bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type III secretion as a generalizable strategy for the production of full‐length biopolymer‐forming proteins
Authors: Azam Anum , Li Cheng , Metcalf Kevin J. , Tullman‐Ercek Danielle 
Published: May 2015

ABSTRACTBiopolymer‐forming proteins are integral in the development of customizable biomaterials, but recombinant expression of these proteins is challenging. In particular, biopolymer‐forming proteins have repetitive, glycine‐rich domains and, like many heterologously expressed proteins, are prone to incomplete translation, aggregation, and proteolytic degradation in the production host. This necessitates tailored purification processes to isolate each full‐length protein of interest from the truncated forms as well as other contaminating proteins; owing to the repetitive nature of these proteins, the truncated polypeptides can have very similar chemistry to the full‐length form and are difficult to separate from the full‐length protein. We hypothesized that bacterial expression and secretion would be a promising alternative option for biomaterials‐forming proteins, simplifying isolation of the full‐length target protein. By using a selective secretion system, truncated forms of the protein are not secreted and thus are not found in the culture harvest. We show that a synthetically upregulated type III secretion system leads to a general increase in secretion titer for each protein that we tested. Moreover, we observe a substantial enhancement in the homogeneity of full‐length forms of pro‐resilin, tropo‐elastin crosslinking domains, and silk proteins produced in this manner, as compared with proteins purified from the cytosol. Secretion via the type III apparatus limits co‐purification of truncated forms of the target protein and increases protein purity without extensive purification steps. Demonstrating the utility of such a system, we introduce several modifications to resilin‐based peptides and use an un‐optimized, single‐column process to purify these proteins. The resulting materials are of sufficiently high quantity and yield for the production of antimicrobial hydrogels with highly reproducible rheological properties. The ease of this process and its applicability to an array of engineered biomaterial‐forming peptides lend support for the application of bacterial expression and secretion for other proteins that are traditionally difficult to express and isolate from the bacterial cytoplasm. Biotechnol. Bioeng. 2016;113: 2313–2320. © 2015 Wiley Periodicals, Inc.
Serial type‐specific human papillomavirus (HPV) load measurement allows differentiation between regressing cervical lesions and serial virion productive transient infections
Authors: Depuydt Christophe E. , Jonckheere Jef , Berth Mario , Salembier Geert M. , Vereecken Annie J. , Bogers Johannes J. 
Published: May 2015

AbstractPersistent high‐risk human papillomavirus (HPV) infection is strongly associated with the development of high‐grade cervical intraepithelial neoplasia (CIN) or cancer. Not all persistent infections lead to cancer. Viral load measured at a single time‐point is a poor predictor of the natural history of HPV infections. However the profile of viral load evolution over time could distinguish nonprogressive from progressive (carcinogenic) infections. A retrospective natural history study was set up using a Belgian laboratory database including more than 800,000 liquid cytology specimens. All samples were submitted to qPCR identifying E6/E7 genes of 18 HPV types. Viral load changes over time were assessed by the linear regression slope. Database search identified 261 untreated women with persistent type‐specific HPV DNA detected (270 infections) in at least three of the last smears for a average period of 3.2 years. Using the coefficient of determination (R²) infections could be subdivided in a latency group (n = 143; R² < 0.85) and a regressing group (n = 127; R² ≥ 0.85). In (≥3) serial viral load measurements, serial transient infections with latency is characterized by a nonlinear limited difference in decrease or increase of type‐specific viral load (R² < 0.85 and slopes between 2 measurements 0.0010 and −0.0010 HPV copies/cell per day) over a longer period of time (1553 days), whereas regression of a clonal cell population is characterized by a linear (R² ≥ 0.85) decrease (−0.0033 HPV copies/cell per day) over a shorter period of time (708 days; P < 0.001). Using serial HPV type‐specific viral load measurements we could for the first time identify regressing CIN2 and CIN3 lesions. Evolution of the viral load is an objective measurable indicator of the natural history of HPV infections and could be used for future triage in HPV‐based cervical screening programs.
Breast cancer incidence and menopausal hormone therapy in Norway from 2004 to 2009: a register‐based cohort study
Authors: Suhrke Pål , Zahl Per‐Henrik 
Published: May 2015

AbstractIn Norway, the breast cancer incidence increased by 50% in the 1990s, during a period with initiation of mammography screening as well as a fourfold increase in use of menopausal hormone therapy (HT). After 2002, the HT use has dropped substantially; however, the breast cancer incidence has declined only marginally. How much mammography screening contributed to the breast cancer incidence increase in the 1990s compared with HT use and specifically different types of HT use, has thus been discussed. Whether HT affects the incidence of subtypes of breast cancer differently has also been questioned. We have linked individual data from several national registries from 2004 to 2009 on 449,717 women aged 50–65 years. 4597 cases of invasive cancer and 681 cases of ductal carcinoma in situ (DCIS) were included in the analysis. We used Cox regression to estimate hazard ratio (HR) as a measure of the relative risk of breast cancer associated with use of HT. The HRs associated with prescriptions of HT for more than 1 year were 2.06 (1.90–2.24) for estrogen and progesterone combinations, 1.03 (0.85–1.25) for systemic estrogens, and 1.23 (1.01–1.51) for tibolone. Invasive lobular carcinoma was more strongly associated with use of estrogen and progesterone combinations, HR = 3.10 (2.51–3.81), than nonlobular carcinoma, HR = 1.94 (1.78–2.12). The corresponding value for DCIS was 1.61 (1.28–2.02). We estimated the population attributable fraction to 8.2%, corresponding to 90 breast cancer cases in 2006 indicating that HT use still caused a major number of breast cancer cases.
Synchronous adenomyomas of the ileum in an adult‐an exceptional cause of intussusception
Authors: Khmou Mouna , Znati Kaoutar , Zouaidia Fouad , Jahid Ahmed , Bernoussi Zakiya , Mahassini Najat 
Published: May 2015

Key Clinical MessageIn this article, we report a case of two synchronous ileal adenomyomas leading to intussusception. This rare occurrence has never been reported in the literature. Our case is noteworthy, because the lesion is rare and should be considered in the differential diagnosis of intussusception in adults.
In Situ Techniques to Study the Effects of Anode or Cathode Gas‐Exchange Cycles on the Deterioration of Pt/C Cathode Catalysts in PEFCs
Authors: Samjeské Gabor , Higashi Kotaro , Takao Shinobu , Nagamatsu Shin‐ichi , Nagasawa Kensaku , Sekizawa Oki , Kaneko Takuma , Uruga Tomoya , Iwasawa Yasuhiro 
Published: May 2015

AbstractRepeated, quick anode gas‐exchange (AGEX) or cathode gas‐exchange (CGEX) cycles were applied to polymer electrolyte fuel cell (PEFC) membrane electrode assemblies (MEAs) with Pt/C cathode catalysts to simulate start‐up/shut‐down conditions and to examine a possible countermeasure for their effects on MEA cathode catalyst degradation. The peak height of the white line during in situ time‐resolved X‐ray absorption near‐edge structure (XANES) spectra at the Pt LIII‐edge decreased with an increasing number of AGEX cycles and only in the top region of the MEA cathode layer (close to the gas inlet of the fuel cell), not in the whole MEA area. End‐of‐life analysis after AGEX by using SEM and TEM revealed isolated Pt nanoparticles in micro‐cracks and voids produced in the top region of the MEA cathode layer. The nanoparticle sizes remained almost unchanged for top, middle, and bottom regions of the MEA cathode layer. In the case of CGEX, a small increase in the Pt nanoparticle sizes in the top and bottom positions of the MEA cathode layer was observed. These findings support the role of carbon corrosion, leaving isolated, electrochemically inactive Pt nanoparticles as a consequence of the harsh reaction conditions caused by the reverse current decay mechanism during the start‐up/shut‐down phase, as in the case of AGEX cycles, to be the main cause for the cathode catalyst deterioration close to the anode gas inlet. On the other hand, the hydrogen gas feed to both the anode and cathode during start‐up and shut‐down processes seems to effectively suppress carbon corrosion and prevents a decrease in the performance.
Simultaneous Enantioseparation of Aldohexoses and Aldopentoses Derivatized With L‐Tryptophanamide by Reversed Phase HPLC Using Butylboronic Acid as a Complexation Reagent of Monosaccharides
Authors: Shou Mirei , Terashima Hiroyuki , Aizawa Sen‐Ichi , Taga Atsushi , Yamamoto Atsushi , Kodama Shuji 
Published: May 2015

AbstractThree aldohexoses, glucose, galactose, and mannose, and three aldopentoses, arabinose, xylose, and ribose, were derivatized with L‐tryptophanamide (L‐TrpNH2) under alkaline conditions. Using a basic mobile phase (pH 9.2), the three aldohexoses or the three aldopentoses were simultaneously enantioseparated, respectively, but all the six monosaccharides could not be simultaneously enantioseparated. A large amount of nonreacted L‐TrpNH2 was detected after the derivatized monosaccharides. In order to widen the separation window, a large portion of nonreacted L‐TrpNH2 could be eliminated by liquid–liquid extraction with ethylacetate, and elution order of the derivatized monosaccharides and nonreacted L‐TrpNH2 was found to be reversed using a neutral mobile phase. All of the six monosaccharides were simultaneously enantioseparated by reversed phase high‐performance liquid chromatography (HPLC) using InertSustainSwift C18 column (4.6 mm i.d. × 150 mm) and a mobile phase containing 180 mM phosphate buffer (pH 7.6), 1.5 mM butylboronic acid, and 5% acetonitrile at 40 °C. Nomenclature of D and L for monosaccharides is based on the configurations of the asymmetric C4 center for aldopentoses and C5 center for aldohexoses. It was found that the enantiomer elution order of these six monosaccharides and fucose in the proposed method conformed to be the absolute configuration of the C2 center. Chirality 27:417–421, 2015. © 2015 Wiley Periodicals, Inc.
HybridMR: a new approach for hybrid MapReduce combining desktop grid and cloud infrastructures
Authors: Tang Bing , He Haiwu , Fedak Gilles 
Published: May 2015

SummaryThis paper introduces HybridMR, a novel model for the execution of MapReduce (MR) computation on hybrid computing environment. Using this model, high performance cloud resources and heterogeneous desktop personal computers (PCs) in Internet or Intranet can be integrated to form a hybrid computing environment. Thanks to HybridMR, the computation and storage capability of large scale desktop PCs can be fully utilized to process large scale datasets. HybridMR relies on two innovative solutions to enable such large scale data‐intensive computation. The first one is HybridDFS, which is a hybrid distributed file system. HybridDFS features reliable distributed storage that alleviates the volatility of desktop PCs, thanks to fault tolerance and file replication mechanism. The second innovation is a new node priority‐based fair scheduling (NPBFS) algorithm has been developed in HybridMR to achieve both data storage balance and job assignment balance by assigning each node a priority through quantifying CPU speed, memory size, and input and output capacity. In this paper, we describe the HybridMR, HybridDFS, and NPBFS. We report on performance evaluation results, which show that the proposed HybridMR not only achieves reliable MR computation, reduces task response time, and improves the performance of MR, but also reduces the computation cost and achieves a greener computing mode. Copyright © 2015 John Wiley & Sons, Ltd.
Science gateways today and tomorrow: positive perspectives of nearly 5000 members of the research community
Authors: Lawrence Katherine A. , Zentner Michael , Wilkins‐Diehr Nancy , Wernert Julie A. , Pierce Marlon , Marru Suresh , Michael Scott 
Published: May 2015

SummaryScience gateways are digital interfaces to advanced technologies that support science/engineering research/education. Frequently implemented as Web and mobile applications, they provide access to community resources such as software, data, collaboration tools, instrumentation, and high‐performance computing. We anticipate opportunities for growth within a fragmented community. Through a large‐scale survey, we measured the extent and characteristics of the gateway community (reliance on gateways and nature of existing resources) to understand useful services and support for builders and users. We administered an online survey to nearly 29,000 principal investigators, senior administrators, and people with gateway affiliations. Nearly 5000 respondents represented diverse expertise and geography. The majority of researchers/educators indicated that specialized online resources were important to their work. They choose technologies by asking colleagues and looking for documentation, demonstrated reliability, and technical support; adaptability via customizing or open‐source standards was another priority. Research groups commonly provide their own resources, but public/academic institutions and commercial services also provide substantial offerings. Application creators and administrators welcome external services providing guidance such as technology selection, sustainability planning, evaluation, and specialized expertise (e.g., quality assurance and design). Technologies are diverse, so flexibility and ongoing community input are essential, as is offering specific, easy‐to‐access training, community support, and professional development. Copyright © 2015 John Wiley & Sons, Ltd.
A high‐performance distributed file system for large‐scale concurrent HD video streams
Authors: Duan Hancong , Zhan Wenhan , Min Geyong , Guo Hui , Luo Shengmei 
Published: May 2015

SummaryWith the rapid development of intelligent transportation technology, high‐definition data storage, and processing of massive amounts of video surveillance have become key issues. When thousands of high‐bit‐rate video streaming concurrently writes, disk I/O throughput becomes a bottleneck. In addition, this leads to serious energy consumption and disk abrasion. To solve these problems, a new distributed file system for high concurrent and high‐bit‐rate writing is designed. It combines an optimized data storage model, efficient metadata management, and exquisite disk schedule mechanism. The optimized data storage model uses a file pre‐allocation strategy and multiple‐stream input modulating technology to convert the randomly concurrent writes on the disk into sequential writes; the metadata management provides an efficient means of retrieving the specified data; and the dual‐partition schedule mechanism can ensure the disk stability with less abrasion. Through this distributed file system, the disk I/O throughput can be saturated in a high concurrent writing environment. The performance evaluation results demonstrate that the I/O throughput of a normal 7200RPM SATA III disk in our scheme can be stabilized at 150MB/s, easily to support 300 concurrent high‐definition video streams (4Mbit/s each). The distributed file system with eight commodity servers can afford the ability of supporting 8000 high‐definition video streams concurrently writing, which is far greater than the existing video surveillance storage solutions. Copyright © 2015 John Wiley & Sons, Ltd.
Performance tuning and sparse traversal technique for a cell‐based fetch length algorithm on a GPU
Authors: Murtojärvi Mika , Nevalainen Olli S. , Leppänen Ville 
Published: May 2015

SummaryFor determining distances (fetch lengths) from points to polygons in a two‐dimensional Euclidean plane, cell‐based algorithms provide a simple and effective solution. They divide the input area into a grid of cells that cover the area. The objects are stored into the appropriate cells, and the resulting structure is used for solving the problem. When the input objects are distributed unevenly or the cell size is small, most of the cells may be empty. The representation is then called sparse. In the method proposed in this work, each cell contains information about its distance to the nonempty cells. It is then possible to skip over several empty cells at a time without memory accesses. A cell‐based fetch length algorithm is implemented on a graphics processing unit (GPU). Because control flow divergence reduces its performance, several methods to reduce the divergence are studied. While many of the explicit attempts turn out to be unsuccessful, sorting of the input data and sparse traversal are observed to greatly improve performance: compared with the initial GPU implementation, up to 45‐fold speedup is reached. The speed improvement is greatest when the map is very sparse and the points are given in a random order. Copyright © 2015 John Wiley & Sons, Ltd.
Araport: an application platform for data discovery
Authors: Hanlon Matthew R. , Vaughn Matthew , Mock Stephen , Dooley Rion , Moreira Walter , Stubbs Joe , Town Chris , Miller Jason , Krishnakumar Vivek , Ferlanti Erik , Pence Eleanor 
Published: May 2015

SummaryAraport is an open‐source, online community resource for research on the Arabidopsis thaliana genome and related data. Araport is developed through a partnership between J. Craig Venter Institute, the Texas Advanced Computing Center at The University of Texas at Austin, and The University of Cambridge. Part of the open architecture of Araport is the Science Applications Workspace. Taking an ‘app store’ approach, users can choose applications developed both by the Araport team and community developers to create a customized environment for their work. Araport also provides tooling and support for developing applications for Araport, including an application generator, a rapid development and testing tool, and a straightforward deployment path for publishing applications into the Araport workspace. Copyright © 2015 John Wiley & Sons, Ltd.
Energy Aspects of Thermal Molecular Switching: Molecular Thermal Hysteresis of Helicene Oligomers
Authors: Shigeno Masanori , Kushida Yo , Yamaguchi Masahiko 
Published: May 2015

AbstractMolecular switching is a phenomenon by which a molecule reversibly changes its structure and state in response to external stimuli or energy. Herein, molecular switching is discussed from thermodynamic and kinetic aspects in terms of energy supply with an emphasis on the thermal switching exhibited by helicene oligomers. It includes the inversion of relative thermodynamic stability induced by temperature changes and molecular thermal hysteresis in a closed system. The thermal phenomenon associated with the oligomers involves population/concentration changes between metastable states under nonequilibrium thermodynamic control.
Dimethylaminopyridine‐Supported Graft Polymer Catalyst and its Flow System
Authors: Okuno Yoshinori , Isomura Shigeki , Kamakura Takahiro , Sano Fumiaki , Tamahori Kaoru , Goto Takahiro , Hayashida Takahiro , Kitagawa Yuuichi , Fukuhara Ami , Takeda Kazuyoshi 
Published: May 2015

AbstractInvited for this month’s cover is the group of Prof. Kazuyoshi Takeda at Yokohama University of Pharmacy. The image shows continuous acylation catalyzed by using a graft polymer catalyst together with parallel fixed bed reactors. The Full Paper itself is available at 10.1002/cssc.201500092.
Dispersal depends on body condition and predation risk in the semi‐aquatic insect,Notonecta undulata
Authors: Baines Celina B. , McCauley Shannon J. , Rowe Locke 
Published: May 2015

AbstractDispersal is the movement of organisms across space, which has important implications for ecological and evolutionary processes, including community composition and gene flow. Previous studies have demonstrated that dispersal is influenced by body condition; however, few studies have been able to separate the effects of body condition from correlated variables such as body size. Moreover, the results of these studies have been inconsistent with respect to the direction of the relationship between condition and dispersal. We examined whether body condition influences dispersal in backswimmers (Notonecta undulata). We also tested whether an interaction between body condition and predation risk (another proximate factor that influences dispersal) could contribute to the previously observed inconsistent relationship between condition and dispersal. We imposed diet treatments on backswimmers in the laboratory, and measured the effects of food availability on body condition and dispersal in the field. We found that dispersal was a positive function of body condition, which may have important consequences for population characteristics such as the rate of gene flow and population growth. However, the effects of body condition and predation risk were additive, not interactive, and therefore, our data do not support the hypothesis that the interaction between condition and predation risk contributes to the inconsistency in the results of previous condition‐dependent dispersal studies.
Bank erosion of legacy sediment at the transition from vertical to lateral stream incision
Authors: Lyons Nathan J. , Starek Michael J. , Wegmann Karl W. , Mitasova Helena 
Published: May 2015

AbstractStreambank erosion is a primary source of suspended sediments in many waterways of the US Atlantic Piedmont. This problem is exacerbated where banks are comprised of fine sediment produced by the intensive land use practices of early European settlers. A stream in this region, Richland Creek incises into banks comprised of three stratigraphic layers associated with historic land use: pre‐European settlement, early European agriculture and development, and water‐powered milldam operation. This study aims to identify the bank processes along a reach of Richland Creek that is eroding towards its pre‐disturbance elevation. The volume of material that has eroded along this stream since the milldam breached was calculated by differencing a reconstructed surface of the pond bed and an aerial lidar digital terrain model (DTM). Immediately downstream from the study reach, the channel is floored by bedrock and immediately upstream the rate of channel erosion approximately doubled along the longitudinal profile of Richland Creek, which indicate that the study reach spans the transition from a channel dominated by vertical incision in the upstream direction to horizontal widening in the downstream direction.The combined hydrometeorological conditions and dominant processes causing reach‐scale cut bank erosion were investigated with analyses of stream stage, precipitation, and streambank volumetric and surfaces change that was measured during nine terrestrial lidar surveys in 2010–2012. The spatial variability of erosion during a simulated precipitation event was examined in a field‐based experiment. Erosion was greatest where mill pond sediment columns detached along vertical desiccation and horizontal seepage cracks. This sediment accumulated on the bank toe throughout the study and was a source of readily‐entrained fine sediment contrary to the upper reaches where depositional accommodation space is more limited. Findings suggest that hotspots of sediment excavation progress upstream, indicating that restoration efforts should focus upon stabilizing banks at these locations. Copyright © 2015 John Wiley & Sons, Ltd.