bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach
Authors: Lu Gui-Hua , Hua Xiao-Mei , Liang Li , Wen Zhong-Ling , Du Mei-Hang , Meng Fan-Fan , Pang Yan-Jun , Qi Jin-Liang , Tang Cheng-Yi , Yang Yong-Hua
Published: April 2018

The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira.
Effects of pH-Induced Changes in Soil Physical Characteristics on the Development of Soil Water Erosion
Authors: Matsumoto Shinji , Ogata Shunta , Shimada Hideki , Sasaoka Takashi , Hamanaka Akihiro , Kusuma Ginting
Published: April 2018

Soil water erosion is frequently reported as serious problem in soils in Southeast Asia with tropical climates, and the variations in pH affect the development of the erosion. This study investigated the effects of changes in pH on soil water erosion based on changes in the physical properties of the simulated soils with pH adjusted from 2.0 to 10.0 through artificial rainfall tests. The zeta potential was entirely shifted to positive direction at each pH condition due to Al, Ca, and Mg. In the pH range of 6.0 to 2.0, the aggregation of soil particles resulting from the release of Al3+ from clay minerals and/or molecular attraction between soil particles caused the plastic index (IP) of the soil to decrease. The decrease in IP led to the development of soil water erosion at the pH range. When the pH exceeded 6.0, the repulsive force generated by the negative charges on soil particles decreased IP, resulting in accelerated erosion by water. The results suggest that changes in pH causes physical properties of the soil to change through changes of the zeta potential in the clayey soil rich in Al, Ca, and Mg, leading to the development of soil water erosion.
Coronial Practice, Indigeneity and Suicide
Authors: Tait Gordon , Carpenter Belinda , Jowett Stephanie
Published: April 2018

All available data suggest that, like many other Indigenous peoples, Australian Aborigines are significantly more likely to kill themselves than are non-Aboriginal Australians. This statistical disparity is normally positioned an objective, ontological and undeniable social fact, a fact best explained as a function of endemic community disadvantage and disenfranchisement. This research explores the possibility that higher-than-normal Aboriginal suicide rates may also be a function of coronial decision-making practices. Based upon in-depth interviews with 32 coroners from across Australia, the following conclusions emerged from the data. First, coroners have differing perceptions of Indigenous capacity, and are less likely to have concerns about intent when the suicide is committed by an Indigenous person. Second, coroners have identified divergent scripts of Indigenous suicide, particularly its spontaneity and public location, and this supports rather than challenges, a finding of suicide. Third, the coronial perception of Indigenous life is a factor which influences a suicide determination for Indigenous deaths. Finally, the low level of Indigenous engagement with the coronial system, and the unlikelihood of a challenge to the finding of suicide by Indigenous families, means that a coronial determination of suicide is more likely.
MicroRNAs Targeting Caspase-3 and -7 in PANC-1 Cells
Authors: Park Jong Kook , Doseff Andrea I. , Schmittgen Thomas D.
Published: April 2018

MicroRNAs (miRNAs), a critical part of the RNA silencing machinery, are known to play important regulatory roles in cancer. However, the consequence of miRNA deregulation in cancer is unknown for many miRNAs. Here, we define that miRNAs, miR-17-5p, miR-132-3p/-212-3p, and miR-337-3p are significantly up-regulated in the pancreatic ductal adenocarcinomas (PDAC) compared to the normal and benign tissues. Furthermore, by using PANC-1 cells, we demonstrate that overexpressed miR-337-3p and miR-17-5p/miR-132-3p/-212-3p can regulate executioner caspases-3 and -7, respectively. In addition, over-expression of miRNAs, especially miR-337-3p, attenuates tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) cytotoxicity in PANC-1 cells. Our findings unveil an important biological function for miRNAs up-regulated in PDAC in coordinately regulating caspases, potentially contributing to the malignant progression of PDAC.
Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data
Authors: Ropka-Molik Katarzyna , Pawlina-Tyszko Klaudia , Żukowski Kacper , Piórkowska Katarzyna , Żak Grzegorz , Gurgul Artur , Derebecka Natalia , Wesoły Joanna
Published: April 2018

Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.
Antibacterial Efficacy of Silver Nanoparticles on Endometritis Caused by Prevotella melaninogenica and Arcanobacterum pyogenes in Dairy Cattle
Authors: Gurunathan Sangiliyandi , Choi Yun-Jung , Kim Jin-Hoi
Published: April 2018

Bovine postpartum diseases remain one of the most significant and highly prevalent illnesses with negative effects on the productivity, survival, and welfare of dairy cows. Antibiotics are generally considered beneficial in the treatment of endometritis; however, frequent usage of each antibiotic drug is reason for the emergence of multidrug resistance (MDR) of the pathogenic microorganisms, representing a major impediment for the successful diagnosis and management of infectious diseases in both humans and animals. We synthesized silver nanoparticles (AgNPs) with an average size of 10 nm using the novel biomolecule apigenin as a reducing and stabilizing agent, and evaluated the efficacy of the AgNPs on the MDR pathogenic bacteria Prevotella melaninogenica and Arcanobacterium pyogenes isolated from uterine secretion samples. AgNPs inhibited cell viability and biofilm formation in a dose- and time-dependent manner. Moreover, the metabolic toxicity of the AgNPs was assessed through various cellular assays. The major toxic effect of cell death was caused by an increase in oxidative stress, as evidenced by the increased generation of reactive oxygen species (ROS), malondialdehyde, protein carbonyl content, and nitric oxide. The formation of ROS is considered to be the primary mechanism of bacterial death. Therefore, the biomolecule-mediated synthesis of AgNPs shows potential as an alternative antimicrobial therapy for bovine metritis and endometritis.
An Ensemble of Condition Based Classifiers for Device Independent Detailed Human Activity Recognition Using Smartphones †
Authors: Saha Jayita , Chowdhury Chandreyee , Roy Chowdhury Ishan , Biswas Suparna , Aslam Nauman
Published: April 2018

Human activity recognition is increasingly used for medical, surveillance and entertainment applications. For better monitoring, these applications require identification of detailed activity like sitting on chair/floor, brisk/slow walking, running, etc. This paper proposes a ubiquitous solution to detailed activity recognition through the use of smartphone sensors. Use of smartphones for activity recognition poses challenges such as device independence and various usage behavior in terms of where the smartphone is kept. Only a few works address one or more of these challenges. Consequently, in this paper, we present a detailed activity recognition framework for identifying both static and dynamic activities addressing the above-mentioned challenges. The framework supports cases where (i) dataset contains data from accelerometer; and the (ii) dataset contains data from both accelerometer and gyroscope sensor of smartphones. The framework forms an ensemble of the condition based classifiers to address the variance due to different hardware configuration and usage behavior in terms of where the smartphone is kept (right pants pocket, shirt pockets or right hand). The framework is implemented and tested on real data set collected from 10 users with five different device configurations. It is observed that, with our proposed approach, 94% recognition accuracy can be achieved.
Baseline Apparent Diffusion Coefficient as a Predictor of Response to Liver-Directed Therapies in Hepatocellular Carcinoma
Authors: Niekamp Andrew , Abdel-Wahab Reham , Kuban Joshua , Odisio Bruno , Mahvash Armeen , Hassan Manal , Qayyum Aliya , Kaseb Ahmed , Sheth Rahul
Published: April 2018

Predicting outcomes in patients with hepatocellular carcinoma (HCC) who undergo locoregional therapies remains a substantial clinical challenge. The purpose of this study was to investigate pre-procedure diffusion weighted magnetic resonance imaging (DW-MRI) as an imaging biomarker for tumoral response to therapy for patients with HCC undergoing drug eluting embolic (DEE) chemoembolization and radioembolization. A retrospective review of HCC patients who underwent DEE chemoembolization or radioembolization was performed. Of the 58 patients who comprised the study population, 32 underwent DEE chemoembolization and 26 underwent radioembolization. There was no significant difference in median apparent diffusion coefficient (ADC) values across the two treatment groups (1.01 × 10−3 mm2/s, P = 0.25). The immediate objective response (OR) rate was 71% (40/56). Tumors with high ADC values were found to have a higher probability of OR within 90 days (odds ratio 4.4, P = 0.03). Moreover, index lesion specific progression free survival (PFS) was greater for high ADC tumors, independent of conventional predictors of treatment response (hazard ratio 0.44, P = 0.01). Low ADC was associated with poorer PFS (P = 0.02). Pre-procedure ADC < 1.01 × 10−3 mm2/s is an independent predictor of poorer immediate OR and index lesion specific PFS in patients with HCC undergoing DEE chemoembolization or radioembolization.
Individual Mental Abiities vs. the World’s Problems
Authors: Baron Jonathan
Published: April 2018

The major problems in the world today are problems of government or the lack of it. Thus, the relevant parts of intelligence are those that make for good citizenship, such as supporting the best candidates and policies. I argue that dispositions, as well as capacities, are part of intelligence, and that some dispositions are the ones most crucial for citizenship, particularly the disposition to engage in actively open-minded thinking (AOT) and to apply it as a standard for the evaluation of the qualifications of authorities and leaders. AOT is a general prescriptive theory that applies to all thinking. It affects the aptness of conclusions and the accuracy of confidence judgments, and it reduces overconfidence when extreme confidence is not warranted. AOT may be affected by different factors from those that affect other components of intelligence and thus may undergo different changes over time. Whatever has happened in the past, we need more of it now.
Coupling Numerical Methods and Analytical Models for Ducted Turbines to Evaluate Designs
Authors: Knight Bradford , Freda Robert , Young Yin Lu , Maki Kevin
Published: April 2018

Hydrokinetic turbines extract energy from currents in oceans, rivers, and streams. Ducts can be used to accelerate the flow across the turbine to improve performance. The objective of this work is to couple an analytical model with a Reynolds averaged Navier–Stokes (RANS) computational fluid dynamics (CFD) solver to evaluate designs. An analytical model is derived for ducted turbines. A steady-state moving reference frame solver is used to analyze both the freestream and ducted turbine. A sliding mesh solver is examined for the freestream turbine. An efficient duct is introduced to accelerate the flow at the turbine. Since the turbine is optimized for operation in the freestream and not within the duct, there is a decrease in efficiency due to duct-turbine interaction. Despite the decrease in efficiency, the power extracted by the turbine is increased. The analytical model under-predicts the flow rejection from the duct that is predicted by CFD since the CFD predicts separation but the analytical model does not. Once the mass flow rate is corrected, the model can be used as a design tool to evaluate how the turbine-duct pair reduces mass flow efficiency. To better understand this phenomenon, the turbine is also analyzed within a tube with the analytical model and CFD. The analytical model shows that the duct’s mass flow efficiency reduces as a function of loading, showing that the system will be more efficient when lightly loaded. Using the conclusions of the analytical model, a more efficient ducted turbine system is designed. The turbine is pitched more heavily and the twist profile is adapted to the radial throat velocity profile.
Adoption of Small-Scale Irrigation Farming as a Climate-Smart Agriculture Practice and Its Influence on Household Income in the Chinyanja Triangle, Southern Africa
Authors: Mango Nelson , Makate Clifton , Tamene Lulseged , Mponela Powell , Ndengu Gift
Published: April 2018

This article is concerned with the adoption of small-scale irrigation farming as a climate-smart agriculture practice and its influence on household income in the Chinyanja Triangle. Chinyanja Triangle is a region that is increasingly experiencing mid-season dry spells and an increase in occurrence of drought, which is attributed largely to climate variability and change. This poses high agricultural production risks, which aggravate poverty and food insecurity. For this region, adoption of small-scale irrigation farming as a climate-smart agriculture practice is very important. Through a binary logistic and ordinary least squares regression, this article determines factors that influence the adoption of small-scale irrigation farming as a climate-smart agriculture practice and its influence on income among smallholder farmers. The results show that off-farm employment, access to irrigation equipment, access to reliable water sources and awareness of water conservation practices, such as rainwater harvesting, have a significant influence on the adoption of small-scale irrigation farming. On the other hand, the farmer’s age, distance travelled to the nearest market and nature of employment negatively influence the adoption of small-scale irrigation farming decisions. Ordinary least squares regression results showed that the adoption of small-scale irrigation farming as a climate-smart agriculture practice has a significant positive influence on agricultural income. We therefore conclude that to empower smallholder farmers to respond quickly to climate variability and change, practices that will enhance the adoption of small-scale irrigation farming in the Chinyanja Triangle are critical, as this will significantly affect agricultural income. In terms of policy, we recommend that the governments of Zambia, Malawi and Mozambique, which cover the Chinyanja Triangle, formulate policies that will enhance the adoption of sustainable small scale-irrigation farming as a climate-smart agriculture practice. This will go a long way in mitigating the adverse effects that accompany climate variability and change in the region.
Exploring Long-Term Livelihood and Landscape Change in Two Semi-Arid Sites in Southern Africa: Drivers and Consequences for Social–Ecological Vulnerability
Authors: Masunungure Current , Shackleton Sheona E.
Published: April 2018

This paper investigates the drivers and dynamics of livelihood and landscape change over a 30-year period in two sites in the communal drylands of Zimbabwe (Marwendo) and South Africa (Tshivuhulani). Of particular interest to us was how access to social protection and a wider range of options may mitigate increased vulnerability under a changing climate. A mixed methods approach (using household surveys, focus group discussions, life history interviews, transect walks and secondary sources of data) was applied to develop human–environment timelines for each study site. Findings indicate that prolonged periods of droughts, unreliable rainfall, changing socioeconomic policies and development-related projects were among the major drivers of both positive and negative change in both villages. Marwendo, in particular, experienced a suite of negative drivers in the last 10 years that increased vulnerability and forced households to diversify into potentially maladaptive activities. In contrast, the expansion in social grants in Tshivhulani provided an important safety net that reduced vulnerability, but also led to a decline in farming and a narrowing of livelihood activities for some households. We demonstrate that rural development initiatives such as electrification and road construction can strengthen local people’s capacity to respond to drivers of change, while new methods of farming and diversification of the livelihood portfolio can make them more climate-resilient. However, long-term changes in landscapes and ecosystem services and feedbacks on livelihoods could reverse some of the benefits of development by eroding the natural capital many households still depend on.
Biochemical Characterization and Degradation Pattern of a Unique pH-Stable PolyM-Specific Alginate Lyase from Newly Isolated Serratia marcescens NJ-07
Authors: Zhu Benwei , Hu Fu , Yuan Heng , Sun Yun , Yao Zhong
Published: April 2018

Enzymatic preparation of alginate oligosaccharides with versatile bioactivities by alginate lyases has attracted increasing attention due to its featured characteristics, such as wild condition and specific products. In this study, AlgNJ-07, a novel polyM-specific alginate lyase with high specific activity and pH stability, has been purified from the newly isolated marine bacterium Serratia marcescens NJ-07. It has a molecular weight of approximately 25 kDa and exhibits the maximal activity of 2742.5 U/mg towards sodium alginate under 40 °C at pH 9.0. Additionally, AlgNJ-07 could retain more than 95% of its activity at pH range of 8.0–10.0, indicating it possesses excellent pH-stability. Moreover, it shows high activity and affinity towards polyM block and no activity to polyG block, which suggests that it is a strict polyM-specific alginate lyase. The degradation pattern of AlgNJ-07 has also been explored. The activity of AlgNJ-07 could be activated by NaCl with a low concentration (100–300 mM). It can be observed that AlgNJ-07 can recognize the trisaccharide as the minimal substrate and hydrolyze the trisaccharide into monosaccharide and disaccharide. The TLC and ESI-MS analysis indicate that it can hydrolyze substrates in a unique endolytic manner, producing not only oligosaccharides with Dp of 2–5 but also a large fraction of monosaccharide. Therefore, it may be a potent tool to produce alginate oligosaccharides with lower Dps (degree of polymerization).
Antartin, a Cytotoxic Zizaane-Type Sesquiterpenoid from a Streptomyces sp. Isolated from an Antarctic Marine Sediment
Authors: Kim Dayoung , Lee Eun Ju , Lee Jihye , Leutou Alain S. , Shin Yern-Hyerk , Choi Bomi , Hwang Ji Sun , Hahn Dongyup , Choi Hyukjae , Chin Jungwook , Cho Sung Jin , Hong Yong Deog , Ko Jaeyoung , Seong Chi Nam , Maloney Katherine N. , Oh Dong-Chan , Yang Inho , Hwang Hayoung , Nam Sang-Jip
Published: April 2018

Antartin (1), a new zizaane-type sesquiterpene, was isolated from Streptomyces sp. SCO736. The chemical structure of 1 was assigned from the interpretation of 1D and 2D NMR in addition to mass spectrometric data. The relative stereochemistry of 1 was determined by analysis of NOE data, while the absolute stereochemistry was decided based on a comparison of experimental and calculated electronic circular dichroism (ECD) spectra. Antartin (1) showed cytotoxicity against A549, H1299, and U87 cancer cell lines by causing cell cycle arrest at the G1 phase.
An Incremental Physically-Based Model of P91 Steel Flow Behaviour for the Numerical Analysis of Hot-Working Processes
Authors: Murillo-Marrodán Alberto , Puchi-Cabrera Eli , García Eduardo , Dubar Mirentxu , Cortés Fernando , Dubar Laurent
Published: April 2018

This paper is aimed at modelling the flow behaviour of P91 steel at high temperature and a wide range of strain rates for constant and also variable strain-rate deformation conditions, such as those in real hot-working processes. For this purpose, an incremental physically-based model is proposed for the P91 steel flow behavior. This formulation considers the effects of dynamic recovery (DRV) and dynamic recrystallization (DRX) on the mechanical properties of the material, using only the flow stress, strain rate and temperature as state variables and not the accumulated strain. Therefore, it reproduces accurately the flow stress, work hardening and work softening not only under constant, but also under transient deformation conditions. To accomplish this study, the material is characterised experimentally by means of uniaxial compression tests, conducted at a temperature range of 900–1270 °C and at strain rates in the range of 0.005–10 s−1. Finally, the proposed model is implemented in commercial finite element (FE) software to provide evidence of the performance of the proposed formulation. The experimental compression tests are simulated using the novel model and the well-known Hansel–Spittel formulation. In conclusion, the incremental physically-based model shows accurate results when work softening is present, especially under variable strain-rate deformation conditions. Hence, the present formulation is appropriate for the simulation of the hot-working processes typically conducted at industrial scale.
Microstructure of Semi-Solid Billets Produced by Electromagnetic Stirring and Behavior of Primary Particles during the Indirect Forming Process
Authors: Jin Chul Kyu
Published: April 2018

An A356 alloy semi-solid billet was fabricated using electromagnetic stirring. After inserting the semi-solid billet into an indirect die, a thin plate of 1.2 mm thickness was fabricated by applying compression. The microstructure of the semi-solid billets fabricated in various stirring conditions (solid fraction and stirring force) were analyzed. The deformation and behavior of the primary α-Al particles were analyzed for various parameters (solid fraction, die friction, compression rate, and compression pressure). In the stirred billets, a globular structure was dominant, while a dendrite structure was dominant in the unstirred billets. As the solid fraction decreased and the stirring current increased, the equivalent diameter and roundness of the primary α-Al particles decreased. The primary α-Al particle sizes were reduced as the compressing velocity increased, while a greater number of particles could move as the compressing pressure increased. As the path over which the motion occurred became smoother, the fluidity of the particles improved. Under compression, bonded primary α-Al particles became separated into individual particles again, as the bonds were broken. As wearing caused by friction and collisions between the particles during this motion occurred, the particle sizes were reduced, and the particle shapes become increasingly spheroid.
Effects of Cryogenic Treatment on the Microstructure and Residual Stress of 7075 Aluminum Alloy
Authors: Wei Lijun , Wang Dawei , Li Haisheng , Xie Di , Ye Fan , Song Ruokang , Zheng Gang , Wu Sujun
Published: April 2018

The effect of cryogenic treatment (CT) on the microstructure, residual stress, and dimensional stability of 7075 aluminum alloy under temperatures of 0 °C, −60 °C, −120 °C, and −196 °C were studied, using optical microscopy (OM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), an X-ray diffractometer, and an X-ray stress tester. The results indicated that CT can facilitate the dissolution of the coarse secondary phase into the α(Al) matrix, promote uniform distribution of Mg, Cu, Zn elements, and increase the density of fine secondary phases in the 7075 Al alloy. The CT can also induce the rotation of the α(Al) grain towards (200), through the processes of recovery and recrystallization. It was found that the residual stress was released, and a higher dimensional stability of the 7075 aluminum alloy was achieved, after CT. Experimental results demonstrated that the optimum CT temperature for the 7075 aluminum alloy is −120 °C.
Topology Optimization of Spatially Compliant Mechanisms with an Isomorphic Matrix of a 3-UPC Type Parallel Prototype Manipulator
Authors: Zhu Dachang , Zhan Wanghu , Wu Fupei , Simeone Alessandro
Published: April 2018

A novel topology optimization approach is proposed in this paper for the design of three rotational degree-of-freedom (DOF) spatially compliant mechanisms, combining the Jacobian isomorphic mapping matrix with the solid isotropic material with penalization (SIMP) topological method. In this approach, the isomorphic Jacobian matrix of a 3-UPC (U: universal joint, P: prismatic joint, C: cylindrical joint) type parallel prototype manipulator is formulated. Subsequently, the orthogonal triangular decomposition and differential kinematic method is applied to uncouple the Jacobian matrix to construct a constraint for topology optimization. Firstly, with respect to the 3-UPC type parallel prototype manipulator, the Jacobian matrix is derived to map the inputs and outputs to be used for initializing the topology optimization process. Secondly, the orthogonal triangular decomposition with the differential kinematic method is used to reconstruct the uncoupled mapping matrix to derive the 3-UPC type parallel prototype manipulator. Finally, a combination of the solid isotropic material with penalization (SIMP) method and the isomorphic mapping matrix is applied to construct the topological model. A typical three rotational DOF spatially compliant mechanism is reported as a numerical example to demonstrate the effectiveness of the proposed method.
Fabrication of an Anti-Reflective and Super-Hydrophobic Structure by Vacuum Ultraviolet Light-Assisted Bonding and Nanoscale Pattern Transfer
Authors: Hashimoto Yuki , Yamamoto Takatoki
Published: April 2018

The application of subwavelength, textured structures to glass surfaces has been shown to reduce reflectivity and also results in self-cleaning due to super-hydrophobicity. However, current methods of producing such textures are typically either expensive or difficult to scale up. Based on prior work by the authors, the present study employed a combination of vacuum ultraviolet (VUV) light-assisted bonding and release agent-free pattern transfer to fabricate a moth-eye texture on a glass substrate. This was accomplished by forming a cyclic olefin polymer mold master with a moth-eye pattern, transferring this pattern to a polydimethylsiloxane (PDMS) spin coating, activating both the PDMS and a glass substrate with VUV light, and then bonding the PDMS to the glass before releasing the mold. Atomic force microscopy demonstrated that the desired pattern was successfully replicated on the PDMS surface with a high degree of accuracy, and the textured glass specimen exhibited approximately 3% higher transmittance than untreated glass. Contact angle measurements also showed that the hydrophobicity of the textured surface was significantly increased. These results confirm that this new technique is a viable means of fabricating optical nanostructures via a simple, inexpensive process.
Iron Is the Active Site in Nickel/Iron Water Oxidation Electrocatalysts
Authors: Hunter Bryan M. , Winkler Jay R. , Gray Harry B.
Published: April 2018

Efficient catalysis of the oxygen-evolution half-reaction (OER) is a pivotal requirement for the development of practical solar-driven water splitting devices. Heterogeneous OER electrocatalysts containing first-row transition metal oxides and hydroxides have attracted considerable recent interest, owing in part to the high abundance and low cost of starting materials. Among the best performing OER electrocatalysts are mixed Fe/Ni layered double hydroxides (LDH). A review of the available experimental data leads to the conclusion that iron is the active site for [NiFe]-LDH-catalyzed alkaline water oxidation.
Complexes of CO2 with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions
Authors: Del Bene Janet , Elguero José , Alkorta Ibon
Published: April 2018

Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the complexes of CO2 with the azoles pyrrole, pyrazole, imidazole, 1,2,3- and 1,2,4-triazole, tetrazole and pentazole. Three types of complexes have been found on the CO2:azole potential surfaces. These include ten complexes stabilized by tetrel bonds that have the azole molecule in the symmetry plane of the complex; seven tetrel-bonded complexes in which the CO2 molecule is perpendicular to the symmetry plane; and four hydrogen-bonded complexes. Eight of the planar complexes are stabilized by Nx···C tetrel bonds and by a secondary interaction involving an adjacent Ny-H bond and an O atom of CO2. The seven perpendicular CO2:azole complexes form between CO2 and two adjacent N atoms of the ring, both of which are electron-pair donors. In three of the four hydrogen-bonded complexes, the proton-donor Nz-H bond of the ring is bonded to two C-H bonds, thereby precluding the planar and perpendicular complexes. The fourth hydrogen-bonded complex forms with the strongest acid pentazole. Binding energies, charge-transfer energies and changes in CO2 stretching and bending frequencies upon complex formation provide consistent descriptions of these complexes. Coupling constants across tetrel bonds are negligibly small, but 2hJ(Ny-C) across Nz-H···C hydrogen bonds are larger and increase as the number of N atoms in the ring increases.
PKIDB: A Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials
Authors: Carles Fabrice , Bourg Stéphane , Meyer Christophe , Bonnet Pascal
Published: April 2018

The number of protein kinase inhibitors (PKIs) approved worldwide continues to grow steadily, with 39 drugs approved in the period between 2001 and January 2018. PKIs on the market have been the subject of many reviews, and structure-property relationships specific to this class of drugs have been inferred. However, the large number of PKIs under development is often overlooked. In this paper, we present PKIDB (Protein Kinase Inhibitor Database), a monthly-updated database gathering approved PKIs as well as PKIs currently in clinical trials. The database compiles currently 180 inhibitors ranging from phase 0 to 4 clinical trials along with annotations extracted from seven public resources. The distribution and property ranges of standard physicochemical properties are presented. They can be used as filters to better prioritize compound selection for future screening campaigns. Interestingly, more than one-third of the kinase inhibitors violate at least one Lipinski’s rule. A Principal Component Analysis (PCA) reveals that Type-II inhibitors are mapped to a distinct chemical space as compared to orally administrated drugs as well as to other types of kinase inhibitors. Using a Principal Moment of Inertia (PMI) analysis, we show that PKIs under development tend to explore new shape territories as compared to approved PKIs. In order to facilitate the analysis of the protein space, the kinome tree has been annotated with all protein kinases being targeted by PKIs. Finally, we analyzed the pipeline of the pharmaceutical companies having PKIs on the market or still under development. We hope that this work will assist researchers in the kinase field in identifying and designing the next generation of kinase inhibitors for still untargeted kinases. The PKIDB database is freely accessible from a website at http://www.icoa.fr/pkidb and can be easily browsed through a user-friendly spreadsheet-like interface.
Pharmacokinetic–Pharmacodynamic Model for the Testosterone-Suppressive Effect of Leuprolide in Normal and Prostate Cancer Rats
Authors: Lee Dong-Seok , Kim Sook-Jin , Choi Go-Wun , Lee Yong-Bok , Cho Hea-Young
Published: April 2018

This study developed the pharmacokinetic (PK)–pharmacodynamic (PD) model of the testosterone-suppressive effect of leuprolide for evaluation of the sustained release (SR) depot and leuprolide solution in rats with or without prostate cancer. Six groups of rats were divided by the routes of administration (intravenous and subcutaneous injection) and kinds of formulation (vehicle, leuprolide solution, and SR depot). The PK profile after subcutaneous injection of leuprolide solution could be well-described by the one-compartment model. The absorption rate constant, the total body clearance, and the volume of distribution were estimated at 16.67 h−1, 514.46 mL/h, and 487.40 mL. Using PK parameters in the solution-administered group, the PK model for the SR depot was developed. The PK–PD model was constructed by describing the testosterone-suppressive effect of leuprolide using the feedback turnover model. The response of testosterone after administration of each formulation was well described using this PK–PD model for the estimation of PD parameters (EC50, Emax, h) and systemic parameters (kin, kout, kf on, kf off). The developed PK–PD model containing an inhibitory feedback system could successfully describe the testosterone-suppressive effect of leuprolide in the type of formulation. The PK–PD model developed would be useful for evaluating the formulation of similar drugs whose effect is regulated through the feedback mechanism.
Stryphnodendron Species Known as “Barbatimão”: A Comprehensive Report
Authors: Souza-Moreira Tatiana , Queiroz-Fernandes Geisiany , Pietro Rosemeire
Published: April 2018

Stryphnodendron spp., popularly known as “barbatimão”, is the native Brazilian tree most often employed to treat wounds and infections. The aim of the present study was to highlight the importance of S. adstringens, as well as other Stryphnodendron species recognized as “barbatimão”, to human health, depicting the relevance of ethnopharmacological knowledge to scientific evidence for uses, related chemical compounds, development of pharmaceutical formulations, and the establishment of toxicity parameters. For this purpose, the literature databases PubMed, Scielo, Lilacs, CAPES Thesis and Google Scholar were searched until 2017. It was observed that stem bark was the primary part of the plant used, mainly as a decoction, for wound healing and treatment of infectious and inflammatory disorders. Confirmed biological activities, including wound healing, anti-inflammatory, antioxidant, and antimicrobial activities, were related to the presence of compounds from tannin class, mostly proanthocyanidins. Toxicity parameters for stem bark were inconclusive, but toxicity was observed to a significant extent when seeds were ingested by cattle or other animals. Due to these important and confirmed biological activities, government policy encourages the phytotherapic use of S. adstringens, and some formulations with stem bark extracts were developed and patented. Furthermore, antiprotozoal, hypoglycemic and antiviral activities were identified as promising.
Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability
Authors: Chen Chen-Peng , Chen Chan-Cheng , Huang Chia-Wen , Chang Yen-Ching
Published: April 2018

The skin permeability (Kp) defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR) based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical’s skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.
Electrochemical Aptamer-Based Sensors for Rapid Point-of-Use Monitoring of the Mycotoxin Ochratoxin A Directly in a Food Stream
Authors: Somerson Jacob , Plaxco Kevin
Published: April 2018

The ability to measure the concentration of specific small molecules continuously and in real-time in complex sample streams would impact many areas of agriculture, food safety, and food production. Monitoring for mycotoxin taint in real time during food processing, for example, could improve public health. Towards this end, we describe here an inexpensive electrochemical DNA-based sensor that supports real-time monitor of the mycotoxin ochratoxin A in a flowing stream of foodstuffs.
Poly(vinyl Chloride) Photostabilization in the Presence of Schiff Bases Containing a Thiadiazole Moiety
Authors: Shaalan Naser , Laftah Nawres‎‏ , El-Hiti Gamal , Alotaibi Mohammad , Muslih Raad , Ahmed Dina , Yousif Emad
Published: April 2018

Five Schiff bases containing a thiadiazole moiety have been used as poly(vinyl chloride) photostabilizers at low concentrations. The efficiency of Schiff bases as photostabilizers was investigated using various techniques, for example, the changes in poly(vinyl chloride) infrared spectra, molecular weight, chain scission quantum yield, and surface morphology were monitored upon irradiation with an ultraviolet light. Evidently, all the additives used inhibited poly(vinyl chloride) photodegradation at a significant level. The most efficient Schiff base exhibited a high level of aromaticity and contained a hydroxyl group. It seems possible that such photostabilization could be due to the direct absorption of ultraviolet radiation by the additives. In addition, Schiff bases could act as radical scavengers and proton transfer facilitators to stabilize the polymeric materials.
One-Pot, Highly Stereoselective Synthesis of Dithioacetal-α,α-Diglycosides
Authors: Céspedes Dávila Maria F. , Schneider Jérémy P. , Godard Amélie , Hazelard Damien , Compain Philippe
Published: April 2018

A one-step access to dithioacetal-α,α-diglycosides is reported. The synthetic strategy is based on the thioacetalization of aldehydes or ketones via highly stereoselective ring-opening of 1,6 anhydrosugars with bis(trimethylsilyl)sulfide.
Cultivar and Harvest Month Influence the Nutrient Content of Opuntia spp. Cactus Pear Cladode Mucilage Extracts
Authors: Du Toit Alba , De Wit Maryna , Hugo Arno
Published: April 2018

Mucilage extracted from cactus pear cladodes is a hydrocolloid gum. It is a novel, natural, low-kilojoule, cost-effective texture-modifying ingredient in functional food products. Yet, the cultivar with the most optimal nutrient content and the preferred harvest times are as yet unknown. For this reason, mucilage from three Opuntia ficus-indica (Algerian, Morado and Gymno-Carpo) and one Opuntia robusta (Robusta) cultivar were investigated to determine their nutrient content over six months. Nutrients that contribute energy (10.2 kJ/g) were low. The mineral content was high (ash 17.7/100 g), particularly calcium (3.0 g/100 g) and phosphorous (109.5 mg/kg). Low insoluble acid-detergent fibre (1.4 g/kg) and neutral-detergent fibre (2.1 g/kg) values indicated that mucilage was mostly soluble fibre. Calcium oxalate crystals were not detected in dried mucilage. Opuntia robusta powders had higher protein, extractable fat and potassium content, while Opuntia ficus-indica mucilage powders had higher polyunsaturated (Linoleic and α-Linolenic acid) fat content. O. robusta Robusta mucilage, harvested after the fruit harvest (February) had the lowest energy content and the highest mineral and protein content. Mucilage powders were highly soluble, low-kilojoule and mineral-rich. This is a functional ingredient that is produced from an easily cultivated crop, as cactus pears grow in areas with poor soil, extremely high daytime temperatures and limited water supplies.
A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates
Authors: Li Yanping , Lv Yunyun , Bian Chao , You Xinxin , Deng Li , Shi Qiong
Published: April 2018

Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad-like gene, which formed a novel AAAD family. However, in tetraploid teleosts, there were two copies of the aaad gene due to whole genome duplication. A subsequent synteny analysis investigated 81 aaad sequences and revealed their collinearity and systematic evolution. Interestingly, we discovered that platypus (Ornithorhynchus anatinus), Atlantic cod (Guadus morhua), Mexican tetra (Astyanax mexicanus), and a Sinocyclocheilus cavefish (S. anshuiensis) have long evolutionary branches in the phylogenetic topology. We also performed pseudogene identification and selection pressure analysis; however, the results revealed a deletion of 37 amino acids in Atlantic cod and premature stop codons in the cave-restricted S. anshuiensis and A. mexicanus, suggesting weakening or disappearing rhythms in these cavefishes. Selective pressure analysis of aaad between platypus and other tetrapods showed that rates of nonsynonymous (Ka) and synonymous (Ks) substitutions were higher when comparing the platypus to other representative tetrapods, indicating that, in this semiaquatic mammal, the aaad gene experienced selection during the process of evolution. In summary, our current work provides novel insights into aaad genes in vertebrates from a genome-wide view.
The Stability of Medicinal Plant microRNAs in the Herb Preparation Process
Authors: Xie Wenyan , Melzig Matthias F.
Published: April 2018

Herbal medicine is now globally accepted as a valid alternative system of pharmaceutical therapies. Various studies around the world have been initiated to develop scientific evidence-based herbal therapies. Recently, the therapeutic potential of medicinal plant derived miRNAs has attracted great attraction. MicroRNAs have been indicated as new bioactive ingredients in medicinal plants. However, the stability of miRNAs during the herbal preparation process and their bioavailability in humans remain unclear. Viscum album L. (European mistletoe) has been widely used in folk medicine for the treatment of cancer and cardiovascular diseases. Our previous study has indicated the therapeutic potential of mistletoe miRNAs by using bioinformatics tools. To evaluate the stability of these miRNAs, various mistletoe extracts that mimic the clinical medicinal use as well as traditional folk medicinal use were prepared. The mistletoe miRNAs including miR166a-3p, miR159a, miR831-5p, val-miR218 and val-miR11 were quantified by stem-loop qRT-PCR. As a result, miRNAs were detectable in the majority of the extracts, indicating that consumption of medicinal plant preparations might introduce miRNAs into mammals. The factors that might cause miRNA degradation include ultrasonic treatment, extreme heat, especially RNase treatment, while to be associated with plant molecules (e.g., proteins, exosomes) might be an efficient way to protect miRNAs against degradation. Our study confirmed the stability of plant derived miRNAs during herb preparations, suggesting the possibility of functionally intact medicinal plant miRNAs in mammals.