bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal Deep Learning LSTM Model for Electric Load Forecasting using Feature Selection and Genetic Algorithm: Comparison with Machine Learning Approaches †
Authors: Bouktif Salah , Fiaz Ali , Ouni Ali , Serhani Mohamed
Published: June 2018

Background: With the development of smart grids, accurate electric load forecasting has become increasingly important as it can help power companies in better load scheduling and reduce excessive electricity production. However, developing and selecting accurate time series models is a challenging task as this requires training several different models for selecting the best amongst them along with substantial feature engineering to derive informative features and finding optimal time lags, a commonly used input features for time series models. Methods: Our approach uses machine learning and a long short-term memory (LSTM)-based neural network with various configurations to construct forecasting models for short to medium term aggregate load forecasting. The research solves above mentioned problems by training several linear and non-linear machine learning algorithms and picking the best as baseline, choosing best features using wrapper and embedded feature selection methods and finally using genetic algorithm (GA) to find optimal time lags and number of layers for LSTM model predictive performance optimization. Results: Using France metropolitan’s electricity consumption data as a case study, obtained results show that LSTM based model has shown high accuracy then machine learning model that is optimized with hyperparameter tuning. Using the best features, optimal lags, layers and training various LSTM configurations further improved forecasting accuracy. Conclusions: A LSTM model using only optimally selected time lagged features captured all the characteristics of complex time series and showed decreased Mean Absolute Error (MAE) and Root Mean Square Error (RMSE) for medium to long range forecasting for a wider metropolitan area.
Mechanized Tree Planting in Sweden and Finland: Current State and Key Factors for Future Growth
Authors: Ersson Back Tomas , Laine Tiina , Saksa Timo
Published: June 2018

In Fennoscandia, mechanized tree planting is time-efficient and produces high-quality regeneration. However, because of low cost-efficiency, the mechanization of Fennoscandian tree planting has been struggling. To determine key factors for its future growth, we compared the operational, planning, logistical, and organizational characteristics of mechanized planting in Sweden and Finland. Through interviews with planting machine contractors and client company foresters, we establish that mechanized tree planting in Sweden and Finland presently shares more similarities than differences. Some notable differences include typically longer planting seasons in Sweden, and a tendency towards two-shift operation and less frequent worksite pre-inspection by contractors in Finland. Because of similar challenges, mechanized planting in both countries can improve cost-efficiency through education of involved foresters, flexible information systems, efficient seedling logistics, and continued technical development of planting machines. By striving to have multiple client companies, contractors can reduce their operating radii and increase their machine utilization rates. Above all, our results provide international readers with unprecedented detailed and comprehensive figures and characteristics of Swedish and Finnish mechanized tree-planting activities. We conclude that cooperation between Sweden’s and Finland’s forest industries and research institutes could enhance the mechanization level of Fennoscandian tree planting.
Effects of Plot Positioning Errors on the Optimality of Harvest Prescriptions When Spatial Forest Planning Relies on ALS Data
Authors: Pascual Adrián , Pukkala Timo , De-Miguel Sergio
Published: June 2018

Forest management planning is increasingly relying on airborne laser scanning (ALS) in forest inventory. The area-based method to interpret ALS data requires sample plots measured in the field. The aim of this study was to assess and trace the impacts of the positioning errors of field plots along the entire forest management planning process, from their effect on forest inventory results to the outcome of forest management planning. This research links plot positioning errors with the spatio-temporal allocation of forest treatments and calculates the inoptimality losses arising from plot positioning errors in ALS-based forest inventory. The study area was a forest management unit in Central Spain. Growing stock attributes were predicted for a grid of square-shaped cells. Alternative management schedules were simulated for the grid cells by using growth and yield models. Then, a spatial forest planning problem aiming at maximizing timber production with even-flow cuttings was formulated. Spatial objective variables were used to cluster management prescriptions into dynamic treatment units. We used simulated annealing to conduct spatial optimization. First, the true plot locations were used and then the whole process was repeated with normally distributed random errors with standard deviation equal to 2.5, 5 and 10 m, resulting in an average error of 1.47, 3.06 and 8.34 m, respectively. Increasing the level of positioning errors resulted in higher variability in the estimated growing stock attributes and in the achieved values of management goals. Sub-optimal prescriptions caused by the tested plot positioning errors caused up to 4.62% losses in timber production and up to 3.35% losses in utility. The losses increased with increasing plot positioning error.
Genetic Diversity and Structure through Three Cycles of a Eucalyptus urophylla S.T.Blake Breeding Program
Authors: Lu Wanhong , Arnold Roger J. , Zhang Lei , Luo Jianzhong
Published: June 2018

Eucalyptus urophylla S.T.Blake is an important commercial tropical plantation species worldwide. In China, a breeding program for this species has progressed through three cycles but genetic diversity and structure in the breeding populations are uncertain. A sampling of field trials from these populations was carried out to evaluate their genetic diversity and structure using 16 microsatellite loci. Significant deviations from Hardy-Weinberg equilibrium were recorded at all 16 loci in the populations. Overall expected and observed heterozygosity (He and Ho) estimates of 0.87 and 0.59 respectively for the first cycle population, and 0.88 and 0.60 respectively for the third cycle population, revealed reasonably high levels of genetic diversity. The genetic differentiation coefficient (Fst) revealed low differentiation among pairs of provenances (from the species’ native range) comprising the first cycle population (range: 0.012–0.108), and AMOVA results showed that the majority of molecular genetic variation existed among individuals rather than among provenances for the first cycle population and among individuals rather than among field trial sources in the third cycle population. Levels of genetic diversity appeared to remain unchanged from the first to third cycle populations, and the results indicate prospects for maintaining if not increasing diversity through recurrent breeding. Likely effects of artificial directional selection, prior to sampling, on both populations examined are discussed along with implications for future E. urophylla breeding.
Ungulate Browsing Limits Bird Diversity of the Central European Hardwood Floodplain Forests
Authors: Machar Ivo , Cermak Petr , Pechanec Vilem
Published: June 2018

Temperate hardwood floodplain forests along lowland rivers are considered important forest biodiversity refugia in the European cultural landscape. The absence of apex predators combined with an artificial feeding of herbivore populations in winter seasons has caused an increase in browsing pressure on hardwood trees, nearly preventing their regeneration in some localities. There are still important knowledge gaps in understanding the relationships between deer abundance (and browsing pressure) and the abundance (and diversity) of forest bird species in unmanaged hardwood forests. We have studied the red deer and fallow deer browsing pressure in Central European unmanaged hardwood floodplain forests using a novel method based on monitoring browsing pressure along transects combined with bird census data in the Litovelské Pomoraví Protected Landscape Area (Czech Republic). The monitoring data suggested a very high browsing pressure on hardwood trees, causing a strong reduction of the shrub layer and young tree layer (30–210 cm above ground surface). The bird census data from the study area were collected using the territory mapping method. Our results revealed a bird diversity decline in all study plots and the bush nesters guild was found to be completely absent. As bird species from the bush nesters guild are generally common (usually dominant) in hardwood floodplain forest ecosystems with a rich shrub and young tree layer and low browsing pressure, we conclude that intense browsing by large herbivores represents a limiting factor to the bird diversity (especially bush nesters) of hardwood floodplain forests.
Assessing the Driving Forces in Vegetation Dynamics Using Net Primary Productivity as the Indicator: A Case Study in Jinghe River Basin in the Loess Plateau
Authors: Wang Hao , Liu Guohua , Li Zongshan , Wang Pengtao , Wang Zhuangzhuang
Published: June 2018

An objective and effective method to distinguish the influence of climate change and human activities on vegetation dynamics has great significance in the design and implementation of ecosystem restoration projects. Based on the Moderate Resolution Imaging Spectroradiometer (MODIS) remote data and the Miami and Carnegie–Ames–Stanford Approach (CASA) model, this study simulated and used net primary productivity (NPP) as an indicator to identify vegetation dynamics and their driving forces in the Jinghe River basin from 2000 to 2014. The results showed that: (1) The vegetation in the Jinghe River basin, which accounted for 84.4% of the study area, showed an increasing trend in NPP; (2) Human activities contributed most to vegetation restoration, which accounted for 54.5% of the areas; 24.0% of the areas showed an increasing trend in the NPP that was dominated by climate factors. Degradation dominated by human activities accounted for 4.3% of the study area, and degradation dominated by climate factors resulted in 17.2%; (3) The rate of vegetation degradation in areas dominated by climate factors rose with increased slope, where the arid climate caused shortages of water resources, and the human-dominated vegetation restoration activities exacerbated the vegetation’s water demand further, which surpassed the carrying capacity of regional water resources and led ultimately to vegetation degradation. We recommend that future ecological restoration programs pay more attention to maintaining the balance between ecosystem restoration and water resource demand to maximize the benefits of human activities and ensure the vegetation restoration is ecologically sustainable.
Structural Attributes of Old-Growth and Partially Harvested Northern White-Cedar Stands in Northeastern North America
Authors: Wesely Nathan , Fraver Shawn , Kenefic Laura S. , Weiskittel Aaron R. , Ruel Jean-Claude , Thompson Michael E. , White Alan S.
Published: June 2018

Forestry practitioners often need to identify old-growth stands because of their high conservation value. To identify the structural and compositional characteristics potentially unique to old-growth northern white-cedar (Thuja occidentalis L.) stands, we compared 16 old-growth stands and 17 partially harvested stands in Maine, USA and New Brunswick, Canada. Potential old-growth predictors included common structural metrics such as basal area (BA), quadratic mean diameter (QMD), large tree (≥40 cm diameter at breast height) density, and volumes of coarse woody debris (CWD), along with six structural indices. Using generalized linear mixed-models, we identified two significant structural predictors that differentiate old-growth from partially harvested stands when used in combination: Volume of advanced-decay CWD and live tree QMD. None of the structural indices were useful in distinguishing between old-growth and partially harvested stands, nor did the two types differ with respect to tree species composition. Our results demonstrate that two metrics easily derived from standard inventory data—decayed CWD volume and QMD—effectively characterize the old-growth white-cedar stands sampled in this study. Taken together, these results can improve management decision making for white-cedar, particularly in the context of certification, while also shedding light on the effects of past partial harvesting on current forest structure.
Effects of Growing-Season Drought on Phenology and Productivity in the West Region of Central Hardwood Forests, USA
Authors: Duan Shengwu , He Hong S. , Spetich Marty
Published: June 2018

Studying the effects of drought on forest ecosystems is important in developing a better understanding of forest phenology and productivity. Many previous studies were based on single drought events, whereas effects of recurrent droughts have not been yet fully investigated. This study jointly analyzed the spatial–temporal change of drought patterns with forest phenology and productivity between 2000–2015 in the western Central Hardwood Forests at Missouri, Arkansas Illinois, Oklahoma, and Kansas of the US. Characteristics of forest phenology and productivity were captured by utilizing the Moderate Resolution Imaging Spectroradiometer (MODIS) remote sensing 16-day MOD13Q1 data and Savitsky–Golay (S-G) filtering method. Spatial-temporal drought patterns were assessed by empirical orthogonal function (EOF) on self-calibrating Palmer Drought Severity Index (scPDSI) time series. Our results revealed four drought zones: sporadic severe drought zone, cyclic light drought zone, minor drought zone, and moderate drought zone. The results showed that at the regional scale, drought effects on forest phenology and productivity depended on forest type and drought intensity. The cyclic light drought did not result in a notable decline of growing season length and productivity, while both minor drought and severe drought were followed by a significant decrease of forest growing season length and productivity. This research presents an alternative method to analyze the impacts of drought on regional forest dynamics.
Dynamic Cost-Aware Routing of Web Requests
Authors: Velusamy Gandhimathi , Lent Ricardo
Published: June 2018

Work within next generation networks considers additional network convergence possibilities and the integration of new services to the web. This trend responds to the ongoing growth of end-user demand for services that can be delivered anytime, anywhere, on any web-capable device, and of traffic generated by new applications, e.g., the Internet of Things. To support the massive traffic generated by the enormous user base and number of devices with reliability and high quality, web services run from redundant servers. As new servers need to be regularly deployed at different geographical locations, energy costs have become a source of major concern for operators. We propose a cost aware method for routing web requests across replicated and distributed servers that can exploit the spatial and temporal variations of both electricity prices and the server network. The method relies on a learning automaton that makes per-request decisions, which can be computed much faster than regular global optimization methods. Using simulation and testbed measurements, we show the cost reductions that are achievable with minimal impact on performance compared to standard web routing algorithms.
Geophysical Input to Improve the Conceptual Model of the Hydrogeological Framework of a Coastal Karstic Aquifer: Uley South Basin, South Australia
Authors: Somaratne Nara , Ashman Glyn , Irvine Michelle , Mann Simon
Published: June 2018

A lack of closely spaced datasets on layer elevations, aquifer parameters, identification of areas with high recharge potential, dominant conduit porosity zones, and well defined boundary conditions hampers the ability of groundwater models to produce a reliable water balance. Typically, geological structure, aquifer properties, and groundwater heads are obtained from point measurements which are sparse. The drillhole information in aquifers is usually available at locations far apart, distances ranging from hundreds to thousands of meters. Furthermore, pump tests are usually conducted at limited locations and generalized to the aquifer. This limited knowledge leads to errors in the conceptual understanding of the aquifer. In this study, Airborne Electromagnetic Survey (AEM) was used to define base elevations of the aquifers where drillhole information was lacking. Surface Nuclear Magnetic Resonance (sNMR), borehole NMR, Transient Electromagnetic (TEM), and downhole geophysical surveys have given new insight to the conceptualization of hydrogeological framework. These methods are relatively low in cost compared to traditional well drilling and provide information on layer elevations, aquifer parameters, point and diffuse recharge zones, and conduit porosity zones in the profile, which improves our definition of the boundary conditions. From a practical point of view, combining drillhole information with a variety of geophysical techniques provides sound datasets to develop a comprehensive conceptual model. This in turn can be used to build a robust groundwater model.
Pollution Plume Development in the Primary Aquifer at the Atlantis Historical Solid Waste Disposal Site, South Africa
Authors: Bugan Richard , Tredoux Gideon , Jovanovic Nebo , Israel Sumaya
Published: June 2018

The monitoring of pollution plumes from municipal landfills is essential in order to control and, where necessary, remediate aquifer contamination. The Atlantis historical landfill was established in 1975 and was unlined as it preceded the promulgation of the Minimum Requirements by the Department of Water and Sanitation. As the underlying, unconfined sandy aquifer serves as a water supply source to the town of Atlantis, regular quarterly hydrochemical monitoring was carried out from 1989 to 1997, at irregular intervals until 2003, and resumed in 2015 when new, deep boreholes were drilled. Groundwater monitoring over nearly three decades provided valuable information on the nature of the chemical reactions that take place in the subsurface and the extent of transport of chemical constituents. Ammonium and organic carbon, which are subject to redox reactions, were lagging compared to chloride and sodium, which are transported advectively. The most recent data indicated the plume consisted mainly of salinity (electrical conductivity (EC) > 200 mS m−1) in the form of sodium, calcium, chloride and bicarbonate ions 350–400 m down-gradient of the landfill, and it is still expanding at a maximum rate of about 25 m a−1, with local deviations from the regional flow pattern. It also became evident that the plume migrated to greater depth as it was transported further from the waste pile. The breakthrough of contaminants being observed at different depths highlights the importance of suitably designed monitoring networks.
Optimising Clinical Trial Design in Older Cancer Patients
Authors: Whelehan Shóna , Lynch Orlaith , Treacy Niall , Gleeson Ciara , Oates Andrea , O’Donovan Anita
Published: June 2018

Cancer is predominantly a disease of older patients, with over half of those aged over 65 years of age being diagnosed with cancer at some stage. Despite comprising a significant proportion of the patients that we see in clinical practice, there is a lack of representation of older patients in cancer clinical trials. This is mainly due to restrictive trial inclusion criteria that prevent older patients from participating. Also, trial endpoints, such as overall survival, may not represent the most important and most meaningful endpoints for older patients. The latter may place more significance on quality of life and other outcomes such as functional independence. Baseline assessment using Comprehensive Geriatric Assessment, may provide a better framework for quantifying patient outcomes for varying degrees of fitness or frailty. This short communication makes the case for more age appropriate endpoints, such as quality of life, toxicity and functional independence, and that novel trial designs are necessary to inform evidence-based care of older cancer patients.
An Economic Model of Human Cooperation Based on Indirect Reciprocity and Its Implication on Environmental Protection
Authors: Dai Jugui , Zhang Yiqiang , Shi Victor
Published: June 2018

There has been an urgent challenge for environmental protection due to issues like population increase, climate change, and pollution. To address this challenge, sustained human cooperation is critical. However, how cooperation in human beings evolves is one of the 125 most challenging scientific questions, as announced by Science in its 125th anniversary. In this paper, we contribute to answering this question by building an economic game model based on indirect reciprocity and altruism behavior. In our model, there are three types of participants: cooperator, defector, and discriminator. In every round of the game, the cooperator chooses cooperation, the defector chooses non-cooperation, and the choice of the discriminator depends on the choice of his partner in the last round. Our analysis and main result shows that there is no stable evolution equilibrium in this game, which implies that the proportions of different types of players will keep changing instead of reaching a stable equilibrium. In other words, there is no guarantee that cooperation will be dominant in this game. An implication of this result is that to achieve cooperation and protect the environment more effectively, cooperators and discriminators in our society should be provided with incentives.
A Method for Developing Rapid Screening Values for Active Pharmaceutical Ingredients (APIs) in Water and Results of Initial Application for 119 APIs
Authors: Suchomel Ashley , Goeden Helen , Dady Julia
Published: June 2018

Americans fill upward of four billion prescriptions for pharmaceuticals each year, and many of those pharmaceuticals eventually make their way into the environment. Hundreds of different active pharmaceutical ingredients (APIs) are detected in ambient waters and source water used for drinking water in the U.S. Very few of these drugs have health-based guidance values that suggest a safe level for individuals exposed in the ambient environment through drinking water. The Minnesota Department of Health (MDH) has developed a novel method to derive screening-level human health guidance values for APIs. This method was designed for rapid evaluation and relies on Food and Drug Administration (FDA)-approved drug labels and limited additional public data resources for necessary information. MDH developed an analytical framework using traditional and novel uncertainty and adjustment factors specific to the information available for APIs. This framework, along with an estimated lowest therapeutic dose (LTD), was used to derive screening reference dose (sRfD) values. Water screening values (WSV) were then derived using the sRfD, a relative source contribution factor (RSC), and a water intake rate for infants to represent a highly exposed population. MDH used this new method to derive water screening values for 119 APIs that are commonly prescribed and/or commonly monitored in Minnesota waters, including antibiotics, antidepressants, steroids, and other classes of drugs. The derived WSVs can be used to provide context to environmental detections, prioritize APIs for further health-based guidance development, prioritize APIs for future environmental monitoring studies, and inform the development or refinement of analytical methods.
Incorporating Spatial Statistics into Examining Equity in Health Workforce Distribution: An Empirical Analysis in the Chinese Context
Authors: Zhu Bin , Hsieh Chih-Wei , Zhang Yue
Published: June 2018

Existing measures of health equity bear limitations due to the shortcomings of traditional economic methods (i.e., the spatial location information is overlooked). To fill the void, this study investigates the equity in health workforce distribution in China by incorporating spatial statistics (spatial autocorrelation analysis) and traditional economic methods (Theil index). The results reveal that the total health workforce in China experienced rapid growth from 2004 to 2014. Meanwhile, the Theil indexes for China and its three regions (Western, Central and Eastern China) decreased continually during this period. The spatial autocorrelation analysis shows that the overall agglomeration level (measured by Global Moran’s I) of doctors and nurses dropped rapidly before and after the New Medical Reform, with the value for nurses turning negative. Additionally, the spatial clustering analysis (measured by Local Moran’s I) shows that the low–low cluster areas of doctors and nurses gradually reduced, with the former disappearing from north to south and the latter from east to west. On the basis of these analyses, this study suggests that strategies to promote an equitable distribution of the health workforce should focus on certain geographical areas (low–low and low–high cluster areas).
Integrating Refined Kano Model and QFD for Service Quality Improvement in Healthy Fast-Food Chain Restaurants
Authors: Chen Kai-Jung , Yeh Tsu-Ming , Pai Fan-Yun , Chen Der-Fa
Published: June 2018

People are paying greater attention to health. To maintain a good health status and obtain food fast, customers may go to healthy fast-food chain restaurants such as Subway more often than before in China and Taiwan. Healthy fast-food chain restaurants come with a healthy spin, seeking to differentiate themselves from other fast-food restaurants. This paper combined the refined Kano model and the quality function deployment (QFD) method. The refined Kano model was used to understand how customers perceive service attributes developed based on DINESERV measurements. QFD was employed to describe the relationships among the critical service attributes and corresponding improvements as well as to identify the priority for these improvements. The analysis results revealed that providing limited offers (due to periods, seasons, and regions) should be at the top of their improvement list, followed by staff suggestions for ingredients, and a temperature display to enhance the image of fresh ingredients. Other improvement actions include providing regular launches of new flavors/products, designing new and attractive slogans, and providing restaurant apps.
Rethinking the Role of the Public Health Clinic: Comparison of Outpatient Utilization in the Public Health Clinics and Private Clinics in Korea
Authors: Kim Agnus M. , Cho Seongcheol , Kim Hyun Joo , Jo Min-Woo , Eun Sang Jun , Lee Jin Yong
Published: June 2018

Korea has experienced an overall expansion of access to care in the past few decades, which necessitated the reconsideration of the role of the public health clinics (PHC) as a primary care provider. The recent controversy about the outpatient copayment waiver for the elderly in the PHC is in the same vein. This study compared the outpatient utilization of the PHC and private clinics, and investigated its factors. Data were acquired from the National Patient Sample in 2013. Compared with private clinics, the patients in the PHC were more elderly and had less severe conditions. Being elderly, the status of National Health Insurance (NHI) beneficiaries, less comorbidities, and low total claim costs were found to be factors for choosing the PHC over private clinics. These results suggest that the elderly, who are the main beneficiaries of copayment waivers in the PHC, are the most likely to use the outpatient service by the PHC. The functions of the PHC need to be rearranged according to the recent advancements in the health care system in Korea. Diverting the resources and efforts from outpatient care to functions that best serve the health of the population should be considered.
Decryption of Active Constituents and Action Mechanism of the Traditional Uighur Prescription (BXXTR) Alleviating IMQ-Induced Psoriasis-Like Skin Inflammation in BALB/c Mice
Authors: Pang Xiaobo , Zhang Ke , Huang Jian , Wang Hangyu , Gao Le , Wang Tao , Sun Yingnan , Chen Long , Wang Jinhui
Published: June 2018

Bai Xuan Xia Ta Re Pian (BXXTR) is a traditional Uighur medicine ancient prescription in China widely used in the treatment of psoriasis, presenting a high curative rate and few side effects. Given that the active constituents and action mechanism still remain unclear, the aim of this study is to explore the potential active constituents and mechanism of antipsoriasis of BXXTR. Psoriasis-like lesions model in BALB/c mice was induced by Imiquimod (IMQ), including five treatment groups: control group, IMQ-treated group, IMQ-ACITRETIN group (Positive control group), IMQ-BXXTR low dose group, IMQ-BXXTR medium dose group and IMQ-BXXTR high dose group. The Psoriasis Area and Severity Index (PASI) score, skin and ear thickness, and histologic section were collected. The differentially expressed genes were determined by using RNAseq technology and the relevant pathways were analyzed by KEGG database. The ELISA kit and western blot assays were used to detect the related protein expression levels. In addition, the chemical constituents of BXXTR were determined by UPLC-TOF-MS analysis and the potential active constituents were predicted by SEA DOCK and Gene Ontology (GO). The data demonstrated that BXXTR significantly alleviated IMQ-induced psoriasis. RNA-seq analysis showed that BXXTR induced the expression levels of 31 genes; the KEGG analysis suggested that BXXTR could significantly change IL-17-related inflammatory pathways. The ELISA kit confirmed that the expression level of IL-17A protein was significantly reduced. 75 compounds of BXXTR were determined by UPLC-TOF-MS analysis, 11 of 75 compounds were identified as potential active compounds by similarity ensemble approach docking (SEA DOCK) and Gene Ontology (GO). BXXTR reduced the severity of skin lesions by inhibiting IL-17-related inflammatory pathways. The results indicated that BXXTR could suppress psoriasis inflammation by multiple-constituents-regulated multiple targets synergistically. Collectively, this study could provide important guidance for the elucidation of the active constituents and action mechanism of BXXTR for the treatment of psoriasis.
Unusual Manifestation of Live Staphylococcus saprophyticus, Corynebacterium urinapleomorphum, and Helicobacter pylori in the Gallbladder with Cholecystitis
Authors: Backert Steffen , Tegtmeyer Nicole , Oyarzabal Omar A. , Osman Dana , Rohde Manfred , Grützmann Robert , Vieth Michael
Published: June 2018

Culture-independent studies have identified DNA of bacterial pathogens in the gallbladder under pathological conditions, yet reports on the isolation of corresponding live bacteria are rare. Thus, it is unclear which pathogens, or pathogen communities, can colonize the gallbladder and cause disease. Using light microscopy, scanning electron microscopy, culture techniques, phylogenetic analysis, urease assays and Western blotting, we investigated the presence of live bacterial communities in the gallbladder of a cholecystitis patient after cholecystectomy. 16S rRNA gene sequencing of isolated bacterial colonies revealed the presence of pathogens most closely resembling Corynebacterium urinapleomorphum nov. sp., Staphylococcus saprophyticus and Helicobacter pylori. The latter colonies were confirmed as H. pylori by immunohistochemistry and biochemical methods. H. pylori cultured from the gallbladder exhibited both the same DNA fingerprinting and Western cagA gene sequence with ABC-type EPIYA (Glu-Pro-Ile-Tyr-Ala) phosphorylation motifs as isolates recovered from the gastric mucus of the same patient, suggesting that gastric H. pylori can also colonize other organs in the human body. Taken together, here we report, for the first time, the identification and characterization of a community consisting of live S. saprophyticus; C. urinapleomorphum, and H. pylori in the gallbladder of a patient with acute cholecystitis. Their potential infection routes and roles in pathogenesis are discussed.
The Contribution of EDF1 to PPARγ Transcriptional Activation in VEGF-Treated Human Endothelial Cells
Authors: Cazzaniga Alessandra , Locatelli Laura , Castiglioni Sara , Maier Jeanette
Published: June 2018

Vascular endothelial growth factor (VEGF) is important for maintaining healthy endothelium, which is crucial for vascular integrity. In this paper, we show that VEGF stimulates the nuclear translocation of endothelial differentiation-related factor 1 (EDF1), a highly conserved intracellular protein implicated in molecular events that are pivotal to endothelial function. In the nucleus, EDF1 serves as a transcriptional coactivator of peroxisome proliferator-activated receptor gamma (PPARγ), which has a protective role in the vasculature. Indeed, silencing EDF1 prevents VEGF induction of PPARγ activity as detected by gene reporter assay. Accordingly, silencing EDF1 markedly inhibits the stimulatory effect of VEGF on the expression of FABP4, a PPARγ-inducible gene. As nitric oxide is a marker of endothelial function, it is noteworthy that we report a link between EDF1 silencing, decreased levels of FABP4, and nitric oxide production. We conclude that EDF1 is required for VEGF-induced activation of the transcriptional activity of PPARγ.
Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data
Authors: Vale Filipa , Lehours Philippe
Published: June 2018

The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.
Transcriptomics Analysis of the Chinese Pear Pathotype of Alternaria alternata Gives Insights into Novel Mechanisms of HSAF Antifungal Activities
Authors: He Feng , Li Bingxin , Ai Gan , Kange Alex Machio , Zhao Yancun , Zhang Xiong , Jia Yifan , Dou Daolong , Liu Fengquan , Cao Haiqun
Published: June 2018

Alternaria alternata (Fries) Keissler is a lethal pear pathogen that causes leaf black spot disease of pear in Southern China. Heat-stable activity factor (HSAF) is a polycyclic tetramate macrolactam (PTM) produced by Lysobacter enzymogenes and many other microbes with a broad-spectrum antifungal activity against many filamentous fungi. In this study, we evaluated the antifungal effect of HSAF against A. alternata and proposed its antifungal mechanism in A. alternata. We report that HSAF inhibited the mycelial growth of A. alternata in a dose-dependent manner. Transcriptomics analysis revealed that HSAF treatment resulted in an expression alteration of a wide range of genes, with 3729 genes being up-regulated, and 3640 genes being down-regulated. Furthermore, we observed that HSAF treatment disrupted multiple signaling networks and essential cellular metabolisms in A. alternata, including the AMPK signaling pathway, sphingolipid metabolism and signaling pathway, carbon metabolism and the TCA (tricarboxylic acid) cycle, cell cycle, nitrogen metabolism, cell wall synthesis and a key hub protein phosphatase 2A (PP2A). These observations suggest that HSAF breaches metabolism networks and ultimately induces increased thickness of the cell wall and apoptosis in A. alternata. The improved understanding of the antifungal mechanism of HSAF against filamentous fungi will aid in the future identification of the direct interaction target of HSAF and development of HSAF as a novel bio-fungicide.
The Interplay between Glucose-Regulated Protein 78 (GRP78) and Steroids in the Reproductive System
Authors: Hebert-Schuster Marylise , Rotta Belinda Elisabeth , Kirkpatrick Brenna , Guibourdenche Jean , Cohen Marie
Published: June 2018

The glucose-regulated protein 78 (GRP78) is a molecular chaperone that is responsible for protein folding, which belongs to the heat shock protein 70 kDa (HSPA/HSP70). Because of the conjunction of GRP78 transcription with endoplasmic reticulum stress, the chaperone plays an important role in the unfolded protein response (UPR), which is induced after the accumulation of misfolded proteins. In the last years, a significant body of research concentrated on interplay between GRP78 and sexual steroid hormones. Throughout this review, we describe the mechanisms by which GRP78 regulates steroidogenesis at multiple levels and how steroids modulate GRP78 expression in different mammalian reproductive organs. Finally, we discuss the cooperation between GRP78 and steroids for cell survival and proliferation in the context of reproduction and tumorigenesis. This new paradigm offers significant opportunities for future exploration.
Protective Effects of Xyloglucan in Association with the Polysaccharide Gelose in an Experimental Model of Gastroenteritis and Urinary Tract Infections
Authors: Esposito Emanuela , Campolo Michela , Casili Giovanna , Lanza Marika , Franco Domenico , Filippone Alessia , Peritore Alessio F. , Cuzzocrea Salvatore
Published: June 2018

Acute infectious gastroenteritis (GE) and urinary tract infection (UTI) are common diseases and are normally perceived as mild and limiting illnesses. Xyloglucan is a natural plant polymer with protective barrier properties, also known as “mucosal protectors”, which is the main ingredient of medical devices developed for the management of different diseases, such as gastrointestinal diseases, urinary tract infections, or respiratory allergic diseases. The aim of this study was to evaluate the protective effect of xyloglucan in association with gelose (also called agar) in an experimental model of bacterial GE and UTI in rats. Two kinds of infection were induced by oral administration of Salmonella enterica and Enterococcus hirae for three days. Two days before the bacterial administration, preventive oral treatment with xyloglucan + gelose (10 mg/kg + 5 mg/kg) was performed daily until the seventh day. Twenty-four hours after the last treatment, rats were sacrificed and urinary tracts and intestines for different analysis were collected. The results showed that xyloglucan plus gelose was able to reduce intestinal morphological changes (p < 0.05 for both), tight junctions (TJ) permeability (p < 0.001 for both), and neutrophil infiltration (p < 0.05 for both) induced by bacterial infections, highlighting its barrier proprieties. Moreover, the compound reduced the number of bacterial colonies in the urinary tract favoring elimination by feces. The results obtained in the present study suggest that the protective barrier properties of xyloglucan plus gelose allow the prevention of GE and UTI in models of infections in rats.
Dental Pulp Stem Cell-Derived, Scaffold-Free Constructs for Bone Regeneration
Authors: Tatsuhiro Fukushima , Seiko Tatehara , Yusuke Takebe , Reiko Tokuyama-Toda , Kazuhito Satomura
Published: June 2018

In the present study, a scaffold-free tissue construct was developed as an approach for the regeneration of tissue defects, which produced good outcomes. We fabricated a scaffold-free tissue construct from human dental pulp stem cells (hDPSCs construct), and examined the characteristics of the construct. For its fabrication, basal sheets prepared by 4-week hDPSCs culturing were subjected to 1-week three-dimensional culture, with or without osteogenic induction, whereas hDPSC sheets (control) were fabricated by 1-week culturing of basal sheets on monolayer culture. The hDPSC constructs formed a spherical structure and calcified matrix that are absent in the control. The expression levels for bone-related genes in the hDPSC constructs were significantly upregulated compared with those in the control. Moreover, the hDPSC constructs with osteogenic induction had a higher degree of calcified matrix formation, and higher expression levels for bone-related genes, than those for the hDPSC constructs without osteogenic induction. These results suggest that the hDPSC constructs with osteogenic induction are composed of cells and extracellular and calcified matrices, and that they can be a possible scaffold-free material for bone regeneration.
Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution
Authors: Xie Deng-Feng , Yu Yan , Deng Yi-Qi , Li Juan , Liu Hai-Ying , Zhou Song-Dong , He Xing-Jin
Published: June 2018

Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.
Effective Intrusion Detection System Using XGBoost
Authors: Dhaliwal Sukhpreet Singh , Nahid Abdullah-Al , Abbas Robert
Published: June 2018

As the world is on the verge of venturing into fifth-generation communication technology and embracing concepts such as virtualization and cloudification, the most crucial aspect remains “security”, as more and more data get attached to the internet. This paper reflects a model designed to measure the various parameters of data in a network such as accuracy, precision, confusion matrix, and others. XGBoost is employed on the NSL-KDD (network socket layer-knowledge discovery in databases) dataset to get the desired results. The whole motive is to learn about the integrity of data and have a higher accuracy in the prediction of data. By doing so, the amount of mischievous data floating in a network can be minimized, making the network a secure place to share information. The more secure a network is, the fewer situations where data is hacked or modified. By changing various parameters of the model, future research can be done to get the most out of the data entering and leaving a network. The most important player in the network is data, and getting to know it more closely and precisely is half the work done. Studying data in a network and analyzing the pattern and volume of data leads to the emergence of a solid Intrusion Detection System (IDS), that keeps the network healthy and a safe place to share confidential information.
Document Image Processing
Authors: Likforman-Sulem Laurence , Kavallieratou Ergina
Published: June 2018

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Microscopic View of Defect Evolution in Thermal Treated AlGaInAs Quantum Well Revealed by Spatially Resolved Cathodoluminescence
Authors: Song Yue , Zhang Ligong , Zeng Yugang , Qin Li , Zhou Yinli , Ning Yongqiang , Wang Lijun
Published: June 2018

An aluminum gallium indium arsenic (AlGaInAs) material system is indispensable as the active layer of diode lasers emitting at 1310 or 1550 nm, which are used in optical fiber communications. However, the course of the high-temperature instability of a quantum well structure, which is closely related to the diffusion of indium atoms, is still not clear due to the system’s complexity. The diffusion process of indium atoms was simulated by thermal treatment, and the changes in the optical and structural properties of an AlGaInAs quantum well are investigated in this paper. Compressive strained Al0.07Ga0.22In0.71As quantum wells were treated at 170 °C with different heat durations. A significant decrement of photoluminescence decay time was observed on the quantum well of a sample that was annealed after 4 h. The microscopic cathodoluminescent (CL) spectra of these quantum wells were measured by scanning electron microscope-cathodoluminescence (SEM-CL). The thermal treatment effect on quantum wells was characterized via CL emission peak wavelength and energy density distribution, which were obtained by spatially resolved cathodoluminescence. The defect area was clearly observed in the Al0.07Ga0.22In0.71As quantum wells layer after thermal treatment. CL emissions from the defect core have higher emission energy than those from the defect-free regions. The defect core distribution, which was associated with indium segregation gradient distribution, showed asymmetric character.
Characterization of Graphite Oxide and Reduced Graphene Oxide Obtained from Different Graphite Precursors and Oxidized by Different Methods Using Raman Spectroscopy
Authors: Muzyka Roksana , Drewniak Sabina , Pustelny Tadeusz , Chrubasik Maciej , Gryglewicz Grażyna
Published: June 2018

In this paper, the influences of the graphite precursor and the oxidation method on the resulting reduced graphene oxide (especially its composition and morphology) are shown. Three types of graphite were used to prepare samples for analysis, and each of the precursors was oxidized by two different methods (all samples were reduced by the same method of thermal reduction). Each obtained graphite oxide and reduced graphene oxide was analysed by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy (RS).