bluuebunny/crossref_metadata_2025 huggingface dataset:
Stacked Boosters Network Architecture for Short-Term Load Forecasting in Buildings
Authors: Salmi Tuukka , Kiljander Jussi , Pakkala Daniel
Published: May 2020

This paper presents a novel deep learning architecture for short-term load forecasting of building energy loads. The architecture is based on a simple base learner and multiple boosting systems that are modelled as a single deep neural network. The architecture transforms the original multivariate time series into multiple cascading univariate time series. Together with sparse interactions, parameter sharing and equivariant representations, this approach makes it possible to combat against overfitting while still achieving good presentation power with a deep network architecture. The architecture is evaluated in several short-term load forecasting tasks with energy data from an office building in Finland. The proposed architecture outperforms state-of-the-art load forecasting model in all the tasks.
Investigation of Heat Diffusion at Nanoscale Based on Thermal Analysis of Real Test Structure
Authors: Raszkowski Tomasz , Zubert Mariusz
Published: May 2020

This paper presents an analysis related to thermal simulation of the test structure dedicated to heat-diffusion investigation at the nanoscale. The test structure consists of thin platinum resistors mounted on wafer made of silicon dioxide. A bottom part of the structure contains the silicon layer. Simulations were carried out based on the thermal simulator prepared by the authors. Simulation results were compared with real measurement outputs yielded for the mentioned test structure. The authors also propose the Grünwald–Letnikov fractional space-derivative Dual-Phase-Lag heat transfer model as a more accurate model than the classical Fourier–Kirchhoff (F–K) heat transfer model. The approximation schema of proposed model is also proposed. The accuracy and computational properties of both numerical algorithms are presented in detail.
A LSTM-STW and GS-LM Fusion Method for Lithium-Ion Battery RUL Prediction Based on EEMD
Authors: Mao Ling , Xu Jie , Chen Jiajun , Zhao Jinbin , Wu Yuebao , Yao Fengjun
Published: May 2020

To address inaccurate prediction in remaining useful life (RUL) in current Lithium-ion batteries, this paper develops a Long Short-Term Memory Network, Sliding Time Window (LSTM-STW) and Gaussian or Sine function, Levenberg-Marquardt algorithm (GS-LM) fusion batteries RUL prediction method based on ensemble empirical mode decomposition (EEMD). Firstly, EEMD is used to decompose the original data into high-frequency and low-frequency components. Secondly, LSTM-STW and GS-LM are used to predict the high-frequency and low-frequency components, respectively. Finally, the LSTM-STW and GS-LM prediction results are effectively integrated in order to obtain the final prediction of the lithium-ion battery RUL results. This article takes the lithium-ion battery data published by NASA as input. The experimental results show that the method has higher accuracy, including the phenomenon of sudden capacity increase, and is less affected by the prediction starting point. The performance of the proposed method is better than other typical battery RUL prediction methods.
FPGA-Based System for Electromagnetic Interference Evaluation in Random Modulated DC/DC Converters
Authors: Loschi Hermes , Lezynski Piotr , Smolenski Robert , Nascimento Douglas , Sleszynski Wojciech
Published: May 2020

Field-Programmable Gate Array (FPGA) provides the possibility to design new “electromagnetic compatibility (EMC) friendly” control techniques for power electronic converters. Such control techniques use pseudo-random modulators (RanM) to control the converter switches. However, some issues connected with the FPGA-based design of RanM, such as matching the range of fixed-point numbers, might be challenging. The modern programming tools, such as LabVIEW, may facilitate the design process, but there are still fixed-point operations and limitations in arithmetic operations. This paper presents the design insights on the FPGA-based EMC friendly control system for DC/DC converter. Probability density functions (PDF) are used to analyse and improve pseudo-random algorithms. The theoretical algorithms, hardware details and experimental results are presented and discussed in terms of conducted electromagnetic interference emission.
Wave Exciting Force Maximization of Truncated Cylinders in a Linear Array
Authors: Michailides Constantine , Loukogeorgaki Eva , Chatjigeorgiou Ioannis K.
Published: May 2020

This study focuses on the determination of optimum layout configurations for a linear array of identical mutually interacting truncated cylinders. Optimum configurations correspond to those that maximize either the total heave exciting force acting on all cylinders of the array or the heave exciting force applied on pairs of cylinders within the array. For achieving this goal, we developed and applied an efficient optimization numerical process (ONP), where a robust hydrodynamic numerical model, capable of solving the diffraction problem of the examined multi-body arrangement in the frequency domain, was appropriately coupled with a genetic algorithm solver in an integrated computational environment. Initially, the efficiency of the ONP is demonstrated by comparing results with those of other investigations that resulted from the deployment of classical optimization methods. Then, ONP is applied for a linear array of nine cylinders for determining the optimum layout configurations under the action of the head and perpendicular to the array waves, and for different maximum allowable array lengths. The resulting optimum configurations correspond to a random positioning of the cylinders within the array. Nevertheless, they are characterized by the formation of clusters of closely-positioned cylinders, which induce positive hydrodynamic interactions in terms of maximizing the exciting forces.
Plasticity of Root Traits under Competition for a Nutrient-Rich Patch Depends on Tree Species and Possesses a Large Congruency between Intra- and Interspecific Situations
Authors: Lak Zana A. , Sandén Hans , Mayer Mathias , Godbold Douglas L. , Rewald Boris
Published: May 2020

Belowground competition is an important structuring force in terrestrial plant communities. Uncertainties remain about the plasticity of functional root traits under competition, especially comparing interspecific vs. intraspecific situations. This study addresses the plasticity of fine root traits of competing Acer pseudoplatanus L. and Fagus sylvatica L. seedlings in nutrient-rich soil patches. Seedlings’ roots were grown in a competition chamber experiment in which root growth (biomass), morphological and architectural fine roots traits, and potential activities of four extracellular enzymes were analyzed. Competition chambers with one, two conspecific, or two allospecific roots were established, and fertilized to create a nutrient ‘hotspot’. Interspecific competition significantly reduced fine root growth in Fagus only, while intraspecific competition had no significant effect on the fine root biomass of either species. Competition reduced root nitrogen concentration and specific root respiration of both species. Potential extracellular enzymatic activities of β-glucosidase (BG) and N-acetyl-glucosaminidase (NAG) were lower in ectomycorrhizal Fagus roots competing with Acer. Acer fine roots had greater diameter and tip densities under intraspecific competition. Fagus root traits were generally more plastic than those of Acer, but no differences in trait plasticity were found between competitive situations. Compared to Acer, Fagus roots possessed a greater plasticity of all studied traits but coarse root biomass. However, this high plasticity did not result in directed trait value changes under interspecific competition, but Fagus roots grew less and realized lower N concentrations in comparison to competing Acer roots. The plasticity of root traits of both species was thus found to be highly species- but not competitor-specific. By showing that both con- and allospecific roots had similar effects on target root growth and most trait values, our data sheds light on the paradigm that the intensity of intraspecific competition is greater than those of interspecific competition belowground.
Using Satellite Imagery to Evaluate Bark Beetle-Caused Tree Mortality Reported in Aerial Surveys in a Mixed Conifer Forest in Northern Idaho, USA
Authors: Bright Benjamin C. , Hudak Andrew T. , Egan Joel M. , Jorgensen Carl L. , Rex Franciel E. , Hicke Jeffrey A. , Meddens Arjan J.H.
Published: May 2020

Bark beetles cause significant tree mortality in western North America. The United States Forest Service coordinates annual insect and disease surveys (IDS) by observers in airplanes to map and quantify the tree mortality caused by beetles. The subjective nature of these surveys means that accuracy evaluation is important for characterizing uncertainty. Furthermore, the metric reported for quantifying tree mortality recently changed (2012–2018 depending in region) from killed trees per acre to percent tree mortality within damage polygons, posing challenges for linking older and newer records. Here we evaluated IDS severity estimates in a beetle-affected forest in northern Idaho, USA using fine-resolution satellite imagery, which permitted greater areal coverage than field data. We first used well-established methods to map beetle-caused tree mortality in two WorldView-2 (WV2) images with a high accuracy relative to field observations. Trees-per-acre measurements within collocated IDS polygons were then converted to percent mortality using three methods and evaluated with the WV2 maps. The overall accuracies for the three methods ranged from 35–38% (for methods that used five percent-mortality classes) and 49–56% (three classes). When IDS and WV2 estimates of mortality severity that were within ±15% of each other were considered accurate, overall accuracies were 71–78%. Within the aerial survey damage polygons, the total mortality area tended to be overestimated relative to WV2. WV2 imagery identified ~50% more mortality across the study region compared with the IDS methods, with most of the difference occurring where damage was low severity or in wilderness areas. Severity of Douglas-fir beetle-caused tree mortality was estimated the most accurately, whereas severity of mountain pine beetle-caused tree mortality was estimated the least accurately. Future studies that control for temporal ambiguity between IDS and satellite imagery, as well as IDS spatial error, might provide better assessments of IDS severity accuracy. Our study increases the usefulness of the rich aerial survey database by providing estimates of uncertainty in the IDS database of tree mortality severity.
Nest Survival and Transplantation Success of Formica rufa (Hymenoptera: Formicidae) Ants in Southern Turkey: A Predictive Approach
Authors: Serttaş Ayhan , Bakar Özer , Alkan Uğur Melih , Yılmaz Arif , Yolcu Halil İbrahim , İpekdal Kahraman
Published: May 2020

Research highlights: Formica rufa is used widely for biocontrol in Turkish forests. Although ecological characteristics of red wood ant habitats are well known, the statistical significance of these characteristics and their effects on nest transplantation success are largely unknown. Having such knowledge on a local scale, however, can help to predict the success of a scheduled transplantation effort, and can prevent loss of time and money. Background and objectives: In the present study, we used nest transplantation data from southern Turkey to determine habitat parameters that have a significant impact on nest survival, and to investigate possibility of predicting transplantation success from habitat parameter data. Materials and methods: Algorithms of data mining are widely used in agricultural and forestry applications for a wide range of tasks. In the present study, we used descriptive statistics to summarize the transplantation profile according to six habitat parameters (altitude, aspect, canopy closure, landform, nest substrate, and slope). We also used classification, a data mining approach, with two of its methods (decision tree and naïve Bayes) to determine the most important habitat parameters for nest survival and predict nest transplantation success in southern Turkey. Results: We found that altitude, aspect, and canopy closure were the most important factors affecting transplantation success. We also show that classification methods can be used in not only classifying, but also predicting the success rate of future transplantations. Thus, we show that the possibility of success for a given area can be predicted when certain parameters are known. Conclusions: This method can assist biological control practitioners in planning biocontrol programs and selecting favorable spots for red wood ant nest transplantation.
Deadwood Characteristics in Mature and Old-Growth Birch Stands and Their Implications for Carbon Storage
Authors: Šēnhofa Silva , Jaunslaviete Ieva , Šņepsts Guntars , Jansons Jurģis , Liepa Līga , Jansons Āris
Published: May 2020

As one of the most abundant tree species in the hemiboreal zone, birch is important from both commercial and biodiversity perspectives. While old-growth deciduous stands are important for biodiversity conservation with an emphasis on deadwood availability, the role that deadwood in these stands plays in carbon sequestration remains unclear. We studied mature (71–110 years old) and old-growth (121–150 years old) birch stands on fertile mineral soils. The marginal mean deadwood volume was 43.5 ± 6.4 m3 ha−1 in all mature stands, 51.3 ± 7.1 m3 ha−1 in recently unmanaged mature stands, and 54.4 ± 4.4 m3 ha−1 in old-growth stands; the marginal mean deadwood carbon pool for each stand type was 5.4 ± 0.8 t·ha−1, 6.3 ± 0.9 t·ha−1, and 7.9 ± 0.6 t·ha−1, respectively. Deadwood volume was not related to stand productivity in terms of stand basal area, stand height, or stand age. The difference between mature and old-growth stands remained non-significant (p < 0.05). A high volume of deadwood was almost continuously present throughout the landscape in assessed unmanaged sites; moreover, 88% of sample plots in old-growth stands and 63% of sample plots in mature stands had a deadwood volume higher than 20 m3·ha−1. Old-growth stands had a slightly greater volume of large deadwood than unmanaged mature stands; in both, almost half of the deadwood was more than 30 cm in diameter and approximately one-fifth had a diameter greater than 40 cm. Both groups of stands had similar proportions of coniferous and deciduous deadwood and lying and standing deadwood. Old-growth stands had a higher volume of recently and weakly decayed wood, indicating increased dieback during recent years.
Drought Primarily Reduces Canopy Transpiration of Exposed Beech Trees and Decreases the Share of Water Uptake from Deeper Soil Layers
Authors: Lüttschwager Dietmar , Jochheim Hubert
Published: May 2020

Research Highlights: During drought, reduced soil water availability and increased vapor pressure deficit diminished transpiration in a mature beech stand (Fagus sylvatica L.). Dominant trees were more affected than suppressed trees. The share of soil water uptake from deeper layers decreased. The ability of individual trees in the forest stand to save water during drought was apparently dependent on their social status. This would be relevant for forest management. Objectives: We investigated which basal area classes of trees contribute more or less to total transpiration under wet and dry conditions, and from which soil layers they took up water. We hypothesized that dominant trees have a better adaptability to drought and diminish transpiration more than suppressed trees. Methods: The water budget of the forest stand was continuously monitored throughout the entire observation period. Xylem sap flux measurements using thermal dissipation probes were performed during the vegetation period at different depths in the trunks of ten representative trees. A radial distribution model of the sap flow density pattern was used to compute whole-tree and stand transpiration. Water budget was simulated using a physiology-based model. Results: During drought, the fraction of suppressed trees to whole-canopy transpiration of the forest stand increased and the share of soil water uptake from deeper layers decreased. Conclusions: The behavior of dominant trees under drought conditions could be interpreted as a water-conserving strategy. Thinning by removing suppressed trees should be employed to stabilize forests.
Aromatic Potential of Diverse Non-Conventional Yeast Species for Winemaking and Brewing
Authors: Gamero Amparo , Dijkstra Annereinou , Smit Bart , de Jong Catrienus
Published: May 2020

Traditionally, Saccharomyces species are those used to conduct industrial alcoholic fermentations. Recently, an increasing interest has arisen with respect to the potential of so-called non-conventional yeasts to improve wine and beer aroma profiles, keeping the particular terroir of each region or for the development of craft beers. In this study, the potential of diverse non-conventional yeasts to improve aroma in winemaking and brewing was investigated, testing several pure and mixed culture combinations. In addition, a comparison between microscale and labscale was carried out in order to assess the value of microwine and microbeer as screening tools. The results indicated that non-Saccharomyces yeasts were good candidates to enhance or diversify aroma profiles in alcoholic beverages, especially regarding acetate ester yield and fruity aromas. However, mixed cultures with Saccharomyces spp. are normally required to achieve a successful fermentation. The adjustment of pithing ratios is crucial for this purpose. Microscale is presented as an effective and efficient screening tool to compare different culture combinations, although scaling-up will always be necessary in order to get results closer to real winemaking or brewing processes.
Fermentative Microbes of Khadi, a Traditional Alcoholic Beverage of Botswana
Authors: Motlhanka Koketso , Lebani Kebaneilwe , Boekhout Teun , Zhou Nerve
Published: May 2020

Khadi is a popular traditional alcoholic beverage in rural households in Botswana. The product is produced by fermentation of ripened sun-dried Grewia flava (Malvaceae) fruits supplemented with brown table sugar. Despite its popularity, its growing consumer acceptance, its potential nutritional value, and its contribution to the socio-economic lifestyle of Botswana, the production process remains non-standardized. Non-standardized production processes lead to discrepancies in product quality and safety as well as varying shelf life. Identification of unknown fermentative microorganisms of khadi is an important step towards standardization of its brewing process for entrance into commercial markets. The aim of this study was to isolate and identify bacteria and yeasts responsible for fermentation of khadi. Yeasts and bacteria harbored in 18 khadi samples from 18 brewers in central and northern Botswana were investigated using classic culture-dependent techniques and DNA sequencing methods. Additionally, we used the same techniques to investigate the presence of bacteria and yeasts on six batches of ripened-dried G. flava fruits used for production of the sampled brews. Our results revealed that Saccharomyces cerevisiae closely related to a commercial baker’s yeast strain sold locally was the most predominant yeast species in khadi suggesting a possible non-spontaneous brewing process. However, we also detected diverse non-Saccharomyces yeasts, which are not available commercially in retail shops in Botswana. This suggests that spontaneous fermentation is partially responsible for fermentation of khadi. This study, presenting the first microbiological characterization of a prominent traditional alcoholic beverage in Botswana, is vital for development of starter cultures for the production of a consistent product towards the commercialization of khadi.
Language-Independent Fake News Detection: English, Portuguese, and Spanish Mutual Features
Authors: Abonizio Hugo Queiroz , de Morais Janaina Ignacio , Tavares Gabriel Marques , Barbon Junior Sylvio
Published: May 2020

Online Social Media (OSM) have been substantially transforming the process of spreading news, improving its speed, and reducing barriers toward reaching out to a broad audience. However, OSM are very limited in providing mechanisms to check the credibility of news propagated through their structure. The majority of studies on automatic fake news detection are restricted to English documents, with few works evaluating other languages, and none comparing language-independent characteristics. Moreover, the spreading of deceptive news tends to be a worldwide problem; therefore, this work evaluates textual features that are not tied to a specific language when describing textual data for detecting news. Corpora of news written in American English, Brazilian Portuguese, and Spanish were explored to study complexity, stylometric, and psychological text features. The extracted features support the detection of fake, legitimate, and satirical news. We compared four machine learning algorithms (k-Nearest Neighbors (k-NN), Support Vector Machine (SVM), Random Forest (RF), and Extreme Gradient Boosting (XGB)) to induce the detection model. Results show our proposed language-independent features are successful in describing fake, satirical, and legitimate news across three different languages, with an average detection accuracy of 85.3% with RF.
Laser Sources Based on Rare-Earth Ion Doped Tellurite Glass Fibers and Microspheres
Authors: Anashkina Elena A.
Published: May 2020

In recent years, huge progress has been made in the development of rare-earth ion doped tellurite glass laser sources, ranging from watt- and multiwatt-level fiber lasers to nanowatt level microsphere lasers. Significant success has been achieved in extending the spectral range of tellurite fiber lasers generating at wavelengths beyond 2 μm as well as in theoretical understanding. This review is aimed at discussing the state of the art of neodymium-, erbium-, thulium-, and holmium-doped tellurite glass fiber and microsphere lasers.
Alternative Feed Raw Materials Modulate Intestinal Microbiota and Its Relationship with Digestibility in Yellowtail Kingfish Seriola lalandi
Authors: Dam Chinh Thi My , Booth Mark , Pirozzi Igor , Salini Michael , Smullen Richard , Ventura Tomer , Elizur Abigail
Published: May 2020

Gut microbiota plays a crucial role in nutrient digestibility and fish health. This study aimed to investigate the effects of alternative feed raw materials on the bacterial communities in the distal intestine and its relationship with nutrient digestibility in yellowtail kingfish (YTK), Seriola lalandi. Two 4-week digestibility trials were conducted to evaluate fish meal (FM), two sources of poultry by-product meal (PBM-1 & PBM-2), blood meal (BLM), faba bean meal (FBM), corn gluten meal (CGM), soy protein concentrate (SPC) and wheat flour (WH). The nutrient digestibility value was determined using the stripping fecal collection method. Bacterial communities were characterized by high-throughput sequencing based on V3-V4 region of the 16S rRNA gene. The most abundant phylum identified in the present study was Proteobacteria. A significant change in the distal intestine was observed in fish fed diets containing CGM and BLM, characterized by a reduction of species richness and diversity. Additionally, significant correlation between nutrient digestibility and intestinal microbiota was observed. Allivibrio, Vibrio, Curvibacter, Ruminococcaceae, and Clostridium were positively correlated, whereas Ralstonia genus was negatively correlated with nutrient digestibility. This study demonstrated that intestinal microbiota could be a useful tool for evaluating the digestibility of feed raw materials; however, further culture-based study is needed to confirm this observation.
Kinematic and Dynamic Scaling of Copepod Swimming
Authors: Svetlichny Leonid , Larsen Poul S. , Kiørboe Thomas
Published: May 2020

Calanoid copepods have two swimming gaits, namely cruise swimming that is propelled by the beating of the cephalic feeding appendages and short-lasting jumps that are propelled by the power strokes of the four or five pairs of thoracal swimming legs. The latter may be 100 times faster than the former, and the required forces and power production are consequently much larger. Here, we estimated the magnitude and size scaling of swimming speed, leg beat frequency, forces, power requirements, and energetics of these two propulsion modes. We used data from the literature together with new data to estimate forces by two different approaches in 37 species of calanoid copepods: the direct measurement of forces produced by copepods attached to a tensiometer and the indirect estimation of forces from swimming speed or acceleration in combination with experimentally estimated drag coefficients. Depending on the approach, we found that the propulsive forces, both for cruise swimming and escape jumps, scaled with prosome length (L) to a power between 2 and 3. We further found that power requirements scales for both type of swimming as L3. Finally, we found that the cost of transportation (i.e., calories per unit body mass and distance transported) was higher for swimming-by-jumping than for cruise swimming by a factor of 7 for large copepods but only a factor of 3 for small ones. This may explain why only small cyclopoid copepods can afford this hydrodynamically stealthy transportation mode as their routine, while large copepods are cruise swimmers.
Influence of Cooking Conditions on Nutritional Properties and Sensory Characteristics Interpreted by E-Senses: Case-Study on Selected Vegetables
Authors: Buratti Susanna , Cappa Carola , Benedetti Simona , Giovanelli Gabriella
Published: May 2020

This study investigates the effects of three cooking methods (boiling, steaming and microwaving) on the nutritional and physical properties of cauliflowers, carrots and sweet potatoes; e-senses were applied to interpret the sensory characteristics according to physico-chemical aspects. The nutritional quality was evaluated by determining the concentrations of key components and the antioxidant activity; e-sense data, combined with texture parameters, were processed by a principal component analysis. The cooking method and time significantly influenced the quality of the three products. Boiling, which detrimentally affected ascorbic acid, total phenolic concentration and antioxidant activity, enhanced carotene accessibility. Steaming produced losses in ascorbic acid, increasing total phenolics and carotenoids. Microwaving resulted in minor changes in ascorbic acid concentrations, preserved carotenoids and increased total phenolics. The nutritional quality was better preserved or enhanced using shorter cooking times. The elaboration of the data collected by the e-senses showed a clear evolution according to the cooking method and time. The results helped to determine the cooking method that best preserves the nutritional properties of the vegetables, highlighting the applicability of rapid instrumental methods to interpret the evolution of sensory characteristics.
Assessment of the Miniature Kramer Shear Cell to Measure Both Solid Food and Bolus Mechanical Properties and Their Interplay with Oral Processing Behavior
Authors: Álvarez María Dolores , Paniagua Jaime , Herranz Beatriz
Published: May 2020

This study assessed the usefulness of the miniature Kramer shear cell to determine relevant instrumental parameters of solid foods and bolus counterparts, examining their relationships with oral processing behaviors to obtain greater knowledge about the texture perception process. Six solid foods with different textural properties were tested. Bolus mechanical properties were also determined by means of cone penetration tests and rheological measurements, and their particle size distributions by sieving. Oral processing behavior (chewing time, number of chews, chewing rate, eating rate) and food saliva uptake (SU) of a young volunteer and a panel of 39 untrained participants were analyzed. The Kramer mechanical properties were very suitable for detecting different levels of food and bolus textural hardness and fracturability and the associated degrees of fragmentation achieved during mastication. Chewing time and number of chews were highly correlated with Kramer food and bolus mechanical properties for the single subject and for the panel’s oral processing behaviors. For the single subject, SU and eating rate also showed strong correlations with food and bolus mechanical properties, unlike chewing rate and food moisture content (FMC). In contrast, eating rate, FMC, and SU did not vary with the oral activities of the panel.
Challenges Associated with Byproducts Valorization—Comparison Study of Safety Parameters of Ultrasonicated and Fermented Plant-Based Byproducts
Authors: Bartkiene Elena , Bartkevics Vadims , Pugajeva Iveta , Borisova Anastasija , Zokaityte Egle , Lele Vita , Sakiene Vytaute , Zavistanaviciute Paulina , Klupsaite Dovile , Zadeike Daiva , Özogul Fatih , Juodeikiene Grazina
Published: May 2020

In order to promote the efficient use of byproducts from the production of plant-based beverages, which still contain a large amount of nutritional and functional compounds, microbiological and chemical safety characteristics should be evaluated and, if needed, improved. Many challenges are associated with byproducts valorization, and the most important ones, which should be taken into account at the further steps of valorization, are biological and chemical safety. For safety improving, several technological treatments (biological, physical etc.) can be used. In this study, the influence of low-frequency ultrasonication (US) and fermentation with Lactobacillus casei LUHS210 strain, as physical and biotechnological treatments, on the safety characteristics of the byproducts (BYs) from the processing of rice, soy, almond, coconut, and oat drinks was compared. Ultrasonication, as well as fermentation, effectively improved the microbiological safety of BYs. Ultrasonication and fermentation reduced the concentration of deoxynivalenol, on average, by 24% only in soy BYs. After fermentation, 15-acetyldeoxynivalenol was formed in all samples (<12 µg kg−1), except for soy BYs. The lowest total biogenic amines content was found in fermented rice BYs and ultrasonicated coconut BYs. When comparing untreated and fermented BYs, significant changes in macro- and micro-elements content were found. Ultrasonication at 37 kHz did not significantly influence the concentrations of macro- and micro-elements, while fermentation affected most of the essential micro-elements. Consequently, while ultrasonication and fermentation can enhance the safety of BYs, the specific effects must be taken into account on biogenic amines, mycotoxins, and micro and macro elements.
Evolutionary Variability of W-Linked Repetitive Content in Lacertid Lizards
Authors: Suwala Grzegorz , Altmanová Marie , Mazzoleni Sofia , Karameta Emmanouela , Pafilis Panayiotis , Kratochvíl Lukáš , Rovatsos Michail
Published: May 2020

Lacertid lizards are a widely radiated group of squamate reptiles with long-term stable ZZ/ZW sex chromosomes. Despite their family-wide homology of Z-specific gene content, previous cytogenetic studies revealed significant variability in the size, morphology, and heterochromatin distribution of their W chromosome. However, there is little evidence about the accumulation and distribution of repetitive content on lacertid chromosomes, especially on their W chromosome. In order to expand our knowledge of the evolution of sex chromosome repetitive content, we examined the topology of telomeric and microsatellite motifs that tend to often accumulate on the sex chromosomes of reptiles in the karyotypes of 15 species of lacertids by fluorescence in situ hybridization (FISH). The topology of the above-mentioned motifs was compared to the pattern of heterochromatin distribution, as revealed by C-banding. Our results show that the topologies of the examined motifs on the W chromosome do not seem to follow a strong phylogenetic signal, indicating independent and species-specific accumulations. In addition, the degeneration of the W chromosome can also affect the Z chromosome and potentially also other parts of the genome. Our study provides solid evidence that the repetitive content of the degenerated sex chromosomes is one of the most evolutionary dynamic parts of the genome.
Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq Data
Authors: Chi Weilai , Deng Minghua
Published: May 2020

Single-cell RNA-seq (scRNA-seq) is quite prevalent in studying transcriptomes, but it suffers from excessive zeros, some of which are true, but others are false. False zeros, which can be seen as missing data, obstruct the downstream analysis of single-cell RNA-seq data. How to distinguish true zeros from false ones is the key point of this problem. Here, we propose sparsity-penalized stacked denoising autoencoders (scSDAEs) to impute scRNA-seq data. scSDAEs adopt stacked denoising autoencoders with a sparsity penalty, as well as a layer-wise pretraining procedure to improve model fitting. scSDAEs can capture nonlinear relationships among the data and incorporate information about the observed zeros. We tested the imputation efficiency of scSDAEs on recovering the true values of gene expression and helping downstream analysis. First, we show that scSDAE can recover the true values and the sample–sample correlations of bulk sequencing data with simulated noise. Next, we demonstrate that scSDAEs accurately impute RNA mixture dataset with different dilutions, spike-in RNA concentrations affected by technical zeros, and improves the consistency of RNA and protein levels in CITE-seq data. Finally, we show that scSDAEs can help downstream clustering analysis. In this study, we develop a deep learning-based method, scSDAE, to impute single-cell RNA-seq affected by technical zeros. Furthermore, we show that scSDAEs can recover the true values, to some extent, and help downstream analysis.
Spatio-Temporal Roles of ASD-Associated Variants in Human Brain Development
Authors: Kim Yujin , An Joon-Yong
Published: May 2020

Transcriptional regulation of the genome arguably provides the basis for the anatomical elaboration and dynamic operation of the human brain. It logically follows that genetic variations affecting gene transcription contribute to mental health disorders, including autism spectrum disorder (ASD). A number of recent studies have shown the role of de novo variants (DNVs) in disrupting early neurodevelopment. However, there is limited knowledge concerning the role of inherited variants during the early brain development of ASD. In this study, we investigate the role of rare inherited variations in neurodevelopment. We conducted co-expression network analyses using an anatomically comprehensive atlas of the developing human brain and examined whether rare coding and regulatory variants, identified from our genetic screening of Australian families with ASD, work in different spatio-temporal functions.
The Microbiome in Cystic Fibrosis Pulmonary Disease
Authors: Françoise Alice , Héry-Arnaud Geneviève
Published: May 2020

Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.
Metabolomics: A Tool to Understand the Impact of Genetic Mutations in Amyotrophic Lateral Sclerosis
Authors: Lanznaster Débora , Veyrat-Durebex Charlotte , Vourc’h Patrick , Andres Christian R. , Blasco Hélène , Corcia Philippe
Published: May 2020

Metabolomics studies performed in patients with amyotrophic lateral sclerosis (ALS) reveal a set of distinct metabolites that can shed light on the pathological alterations taking place in each individual. Metabolites levels are influenced by disease status, and genetics play an important role both in familial and sporadic ALS cases. Metabolomics analysis helps to unravel the differential impact of the most common ALS-linked genetic mutations (as C9ORF72, SOD1, TARDBP, and FUS) in specific signaling pathways. Further, studies performed in genetic models of ALS reinforce the role of TDP-43 pathology in the vast majority of ALS cases. Studies performed in differentiated cells from ALS-iPSC (induced Pluripotent Stem Cells) reveal alterations in the cell metabolism that are also found in ALS models and ultimately in ALS patients. The development of metabolomics approaches in iPSC derived from ALS patients allow addressing and ultimately understanding the pathological mechanisms taking place in any patient. Lately, the creation of a “patient in a dish” will help to identify patients that may benefit from specific treatments and allow the implementation of personalized medicine.
Diverse LEF/TCF Expression in Human Colorectal Cancer Correlates with Altered Wnt-Regulated Transcriptome in a Meta-Analysis of Patient Biopsies
Authors: Mayer Claus-Dieter , Magon de La Giclais Soizick , Alsehly Fozan , Hoppler Stefan
Published: May 2020

Aberrantly activated Wnt signaling causes cellular transformation that can lead to human colorectal cancer. Wnt signaling is mediated by Lymphoid Enhancer Factor/T-Cell Factor (LEF/TCF) DNA-binding factors. Here we investigate whether altered LEF/TCF expression is conserved in human colorectal tumor sample and may potentially be correlated with indicators of cancer progression. We carried out a meta-analysis of carefully selected publicly available gene expression data sets with paired tumor biopsy and adjacent matched normal tissues from colorectal cancer patients. Our meta-analysis confirms that among the four human LEF/TCF genes, LEF1 and TCF7 are preferentially expressed in tumor biopsies, while TCF7L2 and TCF7L1 in normal control tissue. We also confirm positive correlation of LEF1 and TCF7 expression with hallmarks of active Wnt signaling (i.e., AXIN2 and LGR5). We are able to correlate differential LEF/TCF gene expression with distinct transcriptomes associated with cell adhesion, extracellular matrix organization, and Wnt receptor feedback regulation. We demonstrate here in human colorectal tumor sample correlation of altered LEF/TCF gene expression with quantitatively and qualitatively different transcriptomes, suggesting LEF/TCF-specific transcriptional regulation of Wnt target genes relevant for cancer progression and survival. This bioinformatics analysis provides a foundation for future more detailed, functional, and molecular analyses aimed at dissecting such functional differences.
The North Pacific Diatom Species Neodenticula seminae in the Modern and Holocene Sediments of the North Atlantic and Arctic
Authors: Matul Alexander , Kazarina Galina Kh.
Published: May 2020

The paper presents micropaleontological information and observations of the North Pacific diatom species Neodenticula (N.) seminae (Simonsen and Kanaya) Akiba and Yanagisawa in the surface and Holocene sediments from the North Atlantic, Nordic, and Arctic Seas. The compilation of previously published data and new findings of this study on N. seminae in the surface sediments shows its broad occurrence as a usual element of the modern diatom microflora in the Nordic, Labrador, and Irminger Seas. The recent migration of N. seminae from its native area, the Subarctic Pacific, reflects the oceanographic shift in the late 1990s as greater transport of the warmer surface Pacific water to the Arctic causes Arctic sea-ice reduction. Micropaleontological studies of the Holocene sediments document the multiple events of N. seminae appearance in the Arctic during the latest Pleistocene and Holocene warming intervals. These observations can suggest the events of the increased influence of the North Pacific water on the Arctic environments in the past, not just during the recent warm climate amplification.
Design of Medium Depth Drainage Trench Systems for the Mitigation of Deep Landsliding
Authors: Cotecchia Federica , Petti Rossella , Milella Dario , Lollino Piernicola
Published: May 2020

For those slopes where the piezometric regime acts as internal landslide predisposing factor, drainage may represent a more effective mitigation measure than other structural interventions. However, drainage trenches have been generally considered as mitigation measure solely for shallow landslides. More recently, instead, some authors show that the variation in piezometric conditions at large depth is not negligible when medium depth drainage trenches are involved. The paper presents the results of finite element analyses of the transient seepage induced by the installation of systems of drainage trenches of different geometric parameters, and the effect of the drainage system on the stability factor of the slip surface, through 2D limit equilibrium analyses. The pilot region is the Daunia Apennines, where field studies have led to recognize for most of the landslides a “bowl-shaped” slip surface; the results accounting for the Fontana Monte slope at Volturino (Italy), selected as prototype landslide in the assessment of the stabilization efficacy of deep drainage trench systems, is discussed in the following. The study aims at providing indications about the design of the drainage trenches to reduce the pore water pressures on a deep slip surface of such type.
Assessment of Infrastructure Vulnerability to Tsunamis upon the Coastal Zone of Oman Using GIS
Authors: Hereher Mohamed E.
Published: May 2020

The coastal zones of Oman are frequently exposed to tropical cyclones and are expected to be overwhelmed by tsunami waves that originate from marine earthquakes in the Indian Ocean. Inundation of low-lying coastal lands is, hence, inevitable. This study aims to provide a spatial database of the major infrastructure of Oman in relation to their vulnerability to the sea-level rise by tsunamis. This investigation relied on high-resolution elevation data obtained from the Advanced Spaceborne Thermal Emission and Reflection Radiometer-Global Digital Elevation Model (ASTER GDEM) and eleven infrastructure variables acquired from the Oman National Spatial Data Infrastructure. These variables include: schools, hospitals, banks, mosques, fuel stations, police centers, shopping centers, archeological sites, vegetation cover, roads and built-up areas. A Geographical Information System (GIS) analysis was carried out to delineate and quantify the features along the coast with elevation ranges between 1 and 10 m above the current sea-level. Four tsunami scenarios were investigated depending on historical and expected estimations of tsunami heights of 2, 5, 8 and 10 m at the shoreline from previous studies. Results provide spatial vulnerability maps and databases that could be of the utmost importance to planners and developers. Al-Batinah coastal plain of northern Oman is the most vulnerable location to tsunami hazards due to its low-elevated coastal plain and high concentration of population, infrastructure and services. The study asserts the benefits of GIS as a geospatial analysis tool for risk assessment.
The Functioning of Erosion-channel Systems of the River Basins of the South of Eastern Siberia
Authors: Bazhenova Olga I. , Bardash Aleksandr V. , Makarov Stanislav A. , Opekunova Marina Yu. , Tukhta Sergei A. , Tyumentseva Elizaveta M.
Published: May 2020

We revealed the regional features of the functioning of the erosion-channel systems of the Angara, Upper Lena, Selenga, and Upper Amur basins in the south of Eastern Siberia and examined the action of sloping non-channel, temporary, and permanent channel water flows, and presented the patterns of the spatial distribution of soil and gully erosion belts. The development conditions and factors of fluvial processes are considered and the role of cryogenic processes in the increasing activity of water flows is emphasized. The interdecadal dynamic cycles of the erosion-accumulative processes are revealed. A quantitative assessment of soil loss from erosion on agricultural land in the forest-steppe basins was carried out. We made an assessment of the plane deformation of the upper course of the Lena river (Siberian platform) and Irkut (Baikal rift zone and the Irkutsk-Cheremkhovo plain) using cartographic sources of different times, aerial photographs, and satellite imagery. The contribution of extreme fluvial events to sediment redistribution in river basins is shown. Particular attention is paid to the mudflow impact, floods, and channel deformations on the ecological state of the basin systems.
Relationship Between Lumbar Motor Control Ability and Spinal Curvature in Elderly Individuals
Authors: Miyachi Ryo , Miyazaki Junya
Published: May 2020

This study aimed to clarify the relationship between spine curvature and the movement pattern/motor control ability of the lumbar and hip joints during prone hip extension in elderly individuals. The participants were 14 elderly people who attended a community health class. We measured the motion angle, motion ratio (movement pattern), and motor control ability of the lumbar and hip joints during prone hip extension. In addition, the lumbar lordosis angle and thoracic kyphosis angle were measured in the standing position. There was no correlation between the spinal curvature in the standing position and the lumbar/hip joint movement pattern and motor control ability during prone hip extension. When evaluating the lumbar spine, it is necessary to perform a comprehensive evaluation by interpreting static evaluations such as spinal alignment or dynamic evaluations such as movement patterns and motor control abilities.
Study on the Improved Method of Urban Subcatchments Division Based on Aspect and Slope- Taking SWMM Model as Example
Authors: Wu Zening , Ma Bingyan , Wang Huiliang , Hu Caihong
Published: May 2020

The storm water management model (SWMM) is widely used in urban rainfall runoff simulations, but there are no clear rules for the division of its sub catchment areas. At present, the popular sub catchment area division method takes the average slope as the slope parameter of the sub catchment area, which brings errors to the model in mechanism. Based on the current method, this paper proposes a new method to further subdivide the sub catchment area of the SWMM model, according to the Digital Elevation Model (DEM) data of underlying surface, slope and aspect information. By comparing with the previous methods, it was found that the division method based on slope and aspect can make the setting of model parameters and hydraulic exchange conditions clearer, and improve the accuracy of the model on a certain level.