bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphofunctional characteristics of the tomato male gametophyte under conditions of viral pathogenesis
Authors: Saltanovish T. I. , Andronic L. I. , Antosh L. P. , Doncila A. N. 
Published: May 2021

Relevance. The action of viral phytopathogens changes the quality of the male gametophyte, which ultimately leads to a decrease in plant productivity. So, information on the features of the variability of morphofunctional characteristics of the microgametophyte becomes topical. Taking into account the expression of a part of the plant genome in pollen, the male gametophyte can be used as a reliable system for assessing the response of genotypes to the action of viral pathogens. Presuming that the problems of variability of characteristics of the male gametophyte in conditions of viral pathogenesis have not been enough studied, as well as the main factors determining the variability have not been identified, the aim of the research was to study the effect of viral phytopathogens on the male gametophyte characters in tomato.Material and methods. Hybrids F1 and varieties of tomato were used in the experiments. Plants were grown in a greenhouse. They were inoculated with tobacco mosaic virus (TMV) or tomato aspermia virus (TAV) in the 4-5 leaf phase. To determine the quality of pollen, flowers of control and infected plants were collected; pollen was isolated and sown on a nutrient medium. The preparations were analyzed under microscope. The viability of the pollen and the length of the pollen tubes were assessed, and the ratio of these indicators was calculated.Results. Infection of plants with viruses changes some functional characteristics of the male gametophyte. The responses manifested as stimulation, inhibition, or neutral effect. The main sources of variability in characters of pollen were the genotype and viral agents. In viral pathogenesis, unequal indicators of pollen grains were found in terms of the rate of germination and growth of pollen tubes (PT). Analysis of the heritability coefficients of the ratio of pollen viability and PT length (experiment / control) revealed positive dominance and overdominance in 70% of cases. Genotypes have been identified that combine a high level of viability when infected with different viruses. The prospect of their use in further research is proposed.
Application of machine learning algorithms to predict permeability in tight sandstone formations
Authors:   Instytut Nafty i Gazu – Państwowy Instytut Badawczy, Topór Tomasz 
Published: May 2021

The application of machine learning algorithms in petroleum geology has opened a new chapter in oil and gas exploration. Machine learning algorithms have been successfully used to predict crucial petrophysical properties when characterizing reservoirs. This study utilizes the concept of machine learning to predict permeability under confining stress conditions for samples from tight sandstone formations. The models were constructed using two machine learning algorithms of varying complexity (multiple linear regression [MLR] and random forests [RF]) and trained on a dataset that combined basic well information, basic petrophysical data, and rock type from a visual inspection of the core material. The RF algorithm underwent feature engineering to increase the number of predictors in the models. In order to check the training models’ robustness, 10-fold cross-validation was performed. The MLR and RF applications demonstrated that both algorithms can accurately predict permeability under constant confining pressure (R2 0.800 vs. 0.834). The RF accuracy was about 3% better than that of the MLR and about 6% better than the linear reference regression (LR) that utilized only porosity. Porosity was the most influential feature of the models’ performance. In the case of RF, the depth was also significant in the permeability predictions, which could be evidence of hidden interactions between the variables of porosity and depth. The local interpretation revealed the common features among outliers. Both the training and testing sets had moderate-low porosity (3–10%) and a lack of fractures. In the test set, calcite or quartz cementation also led to poor permeability predictions. The workflow that utilizes the tidymodels concept will be further applied in more complex examples to predict spatial petrophysical features from seismic attributes using various machine learning algorithms.
Protocolo de Prevenção e Tratamento de Infeções Associadas à Terapêutica Imunossupressora de Doenças Autoimunes
Authors: Valdoleiros Sofia R. , Furtado Isabel , Silva Carolina , Correia Gonçalves Inês , Santos Silva André , Vasconcelos Olga , Aboim Horta Ana , Vasconcelos A. Ludgero , Xará Sandra , Gonçalves Maria João , Araújo Abreu Miguel , Sarmento-Castro Rui 
Published: May 2021

O presente protocolo aborda o risco, prevenção e tratamento da infeção no doente sob terapêutica imunomoduladora ou imunossupressora em contexto de doença autoimune ou autoinflamatória. Subdivide-se nas seguintes secções: fármacos e risco associado de infeção; imunizações; risco, prevenção e tratamento de infeções específicas. Com um número crescente de novos fármacos em utilização nos últimos anos, o tratamento de doenças autoimunes envolve a utilização de terapêuticas imunossupressoras ou imunomoduladoras e associa-se a aumento do risco de infeção, que pode estar presente de uma forma global ou apenas para infeções por agentes específicos, variando amplamente consoante a classe farmacológica e mesmo dentro desta. Na estruturação da estratégia preventiva são fundamentais a caracterização da patologia que motiva a imunossupressão, a compreensão do mecanismo de ação do imunossupressor, a aferição de infeções prévias, o reconhecimento de fatores de risco, a realização de rastreios laboratoriais, a administração de vacinas, a educação do doente e a monitorização de sintomas e sinais clínicos, na dependência de uma gestão clínica necessariamente individualizada.
Partition Dimension of Dutch Windmill Graph
Authors: Hasmawati Hasmawati , Nurwahyu Budi , Daming Ahmad Syukur , Amir Amir Kamal 
Published: May 2021

Let be a connected graph G and -partition of end . The coordinat to is definition . If every twovertex is distinct applies, then is a called partition of . The minimum k for which k-resolving partition of is the partition dimension and denoted with . In this paper, we investigates the partition dimensionfor a large Dutch windmill graph for and . We show that if for some, forany.
Pilot Study On The Value of Echocardiography Combined With Lung Ultrasound In The Diagnosis And Treatment of COVID-19 Pneumonia
Authors: Han Jing , Yang Xi , Xu Wei , Jin Ronghua , Liu Weiyuan , Ding Lei , Meng Sha , Li Jin , Zheng Ying , Li Haowen , Meng Fankun 
Published: May 2021

Abstract
Background: This study aimed to investigate the relationship between echocardiography results and lung ultrasound score (LUS) in coronavirus diseases 2019 (COVID-19) pneumonia patients and to evaluate the impact of their combined application in the diagnosis and treatment of COVID-19 pneumonia.Methods: Hospitalized COVID-19 pneumonia patients who underwent lung ultrasound and echocardiography daily were included in this study. Patients with tricuspid regurgitation within 3 days of admission were enrolled, and the correlation and differences between their pulmonary artery pressure (PAP) and LUS on days 3, 8, and 13 were compared. The inner diameter of the pulmonary artery root and the size of the atria and ventricles were also observed.Results: Pulmonary artery pressure within 3 days (on day 3, 8 and 13) of admission was positively correlated with LUS (r = 0.448, p = 0.003; r = 0.738, p = 0.000; r = 0.325, p = 0.036). On day 8 the values of both PAP and LUS were higher than their corresponding values on days 3 and 13 (p < 0.01). On day 8 the positive rate for increased PAP and LUS was 92.9% (39/42) and 90.5% (38/42), respectively, and the combined positive rate for these two was 97.6% (41/42). On day 8 the inner diameters of the right atrium, right ventricle, and pulmonary artery differed significantly from their corresponding values on days 3 and 13 (p < 0.05).Conclusions: PAP is positively correlated with LUS. The two should be combined for a more informative assessment of the status of recovery from COVID-19 pneumonia.
DeephageTP: A Convolutional Neural Network Framework For Identifying Phage-Specific Proteins From Metagenomic Sequencing Data
Authors: Chu Yunmeng , Guo Shun , Cui Dachao , Fu Xiongfei , Ma Yingfei 
Published: May 2021

Abstract
Backgroud: Bacteriophage (phage) is the most abundant and diverse biological entity on the Earth. This makes it a challenge to identify and annotate phage genomes efficiently on a large scale.Results: Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are the three specific proteins of the tailed phage. Here, we develop a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three protein sequences encoded by the metagenome data. The framework takes one-hot encoding data of the original protein sequences as the input and extracts the predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of the sequences within the same category. The proposed model with the set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the result shows that compared to the conventional alignment-based methods, our proposed framework has a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training dataset.Conclusions: In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP.
Race/ethnicity is an Important Predictor of Life Expectancy in Localized Prostate Cancer Patients
Authors: Würnschimmel Christoph , Nocera Luigi , Wenzel Mike , Ruvolo Claudia Collà , Tian Zhe , Saad Fred , Briganti Alberto , Shariat Sharokh F. , Mirone Vincenzo , Chun Felix K.H. , Tilki Derya , Graefen Markus , Karakiewicz Pierre I. 
Published: May 2021

Abstract
PURPOSE:To test the effect of race/ethnicity on Social Security Administration (SSA) life tables’ life-expectancy (LE) predictions in localized prostate cancer (PCa) patients treated with either radical prostatectomy (RP) or external beam radiotherapy (EBRT). We hypothesized that LE will be affected by race/ethnicity. PATIENTS AND METHODS:We relied on the 2004-2006 Surveillance, Epidemiology, and End Results database to identify D’Amico intermediate- and high-risk PCa patients treated with either RP or EBRT. SSA life tables were used to compute 10-year LE predictions and were compared to OS. Stratification was performed according to treatment type (RP/EBRT) and race/ethnicity (Caucasian, African-American, Hispanic/Latino and Asian). RESULTS:Of 55,383 assessable patients, 40,490 were Caucasian (RP 49.3% vs. EBRT 50.7%), 7,194 African-American (RP 41.3% vs. EBRT 50.7%), 4,716 Hispanic/Latino (RP 51.0% vs. EBRT 49.0%) and 2,983 were Asian (RP 41.6% vs. EBRT 58.4%). In both RP and EBRT patients, OS exceeded life tables’ LE predictions, except for African-Americans. However, in RP patients, the magnitude of the difference was greater than in EBRT. Moreover, in RP patients, OS of African-Americans virtually perfectly followed predicted LE. Conversely, in EBRT patients, the OS of African-American patients was worse than predicted LE. CONCLUSIONS:OS in RP and EBRT treated PCa patients is invariably better than respective life tables’ derived LE predictions for Caucasians, Hispanic/Latinos and Asians, but not for African-Americans. The recorded survival disadvantage in African-American RP and EBRT patients, and if applicable also in other African-American populations, warrants detailed consideration and possibly corrective measures.
Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.
Authors: Chinchilla-Vargas Josue , Meerbeek Jonathan R. , Rothschild Max F. , Bertolini Francesca 
Published: May 2021

Abstract

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with Fst values larger than 0.9. Canadian inbreeding rate (Froh=0.32) appears to be higher to the inbreeding of Iowa population (Froh=0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canada population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.
Identification of a Novel Interaction of FUS and Syntaphilin May Explain Synaptic and Mitochondrial Abnormalities Caused by ALS Mutations
Authors: Vance Caroline , Salam Shaakir , Tacconelli Sara , Smith Bradley , Mitchell Jacqueline , Glennon Elizabeth , Nikolaou Nikolas , Houart Corinne 
Published: May 2021

Abstract
Aberrantly expressed fused in sarcoma (FUS) is a hallmark of FUS-related amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Wildtype FUS localises to synapses and interacts with mitochondrial proteins while mutations have been shown to cause to pathological changes affecting mitochondria, synapses and the neuromuscular junction (NMJ). This indicates a crucial physiological role for FUS in regulating synaptic and mitochondrial function that is currently poorly understood. In this paper we provide evidence that mislocalised cytoplasmic FUS causes mitochondrial and synaptic changes and that FUS plays a vital role in maintaining neuronal health in vitro and in vivo. Overexpressing mutant FUS altered synaptic numbers and neuronal complexity in both primary neurons and zebrafish models. The degree to which FUS was mislocalised led to differences in the synaptic changes which was mirrored by changes in mitochondrial numbers and transport. Furthermore, we showed that FUS interacts with the mitochondrial tethering protein Syntaphilin (SNPH), and that mutations in FUS affect this relationship. Finally, we demonstrated mutant FUS led to changes in global protein translation. This interaction between FUS and SNPH could explain the synaptic and mitochondrial defects observed leading to global protein translation defects. Importantly, our results support the ‘gain-of-function’ hypothesis for disease pathogenesis in FUS-related ALS.
Determinants of Elevated D-dimer Levels and Long-Term Outcome in Elderly Patients with End-Stage Heart Failure
Authors: Tian Aiju , Yang Chengzhi , Weng Shengfeng , Chen Xiaoli , Liu Hong , Luo Zhi 
Published: May 2021

Abstract
Background: Previous studies have shown that heart failure is associated with hemostatic abnormalities and hypercoagulable state. Plasma D-dimer levels reflect both fibrin formation and degradation, and elevated D-dimer levels have been associated with poor prognosis in patients with heart failure. However, little is known about their roles in elderly patients with end-stage HF. In present study, we aimed to explore the clinical significance and determinants of plasma D-dimer in elderly patients with end-stage heart failure. Methods: A total of 177 patients with heart failure at Beijing Geriatric Hospital from November 1, 2015 to December 30, 2018 were enrolled. All hospitalized patients were obtained D-dimer levels within the first 24 h following admission after obtaining informed consent. Primary endpoint was all-cause mortality. Results: A total of 60 patients had elevated D-dimer levels. Blood urea nitrogen (β=1.106, 95% CI: 1.029-1.190, p = 0.006), NYHA functional class (β=2.179, 95% CI: 1.170-4.056, p = 0.014) and white blood cell counts (β = 1.188, 95% CI: 1.040-1.358, p = 0.011) were independent risk factors for elevated D-dimer in elderly patients with end-stage heart failure. Albumin (β=0.803, 95% CI: 0.728-0.885, P ＜ 0.001) was negative risk factor for elevated D-dimer in elderly patients with end-stage heart failure. Elevated D-dimer level was independently associated with increased risk of long-term all-cause mortality (P = 0.048). Conclusions: For elderly patients with end-stage heart failure, D-dimer levels were associated with white blood cell counts, blood urea nitrogen, albumin and NYHA functional class and elevated D-dimer level was independently associated with poor long-term outcome.
Topoarchitected polymer networks expand the space of material properties
Authors: Liu Xiao , Wu Jingping , Qiao Keke , Liu Guohan , Wang Zhengjin , Lu Tongqing , Suo Zhigang , Hu Jian 
Published: May 2021

Abstract
Many living tissues achieve functions through architected constituents with strong adhesion. An Achilles tendon, for example, transmits force, elastically and repeatedly, from a muscle to a bone through staggered alignment of stiff collagen fibrils in a soft proteoglycan matrix. The collagen fibrils align orderly and adhere to the proteoglycan strongly. However, synthesizing architected materials with strong adhesion has been challenging. Here we fabricate architected polymer networks by sequential polymerization and photolithography, and attain adherent interface by topological entanglement. We fabricate tendon-inspired hydrogels by embedding hard blocks in topological entanglement with a soft matrix. The staggered architecture and strong adhesion enable high elastic limit strain and high toughness simultaneously. This combination of attributes is commonly desired in applications, but rarely achieved in synthetic materials. We further demonstrate architected polymer networks of various geometric patterns and material combinations to show the potential for expanding the space of material properties.
Bioenergy-induced land-use change emissions with sectorally fragmented policies
Authors: Merfort Leon , Bauer Nico , Humpenöder Florian , Klein David , Strefler Jessica , Popp Alexander , Luderer Gunnar , Kriegler Elmar 
Published: May 2021

Abstract
We assess the impact of different land-use emission policies within a broader climate policy framework on bioenergy production and associated land-use carbon emissions. We use the global Integrated Assessment Model REMIND-MAgPIE integrating the energy and land-use sectors and derive alternative climate change mitigation scenarios over the 21st century. If CO2 emissions are regulated consistently across sectors, land-use change emissions of biofuels are limited to 12 kgCO2/GJ. Without land-use emission regulations applied, bioenergy-induced emissions increase substantially and the emission factor per energy unit raises to levels slightly below diesel combustion (64 kg CO2/GJ). Pricing these emissions on the level of bioenergy consumption diminishes bioenergy deployment and the associated CO2 emissions, while failing to reduce the average emission factor. Despite effective reduction of land-use emissions, undifferentiated penalization of bioenergy use substantially increases mitigation costs. If supply side policies comprehensively regulate direct and indirect emissions, bioenergy can be produced much more sustainably.
Potential Roles of IGF2BP3 in Bladder Cancer
Authors: Ye Yu , Huang Haoxuan , Huang Rong , Wang Xi , Xie Yuanliang , Deng Caiwang , Li Tianyu , Wang Qiuyan , Mo Zengnan 
Published: May 2021

Abstract
The IGF2BP3 can affect cancer cells through the regulation of m6A. In this study, we combined the RNA sequencing and the RNA methylation sequencing to investigate the role and the mechanism of the IGF2BP3 in bladder cancer.TCGA data showed that the intersection genes of RBP differentially expressed and RBP involved in m6A modification were IGF2BP1 and IGF2BP3, only IGF2BP3 was significantly associated with short survival time (P < 0.01). Then immunohistochemistry and qRT-PCR detection showed that IGF2BP3 is highly expressed in bladder cancer (P < 0.05). The T24 knockout IGF2BP3 cell line was successfully constructed, with cell proliferation decreased and the apoptosis increased (P < 0.05). RNA sequencing results of clinical bladder tissue from 53 cases showed that the expression of IGF2BP3 samples were associated with the high levels of proliferation-related genes. The analysis of combined RNA and M6a level showed the differential genes related to cell growth and proliferation: SPHK1, POMT2, MRPS18a in T24 and T24-KO. Our study suggests that the IGF2BP3 is highly expressed in bladder cancer and related to tumor metastasis and invasion, the IGF2BP3 expression is related to cell proliferation genes, which affects the growth, proliferation, and apoptosis of T24 cells, and SpHK1, POMT2, and MRPS18a may be potential targets of IGF2BP3.
Prediction of Transmission Coefficients of Regular Wave Attenuation by Emergent Vegetation
Authors: Gong Shangpeng , CHEN JIE , Jiang Changbo , He Fei , Wu Zhiyuan 
Published: May 2021

Abstract
Transmission coefficient (Kt) for wave attenuation by vegetation is essential parameter for predicting the wave height. In this paper, based on the experimental data of three kind of artificial vegetation model, genetic programming (GP), artificial neural networks (ANNs) and multivariate non-linear regression (MNLR) were used to analyze the dimensionless factors including Ursell number (Ur), relative width (RB) relative height (α) and volume fraction (φ). The proposed GP formulae were compared with MNLR and ANNs. The predictions of GP models were in good agreement with measured data, and outperformed MNLR equations. Otherwise, GP and ANNs were used to obtain the weight of each factor. The results can provide a reference for the artificial planting of the three plants.