bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiconductor Electronic Label-Free Assay for Predictive Toxicology
Authors: Mao Yufei , Shin Kyeong-Sik , Wang Xiang , Ji Zhaoxia , Meng Huan , Chui Chi On 
Published: April 2016

AbstractWhile animal experimentations have spearheaded numerous breakthroughs in biomedicine, they also have spawned many logistical concerns in providing toxicity screening for copious new materials. Their prioritization is premised on performing cellular-level screening in vitro. Among the screening assays, secretomic assay with high sensitivity, analytical throughput and simplicity is of prime importance. Here, we build on the over 3-decade-long progress on transistor biosensing and develop the holistic assay platform and procedure called semiconductor electronic label-free assay (SELFA). We demonstrate that SELFA, which incorporates an amplifying nanowire field-effect transistor biosensor, is able to offer superior sensitivity, similar selectivity and shorter turnaround time compared to standard enzyme-linked immunosorbent assay (ELISA). We deploy SELFA secretomics to predict the inflammatory potential of eleven engineered nanomaterials in vitro and validate the results with confocal microscopy in vitro and confirmatory animal experiment in vivo. This work provides a foundation for high-sensitivity label-free assay utility in predictive toxicology.
Generation of exogenous germ cells in the ovaries of sterile NANOS3-null beef cattle
Authors: Ideta Atsushi , Yamashita Shiro , Seki-Soma Marie , Yamaguchi Ryosaku , Chiba Shiori , Komaki Haruna , Ito Tetsuya , Konishi Masato , Aoyagi Yoshito , Sendai Yutaka 
Published: April 2016

AbstractBlastocyst complementation (BC) systems have enabled in vivo generation of organs from allogeneic pluripotent cells, compensating for an empty germ cell niche in gene knockout (KO) animals. Here, we succeeded in producing chimeric beef cattle (Wagyu) by transferring allogenic germ cells into ovaries using somatic cell nuclear transfer and BC technology. The KO of NANOS3 (NANOS3−/−) in Wagyu bovine ovaries produced a complete loss of germ cells. Holstein blastomeres (NANOS3+/+) were injected into NANOS3−/− Wagyu embryos. Subsequently, exogenous germ cells (NANOS3+/+) were identified in the NANOS3−/− ovary. These results clearly indicate that allogeneic germ cells can be generated in recipient germ cell-free gonads using cloning and BC technologies.
Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity
Authors: Ayres Cory M. , Scott Daniel R. , Corcelli Steven A. , Baker Brian M. 
Published: April 2016

AbstractComplementarity determining region (CDR) loop flexibility has been suggested to play an important role in the selection and binding of ligands by T cell receptors (TCRs) of the cellular immune system. However, questions remain regarding the role of loop motion in TCR binding, and crystallographic structures have raised questions about the extent to which generalizations can be made. Here we studied the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5. We found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity. While the loops of A6 move rapidly in an uncorrelated fashion, those of DMF5 are substantially less mobile. Accordingly, the mechanisms of binding and cross-reactivity are very different between the two TCRs: whereas A6 relies on conformational selection to select and bind different ligands, DMF5 uses a more rigid, permissive architecture with greater reliance on slower motions or induced-fit. In addition to binding site flexibility, we also explored whether ligand-binding resulted in common dynamical changes in A6 and DMF5 that could contribute to TCR triggering. Although binding-linked motional changes propagated throughout both receptors, no common features were observed, suggesting that changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling.
Platelet-cytokine Complex Suppresses Tumour Growth by Exploiting Intratumoural Thrombin-dependent Platelet Aggregation
Authors: Li Yu-Tung , Nishikawa Tomoyuki , Kaneda Yasufumi 
Published: April 2016

AbstractTumours constitute unique microenvironments where various blood cells and factors are exposed as a result of leaky vasculature. In the present study, we report that thrombin enrichment in B16F10 melanoma led to platelet aggregation and this property was exploited to administer an anticancer cytokine, interferon-gamma induced protein 10 (IP10), through the formation of a platelet-IP10 complex. When intravenously infused, the complex reached platelet microaggregates in the tumour. The responses induced by the complex were solely immune-mediated and tumour cytotoxicity was not observed. The complex suppressed the growth of mouse melanoma in vivo, while both platelets and the complex suppressed the accumulation of FoxP3+ regulatory T cells in the tumour. These results demonstrated that thrombin-dependent platelet aggregation in B16F10 tumours defines platelets as a vector to deliver anticancer cytokines and provide specific treatment benefits.
Integral Light-Harvesting Complex Expression In Symbiodinium Within The Coral Acropora aspera Under Thermal Stress
Authors: Gierz Sarah L. , Gordon Benjamin R. , Leggat William 
Published: April 2016

AbstractCoral reef success is largely dependent on the symbiosis between coral hosts and dinoflagellate symbionts belonging to the genus Symbiodinium. Elevated temperatures can result in the expulsion of Symbiodinium or loss of their photosynthetic pigments and is known as coral bleaching. It has been postulated that the expression of light-harvesting protein complexes (LHCs), which bind chlorophylls (chl) and carotenoids, are important in photobleaching. This study explored the effect a sixteen-day thermal stress (increasing daily from 25–34 °C) on integral LHC (chlorophyll a-chlorophyll c2-peridinin protein complex (acpPC)) gene expression in Symbiodinium within the coral Acropora aspera. Thermal stress leads to a decrease in Symbiodinium photosynthetic efficiency by day eight, while symbiont density was significantly lower on day sixteen. Over this time period, the gene expression of five SymbiodiniumacpPC genes was quantified. Three acpPC genes exhibited up-regulated expression when corals were exposed to temperatures above 31.5 °C (acpPCSym_1:1, day sixteen; acpPCSym_15, day twelve; and acpPCSym_18, day ten and day sixteen). In contrast, the expression of acpPCSym_5:1 and acpPCSym_10:1 was unchanged throughout the experiment. Interestingly, the three acpPC genes with increased expression cluster together in a phylogenetic analysis of light-harvesting complexes.
Image-based compound profiling reveals a dual inhibitor of tyrosine kinase and microtubule polymerization
Authors: Tanabe Kenji 
Published: April 2016

AbstractSmall-molecule compounds are widely used as biological research tools and therapeutic drugs. Therefore, uncovering novel targets of these compounds should provide insights that are valuable in both basic and clinical studies. I developed a method for image-based compound profiling by quantitating the effects of compounds on signal transduction and vesicle trafficking of epidermal growth factor receptor (EGFR). Using six signal transduction molecules and two markers of vesicle trafficking, 570 image features were obtained and subjected to multivariate analysis. Fourteen compounds that affected EGFR or its pathways were classified into four clusters, based on their phenotypic features. Surprisingly, one EGFR inhibitor (CAS 879127-07-8) was classified into the same cluster as nocodazole, a microtubule depolymerizer. In fact, this compound directly depolymerized microtubules. These results indicate that CAS 879127-07-8 could be used as a chemical probe to investigate both the EGFR pathway and microtubule dynamics. The image-based multivariate analysis developed herein has potential as a powerful tool for discovering unexpected drug properties.
Potential of the beneficial fungus Trichoderma to enhance ecosystem-service provision in the biofuel grass Miscanthus x giganteus in agriculture
Authors: Chirino-Valle Ivan , Kandula Diwakar , Littlejohn Chris , Hill Robert , Walker Mark , Shields Morgan , Cummings Nicholas , Hettiarachchi Dilani , Wratten Stephen 
Published: April 2016

AbstractThe sterile hybrid grass Miscanthus x giganteus (Mxg) can produce more than 30 t dry matter/ha/year. This biomass has a range of uses, including animal bedding and a source of heating fuel. The grass provides a wide range of other ecosystem services (ES), including shelter for crops and livestock, a refuge for beneficial arthropods, reptiles and earthworms and is an ideal cellulosic feedstock for liquid biofuels such as renewable (drop-in) diesel. In this study, the effects of different strains of the beneficial fungus Trichoderma on above- and below-ground biomass of Mxg were evaluated in glasshouse and field experiments, the latter on a commercial dairy farm over two years. Other ES benefits of Trichoderma measured in this study included enhanced leaf chlorophyll content as well as increased digestibility of the dried material for livestock. This study shows, for the first time for a biofuel feedstock plant, how Trichoderma can enhance productivity of such plants and complements other recent work on the wide-ranging provision of ES by this plant species.
A new type of power energy for accelerating chemical reactions: the nature of a microwave-driving force for accelerating chemical reactions
Authors: Zhou Jicheng , Xu Wentao , You Zhimin , Wang Zhe , Luo Yushang , Gao Lingfei , Yin Cheng , Peng Renjie , Lan Lixin 
Published: April 2016

AbstractThe use of microwave (MW) irradiation to increase the rate of chemical reactions has attracted much attention recently in nearly all fields of chemistry due to substantial enhancements in reaction rates. However, the intrinsic nature of the effects of MW irradiation on chemical reactions remains unclear. Herein, the highly effective conversion of NO and decomposition of H2S via MW catalysis were investigated. The temperature was decreased by several hundred degrees centigrade. Moreover, the apparent activation energy (Ea’) decreased substantially under MW irradiation. Importantly, for the first time, a model of the interactions between microwave electromagnetic waves and molecules is proposed to elucidate the intrinsic reason for the reduction in the Ea’ under MW irradiation and a formula for the quantitative estimation of the decrease in the Ea’ was determined. MW irradiation energy was partially transformed to reduce the Ea’ and MW irradiation is a new type of power energy for speeding up chemical reactions. The effect of MW irradiation on chemical reactions was determined. Our findings challenge both the classical view of MW irradiation as only a heating method and the controversial MW non-thermal effect and open a promising avenue for the development of novel MW catalytic reaction technology.
Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers
Authors: Zarzycki Piotr , Gilbert Benjamin 
Published: April 2016

AbstractWater diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.
Astrocytes regulate heterogeneity of presynaptic strengths in hippocampal networks
Authors: Letellier Mathieu , Park Yun Kyung , Chater Thomas E. , Chipman Peter H. , Gautam Sunita Ghimire , Oshima-Takago Tomoko , Goda Yukiko 
Published: April 2016

Significance
We addressed the basic mechanisms underlying synapse heterogeneity, and we identified a form of regulation that serves to increase the variations in the efficacy with which neurons communicate with each other through synapses. We demonstrate that this process requires astrocytes, which, previously, have been thought to play mostly a passive role in maintaining neuronal functions. The cellular mechanism that regulates synaptic efficacy requires astrocyte membrane depolarization, activation of astrocyte NMDA receptors, and astrocyte calcium signaling. The fundamental nature of the regulation is underscored by the preservation of the mechanism from acute brain slices down to dissociated cultures that lack the native topology of brain networks.
Can Weighted Useable Area Predict Flow Requirements of Drift‐Feeding Salmonids? Comparison with a Net Rate of Energy Intake Model Incorporating Drift–Flow Processes
Authors: Hayes John W. , Goodwin Eric , Shearer Karen A. , Hay Joe , Kelly Lon 
Published: April 2016

AbstractWe compared a process‐based invertebrate drift and drift‐feeding net rate of energy intake (NREI) model and a traditional hydraulic‐habitat model (using the RHYHABSIM [River Hydraulics and Habitat Simulation] software program) for predicting the flow requirements of 52‐cm Brown Trout Salmo trutta in a New Zealand river. Brown Trout abundance predicted by the NREI model for the constant drift concentration–flow scenarios were asymptotic or linear, depending on drift concentration, increasing through the mean annual low flow (MALF; 17 m3/s). However, drift concentration increased with flow, consistent with passive entrainment. The predicted fish abundance–flow relationship based on flow‐varying drift concentration increased logistically, and more steeply, with flow through the MALF and beyond. Predictions for the relationship between weighted useable area (WUA) and flow were made for three sets of drift‐feeding habitat suitability criteria (HSC) developed on three midsized and one large New Zealand river (flow at sampling was 2.8–4.6 m3/s and ~100 m3/s, respectively) and the South Platte River, Colorado (flow at sampling, 7–18 m3/s). The midsized‐river HSC ascribe lower suitability to water velocities > 0.6 m/s. They predicted WUA peaking at 10–11 m3/s, well below the MALF. The WUA–flow relationships for the two large‐river HSC were asymptotic at about 22 m3/s. Overall, WUA appears to underestimate the flow needs of drift‐feeding salmonids. The NREI model showed that assessing flow needs of drift‐feeding fish is more complex than interpreting a WUA–flow relationship based only on physical habitat suitability. The relationship between predicted fish abundance and flow is an emergent property of flow‐dependent drift‐foraging dynamics interacting with flow‐dependent drift concentration and drift flux, local depletion of drift by feeding fish, and flow‐related replenishment of drift from the bed and dispersion. It is time that the principles and predictions of drift–NREI models influence assessments of habitat capacity and instream flow needs of drift‐feeding fish.Received April 10, 2015; accepted November 10, 2015 Published online April 27, 2016
Maximum Likelihood Estimation of the Proportion of Hatchery‐Origin Fish on Spawning Grounds Using Coded Wire Tagging and Parentage‐Based Tagging
Authors: Hinrichsen Richard A. , Steele Craig A. , Ackerman Michael W. , Campbell Matthew R. , Narum Shawn R. , Hess Maureen A. , Young William P. , Shields Barbara A. , Maschhoff Brian L. 
Published: April 2016

AbstractFor salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery‐origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery‐ and natural‐origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage‐based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage‐based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of expected tag recoveries on precision, to simulated PBT data for fall Chinook Salmon spawning in the Hanford Reach of the Columbia River. Precision of p from maximum likelihood estimation increased with the expected number of tag recoveries in a carcass survey, whether CWTs or PBTs. In the South Fork Salmon River application, there were 340% more PBT recoveries than CWT recoveries, leading to greater precision in release‐specific values of p from maximum likelihood estimation. The maximum likelihood estimation procedure provides fisheries managers a method to design a tagging and sampling program aimed at estimating p, a valuable measure of the potential for interaction of wild‐ and hatchery‐origin fish on the spawning grounds. To design a program for estimating p, we recommend selecting a target level of precision and then choosing a tagging fraction and sampling rate that delivers that precision in the most cost‐effective way.Received August 21, 2015; accepted January 19, 2016 Published online April 27, 2016
Modelling of 3D fields due to ferritic inserts and test blanket modules in toroidal geometry at ITER
Authors: Liu Yueqiang , Äkäslompolo Simppa , Cavinato Mario , Koechl Florian , Kurki-Suonio Taina , Li Li , Parail Vassili , Saibene Gabriella , Särkimäki Konsta , Sipilä Seppo , Varje Jari 
Published: April 2016

Abstract
Computations in toroidal geometry are systematically performed for the plasma response to 3D magnetic perturbations produced by ferritic inserts (FIs) and test blanket modules (TBMs) for four ITER plasma scenarios: the 15 MA baseline, the 12.5 MA hybrid, the 9 MA steady state, and the 7.5 MA half-field helium plasma. Due to the broad toroidal spectrum of the FI and TBM fields, the plasma response for all the n  =  1–6 field components are computed and compared. The plasma response is found to be weak for the high-n (n  >  4) components. The response is not globally sensitive to the toroidal plasma flow speed, as long as the latter is not reduced by an order of magnitude. This is essentially due to the strong screening effect occurring at a finite flow, as predicted for ITER plasmas. The ITER error field correction coils (EFCC) are used to compensate the n  =  1 field errors produced by FIs and TBMs for the baseline scenario for the purpose of avoiding mode locking. It is found that the middle row of the EFCC, with a suitable toroidal phase for the coil current, can provide the best correction of these field errors, according to various optimisation criteria. On the other hand, even without correction, it is predicted that these n  =  1 field errors will not cause substantial flow damping for the 15 MA baseline scenario.
On the fusion triple product and fusion power gain of tokamak pilot plants and reactors
Authors: Costley A.E. 
Published: April 2016

Abstract
The energy confinement time of tokamak plasmas scales positively with plasma size and so it is generally expected that the fusion triple product, nTτ
E, will also increase with size, and this has been part of the motivation for building devices of increasing size including ITER. Here n, T, and τ
E are the ion density, ion temperature and energy confinement time respectively. However, tokamak plasmas are subject to operational limits and two important limits are a density limit and a beta limit. We show that when these limits are taken into account, nTτ
E becomes almost independent of size; rather it depends mainly on the fusion power, P
fus. In consequence, the fusion power gain, Q
fus, a parameter closely linked to nTτ
E is also independent of size. Hence, P
fus and Q
fus, two parameters of critical importance in reactor design, are actually tightly coupled. Further, we find that nTτ
E is inversely dependent on the normalised beta, β
N; an unexpected result that tends to favour lower power reactors. Our findings imply that the minimum power to achieve fusion reactor conditions is driven mainly by physics considerations, especially energy confinement, while the minimum device size is driven by technology and engineering considerations. Through dedicated R&D and parallel developments in other fields, the technology and engineering aspects are evolving in a direction to make smaller devices feasible.
Soluble Tumor Necrosis Factor-α Receptor 2 in Urine Is a Potential Biomarker for Noninvasive Diagnosis of Malaria During Pregnancy
Authors: Tassi Yunga Samuel , Thévenon Audrey Davidson , Leke Rose Gana Fomban , Taylor Diane Wallace 
Published: April 2016

AbstractBackground.  During pregnancy, the placenta is inaccessible for diagnosis of placental malaria (PM), but soluble tumor necrosis factor-α receptors (sTNFR) are elevated in the plasma of women with PM.Methods.  In this study, sTNFR-1 and sTNFR-2 were quantified in urine of pregnant and nonpregnant Cameroonian women who were positive or negative for malaria by blood-smear microscopy.Results.  We found that levels of both sTNFR in urine were higher in pregnant compared with nonpregnant women, but malaria-positive pregnant women excreted substantially more sTNFR-1 (P = .005) and sTNFR-2 (P &lt; .001) than malaria-negative pregnant women. The amount of sTNFR-1(rs = 0.784, P &lt; .001) and sTNFR-2 (rs = 0.816, P &lt; .001) in urine correlated with parasitemia, even in afebrile pregnant women. Urine sTNFR-2 predicted maternal malaria with an area under curve of 0.892 (95% confidence interval, .787–.898). At cutoff concentrations of 9.8 ng and 13.6 ng of sTNFR-2 per mL urine, the sensitivity/specificity were 82.6%/87.0% and 78.3%/95.7%, respectively.Conclusions.  The sTNFR-2 in noninvasive urine samples may be useful for diagnosis of malaria during pregnancy.
Occurrence of Phytophthora Species in Commercial Nursery Production
Authors: Junker Corina , Goff Patrick , Wagner Stefan , Werres Sabine 
Published: April 2016

Two commercial woody ornamental nurseries were sampled for the presence of Phytophthora species over a period of three years between 2011 and 2014. The samples were taken every two months at different propagation (greenhouses, plastic tunnels) and cultivation (container stands) areas as well as from nearby pathways and from a water recycling system with a slow sand filter. Furthermore, different materials like soil, substrates, residues, wind-carried leaves, water and sediment were sampled. In total, 12 known Phytophthora species could be detected. Further, three isolates did not match any of the known species. Phytophthora ramorum, P. gonapodyides, and P. plurivora were the species with the highest detection rates. Phytophthora ramorum could be detected during all seasons of the year. In total, the puddles on the pathways had the highest percentage of positive detections. Residues, wind-carried leaves and water and sediment from the water runoffs were also good places for Phytophthora survival. In both nurseries, the plant samples showed very low infection rates. Ideas for surveys and management are discussed. Accepted for publication 14 March 2016. Published 11 April 2016.