bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consensus engineering of sucrose phosphorylase: The outcome reflects the sequence input
Authors: Aerts Dirk , Verhaeghe Tom , Joosten Henk‐Jan , Vriend Gert , Soetaert Wim , Desmet Tom 
Published: April 2013

ABSTRACTConsensus engineering, which is replacing amino acids by the most frequently occurring one at their positions in a multiple sequence alignment (MSA), is a known strategy to increase the stability of a protein. The application of this concept to the entire sequence of an enzyme, however, has been tried only a few times mainly because of the problems determining the consensus in highly variable regions. We show that this problem can be solved by replacing such problematic regions by the corresponding sequence of the natural homologue closest to the consensus. When one or a few sub‐families are overrepresented in the MSA the consensus sequence is a biased representation of the sequence space. We examine the influence of this bias by constructing three consensus sequences using different MSAs of sucrose phosphorylase (SP). Each consensus enzyme contained about 70 mutations compared to its closest natural homologue and folded correctly and displayed activity on sucrose. Correlation analysis revealed that the family's co‐evolution network was kept intact, which is one of the main advantages of full‐length consensus design. The consensus enzymes displayed an “average” thermostability, that is, one that is higher than some but not all known representatives. We cautiously present practical rules for the design of consensus sequences, but warn that the measure of success depends on which natural enzyme is used as point of comparison. Biotechnol. Bioeng. 2013;110: 2563–2572. © 2013 Wiley Periodicals, Inc.
Adenoma detection in patients undergoing a comprehensive colonoscopy screening
Authors: Raju Gottumukkala S. , Vadyala Vikram , Slack Rebecca , Krishna Somashekar G. , Ross William A. , Lynch Patrick M. , Bresalier Robert S. , Hawk Ernest , Stroehlein John R. 
Published: April 2013

AbstractMeasures shown to improve the adenoma detection during colonoscopy (excellent bowel preparation, cecal intubation, cap fitted colonoscope to examine behind folds, patient position change to optimize colon distention, trained endoscopy team focusing on detection of subtle flat lesions, and incorporation of optimum endoscopic examination with adequate withdrawal time) are applicable to clinical practice and, if incorporated are projected to facilitate comprehensive colonoscopy screening program for colon cancer prevention. To determine adenoma and serrated polyp detection rate under conditions designed to optimize quality parameters for comprehensive screening colonoscopy. Retrospective analysis of data obtained from a comprehensive colon cancer screening program designed to optimize quality parameters. Academic medical center. Three hundred and forty‐three patients between the ages of 50 years and 75 years who underwent first screening colonoscopy between 2009 and 2011 among 535 consecutive patients undergoing colonoscopy. Comprehensive colonoscopy screening program was utilized to screen all patients. Cecal intubation was successful in 98.8% of patients. The Boston Bowel Preparation Scale for quality of colonoscopy was 8.97 (95% confidence interval [CI]; 8.94, 9.00). The rate of adenoma detection was 60% and serrated lesion (defined as serrated adenomas or hyperplastic polyps proximal to the splenic flexure) detection was 23%. The rate of precancerous lesion detection (adenomas and serrated lesions) was 66%. The mean number of adenomas per screening procedure was 1.4 (1.2, 1.6) and the mean number of precancerous lesions (adenomas or serrated lesions) per screening procedure was 1.6 (1.4, 1.8). Retrospective study and single endoscopist experience. A comprehensive colonoscopy screening program results in high‐quality screening with high detection of adenomas, advanced adenomas, serrated adenomas, and multiple adenomas.
Heterometallic Clusters [CuSn3S9]5− and [Cu6Sn6S20]10−: Solvothermal Synthesis and Characterization of 4f–3d Thiostannates
Authors: Chen Ruihong , Wang Fang , Tang Chunying , Zhang Yong , Jia Dingxian 
Published: April 2013

AbstractTwo types of 4f–3d thiostannates with general formula [Hen]2[Ln(en)4(CuSn3S9)]⋅0.5 en (Ln1; Ln=La, 1; Ce, 2) and [Hen]4[Ln(en)4]2[Cu6Sn6S20]⋅3 en (Ln2; Ln=Nd, 3; Gd, 4; Er, 5) were prepared by reactions of Ln2O3, Cu, Sn, and S in ethylenediamine (en) under solvothermal conditions between 160 and 190 °C. However, reactions performed in the range from 120 to 140 °C resulted in crystallization of [Sn2S6]4− compounds and CuS powder. In 1 and 2, three SnS4 tetrahedra and one CuS3 triangle are joined by sharing sulfur atoms to form a novel [CuSn3S9]5− cluster that coordinates to the Ln3+ ion of [Ln(en)4]3+ (Ln=La, Ce) as a monodentate ligand. The [CuSn3S9]5− unit is the first thio‐based heterometallic adamantane‐like cluster coordinating to a lanthanide center. In 3–5, six SnS4 tetrahedra and six CuS3 triangles are connected by sharing common sulfur atoms to form the ternary [Cu6Sn6S20]10− cluster, in which a Cu6 core is enclosed by two Sn3S10 fragments. The topological structure of the novel Cu6 core can be regarded as two Cu4 tetrahedra joined by a common edge. The Ln3+ ions in Ln1 and Ln2 are in nine‐ and eightfold coordination, respectively, which leads to the formation of the [CuSn3S9]5− and [Cu6Sn6S20]10− clusters under identical synthetic conditions. The syntheses of Ln1 and Ln2 show the influence of the lanthanide contraction on the quaternary Ln/Cu/Sn/S system in ethylenediamine. Compounds 1–5 exhibit bandgaps in the range of 2.09–2.48 eV depending on the two different types of clusters in the compounds. Compounds 1, 3, and 4 lost their organic components in the temperature range of 110–350 °C by multistep processes.
Using buffered playtime for QoE‐oriented resource management of YouTube video streaming
Authors: Wamser F. , Hock D. , Seufert M. , Staehle B. , Pries R. , Tran‐Gia P. 
Published: April 2013

ABSTRACTYouTube is the most important online platform for streaming video clips. The popularity and the continuously increasing number of users pose new challenges for Internet service providers. In particular, in access networks where the transmission resources are limited and the providers are interested in reducing their operational expenditure, it is worth to efficiently optimise the network for popular services such as YouTube. In this paper, we propose different resource management mechanisms to improve the quality of experience (QoE) of YouTube users. In particular, we investigate the benefit of cross‐layer resource management actions at the client and in the access network for YouTube video streaming. The proposed algorithms are evaluated in a wireless mesh testbed. The results show how to improve the YouTube QoE for the users with the help of client‐based or network‐based control actions. Copyright © 2013 John Wiley & Sons, Ltd.
Altered bone development and turnover in transgenic mice over‐expressing Lipocalin‐2 in bone
Authors: Costa Delfina , Lazzarini Edoardo , Canciani Barbara , Giuliani Alessandra , SpanÒ Raffaele , Marozzi Katia , Manescu Adrian , Cancedda Ranieri , Tavella Sara 
Published: April 2013

AbstractLipocalin‐2 (LCN2) is a protein largely expressed in many tissues, associated with different biological phenomena such as cellular differentiation, inflammation and cancer acting as a survival/apoptotic signal. We found that LCN2 was expressed during osteoblast differentiation and we generated transgenic (Tg) mice over‐expressing LCN2 in bone. Tg mice were smaller and presented bone microarchitectural changes in both endochondral and intramembranous bones. In particular, Tg bones displayed a thinner layer of cortical bone and a decreased trabecular number. Osteoblast bone matrix deposition was reduced and osteoblast differentiation was slowed‐down. Differences were also observed in the growth plate of young transgenic mice where chondrocyte displayed a more immature phenotype and a lower proliferation rate. In bone marrow cell cultures from transgenic mice, the number of osteoclast progenitors was increased whereas in vivo it was increased the number of mature osteoclasts expressing tartrate‐resistant acid phosphatase (TRAP). Finally, while osteoprotegerin (OPG) levels remained unchanged, the expression of the conventional receptor activator of nuclear factor‐κB ligand (RANKL) and of the IL‐6 was enhanced in Tg mice. In conclusion, we found that LCN2 plays a role in bone development and turnover having both a negative effect on bone formation, by affecting growth plate development and interfering with osteoblast differentiation, and a positive effect on bone resorption by enhancing osteoclast compartment. J. Cell. Physiol. 228: 2210–2221, 2013. © 2013 Wiley Periodicals, Inc.
Coupled analysis of Maxwell–Schrödinger equations by using the length gauge: harmonic model of a nanoplate subjected to a 2D electromagnetic field
Authors: Ohnuki Shinichiro , Takeuchi Takashi , Sako Tokuei , Ashizawa Yoshito , Nakagawa Katsuji , Tanaka Masahiro 
Published: April 2013

ABSTRACTA novel algorithm is proposed for solving coupled Maxwell and Schrödinger equations relying on the use of a length gauge form of the coupling between an electromagnetic field and electrons. Numerical simulations using codes implemented with the proposed and conventional algorithms have been performed for a harmonic model of a nanoplate subjected to a pulsed laser field whose central frequency is close to the plasmon frequency. We verify that the proposed algorithm can reduce computational time almost by half as compared with the conventional method. Copyright © 2013 John Wiley & Sons, Ltd.
Fluorescently labeled therapeutic antibodies for detection of microscopic melanoma
Authors: Day Kristine E. , Beck Lauren N. , Deep Nicholas L. , Kovar Joy , Zinn Kurt R. , Rosenthal Eben L. 
Published: April 2013

Objectives/HypothesisDetection of microscopic disease during surgical resection of melanoma remains a significant challenge. To assess real‐time optical imaging for visualization of microscopic cancer, we evaluated three US Food and Drug Administration (FDA)‐approved therapeutic monoclonal antibodies.Study DesignProspective, basic science.MethodsMelanoma cell lines (A375 and SKMEL5) were xenografted into the ears of immunodeficient mice. Bevacizumab, panitumumab, tocilizumab, or a nonspecific immunoglobin G (IgG) were covalently linked to a near‐infrared (NIR) fluorescent probe (IRDye800CW) and systemically injected. Primary tumors were imaged and then resected under fluorescent guidance using the SPY (Novadaq, Toronto, Ontario, Canada), an NIR imaging system used in plastic and reconstructive surgeries to evaluate perfusion. Mice were also imaged with the Pearl Impulse small animal imager (LI‐COR Biosciences, Lincoln, NE), an NIR imaging system designed for use with IRDye800CW. Postresection, small tissue fragments were fluorescently imaged and the presence of tumor subsequently confirmed by correlation with histology.ResultsAll fluorescently labeled therapeutic monoclonal antibodies could adequately delineate tumor from normal tissue based on tumor‐to‐background ratios (TBR) compared to IgG‐IRDye800CW. On serial imaging, panitumumab achieved the highest TBRs with both SPY and Pearl (3.8 and 6.6, respectively). When used to guide resections, the antibody‐dye conjugates generated TBRs in the range of 1.3 to 2.2 (average, 1.6) using the SPY and 1.9 to 6.3 (average, 2.7) using the Pearl. There was no significant difference among the antibodies with either imaging modality or cell line (one‐way analysis of variance).ConclusionsOur data suggest that FDA‐approved antibodies may be suitable targeting agents for the intraoperative fluorescent detection of melanoma. Laryngoscope, 123:2681–2689, 2013
GLOBAL DRIVERS SETTING DESERTIFICATION RESEARCH PRIORITIES: INSIGHTS FROM A STAKEHOLDER CONSULTATION FORUM
Authors: Bisaro Alexander , Kirk Michael , Zdruli Pandi , Zimmermann Willi 
Published: April 2013

ABSTRACTRecent rapid changes in global scale drivers of desertification, land degradation and drought (DLDD) have two important consequences for drylands. First, changes in these drivers, for example in food and energy prices, make improving interventions in drylands more urgent because of their potential impacts. Second, these changes introduce new knowledge gaps regarding both the potential impacts on social‐ecological dryland systems and the design of options to take advantage of opportunities. This paper identifies the most salient research needs in DLDD in drylands brought on by global drivers. The question was addressed through an iterative stakeholder consultative forum. First, relevant global scale drivers were identified through a literature review and preliminary consultation. Next, stakeholders and experts were further consulted to identify research priorities given rise to by these drivers. Identified research priorities were as follows: (i) assessing impacts of rising prices on DLDD in mixed market and subsistence production contexts; (ii) assessing options and limits of agricultural modernisation on fragile lands; (iii) developing methods for assessing land‐use trade‐offs and mapping productive lands; (iv) modelling and participatory methods for monitoring and evaluating soil carbon sequestration; (v) developing policy frameworks to regulate impacts of investment on the environment and local livelihoods; (vi) participatory modelling for regional and local adaptation planning; and (vii) valuation of non‐market land degradation outcomes including biodiversity loss. Concluding, we call for a forward‐looking interdisciplinary drylands research agenda with an increased emphasis on governance to address these priorities. Copyright © 2013 John Wiley & Sons, Ltd.
An Exceptional Rainfall Event in the Central Western Pyrenees: Spatial Patterns in Discharge and Impact
Authors: Serrano‐Muela Maria Pilar , Nadal‐Romero Estela , Lana‐Renault Noemí , González‐Hidalgo José Carlos , López‐Moreno Juan Ignacio , Beguería Santiago , Sanjuan Yasmina , García‐Ruiz José María 
Published: April 2013

AbstractAn exceptional rainfall and hydrological event occurred on 19–21 October 2012 in the central western Pyrenees and was particularly significant in the Upper Aragón River basin and its tributaries, mainly the Irati River. Analysis of historical records showed that, considered separately, the event of 19 and 20 October ranked between the second and fifth highest most extreme daily precipitation events. For the two days combined (with a total between 200 and 260 mm), the precipitation event was the most extreme 2‐day event among all observation stations but one. The consequent flood destroyed part of an urban area, and a long stretch of a national road triggered landslides, enlarged the alluvial plain and caused generalised soil erosion in cultivated fields cropped with winter cereals. Badlands in the marls of the Inner Depression yielded high volumes of sediment. The floods in the tributaries were relatively moderate (return periods of 14–42 years), whereas in the Upper Aragón River, the flood corresponded to a return period of approximately 400–500 years and to 142 years at the end of the Yesa reservoir, although difficulties in estimating the discharge increased the uncertainty of these values. The Yesa and Itoiz reservoirs considerably reduced the intensity of the flood in the middle and lower Aragón River and confirmed the importance of the water level in the reservoirs when such rainfall events occur. The water storage in the Yesa reservoir increased from 16% to 53% as a consequence of the event. More integrated studies are necessary to decrease the risks associated with flood hazards. This is particularly the case in mountain areas, where the steep slopes and longitudinal gradients of the rivers shorten the concentration time of floods and increase the energy that erodes channels and riverbanks. Copyright © 2013 John Wiley & Sons, Ltd.
Nuchal translucency measurement: are qualitative and quantitative quality control processes related?
Authors: Hermann Monika , Fries Nicolas , Mangione Raphaëlle , Boukobza Philippe , Ville Yves , Salomon Laurent J. 
Published: April 2013

ABSTRACTObjectivesTwo types of quality assurance processes for nuchal translucency (NT) measurement have been described: qualitative through review of images and quantitative comparison of operator's specific NT distribution to reference distributions. The aim of this study was to assess the results of these two approaches.MethodsProspective evaluation of sonologists affiliated to the French Ultrasound College who first underwent qualitative evaluation based on the College Français d'Echographie Foetale (CFEF) score. During one year, those same sonologists measured the NT for Down syndrome screening purposes. The operator's specific NT distributions were compared to their CFEF score, their number of unsatisfactory images and their number of NT measurements per year.ResultsThe study involved 1726 sonologists who performed 174 722 first‐trimester examinations. Mean (SD) quantitative score was 23.4/32 (+/−7.4). The median [inter‐quantile range] number of examinations per sonologist was 69 [37; 123]. The median [range] NT multiples of the mean (MoM) value was 0.81 [0.46; 1.22]. NT (MoM) absolute deviation from 1 MoM was significantly correlated with mean score obtained (R2 = −0.17, p < 0.0001), number of unacceptable images (R2 = 0.14, p < 0.0001) and number of ultrasound scans performed per year (R2 = −0.19, p < 0.0001).ConclusionOur results suggest that both processes are clearly related. © 2013 John Wiley & Sons, Ltd.
Reviving Community: The Difficult Practice of Prioritizing Social Capital in Disaster Responses
Authors: Gannon James 
Published: April 2013

AbstractDrawing on his experiences coordinating among overseas donors and local aid groups responding to Japan's 2011 earthquake and tsunami, James Gannon gives high marks to Daniel Aldrich's Building Resilience: Social Capital in Post‐Disaster Recovery. He agrees with the importance of prioritizing social capital in disaster responses, but points out some of the practical challenges and pressures that make this difficult to do. Maintaining social capital sometimes involves difficult trade‐offs, it is less politically appealing than shortsighted “quick fixes,” and when nongovernmental organizations (NGOs) are playing a growing role in the disaster response, it is more difficult for them to convince donors and other stakeholders of the need to prioritize approaches that strengthen social capital over other more tangible and easily understood interventions. Nonetheless, he argues that approaches that harness social capital are essential for sustainable and effective disaster responses.
Age distribution of patients with advanced non-melanoma skin cancer in the United States
Authors: Dacosta Byfield Stacey , Chen Diana , Yim Yeun Mi , Reyes Carolina 
Published: April 2013

AbstractThe epidemiology of non-melanoma skin cancer (NMSC) is not well understood due to exclusion from most US cancer registries. Patients with at least two claims with a NMSC diagnosis (ICD-9-CM 173.xx) at least 60 days apart, or at least one claim for a NMSC-specific treatment from 1/2010 to 12/2010, were identified from a large US commercial insurance claims database and grouped into one of three cohorts: metastatic (MET), locally advanced (LA), or “all other”. MET patients had at least two claims with a metastasis code at least 30 days apart. LA patients had at least two visits to a medical oncologist, one diagnostic imaging service, two radiation therapy services, or one visit to two or more physician specialties. Remaining patients were “all other”. Incidence and prevalence of NMSC were calculated from among the total number of persons continuously enrolled in the plan during the study period and standardized to the 2010 US population. From among 6,610,256 patients, there were 47,451 incident cases of NMSC (MET n = 16, LA n = 387, all other n = 47,048). The age-adjusted incidence rate of 693 per 100,000 persons (2010 population) approximates to 2,139,535 total NMSC cases in the US (0.7 % of population). 671 prevalent cases had advanced disease (MET n = 43, LA n = 628); an age-adjusted rate of 0.6 and 10 per 100,000 US persons equivalent to 1,993 and 29,841 MET and LA cases, respectively. Although NMSCs rarely progress, the number of patients with advanced disease is significant. Further studies to determine proportions of advanced NMSC by subtype are needed.
The Decision to Continue a Pregnancy Affected by Down Syndrome: Timing of Decision and Satisfaction with Receiving a Prenatal Diagnosis
Authors: Hurford Emily , Hawkins Anne , Hudgins Louanne , Taylor Joanne 
Published: April 2013

AbstractIn order to provide the best genetic counseling possible for women who learn of a diagnosis of Down syndrome prenatally, we sought to assess the timing of the decision to continue a pregnancy and the satisfaction these women had with learning this information. Fifty‐six mothers of children with Down syndrome diagnosed prenatally between 2007 and 2010 completed a survey regarding their experience with decision‐making after prenatal diagnosis. Approximately one third (17/56) of participants reported they knew before getting pregnant that they would not terminate for any reason, and almost half of the participants (24/56) reported they did not decide to continue their pregnancy until after the diagnosis. Many participants (82 %; 42/56) stated that learning the diagnosis during pregnancy increased their anxiety. The majority (88 %; 45/56) also reported that if they could do it over again, they would undergo prenatal testing for preparation purposes, despite increased anxiety. Religious and spiritual beliefs as well as feeling attached to the baby were the personal factors that had the greatest impact on most women's decision‐making. Despite increased anxiety caused by learning the diagnosis prenatally, most women favored prenatal diagnosis as it allowed them time to process the information and prepare for the birth of their child.
Combined Use of Ozonation and Biodegradation of Anionic and Non‐ionic Surfactants
Authors: Lechuga Manuela , Fernández‐Arteaga Alejandro , Fernández‐Serrano Mercedes , Jurado Encarnación , Burgos Alejandro , Ríos Francisco 
Published: April 2013

AbstractThis study investigated the extent of primary and final biodegradation of anionic and non‐ionic surfactants to evaluate the combined use of ozonation and biodegradation in surfactant removal. The surfactants used were alkylpolyglucosides and linear alkyl benzene sulfonates. The anionic surfactant containing a benzene ring on its structure was oxidized faster than was the non‐ionic surfactant. Both surfactants showed poor mineralization due to ozonation indicating an ozone attack primarily on carbon bonds. The results indicate that the removal of surfactants and of the total organic carbon is increased by the consecutive use of ozonation and biodegradation.