bluuebunny/crossref_metadata_2025 huggingface dataset:
Rolling Circle Amplification (RCA)-Mediated Genome-Wide ihpRNAi Mutant Library Construction in Brassica napus
Authors: Zhao Shengbo , Luo Junling , Zeng Xinhua , Li Keqi , Yuan Rong , Zhu Li , Li Xiaofei , Wu Gang , Yan Xiaohong
Published: October 2020

With the successful completion of genomic sequencing for Brassica napus, identification of novel genes, determination of functions performed by genes, and exploring the molecular mechanisms underlying important agronomic traits were challenged. Mutagenesis-based functional genomics techniques including chemical, physical, and insertional mutagenesis have been used successfully in the functional characterization of genes. However, these techniques had their disadvantages and inherent limitations for allopolyploid Brassica napus, which contained a large number of homologous and redundant genes. Long intron-spliced hairpin RNA (ihpRNA) constructs which contained inverted repeats of the target gene separated by an intron, had been shown to be very effective in triggering RNAi in plants. In the present study, the genome-wide long ihpRNA library of B. napus was constructed with the rolling circle amplification (RCA)-mediated technology. Using the phytoene desaturase (PDS) gene as a target control, it was shown that the RCA-mediated long ihpRNA construct was significantly effective in triggering gene silence in B. napus. Subsequently, the resultant long ihpRNA library was transformed into B. napus to produce corresponding RNAi mutants. Among the obtained transgenic ihpRNA population of B. napus, five ihpRNA lines with observable mutant phenotypes were acquired including alterations in the floral model and the stamen development. The target genes could be quickly identified using specific primers. These results showed that the RCA-mediated ihpRNA construction method was effective for the genome-wide long ihpRNA library of B. napus, therefore providing a platform for study of functional genomics in allopolyploid B. napus.
Peroxisome Proliferator-Activated Receptor γ Coactivator 1α Activates Vascular Endothelial Growth Factor That Protects Against Neuronal Cell Death Following Status Epilepticus through PI3K/AKT and MEK/ERK Signaling
Authors: Huang Jyun-Bin , Hsu Shih-Pin , Pan Hsiu-Yung , Chen Shang-Der , Chen Shu-Fang , Lin Tsu-Kung , Liu Xuan-Ping , Li Jie-Hau , Chen Nai-Ching , Liou Chia-Wei , Hsu Chung-Yao , Chuang Hung-Yi , Chuang Yao-Chung
Published: October 2020

Status epilepticus may cause molecular and cellular events, leading to hippocampal neuronal cell death. Peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) is an important regulator of vascular endothelial growth factor (VEGF) and VEGF receptor 2 (VEGFR2), also known as fetal liver kinase receptor 1 (Flk-1). Resveratrol is an activator of PGC-1α. It has been suggested to provide neuroprotective effects in epilepsy, stroke, and neurodegenerative diseases. In the present study, we used microinjection of kainic acid into the left hippocampal CA3 region in Sprague Dawley rats to induce bilateral prolonged seizure activity. Upregulating the PGC-1α pathway will increase VEGF/VEGFR2 (Flk-1) signaling and further activate some survival signaling that includes the mitogen activated protein kinase kinase (MEK)/mitogen activated protein kinase (ERK) and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathways and offer neuroprotection as a consequence of apoptosis in the hippocampal neurons following status epilepticus. Otherwise, downregulation of PGC-1α by siRNA against pgc-1α will inhibit VEGF/VEGFR2 (Flk-1) signaling and suppress pro-survival PI3K/AKT and MEK/ERK pathways that are also accompanied by hippocampal CA3 neuronal cell apoptosis. These results may indicate that the PGC-1α induced VEGF/VEGFR2 pathway may trigger the neuronal survival signaling, and the PI3K/AKT and MEK/ERK signaling pathways. Thus, the axis of PGC-1α/VEGF/VEGFR2 (Flk-1) and the triggering of downstream PI3K/AKT and MEK/ERK signaling could be considered an endogenous neuroprotective effect against apoptosis in the hippocampus following status epilepticus.
Bone Marrow-Derived Mononuclear Cell Transplants Decrease Retinal Gliosis in Two Animal Models of Inherited Photoreceptor Degeneration
Authors: Di Pierdomenico Johnny , García-Ayuso Diego , González-Herrero María Elena Rodríguez , García-Bernal David , Blanquer Miguel , Bernal-Garro José Manuel , García-Hernández Ana M. , Vidal-Sanz Manuel , Villegas-Pérez María P.
Published: October 2020

Inherited photoreceptor degenerations are not treatable diseases and a frequent cause of blindness in working ages. In this study we investigate the safety, integration and possible rescue effects of intravitreal and subretinal transplantation of adult human bone-marrow-derived mononuclear stem cells (hBM-MSCs) in two animal models of inherited photoreceptor degeneration, the P23H-1 and the Royal College of Surgeons (RCS) rat. Immunosuppression was started one day before the injection and continued through the study. The hBM-MSCs were injected in the left eyes and the animals were processed 7, 15, 30 or 60 days later. The retinas were cross-sectioned, and L- and S- cones, microglia, astrocytes and Müller cells were immunodetected. Transplantations had no local adverse effects and the CD45+ cells remained for up to 15 days forming clusters in the vitreous and/or a 2–3-cells-thick layer in the subretinal space after intravitreal or subretinal injections, respectively. We did not observe increased photoreceptor survival nor decreased microglial cell numbers in the injected left eyes. However, the injected eyes showed decreased GFAP immunoreactivity. We conclude that intravitreal or subretinal injection of hBM-MSCs in dystrophic P23H-1 and RCS rats causes a decrease in retinal gliosis but does not have photoreceptor neuroprotective effects, at least in the short term. However, this treatment may have a potential therapeutic effect that merits further investigation.
Streamlining Quantitative Analysis of Long RNA Sequencing Reads
Authors: Oeck Sebastian , Tüns Alicia I. , Hurst Sebastian , Schramm Alexander
Published: October 2020

Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often lacks cost- and time-efficient workflows. Although kit-based workflows and benchtop platforms for RNA sequencing provide software options, e.g., cloud-based tools to analyze basecalled reads, quantitative, and easy-to-use solutions for transcriptome analysis, especially for non-human data, are missing. We therefore developed a user-friendly tool, termed Alignator, for rapid analysis of long RNA reads requiring only FASTQ files and an Ensembl cDNA database reference. After successful mapping, Alignator generates quantitative information for each transcript and provides a table in which sequenced and aligned RNA are stored for further comparative analyses.
Strain-Dependent Prion Infection in Mice Expressing Prion Protein with Deletion of Central Residues 91–106
Authors: Uchiyama Keiji , Miyata Hironori , Yamaguchi Yoshitaka , Imamura Morikazu , Okazaki Mariya , Pasiana Agriani Dini , Chida Junji , Hara Hideyuki , Atarashi Ryuichiro , Watanabe Hitomi , Kondoh Gen , Sakaguchi Suehiro
Published: October 2020

Conformational conversion of the cellular prion protein, PrPC, into the abnormally folded isoform, PrPSc, is a key pathogenic event in prion diseases. However, the exact conversion mechanism remains largely unknown. Transgenic mice expressing PrP with a deletion of the central residues 91–106 were generated in the absence of endogenous PrPC, designated Tg(PrP∆91–106)/Prnp0/0 mice and intracerebrally inoculated with various prions. Tg(PrP∆91–106)/Prnp0/0 mice were resistant to RML, 22L and FK-1 prions, neither producing PrPSc∆91–106 or prions in the brain nor developing disease after inoculation. However, they remained marginally susceptible to bovine spongiform encephalopathy (BSE) prions, developing disease after elongated incubation times and accumulating PrPSc∆91–106 and prions in the brain after inoculation with BSE prions. Recombinant PrP∆91-104 converted into PrPSc∆91–104 after incubation with BSE-PrPSc-prions but not with RML- and 22L–PrPSc-prions, in a protein misfolding cyclic amplification assay. However, digitonin and heparin stimulated the conversion of PrP∆91–104 into PrPSc∆91–104 even after incubation with RML- and 22L-PrPSc-prions. These results suggest that residues 91–106 or 91–104 of PrPC are crucially involved in prion pathogenesis in a strain-dependent manner and may play a similar role to digitonin and heparin in the conversion of PrPC into PrPSc.
The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity
Authors: Kreimendahl Sebastian , Rassow Joachim
Published: October 2020

Tom70 is a versatile adaptor protein of 70 kDa anchored in the outer membrane of mitochondria in metazoa, fungi and amoeba. The tertiary structure was resolved for the Tom70 of yeast, showing 26 α-helices, most of them participating in the formation of 11 tetratricopeptide repeat (TPR) motifs. Tom70 serves as a docking site for cytosolic chaperone proteins and co-chaperones and is thereby involved in the uptake of newly synthesized chaperone-bound proteins in mitochondrial biogenesis. In yeast, Tom70 additionally mediates ER-mitochondria contacts via binding to sterol transporter Lam6/Ltc1. In mammalian cells, TOM70 promotes endoplasmic reticulum (ER) to mitochondria Ca2+ transfer by association with the inositol-1,4,5-triphosphate receptor type 3 (IP3R3). TOM70 is specifically targeted by the Bcl-2-related protein MCL-1 that acts as an anti-apoptotic protein in macrophages infected by intracellular pathogens, but also in many cancer cells. By participating in the recruitment of PINK1 and the E3 ubiquitin ligase Parkin, TOM70 can be implicated in the development of Parkinson’s disease. TOM70 acts as receptor of the mitochondrial antiviral-signaling protein (MAVS) and thereby participates in the corresponding system of innate immunity against viral infections. The protein encoded by Orf9b in the genome of SARS-CoV-2 binds to TOM70, probably compromising the synthesis of type I interferons.
Growth Factors in the Carotid Body—An Update
Authors: Stocco Elena , Barbon Silvia , Tortorella Cinzia , Macchi Veronica , De Caro Raffaele , Porzionato Andrea
Published: October 2020

The carotid body may undergo plasticity changes during development/ageing and in response to environmental (hypoxia and hyperoxia), metabolic, and inflammatory stimuli. The different cell types of the carotid body express a wide series of growth factors and corresponding receptors, which play a role in the modulation of carotid body function and plasticity. In particular, type I cells express nerve growth factor, brain-derived neurotrophic factor, neurotrophin 3, glial cell line-derived neurotrophic factor, ciliary neurotrophic factor, insulin-like-growth factor-I and -II, basic fibroblast growth factor, epidermal growth factor, transforming growth factor-α and -β, interleukin-1β and -6, tumor necrosis factor-α, vascular endothelial growth factor, and endothelin-1. Many specific growth factor receptors have been identified in type I cells, indicating autocrine/paracrine effects. Type II cells may also produce growth factors and express corresponding receptors. Future research will have to consider growth factors in further experimental models of cardiovascular, metabolic, and inflammatory diseases and in human (normal and pathologic) samples. From a methodological point of view, microarray and/or proteomic approaches would permit contemporary analyses of large groups of growth factors. The eventual identification of physical interactions between receptors of different growth factors and/or neuromodulators could also add insights regarding functional interactions between different trophic mechanisms.
Nitrite Reductase 1 Is a Target of Nitric Oxide-Mediated Post-Translational Modifications and Controls Nitrogen Flux and Growth in Arabidopsis
Authors: Costa-Broseta Álvaro , Castillo MariCruz , León José
Published: October 2020

Plant growth is the result of the coordinated photosynthesis-mediated assimilation of oxidized forms of C, N and S. Nitrate is the predominant N source in soils and its reductive assimilation requires the successive activities of soluble cytosolic NADH-nitrate reductases (NR) and plastid stroma ferredoxin-nitrite reductases (NiR) allowing the conversion of nitrate to nitrite and then to ammonium. However, nitrite, instead of being reduced to ammonium in plastids, can be reduced to nitric oxide (NO) in mitochondria, through a process that is relevant under hypoxic conditions, or in the cytoplasm, through a side-reaction catalyzed by NRs. We use a loss-of-function approach, based on CRISPR/Cas9-mediated genetic edition, and gain-of-function, using transgenic overexpressing HA-tagged Arabidopsis NiR1 to characterize the role of this enzyme in controlling plant growth, and to propose that the NO-related post-translational modifications, by S-nitrosylation of key C residues, might inactivate NiR1 under stress conditions. NiR1 seems to be a key target in regulating nitrogen assimilation and NO homeostasis, being relevant to the control of both plant growth and performance under stress conditions. Because most higher plants including crops have a single NiR, the modulation of its function might represent a relevant target for agrobiotechnological purposes.
LncLocation: Efficient Subcellular Location Prediction of Long Non-Coding RNA-Based Multi-Source Heterogeneous Feature Fusion
Authors: Feng Shiyao , Liang Yanchun , Du Wei , Lv Wei , Li Ying
Published: October 2020

Recent studies uncover that subcellular location of long non-coding RNAs (lncRNAs) can provide significant information on its function. Due to the lack of experimental data, the number of lncRNAs is very limited, experimentally verified subcellular localization, and the numbers of lncRNAs located in different organelle are wildly imbalanced. The prediction of subcellular location of lncRNAs is actually a multi-classification small sample imbalance problem. The imbalance of data results in the poor recognition effect of machine learning models on small data subsets, which is a puzzling and challenging problem in the existing research. In this study, we integrate multi-source features to construct a sequence-based computational tool, lncLocation, to predict the subcellular location of lncRNAs. Autoencoder is used to enhance part of the features, and the binomial distribution-based filtering method and recursive feature elimination (RFE) are used to filter some of the features. It improves the representation ability of data and reduces the problem of unbalanced multi-classification data. By comprehensive experiments on different feature combinations and machine learning models, we select the optimal features and classifier model scheme to construct a subcellular location prediction tool, lncLocation. LncLocation can obtain an 87.78% accuracy using 5-fold cross validation on the benchmark data, which is higher than the state-of-the-art tools, and the classification performance, especially for small class sets, is improved significantly.
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Authors: Preto A. J. , Moreira Irina S.
Published: October 2020

Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein–protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) prediction methods. However, the availability of a much larger array of protein sequences in comparison to determined tree-dimensional structures indicates that a sequence-based HS predictor has the potential to be more useful for the scientific community. Herein, we present SPOTONE, a new ML predictor able to accurately classify protein HS via sequence-only features. This algorithm shows accuracy, AUROC, precision, recall and F1-score of 0.82, 0.83, 0.91, 0.82 and 0.85, respectively, on an independent testing set. The algorithm is deployed within a free-to-use webserver, only requiring the user to submit a FASTA file with one or more protein sequences.
A Systematic Review of the Application of Maturity Models in Universities
Authors: Tocto-Cano Esteban , Paz Collado Sandro , López-Gonzales Javier Linkolk , Turpo-Chaparro Josué E.
Published: October 2020

A maturity model is a widely used tool in software engineering and has mostly been extended to domains such as education, health, energy, finance, government, and general use. It is valuable for evaluations and continuous improvement of business processes or certain aspects of organizations, as it represents a more organized and systematic way of doing business. In this paper, we only focus on college higher education. For this reason, we present a novel approach that allows detecting some gaps in the existing maturity models for universities, as they are not models that address the dimensions in their entirety. To identify these models and their validities, as well as a classification of models that were identified in universities, we carried out a systematic literature review on 27,289 articles retrieved with respect to maturity models and published in peer-reviewed journals between 2007 and 2020. We found 23 articles that find maturity models applied in universities, through exclusion and inclusion criteria. We then grouped these items into nine categories with specific purposes. We concluded that maturity models used in Universities move towards agility, which is supported by the semantic web.
Design of Distributed Discrete-Event Simulation Systems Using Deep Belief Networks
Authors: Cortes Edwin , Rabelo Luis , Sarmiento Alfonso T. , Gutierrez Edgar
Published: October 2020

In this research study, we investigate the ability of deep learning neural networks to provide a mapping between features of a parallel distributed discrete-event simulation (PDDES) system (software and hardware) to a time synchronization scheme to optimize speedup performance. We use deep belief networks (DBNs). DBNs, which due to their multiple layers with feature detectors at the lower layers and a supervised scheme at the higher layers, can provide nonlinear mappings. The mapping mechanism works by considering simulation constructs, hardware, and software intricacies such as simulation objects, concurrency, iterations, routines, and messaging rates with a particular importance level based on a cognitive approach. The result of the mapping is a synchronization scheme such as breathing time buckets, breathing time warp, and time warp to optimize speedup. The simulation-optimization technique outlined in this research study is unique. This new methodology could be realized within the current parallel and distributed simulation modeling systems to enhance performance.
In Full Force. Mechanotransduction and Morphogenesis during Homeostasis and Tissue Regeneration
Authors: Tsata Vasiliki , Beis Dimitris
Published: October 2020

The interactions of form and function have been the focus of numerous studies in the context of development and more recently regeneration. Our understanding on how cells, tissues and organs sense and interpret external cues, such as mechanical forces, is becoming deeper as novel techniques in imaging are applied and the relevant signaling pathways emerge. These cellular responses can be found from bacteria to all multicellular organisms such as plants and animals. In this review, we focus on hemodynamic flow and endothelial shear stress during cardiovascular development and regeneration, where the interactions of morphogenesis and proper function are more prominent. In addition, we address the recent literature on the role of extracellular matrix and fibrotic response during tissue repair and regeneration. Finally, we refer to examples where the integration of multi-disciplinary approaches to understand the biomechanics of cellular responses could be utilized in novel medical applications.
Application of A Convolutional Neural Network in The Diagnosis of Gastric Mesenchymal Tumors on Endoscopic Ultrasonography Images
Authors: Kim Yoon Ho , Kim Gwang Ha , Kim Kwang Baek , Lee Moon Won , Lee Bong Eun , Baek Dong Hoon , Kim Do Hoon , Park Jun Chul
Published: September 2020

Background and Aims: Endoscopic ultrasonography (EUS) is a useful diagnostic modality for evaluating gastric mesenchymal tumors; however, differentiating gastrointestinal stromal tumors (GISTs) from benign mesenchymal tumors such as leiomyomas and schwannomas remains challenging. For this reason, we developed a convolutional neural network computer-aided diagnosis (CNN-CAD) system that can analyze gastric mesenchymal tumors on EUS images. Methods: A total of 905 EUS images of gastric mesenchymal tumors (pathologically confirmed GIST, leiomyoma, and schwannoma) were used as a training dataset. Validation was performed using 212 EUS images of gastric mesenchymal tumors. This test dataset was interpreted by three experienced and three junior endoscopists. Results: The sensitivity, specificity, and accuracy of the CNN-CAD system for differentiating GISTs from non-GIST tumors were 83.0%, 75.5%, and 79.2%, respectively. Its diagnostic specificity and accuracy were significantly higher than those of two experienced and one junior endoscopists. In the further sequential analysis to differentiate leiomyoma from schwannoma in non-GIST tumors, the final diagnostic accuracy of the CNN-CAD system was 75.5%, which was significantly higher than that of two experienced and one junior endoscopists. Conclusions: Our CNN-CAD system showed high accuracy in diagnosing gastric mesenchymal tumors on EUS images. It may complement the current clinical practices in the EUS diagnosis of gastric mesenchymal tumors.
18F-FDG PET/MR versus MR Alone in Whole-Body Primary Staging and Restaging of Patients with Rectal Cancer: What Is the Benefit of PET?
Authors: Li Yan , Mueller Laura Isabel , Neuhaus Jan Peter , Bertram Stefanie , Schaarschmidt Benedikt Michael , Demircioglu Aydin , Ludwig Johannes Maximilian , Kirchner Julian , Rischpler Christoph , Herrmann Ken , Catalano Onofrio Antonio , Umutlu Lale
Published: September 2020

Background: To investigate and compare the diagnostic performance of 18F-Fluorodeoxyglucose (18F-FDG) PET/MR and MR alone in whole-body primary staging and restaging of patients with rectal cancer. Methods: A retrospective analysis was performed to evaluate diagnostic accuracies of combined reading of PET/MR and MR alone in T, N and M staging against the reference standard. Inter-observer agreement regarding TNM staging was calculated separately for PET/MR and MR alone. Results: A total of 39 studies of 34 patients could be evaluated. Diagnostic accuracies of PET/MR and MR alone were the same in locoregional T staging. For predicting N+ stage, the specificity of combined reading of PET and MR (0.917 and 0.833 for reader 1 and 2, respectively) was slightly higher than MR alone (0.833 and 0.75) without significantly increasing the overall accuracy (0.783 vs. 0.783 and 0.783 vs. 0.739). For detecting distant metastasis, the sensitivities of PET/MR and MR alone were shown equal (1.0 vs. 1.0 and 0.938 vs. 0.938), while the specificity of PET/MR was marginally lower (0.87 vs. 0.913 and 0.826 vs. 0.87). The inter-observer agreements were good to excellent in M (κ = 0.64 and 0.637 for PET/MR and MR alone, p < 0.001) and N staging (0.819 and 0.738, p < 0.001).Conclusion: PET did not yield a significant improvement in diagnostic accuracy of PET/MR in TNM staging of rectal cancer, since MR alone facilitated accurate classification of disease stage with good to excellent inter-observer agreement.
PkMin: Peak Power Minimization for Multi-Threaded Many-Core Applications
Authors: Maity Arka , Pathania Anuj , Mitra Tulika
Published: September 2020

Multiple multi-threaded tasks constitute a modern many-core application. An accompanying generic Directed Acyclic Graph (DAG) represents the execution precedence relationship between the tasks. The application comes with a hard deadline and high peak power consumption. Parallel execution of multiple tasks on multiple cores results in a quicker execution, but higher peak power. Peak power single-handedly determines the involved cooling costs in many-cores, while its violations could induce performance-crippling execution uncertainties. Less task parallelization, on the other hand, results in lower peak power, but a more prolonged deadline violating execution. The problem of peak power minimization in many-cores is to determine task-to-core mapping configuration in the spatio-temporal domain that minimizes the peak power consumption of an application, but ensures application still meets the deadline. All previous works on peak power minimization for many-core applications (with or without DAG) assume only single-threaded tasks. We are the first to propose a framework, called PkMin, which minimizes the peak power of many-core applications with DAG that have multi-threaded tasks. PkMin leverages the inherent convexity in the execution characteristics of multi-threaded tasks to find a configuration that satisfies the deadline, as well as minimizes peak power. Evaluation on hundreds of applications shows PkMin on average results in 49.2% lower peak power than a similar state-of-the-art framework.
A Method to Minimize the Data Size of a Lightweight Model for Ship and Offshore Plant Structure Using Part Characteristics
Authors: Kwon Kiyoun , Mun Duhwan
Published: September 2020

One of the most widely used methods for representing the shapes of ships and offshore plants is triangular mesh, which has a simple structure and is easy to visualize. In particular, lightweight models composed of triangular meshes are often used as a sharing medium for three-dimensional (3D) shape design results in the collaboration process among many stakeholders participating in the construction process. Currently, there are demands for visualizing the total shapes of ships or offshore plants for design review, interference check, construction monitoring, and securing maintenance space. However, this requires high computing power and much time due to the large size of the triangular mesh model. We have two general solutions as follows: simplifying the shape of the ship and offshore plant structure and reducing the size of the lightweight file itself. Between them, this study proposes a method for reducing the lightweight file. This method classifies the part types of the ship or offshore plant structure and then only stores the minimum triangular mesh information for each part type, excluding unnecessary information. Then, the topographic information of triangular meshes is stored together in the lightweight file to shorten the time required for restoration of the lightweight file.
Southern African Wave Model Sensitivities and Accuracies
Authors: Rautenbach Christo , Barnes Michael A. , Wang David W. , Dykes James
Published: October 2020

Numerous studies have identified the complexities of the wave climatology around the South African coast, but limited studies have investigated these complex dynamics in the available literature. Several freely available parameterized wave boundary conditions are produced around southern Africa. However, none of these are fully spectral outputs from global or larger regional spectral wave models. This constraint results in local engineering and scientific organizations, reconstructing their own spectral boundary conditions. For coastal models, this is a reasonable assumption, assuming that the single parameterization is accurate and a representation of a non-multimodal sea state. The South African Weather Service (SAWS) Marine unit recently launched their coupled, operational wave and storm surge forecasting model. The aim of the SAWS Wave and Storm Surge (SWaSS) platform was to provide accurate, high-resolution coastal forecasts for the entire South African coastline. The present investigation thus presents the validation of the spectral wave component of the coupled system, developed in Delft3D. Various wave boundary reconstructions are investigated together with the two most used and well-known whitecapping formulations. Validation is performed with both in situ wave-rider buoy data (at nine locations along the coastline) and regional remotely sensed, along track, altimetry data. Full model performance statistics are provided, and the accuracy of the model is discussed.
Susceptibility of the Candida haemulonii Complex to Echinocandins: Focus on Both Planktonic and Biofilm Life Styles and a Literature Review
Authors: Ramos Lívia S. , Silva Laura N. , Branquinha Marta H. , Santos André L. S.
Published: October 2020

Candida haemulonii complex (C. haemulonii, C. duobushaemulonii and C. haemulonii var. vulnera) is well-known for its resistance profile to different available antifungal drugs. Although echinocandins are the most effective class of antifungal compounds against the C. haemulonii species complex, clinical isolates resistant to caspofungin, micafungin and anidulafungin have already been reported. In this work, we present a literature review regarding the effects of echinocandins on this emergent fungal complex. Published data has revealed that micafungin and anidulafungin were more effective than caspofungin against the species forming the C. haemulonii complex. Subsequently, we investigated the susceptibilities of both planktonic and biofilm forms of 12 Brazilian clinical isolates of the C. haemulonii complex towards caspofungin and micafungin (anidulafungin was unavailable). The planktonic cells of all the fungal isolates were susceptible to both of the test echinocandins. Interestingly, echinocandins caused a significant reduction in the biofilm metabolic activity (viability) of almost all fungal isolates (11/12, 91.7%). Generally, the biofilm biomasses were also affected (reduction range 20–60%) upon exposure to caspofungin and micafungin. This is the first report of the anti-biofilm action of echinocandins against the multidrug-resistant opportunistic pathogens comprising the C. haemulonii complex, and unveils the therapeutic potential of these compounds.
The Economic Resilience of the Austrian Agriculture since the EU Accession
Authors: Quendler Erika , Morkūnas Mangirdas
Published: October 2020

Ensuring sustainable and economically viable agriculture requires economic resilience before, throughout, and after a shock. This paper studies the economic resilience of Austrian agriculture within the period of 1995 to 2019. However, methods for tracking changes in economic resilience have so far seen only limited application in agriculture. The index for the analysis and measurement of economic resilience is based on four areas: financial flexibility, stability in following the development path, diversification of activities, and diversification of export markets. As results show, Austrian agriculture is of interest because of the very high level of economic resilience, ranging from 0.83 to 0.92 in the period researched, thereby displaying a high capacity to absorb shocks. Generally, these results indicate that Austrian agriculture is forgiving of shocks and thus very economically resilient. These results provide context for developing generalizations on economic resilience in agriculture and its fundamental function for producing effective food security within a sustainable transition path. Some concluding suggestions propose possible future areas of research.
Agroforestry Innovation through Planned Farmer Behavior: Trimming in Pine–Coffee Systems
Authors: Cahyono Edi Dwi , Fairuzzana Salsabila , Willianto Deltanti , Pradesti Eka , McNamara Niall P. , Rowe Rebecca L. , Noordwijk Meine van
Published: September 2020

Knowledge transfer depends on the motivations of the target users. A case study of the intention of Indonesian coffee farmers to use a tree canopy trimming technique in pine–based agroforestry highlights path-dependency and complexity of social-ecological relationships. Farmers have contracts permitting coffee cultivation under pine trees owned by the state forestry company but have no right to fell trees. A multidisciplinary international team of scientists supported farmers at the University of Brawijaya Forest in East Java to trial canopy trimming to improve light for coffee production while maintaining tree density. Data were collected using surveys through interviews, case study analysis using in-depth interviews, focus group discussions and nonparticipant observations. Using the Theory of Planned Behavior, we found that though farmer attitudes toward trimming techniques were positive, several factors needed to be scrutinized: perceived limited socio-policy support and resources. While there is hope that canopy trimming can improve coffee production and local ecosystem services, a participatory and integrative extension and communication strategy will be needed. In the relationship between farmers as agents and forest authorities as principals, any agroforestry innovation needs to incorporate knowledge and concerns in the triangle of farmers, policymakers and empirical science.
Development of Postoperative Pain in Patients with End-Stage Knee Osteoarthritis Is Associated with Upregulation of Genes Related to Extracellular Matrix Degradation, Inflammation, and Apoptosis Measured in the Peripheral Blood before Knee Surgery
Authors: Tchetina Elena V. , Glemba Kseniya E. , Markova Galina A. , Naryshkin Evgeniy A. , Taskina Elena A. , Makarov Maksim A. , Lila Aleksandr M.
Published: September 2020

Osteoarthritis (OA) pain implies an indication for joint replacement in patients with end-stage OA. However, chronic postoperative pain is observed in 10–40% of patients with OA. Here, we identified genes whose expression in the peripheral blood before surgery could denote the risk of postoperative pain development. We examined the peripheral blood of 26 healthy subjects and 50 patients with end-stage OA prior to joint replacement surgery. Pain was evaluated before surgery using the visual analog scale (VAS) index and neuropathic pain questionnaires, Douleur Neuropathique 4 Questions (DN4) and PainDETECT questionnaires. Functional activity was assessed using the Western Ontario and McMaster Universities osteoarthritis index (WOMAC). Three and six months after surgery, pain indices according to VAS of 30% and higher were considered. Metalloproteinase (MMP)-9 and tissue inhibitor of metalloproteinase (TIMP)1 protein levels were measured using ELISA in the peripheral blood mononuclear cells (PBMCs). Total RNA isolated from whole blood was analysed using quantitative real-time RT-PCR for caspase-3, MMP-9, TIMP1, cathepsins K and S, tumour necrosis factor (TNF)α, interleukin (IL)-1β, and cyclooxygenase (COX)-2 gene expression. Seventeen patients reported post-surgical pain. Expression of cathepsins K and S, caspase-3, TIMP1, IL-1β, and TNFα genes before surgery was significantly higher in these patients compared to pain-free patients with OA. Receiver-operating characteristic (ROC) curve analyses confirmed significant associations between these gene expressions and the likelihood of pain development after arthroplasty. High baseline expression of genes associated with extracellular matrix destruction (cathepsins S and K, TIMP1), inflammation (IL-1β, TNFα), and apoptosis (caspase-3) measured in the peripheral blood of patients with end-stage OA before knee arthroplasty might serve as an important biomarker of postoperative pain development.
Numerical Analysis of Bowing Phenomenon Due to Thermal Stresses in Marble Slabs
Authors: Ito William Hideki , Ferrero Anna Maria , de Queiroz Paulo Ivo Braga
Published: October 2020

Bowing is a pathology known by the deformation experienced in some external covering systems in ornamental stones, especially in marble, and thermal action is one of the key factors that lead to this degradation. Previous studies presented remarkable contributions about the mechanical behavior of bowing but they were based on classical beam’s theory and improper assumptions might mislead the evaluation of internal stresses. This study proposes to evaluate internal stresses in bowing due to thermal loading considering the true deformed shape in continuum media. Finite displacement concepts are proposed to calculate stress-strain relationship and comparison with linear elastic theory is also addressed. Internal stresses not predictable in the Euler-Bernoulli beam were found in parametric analyses. Moreover, the numerical analysis accomplished in this paper indicates that transient heat flux should induce higher stresses than just considering higher gradients of temperature in steady flux which could explain the larger decohesion through width in bowing tests.
Curcumin Incorporated Poly(Butylene Adipate-co-Terephthalate) Film with Improved Water Vapor Barrier and Antioxidant Properties
Authors: Roy Swarup , Rhim Jong-Whan
Published: October 2020

Curcumin incorporated poly(butylene adipate-co-terephthalate) (PBAT) based film was fabricated. Curcumin has uniformly distributed in the PBAT matrix to form a bright yellow PBAT/curcumin film. The PBAT/curcumin film has slightly reduced tensile strength and flexibility than the neat PBAT film, while the thermal stability of the film has not changed significantly. The blending of curcumin significantly decreased the water vapor permeability of the PBAT film. Additionally, the PBAT/curcumin film showed potent antioxidant activity with some antimicrobial activity. The PBAT/curcumin films with improved water vapor barrier and additional functions can be used for active packaging applications.
Preparation and Properties of Microcrystalline Cellulose/Fish Gelatin Composite Film
Authors: Pan Ling , Li Peng , Tao Yubo
Published: October 2020

As a natural macromolecule-based biomaterial, fish gelatin is used in medical materials for its low pathogen infection risk. However, because of poor mechanical properties, its application has been limited. In this study, microcrystalline cellulose-reinforced fish gelatin (FG/MCC) composite films were prepared with a biological cross-linking agent (genipin) under ultrasonic treatment. SEM micrographs showed that the smooth microstructure of FG film became increasingly disordered with the addition of MCC. The infrared spectrum analysis (FTIR) demonstrated the existence of hydrogen bond interaction between MCC and FG. Compared with the pure FG film, the tensile strength (TS) and modulus of elasticity (MOE) of composite films with MCC were improved, and the elongation at break (EAB) and swelling ratios (SR) were decreased. Ultrasonic treatment could further improve TS, MOE, and SR. When the composite film was prepared with 15% MCC and treated with ultrasound, the TS and MOE increased by 115% and 227%, respectively, while the EAB decreased by 35% and the SR decreased by 4% in comparison with pure FG films. Thermo-gravimetric analysis (TGA) showed that the FG/MCC composite films were stable below 100 °C. The above results indicate that the FG/MCC films have optimistic application prospects in the biomedical field.
Corrosion Resistance of Inconel 625 CMT-Cladded Layers after Long-Term Exposure to Biomass and Waste Ashes in High-Temperature Conversion Processes
Authors: Błoniarz Aleksandra , Schreiner Marcus , Reinmöller Markus , Kopia Agnieszka
Published: October 2020

The present study investigated the effect of corrosion on an Inconel 625-cladded layer using the cold metal transfer (CMT) method. The corrosion was caused by various ashes and high process temperatures. The ashes were obtained from the biomasses of mixed wood and oat straw, as well as from sewage sludge, by ashing. Long-term corrosion tests were carried out at 650 °C over a period of 1000 h. The chemical composition, mineral phases, and corrosion effects were studied by X-ray fluorescence (XRF), scanning electron microscopy equipped with energy-dispersive X-rays (SEM–EDX), and X-ray diffraction (XRD) from the surface and on the cross-section of the samples. The chemical composition of the ashes was quite different, but representative of their particular fuel. Together with the effects of the operating temperature and mass transfer, significant differences in the degree of the corrosion depth were detected for the various ashes. For the investigated samples, the corrosion mechanisms were inferred based on the identified corrosion products.
Characterisation of Wheat Straw Pellets Individually and in Combination with Cassava Starch or Calcium Carbonate under Various Compaction Conditions: Determination of Pellet Strength and Water Absorption Capacity
Authors: Matkowski Patryk , Lisowski Aleksander , Świętochowski Adam
Published: October 2020

This study aimed to optimise the production conditions of wheat straw (WS) pellets and pellets with the additives of cassava starch (CS) or calcium carbonate (CC) based on the criteria of pellet strength and water absorption by crushed pellets. The pellets produced using a 2–10%-wt/wt additive ratio, material moisture of 10–30% w.b., die height of 66–86 mm, and material temperature of 78–108 °C were tested. The influence these factors on the strength parameters of pellets was different than on the water absorption by the crushed pellets. The pellets made of WS blended with CC additive were characterised by better strength parameters and the compressed pellets were characterised by better water absorption than those with CS. High and positive correlation among specific pellet compression work, elasticity modulus for pellet compression, and tensile strength values were observed. As the strength parameters of pellets showed high correlation with single pellet density, for the consistency of conclusions, the optimal conditions for pellet production were assumed based on the density. For optimal conditions at 4% wt/wt additive ratio, 23% w.b. material moisture, 78 mm die height, and 80 °C material temperature, the specific pellet compression work was 3.22 mJ·mm−2, elasticity modulus was 5.78 MPa, and maximum tensile strength of the pellets was 2.68 MPa; moreover, the water absorption by crushed pellets amounted to 2.60 g H2O·g−1 of dry matter.
Modulus and Strength of Concretes with Alternative Materials
Authors: Jacintho Ana Elisabete Paganelli Guimarães de Avila , Cavaliere Ivanny Soares Gomes , Pimentel Lia Lorena , Forti Nádia Cazarim Silva
Published: October 2020

This paper presents a study with concretes produced with natural aggregates, recycled concrete aggregates (RCA) and waste porcelain aggregates (WPA). The study analyzed the influence of recycled aggregates in the mechanical properties of conventional concretes and evaluated the difference between measured and predicted values of elasticity modulus. The incorporation of WPA in concrete showed better mechanical results compared to the concretes produced with RCA. Measured elasticity moduli were lower than moduli predicted by NBR 6118:2014 and fib Model Code 2010, while measured results were greater than values predicted by Eurocode 2:2004 and ACI 318:2014, as expected, which indicated the safety of the latter two standards.
Thermal Insulation of YSZ and Erbia-Doped Yttria-Stabilised Zirconia EB-PVD Thermal Barrier Coating Systems after CMAS Attack
Authors: Boissonnet Germain , Chalk Christine , Nicholls John R. , Bonnet Gilles , Pedraza Fernando
Published: October 2020

The impact of small deposits of calcium–magnesium–aluminium silicates (CMAS) on the top of thermal barrier coatings (TBCs) made of yttria-stabilised zirconia (YSZ) produced via electron-beam physical vapour deposition (EB-PVD) is shown to play a role in the microstructural and chemical stability of the coatings; hence, it also affects the thermal insulation potential of TBCs. Therefore, the present work investigates the degradation potential of minor CMAS deposits (from 0.25 to 5 mg·cm−2) annealed at 1250 °C for 1 h on a novel Er2O3-Y2O3 co-stabilised ZrO2 (ErYSZ) EB-PVD TBC, which is compared to the standard YSZ coating. Due to the higher reactivity of ErYSZ coatings with CMAS, its penetration is limited in comparison with the standard YSZ coatings, hence resulting in a better thermal insulation of the former after ageing.
Investigation on Hydration and Mechanical Properties of Mortar Containing Limestone Powder and Fly Ash Based on the Coupled Chemical–Thermal–Mechanical Method
Authors: Zhou Wei , Tian Wenxiang , Qi Tianqi , Liu Shuhua , Feng Chuqiao , Ma Gang , Chang Xiaolin
Published: October 2020

The composited cementitious materials usually have superior performance; for example, using limestone powder (LP) and fly ash (FA) as the admixtures of cement in concrete/mortar is a popular way of improving the properties of concrete/mortar structures. In this work, we performed experimental tests to study the hydration process and pore distribution in mortar containing different ratios of LP and FA. Based on the results of mercury intrusion porosimetry (MIP), a numerical mortar model with random pore is built. The model can reflect the synergistic hydration interaction and filling effect caused by the admixtures of LP and FA. After analyzing the hydration process, the coupled chemical–thermal–mechanical method was used to simulate the characteristics of mortar containing LP and FA. The coupling model can simulate the “hump-type” hydration acceleration stage of the mortar at early age, which is specifically caused by the LP, proved in the experimental test. Additionally, the special, “hump-type” stage is important to enhance the early strength of the mortar. At different levels of admixture content, the random pore model and coupled method can predict the evolution process of the mechanical properties well, at early age and for long-term strength. Both experimental and numerical results suggest that the mortar containing admixtures of the proper ratio of LP to FA have good mechanical properties, which can be applied to engineering structures.
Electrochemical Activation of Li2MnO3 Electrodes at 0 °C and Its Impact on the Subsequent Performance at Higher Temperatures
Authors: Susai Francis Amalraj , Talianker Michael , Liu Jing , Rosy  , Paul Tanmoy , Grinblat Yehudit , Erickson Evan , Noked Malachi , Burstein Larisa , Frenkel Anatoly I. , Tsur Yoed , Markovsky Boris , Aurbach Doron
Published: October 2020

This work continues our systematic study of Li- and Mn- rich cathodes for lithium-ion batteries. We chose Li2MnO3 as a model electrode material with the aim of correlating the improved electrochemical characteristics of these cathodes initially activated at 0 °C with the structural evolution of Li2MnO3, oxygen loss, formation of per-oxo like species (O22−) and the surface chemistry. It was established that performing a few initial charge/discharge (activation) cycles of Li2MnO3 at 0 °C resulted in increased discharge capacity and higher capacity retention, and decreased and substantially stabilized the voltage hysteresis upon subsequent cycling at 30 °C or at 45 °C. In contrast to the activation of Li2MnO3 at these higher temperatures, Li2MnO3 underwent step-by-step activation at 0 °C, providing a stepwise traversing of the voltage plateau at >4.5 V during initial cycling. Importantly, these findings agree well with our previous studies on the activation at 0 °C of 0.35Li2MnO3·0.65Li[Mn0.45Ni0.35Co0.20]O2 materials. The stability of the interface developed at 0 °C can be ascribed to the reduced interactions of the per-oxo-like species formed and the oxygen released from Li2MnO3 with solvents in ethylene carbonate–methyl-ethyl carbonate/LiPF6 solutions. Our TEM studies revealed that typically, upon initial cycling both at 0 °C and 30 °C, Li2MnO3 underwent partial structural layered-to-spinel (Li2Mn2O4) transition.