bluuebunny/crossref_metadata_2025 huggingface dataset:
Intranasal Administration of PACAP Is an Efficient Delivery Route to Reduce Infarct Volume and Promote Functional Recovery After Transient and Permanent Middle Cerebral Artery Occlusion
Authors: Cherait Asma , Maucotel Julie , Lefranc Benjamin , Leprince Jérôme , Vaudry David
Published: January 2021

Intranasal (IN) administration appears to be a suitable route for clinical use as it allows direct delivery of bioactive molecules to the central nervous system, reducing systemic exposure and sides effects. Nevertheless, only some molecules can be transported to the brain from the nasal cavity. This led us to compare the efficiency of an IN, intravenous (IV), and intraperitoneal (IP) administration of pituitary adenylate cyclase-activating polypeptide (PACAP) after transient or permanent middle cerebral artery occlusion (MCAO) in C57BL/6 mice. The results show that the neuroprotective effect of PACAP is much more efficient after IN administration than IV injection while IP injection had no effect. IN administration of PACAP reduced the infarct volume when injected within 6 h after the reperfusion and improved functional recovery up to at least 1 week after the ischemia.
Elevation Correlates With Significant Changes in Relative Abundance in Hummingbird Fecal Microbiota, but Composition Changes Little
Authors: Herder Elizabeth A. , Spence Austin R. , Tingley Morgan W. , Hird Sarah M.
Published: January 2021

The microbial communities living on and in vertebrate hosts have myriad effects on their hosts, potentially including fitness and speciation. Microbiomes are influenced by both intrinsic (from the host) and extrinsic (from the environment) factors, but the relative contributions of each are unknown for most non-model species. Abiotic environmental factors can influence the microbiome directly but it is less clear how abiotic gradients shape microbiome communities in the wild. Here, we captured eight wild Anna’s hummingbirds from three different elevations along their elevational distribution in California and moved them directly to a middle (“Within Range”) elevation. After some time at this elevation, the birds were moved in captivity to an “Above Range” elevation, and two birds were later moved back to the Within Range elevation. Fecal and food samples were collected longitudinally and the V4 region of the 16S rRNA gene analyzed. The most abundant phyla in all samples were Fusobacteria, Firmicutes, Actinobacteria, and Proteobacteria. Individual Bird ID explained the greatest amount of microbiome variation at 27.5%, signifying some amount of stability in the Anna’s hummingbird fecal microbiome. Sample elevation explained 19.6% (p = 0.001) of the variation using weighted UniFrac, but only 2.0% (p = 0.047) using unweighted UniFrac, implying a change in abundance of bacterial lineages in the microbiome but not in the presence or absence of the microbes. Additionally, Fusobacteria were 7.0x more abundant in the Above Range elevation samples while Firmicutes were 0.3x lower. A thorough understanding of how the environment can shape the microbiome may assist in conservation efforts and a general understanding of host-microbiome relationships in an era of rapid and global environmental change.
Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana
Authors: Farooq Muhammad , van Dijk Aalt D. J. , Nijveen Harm , Aarts Mark G. M. , Kruijer Willem , Nguyen Thu-Phuong , Mansoor Shahid , de Ridder Dick
Published: January 2021

Prediction of growth-related complex traits is highly important for crop breeding. Photosynthesis efficiency and biomass are direct indicators of overall plant performance and therefore even minor improvements in these traits can result in significant breeding gains. Crop breeding for complex traits has been revolutionized by technological developments in genomics and phenomics. Capitalizing on the growing availability of genomics data, genome-wide marker-based prediction models allow for efficient selection of the best parents for the next generation without the need for phenotypic information. Until now such models mostly predict the phenotype directly from the genotype and fail to make use of relevant biological knowledge. It is an open question to what extent the use of such biological knowledge is beneficial for improving genomic prediction accuracy and reliability. In this study, we explored the use of publicly available biological information for genomic prediction of photosynthetic light use efficiency (ΦPSII) and projected leaf area (PLA) inArabidopsis thaliana. To explore the use of various types of knowledge, we mapped genomic polymorphisms to Gene Ontology (GO) terms and transcriptomics-based gene clusters, and applied these in a Genomic Feature Best Linear Unbiased Predictor (GFBLUP) model, which is an extension to the traditional Genomic BLUP (GBLUP) benchmark. Our results suggest that incorporation of prior biological knowledge can improve genomic prediction accuracy for both ΦPSIIand PLA. The improvement achieved depends on the trait, type of knowledge and trait heritability. Moreover, transcriptomics offers complementary evidence to the Gene Ontology for improvement when used to define functional groups of genes. In conclusion, prior knowledge about trait-specific groups of genes can be directly translated into improved genomic prediction.
CDAE: A Cascade of Denoising Autoencoders for Noise Reduction in the Clustering of Single-Particle Cryo-EM Images
Authors: Lei Houchao , Yang Yang
Published: January 2021

As an emerging technology, cryo-electron microscopy (cryo-EM) has attracted more and more research interests from both structural biology and computer science, because many challenging computational tasks are involved in the processing of cryo-EM images. An important image processing step is to cluster the 2D cryo-EM images according to their projection angles, then the cluster mean images are used for the subsequent 3D reconstruction. However, cryo-EM images are quite noisy and denoising them is not easy, because the noise is a complicated mixture from samples and hardware. In this study, we design an effective cryo-EM image denoising model, CDAE, i.e., a cascade of denoising autoencoders. The new model comprises stacked blocks of deep neural networks to reduce noise in a progressive manner. Each block contains a convolutional autoencoder, pre-trained by simulated data of different SNRs and fine-tuned by target data set. We assess this new model on three simulated test sets and a real data set. CDAE achieves very competitive PSNR (peak signal-to-noise ratio) in the comparison of the state-of-the-art image denoising methods. Moreover, the denoised images have significantly enhanced clustering results compared to original image features or high-level abstraction features obtained by other deep neural networks. Both quantitative and visualized results demonstrate the good performance of CDAE for the noise reduction in clustering single-particle cryo-EM images.
Vitamin D3-Induced Tolerogenic Dendritic Cells Modulate the Transcriptomic Profile of T CD4+ Cells Towards a Functional Hyporesponsiveness
Authors: Navarro-Barriuso Juan , Mansilla María José , Quirant-Sánchez Bibiana , Teniente-Serra Aina , Ramo-Tello Cristina , Martínez-Cáceres Eva M.
Published: January 2021

The use of autologous tolerogenic dendritic cells (tolDC) has become a promising alternative for the treatment of autoimmune diseases. Among the different strategies available, the use of vitamin D3 for the generation of tolDC (vitD3-tolDC) constitutes one of the most robust approaches due to their immune regulatory properties, which are currently being tested in clinical trials. However, the mechanisms that vitD3-tolDC trigger for the induction of tolerance remain elusive. For this reason, we performed a full phenotypical, functional, and transcriptomic characterization of T cells upon their interaction with autologous, antigen-specific vitD3-tolDC. We observed a strong antigen-specific reduction of T cell proliferation, combined with a decrease in the relative prevalence of TH1 subpopulations and IFN-γ production. The analysis of the transcriptomic profile of T CD4+ cells evidenced a significant down-modulation of genes involved in cell cycle and cell response to mainly pro-inflammatory immune-related stimuli, highlighting the role of JUNB gene as a potential biomarker of these processes. Consequently, our results show the induction of a strong antigen-specific hyporesponsiveness combined with a reduction on the TH1 immune profile of T cells upon their interaction with vitD3-tolDC, which manifests the regulatory properties of these cells and, therefore, their therapeutic potential in the clinic.
Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity
Authors: Raghav Sunil , Ghosh Arup , Turuk Jyotirmayee , Kumar Sugandh , Jha Atimukta , Madhulika Swati , Priyadarshini Manasi , Biswas Viplov K. , Shyamli P. Sushree , Singh Bharati , Singh Neha , Singh Deepika , Datey Ankita , Avula Kiran , Smita Shuchi , Sabat Jyotsnamayee , Bhattacharya Debdutta , Kshatri Jaya Singh , Vasudevan Dileep , Suryawanshi Amol , Dash Rupesh , Senapati Shantibhushan , Beuria Tushar K. , Swain Rajeeb , Chattopadhyay Soma , Syed Gulam Hussain , Dixit Anshuman , Prasad Punit , Pati Sanghamitra , Parida Ajay ,   Odisha COVID-19 Study Group,   ILS COVID-19 Team
Published: January 2021

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers–based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assemblies identified the presence of all the five reported clades 19A, 19B, 20A, 20B, and 20C in the population. The analyses revealed Europe and Southeast Asia as two major routes for introduction of the disease in India followed by local transmission. Interestingly, the19B clade was found to be more prevalent in our sequenced genomes (17%) compared to other genomes reported so far from India. Haplotype network analysis showed evolution of 19A and 19B clades in parallel from predominantly Gujarat state in India, suggesting it to be one of the major routes of disease transmission in India during the months of March and April, whereas 20B and 20C appeared to evolve from 20A. At the same time, 20A and 20B clades depicted prevalence of four common mutations 241 C > T in 5′ UTR, P4715L, F942F along with D614G in the Spike protein. D614G mutation has been reported to increase virus shedding and infectivity. Our molecular modeling and docking analysis identified that D614G mutation resulted in enhanced affinity of Spike S1–S2 hinge region with TMPRSS2 protease, possibly the reason for increased shedding of S1 domain in G614 as compared to D614. Moreover, we also observed an increased concordance of G614 mutation with the viral load, as evident from decreased Ct value of Spike and the ORF1ab gene.
Development of a Fast SARS-CoV-2 IgG ELISA, Based on Receptor-Binding Domain, and Its Comparative Evaluation Using Temporally Segregated Samples From RT-PCR Positive Individuals
Authors: Mehdi Farha , Chattopadhyay Souvick , Thiruvengadam Ramachandran , Yadav Sarla , Kumar Manjit , Sinha Sangita Kumari , Goswami Sandeep , Kshetrapal Pallavi , Wadhwa Nitya , Chandramouli Natchu Uma , Sopory Shailaja , Koundinya Desiraju Bapu , Pandey Anil K. , Das Asim , Verma Nikhil , Sharma Nandini , Sharma Pragya , Bhartia Vandita , Gosain Mudita , Lodha Rakesh , Lamminmäki Urpo , Shrivastava Tripti , Bhatnagar Shinjini , Batra Gaurav
Published: January 2021

SARS-CoV-2 antibody detection assays are crucial for gathering seroepidemiological information and monitoring the sustainability of antibody response against the virus. The SARS-CoV-2 Spike protein’s receptor-binding domain (RBD) is a very specific target for anti-SARS-CoV-2 antibodies detection. Moreover, many neutralizing antibodies are mapped to this domain, linking antibody response to RBD with neutralizing potential. Detection of IgG antibodies, rather than IgM or total antibodies, against RBD is likely to play a larger role in understanding antibody-mediated protection and vaccine response. Here we describe a rapid and stable RBD-based IgG ELISA test obtained through extensive optimization of the assay components and conditions. The test showed a specificity of 99.79% (95% CI: 98.82–99.99%) in a panel of pre-pandemic samples (n = 470) from different groups, i.e., pregnancy, fever, HCV, HBV, and autoantibodies positive. Test sensitivity was evaluated using sera from SARS-CoV-2 RT-PCR positive individuals (n = 312) and found to be 53.33% (95% CI: 37.87–68.34%), 80.47% (95% CI: 72.53–86.94%), and 88.24% (95% CI: 82.05–92.88%) in panel 1 (days 0–13), panel 2 (days 14–20) and panel 3 (days 21–27), respectively. Higher sensitivity was achieved in symptomatic individuals and reached 92.14% (95% CI: 86.38–96.01%) for panel 3. Our test, with a shorter runtime, showed higher sensitivity than parallelly tested commercial ELISAs for SARS-CoV-2-IgG, i.e., Euroimmun and Zydus, even when equivocal results in the commercial ELISAs were considered positive. None of the tests, which are using different antigens, could detect anti-SARS-CoV-2 IgGs in 10.5% RT-PCR positive individuals by the fourth week, suggesting the lack of IgG response.
Immune Regulation of Adult Neurogenic Niches in Health and Disease
Authors: Chintamen Sana , Imessadouene Fatima , Kernie Steven G.
Published: January 2021

Microglia regulate neuronal development during embryogenesis, postnatal development, and in specialized microenvironments of the adult brain. Recent evidence demonstrates that in adulthood, microglia secrete factors which modulate adult hippocampal neurogenesis by inhibiting cell proliferation and survival both in vitro and in vivo, maintaining a balance between cell division and cell death in neurogenic niches. These resident immune cells also shape the nervous system by actively pruning synapses during critical periods of learning and engulfing excess neurons. In neurodegenerative diseases, aberrant microglial activity can impede the proper formation and prevent the development of appropriate functional properties of adult born granule cells. Ablating microglia has been presented as a promising therapeutic approach to alleviate the brain of maladaptive immune response. Here, we review key mechanisms through which the immune system actively shapes neurogenic niches throughout the lifespan of the mammalian brain in both health and disease. We discuss how interactions between immune cells and developing neurons may be leveraged for pharmacological intervention and as a means to preserve adult neurogenesis.
Machine Learning Methods for Diagnosing Autism Spectrum Disorder and Attention- Deficit/Hyperactivity Disorder Using Functional and Structural MRI: A Survey
Authors: Eslami Taban , Almuqhim Fahad , Raiker Joseph S. , Saeed Fahad
Published: January 2021

Here we summarize recent progress in machine learning model for diagnosis of Autism Spectrum Disorder (ASD) and Attention-deficit/Hyperactivity Disorder (ADHD). We outline and describe the machine-learning, especially deep-learning, techniques that are suitable for addressing research questions in this domain, pitfalls of the available methods, as well as future directions for the field. We envision a future where the diagnosis of ASD, ADHD, and other mental disorders is accomplished, and quantified using imaging techniques, such as MRI, and machine-learning models.
Development of a Comorbidity-Based Nomogram to Predict Survival After Salvage Reirradiation of Locally Recurrent Nasopharyngeal Carcinoma in the Intensity-Modulated Radiotherapy Era
Authors: Huang Run-Da , Sun Zhuang , Wang Xiao-Hui , Tian Yun-Ming , Peng Ying-Lin , Wang Jing-Yun , Xiao Wei-Wei , Chen Chun-Yan , Deng Xiao-Wu , Han Fei
Published: January 2021

Purpose

To assess the impact of comorbidity on treatment outcomes in patients with locally recurrent nasopharyngeal carcinoma (lrNPC) using intensity-modulated radiotherapy (IMRT) and to develop a nomogram that combines prognostic factors to predict clinical outcome and guide individual treatment.

Methods

This was a retrospective analysis of patients with lrNPC who were reirradiated with IMRT between 2003 and 2014. Comorbidity was evaluated by Adult Comorbidity Evaluation-27 grading (ACE-27). The significant prognostic factors (P < 0.05) by multivariate analysis using the Cox regression model were adopted into the nomogram model. Harrell concordance index (C-index) calibration curves were applied to assess this model.

Results

Between 2003 and 2014, 469 lrNPC patients treated in our institution were enrolled. Significant comorbidity (moderate or severe grade) was present in 17.1% of patients by ACE-27. Patients with no or mild comorbidity had a 5-year overall survival (OS) rate of 36.2 versus 20.0% among those with comorbidity of moderate or severe grade (P < 0.0001). The chemotherapy used was not significantly different in patients with lrNPC (P > 0.05). For the rT3–4 patients, the 5-year OS rate in the chemotherapy + radiation therapy (RT) group was 30.0 versus 16.7% for RT only (P = 0.005). The rT3–4 patients with no or mild comorbidity were associated with a higher 5-year OS rate in the chemotherapy + RT group than in the RT only group (32.1 and 17.1%, respectively; P=0.003). However, for the rT3–4 patients with a comorbidity (moderate or severe grade), the 5-year OS rate in the chemotherapy + RT group vs. RT alone was not significantly different (15.7 vs. 15.0%, respectively; p > 0.05). Eight independent prognostic factors identified from multivariable analysis were fitted into a nomogram, including comorbidity. The C-index of the nomogram was 0.715. The area under curves (AUCs) for the prediction of 1-, 3-, and 5-year overall survival were 0.770, 0.764, and 0.780, respectively.

Conclusion

Comorbidity is among eight important prognostic factors for patients undergoing reirradiation. We developed a nomogram for lrNPC patients to predict the probability of death after reirradiation and guide individualized management.
Localization and Composition of Fructans in Stem and Rhizome of Agave tequilana Weber var. azul
Authors: Pérez-López Arely V. , Simpson June , Clench Malcolm R. , Gomez-Vargas Alan D. , Ordaz-Ortiz José J.
Published: January 2021

Methodology combining mass spectrometry imaging (MSI) with ion mobility separation (IMS) has emerged as a biological imaging technique due to its versatility, sensitivity and label-free approach. This technique has been shown to separate isomeric compounds such as lipids, amino acids, carboxylic acids and carbohydrates. This report describes mass spectrometry imaging in combination with traveling-wave ion mobility separation and matrix-assisted laser desorption/ionization (MALDI). Positive ionization mode was used to locate fructans on tissue printed sections of Agave rhizome and stem tissue and distinguished fructan isoforms. Here we show the location of fructans ranging from DP3 to DP17 to be differentially abundant across the stem tissue and for the first time, experimental collision cross sections of endogenous fructan structures have been collected, revealing at least two isoforms for fructans of DP4, DP5, DP6, DP7, DP8, DP10, and DP11. This demonstrates that complex fructans such as agavins can be located and their isoforms resolved using a combination of MALDI, IMS, and MSI, without the need for extraction or derivatization. Use of this methodology uncovered patterns of fructan localization consistent with functional differences where higher DP fructans are found toward the central section of the stem supporting a role in long term carbohydrate storage whereas lower DP fructans are concentrated in the highly vascularized central core of rhizomes supporting a role in mobilization of carbohydrates from the mother plant to developing offsets. Tissue specific patterns of expression of genes encoding enzymes involved in fructan metabolism are consistent with fructan structures and localization.
Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana
Authors: Zulkapli Muhammad Mu’izzuddin , Ab Ghani Nur Syatila , Ting Tiew Yik , Aizat Wan Mohd , Goh Hoe-Han
Published: January 2021

Nepenthes is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for Nepenthes. In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes × hookeriana through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid N. × hookeriana were more resembling N. rafflesiana, both of which are insectivorous compared with omnivorous N. ampullaria that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in N. ampullaria, we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of Nepenthes species with distinct dietary habits.
Field Application of Organic Fertilizers Triggers N2O Emissions From the Soil N Pool as Indicated by 15N-Labeled Digestates
Authors: Häfner Franziska , Ruser Reiner , Claß-Mahler Ingrid , Möller Kurt
Published: January 2021

Anaerobic digestion (AD) can generate biogas while simultaneously producing digestate which can be used as fertilizer. Feedstocks used for AD influence digestate composition, which in turn may affect carbon (C) and nitrogen (N) turn-over in soils and subsequently influence nitrous oxide (N2O) emissions after soil application. Assessment of greenhouse gas emissions from digestates can help to evaluate the overall sustainability of an agricultural production system. The objective of this study was therefore to evaluate and understand the effect of differences in digestate composition on in situ N2O emissions within the 1st weeks after application of seven digestates. The digestates were derived from different feedstocks and 15N-labeled, either in total N or only in ammonium-N. Therefore, the experimental design enabled us to differentiate between potential N2O-N sources (i.e., digestate N or soil N). Furthermore, it allowed to distinguish to some extent between organic-N and ammonium-N as potential N sources for denitrification. Digestates were homogeneously incorporated into the upper 5 cm of microplots in an arable Haplic Luvisol in South Germany at a rate of 170 kg N ha−1. After application, N2O fluxes were measured for ~60 days (May-July) using the closed chamber method in 2 experimental years. Mainly due to higher precipitations in the 1st year, cumulative N2O emissions were higher (312–1,580 g N2O-N ha−1) compared to the emissions (133–690 g N2O-N ha−1) in the 2nd year. Between 16–33% (1st year) and 17–38% (2nd year) of N2O emissions originated from digestate N, indicating that digestate application triggered N2O production and release mainly from soil N. This effect was strongest immediately after digestate application. It was concluded that the first (short term) peak in N2O emissions after digestate application is largely related to denitrification of soil-N. However, the experimental setup does not allow to differentiate between the different denitrification pathways. Weather conditions showed a substantial effect on N2O emissions, where the correlation between N2O and CO2 flux rates hinted on denitrification as main N2O source. The effect of digestate composition, particularly organic N from the digestate, on soil N2O emissions seems to be of minor relevance.
PDA Indolylmaleimides Induce Anti-Tumor Effects in Prostate Carcinoma Cell Lines Through Mitotic Death
Authors: Schille Jan Torben , Nolte Ingo , Beck Julia , Jilani Daria , Roolf Catrin , Pews-Davtyan Anahit , Rolfs Arndt , Henze Larissa , Beller Matthias , Brenig Bertram , Junghanss Christian , Schütz Ekkehard , Murua Escobar Hugo
Published: January 2021

Castrate resistant prostate cancer in men shares several characteristics with canine prostate cancer (PCa). Due to current insufficient therapies, evaluating novel therapeutic agents for late-stage PCa is of considerable interest for both species. PDA indolylmaleimides showed anticancer effects in several neoplastic cell lines. Herein, a comparative characterization of PDA-66 and PDA-377 mediated effects was performed in human and canine PCa cell lines, which is also the first detailed characterization of these agents on cells derived from solid tumors in general. While PDA-377 showed only weak growth inhibition on human PCa cell lines, PDA-66 inhibited proliferation and induced apoptosis in human and canine cell lines with concentrations in the low micromolar range. Morphological characterization and whole transcriptome sequencing revealed that PDA-66 induces mitotic death through its microtubule-depolymerizing ability. PDA-66 appears to be a worthwhile anti-mitotic agent for further evaluation. The similarities in cellular and molecular response observed in the cell lines of both origins form a solid basis for the use of canine PCa in vivo models to gain valuable interchangeable data to the advantage of both species.
Longitudinal Axial Flow Rice Thresher Performance Optimization Using the Taguchi Technique
Authors: Abdeen Mohamed Anwer , Salem Abouelnadar Elsayed , Zhang Guozhong
Published: January 2021

Combine harvesters are widely used worldwide in harvesting many crops, and they have many functions that cover the entire harvesting process, such as cutting, threshing, separating, and cleaning. The threshing drum is the core working device of the combine harvester and plays an influential role in rice threshing efficiency, threshing power requirement, and seed loss. In this study, two structures of rice threshers (conical-shaped and cylindrical-shaped) were tested and evaluated for performance under different thresher rotating speeds of 1100, 1300, and 1500 rpm and different feeding rates of 0.8, 1.1, and 1.4 kg/s. The experiment was designed using the Taguchi method, and the obtained results were evaluated using the same technique. The thresher structure and operating parameters were assessed and optimized with reference to threshing efficiency, required power, and productivity. The obtained results revealed that increasing thresher rotating speed and the feeding rate positively related to threshing efficiency, power, and productivity. The highest efficiency of 98% and the maximum productivity of 0.64 kg/s were obtained using the conical-shaped thresher under a 1500 rpm rotating speed and a feed rate of 1.4 kg/s, whereas the minimum required power of 5.45 kW was obtained using the conical thresher under a rotating speed of 1100 rpm and a feed rate of 0.8 kg/s.
Tall Fescue (Schedonorus arundinaceus (Schreb.) Dumort.) Turfgrass Cultivars Performance under Reduced N Fertilization
Authors: Schiavon Marco , Pornaro Cristina , Macolino Stefano
Published: January 2021

The identification of minimal N requirements for sustaining turfgrass quality and functionality became necessary to reduce N fertilization inputs and avoid potential environmental impacts in the European Union. A two year study was conducted at Padova University in Legnaro, northeastern Italy to investigate the performance of four tall fescue (Schedonorus arundinaceus (Schreb.) Dumort.) cultivars (‘Lexington’, ‘Rhambler SRP’, ‘Rhizing star’, and ‘Thunderstruck’) fertilized twice per year at either 75 or 150 kg N ha−1 year−1. Turfgrass was evaluated every two weeks for turfgrass visual quality, percent green cover (PGR) as well as dark green color index (DGCI) through digital image analysis and normalized difference vegetation index (NDVI). ‘Rhizing star’ was the only cultivar that showed poor adaptation to the environment, achieving acceptable turfgrass quality (6.0 or higher) only during June and July 2019. Turf fertilized at 150 kg N ha−1 year−1 generally showed higher performance than 75 kg N ha−1 year−1, however, the increase in turfgrass quality was mostly negligible and detected only during the winter months. Results suggest that well adapted tall fescue cultivars could be fertilized at 75 kg N ha−1 year−1 in Northern Italy.
Direct and Indirect Detoxification Effects of Humic Substances
Authors: Bondareva Lydia , Kudryasheva Nadezhda
Published: January 2021

The review summarizes studies on the detoxification effects of water-soluble humic substances (HS), which are products of the natural transformation of organic substances in soils and bottom sediments that serve as natural detoxifying agents in water solutions. The detoxifying effects of HS on microorganisms are quite complex: HS neutralize free pollutants (indirect bioeffects) and also stimulate the protective response of organisms (direct bioeffects). Prospects and potential problems of bioluminescent bacteria-based assay to monitor toxicity of solutions in the presence of HS are discussed. The main criterion for the bioassay application is versatility and ease of use. The detoxification efficiency of HS in different pollutant solutions was evaluated, and the detoxification mechanisms are discussed. Particular attention was paid to the direct and complex direct + indirect effects of HS. The review focuses on the protective function of HS in solutions of radionuclides and salts of stable metals, with special consideration of the antioxidant properties of HS.
Molecular Characterization of New Haplotype of Genus Sarcocystis in Seabirds from Magdalena Island, Southern Chile
Authors: Acosta Igor C. L. , Gennari Solange M. , Llano Horwald A. B. , Muñoz-Leal Sebastián , Soares Rodrigo M.
Published: January 2021

Evidence of sarcocystid infection was investigated in samples of 16 penguins (Spheniscus. magellanicus), four Dominican gulls (Larus dominicanus) and two Chilean skuas (Stercorarius chilensis) found in Madalenas Islands, Chile, in 2017. Samples of skeletal muscle, cardiac muscle and brain from all birds were screened by a pan-sarcocystid nested-PCR targeting a short fragment of the gene encoding the small ribosomal unit (nPCR-18Sa). The only two positive samples by nPCR-18Sa, both from skuas, were tested by a nested-PCR directed to the internal transcribed spacer 1 (nPCR-ITS1), also a pan-sarcocystidae nested-PCR, and to a nested-PCR directed to the B1 gene (nPCR-B1), for the exclusive detection of Toxoplasma gondii. The two nPCR-18Sa-positive samples were nPCR-ITS1-positive and nPCR-B1-negative. The nPCR-ITS1 nucleotide sequences from the two skuas, which were identical to each other, were revealed closely related to homologous sequences of Sarcocystis halieti, species found in seabirds of northern hemisphere. Larger fragments of genes encoding 18S and partial sequences of genes coding for cytochrome oxidase subunit 1 were also analyzed, corroborating ITS1 data. The haplotypes found in the skuas are unprecedent and closely related to species that use birds as the definitive host. Further studies need to be carried out to detect, identify and isolate this parasite to understand the epidemiology of the infection and its impact on the health of marine fauna.
Case Study: Misdiagnosis of Nonhemolytic Staphylococcus aureus Isolates from Cases of Bovine Mastitis as Coagulase-Negative Staphylococci
Authors: Ryman Valerie E. , Kautz Felicia M. , Nickerson Steve C.
Published: January 2021

Staphylococcus aureus is one of the most concerning mastitis-causing pathogens in dairy cattle. Using basic microbiological techniques, S. aureus is typically identified by colony characteristics and hemolysis on blood agar where isolates without hemolysis are typically considered to be coagulase-negative staphylococci (CNS) isolates. Herein, we present a decade-long case study where suspected S. aureus isolates from one Georgia dairy farm were further tested to confirm presumptive identification. Presumptive identification of bacterial growth from 222 mammary secretions from bred Holstein heifers and lactating cows was conducted at the time of collection. Presumptive identification of S. aureus on blood agar was based on observation of colony morphology, color, and presence or absence of a broad zone of incomplete hemolysis and a smaller zone of complete hemolysis at 48 h. Those without hemolysis were presumptively characterized as CNS. All isolates were further plated on mannitol salt agar and a coagulase test was performed. A positive for both of these tests together was deemed to be S. aureus. A selection of isolates was tested using API® Staph to biochemically confirm S. aureus identification. Data showed that 63.96% of isolates presumed to be CNS isolates were identified as S. aureus, 9.46% of isolates presumed to be CNS isolates were identified as coagulase-positive staphylococci (CPS) species (but not S. aureus), and 26.58% of samples that were presumed to be CNS isolates were identified correctly.
Experimental Evaluation of a Spectral Index to Characterize Temporal Variations in the Direct Normal Irradiance Spectrum
Authors: Nofuentes Gustavo , Gueymard Christian A. , Caballero José A. , Marques-Neves Guilherme , Aguilera Jorge
Published: January 2021

A simple index is desirable to assess the effects on both flat-plate and concentrating photovoltaics of natural changes in the solar spectrum. Some studies have suggested that the relationship between the Average Photon Energy (APE) and the shape of individual global tilted irradiance, global horizontal irradiance, or direct normal irradiance (DNI) spectra is bijective and can therefore be used as a single number to unequivocally replace a complete spectral distribution. This paper reevaluates these studies with a modified methodology to assess whether a one-to-one relationship really exists between APE and spectral DNI. A 12-month dataset collected in Jaén (Spain) using a sun-tracking spectroradiometer provides the necessary spectral DNI data between 350 and 1050 nm. After quality control and filtering, 78,772 valid spectra were analyzed. The methodology is based on a statistical analysis of the spectral distributions binned in 0.02-eV APE intervals, from 1.74 to 1.90 eV. For each interval, both the standard deviation and coefficient of variation (CV) are determined across all 50-nm bands into which the 350–1050-nm waveband is divided. CV stays below 3.5% within the 450–900-nm interval but rises up to 13% outside of it. It is concluded that APE may be approximately assumed to uniquely characterize the DNI spectrum distribution for Jaén (and presumably for locations with similar climates) only over the limited 450–900-nm waveband.
The Neurochaperonopathies: Anomalies of the Chaperone System with Pathogenic Effects in Neurodegenerative and Neuromuscular Disorders
Authors: Scalia Federica , Vitale Alessandra Maria , Santonocito Radha , Conway de Macario Everly , Macario Alberto J. L. , Cappello Francesco
Published: January 2021

The chaperone (or chaperoning) system (CS) constitutes molecular chaperones, co-chaperones, and chaperone co-factors, interactors and receptors, and its canonical role is protein quality control. A malfunction of the CS may cause diseases, known as the chaperonopathies. These are caused by qualitatively and/or quantitatively abnormal molecular chaperones. Since the CS is ubiquitous, chaperonopathies are systemic, affecting various tissues and organs, playing an etiologic-pathogenic role in diverse conditions. In this review, we focus on chaperonopathies involved in the pathogenic mechanisms of diseases of the central and peripheral nervous systems: the neurochaperonopathies (NCPs). Genetic NCPs are linked to pathogenic variants of chaperone genes encoding, for example, the small Hsp, Hsp10, Hsp40, Hsp60, and CCT-BBS (chaperonin-containing TCP-1- Bardet–Biedl syndrome) chaperones. Instead, the acquired NCPs are associated with malfunctional chaperones, such as Hsp70, Hsp90, and VCP/p97 with aberrant post-translational modifications. Awareness of the chaperonopathies as the underlying primary or secondary causes of disease will improve diagnosis and patient management and open the possibility of investigating and developing chaperonotherapy, namely treatment with the abnormal chaperone as the main target. Positive chaperonotherapy would apply in chaperonopathies by defect, i.e., chaperone insufficiency, and consist of chaperone replacement or boosting, whereas negative chaperonotherapy would be pertinent when a chaperone actively participates in the initiation and progression of the disease and must be blocked and eliminated.
New Hydraulic High-Pressure Impulse Generator for Long-Duration Impulse Tests
Authors: Ding Chuan , Huang Yu , Chen Haoqi , Zhang Lichao , Meng Bin , Gao Yuanhao
Published: January 2021

Water hammer wave is widely applied to test hydraulic components in various areas. A new hydraulic high-pressure impulse generator is presented in this paper in order to provide the standard water hammer wave for long-term usage. A combination of a sleeve and a rotary spool was used to build the impulse generator, and a booster piston was applied to amplify the output pressure. Mathematical models were established using commercial software, and a prototype and a test rig were built based on the simulation results. The experimental results for both single wave and repeated periods show the feasibility of the new design and indicate that the new hydraulic high-pressure impulse generator can be used for long-time impulse tests.
Segregation of NiTe2 and NbTe2 in p-Type Thermoelectric Bi0.5Sb1.5Te3 Alloys for Carrier Energy Filtering Effect by Melt Spinning
Authors: Kim Hyun-Sik , Kim TaeWan , An Jiwoo , Kim Dongho , Jeon Ji Hoon , Kim Sang-il
Published: January 2021

The formation of secondary phases of NiTe2 and NbTe2 in p-type Bi0.5Sb1.5Te3 thermoelectric alloys was investigated through in situ phase separation by using the melt spinning process. Adding stoichiometric Ni, Nb, and Te in a solid-state synthesis process of Bi0.5Sb1.5Te3, followed by rapid solidification by melt spinning, successfully segregated NiTe2 and NbTe2 in the Bi0.5Sb1.5Te3 matrix. Since heterointerfaces of Bi0.5Sb1.5Te3 with NiTe2 and NbTe2 form potential barriers of 0.26 and 0.08 eV, respectively, a low energy carrier filtering effect can be expected; higher Seebeck coefficients and power factors were achieved for Bi0.5Sb1.5Te3(NiTe2)0.01 (250 μV/K and 3.15 mW/mK2), compared to those of Bi0.5Sb1.5Te3 (240 μV/K and 2.69 mW/mK2). However, there was no power factor increase for NbTe2 segregated samples. The decrease in thermal conductivity was seen due to the possible additional phonon scattering by the phase segregations. Consequently, zT at room temperature was enhanced to 0.98 and 0.94 for Bi0.5Sb1.5Te3(NiTe2)0.01 and Bi0.5Sb1.5Te3(NbTe2)0.01, respectively, compared to 0.79 for Bi0.5Sb1.5Te3. The carrier filtering effect induced by NiTe2 segregations with an interface potential barrier of 0.26 eV effectively increased the Seebeck coefficient and power factor, thus improving the zT of p-type Bi0.5Sb1.5Te3, while the interface potential barrier of 0.08 eV of NbTe2 segregation appeared to be too small to induce an effective carrier filtering effect.
Relationship between Chemical Weathering Indices and Shear Strength of Highly and Completely Weathered Granite in South Korea
Authors: Lee Seung-Hwan , Chung Choong-Ki , Song Young-Woo , Woo Sang-Inn
Published: January 2021

In South Korea, weathered granite is widely distributed and has been used as a bearing stratum for various structures. Therefore, it is important to determine the shear strength of the weathered granite. However, it is difficult to obtain reliable shear strength parameters with laboratory tests or standard penetration test (SPT) because weathered granite is easily crushed during the sampling process, and the penetrability of SPT is not secured. On the other hand, it is well known that weathering affects the variation of geotechnical properties. Based on this concept, this study reports a correlation between the shear strength parameters and the chemical weathering indices of the weathered granite. In this study, the pressuremeter test (PMT) was adopted to determine the friction angle of the weathered granite. For the identical granite, the chemical weathering indices (Vogt’s Ratio (VR), Chemical Index of Alteration (CIA), and Mobiles Index (Imob)) were measured by X-ray fluorescence (XRF). An estimating model considering both site-specific characteristics and degree of weathering was used, and the CIA showed the best correlation (R2 = 0.66) with friction angle among the weathering indices. Since the ratio of measured friction angle over the predicted one was distributed in the range from 0.8 to 1.2, it is more reasonable to predict friction angles based on CIA comparing to using the SPT-N value. It can contribute to a better estimation of friction angles of weathered granite.
Study on Mechanical Properties and Application of a New Flexible Bolt
Authors: Xie Zhengzheng , Zhang Nong , Wei Qun , Wang Jin , Sharifzadeh Mostafa
Published: January 2021

As mining depth extends continuously, complex geological environment and strong mining stress pose serious challenges against excavation safety and higher demand for bolt support. To meet the challenges, a new type of flexible bolt is developed that is free from the limitation of excavation height and can be installed quickly. The flexible bolts have a tail structure which is squeezed together by the locking casing and the steel-strand rod. The tail structure forms the thread through the rolling process, and then can be quickly installed by the nut rotation type, which avoids the disadvantages of the cable tension installation. Through the flexible long bolts, the thick anchoring layer of the roof can be constructed, and the safety control of the roadway is realized. To obtain the optimal specifications, locking casings of three diameters and lengths were used to prepare bolt samples for static tensile test. Test results show that when the diameter of locking casing is fixed, the peak resistance increases as the length of locking casing increases, but the increased amplitude tends to reduce gradually. When the length of locking casing is fixed, too large a diameter makes the mechanical property unstable. Finally, the optimal length and diameter of locking casing are set at 120 and 30 mm, respectively. In addition, cyclic loading tests were conducted, the results of which indicate that cyclic loading does not change the stress state within the bolts and that flexible bolts display a stable mechanical property. Field results indicate that flexible bolts achieve low damage of the surrounding rock and control the maximum roof fracture depth within 2.1 m, thus guaranteeing the roadway safety.
Exploring the Intracrine Functions of VEGF-A
Authors: Wiszniak Sophie , Schwarz Quenten
Published: January 2021

Vascular endothelial growth factor A (VEGF-A or VEGF) is a highly conserved secreted signalling protein best known for its roles in vascular development and angiogenesis. Many non-endothelial roles for VEGF are now established, with the discovery that VEGF and its receptors VEGFR1 and VEGFR2 are expressed in many non-vascular cell-types, as well as various cancers. In addition to secreted VEGF binding to its receptors in the extracellular space at the cell membrane (i.e., in a paracrine or autocrine mode), intracellularly localised VEGF is emerging as an important signalling molecule regulating cell growth, survival, and metabolism. This intracellular mode of signalling has been termed “intracrine”, and refers to the direct action of a signalling molecule within the cell without being secreted. In this review, we describe examples of intracrine VEGF signalling in regulating cell growth, differentiation and survival, both in normal cell homeostasis and development, as well as in cancer. We further discuss emerging evidence for the molecular mechanisms underpinning VEGF intracrine function, as well as the implications this intracellular mode of VEGF signalling may have for use and design of anti-VEGF cancer therapeutics.
Variability of Human rDNA
Authors: Smirnov Evgeny , Chmúrčiaková Nikola , Liška František , Bažantová Pavla , Cmarko Dušan
Published: January 2021

In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
Genetic Approach to Elucidate the Role of Cyclophilin D in Traumatic Brain Injury Pathology
Authors: Readnower Ryan D. , Hubbard William Brad , Kalimon Olivia J. , Geddes James W. , Sullivan Patrick G.
Published: January 2021

Cyclophilin D (CypD) has been shown to play a critical role in mitochondrial permeability transition pore (mPTP) opening and the subsequent cell death cascade. Studies consistently demonstrate that mitochondrial dysfunction, including mitochondrial calcium overload and mPTP opening, is essential to the pathobiology of cell death after a traumatic brain injury (TBI). CypD inhibitors, such as cyclosporin A (CsA) or NIM811, administered following TBI, are neuroprotective and quell neurological deficits. However, some pharmacological inhibitors of CypD have multiple biological targets and, as such, do not directly implicate a role for CypD in arbitrating cell death after TBI. Here, we reviewed the current understanding of the role CypD plays in TBI pathobiology. Further, we directly assessed the role of CypD in mediating cell death following TBI by utilizing mice lacking the CypD encoding gene Ppif. Following controlled cortical impact (CCI), the genetic knockout of CypD protected acute mitochondrial bioenergetics at 6 h post-injury and reduced subacute cortical tissue and hippocampal cell loss at 18 d post-injury. The administration of CsA following experimental TBI in Ppif-/- mice improved cortical tissue sparing, highlighting the multiple cellular targets of CsA in the mitigation of TBI pathology. The loss of CypD appeared to desensitize the mitochondrial response to calcium burden induced by TBI; this maintenance of mitochondrial function underlies the observed neuroprotective effect of the CypD knockout. These studies highlight the importance of maintaining mitochondrial homeostasis after injury and validate CypD as a therapeutic target for TBI. Further, these results solidify the beneficial effects of CsA treatment following TBI.