bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoelectrocatalytic vs. Photocatalytic Degradation of Organic Water Born Pollutants
Authors: Papagiannis Ioannis , Koutsikou Georgia , Frontistis Zacharias , Konstantinou Ioannis , Avgouropoulos George , Mantzavinos Dionissios , Lianos Panagiotis
Published: October 2018

The azo dye Basic Blue 41 was subjected to photocatalytic and photoelectrocatalytic degradation using nanopararticulate titania films deposited on either glass slides or Fluorine doped Tin Oxide (FTO) transparent electrodes. The degradation was carried out by irradiating titania films with weak ultraviolet (UVA) radiation. The degradation was faster when using FTO as a titania support even without bias and was further accelerated under forward electric bias. This result was explained by enhanced electron-hole separation even in the case of the unbiased titania/FTO combination. This system for organic material photocatalytic degradation was also successfully applied to the degradation of the anti-inflammatory drug piroxicam, which demonstrated a well distinguished degradation behavior in going from a plain glass support to unbiased and biased FTO. The degradation pathway of piroxicam has been additionally studied using liquid chromatography-accurate mass spectrometry analysis.
Ultrasonic-Assisted Synthesis of 2D α-Fe2O3@g-C3N4 Composite with Excellent Visible Light Photocatalytic Activity
Authors: Zhang Huoli , Zhu Changxin , Cao Jianliang , Tang Qingjie , Li Man , Kang Peng , Shi Changliang , Ma Mingjie
Published: October 2018

In this study, α-Fe2O3@g-C3N4 photocatalyst was synthesized using an ultrasonic assisted self-assembly preparation method. The α-Fe2O3@g-C3N4 photocatalyst had a stronger optical absorption in the visible light region than pure graphitic carbon nitride (g-C3N4). The Z-Scheme heterojunction between α-Fe2O3 and g-C3N4 significantly inhibited the recombination of electrons and holes. The photocatalytic performances of α-Fe2O3@g-C3N4 photocatalyst were excellent in degradation of Rhodamine B (RhB) under visible light irradiation. The results indicated that 5 wt.% α-Fe2O3/g-C3N4 had the optimal photocatalytic activity because two-dimension (2D) α-Fe2O3 nanosheets can be well-dispersed on the surface of g-C3N4 layers by ultrasonic assisted treatment. A possible photocatalytic mechanism is also discussed.
Interplay between Endoplasmic Reticular Stress and Survivin in Colonic Epithelial Cells
Authors: Gundamaraju Rohit , Vemuri Ravichandra , Chong Wai Chin , Myers Stephen , Norouzi Shaghayegh , Shastri Madhur D. , Eri Rajaraman
Published: October 2018

Sustained endoplasmic reticular stress (ERS) is implicated in aggressive metastasis of cancer cells and increased tumor cell proliferation. Cancer cells activate the unfolded protein response (UPR), which aids in cellular survival and adaptation to harsh conditions. Inhibition of apoptosis, in contrast, is a mechanism adopted by cancer cells with the help of the inhibitor of an apoptosis (IAP) class of proteins such as Survivin to evade cell death and gain a proliferative advantage. In this study, we aimed to reveal the interrelation between ERS and Survivin. We initially verified the expression of Survivin in Winnie (a mouse model of chronic ERS) colon tissues by using immunohistochemistry (IHC) and immunofluorescence (IF) in comparison with wild type Blk6 mice. Additionally, we isolated the goblet cells and determined the expression of Survivin by IF and protein validation. Tunicamycin was utilized at a concentration of 10 µg/mL to induce ERS in the LS174T cell line and the gene expression of the ERS markers was measured. This was followed by determination of inflammatory cytokines. Inhibition of ERS was carried out by 4Phenyl Butyric acid (4PBA) at a concentration of 10 mM to assess whether there was a reciprocation effect. The downstream cell death assays including caspase 3/7, Annexin V, and poly(ADP-ribose) polymerase (PARP) cleavage were evaluated in the presence of ERS and absence of ERS, which was followed by a proliferative assay (EdU click) with and without ERS. Correspondingly, we inhibited Survivin by YM155 at a concentration of 100 nM and observed the succeeding ERS markers and inflammatory markers. We also verified the caspase 3/7 assay. Our results demonstrate that ERS inhibition not only significantly reduced the UPR genes (Grp78, ATF6, PERK and XBP1) along with Survivin but also downregulated the inflammatory markers such as IL8, IL4, and IL6, which suggests a positive correlation between ERS and the inhibition of apoptosis. Furthermore, we provided evidence that ERS inhibition promoted apoptosis in LS174T cells and shortened the proliferation rate. Moreover, Survivin inhibition by YM155 led to a comparable effect as that of ERS inhibition, which includes attenuation of ERS genes and inflammatory markers as well as the promotion of programmed cell death via the caspase 3/7 pathway. Together, our results propose the interrelation between ERS and inhibition of apoptosis assigning a molecular and therapeutic target for cancer treatment.
IR-783 Labeling of a Peptide Receptor for ‘Turn-On’ Fluorescence Based Sensing
Authors: Kwak Eun-A , Kydd LeNaiya , Lim Butaek , Jaworski Justyn
Published: October 2018

In this study, we examine a means for developing near-IR fluorescent sensors through streamlined, site-specific coupling with peptide-based receptors. As the penultimate step of solid-phase synthesis of a peptide-based receptor, we show a simple means of labeling the N’ terminus with the near IR fluorophore IR-783 to afford a viable fluorescent sensor after cleavage from the resin. The proof-of-concept probe utilized a biotin mimetic peptide sequence as the receptive moiety. Here we revealed a “turn-on” fluorescence enhancement upon binding of the biotin mimetic probe to its intended streptavidin target. Not all peptide-receptive moieties tested were able to generate such an enhancement upon target binding, and as such, the rationale for the observed fluorescence response properties is discussed.
Improvement of Corrosion Protection of Coating System via Inhibitor Response Order
Authors: Yu Mei , Zhao Xiangni , Xiong Liangliang , Xue Bing , Kong Xiangxin , Liu Jianhua , Li Songmei
Published: October 2018

This study aims at investigating the effect of inhibitor response order on anticorrosion properties of AA2024 with coating system. The inhibitor response order was constructed by adding different inhibitor in sol-gel primer or epoxy top coating of the coating system. Nanocontainers of graphene oxide/layered double hydroxides (GO/LDHs) were loaded with 2-mercaptobenzothiazole (MBT) and vanadate separately to get the inhibitors of GO/LDHs-MBT and GO/LDHs-VOx, which were used in this work. The protection performances of the coating systems with different inhibitor combination and different inhibitor response order were investigated. The best protective coating system is composed of sol-gel coating with GO/LDHs-MBT and epoxy coating with GO/LDHs-VOx. It is contributed to inhibitor combination and a proper response order of the inhibitors. When filiform corrosion occurs, MBT anions from the sol-gel coating are close to the alloy and they inhibit the corrosion in anodic areas immediately, and then vanadate anions from the out and thick epoxy coating reduce the kinetics of the cathodic oxygen reduction reaction. Response order enhances the corrosion protection properties provided by inhibitor combination, which gives a promising way to design good anticorrosive coating system.
DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)
Authors: Pfeiler Edward
Published: October 2018

DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology.
Alternation of Defects and Phase Turbulence Induces Extreme Events in an Extended Microcavity Laser
Authors: Barbay Sylvain , Coulibaly Saliya , Clerc Marcel G.
Published: October 2018

Out-of-equilibrium systems exhibit complex spatiotemporal behaviors when they present a secondary bifurcation to an oscillatory instability. Here, we investigate the complex dynamics shown by a pulsing regime in an extended, one-dimensional semiconductor microcavity laser whose cavity is composed by integrated gain and saturable absorber media. This system is known to give rise experimentally and theoretically to extreme events characterized by rare and high amplitude optical pulses following the onset of spatiotemporal chaos. Based on a theoretical model, we reveal a dynamical behavior characterized by the chaotic alternation of phase and amplitude turbulence. The highest amplitude pulses, i.e., the extreme events, are observed in the phase turbulence zones. This chaotic alternation behavior between different turbulent regimes is at contrast to what is usually observed in a generic amplitude equation model such as the Ginzburg–Landau model. Hence, these regimes provide some insight into the poorly known properties of the complex spatiotemporal dynamics exhibited by secondary instabilities of an Andronov–Hopf bifurcation.
Maximum Entropy Probability Density Principle in Probabilistic Investigations of Dynamic Systems
Authors: Náprstek Jiří , Fischer Cyril
Published: October 2018

In this study, we consider a method for investigating the stochastic response of a nonlinear dynamical system affected by a random seismic process. We present the solution of the probability density of a single/multiple-degree of freedom (SDOF/MDOF) system with several statically stable equilibrium states and with possible jumps of the snap-through type. The system is a Hamiltonian system with weak damping excited by a system of non-stationary Gaussian white noise. The solution based on the Gibbs principle of the maximum entropy of probability could potentially be implemented in various branches of engineering. The search for the extreme of the Gibbs entropy functional is formulated as a constrained optimization problem. The secondary constraints follow from the Fokker–Planck equation (FPE) for the system considered or from the system of ordinary differential equations for the stochastic moments of the response derived from the relevant FPE. In terms of the application type, this strategy is most suitable for SDOF/MDOF systems containing polynomial type nonlinearities. Thus, the solution links up with the customary formulation of the finite elements discretization for strongly nonlinear continuous systems.
An Examination of Middle School Organizational Structures in the United States and Australia
Authors: Ellerbrock Cheryl R. , Main Katherine , Falbe Kristina N. , Pomykal Franz Dana
Published: October 2018

The middle school concept, aimed at creating a more developmentally responsive learning environment for young adolescents, gained a stronghold in the later part of the 20th century. Proponents of this concept have argued continually for the holistic implementation of its six key characteristics if its benefits are to be realized. These characteristics include: (a) a challenging, integrative, and exploratory curriculum; (b) varied teaching and learning approaches; (c) assessment and evaluation that promote learning; (d) flexible organizational structures (i.e., including the physical space, scheduling, and grouping of students and teachers); (e) programs and policies that foster health, wellness and safety; and (f) comprehensive guidance and support services. Recently, Ellerbrock, Falbe, and Pomykal Franz identified key middle school organizational structures of people, place, and time as being interconnected and integral to effective middle school practices. Main also demonstrated the interconnected nature of these key characteristics and how organizational structures of people affected the successful implementation of other characteristics. Thus, how these organizational structures can and are being implemented has implications for our understanding of the effectiveness of other middle school practices. In this paper, researchers from both the United States and Australia examine and compare literature published between 2000 and 2018 addressing ways in which middle school/middle years organizational structures have been reported and categorized by structures of people, place, and time in these two countries. Pertinent literature related to organizational structures of middle schools in the United States and to middle years education in Australia was examined. Findings from studies and evaluations from each country are reported to provide an international perspective on the organizational structures of middle schools/middle years education across the two countries. Overall, since 2000, the body of knowledge about middle schools/middle years organizational structures has been surprisingly limited in comparison to their perceived importance in the field. This lack of research is concerning in the midst of educational reform in both countries, resulting in questions about the impact of school organizational structures on young adolescent development and learning.
A Systematic Review of Evidence-Based Video Modeling for Students with Emotional and Behavioral Disorders
Authors: Seok Soonhwa , DaCosta Boaventura , McHenry-Powell Mikayla , Heitzman-Powell Linda S. , Ostmeyer Katrina
Published: October 2018

This systematic review examined eight studies showing that video modeling (VM) can have a positive and significant effect for students with emotional and behavioral disorders (EBD). Building upon meta-analyses that sought evidence of video-based interventions decreasing problem behaviors of students with EBD in K-12 education, the review examined the standards of the Council for Exceptional Children (CEC) for evidence-based practice as well as additional quality indicators, neglected quality indicators, strategies combined with VM, the impact of the independent variables on the dependent variables, and common recommendations offered for future research. Findings revealed that the eight studies met the CEC standards for evidence-based practices as well as other quality indicators. For instance, all studies reported content and setting, participants, intervention agents, description of practice, as well as interobserver agreement and experimental control. According to the findings, fidelity index and effect size were the two most neglected quality indicators. Furthermore, instructions, reinforcement system, and feedback or discussion were the most common strategies used. Finally, generalizability—across settings, populations, treatment agents, target behaviors in the real world, and subject matter—was the most common recommendation for future research. While further investigation is warranted, these findings suggest that VM is an effective evidence-based practice for students with EBD when the CEC standards are met.
A State of Charge Estimation Method Based on Adaptive Extended Kalman-Particle Filtering for Lithium-ion Batteries
Authors: Xia Bizhong , Guo Shengkun , Wang Wei , Lai Yongzhi , Wang Huawen , Wang Mingwang , Zheng Weiwei
Published: October 2018

A state of charge (SOC) estimation method is proposed. An Adaptive Extended Kalman Particle filter (AEKPF) based on Particle Filter (PF) and Adaptive Kalman Filter (AKF) is used in order to decrease the error and reduce calculations. The second-order resistor-capacitor (RC) Equivalent Circuit Model (ECM) is used to identify dynamic parameters of the battery. After testing (include Dynamic Stress test (DST), New European Driving Cycle (NEDC), Federal Urban Dynamic Schedule (FUDS), Urban Dynamometer Driving Schedules (UDDS), etc.) at different temperatures and times, it was found that the AEKPF exhibits greater tolerance for high system noise (10% or higher) and provides more accurate estimations under common operating conditions.
Price and Volatility Spillovers Between the US Crude Oil and Natural Gas Wholesale Markets
Authors: Perifanis Theodosios , Dagoumas Athanasios
Published: October 2018

The paper examines both the time-varying price and volatility transmission between US natural gas and crude oil wholesale markets, over the period 1990–2017. Short iterations suggest that neither commodity determines other’s returns, but sub-periods with very short-lived causal relationships exist. It can be asserted that the markets are decoupled, where unconventional production further enhances the already established commodities’ independence. Using Momentum Threshold Autoregressive (MTAR) cointegration methodology, we find evidence of positive asymmetry from crude oil to natural gas prices, i.e., oil price increases cause faster adjustments to natural gas prices than decreases. We also find that an 1% change of oil price has positive and significantly larger long-term impact (between 0.01% to 0.02%) to the gas price, compared to the negligible impact of gas to oil. Volatility transmission is examined using the Dynamic Conditional Covariance (DCC)-Generalized Autoregressive Conditional Heteroscedasticity (GARCH) methodology, presenting their time-varying correlation. Results show that both commodities influence each other’s volatility at the aggregate level. Finally, we conclude that both regional commodity markets are liquid and integrated, where the market fundamentals drive their price formulation. However, although markets are decoupled and not appropriate for perfect hedging of each other, the existence of bidirectional volatility transmission and their substitutability might be useful for diversified portfolio allocation.
Comparing Crude Oils with Different API Gravities on a Molecular Level Using Mass Spectrometric Analysis. Part 1: Whole Crude Oil
Authors: Santos Jandyson M. , Wisniewski Jr. Alberto , Eberlin Marcos N. , Schrader Wolfgang
Published: October 2018

Different ionization techniques based on different principles have been applied for the direct mass spectrometric (MS) analysis of crude oils providing composition profiles. Such profiles have been used to infer a number of crude oil properties. We have tested the ability of two major atmospheric pressure ionization techniques, electrospray ionization (ESI(±)) and atmospheric pressure photoionization (APPI(+)), in conjunction with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The ultrahigh resolution and accuracy measurements of FT-ICR MS allow for the correlation of mass spectrometric (MS) data with crude oil American Petroleum Institute (API) gravities, which is a major quality parameter used to guide crude oil refining, and represents a value of the density of a crude oil. The double bond equivalent (DBE) distribution as a function of the classes of constituents, as well as the carbon numbers as measured by the carbon number distributions, were examined to correlate the API gravities of heavy, medium, and light crude oils with molecular FT-ICR MS data. An aromaticity tendency was found to directly correlate the FT-ICR MS data with API gravities, regardless of the ionization technique used. This means that an analysis on the molecular level can explain the differences between a heavy and a light crude oil on the basis of the aromaticity of the compounds in different classes. This tendency of FT-ICR MS with all three techniques, namely, ESI(+), ESI(−), and APPI(+), indicates that the molecular composition of the constituents of crude oils is directly associated with API gravity.
A Wireless-Driven, Micro, Axial-Flux, Single-Phase Switched Reluctance Motor
Authors: Pang Da-Chen , Wang Chih-Ting
Published: October 2018

This study proposes a novel, axial-flux, single-phase switched reluctance motor for micro machines with wireless-driven capability. The rotor and stator each have two poles, and the stator utilizes two permanent magnets to provide the required parking position and rotational torque. By reducing the number of magnetic poles and coils in the stator, and by utilizing a cylindrical design for its stator components, the micro motor is able to be easily manufactured and assembled. Safety and convenience are also achieved through the use of a wireless drive, which negates the need for power connections or batteries. This study utilizes the topology method in rotor design to reduce excessive torque ripple. For this study, an actual micro, axial-flux, single-phase switched reluctance motor with a diameter of 5.5 mm and length of 4.4 mm was built in combination with a wireless charging module and motor circuitry found on the market. With an induced current of 0.7 A, the motor achieved a maximum of 900 rpm, indicating possible applications with respect to toys, micro-pumps, dosing pumps, and vessels for gases, liquids, or vacuum that do not require feedthrough.
Assessing Swedish Foundries Energy Management Program
Authors: Sa Aida , Thollander Patrik , Cagno Enrico , Rafiee Majid
Published: October 2018

With regard to increased sustainability, managers not only need to know WHAT is needed for their company to improve, but also HOW to do so in detail is equally important. Energy management (EnM) is a pillar to the transformation of industrial energy systems towards enhanced energy efficiency and increased sustainability. One way to develop more and improve EnM both practically and theoretically is to shed light on how the combination of techniques and operation can contribute to successful EnM. This paper, therefore, through investigation of 10 Swedish foundries aims to present the structure of the energy strategy and associated practices at first; second, to assess industry’s EnM program and maturity level; and third, to identify and understand the nature of energy efficiency promoting factors within studied cases.
Natural and Synthetic Hydrophilic Polymers Enhance Salt and Drought Tolerance of Metasequoia glyptostroboides Hu and W.C.Cheng Seedlings
Authors: Li Jing , Ma Xujun , Sa Gang , Zhou Dazhai , Zheng Xiaojiang , Zhou Xiaoyang , Lu Cunfu , Lin Shanzhi , Zhao Rui , Chen Shaoliang
Published: October 2018

We compared the effects of hydrophilic polymer amendments on drought and salt tolerance of Metasequoia glyptostroboides Hu and W.C.Cheng seedlings using commercially available Stockosorb and Luquasorb synthetic hydrogels and a biopolymer, Konjac glucomannan (KGM). Drought, salinity, or the combined stress of both drought and salinity caused growth retardation and leaf injury in M. glyptostroboides. Under a range of simulated stress conditions, biopolymers and synthetic hydrogels alleviated growth inhibition and leaf injury, improved photosynthesis, and enhanced whole-plant and unit transpiration. For plants subjected to drought conditions, Stockosorb hydrogel amendment specifically caused a remarkable increase in water supply to roots due to the water retention capacity of the granular polymer. Under saline stress, hydrophilic polymers restricted Na+ and Cl− concentrations in roots and leaves. Moreover, root K+ uptake resulted from K+ enrichment in Stockosorb and Luquasorb granules. Synthetic polymers and biopolymers increased the ability of M. glyptostroboides to tolerate combined impacts of drought and salt stress due to their water- and salt-bearing capacities. Similar to the synthetic polymers, the biopolymer also enhanced M. glyptostroboides drought and salt stress tolerance.
Hydrology of Drained Peatland Forest: Numerical Experiment on the Role of Tree Stand Heterogeneity and Management
Authors: Stenberg Leena , Haahti Kersti , Hökkä Hannu , Launiainen Samuli , Nieminen Mika , Laurén Ari , Koivusalo Harri
Published: October 2018

A prerequisite for sustainable peatland forestry is sufficiently low water table (WT) level for profitable tree production. This requires better understanding on controls and feedbacks between tree stand and its evapotranspiration, drainage network condition, climate, and WT levels. This study explores the role of spatial tree stand distribution in the spatiotemporal distribution of WT levels and site water balance. A numerical experiment was conducted by a three-dimensional (3-D) hydrological model (FLUSH) applied to a 0.5 ha peatland forest assuming (1) spatially uniform interception and transpiration, (2) interception and transpiration scaled with spatial distributions of tree crown and root biomass, and (3) the combination of spatially scaled interception and uniform transpiration. Site water balance and WT levels were simulated for two meteorologically contrasting years. Spatial variations in transpiration were found to control WT levels even in a forest with relatively low stand stem volume (<100 m3/ha). Forest management scenarios demonstrated how stand thinning and reduced drainage efficiency raised WT levels and increased the area and duration of excessively wet conditions having potentially negative economic (reduced tree growth) and environmental (e.g., methane emissions, phosphorus mobilization) consequences. In practice, silvicultural treatment manipulating spatial stand structure should be optimized to avoid emergence of wet spots.
Chemical and Biological Sensors for Food-Quality Monitoring and Smart Packaging
Authors: Mustafa Fatima , Andreescu Silvana
Published: October 2018

The growing interest in food quality and safety requires the development of sensitive and reliable methods of analysis as well as technology for freshness preservation and food quality. This review describes the status of chemical and biological sensors for food monitoring and smart packaging. Sensing designs and their analytical features for measuring freshness markers, allergens, pathogens, adulterants and toxicants are discussed with example of applications. Their potential implementation in smart packaging could facilitate food-status monitoring, reduce food waste, extend shelf-life, and improve overall food quality. However, most sensors are still in the development stage and need significant work before implementation in real-world applications. Issues like sensitivity, selectivity, robustness, and safety of the sensing materials due to potential contact or migration in food need to be established. The current development status of these technologies, along with a discussion of the challenges and opportunities for future research, are discussed.
The Global Hepatitis B Virus Genotype Distribution Approximated from Available Genotyping Data
Authors: Velkov Stoyan , Ott Jördis J. , Protzer Ulrike , Michler Thomas
Published: October 2018

Hepatitis B virus (HBV) is divided into nine genotypes, A to I. Currently, it remains unclear how the individual genotypes contribute to the estimated 250 million chronic HBV infections. We performed a literature search on HBV genotyping data throughout the world. Over 900 publications were assessed and data were extracted from 213 records covering 125 countries. Using previously published HBV prevalence, and population data, we approximated the number of infections with each HBV genotype per country and the genotype distribution among global chronic HBV infections. We estimated that 96% of chronic HBV infections worldwide are caused by five of the nine genotypes: genotype C is most common (26%), followed by genotype D (22%), E (18%), A (17%) and B (14%). Genotypes F to I together cause less than 2% of global chronic HBV infections. Our work provides an up-to-date analysis of global HBV genotyping data and an initial approach to estimate how genotypes contribute to the global burden of chronic HBV infection. Results highlight the need to provide HBV cell culture and animal models that cover at least genotypes A to E and represent the vast majority of global HBV infections to test novel treatment strategies.
An Analytic Approach Using Candidate Gene Selection and Logic Forest to Identify Gene by Environment Interactions (G × E) for Systemic Lupus Erythematosus in African Americans
Authors: Wolf Bethany J. , Ramos Paula S. , Hyer J. Madison , Ramakrishnan Viswanathan , Gilkeson Gary S. , Hardiman Gary , Nietert Paul J. , Kamen Diane L.
Published: October 2018

Development and progression of many human diseases, such as systemic lupus erythematosus (SLE), are hypothesized to result from interactions between genetic and environmental factors. Current approaches to identify and evaluate interactions are limited, most often focusing on main effects and two-way interactions. While higher order interactions associated with disease are documented, they are difficult to detect since expanding the search space to all possible interactions of p predictors means evaluating 2p − 1 terms. For example, data with 150 candidate predictors requires considering over 1045 main effects and interactions. In this study, we present an analytical approach involving selection of candidate single nucleotide polymorphisms (SNPs) and environmental and/or clinical factors and use of Logic Forest to identify predictors of disease, including higher order interactions, followed by confirmation of the association between those predictors and interactions identified with disease outcome using logistic regression. We applied this approach to a study investigating whether smoking and/or secondhand smoke exposure interacts with candidate SNPs resulting in elevated risk of SLE. The approach identified both genetic and environmental risk factors, with evidence suggesting potential interactions between exposure to secondhand smoke as a child and genetic variation in the ITGAM gene associated with increased risk of SLE.
How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans
Authors: Subirana Juan A. , Messeguer Xavier
Published: October 2018

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect.
Where, What, When, and Why Is Bottom Mapping Needed? An On-Line Application to Set Priorities Using Expert Opinion
Authors: Kendall Matthew S. , Buja Ken , Menza Charles , Battista Tim
Published: October 2018

Globally, there is a lack of resources to survey the vast seafloor areas in need of basic mapping data. Consequently, smaller areas must be prioritized to address the most urgent needs. We developed a systematic, quantitative approach and on-line application to gather mapping suggestions from diverse stakeholders. Participants are each provided with 100 virtual coins to place throughout a region of interest to convey their mapping priorities. Inputs are standardized into a spatial framework using a grid and pull-down menus. These enabled participants to convey the types of mapping products that they need, the rationale used to justify their needs, and the locations that they prioritize for mapping. This system was implemented in a proposed National Marine Sanctuary encompassing 2784 km2 of Lake Michigan, Wisconsin. We demonstrate key analyses of the outputs, including coin counts, cell ranking, and multivariate cluster analysis for isolating high priority topics and locations. These techniques partition the priorities among the disciplines of the respondents, their selected justifications, and types of desired map products. The results enable respondents to identify potential collaborations to achieve common goals and more effectively invest limited mapping funds. The approach can be scaled to accommodate larger geographic areas and numbers of participants and is not limited to seafloor mapping.
Under-Detection of Lyme Disease in Canada
Authors: Lloyd Vett K. , Hawkins Ralph G.
Published: October 2018

Lyme disease arises from infection with pathogenic Borrelia species. In Canada, current case definition for confirmed Lyme disease requires serological confirmation by both a positive first tier ELISA and confirmatory second tier immunoblot (western blot). For surveillance and research initiatives, this requirement is intentionally conservative to exclude false positive results. Consequently, this approach is prone to false negative results that lead to underestimation of the number of people with Lyme disease. The province of New Brunswick (NB), Canada, can be used to quantify under-detection of the disease as three independent data sets are available to generate an estimate of the true human disease prevalence and incidence. First, detailed human disease incidence is available for the US states and counties bordering Canada, which can be compared with Canadian disease incidence. Second, published national serology results and well-described sensitivity and specificity values for these tests are available and deductive reasoning can be used to query for discrepancies. Third, high-density tick and canine surveillance data are available for the province, which can be used to predict expected human Lyme prevalence. Comparison of cross-border disease incidence suggests a minimum of 10.2 to 28-fold under-detection of Lyme disease (3.6% to 9.8% cases detected). Analysis of serological testing predicts the surveillance criteria generate 10.4-fold under-diagnosis (9.6% cases detected) in New Brunswick for 2014 due to serology alone. Calculation of expected human Lyme disease cases based on tick and canine infections in New Brunswick indicates a minimum of 12.1 to 58.2-fold underestimation (1.7% to 8.3% cases detected). All of these considerations apply generally across the country and strongly suggest that public health information is significantly under-detecting and under-reporting human Lyme cases across Canada. Causes of the discrepancies between reported cases and predicted actual cases may include undetected genetic diversity of Borrelia in Canada leading to failed serological detection of infection, failure to consider and initiate serological testing of patients, and failure to report clinically diagnosed acute cases. As these surveillance criteria are used to inform clinical and public health decisions, this under-detection will impact diagnosis and treatment of Canadian Lyme disease patients.
Chinese National Air Protection Policy Development: A Policy Network Theory Analysis
Authors: Gong Xiao , Mi Jianing , Yang Ruitao , Sun Rui
Published: October 2018

Given its wide involvement in and recognition by international organizations, China has signed many international agreements and negotiations. This study verified how and the extent to which changes in exogenous factors (e.g., international agreements and negotiations) affect Chinese governmental air protection policy development. Previous studies on policy network theory have demonstrated that exogenous factors affected the development of domestic policies significantly, while in this study little evidence was found to demonstrate the influence of exogenous factors on changes in Chinese policy. Rather, internal factors have played an important role in both its development and transformation. These findings differ from study results on wealthy countries and other developing districts. This study then explores the causes of substandard policy outcomes. To probe this further, policy network theory is applied to explain the gap between the guiding principle of central government’s policies and local implementation in actual practice. By analyzing the strategies of policy actors and specific rules in current Chinese context, the associated limitations and obstacles in the process of policy-making and implementation can be explained from the aspect of bureaucratic system, energy market running mechanism and others. This paper recommends alterations in the current policy and structure based on these findings.
Climate Change, Health and Existential Risks to Civilization: A Comprehensive Review (1989–2013)
Authors: Butler Colin D.
Published: October 2018

Background: Anthropogenic global warming, interacting with social and other environmental determinants, constitutes a profound health risk. This paper reports a comprehensive literature review for 1989–2013 (inclusive), the first 25 years in which this topic appeared in scientific journals. It explores the extent to which articles have identified potentially catastrophic, civilization-endangering health risks associated with climate change. Methods: PubMed and Google Scholar were primarily used to identify articles which were then ranked on a three-point scale. Each score reflected the extent to which papers discussed global systemic risk. Citations were also analyzed. Results: Of 2143 analyzed papers 1546 (72%) were scored as one. Their citations (165,133) were 82% of the total. The proportion of annual papers scored as three was initially high, as were their citations but declined to almost zero by 1996, before rising slightly from 2006. Conclusions: The enormous expansion of the literature appropriately reflects increased understanding of the importance of climate change to global health. However, recognition of the most severe, existential, health risks from climate change was generally low. Most papers instead focused on infectious diseases, direct heat effects and other disciplinary-bounded phenomena and consequences, even though scientific advances have long called for more inter-disciplinary collaboration.
Occurrence and Composition of Microplastics in the Seabed Sediments of the Coral Communities in Proximity of a Metropolitan Area
Authors: Cheang Chi Chiu , Ma Yue , Fok Lincoln
Published: October 2018

In marine environments, microplastics have become a focus in scientific research in the last decade due to the global threat this pollutant poses to the marine environment. Corals in Hong Kong are under threat due to the degradation of the marine environment caused by human activities. This study investigated the occurrence, abundance and composition of microplastic debris (0.3–5 mm) in seabed sediments adjacent to coral communities in Hong Kong. Twenty-four benthic sediment samples were collected from four study sites located along the northeastern and eastern shores of Hong Kong. Microplastic concentrations ranged from 169 ± 48 to 221 ± 45 items/kg, and the mean concentration of microplastics in the seabed sediments was 189 ± 50 items/kg, which was comparable to similar studies in other regions. Microplastics accounted for 95.4% of particles extracted from benthic sediment samples using 40× light microscopy. ATR-FTIR spectroscopy analysis showed that polyethylene (PE) and polyethylene terephthalate (PET) comprised the majority of polymer types, contributing 45.3% and 29.3%, respectively. The proportion of microplastics made from PE and PET in seabed sediments was significantly higher than that observed in local beach sediments. The proportion of microplastics made from PE and low-density polyethylene (LDPE) and polypropylene (PP) together in the seabed sediments was much higher than that of PET and polyvinyl chloride (PVC). The results have provided information with reference to environmental concentrations of microplastics for fringe reef habitat close to urban areas, which can be applied in studies concerning ecotoxicity of microplastics.
The Impact on the Ecosystem Services Value of the Ecological Shelter Zone Reconstruction in the Upper Reaches Basin of the Yangtze River in China
Authors: Yu Zhilei , Qin Tianling , Yan Dengming , Yang Meijian , Yu Hexin , Shi Wanli
Published: October 2018

With regional socio-economic development and increasing population, the structure and function of terrestrial ecosystem environments on the earth’s surface have changed markedly. Ecological shelter zone reconstruction (ESZR) is an ecosystem restoration and conservation project, which aims to ensure the safety of the ecological environments of—regions and basins. We selected the upper reaches of the Yangtze River (from Yibin to Chongqing) as the study area and determined the connotation of ESZR. At the same time, the planning scope and construction content of the ecological barrier in this specific region have been preliminarily explored. Meanwhile, a set of related planning methods was proposed, the ecological effects of which were quantitatively assessed and confirmed through the calculation of ESVs. Compared with the conditions in 2005, the study showed that the value of the services of the whole ecosystem augmented significantly under the slope classification, increasing by 103.23%. At the same time, the land use pattern has been optimized, and the vegetation coverage has been enhanced. The ESZR can effectively improve the ecosystem service function of slope land (mainly slope > 25°) and the regional ecological environment, solve the rocky desertification of the study area and provide an effective decision in relation to supporting regional green sustainable development.
Dietary Sodium Restriction Reduces Arterial Stiffness, Vascular TGF-β-Dependent Fibrosis and Marinobufagenin in Young Normotensive Rats
Authors: Grigorova Yulia N. , Wei Wen , Petrashevskaya Natalia , Zernetkina Valentina , Juhasz Ondrej , Fenner Rachel , Gilbert Christian , Lakatta Edward G. , Shapiro Joseph I. , Bagrov Alexei Y. , Fedorova Olga V.
Published: October 2018

High salt (HS) intake stimulates the production of marinobufagenin (MBG), an endogenous steroidal Na/K-ATPase ligand, which activates profibrotic signaling. HS is accompanied by a blood pressure (BP) increase in salt-sensitive hypertension, but not in normotensive animals. Here, we investigated whether HS stimulates MBG production and activates transforming growth factor-beta (TGF-β) profibrotic signaling in young normotensive rats, and whether these changes can be reversed by reducing salt to a normal salt (NS) level. Three-month old male Sprague–Dawley rats received NS for 4 and 8 weeks (0.5% NaCl; NS4 and NS8), or HS for 4 and 8 weeks (4% NaCl; HS4 and HS8), or HS for 4 weeks followed by NS for 4 weeks (HS4/NS4), n = 8/group. Systolic BP (SBP), pulse wave velocity (PWV), MBG excretion, aortic collagen 1α2, collagen 4α1 and TGF-β, Smad2, Smad3, Fli-1 mRNA, and total collagen abundance were measured at baseline (BL), and on weeks 4 and 8. Statistical analysis was performed using one-way ANOVA. SBP was not affected by HS (125 ± 5 and 126 ± 6 vs. 128 ± 7 mmHg, HS4 and HS8 vs. BL, p > 0.05). HS increased MBG (164 ± 19 vs. 103 ± 19 pmol/24 h/kg, HS4 vs. BL, p < 0.05) and PWV (3.7 ± 0.2 vs. 2.7 ± 0.2 m/s, HS4 vs. NS4, p < 0.05). HS8 was associated with a further increase in MBG and PWV, with an increase in aortic Col1a2 80%), Col4a1 (50%), Tgfb1 (30%), Smad2 (30%) and Smad3 (45%) mRNAs, and aortic wall collagen (180%) vs. NS8 (all p < 0.05). NS following HS downregulated HS-induced factors: in HS4/NS4, the MBG level was 91 ± 12 pmol/24 h/kg (twofold lower than HS8, p < 0.01), PWV was 3.7 ± 0.3 vs. 4.7 ± 0.2 m/s (HS4/NS4 vs. HS8, p < 0.05), aortic wall Tgfb1, Col1a2, Col4a1, Smad2, Smad3 mRNAs, and collagen abundance were reversed by salt reduction to the BL levels (p < 0.05). HS was associated with an activation of TGF-β signaling, aortic fibrosis and aortic stiffness accompanied by an MBG increase in the absence of SBP changes in young normotensive rats. The reduction of dietary salt following HS decreased MBG, PWV, aortic wall collagen and TGF-β. Thus, HS-induced aortic stiffness in normotensive animals occurred in the context of elevated MBG, which may activate SMAD-dependent TGF-β pro-fibrotic signaling. This data suggests that a decrease in salt consumption could help to restore aortic elasticity and diminish the risk of cardiovascular disease by reducing the production of the pro-fibrotic factor MBG.
sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data
Authors: Jung Chol-Hee , Park Daniel J. , Georgeson Peter , Mahmood Khalid , Milne Roger L. , Southey Melissa C. , Pope Bernard J.
Published: October 2018

DNA methylation influences predisposition, development and prognosis for many diseases, including cancer. However, it is not uncommon to encounter samples with incorrect sex labelling or atypical sex chromosome arrangement. Sex is one of the strongest influencers of the genomic distribution of DNA methylation and, therefore, correct assignment of sex and filtering of abnormal samples are essential for the quality control of study data. Differences in sex chromosome copy numbers between sexes and X-chromosome inactivation in females result in distinctive sex-specific patterns in the distribution of DNA methylation levels. In this study, we present a software tool, sEst, which incorporates clustering analysis to infer sex and to detect sex-chromosome abnormalities from DNA methylation microarray data. Testing with two publicly available datasets demonstrated that sEst not only correctly inferred the sex of the test samples, but also identified mislabelled samples and samples with potential sex-chromosome abnormalities, such as Klinefelter syndrome and Turner syndrome, the latter being a feature not offered by existing methods. Considering that sex and the sex-chromosome abnormalities can have large effects on many phenotypes, including diseases, our method can make a significant contribution to DNA methylation studies that are based on microarray platforms.
ITGB1b-Deficient Rare Minnows Delay Grass Carp Reovirus (GCRV) Entry and Attenuate GCRV-Triggered Apoptosis
Authors: Chen Geng , Xiong Lv , Wang Yumeng , He Libo , Huang Rong , Liao Lanjie , Zhu Zuoyan , Wang Yaping
Published: October 2018

Integrin β-1 (ITGB1) is a transmembrane protein belonging to the integrin family and it plays an important role in viral entry. In this study, the itgb1b gene of the rare minnow, Gobiocypris rarus, was cloned and analyzed. To investigate the possible role of itgb1b on grass carp reovirus (GCRV) infection, we generated an ITGB1b-deficient rare minnow (ITGB1b−/−) using the CRISPR/Cas9 system. Following stimulation with GCRV, the survival time of the -ITGB1b−/− rare minnows was extended in comparison to the wild-type minnows. Moreover, the relative copy number of GCRV and the level of clathrin-mediated endocytosis-associated and apoptosis-related gene expression in the ITGB1b−/− rare minnows was significantly lower than that of the wild-type minnows. These results suggested that the absence of itgb1b reduced viral entry efficiency and the expression of apoptosis-related genes. Moreover, the data suggested that itgb1b played an important role in mediating the entry of viruses into the cells via clathrin. Therefore, these findings provide novel insight into the function of itgb1b in the process of GCRV infection.