bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dynamic soil chamber system coupled with a tunable diode laser for online measurements of δ13C, δ18O, and efflux rate of soil‐respired CO2
Authors: Powers Heath H. , Hunt John E. , Hanson David T. , McDowell Nate G. 
Published: January 2010

AbstractHigh frequency observations of the stable isotopic composition of CO2 effluxes from soil have been sparse due in part to measurement challenges. We have developed an open‐system method that utilizes a flow‐through chamber coupled to a tunable diode laser (TDL) to quantify the rate of soil CO2 efflux and its δ13C and δ18O values (δ13CR and δ18OR, respectively). We tested the method first in the laboratory using an artificial soil test column and then in a semi‐arid woodland. We found that the CO2 efflux rates of 1.2 to 7.3 µmol m−2 s−1 measured by the chamber‐TDL system were similar to measurements made using the chamber and an infrared gas analyzer (IRGA) (R2 = 0.99) and compared well with efflux rates generated from the soil test column (R2 = 0.94). Measured δ13C and δ18O values of CO2 efflux using the chamber‐TDL system at 2 min intervals were not significantly different from source air values across all efflux rates after accounting for diffusive enrichment. Field measurements during drought demonstrated a strong dependency of CO2 efflux and isotopic composition on soil water content. Addition of water to the soil beneath the chamber resulted in average changes of +6.9 µmol m−2 s−1, −5.0‰, and −55.0‰ for soil CO2 efflux, δ13CR and δ18OR, respectively. All three variables initiated responses within 2 min of water addition, with peak responses observed within 10 min for isotopes and 20 min for efflux. The observed δ18OR was more enriched than predicted from temperature‐dependent H2O‐CO2 equilibration theory, similar to other recent observations of δ18OR from dry soils (Wingate L, Seibt U, Maseyk K, Ogee J, Almeida P, Yakir D, Pereira JS, Mencuccini M. Global Change Biol. 2008; 14: 2178). The soil chamber coupled with the TDL was found to be an effective method for capturing soil CO2 efflux and its stable isotope composition at high temporal frequency. Published in 2010 by John Wiley & Sons, Ltd.
A new class of anthocyanin‐procyanidin condensation products detected in red wine by electrospray ionization multi‐stage mass spectrometry analysis
Authors: Sun Baoshan , Fernandes Tiago A. , Spranger M. Isabel 
Published: January 2010

AbstractIn our previous work, we have identified, in a model wine solution containing malvidin 3‐glucoside, epicatechin and acetaldehyde, a new condensation product – hydroxylethyl‐malvidin‐3‐glucoside‐ethyl‐epicatechin. The objective of this work was to verify the presence of such new condensation products in red wine. For this purpose, red wine was fractionated into various fractions by column chromatography on LiChroprep RP 18 and on Toyopearl 40 (F). The phenolic composition of each fraction was verified by HPLC‐DAD and direct‐infusion ESI‐MSn analysis. In addition to the well‐known anthocyanins and their acetyl and coumaroyl derivatives, and several direct and indirect anthocyanin‐(epi)catechin condensation products, a new class of pigmented products, namely hydroxyethyl‐anthocyanin‐ethyl‐flavanol compounds, have been detected in red wine. The new class of pigmented products would be expected to be the major pigments responsible for the color of aged red wine. Copyright © 2010 John Wiley & Sons, Ltd.
The effects of differentiated water supply after anthesis and nitrogen fertilization on δ15N of wheat grain
Authors: Raimanová Ivana , Haberle Jan 
Published: January 2010

AbstractThe δ15N signature of plants integrates various processes in soil and plant. In this study, the effect of different water regimes applied during the period of grain growth of winter wheat on grain δ15N was examined in a 4‐year field experiment. The treatments comprised water shortage (S), an ample water supply (W), and rain‐fed crop (R). Zero fertilization (N0) and 200 kg N.ha−1 in mineral fertilizer (N1) treatments were studied. The grain 15N was determined during grain growth and at maturity. The water regime, nitrogen application and year had a significant effect on mature grain δ15N (p < 0.001). Water and nitrogen explained 54.6% of the variability of δ15N in the experiment, the year accounted for 10.7% and the interactions for another 19.6% of the total variability. The analysis of non‐mature grain δ15N showed significant effects of N and year but not of water. Nitrogen fertilization reduced the δ15N of mature grain in years by 0.7–6.3‰ in comparison with N0 plants; the reduction was more pronounced under stress (average reduction by 4.1‰) than under rain‐fed (2.4‰) and ample water supply (2.2‰). Water stress decreased the grain δ15N in fertilized wheat, by 0.1–2.1‰ and 0.6–3.6‰ in experimental years, on average by 1.30‰ and 1.79‰ in comparison with the R and W water supply, respectively. The effect of water supply was not significant in non‐fertilized wheat. A significant negative linear relationship between grain N concentration and δ15N in maturity or during the grain growth (R2 = 0.83, R2 = 0.76, respectively) was found. The observed sources of grain δ15N variability should be taken into consideration when analyzing and interpreting the data on the δ15N signature of plant material from field conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Desulfurization of cysteine‐containing peptides resulting from sample preparation for protein characterization by mass spectrometry
Authors: Wang Zhouxi , Rejtar Tomas , Zhou Zhaohui Sunny , Karger Barry L. 
Published: January 2010

AbstractIn this study, we have examined two cysteine modifications resulting from sample preparation for protein characterization by mass spectrometry (MS): (1) a previously observed conversion of cysteine into dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine into alanine. Using model peptides, the conversion of cysteine into dehydroalanine via β‐elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37°C, pH 7.0–9.0) without disulfide reduction and alkylation. Furthermore, the surprising conversion of cysteine into alanine was shown to occur by heating cysteine‐containing peptides in the presence of a phosphine (tris(2‐carboxyethyl)phosphine hydrochloride (TCEP)). The formation of alanine from cysteine, investigated by performing experiments in H2O or D2O, suggested a radical‐based desulfurization mechanism unrelated to β‐elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluation and performance of desorption electrospray ionization using a triple quadrupole mass spectrometer for quantitation of pharmaceuticals in plasma
Authors: Kennedy Joseph H. , Wiseman Justin M. 
Published: January 2010

AbstractThe present work describes the methodology and investigates the performance of desorption electrospray ionization (DESI) combined with a triple quadrupole mass spectrometer for the quantitation of small drug molecules in human plasma. Amoxepine, atenolol, carbamazepine, clozapine, prazosin, propranolol and verapamil were selected as target analytes while terfenadine was selected as the internal standard common to each of the analytes. Protein precipitation of human plasma using acetonitrile was utilized for all samples. Limits of detection were determined for all analytes in plasma and shown to be in the range 0.2–40 ng/mL. Quantitative analysis of amoxepine, prazosin and verapamil was performed over the range 20–7400 ng/mL and shown to be linear in all cases with R2 >0.99. In most cases, the precision (relative standard deviation) and accuracy (relative error) of each method were less than or equal to 20%, respectively. The performance of the combined techniques made it possible to analyze each sample in 15 s illustrating DESI tandem mass spectrometry (MS/MS) as powerful tool for the quantitation of analytes in deproteinized human plasma. Copyright © 2010 John Wiley & Sons, Ltd.
Real‐time measurement of peroxyacetyl nitrate using selected ion flow tube mass spectrometry
Authors: Hastie Donald R. , Gray John , Langford Vaughan S. , Maclagan Robert G. A. R. , Milligan Daniel B. , McEwan Murray J. 
Published: January 2010

AbstractThe on‐line detection of gaseous peroxyacetyl nitrate (PAN) using selected ion flow tube mass spectrometry (SIFT‐MS) has been investigated using a synthetic sample of PAN in air at a humidity of ∼30%. Using the H3O+ reagent ion, signals due to PAN at m/z 122, 77 and 95 have been identified. These correspond to protonated PAN, protonated peractetic acid and its water cluster, respectively. These products and their energetics have been probed through quantum mechanical calculations. The rate coefficient of H3O+ has been estimated to be 4.5 × 10−9 cm3 s−1, leading to a PAN sensitivity of 138 cps/ppbv. This gives a limit of detection of 20 pptv in 10 s using the [M+H]+ ion of PAN at m/z 122. Copyright © 2010 John Wiley & Sons, Ltd.
A quick and easy method to identify bacteria by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry
Authors: Pennanec Xaviera , Dufour Alain , Haras Dominique , Réhel Karine 
Published: January 2010

AbstractConcerns with water quality have increased in recent years, in part due to the more frequent contamination of water by pathogens like E. coli and L. pneumophila. Current methods for the typing of bacteria in water samples are based on culture of samples on specific media. These techniques are time‐consuming, subject to the impact of interferents and do not totally meet all the requirements of prevention. There is a need for accurate and rapid identification of these microorganisms. This report deals with the detection of bacteria, more precisely of Legionella spp., and the development of an analytical strategy for a rapid and unambiguous identification of these pathogens in water from diverse origins. Therefore, a protein mass mapping using matrix‐assisted laser desorption/ionisation mass spectrometry (MALDI MS) of whole bacteria combined with a home‐made database of bacteria spectra is applied. A large variety of different bacteria and microorganisms is used to approach the actual composition of samples with numerous interferents. The objective is to propose a universal method for sampling preparation before MALDI MS analysis and optimised spectrometric conditions for reproducible intense peaks. Several experimental factors known to influence signal quality such as time and media of culture have been studied. The proposed method gives promising results for a sure differentiation of Legionella species and subspecies and a rapid identification of bacteria which are the most dangerous or difficult to eradicate. This method is easy to perform with an excellent reproducibility. The analytical protocol and the corresponding database were validated on samples from different origins (cooling tower, plumbing hot water). Copyright © 2010 John Wiley & Sons, Ltd.
Anti‐retroviral activity of TRIM5α
Authors: Nakayama Emi E. , Shioda Tatsuo 
Published: January 2010

AbstractHuman immunodeficiency virus type 1 (HIV‐1) shows a very narrow host range limited to humans and chimpanzees. Experimentally, HIV‐1 does not infect Old World monkeys, such as rhesus (Rh) and cynomolgus (CM) monkeys, and fails to replicate in activated CD4 positive T lymphocytes obtained from these monkeys. In contrast, simian immunodeficiency virus isolated from a macaque monkey (SIVmac) can replicate well in both Rh and CM. In 2004, tripartite motif 5α (TRIM5α) was identified as a host factor which plays an important role in the restricted host range of HIV‐1. Rh and CM TRIM5α restrict HIV‐1 infection but not SIVmac, while in comparison, anti‐viral activity of human TRIM5α against those viruses is very weak. TRIM5α consists of the RING, B‐box 2, coiled‐coil and SPRY (B30.2) domains. The RING domain is frequently found in E3 ubiquitin ligase and TRIM5α is degraded via the ubiquitin‐proteasome pathway during HIV‐1 restriction. TRIM5α recognises the multimerised capsid (viral core) of an incoming virus by its α‐isoform specific SPRY domain and is believed to be involved in innate immunity to control retroviral infection. Differences in amino acid sequences in the SPRY domain of TRIM5α of different monkey species were found to affect species‐specific restriction of retrovirus infection, while differences in amino acid sequences in the viral capsid protein determine viral sensitivity to restriction. Accurate structural analysis of the binding surface between the viral capsid protein and TRIM5α SPRY is thus required for the development of new antiretroviral drugs that enhance anti‐HIV‐1 activity of human TRIM5α. Copyright © 2009 John Wiley & Sons, Ltd.
Kinematic reconfigurability control for an environmental mobile robot operating in the Amazon rain forest
Authors: Freitas Gustavo , Gleizer Gabriel , Lizarralde Fernando , Hsu Liu , dos Reis Ney Robinson Salvi 
Published: January 2010

AbstractThis paper addresses the active control problem of reconfigurable mobile robots on irregular terrain. Different kinematic control strategies to improve robot mobility are proposed based on (a) ground clearance and orientation, (b) ground clearance and stability margin, and (c) wheel traction efficiency. Owing to conflicting objectives associated with these strategies, a multi‐objective optimization approach is formulated to determine a set of optimal solutions and establish a trade‐off optimal solution. The proposed control is validated through numerical simulations and experimental tests using an amphibious wheel‐legged robot, named Environmental Hybrid Robot, designed for environmental monitoring in the Amazon rain forest. © 2010 Wiley Periodicals, Inc.
Analysis of textile fibers by in‐air PIXE
Authors: Jezeršek D. , Jakomin S. , Šmit Ž. 
Published: January 2010

AbstractTrace elements in textile fibers were analyzed by the in‐air particle induced X‐ray emission (PIXE) method. Individual fibers were used as a target, representing minute material available in forensic or archeological applications. For quantification of the concentrations, the X‐ray production was assumed to occur in a thin cylindrical target that intersects the central part of the beam. The irradiated volume and the distribution of escape lengths were calculated in the model. The impact beam intensity was axially symmetric Gaussian, as shown by calculation and cross‐scan measurements. The normalization procedure relied on the argon signal from the air, which was checked by the chopper method. For a set of fibers, elements characteristic of the fibers and their dressings were determined. Copyright © 2010 John Wiley & Sons, Ltd.
A Bayesian approach to joint modeling of protein–DNA binding, gene expression and sequence data
Authors: Xie Yang , Pan Wei , Jeong Kyeong S. , Xiao Guanghua , Khodursky Arkady B. 
Published: January 2010

AbstractThe genome‐wide DNA‐protein‐binding data, DNA sequence data and gene expression data represent complementary means to deciphering global and local transcriptional regulatory circuits. Combining these different types of data can not only improve the statistical power, but also provide a more comprehensive picture of gene regulation. In this paper, we propose a novel statistical model to augment protein–DNA‐binding data with gene expression and DNA sequence data when available. We specify a hierarchical Bayes model and use Markov chain Monte Carlo simulations to draw inferences. Both simulation studies and an analysis of an experimental data set show that the proposed joint modeling method can significantly improve the specificity and sensitivity of identifying target genes as compared with conventional approaches relying on a single data source. Copyright © 2010 John Wiley & Sons, Ltd.
Robust non‐linear mixed modelling of longitudinal PSA levels after prostate cancer treatment
Authors: Subtil F. , Rabilloud M. 
Published: January 2010

AbstractThe objective of this study was to develop a robust non‐linear mixed model for prostate‐specific antigen (PSA) measurements after a high‐intensity focused ultrasound (HIFU) treatment for prostate cancer. The characteristics of these data are the presence of outlying values and non‐normal random effects. A numerical study proved that parameter estimates can be biased if these characteristics are not taken into account. The intra‐patient variability was described by a Student‐t distribution and Dirichlet process priors were assumed for non‐normal random effects; a process that limited the bias and provided more efficient parameter estimates than a classical mixed model with normal residuals and random effects. It was applied to the determination of the best dynamic PSA criterion for the diagnosis of prostate cancer recurrence, but could be used in studies that rely on PSA data to improve prognosis or compare treatment efficiencies and also with other longitudinal biomarkers that, such as PSA, present outlying values and non‐normal random effects. Copyright © 2010 John Wiley & Sons, Ltd.
Hybrid pooled–unpooled design for cost‐efficient measurement of biomarkers
Authors: Schisterman Enrique F. , Vexler Albert , Mumford Sunni L. , Perkins Neil J. 
Published: January 2010

AbstractEvaluating biomarkers in epidemiological studies can be expensive and time consuming. Many investigators use techniques such as random sampling or pooling biospecimens in order to cut costs and save time on experiments. Commonly, analyses based on pooled data are strongly restricted by distributional assumptions that are challenging to validate because of the pooled biospecimens. Random sampling provides data that can be easily analyzed. However, random sampling methods are not optimal cost‐efficient designs for estimating means. We propose and examine a cost‐efficient hybrid design that involves taking a sample of both pooled and unpooled data in an optimal proportion in order to efficiently estimate the unknown parameters of the biomarker distribution. In addition, we find that this design can be used to estimate and account for different types of measurement and pooling error, without the need to collect validation data or repeated measurements. We show an example where application of the hybrid design leads to minimization of a given loss function based on variances of the estimators of the unknown parameters. Monte Carlo simulation and biomarker data from a study on coronary heart disease are used to demonstrate the proposed methodology. Published in 2010 by John Wiley & Sons, Ltd.
Hierarchical multicast in wireless sensor networks with mobile sinks
Authors: Hwang Shiow‐Fen , Lu Kun‐Hsien , Su Yi‐Yu , Hsien Chi‐Sen , Dow Chyi‐Ren 
Published: January 2010

AbstractIn most studies of wireless sensor networks (WSNs), sensor nodes and sinks are typically stationary. However, mobile sinks are required in various applications of real‐life environments, and delivering sensed data to mobile sinks using ordinary routing protocols is very inefficient. Multicasting is an important process in the minimization of the number of transmissions in WSNs. Since sensor nodes have limited resources, many studies have focused on how to send data to specific receivers efficiently. This work presents a grid‐based hierarchical multicast (HM) routing protocol for WSNs with mobile sinks. Location servers (LSs) are adopted to manage the information about the locations of receivers and then a multicast tree is constructed distributively to reduce the update cost and energy consumed by sink mobility. The multicast tree can be shared by multiple sources, reducing the path construction overhead. Furthermore, effective maintenance mechanisms that make the multicast tree more stable and robust are presented. Finally, the performance of the proposed HM is investigated by simulation. Simulation results demonstrate that the proposed protocol has a lower energy consumption and higher multicast efficiency than distributed multicast routing protocol (DMRP) and hierarchical geographic multicast routing (HGMR), especially when many sources and receivers are involved. Copyright © 2010 John Wiley & Sons, Ltd.
Standard Outpatient Re‐Evaluation for Patients Not Admitted to the Hospital After Emergency Department Evaluation for Acute Abdominal Pain
Authors: Toorenvliet Boudewijn R. , Bakker Rutger F. R. , Flu Hans C. , Merkus Jos W. S. , Hamming Jaap F. , Breslau Paul J. 
Published: January 2010

AbstractBackgroundThe aim of the present study was to investigate the efficacy and safety of standard outpatient re‐evaluation for patients who are not admitted to the hospital after emergency department surgical consultation for acute abdominal pain.MethodsAll patients seen at the emergency department between June 2005 and July 2006 for acute abdominal pain were included in a prospective study using a structured diagnosis and management flowchart. Patients not admitted to the hospital were given appointments for re‐evaluation at the outpatient clinic within 24 h. All clinical parameters, radiological results, diagnostic considerations, and management proposals were scored prospectively.ResultsFive‐hundred patients were included in this analysis. For 148 patients (30%), the final diagnosis was different from the diagnosis after initial evaluation. Eighty‐five patients (17%) had a change in management after re‐evaluation, and 20 of them (4%) were admitted to the hospital for an operation. Only 6 patients (1.2%) had a delay in diagnosis and treatment, which did not cause extra morbidity.ConclusionsStandard outpatient re‐evaluation is a safe and effective means of improving diagnostic accuracy and helps to adapt management for patients that are not admitted to the hospital after surgical consultation for acute abdominal pain at the emergency department.
An Algorithm Informed by the Parathyroid Hormone Level Reduces Hypocalcemic Complications of Thyroidectomy
Authors: Wiseman James E. , Mossanen Matthew , Ituarte Philip H. G. , Bath Jonathan M. T. , Yeh Michael W. 
Published: January 2010

AbstractBackgroundMeasurement of the parathyroid hormone (PTH) level following total thyroidectomy (TTx) may allow prediction of postoperative hypocalcemia. We present an algorithmic method of managing hypocalcemia pre‐emptively, based on the PTH level 1 h after operation.Materials and methodsWe examined 423 consecutive patients undergoing TTx at a single institution. A subset of patients were managed using an algorithm involving routine postoperative oral calcium administration and the early addition of oral calcitriol in patients with a low 1‐h postoperative PTH level. Algorithm patients were compared to a concurrent, conventionally managed group. Outcomes measured included serum calcium levels, symptoms of hypocalcemia, postoperative complications, and receipt of intravenous (IV) calcium.ResultsThe algorithm was applied in 135 patients, and 288 patients were managed conventionally. Critically low calcium levels (total calcium <7.5 mg/dl [1.88 mmol/l] or ionized calcium <0.94 mmol/l) were less common in algorithm patients (10.6% vs. 25.3%; p < 0.005). Much of this difference was attributable to the protective impact of the algorithm on patients undergoing TTx for cancer, 30% of whom developed critically low calcium levels when managed conventionally. Among patients requiring IV calcium, algorithm patients received fewer doses (1.29 vs. 1.86; p < 0.05). Low 1‐h PTH levels were found in 21% (28/133) of algorithm patients, but these did not correlate with low calcium levels, suggesting that the algorithm compensated adequately for temporary hypoparathyroidism. No patients developed hypercalcemia.ConclusionsAn algorithmic approach incorporating early postoperative PTH levels and routine administration of oral calcium reduces the risk of severe hypocalcemia after total thyroidectomy.