bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solvent detergent vs. fresh frozen plasma in cirrhotic patients undergoing liver transplant surgery: a prospective randomized control study
Authors: Bindi M. L. , Miccoli M. , Marietta M. , Meacci L. , Esposito M. , Bisà M. , Mozzo R. , Mazzoni A. , Baggiani A. , Scatena F. , Filipponi F. , Biancofiore G. 
Published: March 2013

BackgroundAlthough orthotopic liver transplantation (OLT) is nowadays considered standard practice at experienced centres, it can still be affected by a significant risk of massive bleeding and its related complications. Solvent/detergent plasma (S/D Plasma) has been proposed as an alternative to fresh frozen plasma (FFP) to curtail such complications. This study aimed at evaluating the efficacy of S/D Plasma in OLT patients by comparing it to FFP.Materials and MethodsSixty‐three OLT patients were randomized into two groups depending on whether they were transfused with FFP or S/D plasma. A thromboelastography‐based protocol aimed at achieving and maintaining predetermined coagulation goals was used to guide plasma transfusions. At the beginning and the end of surgery, standard laboratory coagulation tests were performed together with the assessment of the VII, VIII, V, XII factors and S protein blood levels.ResultsThe two study groups equally achieved the thromboelastography goals but with a reduced amount of transfusions in the S/D plasma group (P < 0·0001). At the end of surgery, factors V and XII and S protein blood levels were lower in the S/D plasma patients who also showed lower INR, aPTT and antithrombin III levels.ConclusionIn cirrhotic patients undergoing OLT, the use of S\D plasma associated with thromboelastography allows the same clinical results but with a significant reduction in the amount of plasma transfusions.
A low dose simulation tool for CT systems with energy integrating detectors
Authors: Žabić Stanislav , Wang Qiu , Morton Thomas , Brown Kevin M. 
Published: March 2013

Purpose:This paper introduces a new strategy for simulating low‐dose computed tomography (CT) scans using real scans of a higher dose as an input. The tool is verified against simulations and real scans and compared to other approaches found in the literature.Methods:The conditional variance identity is used to properly account for the variance of the input high‐dose data, and a formula is derived for generating a new Poisson noise realization which has the same mean and variance as the true low‐dose data. The authors also derive a formula for the inclusion of real samples of detector noise, properly scaled according to the level of the simulated x‐ray signals.Results:The proposed method is shown to match real scans in number of experiments. Noise standard deviation measurements in simulated low‐dose reconstructions of a 35 cm water phantom match real scans in a range from 500 to 10 mA with less than 5% error. Mean and variance of individual detector channels are shown to match closely across the detector array. Finally, the visual appearance of noise and streak artifacts is shown to match in real scans even under conditions of photon‐starvation (with tube currents as low as 10 and 80 mA). Additionally, the proposed method is shown to be more accurate than previous approaches (1) in achieving the correct mean and variance in reconstructed images from pure‐Poisson noise simulations (with no detector noise) under photon‐starvation conditions, and (2) in simulating the correct noise level and detector noise artifacts in real low‐dose scans.Conclusions:The proposed method can accurately simulate low‐dose CT data starting from high‐dose data, including effects from photon starvation and detector noise. This is potentially a very useful tool in helping to determine minimum dose requirements for a wide range of clinical protocols and advanced reconstruction algorithms.
Quantitative material characterization from multi‐energy photon counting CT
Authors: Alessio Adam M. , MacDonald Lawrence R. 
Published: March 2013

Purpose:To quantify the concentration of soft‐tissue components of water, fat, and calcium through the decomposition of the x‐ray spectral signatures in multi‐energy CT images.Methods:Decomposition of dual‐energy and multi‐energy x‐ray data into basis materials can be performed in the projection domain, image domain, or during image reconstruction. In this work, the authors present methodology for the decomposition of multi‐energy x‐ray data in the image domain for the application of soft‐tissue characterization. To demonstrate proof‐of‐principle, the authors apply several previously proposed methods and a novel content‐aware method to multi‐energy images acquired with a prototype photon counting CT system. Data from phantom andex vivo specimens are evaluated.Results:The number and type of materials in a region can be limited based ona priori knowledge or classification strategies. The proposed difference classifier successfully classified the image into air only, water+fat, water+fat+iodine, and water+calcium regions. Then, the content‐aware material decomposition based on weighted least‐square optimization generated quantitative maps of concentration. Bias in the estimation of the concentration of water and oil components in a phantom study was <0.10 ± 0.15 g/cc on average. Decomposition of ex vivo carotid endarterectomy specimens suggests the presence of water, lipid, and calcium deposits in the plaque walls.Conclusions:Initial application of the proposed methodology suggests that it can decompose multi‐energy CT images into quantitative maps of water, adipose, iodine, and calcium concentrations.
Proton‐minibeam radiation therapy: A proof of concept
Authors: Prezado Y. , Fois G. R. 
Published: February 2013

Purpose:This Monte Carlo simulation work aims at studying a new radiotherapy approach called proton‐minibeam radiation therapy (pMBRT). The main objective of this proof of concept was the evaluation of the possible gain in tissue sparing, thanks to the spatial fractionation of the dose, which could be used to deposit higher and potentially curative doses in clinical cases where tissue tolerances are a limit for conventional methods.Methods:Monte Carlo simulations (GATE v.6) have been used as a method to calculate the ratio of the peak‐to‐valley doses (PVDR) for arrays of proton minibeams of 0.7 mm width and several center‐to‐center distances, at different depths in a water phantom. The beam penumbras were also evaluated as an important parameter for tissue sparing, for example, in the treatment of non‐cancer diseases like epilepsy. Two proton energies were considered in this study: a clinically relevant energy (105 MeV) and a very high energy (1 GeV), to benefit from a reduced lateral scattering. For the latter case, an interlaced geometry was also evaluated.Results:Higher or similar PVDR than the ones obtained in x‐rays minibeam radiation therapy were achieved in several pMBRT configurations. In addition, for the two energies studied, the beam penumbras are smaller than in the case of Gamma Knife radiosurgery.Conclusions:The high PVDR obtained for some configurations and the small penumbras in comparison with existing radiosurgery techniques, suggest a potential gain in healthy tissue sparing in this new technique. Biological studies are warranted to assess the effects of pMBRT on both normal and tumoral tissues.
Evaluation of the microangiographic fluoroscope (MAF) using generalized system performance metrics
Authors: Jain Amit , Bednarek Daniel R. , Rudin Stephen 
Published: March 2013

Purpose:The performance of a newly developed, high resolution, microangiographic fluoroscope (MAF) (35μm pixel pitch and 300 μm thick CsI phosphor) was evaluated using a generalized linear system analysis and compared with that of a standard amorphous Si thin film transistor flat panel detector (FPD) (194 μm pixel pitch and 600 μm thick CsI phosphor). The linear system metrics such as modulation transfer function (MTF), noise power spectrum, and detection quantum efficiency (DQE) are commonly used to gauge the intrinsic detector performance in the detector plane. However, these linear system metrics do not provide information about the image receptor performance in a real system since they do not include the effects of other parameters such as focal spot distribution, scatter radiation, and geometric unsharpness, which may compromise detector performance characteristics. Use of generalized linear system metrics [generalized modulation transfer function (GMTF), generalized normalized noise power spectrum (GNNPS), and generalized detection quantum efficiency (GDQE)] that include these effects gives a more meaningful, complete, and appropriate evaluation of detector performance as part of the imaging system.Methods:A uniform head equivalent phantom was used to simulate realistic clinical parameters and x‐ray spectra. The detector MTFs were measured using the slanted edge method and the focal spot MTFs were measured using a pinhole assembly. The scatter MTF was simulated and the scatter fraction was measured for a head‐equivalent phantom. The generalized system metrics were calculated for different combinations of three choices of focal spots and three different magnifications with two different air‐gaps. The performance of the MAF was also illustrated using stent images obtained with different focal spots under similar conditions.Results:Results for the generalized metrics provide a quantitative description of the performance of the imaging system for both detectors. This generalized analysis demonstrated that both detectors have similar imaging capabilities at lower spatial frequencies, but that the MAF has superior performance over the FPD at higher frequencies even when considering focal spot blurring and scatter.Conclusions:This generalized performance analysis demonstrates the significance of focal spot size, magnification, and scatter on the system performance metrics (GMTF, GNNPS, and GDQE). Although the ideal detector performance characteristics of the MAF are not fully realized due to these other system factors, it still retains an advantage in DQE at high spatial frequencies over the FPD. Similar studies based on the generalized linear system metrics can serve as an efficient tool to evaluate total system capabilities under different realistic conditions to enable optimal design for specific imaging tasks.
Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment
Authors: Caspers Martien P. M. , Boekhorst Jos , Abee Tjakko , Siezen Roland J. , Kort Remco 
Published: March 2013

ABSTRACT

Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain
Anoxybacillus flavithermus
TNO-09.006 from a milk-processing plant, and we report the complete genome of this isolate consisting of a single chromosome of 2.65 Mb.
Draft Genome Sequence of Escherichia coli Strain Nissle 1917 (Serovar O6:K5:H1)
Authors: Cress Brady F. , Linhardt Robert J. , Koffas Mattheos A. G. 
Published: March 2013

ABSTRACT

We announce the availability of the 5.023-Mbp high-quality draft assembly of the
Escherichia coli
strain Nissle 1917 (serovar O6:K5:H1) genome. Short genomic segments from this important probiotic strain have been available in public databases, but the full genome sequence has remained inaccessible. Thus, high-coverage, whole genome sequencing of
E. coli
Nissle 1917 is presented herein. Reannotation and metabolic reconstruction will enable comparative genomics analysis and model-guided predictions of genetic manipulations leading to increased production of the K5 capsular polysaccharide known as
N
-acetyl heparosan, a precursor to the anticoagulant pharmaceutical heparin.
Draft Genome Sequence of Pseudoalteromonas luteoviolacea Strain B (ATCC 29581)
Authors: Cress Brady F. , Erkert Kelly A. , Barquera Blanca , Koffas Mattheos A. G. 
Published: March 2013

ABSTRACT

We report the 4.049-Mbp high-quality draft assembly of the
Pseudoalteromonas luteoviolacea
strain B (ATCC 29581) genome. This marine species is known to biosynthesize several antimicrobial compounds, including the purple pigment violacein. Whole-genome sequencing and genome mining will complement experimental studies aimed at elucidating novel biosynthetic pathways capable of producing pharmaceutically relevant molecules. Based upon 16S rRNA phylogenetic analysis, we propose that strain ATCC 29581 be classified as a distinct phylogenetic species of the genus
Pseudoalteromonas
.
Deep Sequencing Analysis of Defective Genomes of Parainfluenza Virus 5 and Their Role in Interferon Induction
Authors: Killip M. J. , Young D. F. , Gatherer D. , Ross C. S. , Short J. A. L. , Davison A. J. , Goodbourn S. , Randall R. E. 
Published: March 2013

ABSTRACT
Preparations of parainfluenza virus 5 (PIV5) that are potent activators of the interferon (IFN) induction cascade were generated by high-multiplicity passage in order to accumulate defective interfering virus genomes (DIs). Nucleocapsid RNA from these virus preparations was extracted and subjected to deep sequencing. Sequencing data were analyzed using methods designed to detect internal deletion and “copyback” DIs in order to identify and characterize the different DIs present and to approximately quantify the ratio of defective to nondefective genomes. Trailer copybacks dominated the DI populations in IFN-inducing preparations of both the PIV5 wild type (wt) and PIV5-VΔC (a recombinant virus that does not encode a functional V protein). Although the PIV5 V protein is an efficient inhibitor of the IFN induction cascade, we show that nondefective PIV5 wt is unable to prevent activation of the IFN response by coinfecting copyback DIs due to the interfering effects of copyback DIs on nondefective virus protein expression. As a result, copyback DIs are able to very rapidly activate the IFN induction cascade prior to the expression of detectable levels of V protein by coinfecting nondefective virus.
A Fully Attenuated Recombinant Salmonid Alphavirus Becomes Pathogenic through a Single Amino Acid Change in the E2 Glycoprotein
Authors: Mérour Emilie , Lamoureux Annie , Bernard Julie , Biacchesi Stéphane , Brémont Michel 
Published: March 2013

ABSTRACT
A recombinant sleeping disease virus (rSDV) was previously shown to be totally attenuated and provide long-term protection in trout (C. Moriette, M. Leberre, A. Lamoureux, T. L. Lai, M. Brémont, J. Virol. 80:4088–4098, 2006). Sequence comparison of the rSDV to wild-type genomes exhibited a number of nucleotide changes. In the current study, we demonstrate that the virulent phenotype of SDV was essentially associated with two amino acid changes, V8A and M136T, in the E2 glycoprotein, with the V8A change mostly being involved in the acquisition of the virulent phenotype.
Variation of HIV-1 Mutation Spectra among Cell Types
Authors: Holtz Colleen M. , Mansky Louis M. 
Published: March 2013

ABSTRACT
The high rates of mutation, recombination, and replication drive HIV-1 diversity. In this study, we investigated how cell type affects viral mutation rate and mutation spectra. In studying four different cell types, no differences in mutation rate were observed, but intriguingly cell type differences impacted HIV-1 mutation spectra. This is the first description of significant differences in HIV-1 mutation spectra observed in different cell types in the absence of changes in the viral mutation rate.
PRAME-Induced Inhibition of Retinoic Acid Receptor Signaling-Mediated Differentiation—A Possible Target for ATRA Response in AML without t(15;17)
Authors: Bullinger Lars , Schlenk Richard F. , Götz Marlies , Botzenhardt Ursula , Hofmann Susanne , Russ Annika C. , Babiak Anna , Zhang Lu , Schneider Vanessa , Döhner Konstanze , Schmitt Michael , Döhner Hartmut , Greiner Jochen 
Published: February 2013

Abstract
Purpose: In acute myeloid leukemia (AML) without retinoic acid receptor (RAR) rearrangement, the effect of all-trans-retinoic acid (ATRA) is still poorly understood despite an association of NPM1 mutation and ATRA response. Recently, preferentially expressed antigen in melanoma (PRAME) has been shown to be a dominant repressor of RAR signaling.
Experimental Design: Thus, we further investigated ATRA response mechanisms, especially the impact of PRAME expression on ATRA responsiveness. We profiled gene expression in diagnostic samples derived from our AML HD98B trial, in which ATRA was administered in addition to intensive chemotherapy.
Results: Our data revealed a PRAME expression-associated gene pattern to be significantly enriched for genes involved in the retinoic acid metabolic process. In leukemia cell line models, we could show that retinoic acid-regulated cell proliferation and differentiation are impacted by PRAME expression. In patients with primary AML, repressor activity of high-PRAME levels might be overcome by the addition of ATRA as indicated by better outcome in 2 independent studies (P = 0.029).
Conclusions: PRAME seems to impair differentiation and to increase proliferation likely via blocking RAR signaling, which might be reversed by ATRA. PRAME therefore represents a promising target for both ATRA treatment and possibly future immunotherapeutic approaches in AML. Clin Cancer Res; 19(9); 2562–71. ©2013 AACR.
Human Lung Epithelial Cells Progressed to Malignancy through Specific Oncogenic Manipulations
Authors: Sato Mitsuo , Larsen Jill E. , Lee Woochang , Sun Han , Shames David S. , Dalvi Maithili P. , Ramirez Ruben D. , Tang Hao , DiMaio John Michael , Gao Boning , Xie Yang , Wistuba Ignacio I. , Gazdar Adi F. , Shay Jerry W. , Minna John D. 
Published: March 2013

Abstract
We used CDK4/hTERT–immortalized normal human bronchial epithelial cells (HBEC) from several individuals to study lung cancer pathogenesis by introducing combinations of common lung cancer oncogenic changes (p53, KRAS, and MYC) and followed the stepwise transformation of HBECs to full malignancy. This model showed that: (i) the combination of five genetic alterations (CDK4, hTERT, sh-p53, KRASV12, and c-MYC) is sufficient for full tumorigenic conversion of HBECs; (ii) genetically identical clones of transformed HBECs exhibit pronounced differences in tumor growth, histology, and differentiation; (iii) HBECs from different individuals vary in their sensitivity to transformation by these oncogenic manipulations; (iv) high levels of KRASV12 are required for full malignant transformation of HBECs, however, prior loss of p53 function is required to prevent oncogene-induced senescence; (v) overexpression of c-MYC greatly enhances malignancy but only in the context of sh-p53+KRASV12; (vi) growth of parental HBECs in serum-containing medium induces differentiation, whereas growth of oncogenically manipulated HBECs in serum increases in vivo tumorigenicity, decreases tumor latency, produces more undifferentiated tumors, and induces epithelial-to-mesenchymal transition (EMT); (vii) oncogenic transformation of HBECs leads to increased sensitivity to standard chemotherapy doublets; (viii) an mRNA signature derived by comparing tumorigenic versus nontumorigenic clones was predictive of outcome in patients with lung cancer. Collectively, our findings show that this HBEC model system can be used to study the effect of oncogenic mutations, their expression levels, and serum-derived environmental effects in malignant transformation, while also providing clinically translatable applications such as development of prognostic signatures and drug response phenotypes.
Visual Overview: http://mcr.aacrjournals.org/content/11/6/638/F1.large.jpg.
Mol Cancer Res; 11(6); 638–50. ©2013 AACR.
Human Umbilical Vein Endothelial Cells Protect Against Hypoxic-Ischemic Damage in Neonatal Brain via Stromal Cell-derived Factor 1/C-X-C Chemokine Receptor Type 4
Authors: Wu Chia-Ching , Chen Yi-Chi , Chang Ying-Chao , Wang Lan-Wan , Lin Yung-Chieh , Chiang Yi-Lun , Ho Chien-Jung , Huang Chao-Ching 
Published: March 2013

Background and Purpose—
Agents that protect against neurovascular damage provide a powerful neuroprotective strategy. Human umbilical vein endothelial cells (HUVECs) may be used to treat neonates with hypoxic-ischemia (HI) because of its autologous capability. We hypothesized that peripherally injected HUVECs entered the brain after HI, protected against neurovascular damage, and provided protection via stromal cell–derived factor 1/C-X-C chemokine receptor type 4 pathway in neonatal brain.

Methods—
Postpartum day 7 rat pups received intraperitoneal injections of low-passage HUVEC-P4, high-passage HUVEC-P8, or conditioned medium before and immediately after HI. HUVECs were transfected with adenovirus-green fluorescent protein for cell tracing. Oxygen–glucose deprivation was established by coculturing HUVEC-P4 with mouse neuroblastoma neuronal cells (Neuro-2a) and with mouse immortalized cerebral vascular endothelial cells (b.End3).

Results—
HUVEC-P4–treated group had more blood levels of green fluorescent protein–positive cells than HUVEC-P8–treated group 3 hours postinjection. Intraperitoneally injected HUVEC-P4, but not HUVEC-P8, entered the cortex after HI and positioned closed to the neurons and microvessels. Compared with the condition medium–treated group, the HUVEC-P4–treated but not the HUVEC-P8–treated group showed significantly less neuronal apoptosis and blood–brain barrier damage and more preservation of microvessels in the cortex 24 hours after HI. On postpartum day 14, the HUVEC-P4–treated group showed significant neuroprotection compared with the condition medium–treated group. Stromal cell–derived factor 1 was upregulated in the ipsilateral cortex 3 hours after HI, and inhibiting the stromal cell–derived factor 1/C-X-C chemokine receptor type 4 reduced the protective effect of HUVEC-P4. In vitro transwell coculturing of HUVEC-P4 also significantly protected against oxygen–glucose deprivation cell death in neurons and endothelial cells.

Conclusions—
Cell therapy using HUVECs may provide a powerful therapeutic strategy in treating neonates with HI.
Coronary Artery Calcification Is an Independent Stroke Predictor in the General Population
Authors: Hermann Dirk M. , Gronewold Janine , Lehmann Nils , Moebus Susanne , Jöckel Karl-Heinz , Bauer Marcus , Erbel Raimund 
Published: March 2013

Background and Purpose—
Coronary artery calcification (CAC) is a noninvasive marker of plaque load that predicts myocardial infarcts in the general population. Herein, we investigated whether CAC predicts stroke events in addition to established risk factors that are part of the Framingham risk score.

Methods—
A total of 4180 subjects from the population-based Heinz Nixdorf Recall study (45–75 years of age; 47.1% men) without previous stroke, coronary heart disease, or myocardial infarction were evaluated for stroke events over 94.9±19.4 months. Cox proportional hazards regressions were used to examine CAC as stroke predictor in addition to established vascular risk factors (age, sex, systolic blood pressure, low-density lipoprotein, high-density lipoprotein, diabetes mellitus, smoking, and atrial fibrillation).

Results—

Ninety-two incident strokes occurred (82 ischemic, 10 hemorrhagic). Subjects suffering a stroke had significantly higher CAC values at baseline than the remaining subjects (median, 104.8[Q1;Q3, 14.0;482.2] vs 11.2[0;106.2];
P
<0.001). In a multivariable Cox regression, log
10
(CAC+1) was an independent stroke predictor (hazards ratio, 1.52 [95% confidence interval, 1.19–1.92];
P
=0.001) in addition to age (1.35 per 5 years [1.15–1.59];
P
<0.001), systolic blood pressure (1.25 per 10 mm Hg [1.14–1.37];
P
<0.001), and smoking (1.75 [1.07–2.87];
P
=0.025). CAC predicted stroke in men and women, particularly in subjects <65 years of age and independent of atrial fibrillation. CAC discriminated stroke risk specifically in participants belonging to the low (<10%) and intermediate (10%–20%) Framingham risk score categories.

Conclusions—
CAC is an independent stroke predictor in addition to classical risk factors in subjects at low or intermediate vascular risk.