needed. Here, we present a semi-automaticde novostructure determination method using a deep learning-based framework, named as DeepMM, which builds atomic-accuracy all-atom models from cryo-EM maps at near-atomic resolution. In our method, the main-chain and Cα positions as well as their amino acid and secondary structure types are predicted in the EM map using Densely Connected Convolutional Networks. DeepMM was extensively validated on 40 simulated maps at 5 Å resolution and 30 experimental maps at 2.6-4.8 Å resolution as well as an EMDB-wide data set of 2931 experimental maps at 2.6-4.9 Å resolution, and compared with state-of-the-art algorithms including RosettaES, MAINMAST, and Phenix. Overall, our DeepMM algorithm obtained a significant improvement over existing methods in terms of both accuracy and coverage in building full-length protein structures on all test sets, demonstrating the efficacy and general applicability of DeepMM.Availabilityhttps://github.com/JiahuaHe/DeepMMSupplementary informationSupplementary data are available.
Dissection of PRC1 and PRC2 recruitment in Arabidopsis connects EAR repressome to PRC2 anchoring
Authors: Baile Fernando , Merini Wiam , Hidalgo Inés , Calonje Myriam 
Published: August 2020

AbstractPcG complexes ensure that every cell in an organism expresses the genes needed at a particular stage, time or condition. However, it is still not fully understood how PRC1 and PRC2 are recruited to target genes in plants. Recent results in Arabidopsis support that PRC2 recruitment is mediated by different TFs. However, it is unclear how all these TFs interact with PRC2 and whether they can also recruit PRC1 activity. Here, by using a system toin vivobind selected factors to a synthetic promoter lacking the complexity of PcG target promoters, we show that while VAL1 binding recapitulates PRC1 and PRC2 marking, the binding of other TFs only render PRC2 marking. Interestingly, all these TFs contain an EAR domain that acts as docking point for PRC2 and HDACs, connecting two different repressive mechanisms. Furthermore, we show that different TFs act synergistically in PRC2 anchoring to maintain a long-term repression.
Rest is Required to Learn an Appetitively-Reinforced Operant Task inDrosophila
Authors: Wiggin Timothy D. , Hsiao Yung-Yi , Liu Jeffrey B. , Huber Robert , Griffith Leslie C. 
Published: August 2020

ABSTRACTMaladaptive operant conditioning contributes to development of neuropsychiatric disorders. Candidate genes have been identified that contribute to this maladaptive plasticity, but the neural basis of operant conditioning in genetic model organisms remains poorly understood. The fruit flyDrosophila melanogasteris a versatile genetic model organism that readily forms operant associations with punishment stimuli. However, operant conditioning with a food reward has not been demonstrated in flies, limiting the types of neural circuits that can be studied. Here we present the first sucrose-reinforced operant conditioning paradigm for flies. In the paradigm, flies walk along a Y-shaped track with reward locations at the terminus of each hallway. When flies turn in the reinforced direction at the center of the track, sucrose is presented at the end of the hallway. Only flies that rest early in training learn the reward contingency normally. Flies rewarded independently of their behavior do not form a learned association but have the same amount of rest as trained flies, showing that rest is not driven by learning. Optogenetically-induced sleep does not promote learning, indicating that sleep itself is not sufficient for learning the operant task. We validated the sensitivity of this assay to detect the effect of genetic manipulations by testing the classic learning mutantdunce.Dunceflies are learning impaired in the Y-Track task, indicating a likely role for cAMP in the operant coincidence detector. This novel training paradigm will provide valuable insight into the molecular mechanisms of disease and the link between sleep and learning.
CyAnno: A semi-automated approach for cell type annotation of mass cytometry datasets
Authors: Kaushik Abhinav , Dunham Diane , He Ziyuan , Manohar Monali , Desai Manisha , Nadeau Kari C , Andorf Sandra 
Published: August 2020

AbstractFor immune system monitoring in large-scale studies at the single-cell resolution using CyTOF, (semi-)automated computational methods are applied for annotating live cells of mixed cell types. Here, we show that the live cell pool can be highly enriched with undefined heterogeneous cells, i.e. ‘ungated’ cells, and that current (semi-)automated approaches ignore their modeling resulting in misclassified annotations. Therefore, we introduce ‘CyAnno’, a novel semi-automated approach for deconvoluting the unlabeled cytometry dataset based on a machine learning framework utilizing manually gated training data that allows the integrative modeling of ‘gated’ cell types and the ‘ungated’ cells. By applying this framework on several CyTOF datasets, we demonstrated that including the ‘ungated’ cells can lead to a significant increase in the prediction accuracy of the ‘gated’ cell types. CyAnno can be used to identify even a single cell type, including rare cells, with higher efficacy than current state-of-the-art semi-automated approaches.
RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development
Authors: Ivanchenko Maria G. , Ozguc Olivia R. , Bollmann Stephanie R. , Fraser Valerie N. , Megraw Molly 
Published: August 2020

AbstractCyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (‘Ailsa Craig’) anddgttissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.
Glucose restriction drives spatial re-organization of mevalonate metabolism and liquid-crystalline lipid droplet biogenesis
Authors: Rogers Sean , Hariri Hanaa , Gui Long , Wood N. Ezgi , Speer Natalie , Nicastro Daniela , Henne W. Mike 
Published: August 2020

AbstractEukaryotes compartmentalize metabolic pathways into sub-cellular domains, but the role of inter-organelle contacts in organizing metabolic reactions remains poorly understood. Here, we show that in response to acute glucose restriction (AGR) yeast undergo metabolic remodeling of their mevalonate pathway that is spatially coordinated at nucleus-vacuole junctions (NVJs). The NVJ serves as a metabolic platform by selectively retaining HMG-CoA Reductases (HMGCRs), driving mevalonate pathway flux in an Upc2-dependent manner. AGR-induced HMGCR compartmentalization enhances mevalonate metabolism and sterol-ester biosynthesis that generates lipid droplets (LDs) with liquid-crystalline sub-architecture. Loss of NVJ-dependent HMGCR partitioning affects yeast growth, but can be bypassed by artificially multimerizing HMGCRs, indicating NVJ compartmentalization enhances mevalonate pathway flux by promoting HMGCR inter-enzyme associations. We propose a non-canonical mechanism regulating mevalonate metabolism via the spatial compartmentalization of rate-limiting HMGCR enzymes, and reveal that AGR creates LDs with remarkable phase transition properties.One Sentence SummarySpatial compartmentalization of HMG-CoA Reductases at ER-lysosome contacts modulates mevalonate pathway flux
Microtubule-independent movement of the fission yeast nucleus
Authors: Ashraf Sanju , Kelly David A. , Sawin Kenneth E. 
Published: August 2020

ABSTRACTMovement of the cell nucleus typically involves the cytoskeleton and either polymerization-based pushing forces or motor-based pulling forces. In fission yeastSchizosaccharomyces pombe, nuclear movement and positioning are thought to depend on microtubule polymerization-based pushing forces. Here we describe a novel, microtubule-independent, form of nuclear movement in fission yeast. Microtubule-independent nuclear movement is directed towards growing cell tips, and it is strongest when the nucleus is close to a growing cell tip, and weakest when the nucleus is far from that tip. Microtubule-independent nuclear movement requires actin cables but does not depend on actin polymerization-based pushing or myosin V-based pulling forces. Vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) Scs2 and Scs22, which are critical for endoplasmic reticulum-plasma membrane contact sites in fission yeast, are also required for microtubule-independent nuclear movement. We also find that in cells in which microtubule-based pushing forces are present, disruption of actin cables leads to increased fluctuations in interphase nuclear positioning and subsequent altered septation. Our results suggest two non-exclusive mechanisms for microtubule-independent nuclear movement, which may help illuminate aspects of nuclear positioning in other cells.