bluuebunny/crossref_metadata_2025_split huggingface dataset:
Micro‐ to nanostructure and geochemistry of extant crinoidal echinoderm skeletons
Authors: Gorzelak P. , Stolarski J. , Mazur M. , Meibom A. 
Published: November 2012

AbstractThis paper reports the results of micro‐ to nanostructural and geochemical analyses of calcitic skeletons from extant deep‐sea stalked crinoids. Fine‐scale (SEM, FESEM, AFM) observations show that the crinoid skeleton is composed of carbonate nanograins, about 20–100 nm in diameter, which are partly separated by what appears to be a few nm thick organic layers. Sub‐micrometre‐scale geochemical mapping of crinoid ossicles using a NanoSIMS ion microprobe, combined with synchrotron high‐spatial‐resolution X‐ray micro‐fluorescence (μ‐XRF) maps and X‐ray absorption near‐edge structure spectroscopy (XANES) show that high Mg concentration in the central region of the stereom bars correlates with the distribution of S‐sulphate, which is often associated with sulphated polysaccharides in biocarbonates. These data are consistent with biomineralization models suggesting a close association between organic components (including sulphated polysaccharides) and Mg ions. Additionally, geochemical analyses (NanoSIMS, energy dispersive spectroscopy) reveal that significant variations in Mg occur at many levels: within a single stereom trabecula, within a single ossicle and within a skeleton of a single animal. Together, these data suggest that physiological factors play an important role in controlling Mg content in crinoid skeletons and that great care should be taken when using their skeletons to reconstruct, for example, palaeotemperatures and Mg/Ca palaeo‐variations of the ocean.
Relationship Between Helicobacter pylori Infection and Serum Interleukin‐18 in Patients with Carotid Atherosclerosis
Authors: Chen Bao‐Feng , Xu Xin , Deng Yun , Ma Shao‐Chun , Tang Liang‐Qiu , Zhang She‐Bing , Chen Ze‐Fang 
Published: November 2012

AbstractBackgroundHelicobacter pylori (H. pylori) infection stimulates the production of proinflammatory cytokines associated with the development of atherosclerosis. Levels of circulating interleukin‐18 (IL‐18) have been positively correlated with carotid intima‐media thickness (IMT) and coronary plaque area and have identified IL‐18 levels as important predictors of coronary events and cardiovascular mortality. This study aimed to examine the relationship between serum IL‐18 and H. pylori‐IgG antibody as a sign of H. pylori infection in patients with carotid atherosclerosis.MethodsThe carotid IMT, traditional atherosclerotic risk factors, levels of serum H. pylori‐IgG and IL‐18 were measured in 573 health checkup examinees.ResultsSerum IL‐18 and H. pylori‐IgG levels were significantly increased in subjects with increased IMT in comparison with those with normal IMT. In subjects with increased IMT, serum H. pylori‐IgG was positively correlated with serum IL‐18 (r = .402, p = .002), and the association was independent of traditional atherosclerotic risk factors (β = 0.310, p < .001).ConclusionsIn health checkup examinees with increased IMT, serum IL‐18 and H. pylori‐IgG were independently correlated and were significantly higher than in subjects with normal IMT.
Comparison of Hybrid and Sequential Therapies for Helicobacter pylori Eradication in Iran: A Prospective Randomized Trial
Authors: Sardarian Hossein , Fakheri Hafez , Hosseini Vahid , Taghvaei Tarang , Maleki Iradj , Mokhtare Marjan 
Published: November 2012

AbstractBackgroundThe eradication of Helicobacter pylori has been always a concern. In the present study, we aimed to compare two novel treatments in Iran.MethodFour hundred and twenty patients with peptic ulcer and naïve H. pylori infection were randomized in the study. Two hundred and ten patients received hybrid therapy: pantoprazole 40 mg/b.i.d. and amoxicillin 1 g/b.i.d. for 14 days plus 500 mg clarithromycin and 500 mg tinidazole, both twice daily for the last 7 days. The other 210 patients received sequential therapy: 40 mg pantoprazole/b.i.d. for 10 days and 1 g amoxicillin/b.i.d. for the first 5 days, followed by 500 mg clarithromycin/b.i.d. and 500 mg tinidazole/b.i.d. for the last 5 days. C¹⁴‐urea breath test was performed 8 weeks after the treatment.ResultsThree hundred and ninety‐six patients (197 patients in the hybrid group and 199 patients in the sequential group) completed the study. The compliance rates were 96.7 and 98.6% for the two groups, respectively. The intention‐to‐treat eradication rate was 89.5% (95% CI = 85.4–93.6) for the hybrid group and 76.7% (95% CI = 71–82.4) for the sequential group (p = .001), and the per‐protocol eradication rates were 92.9% (95% CI = 89.2–96.5) and 79.9% (95% CI = 74.1–85.4) for the hybrid and sequential groups (p = .001), respectively. Severe adverse effects were observed in 2.4% of patients in the hybrid group and 3.8% of those in the sequential group.ConclusionAccording to our results, sequential regimen does not seem to be an appropriate therapy for H. pylori eradication in the Iranian population, whereas hybrid therapy showed to be more effective. However, considering the high cost of clarithromycin in Iran, we recommend further studies to compare hybrid therapy with bismuth‐containing regimens or to assess the effects of hybrid therapies with periods shorter than 14 days.
Serum peptides, represented by complement 3f des‐arginine, are useful for prediction of the response to pegylated interferon‐α plus ribavirin in patients with chronic hepatitis C
Authors: Noguchi Yohei , Kurokawa Manae S. , Okuse Chiaki , Matsumoto Nobuyuki , Nagai Kouhei , Sato Toshiyuki , Arito Mitsumi , Suematsu Naoya , Okamoto Kazuki , Suzuki Michihiro , Itoh Fumio , Kato Tomohiro 
Published: November 2012

AimBiomarkers predicting sustained virological response (SVR) to pegylated interferon‐α plus ribavirin (PEG IFN‐α/RBV) were investigated.MethodsPeptides in pretreatment sera from 107 patients with hepatitis C virus (HCV) genotype 1 were comprehensively analyzed by mass spectrometry. Ion intensity of the peptides was used to generate discriminant models between the responders who achieved SVR (R) and the non‐responders (NR) to PEG IFN‐α/RBV.ResultsIn total, 107 peptides were detected in a training set (n = 23). A discriminant model using a peptide, complement 3f des‐arginine (C3f‐dR), showed sensitivity of 35% and specificity of 94% for SVR prediction in a testing set (n = 68). In all the R and NR (n = 96), an area under the receiver–operator curve (AUROC) of 0.64 in the C3f‐dR model was increased to 0.78 by addition of platelet (PLT) counts (C3f‐dR/PLT model). Another model using the 107 peptides (AUROC, 0.77) also showed higher AUROC (0.79) by addition of hemoglobin (Hb), body mass index (BMI) and age (107P/Hb/BMI/Age model). The sensitivity and specificity of the C3f‐dR/PLT model were 59% and 88%, and those of the 107P/Hb/BMI/Age model were 70% and 92%, respectively. The C3f‐dR/PLT model showed high AUROC (0.82), similar to that of interleukin‐28B rs8099917 genotype analysis (0.86) in the 45 tested patients. Prediction by the combination of the C3f‐dR/PLT model, the 107P/Hb/BMI/Age model and the rs8099917 genotype analysis was accurate in 44 out of the 45 patients (AUROC, 0.95).ConclusionSerum peptides, especially C3f‐dR, would be useful predictors for SVR to PEG IFN‐α/RBV. The complements may be involved in the HCV elimination.
Structure of Rhenium‐Containing Sodium Borosilicate Glass
Authors: Goel Ashutosh , McCloy John S. , Windisch Charles F. , Riley Brian J. , Schweiger Michael J. , Rodriguez, Carmen P. , Ferreira José M.F. 
Published: November 2012

A series of sodium borosilicate glasses were synthesized with KReO4 or Re2O7, to 10,000 ppm (1 mass%) target Re, to assess effects of large concentrations of rhenium on glass structure and fto estimate solubility of 99Tc, a radioactive component in low active waste nuclear glasses. Rhenium was used as a surrogate for 99Tc for laboratory testing, due to similarities in chemistry, ionic size, and redox. Magic angle spinning nuclear magnetic resonance, Fourier transform infrared spectroscopy, and Raman spectroscopy were performed to characterize the glasses. Si was coordinated in Q2 and Q3 units, Al was four‐coordinated, and B was mostly three‐coordinated. The rhenium additions did not have significant effects on the glass structure up to approximately 3000 ppm Re by mass, the maximum concentration that remained dissolved in glass. Rhenium likely exists in isolated anions in the interstices of the glass network, as evidenced by polarized Raman spectrum of the Re glass in the absence of sulfate. Analogous to in similar glasses, is a network modifier and above solubility forms alkali salt phases on the surface and in the bulk. Comparisons of phase separation and crystallization in containing borosilicate glasses can also be made to containing glasses.
Slack regulation compliance in the Mediterranean fisheries: a paradigm from the Greek Aegean Sea demersal trawl fishery, modelling discard ogives
Authors: Damalas D. , Vassilopoulou V. 
Published: November 2012

AbstractAnnual discard ogives were estimated using generalised additive models (GAMs) for seven demersal fish species (or taxa) and deep‐water rose shrimp, Parapenaeus longirostris (Lucas). Analysis was based on data collected on board commercial bottom trawlers in the central Aegean Sea from 1995 to 2008. Length of specimens and fishing depth (along with year) were the variables that had the most profound effect on the proportion of fish discarded. Compliance with the established minimum catch size of marine organisms (MS) was very low, a fact attributed to the low selectivity of currently used mesh sizes, the market demand for undersized fish, as well as the low control and enforcement effort.
Genome size and ploidy of Thysanoptera
Authors: Jacobson A. L. , Johnston J. S. , Rotenberg D. , Whitfield A. E. , Booth W. , Vargo E. L. , Kennedy G. G. 
Published: November 2012

AbstractFlow cytometry was used to study the genome sizes and ploidy levels for four thrips species: Franklinothrips orizabensis Johansen (Thysanoptera: Aeolothripidae), Frankliniella occidentalis Pergande, Frankliniella fusca Hinds, and Thrips tabaci Lindeman (Thysanoptera: Thripidae). F. orizabensis males and females had 1C genome sizes of 426 Mb and 422 Mb, respectively. Male and female F. fusca had 1C genome sizes of 392 Mb and 409 Mb, whereas F. occidentalis males and females had smaller 1C genomes that were 345 Mb and 337 Mb, respectively. Male F. orizabensis, F. occidentalis and F. fusca were haploid and females diploid. Five isofemale lines of T. tabaci, initiated from parthenogenetic, thelytokous females and collected from different locations in North Carolina, were included in this study; no males were available. One isofemale line was diploid with a genome size of 1C = 310 Mb, and the other four had a mean genome size of 1C = 482 Mb, which is consistent with evidence from microsatellite data of diploidy and polyploidy, respectively, in these same five thelytokous lines. This is the first study to produce genome size estimates for thysanopteran species, and report polyploidy in T. tabaci populations.
Juvenile hormone III suppresses forkhead of transcription factor in the fat body and reduces fat accumulation in the diapausing mosquito, Culex pipiens
Authors: Sim Cheolho , Denlinger David L. 
Published: November 2012

AbstractJuvenile hormone (JH) controls diverse physiological and developmental events including diapause and nutrient metabolism. The focal point of endocrine regulation in adult reproductive diapause is initiated by a halt of JH synthesis. In diapausing females of the mosquito Culex pipiens, the other key molecular event is the signalling pathway from insulin to forkhead of transcription factor (FOXO). We hypothesized that a halt of JH synthesis is related to activation of FOXO, which results in increasing lipid reserves in the fat body at the onset of the diapause programme. In this study, the full‐length sequence of the foxo gene in C. pipiens was characterized, and the protein abundance pattern of the foxo gene product was analyzed by immunoblotting and immunohistochemistry. FOXO was much more abundant in the fat body of diapausing females than in the fat body of nondiapausing females; much lower levels were present in other adult tissues. When we topically applied JH III to diapause‐destined females, FOXO was suppressed, and fat accumulation was reduced, suggesting an interaction between JH synthesis and FOXO that is critical for expression of the diapause phenotype.
Spontaneous succession on opencast mining sites: implications for bird biodiversity
Authors: Šálek Miroslav 
Published: November 2012

Summary

Remediation of lands devastated by industry includes various forms of restoration, such as technical reclamation and spontaneous succession. These management approaches are debated regarding conservation strategies for postindustrial landscapes. Mining areas consisting of early‐ to late‐developmental stages of both reclaimed and unreclaimed sites offer an opportunity to examine the roles of restoration strategies in a complete successional series for biodiversity and disentangle the contributions of particular biotopes available at postindustrial sites.

Using linear models and multivariate analysis, I tested the effects of (a) developmental stages from early successional sites to mature forests, combined with (b) the initiation process at the sites, which was either technical reclamation or spontaneous succession, and (c) vegetation cover on (i) species richness, (ii) rarity and (iii) species composition of bird communities on 60 plots (100 × 100 m) within opencast mining areas in the lignite basin of north‐western Czech Republic.

Bird communities were consistently more species rich on spontaneously developed sites compared with reclaimed sites throughout all stages of the succession series. Species richness increased with site age due to increasing habitat heterogeneity.

The conservation value of bird communities was generally lower on reclaimed sites than on spontaneously developed sites and decreased with site age. The most valuable communities developed on early successional sites and native shrublands, because these were inhabited by specialists that were scarce in the surrounding landscape. By contrast, technically reclaimed sites resulted in impoverished communities, usually with narrow spectra of common species.

Synthesis and applications. The results highlight the importance of spontaneously established sites and complete succession series for developing valuable bird communities in postindustrial areas such as opencast mining sites. In particular, early successional sites and shrublands create refuges for early successional specialists disappearing from the common landscape and these should be promoted at the expense of reclaimed sites wherever possible. My results support an effort for systematic implementation of early successional sites into conservation practice.
Establishment of medium for laboratory cultivation and maintenance of Fredericella sultana for in vivo experiments with Tetracapsuloides bryosalmonae (Myxozoa)
Authors: Kumar G , Abd‐Elfattah A , Soliman H , El‐Matbouli M 
Published: November 2012

AbstractThe freshwater bryozoan Fredericella sultana (Blumenbach) is the most common invertebrate host of the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in salmonid fish. Culture media play an important role in hatching of statoblasts and maintaining clean bryozoan colonies for Malacosporea research. We developed a novel culture medium, Bryozoan Medium C (BMC), for the cultivation and maintenance of F. sultana under laboratory conditions. Statoblasts of F. sultana were successfully hatched to produce transparent‐walled, specific pathogen‐free (SPF) colonies that were maintained >12 months in BMC at pH 6.65. Tetracapsuloides bryosalmonae was successfully transmitted from infected brown trout, Salmo trutta L., to newly hatched F. sultana colonies in BMC, then from the infected bryozoan to SPF brown trout. This study demonstrated the utility of BMC (pH 6.65) for hatching statoblasts, long‐term cultivation of clean and transparent bryozoan colonies and maintenance of the Tetracapsuloides bryosalmonae life cycle in the laboratory for molecular genetic research and other studies such as host–parasiteinteraction.
3‐D PSF fitting for fluorescence microscopy: implementation and localization application
Authors: KIRSHNER H. , AGUET F. , SAGE D. , UNSER M. 
Published: November 2012

SummaryLocalization microscopy relies on computationally efficient Gaussian approximations of the point spread function for the calculation of fluorophore positions. Theoretical predictions show that under specific experimental conditions, localization accuracy is significantly improved when the localization is performed using a more realistic model. Here, we show how this can be achieved by considering three‐dimensional (3‐D) point spread function models for the wide field microscope. We introduce a least‐squares point spread function fitting framework that utilizes the Gibson and Lanni model and propose a computationally efficient way for evaluating its derivative functions. We demonstrate the usefulness of the proposed approach with algorithms for particle localization and defocus estimation, both implemented as plugins for ImageJ.
Ion beam polishing for three‐dimensional electron backscattered diffraction
Authors: SAOWADEE N. , AGERSTED K. , UBHI H.S. , BOWEN J.R. 
Published: November 2012

SummarySerial sectioning by focused ion beam milling for three‐dimensional electron backscatter diffraction (3D‐EBSD) can create surface damage and amorphization in certain materials and consequently reduce the EBSD signal quality. Poor EBSD signal causes longer data acquisition time due to signal averaging and/or poor 3D‐EBSD data quality. In this work a low kV focused ion beam was successfully implemented to automatically polish surfaces during 3D‐EBSD of La‐ and Nb‐doped strontium titanate of volume 12.6 × 12.6 × 3.0 μm. The key to achieving this technique is the combination of a defocused low kV high current ion beam and line scan milling. The line scan was used to restrict polishing to the sample surface and the ion beam was defocused to ensure the beam contacted the complete sample surface. In this study 1 min polishing time per slice increases total acquisition time by approximately 3.3% of normal 3D‐EBSD mapping compared to a significant increase of indexing percentage and pattern quality. The polishing performance in this investigation is discussed, and two potential methods for further improvement are presented.
Segmenting time‐lapse phase contrast images of adjacent NIH 3T3 cells
Authors: CHALFOUN J. , KOCIOLEK M. , DIMA A. , HALTER M. , CARDONE A. , PESKIN A. , BAJCSY P. , BRADY M. 
Published: November 2012

SummaryWe present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are physically in contact with each other. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting, tracking and lineage modelling in cell biology. The segmentation method presented in this paper consists of (1) background reconstruction to obtain noise‐free foreground pixels and (2) incorporation of biological insight about dividing and nondividing cells into the segmentation process to achieve reliable separation of foreground pixels defined as pixels associated with individual cells. The segmentation results for a time‐lapse image stack were compared against 238 manually segmented images (8219 cells) provided by experts, which we consider as reference data. We chose two metrics to measure the accuracy of segmentation: the ‘Adjusted Rand Index’ which compares similarities at a pixel level between masks resulting from manual and automated segmentation, and the ‘Number of Cells per Field’ (NCF) which compares the number of cells identified in the field by manual versus automated analysis. Our results show that the automated segmentation compared to manual segmentation has an average adjusted rand index of 0.96 (1 being a perfect match), with a standard deviation of 0.03, and an average difference of the two numbers of cells per field equal to 5.39% with a standard deviation of 4.6%.
Intraoperative transfusion threshold and tissue oxygenation: a randomised trial
Authors: Nielsen K. , Dahl B. , Johansson P. I. , Henneberg S. W. , Rasmussen L. S. 
Published: November 2012

AbstractBackground and ObjectivesTransfusion with allogeneic red blood cells (RBCs) may be needed to maintain oxygen delivery during major surgery, but the appropriate haemoglobin (Hb) concentration threshold has not been well established. We hypothesised that a higher level of Hb would be associated with improved subcutaneous oxygen tension during major spinal surgery.Materials and MethodsFifty patients aged 18 years or older scheduled for spinal fusion with instrumentation were included and randomised to receive RBCs at either a Hb concentration of 7·3 g dL−1 (restrictive group) or a Hb concentration of 8·9 g dL−1 (liberal group) (Registration no.: H‐C‐2009‐072). Oxygen tension was measured with a polarographic electrode placed subcutaneously over the left deltoid muscle. The primary endpoint was subcutaneous oxygen tension at the time most patients were still undergoing surgery.ResultsForty‐eight patients were included in the intention‐to‐treat analysis; 25 patients in the restrictive group and 23 patients in the liberal group. The median change in subcutaneous oxygen tension 60 min after surgical incision was −0·79 and −0·75 kPa in the restrictive and the liberal groups, respectively (P = 0·78). No significant difference was found in the lowest subcutaneous oxygen tension; −2·07 vs. −1·95 kPa in the restrictive and the liberal groups, respectively (P = 0·85).ConclusionA Hb concentration transfusion threshold of 8·9 g dL−1 was not associated with a higher subcutaneous oxygen tension during major spinal surgery than a threshold of 7·3 g dL−1, but the trial was compromised by methodological difficulties.
Enantiostyly in Chamaecrista ramosa (Fabaceae‐Caesalpinioideae): floral morphology, pollen transfer dynamics and breeding system
Authors: de Almeida N. M. , de Castro C. C. , de Lima Leite A. V. , Novo R. R. , Machado I. C. 
Published: November 2012

AbstractEnantiostyly is a form of reciprocal herkogamy, in which floral morphs present reciprocal differences in the position of sexual elements, and occurs in monomorphic and dimorphic forms. This polymorphism maximises cross‐pollination and reduces self‐pollination, being very common within the subtribe Cassiinae (Fabaceae). Nevertheless, few studies have investigated the functionality of enantiostyly, particularly in this plant group. The present study aimed to investigate enantiostyly and its functionality in Chamaecrista ramosa, a monomorphic enantiostylous shrub, in an area of coastal vegetation in northeast Brazil. Pollen deposition and capture on the body of floral visitors, the relationship of these data with floral biology and breeding system, and morph ratio were evaluated. Pollen deposition and capture occurred in specific sites of the floral visitor body, showing the functionality of enantiostyly. The floral architecture, associated with the floral visitor behaviour, resulted in indirect pollen deposition on the floral visitor body. This occurred through a loop made by the pollen upon the inner petal surface, similar that generally reported for other Cassiinae. Chamaecrista ramosa is self‐compatible, although no fruit set was observed through spontaneous self‐pollination. The occurrence and number of floral morphs was similar within clumps. Enantiostyly seems to be advantageous for this species, as it results in efficient pollen capture and deposition, reduces the chances of autogamy and maximises intermorph pollen flow.