bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exclusive transmission of the embryonic stem cell‐derived genome through the mouse germline
Authors: Koentgen Frank , Lin Jiangwei , Katidou Markella , Chang Isabelle , Khan Mona , Watts Jacqui , Mombaerts Peter 
Published: March 2016

SummaryGene targeting in embryonic stem (ES) cells remains best practice for introducing complex mutations into the mouse germline. One aspect in this multistep process that has not been streamlined with regard to the logistics and ethics of mouse breeding is the efficiency of germline transmission: the transmission of the ES cell‐derived genome through the germline of chimeras to their offspring. A method whereby male chimeras transmit exclusively the genome of the injected ES cells to their offspring has been developed. The new technology, referred to as goGermline, entails injecting ES cells into blastocysts produced by superovulated homozygous Tsc22d3 floxed females mated with homozygous ROSA26‐Cre males. This cross produces males that are sterile due to a complete cell‐autonomous defect in spermatogenesis. The resulting male chimeras can be sterile but when fertile, they transmit the ES cell‐derived genome to 100% of their offspring. The method was validated extensively and in two laboratories for gene‐targeted ES clones that were derived from the commonly used parental ES cell lines Bruce4, E14, and JM8A3. The complete elimination of the collateral birth of undesired, non‐ES cell‐derived offspring in goGermline technology fulfills the reduction imperative of the 3R principle of humane experimental technique with animals. genesis 54:326–333, 2016. © 2016 The Authors. Genesis Published by Wiley Periodicals, Inc.
Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities
Authors: Saito Victor S. , Cianciaruso Marcus Vinicius , Siqueira Tadeu , Fonseca‐Gessner Alaide A. , Pavoine Sandrine 
Published: March 2016

AbstractThe assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.
The land‐potential knowledge system (landpks): mobile apps and collaboration for optimizing climate change investments
Authors: Herrick Jeffrey E. , Beh Adam , Barrios Edmundo , Bouvier Ioana , Coetzee Marina , Dent David , Elias Emile , Hengl Tomislav , Karl Jason W. , Liniger Hanspeter , Matuszak John , Neff Jason C. , Ndungu Lilian Wangui , Obersteiner Michael , Shepherd Keith D. , Urama Kevin C. , Bosch Rik , Webb Nicholas P. 
Published: March 2016

Abstract
Massive investments in climate change mitigation and adaptation are projected during coming decades. Many of these investments will seek to modify how land is managed. The return on both types of investments can be increased through an understanding of land potential: the potential of the land to support primary production and ecosystem services, and its resilience. A Land‐Potential Knowledge System (LandPKS) is being developed and implemented to provide individual users with point‐based estimates of land potential based on the integration of simple, geo‐tagged user inputs with cloud‐based information and knowledge. This system will rely on mobile phones for knowledge and information exchange, and use cloud computing to integrate, interpret, and access relevant knowledge and information, including local knowledge about land with similar potential. The system will initially provide management options based on long‐term land potential, which depends on climate, topography, and relatively static soil properties, such as soil texture, depth, and mineralogy. Future modules will provide more specific management information based on the status of relatively dynamic soil properties such as organic matter and nutrient content, and of weather. The paper includes a discussion of how this system can be used to help distinguish between meteorological and edaphic drought.
Assessing impact of land use and climate change on regulating ecosystem services in the czech republic
Authors: Krkoška lorencová Eliška , Harmáčková Zuzana V. , Landová Lucie , Pártl Adam , Vačkář David 
Published: March 2016

Abstract

Ecosystem services, defined as benefits provided by ecosystem functioning to society, are essential to human well‐being. Due to global environmental change and related anthropogenic drivers, ecosystems are often degraded, which hinders the delivery of ecosystem services. This study aims to quantify the impacts of land use and climate change on two regulating ecosystem services—carbon sequestration and water purification in terms of nitrogen retention in the Czech Republic. While employing approaches of scenarios and modeling, we illustrate current and potential future status of these ecosystem services. Our results show that among the ecosystem change drivers, one of the dominant domestic land‐use change of (Business‐As‐Might‐Be‐Usual) scenario is change of arable land and grassland to forest area that increases by 4.5% in 2080 compared to 2000. The results of ecosystem service modeling based on scenario for the years 2050 and 2080 indicate that the highest yearly carbon sequestration rate occurred in 2000–2050, reaching 640 GgC·yr
−1
, 2000–2080 shows decline in this regulating service by 16%. Average nitrogen leaching to water streams reached 0.75 kgN·ha
−1
·yr
−1
for in 2050 scenario and 0.80 kgN·ha
−1
·yr
−1
for in 2080 scenario as a result of decreasing nitrogen load, which suggested a decrease in nitrogen pollution compared to 2000. Since ecosystem services have not been extensively mainstreamed into research and policies in eastern European countries, we aim to contribute to improvement of knowledge on current status and potential future pathways of the provision of regulating ecosystem services in the Czech Republic.
Reef to island sediment connections on a Maldivian carbonate platform: using benthic ecology and biosedimentary depositional facies to examine island‐building potential
Authors: Morgan Kyle M. , Kench Paul S. 
Published: March 2016

AbstractReef islands are low‐lying accumulations of unconsolidated sediment formed from the skeletal remains of carbonate‐producing reef organisms and are therefore perceived as highly vulnerable to environmental change. However, basic elements of island composition are not well described and given their high inter‐ and intra‐basinal variability a better understanding of reef and island sedimentary environments (and the connections between them) are needed to predict future morphological response. Here, we use detailed ecological and sedimentological datasets to delineate key sediment production zones and biosedimentary depositional facies across the surface of Vabbinfaru platform, Maldives. Field measurements of platform hydrodynamics are applied to sedimentary deposits to determine the potential mobility of grains and identify transport pathways. Carbonate production was dominated by coral framework (mean: 52%) within a narrow zone on the outer reef rim (22% of platform area) resulting in coral‐rich detrital sediments (reef: 51%, island: 64%) that closely resemble living assemblages. The net transfer of sediment occurred lagoonward by wave‐driven processes leading to a decrease in grain size towards the island (R2 = 0.502) which acts as a major control on depositional facies development within the lagoon. Island sediments were distinct from reefal deposits, comprising a restricted suite of durable sands (mean: 1.34ϕ) throughout long‐term development. Our findings suggest that the production, breakdown and redistribution of coral‐derived sediment by platform currents is fundamental to future island stability at Vabbinfaru, and although alterations away from current ecological states may reduce sediment supply, the timescales over which island morphological response will occur depends upon phase lags between initial coral mortality and the conversion of this material into island‐grade sand. Copyright © 2016 John Wiley & Sons, Ltd.
A variable‐fidelity aerodynamic model using proper orthogonal decomposition
Authors: Mifsud M. J. , MacManus D. G. , Shaw S.T. 
Published: March 2016

SummaryA variable‐fidelity aerodynamic model based on proper orthogonal decomposition (POD) of an ensemble of computational fluid dynamics (CFD) solutions at different parameters is presented in this article. The ensemble of CFD solutions consists of two subsets of numerical solutions or snapshots computed at two different nominal orders of accuracy or discretization. These two subsets are referred to as the low‐fidelity and high‐fidelity solutions or data, whereby the low fidelity corresponds with computations made at the lower nominal order of accuracy or coarser discretization. In this model, the relatively inexpensive low‐fidelity data and the more accurate but expensive high‐fidelity data are considered altogether to devise an efficient prediction methodology involving as few high‐fidelity analyses as possible, while obtaining the desired level of detail and accuracy. The POD of this set of variable‐fidelity data produces an optimal linear set of orthogonal basis vectors that best describe the ensemble of numerical solutions altogether. These solutions are projected onto this set of basis vectors to provide a finite set of scalar coefficients that represent either the low‐fidelity or high‐fidelity solutions. Subsequently, a global response surface is constructed through this set of projection coefficients for each basis vector, which allows predictions to be made at parameter combinations not in the original set of observations. This approach is used to predict supersonic flow over a slender configuration using Navier–Stokes solutions that are computed at two different levels of nominal accuracy as the low‐fidelity and high‐fidelity solutions. The numerical examples show that the proposed model is efficient and sufficiently accurate. Copyright © 2016 John Wiley & Sons, Ltd.
Effect of electro‐activated brine solution on the migration of metallic ions from the cans to the product in sterilized canned sweet corn
Authors: Liato Viacheslav , Labrie Steve , Benali Marzouk , Aider Mohammed 
Published: March 2016

AbstractTinplate cans were used to study if electro‐activated brine solution (EAS) is more corrosive than conventional one by ICP analysis. The results showed different effects of EAS on cans, alone or filled with product. Acidic EAS (pH 2–3) and Redox +900 to +1200 mV highly reacted with the cans. The concentrations of Zn, Fe, and Cu in the solution were 0.028, 28.81, and 0.022 ppm, respectively. No Sn migration was observed in this case. When neutral or acidic chlorine‐free EAS was used, no significant difference was observed in comparison with the corrosivity of standard NaCl brine. Alkaline EAS with pH>10 and negative E (≤−966 mV) did not affect Zn, Fe, and Cu migration. However, it affected tin migration. Nevertheless, it is important to mention that even if some corrosion was observed, it was in the limit of the permitted level of concentration when the cans were filled with a product.
Excision margins and sentinel lymph node status as prognostic factors in thick melanoma of the head and neck: A retrospective analysis
Authors: Ruskin Olivia , Sanelli Alexandra , Herschtal Alan , Webb Angela , Dixon Ben , Pohl Miklos , Donahoe Simon , Spillane John , Henderson Michael A. , Gyorki David E. 
Published: March 2016

ABSTRACTBackgroundRecommended margins for thick cutaneous melanoma (Breslow thickness >4 mm; T4) have decreased over recent decades. Optimal margins and the role of sentinel node biopsy (SNB) in thick head and neck melanoma remain controversial.MethodsA single‐center review was conducted of patients treated between 2002 and 2012 assessing the impact of excision margins and sentinel lymph node status on locoregional recurrence and melanoma‐specific survival (MSS).ResultsOne hundred eight patients were identified. Median age was 71.1 years and median Breslow thickness was 6.0 mm. Median follow‐up was 40 months. Locoregional recurrence occurred in 27% and there was no significant reduction in recurrence with margins ≥2 cm (p = .17). Increasing margins did not improve survival (p = .58). Fifty‐nine patients (55%) underwent SNB, of which 27% were positive. There was a trend toward longer survival for patients who were sentinel lymph node‐negative (p = .097).ConclusionWider margins do not significantly improve locoregional recurrence or MSS. Sentinel lymph node involvement reflects a poor prognosis. © 2016 Wiley Periodicals, Inc. Head Neck 38: 1373–1379, 2016
Ice‐jam flood risk assessment and mapping
Authors: Lindenschmidt Karl‐Erich , Das Apurba , Rokaya Prabin , Chu Thuan 
Published: March 2016

AbstractIn northern regions, river ice‐ jam flooding can be more severe than open‐water flooding causing property and infrastructure damages, loss of human life and adverse impacts on aquatic ecosystems. Very little has been performed to assess the risk induced by ice‐related floods because most risk assessments are limited to open‐water floods. The specific objective of this study is to incorporate ice‐jam numerical modelling tools (e.g. RIVICE, Monte‐Carlo simulation) into flood hazard and risk assessment along the Peace River at the Town of Peace River (TPR) in Alberta, Canada. Adequate historical data for different ice‐jam and open‐water flooding events were available for this study site and were useful in developing ice‐affected stage‐frequency curves. These curves were then applied to calibrate a numerical hydraulic model, which simulated different ice jams and flood scenarios along the Peace River at the TPR. A Monte‐Carlo analysis was then carried out to acquire an ensemble of water level profiles to determine the 1 : 100‐year and 1 : 200‐year annual exceedance probability flood stages for the TPR. These flood stages were then used to map flood hazard and vulnerability of the TPR. Finally, the flood risk for a 200‐year return period was calculated to be an average of $32/m2/a ($/m2/a corresponds to a unit of annual expected damages or risk). Copyright © 2016 John Wiley & Sons, Ltd.
The Novel NF‐κB Inhibitor, MTI‐II Peptide Anti‐Inflammatory Drug, Suppresses Inflammatory Responses in Odontoblast‐Like Cells
Authors: Nakayama Kouhei , Hirata‐Tsuchiya Shizu , Okamoto Kazuki , Morotomi Takahiko , Jimi Eijiro , Kitamura Chiaki 
Published: March 2016

ABSTRACTRegulation of inflammation is important for pulp wound healing, including protective responses by odontoblast‐like cells. However, methods for directly regulating pulp inflammation have not yet been described. The inflammatory response is mediated by a transcription factor, nuclear factor‐κB (NF‐κB), which activates inflammatory cytokines including tumor necrosis factor (TNF)‐α. Macromolecular translocation inhibitor II (MTI‐II) was previously demonstrated as an enhancer of the transcriptional activity of glucocorticoid‐bound glucocorticoid receptor. Recently, a MTI‐II peptide anti‐inflammatory drug (MPAID) was bioengineered from the structure of MTI‐II as an inhibitor of NF‐κB transactivation. Here, we examined the effects of MTI‐II and MPAID on the inflammatory responses of odontoblast‐like cells. TNF‐α inhibited alkaline phosphatase (ALP) activity, a marker of odontoblast/osteogenic differentiation, and induced NF‐κB transcriptional activity in KN‐3 cells, which are odontoblast‐like cells derived from dental papilla cells of rat incisors, without affecting their viability. Exogenous expression of MTI‐II suppressed the NF‐κB transcriptional activity induced by TNF‐α or overexpression of p65 (a main subunit of NF‐κB) in the cells, whereas it failed to inhibit degradation of IκBα and nuclear translocation of p65 after TNF‐α treatment, suggesting that MTI‐II inhibits NF‐κB transcriptional activity by modulating the duration of DNA binding by p65. MPAID also inhibited TNF‐α‐induced NF‐κB transcriptional activity, the mRNA expression of IL‐6 and IL‐8, and IL‐6 production. Furthermore, pretreatment of the cells with MPAID restored the inhibitory effect of TNF‐α on ALP activity. These results suggest that MPAID may be able to regulate the inflammatory response and maintain a protective response of dental pulp. J. Cell. Biochem. 117: 2552–2558, 2016. © 2016 Wiley Periodicals, Inc.
HMGB1 Osteo‐Modulatory Action on Osteosarcoma SaOS‐2 Cell Line: An Integrated Study From Biochemical and ‐Omics Approaches
Authors: Martinotti Simona , Patrone Mauro , Manfredi Marcello , Gosetti Fabio , Pedrazzi Marco , Marengo Emilio , Ranzato Elia 
Published: March 2016

ABSTRACTHigh mobility group box protein‐1 (HMGB1) is released from cells under various pathological conditions and it plays a pivotal role as an alarmin signaling tissue damage. Little is known about the impact of HMGB1 in bone repair and remodeling. To this aim, we focused on HMGB1‐induced effects on the in vitro osteoblast model SaOS‐2. Cell proliferation was stimulated with a maximum at concentration of 2.5 nM, and such a dose also stimulated cell migration and scratch wound healing. We then characterized the modulatory effect of HMGB1 on bone biology, by using osteogenesis/mineralization assays, a PCR array, and the analysis of a series of osteogenic markers. We performed also a proteomic screening using SWATH‐MS on SaOS‐2 cell exposed to HMGB1 and we provide evidence for proteins modulated in HMGB1 exposed cells. Taken together, our data demonstrate that SaOS‐2 cell proliferation, migration, and osteogenic differentiation were increased by HMGB1. We, therefore, propose that HMGB1 could be a potent bone‐remodeling signal but the physiological meaning of this property remains to be more ascertained. J. Cell. Biochem. 117: 2559–2569, 2016. © 2016 Wiley Periodicals, Inc.
Atomic force microscopy as a tool to study the adsorption of DNA onto lipid interfaces
Authors: Luque‐Caballero Germán , Maldonado‐Valderrama Julia , Quesada‐Pérez Manuel , Martín‐Molina Alberto 
Published: March 2016

ABSTRACTThe Atomic Force Microscopy (AFM) technique appears as a central tool for the characterization of DNA adsorption onto lipid interfaces. Regardless of the huge number of surveys devoted to this issue, there are still fascinating phenomena in this field that have not been explored in detail by AFM. For instance, adsorption of DNA onto like‐charged lipid surfaces mediated by cations is still not fully understood even though it is gaining popularity nowadays in gene therapy and nanotechnology. Studies related to the complexation of DNA with anionic lipids as a non‐viral gene delivery vehicle as well as the formation of self‐assembled nanoscale DNA constructs (DNA origami) are two of the most attractive systems. Unfortunately, molecular mechanisms underlying the adsorption of DNA onto anionic lipid interfaces remain unclear so far. In view of that, AFM becomes an appropriate technique to provide valuable information to understand the adsorption of DNA to anionic lipid surfaces. As a second part of this review we provide an illustrative example of application of the AFM technique to probe the DNA adsorption onto a model lipid monolayer negatively charged. Microsc. Res. Tech. 80:11–17, 2017. © 2016 Wiley Periodicals, Inc.
Comparative study on fermentation performance in the genome shuffled Candida versatilis and wild‐type salt tolerant yeast strain
Authors: Qi Wei , Guo Hong‐Lian , Wang Chun‐Ling , Hou Li‐Hua , Cao Xiao‐Hong , Liu Jin‐Fu , Lu Fu‐Ping 
Published: March 2016

AbstractBACKGROUNDThe fermentation performance of a genome‐shuffled strain of Candida versatilis S3‐5, isolated for improved tolerance to salt, and wild‐type (WT) strain were analysed. The fermentation parameters, such as growth, reducing sugar, ethanol, organic acids and volatile compounds, were detected during soy sauce fermentation process.RESULTSThe results showed that ethanol produced by the genome shuffled strain S3‐5 was increasing at a faster rate and to a greater extent than WT. At the end of the fermentation, malic acid, citric acid and succinic acid formed in tricarboxylic acid cycle after S3‐5 treatment elevated by 39.20%, 6.85% and 17.09% compared to WT, respectively. Moreover, flavour compounds such as phenethyl acetate, ethyl vanillate, ethyl acetate, isoamyl acetate, ethyl myristate, ethyl pentadecanoate, ethyl palmitate and phenylacetaldehyde produced by S3‐5 were 2.26, 2.12, 2.87, 34.41, 6.32, 13.64, 2.23 and 78.85 times as compared to WT.CONCLUSIONSS3‐5 exhibited enhanced metabolic ability as compared to the wild‐type strain, improved conversion of sugars to ethanol, metabolism of organic acid and formation of volatile compounds, especially esters, Moreover, S3‐5 might be an ester‐flavour type salt‐tolerant yeast. © 2016 Society of Chemical Industry