bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverse halftoning using super‐resolution image processing
Authors: Minami Yuki , Azuma Shun‐ichi , Sugie Toshiharu 
Published: December 2011

AbstractThis paper focuses on the inverse halftoning problem, that is, the problem of reconstructing continuous‐tone images from halftone images of white and black pixels. In general, the problem does not have a unique solution, since halftoning is a many‐to‐one map from continuous‐tone images to binary ones. To this problem, we provide a simple and useful inverse halftoning method, composed of two steps. The first step is to generate several grayscale images from the original halftone image and low‐pass filters. The next step is to reconstruct a continuous‐tone image from the multiple grayscale images by using super‐resolution image processing. This method allows us to obtain good continuous‐tone images which are comparable to the results of the existing methods. The validity of the proposed method is demonstrated by several experiments. © 2011 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
A wireless sensor network for precision agriculture and its performance
Authors: Sahota Herman , Kumar Ratnesh , Kamal Ahmed 
Published: December 2011

ABSTRACTThe use of wireless sensor networks is essential for implementation of information and control technologies in precision agriculture. We present our design of network stack for such an application where sensor nodes periodically collect data from fixed locations in a field. Our design of the physical layer consists of multiple power modes in both the receive and transmit operations for the purpose of achieving energy savings. In addition, we design our MAC layer to use these multiple power modes to improve the energy efficiency of wake‐up synchronization phase. Our MAC protocol also organizes all the sender nodes to be synchronized with the receiver simultaneously and transmit their data in a time scheduled manner. Next, we design our energy aware routing strategy that balances the energy consumption over the nodes in the entire field and minimizes the number of wake‐up synchronization overheads by scheduling the nodes for transmission in accordance with the structure of the routing tree. We develop analytical models and simulation studies to compare the energy consumption of our MAC protocol with that of the popular S‐MAC protocol for a typical network topology used in our application under our routing strategy. Our MAC protocol is shown to have better energy efficiency as well as latency in a periodic data collection application. We also show the improvements resulting from the use of our routing strategy, in simulations, compared with the case when the next hop is chosen randomly from the set of neighbors that are closer to the sink node. Copyright © 2011 John Wiley & Sons, Ltd.
Proposed new simple scoring system to identify indications for urgent ERCP in acute cholangitis based on the Tokyo Guidelines
Authors: Nishino Takayoshi , Onizawa Shunsuke , Hamano Mie , Shirato Izumi , Shirato Miho , Hamano Tetsuya , Tagata Tomoko , Araida Tatsuo , Mitsunaga Atsushi 
Published: December 2011

AbstractBackground/purposeThe Tokyo Guidelines (TG) have enabled more accurate diagnosis of acute cholangitis (AC). This study was undertaken to develop a new prognostic scoring system to predict the need for urgent endoscopic retrograde cholangiopancreatography (ERCP) based on the clinical findings on admission.MethodsWe prospectively reviewed 40 consecutive cases of AC and divided them into an urgent‐ERCP group and an elective‐ERCP group.ResultsUnivariate analysis identified four factors that predicted the need for urgent ERCP: serum albumin level below 3.0 g/dl, blood urea nitrogen level above 20 mg/dl, platelet count below 120,000/μl, and the presence of systemic inflammatory response syndrome. These four predictors plus four predictors of organ dysfunction in the TG: shock, consciousness disturbance, respiratory failure, and prothrombin time/international normalized ratio >1.5, were used to devise a scoring system in which 1 point was assigned for the first four predictors and 2 points were assigned for the latter four predictors (maximum score possible: 12 points). The receiver‐operator characteristic curve of the scores showed good test performance for predicting the need for urgent ERCP and for predicting a positive blood culture, and the areas under the concentration curves (AUCs) were 0.96 and 0.97, respectively. The optimal cut‐off value for urgent ERCP was 2 points.ConclusionsThis new simple scoring system allows identification of high‐risk AC patients soon after admission to hospital.
Measuring the distance between multiple sequence alignments
Authors: Blackburne Benjamin P. , Whelan Simon 
Published: December 2011

Abstract
Motivation: Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses.
Results: We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them.
Availability: MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.
Contact: simon.whelan@manchester.ac.uk
Read count approach for DNA copy number variants detection
Authors: Magi Alberto , Tattini Lorenzo , Pippucci Tommaso , Torricelli Francesca , Benelli Matteo 
Published: December 2011

Abstract
Motivation: The advent of high-throughput sequencing technologies is revolutionizing our ability in discovering and genotyping DNA copy number variants (CNVs). Read count-based approaches are able to detect CNV regions with an unprecedented resolution. Although this computational strategy has been recently introduced in literature, much work has been already done for the preparation, normalization and analysis of this kind of data.
Results: Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform.
Contact: albertomagi@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
ART: a next-generation sequencing read simulator
Authors: Huang Weichun , Li Leping , Myers Jason R. , Marth Gabor T. 
Published: December 2011

Abstract
Summary: ART is a set of simulation tools that generate synthetic next-generation sequencing reads. This functionality is essential for testing and benchmarking tools for next-generation sequencing data analysis including read alignment, de novo assembly and genetic variation discovery. ART generates simulated sequencing reads by emulating the sequencing process with built-in, technology-specific read error models and base quality value profiles parameterized empirically in large sequencing datasets. We currently support all three major commercial next-generation sequencing platforms: Roche's 454, Illumina's Solexa and Applied Biosystems' SOLiD. ART also allows the flexibility to use customized read error model parameters and quality profiles.
Availability: Both source and binary software packages are available at http://www.niehs.nih.gov/research/resources/software/art
Contact: weichun.huang@nih.gov; gabor.marth@bc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Stroke aetiology and predictors of outcome in patients with heart failure and acute stroke: a 10‐year follow‐up study
Authors: Vemmos Kostas , Ntaios George , Savvari Paraskevi , Vemmou Anastasia M. , Koroboki Eleni , Manios Efstathios , Kounali Anna , Lip Gregory Y.H. 
Published: December 2011

AimsThe aim of this study was to investigate stroke aetiology and assess the predictors of early and late outcome in patients with heart failure (HF) and acute stroke.Methods and resultsA total of 2904 patients, admitted between 1993 and 2010, were regularly followed up at months 1, 3, and 6, and yearly thereafter up to 10 years. There were 283 (9.7%) stroke patients with HF; atrial fibrillation (AF) was present in 144 (50.9%) of them. Stroke aetiology in patients with HF and AF was mainly cardioembolism (82%) regardless of HF aetiology. In contrast, in the 139 non‐AF patients with HF, the stroke mechanism was associated with the aetiology of HF: valvular heart disease and dilated cardiomyopathy were related to cardioembolism in 60% and 66.7% of patients, respectively, whereas HF due to coronary artery disease or hypertension was associated with atherosclerotic and lacunar stroke in 40.8% and 61.5%, respectively. In the overall population, HF was an independent predictor of 10‐year mortality [hazard ratio = 1.54, 95% confidence interval (CI) 1.29–1.83; P < 0.001]. Probability of 10‐year survival was 19.4% (95% CI 14.5–23.5) for HF patients and 44.1% (95% CI 41.4–46.8) for non‐HF patients (P < 0.0001). Ten‐year mortality in HF patients was associated with functional class of HF, age, diabetes, stroke severity, and in‐hospital aspirin use. The presence of AF in HF stroke patients did not influence 10‐year survival and composite cardiovascular events (P = 0.429 and P = 0.406, respectively).ConclusionsIn patients with HF, stroke aetiology is influenced by the presence of AF and the underlying cause of HF. Early and late stroke outcome is associated with HF severity but not with the presence of AF.
Muscle pain and serum creatine kinase are not associated with low serum 25(OH) vitamin D levels in patients receiving statins
Authors: Kurnik Daniel , Hochman Israel , Vesterman‐Landes Janet , Kenig Tali , Katzir Itzhak , Lomnicky Yosef , Halkin Hillel , Loebstein Ronen 
Published: December 2011

SummaryObjective  Vitamin D deficiency has been associated in some studies with nonspecific musculoskeletal pain and, more specifically, with statin‐induced myalgia, which was ameliorated by high‐dose vitamin D supplements. Our objective was to explore the association between vitamin D status and statin‐induced myalgia and elevation of serum creatine kinase (CK).Design  Retrospective cohort study, based on the electronic database of a health maintenance organization.Patients  Six thousand eight hundred and eight patients (71·5% women) to whom statins were dispensed during 2008 and who had ≥1 CK and 25‐hydroxy vitamin D (25OHD) levels measured during statin exposure. Of these, 376 patients (5·5%) had switched from a first‐line statin to atorvastatin because of muscle pain (n = 220) or other reasons (n = 156).Measurements  In the entire cohort, we compared serum CK levels among serum 25OHD quartiles. In addition, we compared CK and 25OHD levels among patients with myalgia, other switchers and nonswitchers.Results  The median 25OHD level in the entire cohort was 21·8 ng/ml [interquartile range (IQR), 16·3–27·4]. CK levels were marginally lower in patients in the lowest 25OHD quartile [median CK (IQR) in 25OHD quartiles 1–4, 87 (61–130), 90 (65–131), 91 (65–132) and 91 (67–131) IU/ml, respectively; P = 0·007]. 25OHD levels in statin switchers were similar to those in nonswitchers; moreover, there were no differences in 25OHD among switchers with muscle pain and other switchers.Conclusion  Our findings do not support an association between low 25OHD levels and statin‐induced myalgia or CK elevation.
Changes in heart valve structure and function in patients treated with dopamine agonists for prolactinomas, a 2‐year follow‐up study
Authors: Delgado Victoria , Biermasz Nienke R. , van Thiel Sjoerd W. , Ewe See H. , Marsan Nina Ajmone , Holman Eduard R. , Feelders Richard A. , Smit Johannes W. A. , Bax Jeroen J. , Pereira Alberto M. 
Published: December 2011

SummaryObjective  The use of ergot‐derived dopamine agonists (DA) to treat patients with prolactinomas has not been associated with an increased risk of significant heart valve dysfunction. Accordingly, the present study evaluated whether the long‐term use of DA for hyperprolactinaemia may be associated with increased risk of significant valvular heart disease.Methods  A total of 74 patients (mean age 48 ± 1·4 years, 23% male) with prolactinoma treated with DA for at least 1 year were evaluated with 2‐dimensional echocardiography at baseline. After 2 years of follow‐up, a repeat echocardiography was performed to evaluate significant changes in valvular heart structure (thickening, calcifications and leaflet motion abnormalities) and function (regurgitation or stenosis). Patients were classified according to treatment: patients treated with cabergoline (group 1: n = 45), and patients not treated with cabergoline (group 2: n = 29).Results  At 2‐year follow‐up, no significant valvular stenosis was observed in any patient. In addition, the prevalence of any significant valve regurgitation did not change significantly (from 12% to 15%, P = NS). However, there was a significant increase in the prevalence of valvular calcifications (from 48% to 58%, P = 0·004) and, particularly, in the prevalence of aortic valve calcifications (from 39% to 53%, P = 0·002). In a per‐treatment‐based analysis, the group of patients treated with cabergoline had significantly higher prevalence of aortic valve calcification at 2 years follow‐up as compared to the group of patients not treated with cabergoline (63%vs 38%, P = 0·016).Conclusions  The long‐term therapy with DA (cabergoline) of patients with prolactinoma is associated with an increased prevalence of valvular calcification. However, these structural changes were not accompanied by an increased prevalence of valvular dysfunction.
Volatile and nonvolatile chemical composition of some date fruits (Phoenix dactylifera L.) harvested at different stages of maturity
Authors: El Arem Amira , Saafi Emna B. , Flamini Guido , Issaoui Manel , Ferchichi Ali , Hammami Mohamed , Helall Ahmed N. , Achour Lotfi 
Published: December 2011

SummaryPhysico‐chemical and aroma volatile compositions of three date palm cultivars were studied throughout fruit maturation (besser, rutab and tamr stages) during 2008 harvest season. The studied parameters varied significantly through the different stages, with some variations also depending on the cultivar. Length and width of the three types of dates showed a progressive decrease during ripening. The pH level, total sugars and ash contents significantly increased up to tamr stage. Conversely, moisture, lipid and protein contents decreased. The profile of the volatile aroma compounds was evaluated using solid‐phase micro‐extraction. Sixty‐nine compounds were detected during maturation, accounting from 98.5% to 99.6% at besser, 93.1% to 99.2% at rutab and 94.3% to 98.4% at tamr stages of the total identified volatiles. The present study sheds more light on chemical characteristics of the studied cultivars that can be used in many industrial processes.
New ecological nixtamalisation process for tortilla production and its impact on the chemical properties of whole corn flour and wastewater effluents
Authors: Campechano Carrera Elsa María , de Dios Figueroa Cárdenas Juan , Arámbula Villa Gerónimo , Martínez Flores Héctor Eduardo , Jiménez Sandoval Sergio J. , Luna Bárcenas J. Gabriel 
Published: December 2011

SummaryAn ecological nixtamalisation process (EP) for making whole corn flour for tortillas was compared with the traditional nixtamalisation process (TP). One of the problems of TP is high level of solid losses. The aim was to evaluate the composition of these losses. In EP, dry matter losses of nejayote were from 1.2% to 1.4%, while in TP 3.2%. Nejayote from TP showed a pH of 11.9, whereas EP showed a pH close to neutral. The pericarp was retained in EP with the use of calcium salts, whereas in TP lime destroyed it almost completely. Losses of total dietary fibre in nejayote solids were about 41.2% for TP compared to an average of 17.4% for EP. Most of nejayote losses in TP were soluble fibre (30.4%), compared with EP that ranged from 6.2% to 7.9%. All compounds retained by nixtamal from EP are important sources of nutrients and dietary fibre.
Effect of nanocomposite‐based packaging on preservation quality of green tea
Authors: Zhao Liyan , Li Feng , Chen Guitang , Fang Yong , An Xinxin , Zheng Yonghua , Xin Zhihong , Zhang Min , Yang Yanting , Hu Qiuhui 
Published: December 2011

SummaryAn improved nanocomposite‐based packaging material (NCP) was prepared by blending polyethylene with nano‐Ag, nano‐TiO2 and attapulgite. And its effect on preservation quality of green tea (Biluochun and Qingfeng) during one‐year ambient storage was investigated. The results showed that adding nanoparticles to the polyethylene could significantly improve the barrier property. After one‐year ambient storage, the moisture of Biluochun and Qingfeng with NCP was decreased by 10.3% and 6.1% compared with the normal packaging material. Meanwhile, the contents of amino acid, tea polyphenols, chlorophyll and ascorbic acid were increased by 22.8%, 9.4%, 30.4% and 9.5% for Biluochun and 19.2%, 9.3%, 27.3% and 21.6% for Qingfeng, respectively, compared with the normal packaging material. Moreover, the sensory quality of NCP was also superior to that with the control. Therefore, the improved NCP material probably provides an attractive alternative to maintain the preservation quality of green tea at a high level during storage.
Development of made‐in‐transit set culture yoghurt: effect of increasing the concentration of reconstituted skim milk as the milk base
Authors: Nor‐Khaizura Mahmud‐Ab‐Rashid , Flint Steve H. , McCarthy Owen J. , Palmer Jon S. , Golding Matt , Jaworska Agata 
Published: December 2011

SummaryThe fermentation time, yoghurt acidity expressed as lactic acid, starter culture growth, viscosity and firmness of made‐in‐transit (MIT) set culture yoghurt produced using different concentrations of reconstituted skim milk powder (SMP) from 12% to 20% (w/v) as the milk base were investigated. All milk base formulations were ultra‐high temperature sterilised at 138 °C for 6 s. The results revealed that increasing the SMP concentration increased the viscosity and firmness of MIT set culture yoghurt. At 20% SMP, viscosity and firmness were 4650.8 cP and 1.266 N, respectively. Fermentation of MIT set culture yoghurt with 20% SMP was observed to be faster than with the other conditions. The fermentation time for a medium containing from 14% to 20% SMP could be extended to 168 h, reaching a final pH of 4.50–4.37 and at the same time improving the texture of the MIT set culture yoghurt. The SMP concentration had no influence on the total viable counts of starter bacteria in the yoghurt. The texture of MIT set culture yoghurt may be improved by increasing the concentration of SMP.
Moringa oleiferia leaves extract: a natural antioxidant for retarding lipid peroxidation in cooked goat meat patties
Authors: Das Arun Kumar , Rajkumar Vincent , Verma Arun Kumar , Swarup Devendra 
Published: December 2011

SummaryThe effective utilisation of Moringa oleiferia mature leaves (MOL) extract as an antioxidant in cooked goat meat patties during refrigerated storage was investigated, and its efficiency was evaluated against butylated hydroxytoluene (BHT). The extract exhibited high phenolic content (48.36 mg of gallic acid equivalent per g), flavonoid (31.42 mg g−1 of sample) being the major component. Moringa oleiferia mature leaves extract showed excellent antioxidant activity as determined by radical‐scavenging activity of 1, 1‐diphenyl 2 picrylhydrazyl (DPPH). The IC50 value of MOL extract for 2, 2‐diphenyl‐1‐picrylhydrazyl radical scavenging was 18.54 μg mL−1. Total phenolic content (as gallic acid equivalent) significantly (P < 0.05) increased from 285.56 in control to 379.45 in patties with MOL extract. MOL extract (0.1%) when added to meat was found to retard lipid peroxidation of cooked goat meat patties as measured by TBARS number during refrigerated storage. The increase in TBARS number in MOL extract–treated samples was very slow and remained lowest (0.53 mg malonaldehyde per kg sample) up to 15 days. The antioxidant activity of MOL extract was found to be comparable to BHT. Addition of MOL extract did not affect any of the sensory attributes of patties. The MOL extract at a level of 100 mg/100 g meat was sufficient to protect goat meat patties against oxidative rancidity for periods longer than the most commonly used synthetic antioxidant like BHT.
Antioxidant activity and consumer acceptance of grape seed flour‐containing food products
Authors: Rosales Soto Maria U. , Brown Kelsie , Ross Carolyn F. 
Published: December 2011

SummaryGrape seed flour (GSF) is produced from the pomace waste generated during winemaking. The inclusion of Merlot and Cabernet Sauvignon GSFs in cereal bars, pancakes and noodles was evaluated using antioxidant activity measurements [2,2 diphenyl‐1‐picrylhydrazyl (DPPH) radical scavenging]. Each product (noodles, pancakes and cereal bars) was also evaluated on separate days for consumer acceptance (n = 100 per panel). In comparing antioxidant activities, the highest DPPH radical‐scavenging activity was in pancakes containing Cabernet Sauvignon GSF (25% and 30%), noodles containing Cabernet Sauvignon GSF (20%) and cereal bars containing Merlot GSF (5%). From consumer sensory evaluation, cereal bars made with Merlot GSF, control pancakes and control noodles had high consumer acceptance. Products with low consumer acceptance included pancakes containing 25% Cabernet Sauvignon GSF and noodles containing 20% Cabernet Sauvignon GSF. Overall, the cereal bar containing 5% Merlot GSF showed a good balance of high antioxidant activity with consumer acceptability, making this a promising GSF‐containing new food product.