bluuebunny/crossref_metadata_2025 huggingface dataset:
Newly identified bacteriolytic enzymes that target a wide range of clinical isolates of Clostridium difficile
Authors: Mehta Krunal K. , Paskaleva Elena E. , Wu Xia , Grover Navdeep , Mundra Ruchir V. , Chen Kevin , Zhang Yongrong , Yang Zhiyong , Feng Hanping , Dordick Jonathan S. , Kane Ravi S.
Published: June 2016

Clostridium difficile has emerged as a major cause of infectious diarrhea in hospitalized patients, with increasing mortality rate and annual healthcare costs exceeding $3 billion. Since C. difficile infections are associated with the use of antibiotics, there is an urgent need to develop treatments that can inactivate the bacterium selectively without affecting commensal microflora. Lytic enzymes from bacteria and bacteriophages show promise as highly selective and effective antimicrobial agents. These enzymes often have a modular structure, consisting of a catalytic domain and a binding domain. In the current work, using consensus catalytic domain and cell‐wall binding domain sequences as probes, we analyzed in silico the genome of C. difficile, as well as phages infecting C. difficile. We identified two genes encoding cell lytic enzymes with possible activity against C. difficile. We cloned the genes in a suitable expression vector, expressed and purified the protein products, and tested enzyme activity in vitro. These newly identified enzymes were found to be active against C. difficile cells in a dose‐dependent manner. We achieved a more than 4‐log reduction in the number of viable bacteria within 5 h of application. Moreover, we found that the enzymes were active against a wide range of C. difficile clinical isolates. We also characterized the biocatalytic mechanism by identifying the specific bonds cleaved by these enzymes within the cell wall peptidoglycan. These results suggest a new approach to combating the growing healthcare problem associated with C. difficile infections. Biotechnol. Bioeng. 2016;113: 2568–2576. © 2016 Wiley Periodicals, Inc.
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

This 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

Recently, 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

Hadoop 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

The 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

This 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

We 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

With 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

For 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

The 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

Conservation 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

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

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.
Pesticide exposures and the risk of multiple myeloma in men: An analysis of the North American Pooled Project
Authors: Presutti Roseanna , Harris Shelley A. , Kachuri Linda , Spinelli John J. , Pahwa Manisha , Blair Aaron , Zahm Shelia Hoar , Cantor Kenneth P. , Weisenburger Dennis D. , Pahwa Punam , McLaughlin John R. , Dosman James A. , Freeman Laura Beane
Published: June 2016

Multiple myeloma (MM) has been consistently linked with agricultural activities, including farming and pesticide exposures. Three case‐control studies in the United States and Canada were pooled to create the North American Pooled Project (NAPP) to investigate associations between pesticide use and haematological cancer risk. This analysis used data from 547 MM cases and 2700 controls. Pesticide use was evaluated as follows: ever/never use; duration of use (years); and cumulative lifetime‐days (LD) (days/year handled × years of use). Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using logistic regression adjusted for age, province/state of residence, use of proxy respondents and selected medical conditions. Increased MM risk was observed for ever use of carbaryl (OR = 2.02, 95% CI = 1.28–3.21), captan (OR = 1.98, 95% CI = 1.04–3.77) and DDT (OR = 1.44, 95% CI = 1.05–1.97). Using the Canadian subset of NAPP data, we observed a more than threefold increase in MM risk (OR = 3.18, 95% CI = 1.40–7.23) for ≤10 cumulative LD of carbaryl use. The association was attenuated but remained significant for >10 LD of carbaryl use (OR = 2.44; 95% CI = 1.05–5.64; ptrend = 0.01). For captan, ≤17.5 LD of exposure was also associated with a more than threefold increase in risk (OR = 3.52, 95% CI = 1.32–9.34), but this association was attenuated in the highest exposure category of >17.5 LD (OR = 2.29, 95% CI = 0.81–6.43; ptrend = 0.01). An increasing trend (ptrend = 0.04) was observed for LD of DDT use (LD > 22; OR = 1.92, 95% CI = 0.95–3.88). In this large North American study of MM and pesticide use, we observed significant increases in MM risk for use of carbaryl, captan and DDT.
Targeting Intrinsic and Extrinsic Vulnerabilities for the Treatment of Multiple Myeloma
Authors: Anreddy Nagaraju , Hazlehurst Lori A.
Published: June 2016

Multiple myeloma (MM) is a malignant plasma cell disorder, clinically characterized by osteolytic lesions, immunodeficiency, and renal disease. Over the past decade, MM therapy is significantly improved by the introduction of novel therapeutics such as immunomodulatory agents (thalidomide, lenalidomide, and pomalidomide), proteasome inhibitors (bortezomib, carfilzomib, and ixazomib), monoclonal antibodies (daratumumab and elotuzumab), histone deacetylase (HDAC) inhibitors (Panobinostat). The clinical success of these agents has clearly identified vulnerabilities intrinsic to the MM cell, as well as targets that emanate from the tumor microenvironment. Despite these significant improvements, MM remains incurable due to the development of drug resistance. This perspective will discuss more recent strategies which take advantage of multiple targets within the proteome recycling pathway, chromatin remodeling, and disruption of nuclear export. In addition, we will review the development of strategies designed to block opportunistic survival signaling that occurs between the MM cell and the tumor microenvironment including strategies for inhibiting myeloma‐induced immune suppression. It has become clear that MM tumors continue to evolve on therapy leading to drug resistance. It will be important to understand the emerging drug resistant mechanisms and additional vulnerabilities that occur due to the development of clinical resistance. J. Cell. Biochem. 118: 15–25, 2017. © 2016 Wiley Periodicals, Inc.
High Quality Independent From a Donor: Human Amniotic Fluid Derived Stem Cells—A Practical Analysis Based on 165 Clinical Cases
Authors: Bajek Anna , Olkowska Joanna , Walentowicz‐Sadłecka Małgorzata , Walentowicz Paweł , Sadłecki Paweł , Grabiec Marek , Bodnar Magdalena , Marszałek Andrzej , Dębski Robert , Porowińska Dorota , Czarnecka Joanna , Kaźmierski Łukasz , Drewa Tomasz
Published: June 2016

The aim of the study was to extend the potential use of human stem cells isolated from amniotic fluid in medical applications by confirming their high homogeneity and quality. Amniotic fluid samples were collected during amniocentesis from 165 women during pregnancy. The proliferation rate, clonogenicity, karyotype, aging process, pluripotent cell markers, expression of surface markers, and the potential to differentiate into adipose, bone and cartilage cells of hAFSCs were analyzed. Obtained results revealed that mesenchymal stem cells could be derived successfully from amniotic fluid, which exhibit properties comparable with MSCs of other origins. It is the first study, in which such a large group of patients was involved. Comprehensive statistical and biological analysis were conducted some of which clearly being innovative in relation to human amniotic fluid‐derived stem cells. J. Cell. Biochem. 118: 116–126, 2017. © 2016 Wiley Periodicals, Inc.
Spatial characteristics of residential development shift large carnivore prey habits
Authors: Smith Justine A. , Wang Yiwei , Wilmers Christopher C.
Published: June 2016

Understanding how anthropogenic development affects food webs is essential to implementing sustainable growth measures, yet little is known about how the spatial configuration of residential development affects the foraging behavior and prey habits of top predators. We examined the influence of the spatial characteristics of residential development on prey composition in the puma (Puma concolor). We located the prey remains of kills from 32 pumas fitted with global positioning system (GPS) satellite collars to determine the housing characteristics most influencing prey size and species composition. We examined how differences in housing density, proximity, and clustering influenced puma prey size and diversity. We found that at both local (150 m) and regional (1 km) spatial scales surrounding puma kill sites, housing density (but not the clustering of housing) was the greatest contributor to puma consumption of small prey (<20 kg), which primarily comprised human commensals or pets. The species‐specific relationships between housing density and prey occupancy and detection rates assessed using camera traps were not always similar to those between housing density and proportions of diet, suggesting that pumas may exercise some diet selectivity. The influence of development on puma diet may affect puma disease risk, energetics, and demographics because of altered species interactions and prey‐specific profiles of energetic gain and cost. Our results can help guide future land‐use planners seeking to minimize the impacts of development on wild species interactions and community dynamics. © 2016 The Wildlife Society.
Grasslands bird occupancy of native warm‐season grass
Authors: West Andrew S. , Keyser Patrick D. , Lituma Christopher M. , Buehler David A. , Applegate Roger D. , Morgan John
Published: June 2016

Grassland birds have declined more than any other guild in the United States because of loss and degradation of native grasslands. The United States Department of Agriculture Farm Bill programs have restored some native warm‐season grasses (NWSG), but populations of many grassland bird species continue to decline. Market‐based NWSG uses focused on hay, pasture, and biofuel feedstock may be more appealing to landowners, and may still provide grassland bird habitat on the landscape. We examined breeding grassland bird occupancy of 102 NWSG production fields including 5 treatments (control [n = 37], grazing [n = 7], hay [n = 22], seed [n = 21], and biofuel [n = 15] production) in Kentucky and Tennessee during 2009–2010 breeding seasons. We used a robust design model in Program MARK to determine occupancy and detection rates for grassland birds. We modeled occupancy differences among treatments and sites (i.e., KY, TN), and included covariates (i.e., field‐level vegetation metrics and landscape composition at 3 scales [250 m, 500 m, and 1 km]) for eastern meadowlark (Sturnella magna), field sparrow (Spizella pusilla), grasshopper sparrow (Ammodramus savannarum), northern bobwhite (Colinus virginianus), and red‐winged blackbird (Agelaius phoeniceus). Covariates that influenced occupancy included treatment (field sparrow, 2009 only), site (eastern meadowlark, grasshopper sparrow, and northern bobwhite), percent NWSG cover (positive, red‐winged blackbird), and percent forest cover within 250 m (negative for eastern meadowlark, grasshopper sparrow, northern bobwhite, and red‐winged blackbird) or within 1 km (negative, field sparrow). Our results suggest that forest cover in the surrounding landscape negatively influences species occupancy, and species occupancy generally did not differ among NWSG production treatments. These treatments could be an alternative means to provide grassland bird habitat within an agriculture production landscape. © 2016 The Wildlife Society.
Age‐related changes in mastication are not improved by tongue exercise in a rat model
Authors: Krekeler Brittany N. , Connor Nadine P.
Published: June 2016

Objectives/Hypothesis

Aging results in progressive changes in deglutitive functions, which may be due in part to alterations in muscle morphology and physiology. Mastication is a critical component of bolus formation and swallowing, but aging effects on masticatory function have not been well studied.

Study Design

The purpose of this study was to 1) quantify the effects of aging on mastication, and 2) determine the effects of tongue exercise on mastication in young adult and old rats. We hypothesized that there would be significant differences in mastication characteristics (number of bites, interval between bites, time to eat) as a function of age, and that tongue exercise would resolve preexercise differences between age groups.

Methods

We expanded the established model of progressive, 8‐week tongue exercise to include a mastication measurement: acoustic recordings of vermicelli pasta biting from 17 old and 17 young adult rats, randomized into exercise and control groups.

Results

We found the following: 1) Mastication characteristics were impacted by age. Specifically in older rats, there was an increase in time to eat and number of bites and intervals between bites decreased, suggesting increased oral motor‐processing requirements for bolus formation. 2) tongue exercise did not impact mastication behaviors in young adult or old rats.

Conclusion

Tongue exercise may not have been specific enough to result in behavioral changes in mastication or exercise dose may not have been sufficient. Nevertheless, results were noteworthy in expanding the established rat model of aging and have relevant clinical implications for future translation to human populations.

Level of Evidence

NA Laryngoscope, 127:E29–E34, 2017
Long‐term Effects of Pine Plantations on Soil Quality in Southern Spain
Authors: Martín‐Peinado Francisco J. , Navarro Francisco Bruno , Jiménez Maria Noelia , Sierra Manuel , Martínez Francisco J. , Romero‐Freire Ana , Rojo Leopoldo , Fernández‐Ondoño Emilia
Published: June 2016

This work evaluated how pine plantations established on old fields and degraded lands influence soil properties in comparison with adjacent unplanted areas that undergo into secondary succession, and native forests, analysing the effects of abiotic variables and stand characteristics in the afforestation process. Thirty‐two paired sites (pine plantations versus unplanted areas) and 10 native forests were selected in the SE Spain. In total, 74 soil profiles were studied, and 222 composite soil samples were collected at three different depths. Soil organic carbon, cation exchange capacity, and C : N ratio showed significantly greater values in pine plantations in relation to the unplanted areas (0–5 cm), and the mean values of soil organic carbon, nitrogen (N), C : N ratio, and cation exchange capacity in these pine plantations were similar to those found under native forests. Only K+ concentrations were clearly higher in the native forests than in the other land uses for all depths analysed. Pine plantations in the drier and warmer areas showed lower soil quality in relation to the paired unplanted areas, as well as the younger and denser ones; it may be because under these situations, more time is needed to produce an improvement. In fact, the paired net variations increased with the stand age and/or tree size. In conclusion, pine plantations were in general more efficient in improving parameters related to soil quality, especially in locations with high soil water retention capacity, which in our study area were found at higher and cooler elevations. Copyright © 2016 John Wiley & Sons, Ltd.
Effect of cooling on crystallization and microstructure of polypropylene
Authors: Dietz Wolfgang
Published: June 2016

The cooling of polypropylene melts and their solidification is analyzed taking into account the mutual dependency of crystallization and heat transfer. A single equation for the crystallinity is used. This equation also provides information for the ensuing microstructure. No restrictive assumption is necessary when nucleation kinematics and growth rates are known. Crystallization itself has a strong influence on heat transfer and cooling time during processing because all material parameters depend on crystallinity. The theoretical results obtained with these parameters compare favorably with the temperature drop and the increase of crystallinity observed during cooling experiments. The potential of a simple method for evaluating the spherulitic structure at the end of crystallization is demonstrated by comparing the calculated and the measured size distribution of spherulites in a solidified slab. The combined computation of heat transfer and crystallization presented in this study is important for calculating the cooling time of plastics processing operations. POLYM. ENG. SCI., 56:1291–1302, 2016. © 2016 Society of Plastics Engineers
Nanocomposites of PBAT and cellulose nanocrystals modified by in situ polymerization and melt extrusion
Authors: Morelli Carolina L. , Belgacem Mohamed N. , Branciforti Márcia C. , C. B. Salon Marie , Bras Julien , Bretas Rosario E. S.
Published: June 2016

Cellulose nanocrystals (CNC) were successfully grafted with a low molecular weight poly(butylene glutarate) through an in situ polymerization procedure. The grafting treatment decreased the CNC hydrophilic character and increased the onset of their thermal degradation by approximately 20°C, thus increasing the possibilities of CNC application. Composites of grafted and nongrafted CNC with a poly(butylene‐adipate‐co‐terephthalate) (PBAT) matrix were prepared by melt extrusion. The CNC addition led to an increase of 50% of the tensile elastic modulus of the PBAT. In addition, dynamic mechanical thermal analysis showed that the composite with CNC retained its high modulus even at temperatures far above the glass transition temperature of PBAT. At 60°C the storage modulus of the composite with CNC was approximately 200% higher than that of the pure PBAT. Thus, in this work, nanocomposites of improved properties were obtained through a combination of in situ polymerization and melt extrusion. POLYM. ENG. SCI., 56:1339–1348, 2016. © 2016 Society of Plastics Engineers
On methylene‐bridged cysteine and lysine residues in proteins
Authors: Ruszkowski Milosz , Dauter Zbigniew
Published: June 2016

Cysteine residues ubiquitously stabilize tertiary and quaternary protein structure by formation of disulfide bridges. Here we investigate another linking interaction that involves sulfhydryl groups of cysteines, namely intra‐ and intermolecular methylene‐bridges between cysteine and lysine residues. A number of crystal structures possessing such a linkage were identified in the Protein Data Bank. Inspection of the electron density maps and re‐refinement of the nominated structures unequivocally confirmed the presence of Lys‐CH2‐Cys bonds in several cases.
Destruction‐and‐diffraction by X‐ray free‐electron laser
Authors: Wang Jimin
Published: June 2016

It is common knowledge that macromolecular crystals are damaged by the X‐rays they are exposed to during conventional data collection. One of the claims made about the crystallographic data collection now being collected using X‐ray free‐electron lasers (XFEL) is that they are unaffected by radiation damage. XFEL data sets are assembled by merging data obtained from a very large number of crystals, each of which is exposed to a single femtosecond pulse of radiation, the duration of which is so short that diffraction occurs before the damage done to the crystal has time to become manifest, i.e. “diffraction‐before‐destruction.” However, recent theoretical studies have shown that many of the elemental electronic processes that ultimately result in the destruction of such crystals occur during a single pulse. It is predicted that the amplitudes of atomic scattering factor could be reduced by as much as 75% within the first 5 femtoseconds of such pulses, and that different atoms will respond in different ways. Experimental evidence is provided here that these predictions are correct.
Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin
Authors: Bhutoria Savita , Kalpana Ganjam V. , Acharya Seetharama A.
Published: June 2016

The structure of a protein can be very informative of its function. However, determining protein structures experimentally can often be very challenging. Computational methods have been used successfully in modeling structures with sufficient accuracy. Here we have used computational tools to predict the structure of an evolutionarily conserved and functionally significant domain of Integrase interactor (INI)1/hSNF5 protein. INI1 is a component of the chromatin remodeling SWI/SNF complex, a tumor suppressor and is involved in many protein‐protein interactions. It belongs to SNF5 family of proteins that contain two conserved repeat (Rpt) domains. Rpt1 domain of INI1 binds to HIV‐1 Integrase, and acts as a dominant negative mutant to inhibit viral replication. Rpt1 domain also interacts with oncogene c‐MYC and modulates its transcriptional activity. We carried out an ab initio modeling of a segment of INI1 protein containing the Rpt1 domain. The structural model suggested the presence of a compact and well defined ββαα topology as core structure in the Rpt1 domain of INI1. This topology in Rpt1 was similar to PFU domain of Phospholipase A2 Activating Protein, PLAA. Interestingly, PFU domain shares similarity with Ubiquitin and has ubiquitin binding activity. Because of the structural similarity between Rpt1 domain of INI1 and PFU domain of PLAA, we propose that Rpt1 domain of INI1 may participate in ubiquitin recognition or binding with ubiquitin or ubiquitin related proteins. This modeling study may shed light on the mode of interactions of Rpt1 domain of INI1 and is likely to facilitate future functional studies of INI1.
Subsidized commercial harvesting for cost‐effective wildlife management in urban areas: A case study with kangaroo sharpshooting
Authors: Mawson Peter R. , Hampton Jordan O. , Dooley Brendan
Published: June 2016

The management of overabundant urban fauna is a contentious issue worldwide, particularly for populations of white‐tailed deer (Odocoileus virginianus) in North America and kangaroos (Macropus spp.) in Australia. To be successful, management programs in such settings must be cost‐effective, humane, and publicly acceptable. Here, we describe the management of a fenced, urban population of western grey kangaroos (M. fuliginosus) in southwestern Australia, with an estimated population density of 189 kangaroos/km2. After a period of >12 months of solicited public involvement by key stakeholder groups, a licensed professional shooting team, observing a national code of practice, conducted night‐time sharpshooting. Over an 11‐month period in 2006–2007, 1,009 kangaroos were shot in 43 shooting nights, a mean (±SE) culling rate of 23 ± 3 kangaroos/night or harvest rate of 12 ± 2 kangaroos/hr. Inspectors under the relevant Western Australian legislation functioned as animal welfare observers to ensure that the methods employed for the culling program met the national code of practice and that all license conditions were met. No accidents or injuries occurred during the program. The program produced 17 kg/kangaroo of harvestable meat and biological samples for several research projects. The operational costs of the project were very low, at AU$36/kangaroo, with payments largely limited to incentives paid to commercial harvesters and management staff monitoring public safety and animal welfare. This case study is an example of a publicly acceptable, cost‐effective, humane, and lethal urban wildlife control operation. It demonstrates that public acceptance of a cull of wildlife can be forthcoming with appropriate prior consultation and high professional standards. © 2016 The Wildlife Society.
A noninvasive method to detect Mexican wolves and estimate abundance
Authors: Piaggio Antoinette J. , Cariappa Chip A. , Straughan Dyan J. , Neubaum Melissa A. , Dwire Margaret , Krausman Paul R. , Ballard Warren B. , Bergman David L. , Breck Stewart W.
Published: June 2016

Monitoring wolf abundance is important for recovery efforts of Mexican wolves (Canis lupus baileyi) in the Blue Range Wolf Recovery Area in Arizona and New Mexico, USA. Although radiotelemetry has been a reliable method, collaring and tracking wolves in an expanding population will be prohibitively expensive and alternative methods to estimate abundance will become necessary. We applied 10 canid microsatellite loci to 235 Mexican wolf samples, 48 coyote (C. latrans) samples, and 14 domestic dog (C. lupus familiaris) samples to identify alleles that provide reliable separation of these species. We then evaluated an approach for prescreening, noninvasively collected DNA obtained from fecal samples to identify Mexican wolves. We generated complete genotypes for only those samples identified as probable Mexican wolves. We used these genotypes to estimate mark–recapture population estimates of Mexican wolves and compared these to known numbers of wolves in the study area. We collected fecal samples during 3 sampling periods in 2007–2008 and used Huggins‐type mark–recapture models to estimate Mexican wolf abundance. We were able to generate abundance estimates with 95% confidence for 2 of 3 sampling periods. We estimated abundance to be 10 (95% CI = 6–34) during one sampling period when the known abundance was 10 and we estimated abundance to be 9 (95% CI = 6–30) during the other sampling period when the known abundance was 10. The application of this noninvasive method to estimate Mexican wolf abundance provides an alternative monitoring tool that could be useful for long‐term monitoring of this and other recovering populations. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.