bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of direct and counter‐current flow‐through delignification on enzymatic hydrolysis of wheat straw, and flow limits due to compressibility
Authors: Pihlajaniemi Ville , Sipponen Mika Henrikki , Pastinen Ossi , Nyyssölä Antti , Laakso Simo 
Published: June 2016

ABSTRACTThis article compares the processes for wheat straw lignocellulose fractionation by percolation, counter‐current progressing batch percolation and batch reaction at low NaOH‐loadings (3–6% of DM). The flow‐through processes were found to improve delignification and subsequent enzymatic saccharification, reduce NaOH‐consumption and allow reduction of thermal severity, whereas hemicellulose dissolution was unaffected. However, contrary to previous expectations, a counter‐current process did not provide additional benefits to regular percolation. The compressibility and flow properties of a straw bed were determined and used for simulation of the packing density profile and dynamic pressure in an industrial scale column. After dissolution of 30% of the straw DM by delignification, a pressure drop above 100 kPa m−1 led to clogging of the flow due to compaction of straw. Accordingly, the maximum applicable feed pressure and volumetric straw throughput was determined as a function of column height, indicating that a 10 m column can be operated at a maximum feed pressure of 530 kPa, corresponding to an operation time of 50 min and a throughput of 163 kg m−3 h−1. Biotechnol. Bioeng. 2016;113: 2605–2613. © 2016 Wiley Periodicals, Inc.
Insight into the mechanisms of enhanced retinal transduction by the engineered AAV2 capsid variant ‐7m8
Authors: Khabou Hanen , Desrosiers Mélissa , Winckler Céline , Fouquet Stéphane , Auregan Gwenaëlle , Bemelmans Alexis‐Pierre , Sahel José‐Alain , Dalkara Deniz 
Published: June 2016

ABSTRACTRecently, we described a modified AAV2 vector—AAV2‐7m8—having a capsid‐displayed peptide insertion of 10 amino acids with enhanced retinal transduction properties. The insertion of the peptide referred to as 7m8 is responsible for high‐level gene delivery into deep layers of the retina when virus is delivered into the eye's vitreous. Here, we further characterize AAV2‐7m8 mediated gene delivery to neural tissue and investigate the mechanisms by which the inserted peptide provides better transduction away from the injection site. First, in order to understand if the peptide exerts its effect on its own or in conjunction with the neighboring amino acids, we inserted the 7m8 peptide at equivalent positions on three other AAV capsids, AAV5, AAV8, and AAV9, and evaluated its effect on their infectivity. Intravitreal delivery of these peptide insertion vectors revealed that only AAV9 benefited from 7m8 insertion in the context of the retina. We then investigated AAV2‐7m8 and AAV9‐7m8 properties in the brain, to better evaluate the spread and efficacy of viral transduction in view of the peptide insertion. While 7m8 insertion led to higher intensity gene expression, the spread of gene expression remained unchanged compared to the parental serotypes. Our results indicate that the 7m8 peptide insertion acts by increasing efficacy of cellular entry, with little effect on the spread of viral particles in neural tissue. The effects of peptide insertion are capsid and tissue dependent, highlighting the importance of the microenvironment in gene delivery using AAV. Biotechnol. Bioeng. 2016;113: 2712–2724. © 2016 Wiley Periodicals, Inc.
Small files storing and computing optimization in Hadoop parallel rendering
Authors: Zhang Yizhi , Zhu Zhengdong , Cui Honglin , Dong Xiaoshe , Chen Heng 
Published: June 2016

SummaryHadoop framework has been widely used in animation industries to build a large scale, high performance parallel rendering system. However, Hadoop Distributed File System (HDFS) and the MapReduce programming model are designed to manage large files and suffer performance penalty while rendering and storing small files in a rendering system. Therefore, a method that merges small files based on two intelligent algorithms is proposed to solve the problem. The method uses Particle Swarm Optimization (PSO) to select the optimal merge values for multiple sets of scenes and then uses Support Vector Machine (SVM) to generate a general SVM model which can be used to get the optimal merge value for any scene, by mainly considering the rendering time, memory limitation and other indicators. Then, the method takes advantage of frame‐to‐frame coherence to merge files in the same scene in an interval‐based way with the optimal merge value. Finally, the proposed method is compared with the naive method under three different render scenes. Experimental results show that the proposed method significantly reduces the number of small files and render tasks, and improves the storage efficiency and computing efficiency. Copyright © 2016 John Wiley & Sons, Ltd.
Collaborating CPU and GPU for the electromagnetic simulations with the FDTD algorithm
Authors: Xu Ying , Ma Huimin , Jiang Rongling 
Published: June 2016

SummaryThe co‐processors with the capability of powerful floating‐point operations have been used to study the electromagnetic (EM) simulations with the finite‐difference time‐domain (FDTD) method, which usually consumes huge computational resources. This work studied the implementation and optimization of the three‐dimensional FDTD algorithm with the uniaxial perfectly matched layer boundary conditions on GPU clusters. In this study, CPUs and GPUs collaborate to solve the different parts of the computation domain concurrently, and a set of techniques are used to optimize the execution efficiency of GPUs, such as the use of GPU texture memory, the pinned host memory, and the asynchronization of data transfer between CPU and GPU. For the CPU‐GPU collaborative mode, the problem size solved is not limited by the size of global memory on GPU because the computational capability of CPU is also used for the calculation of EM field. To keep the load balance between CPU and GPU, 85% of the computation load is assigned to GPU for NVIDIA Tesla K40m, and the collaborative efficiency is found to be less than 75%. Copyright © 2016 John Wiley & Sons, Ltd.
A high‐performance computing framework for Monte Carlo ocean color simulations
Authors: Kajiyama Tamito , D'Alimonte Davide , Cunha José C. 
Published: June 2016

SummaryThis paper presents a high‐performance computing (HPC) framework for Monte Carlo (MC) simulations in the ocean color (OC) application domain. The objective is to optimize a parallel MC radiative transfer code named MOX, developed by the authors to create a virtual marine environment for investigating the quality of OC data products derived from in situ measurements of in‐water radiometric quantities. A consolidated set of solutions for performance modeling, prediction, and optimization is implemented to enhance the efficiency of MC OC simulations on HPC run‐time infrastructures. HPC, machine learning, and adaptive computing techniques are applied taking into account a clear separation and systematic treatment of accuracy and precision requirements for large‐scale MC OC simulations. The added value of the work is the integration of computational methods and tools for MC OC simulations in the form of an HPC‐oriented problem‐solving environment specifically tailored to investigate data acquisition and reduction methods for OC field measurements. Study results highlight the benefit of close collaboration between HPC and application domain researchers to improve the efficiency and flexibility of computer simulations in the marine optics application domain. © 2016 The Authors. Concurrency and Computation: Practice and Experience Published by John Wiley & Sons, Ltd.
Hadoop‐based replica exchange over heterogeneous distributed cyberinfrastructures
Authors: Platania Richard , Shams Shayan , Chiu Chui‐Hui , Kim Nayong , Kim Joohyun , Park Seung‐Jong 
Published: June 2016

SummaryWe present Hadoop‐based replica exchange (HaRE), a Hadoop‐based implementation of the replica exchange scheme developed primarily for replica exchange statistical temperature molecular dynamics, an example of a large‐scale, advanced sampling molecular dynamics simulation. By using Hadoop as a framework and the MapReduce model for driving replica exchange, an efficient task‐level parallelism is introduced to replica exchange statistical temperature molecular dynamics simulations. In order to demonstrate this, we investigate the performance of our application over various distributed cyberinfrastructures (DCI), including several high‐performance computing systems, our cyberinfrastructure for reconfigurable optical networks testbed, the global environment for network innovations testbed, and the CloudLab testbed. Scalability performance analysis is shown in terms of scale‐out and scale‐up over a single high‐performance computing cluster, EC2, and CloudLab and scale‐across with cyberinfrastructure for reconfigurable optical networks and global environment for network innovations. As a result, we demonstrate that HaRE is capable of efficient execution over both homogeneous and heterogeneous DCI of varying size and configuration. Contributing factors to performance are discussed in order to provide insight towards the effects of computing environment on the execution of HaRE. With these contributions, we propose that similar loosely coupled scientific applications can also take advantage of the scalable, task‐level parallelism Hadoop MapReduce provides over various DCI. Copyright © 2016 John Wiley & Sons, Ltd.
Integrity as a service for replicated data on the cloud
Authors: Abo‐alian Alshaimaa , Badr Nagwa L. , Tolba M. F. 
Published: June 2016

SummaryWith the proliferation of cloud storage services, data integrity verification becomes increasingly significant in order to guarantee the availability and correctness of the outsourced data. Recently, many auditing schemes have been proposed to verify data integrity without possessing or downloading the outsourced data files. However, such schemes in existence assume that there is a single data owner that can update the file and compute the integrity tags. They do not consider the efficiency of user revocation when auditing multi‐owner data in the cloud. In addition, existing schemes only support dynamic data operations over fixed‐size and single‐copy data blocks. Thus, every small update may need updating the tags for all file blocks in all replicas, which in turn causes higher storage and communication overheads.This paper proposes a public and dynamic auditing scheme that supports fully dynamic data operations over variable‐size data blocks for replicated and multi‐owner cloud storage. Moreover, the proposed scheme can also support efficient user revocation. By supporting batch auditing, the proposed scheme can handle multiple auditing tasks simultaneously and divide an auditing task into multiple sub‐tasks in order to increase the detection probability. Experimental results prove the effectiveness and efficiency of the proposed system. Copyright © 2016 John Wiley & Sons, Ltd.
Why do we build check dams in Alpine streams? An historical perspective from the French experience
Authors: Piton Guillaume , Carladous Simon , Recking Alain , Tacnet Jean Marc , Liébault Frédéric , Kuss Damien , Quefféléan Yann , Marco Olivier 
Published: June 2016

AbstractFor more than 150 years, humans have tried to limit the geomorphic activity of mountain streams, and the related damage, using torrent control works. Check dams are likely the most emblematic civil engineering structures used in soil conservation programs. Modern mountain societies have inherited thousands of these structures built in upland gullies and streams. To help define their effectiveness and decisions concerning their maintenance or new project designs, a clear understanding of potential effects of check dams on river systems, i.e. their functions, is first needed. The next steps concern quantitative assessments of each function on the flood features and combination of all effects. The present understanding of these sometimes old structures' functions can be complicated because the societal and environmental contexts in which the original structures were built may have changed. To bridge this gap, this paper traces the purposes for which check dams were built, through a detailed analysis of French archives. We first analyze chronologically how each function was theorized and applied in the field. In the nineteenth century, engineers developed a thorough empirical and conceptual knowledge of mountain soil erosion, torrential geomorphology, and sediment transport processes as well as check dam interactions with these natural processes. The second part of this paper synthesizes conceptual descriptions of the check dams' functions, in the light of more than 150 years of experience, with their implication on the features of the structures. The French experience is compared to other countries' pioneering works. Finally, the next steps and remaining research challenges toward a comprehensive analysis of check dams' efficiency in torrent hazard mitigation are presented. This analysis is proposed to remind how, conceptually, check dams may influence geomorphic systems, bearing in mind the knowledge represented in pioneer guidelines and recent works on the subject. Copyright © 2016 John Wiley & Sons, Ltd.
Controls on Holocene denudation rates in mountainous environments under Mediterranean climate
Authors: Molliex S. , Jouet G. , Freslon N. , Bourlès D. L. , Authemayou C. , Moreau J. , Rabineau M. 
Published: June 2016

AbstractThe Mediterranean domain is characterized by a specific climate resulting from the close interplay between atmospheric and marine processes and strongly differentiated regional topographies. Corsica Island, a mountainous area located in the western part of the Mediterranean Sea is particularly suitable to quantify regional denudation rates in the framework of a source‐to‐sink approach. Indeed, fluvial sedimentation in East‐Corsica margin is almost exclusively limited to its alluvial plain and offshore domain and its basement is mainly constituted of quartz‐rich crystalline rocks allowing cosmogenic nuclide 10Be measurements. In this paper, Holocene denudation rates of catchments from the eastern part of the island of Corsica are quantified relying on in situ produced 10Be concentrations in stream sediments and interpreted in an approach including quantitative geomorphology, rock strength measurement (with a Schmidt Hammer) and vegetation cover distribution. Calculated denudation rates range from 15 to 95 mm ka‐1. When compared with rates from similar geomorphic domains experiencing a different climate setting, such as the foreland of the northern European Alps, they appear quite low and temporally stable. At the first order, they better correlate with rock strength and vegetation cover than with morphometric indexes. Spatial distribution of the vegetation is controlled by morpho‐climatic parameters including sun exposure and the direction of the main wet wind, so‐called ‘Libecciu’. This distribution, as well as the basement rock strength seems to play a significant role in the denudation distribution. We thus suggest that the landscape reached a geomorphic steady‐state due to the specific Mediterranean climate and that Holocene denudation rates are mainly sustained by weathering processes, through the amount of regolith formation, rather than being transport‐limited. Al/K measurements used as a proxy to infer present‐day catchment‐wide chemical weathering patterns might support this assumption. Copyright © 2016 John Wiley & Sons, Ltd.
Transpiration from three dominant shrub species in a desert‐oasis ecotone of arid regions of Northwestern China
Authors: Ji Xibin , Zhao Wenzhi , Kang Ersi , Jin Bowen , Xu Shiqin 
Published: June 2016

AbstractConservation management for the water dependent desert‐oasis ecotone in arid northwest China requires information on the water use of the dominant species. However, no studies have quantified their combined water use or linked species composition to ecotone transpiration. Here, the water use of three dominant shelterbelt shrubs (Haloxylon ammodendron, Nitraria tangutorum, and Calligonum mongolicum) within an ecotone was measured throughout the full leaf‐out period for three shrub species from 30 May to 16 October 2014, with sap flow gauges using the stem heat balance approach. Species‐specific transpiration was estimated by scaling up sap flow velocities measured in individual stems, to stand area level, using the frequency distribution of stem diameter and assuming a constant proportionality between sap flow velocity and basal cross‐sectional area for all stems. The mean peak sap flux densities (Jsn) for H. ammodendron, N. tangutorum, and C. mongolicum, were 40.12 g cm−2 h−1, 71.33 g cm−2 h−1, and 60.34 g cm−2 h−1, respectively, and the mean estimated daily area‐averaged transpiration rates (Tdaily) for the same species were 0.56 mm day−1, 0.34 mm day−1, and 0.11 mm day−1. The accumulative stand transpiration was approximately 140.8 mm throughout the measurement period, exceeding precipitation by as much as 42.1 mm. Furthermore, Tdaily of these shrubs appeared to be much less sensitive to soil moisture as compared to atmospheric drivers, and the relationship between Jsn and atmospheric drivers was likely uninfluenced by soil moisture regimes in the whole profile (to 1‐m depth), especially for H. ammodendron and C. mongolicum. Results indicate that these shrubs may use deep soil water recharged by capillary rise, or may directly access shallow groundwater. This study provides quantitative data offering important implications for ecotone conservation and water and land resource management. Copyright © 2016 John Wiley & Sons, Ltd.
Toward refined environmental scenarios for ecological risk assessment of down-the-drain chemicals in freshwater environments
Authors: Franco Antonio , Price Oliver R , Marshall Stuart , Jolliet Olivier , Van den Brink Paul J , Rico Andreu , Focks Andreas , De Laender Frederik , Ashauer Roman 
Published: June 2016

Abstract

Current regulatory practice for chemical risk assessment suffers from the lack of realism in conventional frameworks. Despite significant advances in exposure and ecological effect modeling, the implementation of novel approaches as high-tier options for prospective regulatory risk assessment remains limited, particularly among general chemicals such as down-the-drain ingredients. While reviewing the current state of the art in environmental exposure and ecological effect modeling, we propose a scenario-based framework that enables a better integration of exposure and effect assessments in a tiered approach. Global- to catchment-scale spatially explicit exposure models can be used to identify areas of higher exposure and to generate ecologically relevant exposure information for input into effect models. Numerous examples of mechanistic ecological effect models demonstrate that it is technically feasible to extrapolate from individual-level effects to effects at higher levels of biological organization and from laboratory to environmental conditions. However, the data required to parameterize effect models that can embrace the complexity of ecosystems are large and require a targeted approach. Experimental efforts should, therefore, focus on vulnerable species and/or traits and ecological conditions of relevance. We outline key research needs to address the challenges that currently hinder the practical application of advanced model-based approaches to risk assessment of down-the-drain chemicals. Integr Environ Assess Manag 2017;13:233–248. © 2016 SETAC

Key Points
A scenario-based approach that integrates spatially explicit exposure models with ecological effect models is needed to embrace ecological realism in risk assessment. Global- to catchment-scale spatially explicit models can be used to identify areas of higher exposure hotspots and to generate exposure inputs into effect models. Mechanistic effect models demonstrate that it is feasible to extrapolate from individual-level effects to effects at higher levels of biological organization and from laboratory to environmental conditions. Experimental efforts should focus on vulnerable species and/or traits and ecological conditions of relevance.
State-of-the-lagoon reports as vehicles of cross-disciplinary integration
Authors: Zaucha Jacek , Davoudi Simin , Slob Adriaan , Bouma Geiske , van Meerkerk Ingmar , Oen Amy MP , Breedveld Gijs D 
Published: June 2016

Abstract
An integrative approach across disciplines is needed for sustainable lagoon and estuary management as identified by integrated coastal zone management. The ARCH research project (Architecture and roadmap to manage multiple pressures on lagoons) has taken initial steps to overcome the boundaries between disciplines and focus on cross-disciplinary integration by addressing the driving forces, challenges, and problems at various case study sites. A model was developed as a boundary-spanning activity to produce joint knowledge and understanding. The backbone of the model is formed by the interaction between the natural and human systems, including economy and governance-based subsystems. The model was used to create state-of-the-lagoon reports for 10 case study sites (lagoons and estuarine coastal areas), with a geographical distribution covering all major seas surrounding Europe. The reports functioned as boundary objects to build joint knowledge. The experiences related to the framing of the model and its subsequent implementation at the case study sites have resulted in key recommendations on how to address the challenges of cross-disciplinary work required for the proper management of complex social-ecological systems such as lagoons, estuarine areas, and other land-sea regions. Cross-disciplinary integration is initially resource intensive and time consuming; one should set aside the required resources and invest efforts at the forefront. It is crucial to create engagement among the group of researchers by focusing on a joint, appealing overall concept that will stimulate cross-sectoral thinking and focusing on the identified problems as a link between collected evidence and future management needs. Different methods for collecting evidence should be applied including both quantitative (jointly agreed indicators) and qualitative (narratives) information. Cross-disciplinary integration is facilitated by functional boundary objects. Integration offers important rewards in terms of developing a better understanding and subsequently improved management of complex social-ecological systems. Integr Environ Assess Manag 2016;12:690–700. © 2016 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC.