bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soybean (Glycine max) Oil Bodies and Their Associated Phytochemicals
Authors: Fisk Ian D. , Gray David A. 
Published: November 2011

Abstract:  Soybean oil bodies were isolated from 3 cultivars (Ustie, K98, and Elena) and the occurrence of 2 classes of phytochemicals (tocopherol isoforms and isoflavones) and strength of their association with isolated oil bodies was evaluated. Tocopherol is shown to be closely associated with soybean oil bodies; δ‐tocopherol demonstrated a significantly greater association with oil bodies over other tocopherol isoforms. Isoflavones do not show a significant physical association with oil bodies, although there is some indication of a passive association of the more hydrophobic aglycones during oil body isolation.Practical Application:  Oil bodies are small droplets of oil that are stored as energy reserves in the seeds of oil seeds, and have the potential to be used as future food ingredients. If oil body suspensions are commercialized on a large scale, knowledge of the association of phytochemicals with oil bodies will be valuable in deciding species of preference and predicting shelf life and nutritional value.
Assessment of Some Australian Red Wines for Price, Phenolic Content, Antioxidant Activity, and Vintage in Relation to Functional Food Prospects
Authors: Yoo Yung J. , Prenzler Paul D. , Saliba Anthony J. , Ryan Danielle 
Published: November 2011

Abstract:  Twenty‐three Cabernet Sauvignon wines from the Mudgee region and thirty‐two Shiraz wines from the Hunter Valley region were analyzed for phenolic content and antioxidant activity. Concentrations of (+)‐catechin, quercetin, and transresveratrol, total phenolic content, and DPPH antioxidant activity varied considerably, both within and between varieties. Individual phenols, total phenols, and antioxidant activity were correlated with price and vintage. Shiraz wines showed positive and significant correlations for catechin and quercetin concentrations with total phenols, antioxidant activity, and vintage; and for total phenols and antioxidant activity with vintage. Cabernet Sauvignon wines showed positive and significant correlations for quercetin concentration with total phenols and antioxidant activity. There was a negative and significant correlation found between price and antioxidant activity for Cabernet Sauvignon wines. Results are discussed in terms of the potential for wine to be considered a functional food.Practical Application:  We report on potential health benefits (antioxidant activity) of 55 wines typical of 2 geographically close, but distinct, wine regions of Australia. Our results highlight the variability in functional components as an issue that needs further research and consideration in relation to wine as a functional food. The price of studied wines is not reflective of their health functionality, based on antioxidant activities.
Survival of Salmonella Serovars Introduced as a Post‐Aging Contaminant during Storage of Low‐Salt Cheddar Cheese at 4, 10, and 21 °C
Authors: Shrestha Subash , Grieder James A. , McMahon Donald J. , Nummer Brian A. 
Published: November 2011

Abstract:  The microbiological stability of low‐salt cheese has not been well documented. This study examined the survival of Salmonella in low‐salt compared to regular salt Cheddar cheese with 2 pH levels. Cheddar cheeses were formulated at 0.7% and 1.8% NaCl (wt/wt) with both low and high‐pH and aged for 12 wk resulting in four treatments: 0.7% NaCl and pH 5.1 (low‐salt and low‐pH); 0.7% NaCl and pH 5.5 (low‐salt and high‐pH); 1.8% NaCl and pH 5.7 (standard‐salt and high‐pH); and 1.8% NaCl and pH 5.3 (standard‐salt and low‐pH). Each treatment was comminuted and inoculated with a 5‐serovar cocktail of Salmonella at a target level of 4 log CFU/g, then divided and incubated at 4, 10 and 21 °C for up to 90, 90, and 30 d, respectively. Salmonella counts decreased by 2.8 to 3.9 log CFU/g in all treatments. In the initial period of survival study, standard‐salt treatments exhibited significantly lower Salmonella counts compared to low‐salt treatments. The pH levels did not exhibit obvious significant effect in the Salmonella survival in low‐salt treatments. Salmonella counts declined gradually regardless of a continuous increase in pH (end pH of 5.3 to 5.9) of low‐salt treatments at all study temperatures. Salmonella counts were reduced faster at 21 °C storage. Although there were significant reductions in Salmonella counts, the treatments demonstrated survival of Salmonella for up to 90 d when stored at 4 or 10 °C and for up to 30 d at 21 °C, the need for good sanitation practices to prevent postmanufacturing cross contamination remains.Practical Application:  Low‐salt aged Cheddar cheese could not support the growth of inoculated Salmonella and in fact gradual reduction in Salmonella count occurred during storage. Besides being nutritionally better, low or reduced salt Cheddar are safe as their full salt counterparts and that salt may only be a minor food safety hurdle regarding the post‐aging contamination and growth of Salmonella. However, the treatments could not demonstrate complete destruction of Salmonella for up to 90 d when stored at 4 or 10 °C and for up to 30 d at 21 °C, the need for good sanitation practices to prevent postmanufacturing cross‐contamination remains.
Scanning electron microscopy analysis of erythrocytes in thromboembolic ischemic stroke
Authors: SWANEPOEL A. C. , PRETORIUS E. 
Published: November 2011

SummaryIntroduction:  Erythrocytes play an important role in hemostasis and disease conditions. During ischemic stroke, erythrocytes undergo oxidative and proteolytic changes resulting in a changed cellular rheology.Methods:  Blood samples were obtained from controls and thromboembolic ischemic stroke patients (within 48 h of stroke). The ultrastructure of erythrocytes was compared, using a scanning electron microscope (SEM). Abnormal morphology included codocytes, knizocytes, stomatocytes, and echinocytes. Percentage of abnormal cells was calculated, and the analyses were performed using the statistical program NCSS with the level of significance set at 0.05. A t‐test was carried out to compare the data from the erythrocyte counts of stroke patients with that of the control subjects.Results:  Ultrastructural SEM results showed that there are a large percentage of erythrocytes in healthy individuals that do not have a typical discoid shape, when studying the cells using a high magnification electron microscope. Furthermore, analysis showed that variation in shape is so subtle that it is not clearly visible using a typical light microscopy blood smear analysis. Thromboembolic ischemic stroke patients presented with a significant amount of erythrocytes with abnormal morphology.Conclusion:  We suggest that in healthy individuals, a typical smear would contain several nondiscoid‐shaped erythrocytes, only clearly visible at high magnification. However, thromboembolic ischemic stroke does significantly impact erythorcyte shape, and this change in morphology may result in an impaired microcirculation, as well as impaired oxygen carrying capacity. This changed morphology may further complicate the restoring of homeostasis caused by acute thromboembolic stroke.
Application of multiplex PCR approaches for shark molecular identification: feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific
Authors: CABALLERO S. , CARDEÑOSA D. , SOLER G. , HYDE J. 
Published: November 2011

AbstractHere we describe the application of new and existing multiplex PCR methodologies for shark species molecular identification. Four multiplex systems (group ID, thresher sharks, hammerhead sharks and miscellaneous shark) were employed with primers previously described and some designed in this study, which allow for species identification after running PCR products through an agarose gel. This system was implemented for samples (bodies and fins) collected from unidentified sharks landed in the port of Buenaventura and from confiscated tissues obtained from illegal fishing around the Malpelo Island Marine Protected Area, Pacific Coast of Colombia. This method has allowed reliable identification, to date, of 407 samples to the genus and/or species levels, most of them (380) identified as the pelagic thresher shark (Alopias pelagicus). Another seven samples were identified as scalloped hammerhead sharks (Sphyrna lewini). This is an easy‐to‐implement and reliable identification method that could even be used locally to monitor shark captures in the main fishing ports of developed and developing countries.
A topological index theorem for manifolds with corners
Authors: Monthubert Bertrand , Nistor Victor 
Published: November 2011

AbstractWe define an analytic index and prove a topological index theorem for a non-compact manifoldM0with poly-cylindrical ends. Our topological index theorem depends only on the principal symbol, and establishes the equality of the topological and analytical index in the groupK0(C*(M)), whereC*(M) is a canonicalC*-algebra associated to the canonical compactificationMofM0. Our topological index is thus, in general, not an integer, unlike the usual Fredholm index appearing in the Atiyah–Singer theorem, which is an integer. This will lead, as an application in a subsequent paper, to the determination of theK-theory groupsK0(C*(M)) of the groupoidC*-algebra of the manifolds with cornersM. We also prove that an elliptic operatorPonM0has an invertible perturbationP+Rby a lower-order operator if and only if its analytic index vanishes.
Contact homology of good toric contact manifolds
Authors: Abreu Miguel , Macarini Leonardo 
Published: November 2011

AbstractIn this paper we show that any good toric contact manifold has a well-defined cylindrical contact homology, and describe how it can be combinatorially computed from the associated moment cone. As an application, we compute the cylindrical contact homology of a particularly nice family of examples that appear in the work of Gauntlett et al. on Sasaki–Einstein metrics. We show in particular that these give rise to a new infinite family of non-equivalent contact structures on S2×S3 in the unique homotopy class of almost contact structures with vanishing first Chern class.
Robust automatic segmentation of multiple implanted cylindrical gold fiducial markers in cone‐beam CT projections
Authors: Fledelius Walther , Worm Esben , Elstrøm Ulrik V. , Petersen Jørgen B. , Grau Cai , Høyer Morten , Poulsen Per R. 
Published: November 2011

Purpose:Implanted fiducial markers, which are used to correct for day‐to‐day variations, may potentially also be used to correct for intrafraction motion measurements. However, before any treatment can make use of, and react to, the position of the inserted markers they have to be segmented, either manually through expert user intervention or automatically from an imaging system. In the current study, we aimed to establish a robust and autonomous segmentation method for implanted cylindrical gold markers in a single set of projections from a cone‐beam computed tomography (CBCT).Methods:Multiple cylindrical gold markers were segmented in the projection images of CBCT scans by five sequential steps. Initially, marker candidates were identified in all projections with a blob detection routine, and then traced in subsequent projections. Traces inconsistent with a 3D marker position were rejected, and the best remaining traces were identified and used for the construction of a 3D marker constellation model, consisting of the size, position and orientation of the markers. Finally, projections of the model were used to generate templates for the final template‐based marker segmentation. Hereby, challenging situations such as overlap of markers and low contrast regions were taken into account. The segmentation method was tested in 63 CBCT scans from 11 patients with 2–4 cylindrical gold markers implanted in the prostate and for 62 CBCT scans from six patients each with 2–3 cylindrical gold markers implanted in the liver and up to two cylindrical markers placed externally on the abdomen. After segmentation all projections of the 125 scans were manually inspected, and a successful segmentation was registered if the segmented position was within the projection of the marker.Results:For prostate markers, the segmentation was successful in 99.8% of the projections. For the liver patients, liver markers and external markers were segmented successfully in 99.9 and 99.8% of the projections, respectively. All markers were identified in the 3D marker constellation model. The most common source of segmentation error was low contrast and motion of markers relative to each other, which resulted in a discrepancy between the template and actual projection appearance during marker overlap. Markers were overlapping in 20, 2.7, and 0.1% of the projections for prostate, liver, and external, respectively.Conclusions:We have successfully implemented a new method that, without prior knowledge on marker size, position, orientation, and number, autonomously segments cylindrical gold markers from CBCT projections with a high success rate, despite overlap, motion, and low contrast.
An improved model for describing the contrast bolus in perfusion MRI
Authors: Patil Vishal , Johnson Glyn 
Published: November 2011

Purpose:Quantification of perfusion measurements using dynamic, susceptibility‐weighted contrast‐enhanced (DSC) MRI depends on estimating the size and shape of the tracer bolus. Typically, the bolus is described as a gamma variate function (GV) fitted to the bolus portion of tracer concentration time curve (CTC). However, the last point to fit is arbitrary which can lead to considerable variation in the fitted curve in the presence of noise. In this technical note, we present a model which takes into account recirculation explicitly and fits robustly to the entire CTC in the presence of noise.Methods:Signal data measurements from ten DSC MRI patients were fitted with our new model and a GV function using four different methods of estimating the end of the bolus. Estimates of the area under the curves (AUC) and first moments (FMs) of the bolus were compared at different noise levels.Results:The new model gave errors similar to or smaller than those of the most effective methods for fitting a GV.Conclusions:The single compartment recirculation (SCR) model is the most robust fitting technique with respect to noise both for bias and variability.
Four‐dimensional magnetic resonance imaging (4D‐MRI) using image‐based respiratory surrogate: A feasibility study
Authors: Cai Jing , Chang Zheng , Wang Zhiheng , Paul Segars William , Yin Fang‐Fang 
Published: November 2011

Purpose:Four‐dimensional computed tomography (4D‐CT) has been widely used in radiation therapy to assess patient‐specific breathing motion for determining individual safety margins. However, it has two major drawbacks: low soft‐tissue contrast and an excessive imaging dose to the patient. This research aimed to develop a clinically feasible four‐dimensional magnetic resonance imaging (4D‐MRI) technique to overcome these limitations.Methods:The proposed 4D‐MRI technique was achieved by continuously acquiring axial images throughout the breathing cycle using fast 2D cine‐MR imaging, and then retrospectively sorting the images by respiratory phase. The key component of the technique was the use of body area (BA) of the axial MR images as an internal respiratory surrogate to extract the breathing signal. The validation of the BA surrogate was performed using 4D‐CT images of 12 cancer patients by comparing the respiratory phases determined using the BA method to those determined clinically using the Real‐time position management (RPM) system. The feasibility of the 4D‐MRI technique was tested on a dynamic motion phantom, the 4D extended Cardiac Torso (XCAT) digital phantom, and two healthy human subjects.Results:Respiratory phases determined from the BA matched closely to those determined from the RPM: mean (±SD) difference in phase: −3.9% (±6.4%); mean (±SD) absolute difference in phase: 10.40% (±3.3%); mean (±SD) correlation coefficient: 0.93 (±0.04). In the motion phantom study, 4D‐MRI clearly showed the sinusoidal motion of the phantom; image artifacts observed were minimal to none. Motion trajectories measured from 4D‐MRI and 2D cine‐MRI (used as a reference) matched excellently: the mean (±SD) absolute difference in motion amplitude: −0.3 (±0.5) mm. In the 4D‐XCAT phantom study, the simulated “4D‐MRI” images showed good consistency with the original 4D‐XCAT phantom images. The motion trajectory of the hypothesized “tumor” matched excellently between the two, with a mean (±SD) absolute difference in motion amplitude of 0.5 (±0.4) mm. 4D‐MRI was able to reveal the respiratory motion of internal organs in both human subjects; superior–inferior (SI) maximum motion of the left kidney of Subject #1 and the diaphragm of Subject #2 measured from 4D‐MRI was 0.88 and 1.32 cm, respectively.Conclusions:Preliminary results of our study demonstrated the feasibility of a novel retrospective 4D‐MRI technique that uses body area as a respiratory surrogate.
A Monomorphic Haplotype of Chromosome Ia Is Associated with Widespread Success in Clonal and Nonclonal Populations of Toxoplasma gondii
Authors: Khan Asis , Miller Natalie , Roos David S. , Dubey J. P. , Ajzenberg Daniel , Dardé Marie Laure , Ajioka James W. , Rosenthal Benjamin , Sibley L. David 
Published: November 2011

ABSTRACT

Toxoplasma gondii
is a common parasite of animals that also causes a zoonotic infection in humans. Previous studies have revealed a strongly clonal population structure that is shared between North America and Europe, while South American strains show greater genetic diversity and evidence of sexual recombination. The common inheritance of a monomorphic version of chromosome Ia (referred to as ChrIa*) among three clonal lineages from North America and Europe suggests that inheritance of this chromosome might underlie their recent clonal expansion. To further examine the diversity and distribution of ChrIa, we have analyzed additional strains with greater geographic diversity. Our findings reveal that the same haplotype of ChrIa* is found in the clonal lineages from North America and Europe and in older lineages in South America, where sexual recombination is more common. Although lineages from all three continents harbor the same conserved ChrIa* haplotype, strains from North America and Europe are genetically separate from those in South America, and these respective geographic regions show limited evidence of recent mixing. Genome-wide, array-based profiling of polymorphisms provided evidence for an ancestral flow from particular older southern lineages that gave rise to the clonal lineages now dominant in the north. Collectively, these data indicate that ChrIa* is widespread among nonclonal strains in South America and has more recently been associated with clonal expansion of specific lineages in North America and Europe. These findings have significant implications for the spread of genetic loci influencing transmission and virulence in pathogen populations.

IMPORTANCE
Understanding parasite population structure is important for evaluating the potential spread of pathogenicity determinants between different geographic regions. Examining the genetic makeup of different isolates of
Toxoplasma gondii
from around the world revealed that chromosome Ia is highly homogeneous among lineages that predominate on different continents and within genomes that were otherwise quite divergent. This pattern of recent shared ancestry is highly unusual and suggests that some gene(s) found on this chromosome imparts an unusual fitness advantage that has resulted in its recent spread. Although the basis for the conservation of this particularly homogeneous chromosome is unknown, it may have implications for the transmission of infection and spread of human disease.
The Escherichia coli Protein YfeX Functions as a Porphyrinogen Oxidase, Not a Heme Dechelatase
Authors: Dailey Harry A. , Septer Alecia N. , Daugherty Lauren , Thames Daniel , Gerdes Svetlana , Stabb Eric V. , Dunn Anne K. , Dailey Tamara A. , Phillips John D. 
Published: November 2011

ABSTRACT

The protein YfeX from
Escherichia coli
has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation of heme, we undertook to characterize YfeX. Our data reveal that YfeX effectively decolorizes the dyes alizarin red and Cibacron blue F3GA and has peroxidase activity with pyrogallal but not guiacol. YfeX oxidizes protoporphyrinogen to protoporphyrin
in vitro
. However, we were unable to detect any dechelation of heme to free porphyrin with purified YfeX or in cellular extracts of
E. coli
overexpressing YfeX. Additionally,
Vibrio fischeri
, an organism that can utilize heme as an iron source when grown under iron limitation, is able to grow with heme as the sole source of iron when its YfeX homolog is absent. Plasmid-driven expression of YfeX in
V. fischeri
grown with heme did not result in accumulation of protoporphyrin. We propose that YfeX is a typical dye-decolorizing peroxidase (or DyP) and not a dechelatase. The protoporphyrin reported to accumulate when YfeX is overexpressed in
E. coli
likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme. Bioinformatic analysis of bacterial YfeX homologs does not identify any connection with iron acquisition but does suggest links to anaerobic-growth-related respiratory pathways. Additionally, some genes encoding homologs of YfeX have tight association with genes encoding a bacterial cytoplasmic encapsulating protein.

IMPORTANCE
Acquisition of iron from the host during infection is a limiting factor for growth and survival of pathogens. Host heme is the major source of iron in infections, and pathogenic bacteria have evolved complex mechanisms to acquire heme and abstract the iron from heme. Recently Létoffé et al. (Proc. Natl. Acad. Sci. U. S. A. 106:11719–11724, 2009) reported that the protein YfeX from
E. coli
is able to dechelate heme to remove iron and leave an intact tetrapyrrole. This is totally unlike any other described biological system for iron removal from heme and, thus, would represent a dramatically new feature with potentially profound implications for our understanding of bacterial pathogenesis. Given that this reaction has no precedent in biological systems, we characterized YfeX and a related protein. Our data clearly demonstrate that YfeX is not a dechelatase as reported but is a peroxidase that oxidizes endogenous porphyrinogens to porphyrins.