bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical Properties of Polyphenol Oxidases from Ready-to-Eat Lentil (Lens culinaris Medik.) Sprouts and Factors Affecting Their Activities: A Search for Potent Tools Limiting Enzymatic Browning
Authors: Sikora Małgorzata , Świeca Michał , Franczyk Monika , Jakubczyk Anna , Bochnak Justyna , Złotek Urszula
Published: May 2019

Enzymatic browning of sprouts during storage is a serious problem negatively influencing their consumer quality. Identifying and understanding the mechanism of inhibition of polyphenol oxidases (PPOs) in lentil sprouts may offer inexpensive alternatives to prevent browning. This study focused on the biochemical characteristics of PPOs from stored lentil sprouts, providing data that may be directly implemented in improving the consumer quality of sprouts. The purification resulted in approximately 25-fold enrichment of two PPO isoenzymes (PPO I and PPO II). The optimum pH for total PPOs, as well as for PPO I and PPO II isoenzymes, was 4.5–5.5, 4.5–5.0, and 5.5, respectively. The optimal temperature for PPOs was 35 °C. Total PPOs and the PPO I and PPO II isoenzymes had the greatest affinity for catechol (Km = 1.32, 1.76, and 0.94 mM, respectively). Ascorbic acid was the most effective in the inhibition of dark color formation by total PPOs, and showed ca. 62%, 43%, and 24% inhibition at 20-, 2-, and 0.2-mM concentrations. Ascorbic acid, l-cysteine, and sodium metabisulfite (20 mM) significantly inhibited color development in the reactions catalyzed by both isoenzymes of PPO. Ba2+, Fe3+, and Mn2+ (10 mM) completely inhibited PPO activity. This study of the effect of antibrowning compounds and cations on PPO activity provides data that can be used to protect lentil sprouts against enzymatic browning during storage and processing.
Genomic Characterization of External Morphology Traits in Kelpies Does Not Support Common Ancestry with the Australian Dingo
Authors: Chew Tracy , Willet Cali E. , Haase Bianca , Wade Claire M.
Published: May 2019

The Kelpie is a breed developed in Australia for use as a livestock herding dog. It has been proposed that the development of the breed included gene flow from the Australian Dingo (Canis dingo), a canid species present on the Australian continent for around 4000 years. The Kelpie breed is split between working and conformation types that have readily recognizable differences in external morphology. We characterize known gene variants relating to external morphology in sequenced representatives of both Kelpie types (Australian Kelpie—conformation; Australian Working Kelpie—herding) and compare the variants present with those in sequenced Australian Dingoes, including 25 canids with locus-constrained data and one with a whole genome sequence. Variants assessed include identified coat color and ear morphology variants. We describe a new variant site in the transcribed region of methionine sulfoxide reductase 3 that may relate to ear phenotype. None of the morphology variants analyzed offer support for co-ancestry of the Kelpie breed with the Australian Dingo.
Global Regulator PhoP is Necessary for Motility, Biofilm Formation, Exoenzyme Production, and Virulence of Xanthomonas citri Subsp. citri on Citrus Plants
Authors: Wei Chudan , Ding Tian , Chang Changqing , Yu Chengpeng , Li Xingwei , Liu Qiongguang
Published: May 2019

Citrus canker caused by Xanthomonas citri subsp. citri is one of the most important bacterial diseases of citrus, impacting both plant growth and fruit quality. Identifying and elucidating the roles of genes associated with pathogenesis has aided our understanding of the molecular basis of citrus-bacteria interactions. However, the complex virulence mechanisms of X. citri subsp. citri are still not well understood. In this study, we characterized the role of PhoP in X. citri subsp. citri using a phoP deletion mutant, ΔphoP. Compared with wild-type strain XHG3, ΔphoP showed reduced motility, biofilm formation, as well as decreased production of cellulase, amylase, and polygalacturonase. In addition, the virulence of ΔphoP on citrus leaves was significantly decreased. To further understand the virulence mechanisms of X. citri subsp. citri, high-throughput RNA sequencing technology (RNA-Seq) was used to compare the transcriptomes of the wild-type and mutant strains. Analysis revealed 1017 differentially-expressed genes (DEGs), of which 614 were up-regulated and 403 were down-regulated in ΔphoP. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that the DEGs were enriched in flagellar assembly, two-component systems, histidine metabolism, bacterial chemotaxis, ABC transporters, and bacterial secretion systems. Our results showed that PhoP activates the expression of a large set of virulence genes, including 22 type III secretion system genes and 15 type III secretion system effector genes, as well as several genes involved in chemotaxis, and flagellar and histidine biosynthesis. Two-step reverse-transcription polymerase chain reaction analysis targeting 17 genes was used to validate the RNA-seq data, and confirmed that the expression of all 17 genes, except for that of virB1, decreased significantly. Our results suggest that PhoP interacts with a global signaling network to co-ordinate the expression of multiple virulence factors involved in modification and adaption to the host environment during infection.
Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures
Authors: Zhang Peng , Liu Chunsheng , Zheng Xiasheng , Wu Lan , Liu Zhixiang , Liao Baosheng , Shi Yuhua , Li Xiwen , Xu Jiang , Chen Shilin
Published: May 2019

DNA barcoding has been used for decades, although it has mostly been applied to some single-species. Traditional Chinese medicine (TCM), which is mainly used in the form of combination-one type of the multi-species, identification is crucial for clinical usage. Next-generation Sequencing (NGS) has been used to address this authentication issue for the past few years, but conventional NGS technology is hampered in application due to its short sequencing reads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) via long-read sequencing, is employed for the identification of biological compositions in herbal compound formulas in adequate and well controlled studies. By directly sequencing the full-length amplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, the biological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the same time, clone-dependent Sanger sequencing was carried out as a parallel control. Further, another formula—Sanwei-Jili-San (SJS)—was analyzed with genes of ITS2 and CO1. All the ingredients in the samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenous species were also checked, some of which were considered as common contaminations in these products. Methodology analysis demonstrated that this method was sensitive, accurate and reliable. FLMB, a superior but feasible approach for the identification of biological complex mixture, was established and elucidated, which shows perfect interpretation for DNA barcoding that could lead its application in multi-species mixtures.
Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome
Authors: Symonová Radka
Published: May 2019

Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.
Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment
Authors: Gavery Mackenzie R. , Nichols Krista M. , Berejikian Barry A. , Tatara Christopher P. , Goetz Giles W. , Dickey Jon T. , Van Doornik Donald M. , Swanson Penny
Published: May 2019

Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.
The Influence of Soil Compaction on Runoff Formation. A Case Study Focusing on Skid Trails at Forested Andosol Sites
Authors: Zemke Julian J. , Enderling Michel , Klein Alexander , Skubski Marc
Published: May 2019

This study discusses the influence of soil compaction on runoff generation with a special focus on forested Andosol sites. Because of their typical soil physical characteristics (low bulk density, high pore volumes) and the existent land use, these areas are expected to show low to no measurable overland flow during heavy rainfall events. However, due to heavy machinery traffic in the course of forestry actions and pumice excavations, skid trails have been established. Here, a distinct shift of soil dry bulk density (DBD) was observable, using a detailed soil mapping and data interpolation in order to generate in-depth DBD-cross profiles. Additionally, infiltration measurements and rainfall simulations (I = 45 mm·h−1, t = 30 min) were conducted to evaluate effects of observed soil compaction on infiltration rates and overland flow formation. Results show that soil compaction was increased by 21% on average in skid trail wheel ruts. As a consequence, observed runoff was 8.5-times higher on skid trails, while saturated hydraulic conductivity was diminished by 36%. These findings show, that soil compaction leads to a higher possibility of runoff formation during heavy rainfall events, especially at sites which showed initial conditions with presumably low tendencies of runoff formation.
Changing Impacts of North Atlantic Tropical Cyclones on Extreme Precipitation Distribution across the Mid-Atlantic United States
Authors: Dhakal Nirajan
Published: May 2019

Almost every year, north Atlantic tropical cyclones (TCs) are responsible for significant socioeconomic losses across the Mid-Atlantic USA. However, the extent to which TC activity contributes to the changes in the probability distributions of the extreme precipitation have not yet been comprehensively characterized for this region. In this study, a quantile regression method was used to investigate the trends of the lower (τ = 0.2) and upper (τ = 0.8) quantiles of annual and seasonal daily maximum precipitation series for the region using the station-based daily precipitation data for the period 1950–2011. Results show that the rates of changes in the upper quantile have greatly strengthened for the region. Analysis of the spatial pattern of the lower and upper quantile trends for TC and non-TC extreme precipitation series shows that trends have larger magnitudes in most of the sites for TC precipitation series as compared with the non-TC precipitation series for both the lower and upper quantiles. Additionally, the highest trends are observed in the upper quantile for TC time series indicating that TC precipitation is contributing more to the upper tails of the extreme precipitation distribution as compared to the non-TC precipitation. Results from this study have implications for the improved design and reassessment of flood-controlling infrastructure.
Children’s Psychological Representation of Earthquakes: Analysis of Written Definitions and Rasch Scaling
Authors: Raccanello Daniela , Vicentini Giada , Burro Roberto
Published: May 2019

Natural disasters have a potential highly traumatic impact on psychological functioning. This is notably true for children, whose vulnerability depends on their level of cognitive and emotional development. Before formal schooling, children possess all the basic abilities to represent the phenomena of the world, including natural disasters. However, scarce attention has been paid to children’s representation of earthquakes, notwithstanding its relevance for risk awareness and for the efficacy of prevention programs. We examined children’s representation of earthquakes using different methodologies. One hundred and twenty-eight second- and fourth-graders completed a written definition task and an online recognition task, analyzed through the Rasch model. Findings from both tasks indicated that, in children’s representation, natural elements such as geological ones were the most salient, followed by man-made elements, and then by person-related elements. Older children revealed a more complex representation of earthquakes, and this was detected through the online recognition task. The results are discussed taking into account their theoretical and applied relevance. Beyond advancing knowledge of the development of the representation of earthquakes, they also inform on strengths and limitations of different methodologies. Both aspects are key resources to develop prevention programs for fostering preparedness to natural disasters and emotional prevention.
A Usable and People-Friendly Cultural Heritage: MAGNA Project, on the Route from Greece to Magna Graecia
Authors: Rovella Natalia , Bruno Fabio , Davidde Petriaggi Barbara , Makris Theodoris , Raxis Polyvios , La Russa Mauro
Published: May 2019

The Western civilization is deeply rooted in the Ancient Greece culture; political, scientific, technological and philosophic knowledge were born in this epoch. Their diffusion was improved upon by the Greek expansionist policy in colonies of Magna Graecia in Mediterranean Basin, leaving important archaeological traces for the community. In this context, the European project “MAGNA, on the route from Greece to Magna Graecia” seeks to develop a transnational thematic touristic route between Greece and the Ionian coast of Calabria (Southern Italy), an ancient Magna Graecia colony, on the basis of cultural and historical connections between these two Mediterranean areas. The project aims to promote the touristic development of the Greek and Calabrian archaeological sites through dissemination activities. These will concern scientific subjects regarding the conservation of cultural heritage, both in sub-aerial and underwater environments; and study of the sea floor, and pollution of seawater by microplastics. This touristic product consists of cruises on a ship equipped with scientific instruments that offer unique cultural experiences, accompanied by multimedia supports. Experts drive people in the proposed activities, creating more awareness of sustainable and responsible tourism.
On the Need for Better Exposure Assessment for Air Pollution with High Spatial and Temporal Variation
Authors: Brugge Doug
Published: May 2019

The mainstay of air pollution health research has been fine particulate matter pollution (PM2 [...]
Biomarker Effects in Carassius auratus Exposure to Ofloxacin, Sulfamethoxazole and Ibuprofen
Authors: Yang Xiaofan , Xu Xiaoping , Wei Xueyu , Wan Jie , Zhang Yu
Published: May 2019

Ofloxacin, sulfamethoxazole and ibuprofen are three commonly used drugs which can be detected in aquatic environments. To assess their ecotoxicity, the effects of these three pharmaceuticals and their mixture on AChE (acetylcholinesterase) activity in the brain, and EROD (7-ethoxyresorufin-O-deethylase) and SOD (superoxide dismutase) activities in the liver of the freshwater crucian carp Carassius auratus were tested after exposure for 1, 2, 4 and 7 days. The results showed that treatments with 0.002–0.01 mg/L ofloxacin and 0.0008–0.004 mg/L sulfamethoxazole did not significantly change AChE, EROD and SOD activities. AChE activity was significantly inhibited in response to treatment with >0.05mg/L ofloxacin and >0.02 mg/L sulfamethoxazole. All three biomarkers were induced significantly in treatments with ibuprofen and the mixture of the three pharmaceuticals at all the tested concentrations. The combined effects of ofloxacin, sulfamethoxazole and ibuprofen were compared with their isolated effects on the three biomarkers, and the results indicated that exposure to ibuprofen and the mixture at environmentally relevant concentrations could trigger adverse impacts on Carassius auratus. The hazard quotient (HQ) index also demonstrated a high risk for ibuprofen. Moreover, the present study showed that the effects of ofloxacin, sulfamethoxazole and ibuprofen might be additive on the physiological indices of Carassius auratus.
Could Crime Risk Be Propagated across Crime Types?
Authors: Wang Zengli , Zhang Hong
Published: May 2019

It has long been acknowledged that crimes of the same type tend to be committed at the same location or proximity in a short period. However, the investigation of whether this phenomenon exists across crime types remains limited. The spatial-temporal clustered patterns for two types of crimes in public areas (pocket-picking and vehicle/motor vehicle theft) are separately examined. Compared with existing research, this study contributes to current research from three aspects: (1) The repeat and near-repeat phenomenon exists in two types of crimes in a large Chinese city. (2) A significant spatial-temporal interaction between pocket-picking and vehicle/motor vehicle theft exists within a range of 100 m. Some cross-crime type interactions seem to have a stronger ability of prediction than does single-crime type interaction. (3) A risk-avoiding activity is identified after spatial-temporal hotspots of another crime type. The spatial extent with increased risk is limited to a certain distance from the previous hotspots. The experimental results are analyzed and interpreted with current criminology theories.
Obtaining Land Cover Type for Urban Storm Flood Model in UAV Images Using MRF and MKFCM Clustering Techniques
Authors: Wang Yanmei , Zhang Chengcai , Zhang Yisheng , Huang He , Feng Lingtong
Published: May 2019

With the accelerated urbanization process, cities are suffering from extremely heavy rain and urban storm water logging disasters in recent years. To provide reliable and effective information for urban management and emergency decision-making, the accuracy of basic data must be guaranteed in any urban rainwater model. This paper presents a novel MKFCM-MRF (Multiple Kernel Fuzzy C Means-Markov Random Field) model to segment high-resolution Unmanned Aerial Vehicle (UAV) images. The core ideas of MKFCM-MRF model are as follows. Firstly, in order to increase the correlation information between pixels, multiple-kernel functions are introduced into Fuzzy C Means (FCM) clustering algorithm, which automatically filters out the optimal weight combination among kernel functions according to the distribution characteristics of pixels in feature space. Secondly, in order to better segment the texture and edge of the image, the clustering results of multiple-kernel FCM clustering algorithm are introduced into Markov Random Field (MRF) model, a novel spatial energy function integrating fuzzy local information is constructed. Finally, based on the total of data and spatial energies, the raw clustering results are regularized by a global minimization of the energy function using its iterated conditional modes (ICM). The effectiveness of MKFCM-MRF is performed by high-resolution UAV images data. The experimental results indicate MKFCM-MRF can refine the classification map in homogeneous areas, while reducing most of the edge blurring artifact, and improving the classification accuracy compared with FCM clustering algorithm. In addition, the validation of the urban storm flood model shows that the trend of the two clustering results is the same, but the runoff producing time and the peak time of FCM clustering results are advanced, the peak flow and the total runoff are larger; the simulation results corresponding to MKFCM-MRF clustering results are more realistic.
Integrated UAV-Based Real-Time Mapping for Security Applications
Authors: Hein Daniel , Kraft Thomas , Brauchle Jörg , Berger Ralf
Published: May 2019

Security applications such as management of natural disasters and man-made incidents crucially depend on the rapid availability of a situation picture of the affected area. UAV-based remote sensing systems may constitute an essential tool for capturing aerial imagery in such scenarios. While several commercial UAV solutions already provide acquisition of high quality photos or real-time video transmission via radio link, generating instant high-resolution aerial maps is still an open challenge. For this purpose, the article presents a real-time processing tool chain, enabling generation of interactive aerial maps during flight. Key element of this tool chain is the combination of the Terrain Aware Image Clipping (TAC) algorithm and 12-bit JPEG compression. As a result, the data size of a common scenery can be reduced to approximately 0.4% of the original size, while preserving full geometric and radiometric resolution. Particular attention was paid to minimize computational costs to reduce hardware requirements. The full workflow was demonstrated using the DLR Modular Airborne Camera System (MACS) operated on a conventional aircraft. In combination with a commercial radio link, the latency between image acquisition and visualization in the ground station was about 2 s. In addition, the integration of a miniaturized version of the camera system into a small fixed-wing UAV is presented. It is shown that the described workflow is efficient enough to instantly generate image maps even on small UAV hardware. Using a radio link, these maps can be broadcasted to on-site operation centers and are immediately available to the end-users.
Spatial Interaction Modeling of OD Flow Data: Comparing Geographically Weighted Negative Binomial Regression (GWNBR) and OLS (GWOLSR)
Authors: Zhang Lianfa , Cheng Jianquan , Jin Cheng
Published: May 2019

Due to the emergence of new big data technology, mobility data such as flows between origin and destination areas have increasingly become more available, cheaper, and faster. These improvements to data infrastructure have boosted spatial and temporal modeling of OD (origin-destination) flows, which require the consideration of spatial dependence and heterogeneity. Both ordinary least square (OLS) and negative binomial (NB) regression methods have been used extensively to calibrate OD flow models by processing flow data as different types of dependent variables. This paper aims to compare both global and local spatial interaction modeling of OD flows between traditional and geographically weighted OLS (GWOLSR) and NB (GWNBR) modeling methods. From this study with empirical data it is concluded that GWNBR outperforms GWOLSR in reducing spatial autocorrelation and in detecting spatial non-stationarity. Although, it is noted that both local modeling methods show improvement when compared against the equivalent global models.
Reliability Analysis of LandScan Gridded Population Data. The Case Study of Poland
Authors: Calka Beata , Bielecka Elzbieta
Published: May 2019

The issue of population dataset reliability is of particular importance when it comes to broadening the understanding of spatial structure, pattern and configuration of humans’ geographical location. The aim of the paper was to estimate the reliability of LandScan based on the official Polish Population Grid. The adopted methodology was based on the change detection approach, spatial pattern and continuity analysis, as well as statistical analysis at the grid-cell level. Our results show that the LandScan data can estimate the Polish population very well. The number of grid cells with equal people counts in both datasets amounts to 10.5%. The most and highly reliable data cover 72% of the country territory, while less reliable ones cover only 4.3%. The LandScan algorithm tends to underestimate people counts, with a total value of 79,735 people (0.21%). The highest underestimation was noticed in densely populated areas as well as in the transition areas between urban and rural, while overestimation was observed in moderately populated regions, along main roads and in city centres. The underestimation results mainly from the spatial pattern and size of Polish rural settlements, namely a big number of shadowed single households dispersed over agricultural areas and in the vicinity of forests. An excessive assessment of the number of people may be a consequence of the well-known blooming effect.
Top-Bounded Spaces Formed by the Built Environment for Navigation Systems
Authors: Yan Jinjin , Diakité Abdoulaye A. , Zlatanova Sisi , Aleksandrov Mitko
Published: May 2019

Navigation systems help agents find the right (optimal) path from the origin to the desired destination. Current navigation systems mainly offer the shortest (distance or time) path as the default optimal path. However, under certain circumstances, having a least-top-exposed path can be more interesting. For instance, on a rainy day, a path with as many places as possible covered by roofs/shelters is more attractive and pragmatic, since roofs/shelters can offer protection from rain. In this paper, we name environments that covered by roofs/shelters but not completely enclosed like indoors as “top-bounded environments/spaces” (e.g., porches), which are generally formed by built structures. This kind of space is completely missing in current navigation models and systems. Thus, we investigate how to use it for space-based navigation. After proposing a definition, a space model, and attributes of top-bounded spaces, we introduce a projection-based approach to generate them. Then, taking a pedestrian as an example agent, we select generated spaces considering whether the agent can visit/use the identified spaces. Finally, examples and a use case study demonstrate that our research can help to include top-bounded spaces in navigation systems/models. More navigation path types (e.g., least-top-exposed) can be offered for different agents (such as pedestrians, drones or robots).
Glycidamide Promotes the Growth and Migratory Ability of Prostate Cancer Cells by Changing the Protein Expression of Cell Cycle Regulators and Epithelial-to-Mesenchymal Transition (EMT)-Associated Proteins with Prognostic Relevance
Authors: Ekanem Titus Ime , Huang Chi-Chen , Wu Ming-Heng , Lin Ding-Yen , Lai Wen-Fu T. , Lee Kuen-Haur
Published: May 2019

Acrylamide (AA) and glycidamide (GA) can be produced in carbohydrate-rich food when heated at a high temperature, which can induce a malignant transformation. It has been demonstrated that GA is more mutagenic than AA. It has been shown that the proliferation rate of some cancer cells are increased by treatment with GA; however, the exact genes that are induced by GA in most cancer cells are not clear. In the present study, we demonstrated that GA promotes the growth of prostate cancer cells through induced protein expression of the cell cycle regulator. In addition, we also found that GA promoted the migratory ability of prostate cancer cells through induced epithelial-to-mesenchymal transition (EMT)-associated protein expression. In order to understand the potential prognostic relevance of GA-mediated regulators of the cell cycle and EMT, we present a three-gene signature to evaluate the prognosis of prostate cancer patients. Further investigations suggested that the three-gene signature (CDK4, TWIST1 and SNAI2) predicted the chances of survival better than any of the three genes alone for the first time. In conclusion, we suggested that the three-gene signature model can act as marker of GA exposure. Hence, this multi-gene panel may serve as a promising outcome predictor and potential therapeutic target in prostate cancer patients.
Presynaptic Calcium Channels
Authors: Mochida Sumiko
Published: May 2019

Presynaptic Ca2+ entry occurs through voltage-gated Ca2+ (CaV) channels which are activated by membrane depolarization. Depolarization accompanies neuronal firing and elevation of Ca2+ triggers neurotransmitter release from synaptic vesicles. For synchronization of efficient neurotransmitter release, synaptic vesicles are targeted by presynaptic Ca2+ channels forming a large signaling complex in the active zone. The presynaptic CaV2 channel gene family (comprising CaV2.1, CaV2.2, and CaV2.3 isoforms) encode the pore-forming α1 subunit. The cytoplasmic regions are responsible for channel modulation by interacting with regulatory proteins. This article overviews modulation of the activity of CaV2.1 and CaV2.2 channels in the control of synaptic strength and presynaptic plasticity.
Oritatami: A Computational Model for Molecular Co-Transcriptional Folding
Authors: Geary Cody , Meunier Pierre-Étienne , Schabanel Nicolas , Seki Shinnosuke
Published: May 2019

We introduce and study the computational power of Oritatami, a theoretical model that explores greedy molecular folding, whereby a molecular strand begins to fold before its production is complete. This model is inspired by our recent experimental work demonstrating the construction of shapes at the nanoscale from RNA, where strands of RNA fold into programmable shapes during their transcription from an engineered sequence of synthetic DNA. In the model of Oritatami, we explore the process of folding a single-strand bit by bit in such a way that the final fold emerges as a space-time diagram of computation. One major requirement in order to compute within this model is the ability to program a single sequence to fold into different shapes dependent on the state of the surrounding inputs. Another challenge is to embed all of the computing components within a contiguous strand, and in such a way that different fold patterns of the same strand perform different functions of computation. Here, we introduce general design techniques to solve these challenges in the Oritatami model. Our main result in this direction is the demonstration of a periodic Oritatami system that folds upon itself algorithmically into a prescribed set of shapes, depending on its current local environment, and whose final folding displays the sequence of binary integers from 0 to N = 2 k − 1 with a seed of size O ( k ) . We prove that designing Oritatami is NP-hard in the number of possible local environments for the folding. Nevertheless, we provide an efficient algorithm, linear in the length of the sequence, that solves the Oritatami design problem when the number of local environments is a small fixed constant. This shows that this problem is in fact fixed parameter tractable (FPT) and can thus be solved in practice efficiently. We hope that the numerous structural strategies employed in Oritatami enabling computation will inspire new architectures for computing in RNA that take advantage of the rapid kinetic-folding of RNA.
An Improved Jacobi-Based Detector for Massive MIMO Systems
Authors: Zhao Xiaoqing , Li Zhengquan , Xing Song , Liu Yang , Wu Qiong , Li Baolong
Published: May 2019

Massive multiple-input-multiple-output (MIMO) is one of the key technologies in the fifth generation (5G) cellular communication systems. For uplink massive MIMO systems, the typical linear detection such as minimum mean square error (MMSE) presents a near-optimal performance. Due to the required direct matrix inverse, however, the MMSE detection algorithm becomes computationally very expensive, especially when the number of users is large. For achieving the high detection accuracy as well as reducing the computational complexity in massive MIMO systems, we propose an improved Jacobi iterative algorithm by accelerating the convergence rate in the signal detection process.Specifically, the steepest descent (SD) method is utilized to achieve an efficient searching direction. Then, the whole-correction method is applied to update the iterative process. As the result, the fast convergence and the low computationally complexity of the proposed Jacobi-based algorithm are obtained and proved. Simulation results also demonstrate that the proposed algorithm performs better than the conventional algorithms in terms of the bit error rate (BER) and achieves a near-optimal detection accuracy as the typical MMSE detector, but utilizing a small number of iterations.
Similarity Measures of Linguistic Cubic Hesitant Variables for Multiple Attribute Group Decision-Making
Authors: Lu Xueping , Ye Jun
Published: May 2019

A linguistic cubic hesitant variable (LCHV) is a hybrid form of linguistic values in group decision-making environments. It is composed of an interval language variable and multiple single-valued language variables given by different decision-makers (DMs). Due to the uncertainty and hesitation of DMs, the numbers of language variables in different LCHVs are unequal. Thus, the least common multiple number (LCMN) extension method was adopted. Based on the included angle and distance of two LCHVs, we presented two cosine similarity measures and developed a multiple attribute group decision-making (MAGDM) approach. An example of engineer selection was used to implement the proposed LCHV MAGDM method and demonstrate the simplicity and feasibility of the proposed method. The sensitivity analysis of weight changes for the two measures showed that the similarity measure based on distance was more stable than the similarity measure based on included angle in this application.
Interactivity in Cybermedia News: An Interview with Journalists in Colombia, Peru, and Ecuador
Authors: Barredo Ibáñez Daniel , Pinto Garzón Karen , Freundt-Thurne Úrsula , Medranda Morales Narcisa
Published: May 2019

Interactivity is a factor on which cyber journalism is based and summarizes participation options between a user and the medium, a user with other users, and a user with editors. In this study, we focus on the latter in three countries—Colombia, Peru, and Ecuador—, which have been identified owing to their technological gap and the emerging importance of online communication for their respective societies. Through 35 in-depth interviews with journalists from these countries, we analyzed the concept of interactivity of these professionals and their relationship with users. The results revealed that the journalists positively valued civic contributions as a space for diagnosis, although they do not perceive its informational value, as they relate them to the context of opinions. These results verify the prevalence of journalism as strongly influenced by conventional offline production routines.
Improving Semantic Similarity with Cross-Lingual Resources: A Study in Bangla—A Low Resourced Language
Authors: Pandit Rajat , Sengupta Saptarshi , Naskar Sudip Kumar , Dash Niladri Sekhar , Sardar Mohini Mohan
Published: May 2019

Semantic similarity is a long-standing problem in natural language processing (NLP). It is a topic of great interest as its understanding can provide a look into how human beings comprehend meaning and make associations between words. However, when this problem is looked at from the viewpoint of machine understanding, particularly for under resourced languages, it poses a different problem altogether. In this paper, semantic similarity is explored in Bangla, a less resourced language. For ameliorating the situation in such languages, the most rudimentary method (path-based) and the latest state-of-the-art method (Word2Vec) for semantic similarity calculation were augmented using cross-lingual resources in English and the results obtained are truly astonishing. In the presented paper, two semantic similarity approaches have been explored in Bangla, namely the path-based and distributional model and their cross-lingual counterparts were synthesized in light of the English WordNet and Corpora. The proposed methods were evaluated on a dataset comprising of 162 Bangla word pairs, which were annotated by five expert raters. The correlation scores obtained between the four metrics and human evaluation scores demonstrate a marked enhancement that the cross-lingual approach brings into the process of semantic similarity calculation for Bangla.
Conceptualization and Non-Relational Implementation of Ontological and Epistemic Vagueness of Information in Digital Humanities
Authors: Martin-Rodilla Patricia , Gonzalez-Perez Cesar
Published: May 2019

Research in the digital humanities often involves vague information, either because our objects of study lack clearly defined boundaries, or because our knowledge about them is incomplete or hypothetical, which is especially true in disciplines about our past (such as history, archaeology, and classical studies). Most techniques used to represent data vagueness emerged from natural sciences, and lack the expressiveness that would be ideal for humanistic contexts. Building on previous work, we present here a conceptual framework based on the ConML modelling language for the expression of information vagueness in digital humanities. In addition, we propose an implementation on non-relational data stores, which are becoming popular within the digital humanities. Having clear implementation guidelines allow us to employ search engines or big data systems (commonly implemented using non-relational approaches) to handle the vague aspects of information. The proposed implementation guidelines have been validated in practice, and show how we can query a vagueness-aware system without a large penalty in analytical and processing power.
Bacillus thuringiensis Spores and Vegetative Bacteria: Infection Capacity and Role of the Virulence Regulon PlcR Following Intrahaemocoel Injection of Galleria mellonella
Authors: Buisson Christophe , Gohar Michel , Huillet Eugénie , Nielsen-LeRoux Christina
Published: May 2019

Bacillus thuringiensis is an invertebrate pathogen that produces insecticidal crystal toxins acting on the intestinal barrier. In the Galleria mellonella larvae infection model, toxins from the PlcR virulence regulon contribute to pathogenicity by the oral route. While B. thuringiensis is principally an oral pathogen, bacteria may also reach the insect haemocoel following injury of the cuticle. Here, we address the question of spore virulence as compared to vegetative cells when the wild-type Bt407cry- strain and its isogenic ∆plcR mutant are inoculated directly into G. mellonella haemocoel. Mortality dose-response curves were constructed at 25 and 37 °C using spores or vegetative cell inocula, and the 50% lethal dose (LD50) in all infection conditions was determined after 48 h of infection. Our findings show that (i) the LD50 is lower for spores than for vegetative cells for both strains, while the temperature has no significant influence, and (ii) the ∆plcR mutant is four to six times less virulent than the wild-type strain in all infection conditions. Our results suggest that the environmental resistant spores are the most infecting form in haemocoel and that the PlcR virulence regulon plays an important role in toxicity when reaching the haemocoel from the cuticle and not only following ingestion.
Insecticidal Properties of Capsaicinoids and Glucosinolates Extracted from Capsicum chinense and Tropaeolum tuberosum
Authors: Claros Cuadrado José L. , Pinillos Elder O. , Tito Richard , Mirones Carlos Seguil , Gamarra Mendoza Norma N.
Published: May 2019

Food security and biodiversity conservation are threatened by the emergence and spread of pest and pathogens, and thus there is a current need to develop pest management strategies that are sustainable and friendly to the environment and human health. Here, we performed laboratory and field bioassays to evaluate the insecticidal effects of several concentrations of capsaicinoids and glucosinolates (separately and mixed) on an aphid pest (Aphis cytisorum). The capsaicinoids were extracted from the fruits of Capsicum chinense and glucosinolates from the tubers of native Andean crop Tropaeolum tuberosum. We found that both capsaicinoids and glucosinolates have a biocidal effect on A. cytisorum, acting within a fairly short time. Under laboratory conditions, the toxicity of the compounds increased in relation to their concentrations, causing a high percentage of mortality (83–99%) when the aphids were exposed to dilutions of 10% capsaicinoids, 75–100% glucosinolates, or a mixture of 10% capsaicinoids and 90% glucosinolates. The mortality of aphids sprayed in the field with 5% capsaicinoids, 50% glucosinolates, or with a mixture of 5% capsaicinoids and 45% glucosinolates reached 87–97%. Results obtained from laboratory and field experiments were consistent. Our results suggest the potential use of bioinsecticides based on capsaicinoids and/or glucosinolates as an effective alternative to synthetic pesticides.
High Prevalence of a Newly Discovered Wutai Mosquito Phasivirus in Mosquitoes from Rio de Janeiro, Brazil
Authors: Ribeiro Mário Sérgio , Ayllón Tania , Malirat Viviana , Câmara Daniel Cardoso Portela , Giordano Dias Cristina Maria , Louzada Guilherme , Fernandes-Ferreira Davis , Medronho Roberto de Andrade , Campos Acevedo Renata
Published: May 2019

Many RNA viruses have recently emerged, threatening humans and causing harm to animals and plants. Bunyaviruses represent one of the largest groups of RNA viruses and are able to infect a wide range of hosts (invertebrates, vertebrates, and plants). Recently, new insect-specific viruses have been isolated from mosquitoes and phlebotomine sandflies worldwide. Little is known regarding the impact of these viruses on the vector life cycles and the stages of oviposition, breeding, blood feeding, and the mosquito’s lifespan. This study describes, for the first time in South America, the detection and characterization of a recently discovered bunyavirus corresponding to the Wutai mosquito phasivirus, confirming its high prevalence in the Culex spp. and Aedes spp. mosquitoes collected in the urban environment of Rio de Janeiro city, Brazil. The knowledge of the mosquito’s insect-specific virus infection can improve virus evolution studies and may contribute to the understanding of intrinsic factors that influence vector competence to transmit pathogenic viruses.
First Operation of a Resistive Shell Liquid Argon Time Projection Chamber: A New Approach to Electric-Field Shaping
Authors: Berner Roman , Chen Yifan , Ereditato Antonio , Koller Patrick P. , Kreslo Igor , Lorca David , Mettler Thomas , Miao Ting , Piastra Francesco , Sinclair James R. , Weber Michael S.
Published: May 2019

We present a new technology for the shaping of the electric field in Time Projection Chambers (TPCs) using a carbon-loaded polyimide foil. This technology allows for the minimisation of passive material near the active volume of the TPC and, thus, is capable to reduce background events originating from radioactive decays or scattering on the material itself. Furthermore, the high and continuous electric resistivity of the foil limits the power dissipation per unit area and minimizes the risks of damages in the case of an electric field breakdown. Replacing the conventional field cage with a resistive plastic film structure called “shell” decreases the number of components within the TPC and, therefore, reduces the potential points of failure when operating the detector. A prototype liquid argon (LAr) TPC with such a resistive shell and with a cathode made of the same material was successfully tested for long-term operation with electric field values up to 1.6 k V cm − 1 . The experiment shows that it is feasible to successfully produce and shape the electric field in liquefied noble-gas detectors with this new technology.