bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic identity best explains variation in body nutrient stoichiometry in a diverse marine animal community
Authors: Allgeier Jacob E. , Wenger Seth , Layman Craig A. 
Published: August 2020

AbstractAnimal-mediated nutrient dynamics are critical processes in ecosystems. Previous research has found animal-mediated nutrient supply (excretion) to be highly predictable based on allometric scaling, but similar efforts to find universal predictive relationships for an organism’s body nutrient content have been inconclusive. We use a large dataset from a diverse tropical marine community to test three frameworks for predicting body nutrient content. We show that body nutrient content does not follow allometric scaling laws and that it is not well explained by trophic status. Instead, we find strong support for taxonomic identity (particularly at the family level) as a predictor of body nutrient content, indicating that evolutionary history plays a crucial role in determining an organism’s composition. We further find that nutrients are “stoichiometrically linked” (e.g., %C predicts %N), but that the direction of these relationships does not always conform to expectations, especially for invertebrates. Our findings demonstrate that taxonomic identity, not trophic status or body size, is the best baseline from which to predict organismal body nutrient content.
Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba
Authors: Zhou Xian , Liao Yongling , Kim Soo-Un , Chen Zexiong , Nie Gongping , Cheng Shuiyuan , Ye Jiabao , Xu Feng 
Published: August 2020

AbstractBasic helix–loop–helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In recent years, many bHLH family genes have been identified and characterized in woody plants. However, a systematic analysis of thebHLHgene family has not been reported inGinkgo biloba, the oldest relic plant species. In this study, we identifed a total of 85GbbHLHgenes from the genomic and transcriptomic databasesof G. biloba, which were classified into 17 subfamilies based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon–intron range inGbbHLHsfrom 0 to 12. The MEME analysis showed that two conserved motifs, motif 1 and motif 2, distributed in most GbbHLH protein. Subcellular localization analysis exhibited that most GbbHLHs located in nucleus and a few GbbHLHs were distributed in chloroplast, plasma membrane and peroxisome. Promotercis-elementanalysis revealed that most of theGbbHLHgenes contained abundantcis-elementsthat involved in plant growth and development, secondary metabolism biosynthesis, various abiotic stresses response. In addition, correlation analysis between gene expression and flavonoid content screened seven candidateGbbHLHgenes involved in flavonoid biosynthesis, providing the targeted gene encoding transcript factor for increase the flavonoid production through genetic engineering inG. biloba.
Toxic metabolite profiling of Inocybe virosa
Authors: Sai Latha S. , Shivanna Naveen , Naika Mahadeva , Anilakumar K. R. , Kaul Ankur , Mittal Gaurav 
Published: August 2020

AbstractWild mushroom foraging involves a high risk of unintentional consumption of poisonous mushrooms which is a serious health concern. This problem arises due to the close morphological resemblances of toxic mushrooms with edible ones. The genus Inocybe comprises both edible and poisonous species and it is therefore important to differentiate them. Knowledge about their chemical nature will unambiguously determine their edibility and aid in an effective treatment in case of poisonings. In the present study, the presence of volatile toxic metabolites was verified in Inocybe virosa by gas chromatography. Methyl palmitate, phenol, 3,5-bis (1,1-dimethyl ethyl) and phytol were the identified compounds with suspected toxicity. The presence of the toxin muscarine was confirmed by liquid chromatography. The in vitro study showed that there was negligible effect of the digestion process on muscarine content or its toxicity. Therefore, the role of muscarine in the toxicity of Inocybe virosa was studied using a bioassay wherein metameters such as hypersalivation, immobility, excessive defecation, heart rate and micturition were measured. Administration of muscarine resulted in an earlier onset of symptoms and the extract showed a slightly stronger muscarinic effect in comparison to an equivalent dose of muscarine estimated in it. Further, the biological fate of muscarine was studied by pharmacokinetics and gamma scintigraphy in New Zealand white rabbits. Significant amount of the toxin was rapidly and effectively concentrated in the thorax and head region. This study closely explains the early muscarinic response such as miosis and salivation in mice. By the end of 24 h, a relatively major proportion of muscarine administered was accumulated in the liver which stands as an explanation to the hepatotoxicity of Inocybe virosa. This is one of the rare studies that has attempted to understand the toxic potential of muscarine which has previously been explored extensively for its pharmaceutical applications.
Switching behaviour of dSTORM dyes in glycerol-containing buffer
Authors: Goossen-Schmidt Nora C. , Schnieder Marco , Hüve Jana , Klingauf Jürgen 
Published: August 2020

AbstractTo suppress optical aberrations caused by refractive index mismatch, we employ glycerol-immersion objectives in conjunction with fused silica cover glasses and imaging buffers with a high glycerol content. Here we demonstrate that the addition of glycerol to the buffer does not degrade the switching behaviour of the dyes Alexa Fluor 647 and Alexa Fluor 568 in dSTORM measurements, which shows that this approach is suitable for dSTORM. Additionally, we report evidence that sealed sample geometries as used in our experiments reduce photobleaching due to the lower influx of oxygen into the imaging buffer.
Unprecedented enhancement of recombinant protein production in sugarcane culms using a combinatorial promoter stacking system
Authors: Damaj Mona B. , Jifon John L. , Woodard Susan L. , Vargas-Bautista Carol , Barros Georgia O. F. , Molina Joe , White Steven G. , Damaj Bassam B. , Nikolov Zivko L. , Mandadi Kranthi K. 
Published: August 2020

AbstractPlants represent a safe and cost-effective platform for producing high-value proteins with pharmaceutical properties; however, the ability to accumulate these in commercially viable quantities is challenging. Ideal crops to serve as biofactories would include low-input, fast-growing, high-biomass species such as sugarcane. The objective of this study was to develop an efficient expression system to enable large-scale production of high-value recombinant proteins in sugarcane culms. Bovine lysozyme (BvLz) is a potent broad-spectrum antimicrobial enzyme used in the food, cosmetics and agricultural industries. Here, we report a novel strategy to achieve high-level expression of recombinant proteins using a combinatorial stacked promoter system. We demonstrate this by co-expressing BvLz under the control of multiple constitutive and culm-regulated promoters on separate expression vectors and combinatorial plant transformation. BvLz accumulation reached 1.4% of total soluble protein (TSP) (10.0 mg BvLz/kg culm mass) in stacked multiple promoter:BvLz lines, compared to 0.07% of TSP (0.56 mg/kg) in single promoter:BvLz lines. BvLz accumulation was further boosted to 11.5% of TSP (82.5 mg/kg) through event stacking by re-transforming the stacked promoter:BvLz lines with additional BvLz expression vectors. The protein accumulation achieved with the combinatorial promoter stacking expression system was stable in multiple vegetative propagations, demonstrating the feasibility of using sugarcane as a biofactory for producing high-value proteins and bioproducts.
Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia
Authors: Telpoukhovskaia Maria A. , Liu Kai , Sayed Faten A. , Etchegaray Jon Iker , Xie Min , Zhan Lihong , Li Yaqiao , Zhou Yungui , Le David , Bahr Ben A. , Bogyo Matthew , Ding Sheng , Gan Li 
Published: August 2020

AbstractPatients with frontotemporal dementia (FTD) resulting from granulin (GRN) haploinsufficiency have reduced levels of progranulin and exhibit dysregulation in inflammatory and lysosomal networks. Microglia produce high levels of progranulin, and reduction of progranulin in microglia alone is sufficient to recapitulate inflammation, lysosomal dysfunction, and hyperproliferation in a cell-autonomous manner. Therefore, targeting microglial dysfunction caused by progranulin insufficiency represents a potential therapeutic strategy to manage neurodegeneration in FTD. Limitations of current progranulin-enhancing strategies necessitate the discovery of new targets. To identify compounds that can reverse microglial defects in Grn-deficient mouse microglia, we performed a compound screen coupled with high throughput sequencing to assess key transcriptional changes in inflammatory and lysosomal pathways. Positive hits from this initial screen were then further narrowed down based on their ability to rescue cathepsin activity, a critical biochemical readout of lysosomal capacity. The screen identified nor-binaltorphimine dihydrochloride (nor-BNI) and dibutyryl-cAMP, sodium salt (DB-cAMP) as two phenotypic modulators of progranulin deficiency. In addition, nor-BNI and DB-cAMP also rescued cell cycle abnormalities in progranulin-deficient cells. These data highlight the potential of a transcription-based platform for drug screening, and advance two novel lead compounds for FTD.
CINENet: deep learning-based 3D cardiac CINE MRI reconstruction with multi-coil complex-valued 4D spatio-temporal convolutions
Authors: Küstner Thomas , Fuin Niccolo , Hammernik Kerstin , Bustin Aurelien , Qi Haikun , Hajhosseiny Reza , Masci Pier Giorgio , Neji Radhouene , Rueckert Daniel , Botnar René M. , Prieto Claudia 
Published: August 2020

AbstractCardiac CINE magnetic resonance imaging is the gold-standard for the assessment of cardiac function. Imaging accelerations have shown to enable 3D CINE with left ventricular (LV) coverage in a single breath-hold. However, 3D imaging remains limited to anisotropic resolution and long reconstruction times. Recently deep learning has shown promising results for computationally efficient reconstructions of highly accelerated 2D CINE imaging. In this work, we propose a novel 4D (3D + time) deep learning-based reconstruction network, termed 4D CINENet, for prospectively undersampled 3D Cartesian CINE imaging. CINENet is based on (3 + 1)D complex-valued spatio-temporal convolutions and multi-coil data processing. We trained and evaluated the proposed CINENet on in-house acquired 3D CINE data of 20 healthy subjects and 15 patients with suspected cardiovascular disease. The proposed CINENet network outperforms iterative reconstructions in visual image quality and contrast (+ 67% improvement). We found good agreement in LV function (bias ± 95% confidence) in terms of end-systolic volume (0 ± 3.3 ml), end-diastolic volume (− 0.4 ± 2.0 ml) and ejection fraction (0.1 ± 3.2%) compared to clinical gold-standard 2D CINE, enabling single breath-hold isotropic 3D CINE in less than 10 s scan and ~ 5 s reconstruction time.
Accelerated spin dynamics using deep learning corrections
Authors: Park Sojeong , Kwak Wooseop , Lee Hwee Kuan 
Published: August 2020

AbstractTheoretical models capture very precisely the behaviour of magnetic materials at the microscopic level. This makes computer simulations of magnetic materials, such as spin dynamics simulations, accurately mimic experimental results. New approaches to efficient spin dynamics simulations are limited by integration time step barrier to solving the equations-of-motions of many-body problems. Using a short time step leads to an accurate but inefficient simulation regime whereas using a large time step leads to accumulation of numerical errors that render the whole simulation useless. In this paper, we use a Deep Learning method to compute the numerical errors of each large time step and use these computed errors to make corrections to achieve higher accuracy in our spin dynamics. We validate our method on the 3D Ferromagnetic Heisenberg cubic lattice over a range of temperatures. Here we show that the Deep Learning method can accelerate the simulation speed by 10 times while maintaining simulation accuracy and overcome the limitations of requiring small time steps in spin dynamic simulations.
Early pregnancy-induced transcripts in peripheral blood immune cells in Bos indicus heifers
Authors: Rocha Cecilia Constantino , da Silva Andrade Sónia Cristina , de Melo Gabriela Dalmaso , Motta Igor Garcia , Coutinho Luiz Lehmann , Gonella-Diaza Angela Maria , Binelli Mario , Pugliesi Guilherme 
Published: August 2020

AbstractImmune cells play a central role in early pregnancy establishment in cattle. We aimed to: (1) discover novel early-pregnancy-induced genes in peripheral blood mononuclear cells (PBMC); and (2) characterize the temporal pattern of early-pregnancy-induced transcription of select genes in PBMC and peripheral blood polymorphonuclear cells (PMN). Beef heifers were artificially inseminated on D0 and pregnancies were diagnosed on D28. On D10, 14, 16, 18, and 20, blood was collected for isolation of PBMC and PMN from heifers that were retrospectively classified as pregnant (P) or non-pregnant (NP). PBMC samples from D18 were submitted to RNAseq and 220 genes were differentially expressed between pregnant (P) and non-pregnant (NP) heifers. The temporal abundance of 20 transcripts was compared between P and NP, both in PBMC and PMN. In PBMC, pregnancy stimulated transcription of IFI6, RSAD2, IFI44, IFITM2, CLEC3B, OAS2, TNFSF13B, DMKN and LGALS3BP as early as D18. Expression of IFI44, RSAD2, OAS2, LGALS3BP, IFI6 and C1R in PMN was stimulated in the P group from D18. The novel early-pregnancy induced genes discovered in beef heifers will allow both the understanding of the role of immune cells during the pre-attachment period and the development of technologies to detect early pregnancies in beef cattle.
Recalibration and validation of the Charlson Comorbidity Index in an Asian population: the National Health Insurance Service-National Sample Cohort study
Authors: Choi Jae Shin , Kim Myoung-Hee , Kim Yong Chul , Lim Youn-Hee , Bae Hyun Joo , Kim Dong Ki , Park Jae Yoon , Noh Junhyug , Lee Jung Pyo 
Published: August 2020

AbstractWeights assigned to comorbidities in predicting mortality may vary based on the type of index disease and advances in the management of comorbidities. We aimed to develop a modified version of the Charlson Comorbidity Index (CCI) using an Asian nationwide database (mCCI-A), enabling the precise prediction of mortality rates in this population. The main data source used in this study was the National Health Insurance Service-National Sample Cohort (NHIS-NSC) obtained from the National Health Insurance database, which includes health insurance claims filed between January 1, 2002, and December 31, 2013, in Korea. Of the 1,025,340 individuals included in the NHIS-NSC, 570,716 patients who were hospitalized at least once were analyzed in this study. In total, 399,502 patients, accounting for 70% of the cohort, were assigned to the development cohort, and the remaining patients (n = 171,214) were assigned to the validation cohort. The mCCI-A scores were calculated by summing the weights assigned to individual comorbidities according to their relative prognostic significance determined by a multivariate Cox proportional hazard model. The modified index was validated in the same cohort. The Cox proportional hazard model provided reassigned severity weights for 17 comorbidities that significantly predicted mortality. Both the CCI and mCCI-A were correlated with mortality. However, compared with the CCI, the mCCI-A showed modest but significant increases in the c statistics. According to the analyses using continuous net reclassification improvement, the mCCI-A improved the net mortality risk reclassification by 44.0% (95% confidence intervals (CI), 41.6–46.5; p < 0.001). The mCCI-A facilitates better risk stratification of mortality rates in Korean inpatients than the CCI, suggesting that the mCCI-A may be a preferable index for use in clinical practice and statistical analyses in epidemiological studies.
Time, space and social interactions: exit mechanisms for the Covid-19 epidemics
Authors: Scala Antonio , Flori Andrea , Spelta Alessandro , Brugnoli Emanuele , Cinelli Matteo , Quattrociocchi Walter , Pammolli Fabio 
Published: August 2020

AbstractWe develop a minimalist compartmental model to study the impact of mobility restrictions in Italy during the Covid-19 outbreak. We show that, while an early lockdown shifts the contagion in time, beyond a critical value of lockdown strength the epidemic tends to restart after lifting the restrictions. We characterize the relative importance of different lockdown lifting schemes by accounting for two fundamental sources of heterogeneity, i.e. geography and demography. First, we consider Italian Regions as separate administrative entities, in which social interactions between age classes occur. We show that, due to the sparsity of the inter-Regional mobility matrix, once started, the epidemic spreading tends to develop independently across areas, justifying the adoption of mobility restrictions targeted to individual Regions or clusters of Regions. Second, we show that social contacts between members of different age classes play a fundamental role and that interventions which target local behaviours and take into account the age structure of the population can provide a significant contribution to mitigate the epidemic spreading. Our model aims to provide a general framework, and it highlights the relevance of some key parameters on non-pharmaceutical interventions to contain the contagion.
Long non-coding RNA FENDRR regulates IFNγ-induced M1 phenotype in macrophages
Authors: Munteanu Maria Cristina , Huang Chaoqun , Liang Yurong , Sathiaseelan Roshini , Zeng Xiangming , Liu Lin 
Published: August 2020

AbstractMacrophages play an essential role in host defense and display remarkable plasticity in switching between classically (pro-inflammatory—M1) and alternatively activated (anti-inflammatory—M2) phenotypes. The molecular mechanisms of macrophage polarization are not fully understood. Long non-coding RNAs (lncRNAs) with a length of > 200 nucleotides have been shown to play diverse roles in biological processes. Aberrant expression of lncRNAs is associated with a variety of pathophysiological conditions such as cancer, diabetes, cardiovascular, pulmonary diseases, and tissue fibrosis. In this study, we investigated the role of lncRNA FENDRR in human and mouse macrophage polarization. Human THP-1 monocytes were activated with phorbol-12-myristate-13-acetate (PMA) and differentiated into M1 macrophages with IFNγ or M2 macrophages with IL4. Real-time PCR analysis revealed that FENDRR was expressed 80-fold higher in M1 macrophages than that in M2 macrophages. Overexpression of FENDRR in PMA-activated THP-1 cells increased the IFNγ-induced expression of M1 markers, including IL1β and TNFα at both mRNA and protein levels. Knockdown of FENDRR had an opposite effect. Similarly, FENDRR overexpression in primary mouse bone marrow-derived macrophages increased mRNA expression of M1 markers. FENDRR overexpression increased, while FENDRR knock-down decreased, the IFNγ-induced phosphorylation of STAT1 in PMA-activated THP-1 cells. Our studies suggest that FENDRR enhances IFNγ-induced M1 macrophage polarization via the STAT1 pathway.
De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway
Authors: Shah Muzammil , Alharby Hesham F. , Hakeem Khalid Rehman , Ali Niaz , Rahman Inayat Ur , Munawar Mohd , Anwar Yasir 
Published: August 2020

AbstractLantana camara L. is an economically important essential oil producing plant belonging to family Verbenaceae. It is used in medication for treating various diseases like cancer, ulcers, tumor, asthma and fever. The plant is a useful source of essential bioactive compounds such as steroids, flavonoids and phenylpropanoid glycosides etc. Nonetheless, very little is known about the genomic or transcriptomic resources of L. camara, and this might be the reason of hindering molecular studies leading to identification of improved lines. Here we used Illumina sequencing platform and performed the L. camara leaf (LCL) and root (LCR) de novo transcriptome analyses. A total of 70,155,594 and 84,263,224 clean reads were obtained and de novo assembly generated 72,877 and 513,985 unigenes from leaf (LCL) and root (LCR) respectively. Furthermore, the pathway analysis revealed the presence of 229 and 943 genes involved in the phenylpropanoid biosynthesis in leaf and root tissues respectively. Similarity search was performed against publically available genome databases and best matches were found with Sesamum indicum (67.5%) that were much higher than that of Arabidopsis thaliana (3.9%). To the best of our knowledge, this is the first comprehensive transcriptomic analysis of leaf and root tissues of this non-model plant from family Verbenaceae and may serve as a baseline for further molecular studies.
Surgical procedures in the pilonidal sinus disease: a systematic review and network meta-analysis
Authors: Bi Siwei , Sun Kaibo , Chen Shanshan , Gu Jun 
Published: August 2020

AbstractThe most appropriate surgical treatment for pilonidal sinus disease (PSD) is still in dispute. This study aims to comprehensively compare the outcomes of surgical interventions using network meta-analysis. Randomized controlled trial studies were searched systematically to identify all eligible studies in multiple databases and previous publications and Bayesian network meta-analysis was performed. Our primary outcome was the recurrence rate. Differences in the findings of the studies were explored in meta regressions and sensitivity analyses. The risk of bias of each study was assessed using the Cochrane risk of bias tool. Confidence in evidence was assessed using CINeMA (Confidence in Network Meta-Analysis). A total of 39 studies and 5,061 patients were identified and the most common surgical intervention was the Limberg flap. In network meta-analysis, modified Limberg flap and off-midline closure were associated with the lowest recurrence rate. However, the Karydakis flap was associated with shorter operation time by several minutes compared with other interventions and few significant results were found in other outcomes. Modified Limberg flap and off-midline closure provided relatively low recurrence and complications rates. Therefore, they could be two promising surgical interventions for PSD patients.