bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences
Authors: Libis Vincent , Antonovsky Niv , Zhang Mengyin , Shang Zhuo , Montiel Daniel , Maniko Jeffrey , Ternei Melinda A. , Calle Paula Y. , Lemetre Christophe , Owen Jeremy G. , Brady Sean F.
Published: August 2019

Sequencing of DNA extracted from environmental samples can provide key insights into the biosynthetic potential of uncultured bacteria. However, the high complexity of soil metagenomes, which can contain thousands of bacterial species per gram of soil, imposes significant challenges to explore secondary metabolites potentially produced by rare members of the soil microbiome. Here, we develop a targeted sequencing workflow termed CONKAT-seq (co-occurrence network analysis of targeted sequences) that detects physically clustered biosynthetic domains, a hallmark of bacterial secondary metabolism. Following targeted amplification of conserved biosynthetic domains in a highly partitioned metagenomic library, CONKAT-seq evaluates amplicon co-occurrence patterns across library subpools to identify chromosomally clustered domains. We show that a single soil sample can contain more than a thousand uncharacterized biosynthetic gene clusters, most of which originate from low frequency genomes which are practically inaccessible through untargeted sequencing. CONKAT-seq allows scalable exploration of largely untapped biosynthetic diversity across multiple soils, and can guide the discovery of novel secondary metabolites from rare members of the soil microbiome.
Inducers of settlement and metamorphosis of the shrimp Hippolyte inermis Leach in Posidonia oceanica
Authors: Zupo Valerio , Mutalipassi Mirko , Glaviano Francesca , Buono Anna Cecilia , Cannavacciuolo Antonio , Fink Patrick
Published: August 2019

Larvae of the caridean shrimp Hippolyte inermis persist in the plankton of the Mediterranean up to about one month. Since they need to reach appropriate coastal areas for their recruitment in seagrass meadows, we hypothesized that leaves of Posidonia oceanica or, alternatively, algae present in their epiphytic biofilms, might be physically recognised as target substrates and trigger larval metamorphosis and settlement. Chemical cues could improve the finding of suitable habitats for settlement. Thus, the effects of leaves of P. oceanica and biofilms of the diatom Cocconeis scutellum parva, seasonally abundant in the leaf epiphytic stratum, were investigated along with the effect of volatile organic compounds (VOCs) extracted from the epiphytic diatom. The physical induction with P. oceanica accelerated larval settlement, stimulating an earlier and faster metamorphosis of larvae. C. scutellum parva produced a weaker effect on settlement; however, diatom’s VOCs had evident influence and accelerated metamorphosis and settlement. We concluded that such chemical cues as the VOCs produced by epiphytic diatoms, reinforce the effect of physical cues for the identification of suitable settlement locations for this shrimp.
fMRI indicates cortical activation through TRPV1 modulation during acute gouty attacks
Authors: Chen Chiao-Chi , Chang Chen , Hsu Yi-Hua , Peng Yi-Jen , Lee Herng-Sheng , Huang Guo-Shu
Published: August 2019

Gout is one of the most painful disease conditions. The central mechanism of pain processing in this condition remains elusive. Cerebral blood volume (CBV) responses are faithful correlates of brain activity changes; the application of CBV-weighted functional magnetic resonance imaging (fMRI) may shed light on the issue of interest. Transient receptor potential vanilloid 1 (TRPV1) is a critical ion channel expressed both peripherally in nociceptors and centrally in the brain. Whether TRPV1 plays a critical role in gout pain was also explored. Results showed that, in rats with gouty arthritis, noxious stimulation induced CBV increases in the primary somatosensory cortex and thalamus. These increases were correlated with up-regulated TRPV1 protein expression and pain behavior. Selective blockage of central TRPV1 channel activity by intrathecal administration of AMG9810 reversed the induced pain, and abolished the induced CBV increase in thalamocortical regions. The findings support that TRPV1 activation in the central pain pathway is crucial to the augmentation of pain in gouty conditions. This new information supports the development of TRPV1-based drugs for treating gout pain, while fMRI can be useful for repeated evaluation of brain activity changes induced by gout.
Drug Screening for Discovery of Broad-spectrum Agents for Soil-transmitted Nematodes
Authors: Elfawal Mostafa A. , Savinov Sergey N. , Aroian Raffi V.
Published: August 2019

Soil-transmitted nematodes (STNs), namely hookworms, whipworms, and ascarids, are extremely common parasites, infecting 1–2 billion of the poorest people worldwide. Two benzimidazoles, albendazole and mebendazole, are currently used in STN mass drug administration, with many instances of low/reduced activity reported. New drugs against STNs are urgently needed. We tested various models for STN drug screening with the aim of identifying the most effective tactics for the discovery of potent, safe and broad-spectrum agents. We screened a 1280-compound library of approved drugs to completion against late larval/adult stages and egg/larval stages of both the human hookworm parasite Ancylostoma ceylanicum and the free-living nematode Caenorhabditis elegans, which is often used as a surrogate for STNs in screens. The quality of positives was further evaluated based on cheminformatics/data mining analyses and activity against evolutionarily distant Trichuris muris whipworm adults. From these data, two pairs of positives, sulconazole/econazole and pararosaniline/cetylpyridinium, predicted to target nematode CYP-450 and HSP-90 respectively, were prioritized for in vivo evaluation against A. ceylanicum infections in hamsters. One of these positives, pararosaniline, showed a significant impact on hookworm fecundity in vivo. Taken together, our results suggest that anthelmintic screening with A. ceylanicum larval stages is superior to C. elegans based on both reduced false negative rate and superior overall quality of actives. Our results also highlight two potentially important targets for the discovery of broad-spectrum human STN drugs.
Pheno-seq – linking visual features and gene expression in 3D cell culture systems
Authors: Tirier Stephan M. , Park Jeongbin , Preußer Friedrich , Amrhein Lisa , Gu Zuguang , Steiger Simon , Mallm Jan-Philipp , Krieger Teresa , Waschow Marcel , Eismann Björn , Gut Marta , Gut Ivo G. , Rippe Karsten , Schlesner Matthias , Theis Fabian , Fuchs Christiane , Ball Claudia R. , Glimm Hanno , Eils Roland , Conrad Christian
Published: August 2019

Patient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce “pheno-seq” to directly link visual features of 3D cell culture systems with profiling their transcriptome. As prototypic applications breast and colorectal cancer (CRC) spheroids were analyzed by pheno-seq. We identified characteristic gene expression signatures of epithelial-to-mesenchymal transition that are associated with invasive growth behavior of clonal breast cancer spheroids. Furthermore, we linked long-term proliferative capacity in a patient-derived model of CRC to a lowly abundant PROX1-positive cancer stem cell subtype. We anticipate that the ability to integrate transcriptome analysis and morphological patho-phenotypes of cancer cells will provide novel insight on the molecular origins of intratumor heterogeneity.
Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction
Authors: Torrisi Mirko , Kaleel Manaz , Pollastri Gianluca
Published: August 2019

Protein Secondary Structure prediction has been a central topic of research in Bioinformatics for decades. In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction accuracy (88–90%), while only a few predict more than the 3 traditional Helix, Strand and Coil classes. In this study we present tests on different models trained both on single sequence and evolutionary profile-based inputs and develop a new state-of-the-art system with Porter 5. Porter 5 is composed of ensembles of cascaded Bidirectional Recurrent Neural Networks and Convolutional Neural Networks, incorporates new input encoding techniques and is trained on a large set of protein structures. Porter 5 achieves 84% accuracy (81% SOV) when tested on 3 classes and 73% accuracy (70% SOV) on 8 classes on a large independent set. In our tests Porter 5 is 2% more accurate than its previous version and outperforms or matches the most recent predictors of secondary structure we tested. When Porter 5 is retrained on SCOPe based sets that eliminate homology between training/testing samples we obtain similar results. Porter is available as a web server and standalone program at http://distilldeep.ucd.ie/porter/ alongside all the datasets and alignments.
Pore Scale Visualization of Drainage in 3D Porous Media by Confocal Microscopy
Authors: do Nascimento Débora F. , Vimieiro Junior José R. , Paciornik Sidnei , Carvalho Marcio S.
Published: August 2019

We visualize the dynamics of immiscible displacement of a high viscosity wetting phase by a low viscosity non-wetting phase in a three-dimensional (3D) glass bead packing using confocal microscopy. Both phases were doped with two different fluorescent dyes, which enabled visualization of both phases simultaneously and quantification of the phase volumes without the need of image subtraction operations. The transient results show details of the displacement process and how pores are invaded by the non-wetting displacing phase. The static images at the end of the displacement process reveal how the trapped ganglia volume and morphology change with capillary number. The wetting phase is trapped as pendular rings spanning one to multiple pore necks. Details of the pore scale flow of oil wet media revealed with the experimental methods presented here can lead to better fundamental understanding of the physical processes and optimized enhanced oil recovery methods, CO2 sequestration and aquifer remediation.
Establishment and characterization of a fucosylated α-fetoprotein-specific monoclonal antibody: a potential application for clinical research
Authors: Egashira Yuriko , Suganuma Masatoshi , Kataoka Yukiko , Higa Yukiko , Ide Nobuyuki , Morishita Koichi , Kamada Yoshihiro , Gu Jianguo , Fukagawa Koji , Miyoshi Eiji
Published: August 2019

The Lens culinaris agglutinin (LCA)-reactive fraction of α-fetoprotein (AFP-L3) is a well-known cancer biomarker for hepatocellular carcinoma (HCC) with very high specificity. Because LCA recognizes only bi-antennary N-glycans with a core fucose, some of fucosylated AFP in HCC patients may not be detected. Then glycan antibodies, which recognize both specific glycan and protein, are desired for glycobiology. Here, we successfully established a novel glycan antibody for fucosylated AFP and demonstrated its potential clinical application. After immunization with a fucosylated AFP peptide, positive screening was performed for fucosylated AFP peptides using solid-phase enzyme-linked immunosorbent assay (ELISA). The newly developed antibody was designated: fucosylated AFP-specific mAb (FasMab). Western blot analysis showed that FasMab reacted with AFP produced by HepG2 cells, but not with AFP produced by α-1,6-fucosyltransferase deficient HepG2 cells. The specific binding of FasMab to fucosylated AFP was confirmed with ELISA as well as western blot analysis. A preliminary high sensitivity chemiluminescence enzyme immunoassay kit showed increased levels of fucosylated AFP in the sera of patients with HCC, but not in the sera of normal patients, or patients with chronic liver diseases. Thus, the novel glycan antibody, FasMab, is a promising tool to study fucosylated AFP with clinical and basic research applications.
Synthesis of Methane Hydrate from Ice Powder Accelerated by Doping Ethanol into Methane Gas
Authors: Chen Yen-An , Chu Liang-Kai , Chu Che-Kang , Ohmura Ryo , Chen Li-Jen
Published: August 2019

Clathrate hydrate is considered to be a potential medium for gas storage and transportation. Slow kinetics of hydrate formation is a hindrance to the commercialized process development of such applications. The kinetics of methane hydrate formation from the reaction of ice powder and methane gas doped with/without saturated ethanol vapor at constant pressure of 16.55 ± 0.20 MPa and constant temperature ranging from −15 to −1.0 °C were investigated. The methane hydrate formation can be dramatically accelerated by simply doping ethanol into methane gas with ultralow ethanol concentration (<94 ppm by mole fraction) in the gas phase. For ethanol-doped system 80.1% of ice powder were converted into methane hydrate after a reaction time of 4 h, while only 26.6% of ice powder was converted into methane hydrate after a reaction time of 24 h when pure methane gas was used. Furthermore, this trace amount of ethanol could also substantially suppress the self-preservation effect to enhance the dissociation rate of methane hydrate (operated at 1 atm and temperatures below the ice melting point). In other words, a trace amount of ethanol doped in methane gas can act as a kinetic promoter for both the methane hydrate formation and dissociation.
Phase-matched multi-layer based polarisation-independent spot-size converter for silicon nanowire
Authors: Jiang Weifeng , Rahman B. M. Azizur
Published: August 2019

The efficient coupling of optical power from a silicon nanowire (NW) to an optical fibre is challenging for both the quasi-TE and quasi-TM polarisations. Here, we propose a polarisation-independent spot-size converter (PI-SSC) based on phase-matched multi-layer waveguides for efficient coupling between a silicon NW and an optical fibre for both the polarisations. The fabrication process of the proposed PI-SSC is compatible with the complementary metal-oxide-semiconductor (CMOS) process. The optimisation for the proposed PI-SSC is studied by using a numerically efficient algorithm, combining a rigorous H-field based full-vectorial finite element method (VFEM) and the least squares boundary residual (LSBR) method. The simulation results show that using an eleven-layer based PI-SSC, the coupling losses between a silicon NW and a lensed fibre of radius 2 μm can be reduced to only 0.34 dB and 0.25 dB for the quasi-TE and quasi-TM polarisations, respectively. Furthermore, the output multi-layer is horizontally tapered, which further reduces the coupling loss for both the polarisations and the end face is easy to be polished.
The subgingival microbial community of feline periodontitis and gingivostomatitis: characterization and comparison between diseased and healthy cats
Authors: Rodrigues Marjory Xavier , Bicalho Rodrigo Carvalho , Fiani Nadine , Lima Svetlana Ferreira , Peralta Santiago
Published: August 2019

Periodontitis is a common and important health problem in domestic cats. The subgingival microbiota of cats diagnosed with chronic periodontitis (CP), aggressive periodontitis (AP), and feline chronic gingivostomatitis (FCGS) are not well characterized. Thus, the aim of the present study was to characterize and compare the periodontal microbiota of periodontally healthy cats versus cats diagnosed with CP, AP, and FCGS by using next-generation sequencing. In total, 44 domestic cats were enrolled, and 139 subgingival samples were subjected to 16S rRNA gene sequencing to investigate the microbiota composition of each periodontal group evaluated. Our results identified several key genera previously described in periodontal disease (e.g. Treponema and Filifactor) and in the oral microbiota (e.g. Moraxella and Capnocytophaga) of healthy cats. Phylogenetic beta diversity analysis showed that the microbiota of periodontally healthy cats were distinguishable from diseased cats. Even though most of the genera known to be associated with periodontal disease were also identified in healthy cats, they were present at significantly lower relative abundance. Remarkably, alpha diversity was found to be higher in the disease groups compared to healthy animals. These results suggest a pathological mechanism involving opportunistic behavior. Our findings corroborate those in the current literature regarding the complexity of the subgingival microbiota of the domestic cat and reveal both differences and similarities among periodontally healthy and diseased cats.
Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing
Authors: Sanada Takahiro , Tsukiyama-Kohara Kyoko , Shin-I Tadasu , Yamamoto Naoki , Kayesh Mohammad Enamul Hoque , Yamane Daisuke , Takano Jun-ichiro , Shiogama Yumiko , Yasutomi Yasuhiro , Ikeo Kazuho , Gojobori Takashi , Mizokami Masashi , Kohara Michinori
Published: August 2019

The northern tree shrew (Tupaia belangeri) possesses high potential as an animal model of human diseases and biology, given its genetic similarity to primates. Although genetic information on the tree shrew has already been published, some of the entire coding sequences (CDSs) of tree shrew genes remained incomplete, and the reliability of these CDSs remained difficult to determine. To improve the determination of tree shrew CDSs, we performed sequencing of the whole-genome, mRNA, and total RNA and integrated the resulting data. Additionally, we established criteria for the selection of reliable CDSs and annotated these sequences by comparison to the human transcriptome, resulting in the identification of complete CDSs for 12,612 tree shrew genes and yielding a more accurate tree shrew genome database (TupaiaBase: http://tupaiabase.org). Transcriptome profiles in hepatitis B virus infected tree shrew livers were analyzed for validation. Gene ontology analysis showed enriched transcriptional regulation at 1 day post-infection, namely in the “type I interferon signaling pathway”. Moreover, a negative regulator of type I interferon, SOCS3, was induced. This work, which provides a tree shrew CDS database based on genomic DNA and RNA sequencing, is expected to serve as a powerful tool for further development of the tree shrew model.
Image processing approaches to enhance perivascular space visibility and quantification using MRI
Authors: Sepehrband Farshid , Barisano Giuseppe , Sheikh-Bahaei Nasim , Cabeen Ryan P. , Choupan Jeiran , Law Meng , Toga Arthur W.
Published: August 2019

Imaging the perivascular spaces (PVS), also known as Virchow-Robin space, has significant clinical value, but there remains a need for neuroimaging techniques to improve mapping and quantification of the PVS. Current technique for PVS evaluation is a scoring system based on visual reading of visible PVS in regions of interest, and often limited to large caliber PVS. Enhancing the visibility of the PVS could support medical diagnosis and enable novel neuroscientific investigations. Increasing the MRI resolution is one approach to enhance the visibility of PVS but is limited by acquisition time and physical constraints. Alternatively, image processing approaches can be utilized to improve the contrast ratio between PVS and surrounding tissue. Here we combine T1- and T2-weighted images to enhance PVS contrast, intensifying the visibility of PVS. The Enhanced PVS Contrast (EPC) was achieved by combining T1- and T2-weighted images that were adaptively filtered to remove non-structured high-frequency spatial noise. EPC was evaluated on healthy young adults by presenting them to two expert readers and also through automated quantification. We found that EPC improves the conspicuity of the PVS and aid resolving a larger number of PVS. We also present a highly reliable automated PVS quantification approach, which was optimized using expert readings.
Facile fabrication of a large-area and cost-effective PDMS-SERS substrate by sandpaper template-assisted lithography
Authors: Sun Ji , Gong Lin , Gong Zhengjun , Wang Dongmei , Yin Xiaosi , Fan Meikun
Published: August 2019

In this study, a highly reproducible Ag NP loaded polydimethylsiloxane (PDMS) SERS substrate was fabricated by a simple template lithography method.
Antigen-enabled facile preparation of MOF nanovaccine to activate the complement system for enhanced antigen-mediated immune response
Authors: Qi Yanxin , Wang Lei , Guo Huanhuan , Pan Yong , Xie Zhigang , Jin Ningyi , Huang Yubin
Published: August 2019

Since current subunit vaccines are limited by a short halflife in vivo and weak immune responses when used alone without adjuvants, there is an unmet need for combing carriers with complement activation signals to interrupt outbreaks in real-time.
In situ photodeposition of amorphous NixP on CdS nanorods for efficient visible-light photocatalytic H2 generation
Authors: Zhu Simeng , Wang Jing , He Yishan , Yu Zhiyang , Wang Xuxu , Su Wenyue
Published: August 2019

Noble metal-free amorphous NixP modified CdS with superior photocatalytic H2 evolution activity has been successfully fabricated.
Selective electrochemical reduction of CO2to CO on CuO/In2O3nanocomposites: role of oxygen vacancies
Authors: Devi Pinki , Malik Karan , Arora Ekta , Bhattacharya Saswata , Kalendra V. , Lakshmi K. V. , Verma Anil , Singh Jitendra P.
Published: August 2019

For the clean and sustainable development, sequestration of carbon dioxide (CO2) through electrocatalytic reduction to produce high-value industrial precursors, such as CO, is a promising avenue.
Theoretical study of the photoconduction and photomagnetism of the BPY[Ni(dmit)2]2 molecular crystal
Authors: Zapata-Rivera Jhon , Sánchez-de-Armas Rocío , Calzado Carmen J.
Published: August 2019

UV-Vis light generates photoexcited (BPY2+)* radicals that interact with the close Ni(dmit)2 units, modifying their magnetic and conducting properties.
Recent advances in ion-imprinted membranes: separation and detection via ion-selective recognition
Authors: Lu Jian , Qin Yingying , Wu Yilin , Meng Minjia , Yan Yongsheng , Li Chunxiang
Published: August 2019

Ionic selectivity is achieved based on ion-imprinted membranes.
A faster and simpler UPLC-MS/MS method for the simultaneous determination of trimethylamine N-oxide, trimethylamine and dimethylamine in different types of biological samples
Authors: Wu Qiu , Zhao Yan , Zhang Xiangnan , Yang Xingbin
Published: August 2019

Gut microbiota-dependent metabolites trimethylamine N-oxide (TMAO), trimethylamine (TMA) and dimethylamine (DMA) from dietary methylamines have recently gained much attention due to their high association with chronic kidney disease risk.
High-fat diet induces mouse liver steatosis with a concomitant decline in energy metabolism: attenuation by eicosapentaenoic acid (EPA) or hydroxytyrosol (HT) supplementation and the additive effects upon EPA and HT co-administration
Authors: Echeverría Francisca , Valenzuela Rodrigo , Bustamante Andrés , Álvarez Daniela , Ortiz Macarena , Espinosa Alejandra , Illesca Paola , Gonzalez-Mañan Daniel , Videla Luis A.
Published: August 2019

High-fat-diet (HFD) feeding is associated with liver oxidative stress (OS), n-3 long-chain polyunsaturated fatty acid (n-3 LCPUFA) depletion, hepatic steatosis and mitochondrial dysfunction.
Carbon nanotube fibers with enhanced longitudinal carrier mobility for high-performance all-carbon thermoelectric generators
Authors: Lee Taemin , Park Kyung Tae , Ku Bon-Cheol , Kim Heesuk
Published: August 2019

We have demonstrated wet-spun CNT fibers with high thermoelectric performance by optimizing the longitudinal carrier mobility.
Photo-annealed amorphous titanium oxide for perovskite solar cells
Authors: Jeon Jae Bum , Kim Byeong Jo , Bang Gi Joo , Kim Min-cheol , Lee Dong Geon , Lee Jae Myeong , Lee Minho , han Hyun Soo , Boschloo Gerrit , Lee Sangwook , Jung Hyun Suk
Published: August 2019

Photo annealing system under dry condition has been developed to fabricate low temperature amorphous TiO2electron extraction layer for perovskite solar cells.
Ultra-narrow bandgap non-fullerene acceptors for organic solar cells with low energy loss
Authors: Liu Dongxue , Wang Ting , Ke Xin , Zheng Nan , Chang Zhitao , Xie Zengqi , Liu Yongsheng
Published: August 2019

Two ultra-narrow bandgap non-fullerene acceptors (NFAs),4TO-T-4Fand4TO-Se-4F, were designed and synthesized for application in organic solar cells (OSCs).
A fluorinated alloy-type interfacial layer enabled by metal fluoride nanoparticle modification for stabilizing Li metal anodes
Authors: Li Feng , Tan Yi-Hong , Yin Yi-Chen , Zhang Tian-Wen , Lu Lei-Lei , Song Yong-Hui , Tian Te , Shen Bao , Zhu Zheng-Xin , Yao Hong-Bin
Published: August 2019

A uniform LiF/Li–M alloy functional interfacial layer based on chemical modification effectively stabilizes LMBs by inhibiting the growth of Li dendrites.
A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging
Authors: Wang Hong , Wang Huimin , Wu Qiong , Liang Meijuan , Liu Xiaoqing , Wang Fuan
Published: August 2019

A rationally and modularly engineered CHA-HCR-DNAzyme circuit was constructed for amplified biosensing and bioimaging with high performance.
Why are photosynthetic reaction centres dimeric?
Authors: Taylor Natasha , Kassal Ivan
Published: August 2019

The dimerisation of photosynthetic reaction centres enhanced their efficiency by improving exciton transfer from an antenna.
Injectable and fast self-healing protein hydrogels
Authors: Zhang Xin , Jiang Shangtong , Yan Tengfei , Fan Xiaotong , Li Fei , Yang Xiaodong , Ren Bo , Xu Jiayun , Liu Junqiu
Published: August 2019

Injectable hydrogels are adapted to irregularities in the desired location by injection as a liquid and gelation in situ.
LiNi0.90Co0.07Mg0.03O2 cathode materials with Mg-concentration gradient for rechargeable lithium-ion batteries
Authors: Zhang Yudong , Li Hang , Liu Junxiang , Zhang Jicheng , Cheng Fangyi , Chen Jun
Published: August 2019

Nickel-rich LiNi0.90Co0.07Mg0.03O2 cathode material with concentration gradient structure exhibits superior high capacity, high-rate capability and cycling stability.
One minute from pristine carbon to an electrocatalyst for hydrogen peroxide production
Authors: Wang Yun-Lu , Li Shi-Song , Yang Xiao-Hong , Xu Guo-Yong , Zhu Zi-Chun , Chen Ping , Li Shan-Qing
Published: August 2019

An excellent electrocatalyst for producing H2O2was prepared from pristine CMK3 by microwave and subsequent liquid nitrogen treatments in 1 minute.
A PdAg-CeO2nanocomposite anchored on mesoporous carbon: a highly efficient catalyst for hydrogen production from formic acid at room temperature
Authors: Zhang Zhujun , Luo Yixing , Liu Shiwen , Yao Qilu , Qing Shaojun , Lu Zhang-Hui
Published: August 2019

Herein, CeO2-modified PdAg alloy nanocomposites were anchored on mesoporous carbon, showing exceedingly high catalytic activity for HCOOH dehydrogenation at room temperature.
Origin of the large electrostrain in BiFeO3-BaTiO3 based lead-free ceramics
Authors: Wang Ge , Fan Zhongming , Murakami Shunsuke , Lu Zhilun , Hall David A. , Sinclair Derek C. , Feteira Antonio , Tan Xiaoli , Jones Jacob L. , Kleppe Annette K. , Wang Dawei , Reaney Ian M.
Published: August 2019

The large electrostrain (1 − x)BiFeO3-0.3BaTiO3-xNd(Li0.5Nb0.5)O3 ceramics is explained by the presence of polar nano-regions which distort in the direction of the applied field within multiple local symmetries.
Electric power generation using paper materials
Authors: Gao Xue , Xu Tong , Shao Changxiang , Han Yuyang , Lu Bing , Zhang Zhipan , Qu Liangti
Published: August 2019

Paper materials are utilized in moist-electric power generation, and a ‘power’ book that harvests moist-electricity is demonstrated.
Pyrazine as a noncovalent conformational lock in semiconducting polymers for enhanced charge transport and stability in thin film transistors
Authors: Ocheje Michael U. , Goodman Renée B. , Onge P. Blake J. St. , Malik Mah-Noor , Yadiki Madhumitha , He Yinghui , Tao Ye , Chu Ta-Ya , Rondeau-Gagné Simon
Published: August 2019

Pyrazine-containing moieties were introduced into a semiconducting polymer to improve backbone planarity through a conformational locking effect, leading to good electronic properties and high stability in thin film transistors.
External and internal grouping characteristics of juvenile walleye pollock in the Eastern Bering Sea
Authors: Stienessen Sarah C. , Wilson Christopher D. , Weber Thomas C. , Parrish Julia K.
Published: August 2019

Size and shape patterns of fish groups are collective outcomes of interactions among members. Consequently, group-level patterns are often affected when any member responds to changes in their internal state, external state, and environment. To determine how groups of fish respond to components of their physical and ecological environment, and whether the response is influenced by a component of their external state (i.e., fish age), we used a multibeam system to collect three-dimensional grouping characteristics of 5 age categories of juvenile walleye pollock (age 1, age 2, age 3, mixed ages 1 and 2, and mixed ages 2 and 3) across the eastern Bering Sea shelf over two consecutive years (2009–2010). Grouping data were expressed as metrics that described group size (length, height), shape (roundness, spread), internal structure (density, internal heterogeneity), and position (depth, distance above bottom). Physical data (water temperature measurements) were collected with temperature-depth probes, and ecological data (densities of predators and prey − adult walleye pollock and euphausiids, respectively) were collected with an EK60 vertical echosounder. Juvenile pollock maintained a relatively constant shape, size-dependent density (number fish/mean body length3), and internal horizontal heterogeneity among age categories and in the presence of predators and prey. There were changes to group structure in the face of local physical forcing. Groups tended to move towards the seafloor when bottom waters became warmer, and groups became vertically shorter, denser, and had more variation in horizontal internal density as group depth increased. These results are explored in relation to the value and limitations of using multibeam data to describe how external and internal group structure map onto environmental influences.
Assessing attribute redundancy in the application of productivity-susceptibility analysis to data-limited fisheries
Authors: Duffy Leanne M. , Griffiths Shane P.
Published: August 2019

Productivity-susceptibility analysis (PSA) is a widely used data-limited method to assess the relative vulnerability of species impacted by fisheries. Despite its widespread use, few authors have evaluated the impacts of attribute weightings and correlation of productivity attributes that may bias species' vulnerability scores. We evaluated the PSA methodology and performed sensitivity analyses to determine the impacts of correlation among productivity attributes used in the PSA, given that several of these attributes are strongly correlated. A PSA for species caught in the eastern Pacific Ocean tuna purse-seine fishery was used as an example to assess potential bias introduced by attribute weightings and correlation of productivity attributes on species' vulnerability scores. Redundancy was observed among three pairs of attributes. We demonstrated that manipulation of attribute weightings and removal of correlated attributes did not appreciably change any species' overall vulnerability status. Our results suggest that after removal of redundant attributes, PSAs can be conducted more rapidly with fewer data inputs than previous implementations, while retaining comparable vulnerability scores.
Nonlocal gradient operators with a nonspherical interaction neighborhood and their applications
Authors: Lee Hwi , Du Qiang
Published: August 2019

Nonlocal gradient operators are prototypical nonlocal differential operators that are very important in the studies of nonlocal models. One of the simplest variational settings for such studies is the nonlocal Dirichlet energies wherein the energy densities are quadratic in the nonlocal gradients. There have been earlier studies to illuminate the link between the coercivity of the Dirichlet energies and the interaction strengths of radially symmetric kernels that constitute nonlocal gradient operators in the form of integral operators. In this work we adopt a different perspective and focus on nonlocal gradient operators with a non-spherical interaction neighborhood. We show that the truncation of the spherical interaction neighborhood to a half sphere helps making nonlocal gradient operators well-defined and the associated nonlocal Dirichlet energies coercive. These become possible, unlike the case with full spherical neighborhoods, without any extra assumption on the strengths of the kernels near the origin. We then present some applications of the nonlocal gradient operators with non-spherical interaction neighborhoods. These include nonlocal linear models in mechanics such as nonlocal isotropic linear elasticity and nonlocal Stokes equations, and a nonlocal extension of the Helmholtz decomposition.
Detection and genetic characterization of Giardia duodenalis in pigs from large-scale farms in Xinjiang, China
Authors: Jing Bo , Zhang Ying , Xu Chunyan , Li Dongfang , Xing Jinming , Tao Dayong , Zhang Longxian , Qi Meng , Wang Haiyan
Published: August 2019

To study the presence of Giardia duodenalis in Xinjiang, northwest China, we collected 801 fecal specimens from seven large-scale pig farms and screened them using PCR targeting the SSU rRNA gene. Twenty-one (2.6%) of the specimens from five farms were G. duodenalis-positive, with a significant difference in prevalence among different farms (0–8.7%) (p < 0.01). Giardia duodenalis prevalence was highest in fattening pigs (5.4%, 7/129), followed by sows (3.2%, 7/222), post-weaning piglets (1.8%, 5/281), and pre-weaning piglets (1.2%, 2/169), but there was no significant difference in prevalence among the age groups (p > 0.05). Sequence analysis of the SSU rRNA gene revealed that the 21 G. duodenalis strains belonged to three assemblages: A (n = 2), B (n = 16), and E (n = 3). Assemblage B was the predominant assemblage and was widely distributed in all G. duodenalis-positive farms and age groups. All G. duodenalis-positive specimens were further assayed at the β-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi) genes, and two tpi, four gdh, and two bg sequences were identified. These data indicate that pigs may be a zoonotic risk and can potentially spread G. duodenalis infection from animals to humans.
Experimenting intermediate lived spaces in residential subdivisions: Action, interaction and storytelling
Authors: Palmieri Teresa , Serre Marion
Published: August 2019

Suburbanization and more precisely the development of residential subdivisions in Europe are at the core of many current debates. Over the years, they have been strongly criticized for the waste of land, increased infrastructure and network costs, car-dependency and the lack of urbanity. In this context, two processes are politically-driven in Europe: the densification of residential areas and the revitalization of the city centers. These political guidelines interrogate the transformation − and possible deterioration − of living environments and ambiances of residential subdivisions. Indeed, beyond the negative perspectives, other investigations have revealed the potentials of residential subdivisions from different points of view: ecology, social, architectural and urban. In order to contribute to these studies, this paper proposes to investigate the intermediate lived spaces in the specific context of residential subdivisions.
Digital Immersion − case studies in virtual reality
Authors: Welty Christopher , Setiawan Arief
Published: August 2019

Digital tools have transformed the ways we generate designs, pushing the boundaries in formal explorations, as well as the ways we represent them. In this vein, the impacts of the digital revolution affect both design practice and design education. We would like to investigate these impacts on our teaching of design studios, focusing on the virtual reality. Our premise is that the use of first-person immersion in a virtual environment is a means for experiencing space. We are interested in ways in which the abilities of virtual reality to simulate ranges of sensorial information could inform design processes. This paper will report in our research in our teaching that speculated about the values and application of these techniques. This paper aims to discuss our learning processes and experiences as well as to reflect on possibilities of digital means effective design pedagogy.
The affective notes of represented space as motors of emotional and sensorial response
Authors: Morselli Elisa
Published: August 2019

The following essay proposes to investigate the perceptual and emotional aspects related to the visualization of architectural images. The field of research is limited to a well-defined category: figurative representations as the photographic and digital images of contemporary architecture. In particular, two types will be analysed: the un-built architecture produced by Studio MIR and Bloomimages compared with the photographed built architecture. Using figurative images as a tool of reading, the aim of this work is to identify and classify three types of affective spaces capable of generating a specific kind of perception, producing a sensorial classification of atmosphere for architecture. The study of the Psychology of Art, as well as Aesthetics and Neuroaesthetics can be a valuable tool in understanding the phenomena of the present, considering the marked pictoriality of these images. The application of the analytic methodology, developed in these disciplines, can suggest a new way of "looking" at the project, paying attention to the representation of the atmospheres, which characterizes the experience of felt space. Keywords: Affective Space, Perception, Representation, Aesthetics, Atmospheres, Design Research, Generators.
Between ambiance and perception: Heritage decoding
Authors: Kępczyńska-Walczak Anetta
Published: August 2019

The aim of the study is to grasp and analyse the intangible process taking place between ambiance and perception. In this regard, ambiance should be understood as a state or aura, as opposed to perception, assumed as a process. The transition of sensorial immersion from ambiance to perception requires the process of decoding. Decoding might be explained as the process running between ambiance and perception and, furthermore, leading to understanding. Therefore, the outcome of the overall process is of cognitive characteristics. Furthermore, it draws research into a relationship between what is projected and actually experienced, between the tangible and the intangible and reveals the process of decoding ambiances where heritage plays a dominant role. The paper discusses the two concepts in the context of the post-industrial heritage in Łódź, Poland. The set of reflections evokes numerous questions: are we into the heritage as it was, or as it is at present, or rather to its projection, tuned to current socio-cultural standards? Does carefully planned and created ambiance give a clear unambiguous sense of a place? Or, it is not ambiance but the processes of decoding and perception that result in various interpretations of the same experience of atmosphere?
Branding Space: Deliberate Formations in Beginning Design
Authors: McManus Margaret
Published: August 2019

Arguably, ambiance in our culture is created in large by architecture and media. The former consumes us as we inhabit spaces both interior and exterior, allowing physical and material constraints — and the programmatic functions they permit — to create ambiance. The latter, media, inhabits us as we consume it. It creates or perhaps manipulates an ambiance within our minds. Through signage, television, and the internet we have graphic design flooding our brains via advertising and marketing: emotionally directing our decisions, telling us to buy this or invest in that. Analogous to material and physical choices that create the ambiance of architecture, we can blame branding strategies and the practices thereof for the strength and power that they give media to create ambiance. While students use branding strategies to assist themselves in creating ambiance through architecture, they are becoming grounded in a process that compels them to carry out objectives and promises made. Ultimately, this undertone of the pedagogical approach is what they can take forward as they embark on more complex projects, where timely decisions must coincide with a singular message and clear vision.
AMBIANTAL ARCHITECTURE − Defining the role of water in the aesthetic experience of sensitive architectural ambiances
Authors: Sioui Gregory Brais
Published: August 2019

As part of an aesthetic approach, this design-driven research crosses two methodologies to determine what is common in the perception of atmospheres. First, a case study of the Vals’ thermal baths led to the selection of five different atmospheres, which were then analyzed through Gaston Bachelard’s lens, using his bookL’Eau et les rêves. Bachelard’s literary symbols echo in the water contained in the massive stone walls of Vals to identify common generators of sensitive atmospheres. Secondly, the construction of this dialogue between Bachelard and Zumthor leads to the elaboration of a conceptual architecture project which is voluntarily emotional. This project introduces the elements that generate five ambiences identified in the case study. This design-driven research is therefore based on Grégoire Chelkoff’s theory offormantsas vectors of transmission of atmosphere, pre-existing to the experienc of a place, of an ambiance, which itself is understood as a sensitive result of the perception of the space. The present work therefore questions the role of water as a sensitive vector, from the architecture to its visitor. The goal is to determine how water, in varying manifestations, can be used by architects to create a “mise en scène” for a voluntarily emotional architecture.
Architectural character in conservation design projects
Authors: Elwazani Salim , Katara Pooja
Published: August 2019

Embracing “character” as a form of spatial ambiance, this study has examined architectural character and the character’s relationship with the cultural values, building configurations, and building integrity. Considered sequentially, cultural values, building configurations, and building integrity are the three conservation cognitive agents that need to be satisfied before and during the intervention process in the first place, and in a post-intervention sense if to keep the heritage quality of the preserved property intact. Therefore, the study deciphered the character interface with each of the three agents and reflected on these interfaces in completed conservation projects. The study culminated with that the building character plays the central role in moderating the workings of the three agents towards successful conservation projects. The study further pointed out to the challenges that conservation professionals and historic architects face in accommodating character, and by extension, cultural values, building configurations, and building integrity in conservation projects. There is a need for defining and “operationalizing” character—and each of the three agents—to move the conservation process forward.
A case of metastatic prostate cancer treated with metastasectomy
Authors: Miyata Yudai , Funahashi Yasuhito , Yamamoto Akiyuki , Sassa Naoto , Matsukawa Yoshihisa , Gotoh Momokazu
Published: August 2019

In general, metastatic prostate cancer is managed medically. Here we present a patient with metastatic prostate cancer who was treated by surgical resection in addition to medical therapies. Local therapies should be considered if metastatic lesions are limited, also in cases of metastatic prostate cancer.
Can Routine Data be used to Determine the Target Population of
Patients with Type 2 Diabetes in Early Benefit Assessments in
Germany?
Authors: Thoren Corinna ten , Schwalm Anja , Mostardt Sarah , Weber Dietmar , Ihle Peter , Altenhofen Lutz
Published: August 2019

Objectives Since 2011, early benefit assessment of all new drugs
launched in Germany is mandatory. The exact determination of the appropriate
target population (i. e. patients eligible for a drug) plays an
important role for subsequent price negotiations. In type 2 diabetes, the
size of the target population varies considerably between company dossiers
submitted for assessment. Our aim was to explore whether routine data from
all persons insured in German statutory health insurance (SHI) funds can be
used to derive information on the size of the target population with type 2
diabetes.

Methods We explored how the data available at the German Institute of
Medical Documentation and Information (DIMDI) can be used to obtain the
information required. A data-based concept was chosen and the selection
criteria were developed in a multidisciplinary project group. Before
finalizing the database query, the criteria were evaluated in a test
database and the database query was then repeatedly modified.

Results At the time of the design of our analysis in 2017, the most
recent data available at DIMDI were for 2013. The algorithm we developed for
identifying patients with type 2 diabetes and classifying them according to
their medication, based primarily on the combination of ICD and ATC codes,
enabled us to determine the size of target populations for different
indications in diabetes mellitus type 2.

Conclusion Our methodological approach seems to be suitable to
determine target populations in type 2 diabetes.
Reduction of Pyrrolizidine Alkaloid Levels in Comfrey (Symphytum officinale) Hairy Roots by RNAi Silencing of Homospermidine Synthase
Authors: Kruse Lars H. , Stegemann Thomas , Jensen-Kroll Julia , Engelhardt Annika , Wesseling Anne-Maria , Lippert Annemarie , Ludwig-Müller Jutta , Ober Dietrich
Published: August 2019

Comfrey is a medicinal plant, extracts of which are traditionally used for the treatment of painful inflammatory muscle and joint problems, because the plant contains allantoin and rosmarinic acid. However, its medicinal use is limited because of its toxic pyrrolizidine alkaloid (PA) content. PAs encompass more than 400 different compounds that have been identified from various plant lineages. To date, only the first pathway-specific enzyme, homospermidine synthase (HSS), has been characterized. HSS catalyzes the formation of homospermidine, which is exclusively incorporated into PAs. HSS has been recruited several times independently in various plant lineages during evolution by duplication of the gene encoding deoxyhypusine synthase (DHS), an enzyme of primary metabolism. Here, we describe the establishment of RNAi knockdown hairy root mutants of HSS in Symphytum officinale. A knockdown of HSS by 60 – 80% resulted in a significant reduction of homospermidine by ~ 86% and of the major PA components 7-acetylintermedine N-oxide and 3-acetylmyoscorpine N-oxide by approximately 60%. The correlation of reduced transcript levels of HSS with reduced levels of homospermidine and PAs provides in planta support for HSS being the central enzyme in PA biosynthesis. Furthermore, the generation of PA-depleted hairy roots might be a cost-efficient way for reducing toxic by-products that limit the medicinal applicability of S. officinale extracts.