bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of elasticity: a stochastic model-based approach in ultrasound elastography
Authors: Lu Minhua , Zhang Heye , Wang Jun , Yuan Jinwei , Hu Zhenghui , Liu Huafeng 
Published: August 2013

Abstract

Background
The convectional strain-based algorithm has been widely utilized in clinical practice. It can only provide the information of relative information of tissue stiffness. However, the exact information of tissue stiffness should be valuable for clinical diagnosis and treatment.

Methods
In this study we propose a reconstruction strategy to recover the mechanical properties of the tissue. After the discrepancies between the biomechanical model and data are modeled as the process noise, and the biomechanical model constraint is transformed into a state space representation the reconstruction of elasticity can be accomplished through one filtering identification process, which is to recursively estimate the material properties and kinematic functions from ultrasound data according to the minimum mean square error (MMSE) criteria. In the implementation of this model-based algorithm, the linear isotropic elasticity is adopted as the biomechanical constraint. The estimation of kinematic functions (i.e., the full displacement and velocity field), and the distribution of Young’s modulus are computed simultaneously through an extended Kalman filter (EKF).

Results
In the following experiments the accuracy and robustness of this filtering framework is first evaluated on synthetic data in controlled conditions, and the performance of this framework is then evaluated in the real data collected from elastography phantom and patients using the ultrasound system. Quantitative analysis verifies that strain fields estimated by our filtering strategy are more closer to the ground truth. The distribution of Young’s modulus is also well estimated. Further, the effects of measurement noise and process noise have been investigated as well.

Conclusions
The advantage of this model-based algorithm over the conventional strain-based algorithm is its potential of providing the distribution of elasticity under a proper biomechanical model constraint. We address the model-data discrepancy and measurement noise by introducing process noise and measurement noise in our framework, and then the absolute values of Young’s modulus are estimated through the EFK in the MMSE sense. However, the initial conditions, and the mesh strategy will affect the performance, i.e., the convergence rate, and computational cost, etc.
Role of hypoxia inducible factor-1 in keratinocyte inflammatory response and neutrophil recruitment
Authors: Leire Emma , Olson Josh , Isaacs Hart , Nizet Victor , Hollands Andrew 
Published: August 2013

Abstract

Background
Hypoxia inducible factor-1 (HIF-1) is a major regulator of the cellular adaption to low oxygen stress and the innate immune function of myeloid cells. Treatment with the novel HIF-1 stabilizing drug AKB-4924 has been shown to enhance the bactericidal activity of keratinocytes as well as phagocytic cells. In this study, we sought to investigate the effect of pharmacological boosting of HIF-1 with AKB-4924 in keratinocytes and their contribution to the innate immune response.

Findings
Treatment with the novel HIF-1 stabilizing drug AKB-4924 can increase keratinocyte production of pro-inflammatory cytokines in vitro and enhance neutrophil recruitment in vivo.

Conclusions
HIF plays an important role in cytokine production by keratinocytes and in neutrophil recruitment to the skin. The HIF-boosting drug AKB-4924 has the potential to enhance the immune response even in the complex environment of bacterial skin infections.
Proteomic analysis of kidneys from selenoprotein M transgenic rats in response to increased bioability of selenium
Authors: Goo Jun Seo , Kim Yo Na , Choi Kyung Mi , Hwang In Sik , Kim Ji Eun , Lee Young Ju , Kwak Moon Hwa , Shim Sun Bo , Jee Seung Wan , Lim Chul Joo , Seong Je Kyung , Hwang Dae Youn 
Published: August 2013

Abstract

Background
To characterize changes in global protein expression in kidneys of transgenic rats overexpressing human selenoprotein M (SelM) in response to increased bioabivility of selenium (Sel), total proteins extracted from kidneys of 10-week-old CMV/hSelM Tg and wild-type rats were separated by 2-dimensional gel electrophoresis and measured for changes in expression.

Results
Ten and three proteins showing high antioxidant enzymatic activity were up- and down-regulated, respectively, in SelM-overexpressing CMV/hSelM Tg rats compared to controls based on an arbitrary 2-fold difference. Up-regulated proteins included LAP3, BAIAP2L1, CRP2, CD73 antigen, PDGF D, KIAA143 homolog, PRPPS-AP2, ZFP313, HSP-60, and N-WASP, whereas down-regulated proteins included ALKDH3, rMCP-3, and STC-1. After Sel treatment, five of the up-regulated proteins were significantly increased in expression in wild-type rats, whereas there were no changes in CMV/hSelM Tg rats. Only two of the down-regulated proteins showed reduced expression in wild-type and Tg rats after Sel treatment.

Conclusions
These results show the primary novel biological evidences that new functional protein groups and individual proteins in kidneys of Tg rats relate to Sel biology including the response to Sel treatment and SelM expression.
Pharmacokinetics and thrombolytic effects of the recombinant tissue-type plasminogen activator in horses
Authors: Bäumer Wolfgang , Herrling Gudrun M , Feige Karsten 
Published: August 2013

Abstract

Background
To test the efficacy of the recombinant tissue-type plasminogen activator (rt-PA) alteplase in horses, the thrombolytic effect was tested in in vitro generated equine thrombi. The extent of lysis was determined by measuring the decrease in thrombi weight over a period of 4 hours. In vivo pharmacokinetics of alteplase were determined in 6 healthy horses. A single dose (1 mg/kg) was applied via intravenous infusion over a period of 30 minutes Coagulation-related variables, blood count and clinical parameters were taken before the treatment and until 48 h after treatment. In addition, plasma rt-PA concentration was measured until 300 min after commencing the infusion.

Results

In vitro, a dose dependent decrease of thrombus weight ranging from a 56 (± 6.5) % decrease for 0.5 μg/ml to 92 (± 2.1) % decrease for 5 μg/ml rt-PA was noted. The D-dimer concentration in the lysis medium correspondingly increased from 0.10 up to 10.8 mg/l.

In vivo, none of the horses showed an adverse reaction to the alteplase infusion. In some horses blood parameters were slightly altered. The 1 mg/kg dose yielded the following pharmacokinetic parameters: Cmax = 1.25 ± 0.27 μg/ml; CL = 21.46 ± 5.67 ml/min/kg; dominant half life (t1/2α) = 6.81 ± 1.48 minutes; median elimination half life (t1/2β) = 171 min (range: 85–1061); AUC = 50.33 ± 17.62 μg · min /ml.

Conclusion
These findings indicate that a single dose of 1 mg/kg alteplase results in rt-PA plasma concentrations comparable to those in humans and might be sufficient for a thrombolytic therapy in horses. Further studies must be performed to determine the alteplase effectiveness in horses with jugular vein thrombosis.
Developmental and Behavioral Pediatricians' Attitudes Toward Screening for Fragile X
Authors: Acharya Kruti , Schindler Abigail 
Published: August 2013

Abstract
Developmental and behavioral pediatricians (DBP) diagnose and care for children with fragile X syndrome. Their attitudes toward FMR1 newborn screening (NBS) and FMR1 carrier testing in childhood could highlight potential pitfalls with FMR1 NBS. We conducted a cross-sectional survey with an adjusted response rate of 61%. Among DBP, 74% supported universal FMR1 NBS, preferring to identify both full mutations and premutations. DBP also support FMR1 testing of asymptomatic siblings. Although DBP support testing for premutations at various points in the lifespan, DBP are not familiar with the array of fragile X–associated disorders (FXAD). Targeted educational interventions are needed to ensure that all health care providers have the knowledge and competence to consent and to counsel families on FXAD.
The value of clinical and laboratory diagnostics for chest pain patients at the emergency department
Authors: Jellema Laurens-Jan C. , Backus Barbra E. , Six A. Jacob , Braam Richard , Groenemeijer Bjorn , van der Zaag-Loonen Hester J. , Tio Rene , van Suijlen Jeroen D.E. 
Published: August 2013

AbstractThe focus during the diagnostic process for patients with acute chest pain is to discriminate patients who can be safely discharged from those who are at risk for an acute coronary syndrome (ACS). In this study the diagnostic value of the clinical examination is compared with laboratory testing of troponin.This study included 710 chest pain patients who presented at the ED of two hospitals in the Netherlands. Clinical examination and laboratory testing were combined in the recently developed HEART-score. The diagnostic values of clinical presentation, troponin and the HEART-score for a major adverse coronary event (MACE) and an ACS within 6 weeks were assessed. Furthermore, the improvement of HEART with the second troponin measurement after 6 h was assessed using the net reclassification improvement (NRI).The use of HEART (AUCThe HEART-score combines clinical evaluation and results from laboratory testing, which should be used together, to discriminate patients at risk of a cardiac event from patients who can be safely discharged. In addition, it is shown that a second troponin measurement slightly improves the discriminative ability of the HEART-score.
Serum Uric Acid and C-reactive Protein in Patients with Metastatic Colorectal Carcinoma During Combination Therapy with High-dose Folinic Acid
Authors: Melichar Bohuslav , Hyšpler Radomír , Kalábová Hana , Holecková Petra , Študentová Hana 
Published: August 2013

Abstract
New spectrum of side effects has emerged with the introduction of targeted therapies, including changes in parameters determining cardiovascular risk. Among other laboratory parameters, hyperuricemia and elevated Creactive protein (CRP) are associated with increased risk of cardiovascular disease. The aim of the present study was to investigate the changes of serum uric acid and CRP during the therapy with cetuximab, combined with 5- fluorouracil and high-dose folinic acid, in patients with metastatic colorectal carcinoma and the association of these changes with the outcome of the therapy. CRP and uric acid were determined using particle-enhanced immunoturbidimetric assay and uricase method, respectively. Measurements before and during the treatment were compared by Wilcoxon signed rank test, and comparison between survivors and non-survivors was performed by Mann-Whitney U test. Compared to baseline (pre-treatment) concentrations, serum uric acid was decreased significantly throughout the course of the combination treatment with irinotecan, 5-fluorouracil, highdose folinic acid and cetuximab. The decrease was evident early in the course of treatment. Serum CRP was also decreased significantly throughout the most of the course of therapy. The significant decrease of serum uric acid and CRP was evident already one week after the start of treatment. Serum CRP was significantly lower in patients who survived 12 months, but no difference of uric acid concentrations between survivors and non-survivors was found. A marked decrease of serum uric acid was observed during the combination therapy. High CRP was associated with poor prognosis, but no association between uric acid and prognosis was noted.
Use of a Pteridine Moiety to Track DNA Uptake in Cells
Authors: Costa Justin A. , Leal-Pinto Edgar , Henderson Scott C. , Zabel Troy , Hawkins Mary E. , Hanss Basil 
Published: August 2013

Abstract
Fluorescence labeled oligonucleotides have a long history of being used to monitor nucleic acid transport and uptake. However, it is not known if the fluorescent moiety itself physically limits the number of pathways that can be used by the cell due to steric, hydrophobic, or other chemical characteristics. Here, we report a method for comparing the uptake kinetics of oligonucleotides labeled either with the fluorescent pteridine, 3-methyl-8-(2- deoxy-b-D-ribofuranosyl) isoxanthopterin (3MI), or the common fluorophore 5-carboxyfluorescein (5-FAM). We use a multiphoton microscopic technique to monitor nucleic acid uptake LLC-PK1, a pig renal tubular cell line that is known to have multiple uptake pathways. We find that the two fluorophores enter the cells at different rates, suggesting that choice of fluorescent moiety influences the uptake pathway used by a cell. Finally, we reconstituted an LLC-PK1 membrane channel that is selective for nucleic acids in planar lipid bilayers, and tested the ability of the labeled nucleic acids to permeate the channel. We find that 3MI, and not 5-FAM labeled oligonucleotides can traverse the plasma membrane through the channel. These results have implications for future studies aimed at delivering pteridine moieties to cells and for tracking nucleic acid transport into tissues.
Evaluation of Serum and Urinary Levels of some Pteridine Pathway Components in Healthy Turkish Children
Authors: Girgin Gözde , Baydar Terken , Fuchs Dietmar , Sahin Gönül , Özmert Elif , Yurdakök Kadriye 
Published: August 2013

Abstract
Neopterin, as a non-conjugated pteridine, is synthesized from guanosine triphosphate and its production is upregulated upon the activation of cellular immune response. Alterations of pteridines in body fluids are known to correlate well with existing diseases and stages, prognosis, clinical outcomes and survival data. It is of advantage to have a pteridine database of healthy volunteers to determine normal values. Thereby, especially in children there is no detailed study on pteridine levels. The aim of this study is to initiate the establishment of pteridine database of healthy children in our country. Serum neopterin levels were analysed by enzyme-linked immunosorbent assay. Urinary neopterin and biopterin levels and serum kynurenine, tryptophan levels and kynurenine/tryptophan ratio as an estimate of tryptophan breakdown were assessed with high-pressure liquid chromatography in serum and urine samples of 55 children aged between 3 months and 10 years. The results were evaluated within the subgroups of different ages and sex. Pteridine pathway components were found to be higher in children compared to adults. Higher levels of pteridine pathway components observed within the first years of life may reflect the rapid maturation of the immune system, and environmental adaptation and/or insufficiency of defence systems. On the other hand, it may also relate to a higher frequency of infections not (yet) manifested clinically.
Herd behavior, bubbles and social interactions in financial markets
Authors: Chang Sheng-Kai 
Published: August 2013

AbstractThis paper studies herd behavior, bubbles and social interactions in financial markets through the asset pricing models with heterogeneous interacting agents. The relationship between social interactions, herd behavior and bubbles is examined. It is found that herd behavior arises naturally when there are strong enough social interactions among individual investors. In addition, an extremely small bubble may cause a sufficiently large number of traders to engage in herd behavior when the social interactions among traders are strong.
The serum 25-hydroxyvitamin D response to vitamin D supplementation is related to genetic factors, BMI, and baseline levels
Authors: Didriksen Allan , Grimnes Guri , Hutchinson Moira Strand , Kjærgaard Marie , Svartberg Johan , Joakimsen Ragnar M , Jorde Rolf 
Published: August 2013

ObjectiveThe serum 25-hydroxyvitamin D (25(OH)D) level is not only dependent on vitamin D intake and production in the skin but also dependent on genetic factors. Thus, in large genome-wide association studies, it has been shown that single nucleotide polymorphisms (SNPs) in the vitamin D binding protein (DBP), as well as in enzymes related to activation or degradation of vitamin D and its metabolites, are as important for the serum 25(OH)D level as the effect of season. How these SNPs affect the serum 25(OH)D response to vitamin D supplementation is uncertain.Design and methodsData were pooled from three randomized controlled trials where 40 000 IU vitamin D/week was given for 6 months. Serum 25(OH)D was measured before and at the end of the intervention, and the subjects were genotyped for SNPs related to the serum 25(OH)D level.ResultsBaseline 25(OH)D levels were significantly related to SNPs in theDBPandCYP2R1genes. Those with SNPs associated with the lowest baseline 25(OH)D levels also had the smallest increase (delta) after supplementation. Those with the lowest baseline serum 25(OH)D (without regard to genotypes) had the highest increase (delta) after supplementation. Subjects with high BMI had lowest baseline 25(OH)D levels and also the smallest increase (delta) after supplementation.ConclusionsThe serum 25(OH)D response to supplementation depends on genes, baseline level, and BMI. However, whether this is clinically important or not depends on the therapeutic window of vitamin D, an issue that is still not settled.
A Novel Approach to Estimating Heterozygosity from Low-Coverage Genome Sequence
Authors: Bryc Katarzyna , Patterson Nick , Reich David 
Published: August 2013

AbstractHigh-throughput shotgun sequence data make it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites within an individual’s genome, which is informative about inbreeding and effective population size. However, in many cases, the available sequence data of an individual are limited to low coverage, preventing the confident calling of genotypes necessary to directly count the proportion of heterozygous sites. Here, we present a method for estimating an individual’s genome-wide rate of heterozygosity from low-coverage sequence data, without an intermediate step that calls genotypes. Our method jointly learns the shared allele distribution between the individual and a panel of other individuals, together with the sequencing error distributions and the reference bias. We show our method works well, first, by its performance on simulated sequence data and, second, on real sequence data where we obtain estimates using low-coverage data consistent with those from higher coverage. We apply our method to obtain estimates of the rate of heterozygosity for 11 humans from diverse worldwide populations and through this analysis reveal the complex dependency of local sequencing coverage on the true underlying heterozygosity, which complicates the estimation of heterozygosity from sequence data. We show how we can use filters to correct for the confounding arising from sequencing depth. We find in practice that ratios of heterozygosity are more interpretable than absolute estimates and show that we obtain excellent conformity of ratios of heterozygosity with previous estimates from higher-coverage data.
Genotype Imputation Reference Panel Selection Using Maximal Phylogenetic Diversity
Authors: Zhang Peng , Zhan Xiaowei , Rosenberg Noah A , Zöllner Sebastian 
Published: August 2013

Abstract
The recent dramatic cost reduction of next-generation sequencing technology enables investigators to assess most variants in the human genome to identify risk variants for complex diseases. However, sequencing large samples remains very expensive. For a study sample with existing genotype data, such as array data from genome-wide association studies, a cost-effective approach is to sequence a subset of the study sample and then to impute the rest of the study sample, using the sequenced subset as a reference panel. The use of such an internal reference panel identifies population-specific variants and avoids the problem of a substantial mismatch in ancestry background between the study population and the reference population. To efficiently select an internal panel, we introduce an idea of phylogenetic diversity from mathematical phylogenetics and comparative genomics. We propose the “most diverse reference panel”, defined as the subset with the maximal “phylogenetic diversity”, thereby incorporating individuals that span a diverse range of genotypes within the sample. Using data both from simulations and from the 1000 Genomes Project, we show that the most diverse reference panel can substantially improve the imputation accuracy compared to randomly selected reference panels, especially for the imputation of rare variants. The improvement in imputation accuracy holds across different marker densities, reference panel sizes, and lengths for the imputed segments. We thus propose a novel strategy for planning sequencing studies on samples with existing genotype data.
Negative Functional Interaction Between Cell Integrity MAPK Pathway and Rho1 GTPase in Fission Yeast
Authors: Viana Raul A , Pinar Mario , Soto Teresa , Coll Pedro M , Cansado Jose , Pérez Pilar 
Published: August 2013

Abstract
Rho1 GTPase is the main activator of cell wall glucan biosynthesis and regulates actin cytoskeleton in fungi, including Schizosaccharomyces pombe. We have obtained a fission yeast thermosensitive mutant strain carrying the rho1-596 allele, which displays reduced Rho1 GTPase activity. This strain has severe cell wall defects and a thermosensitive growth, which is partially suppressed by osmotic stabilization. In a global screening for rho1-596 multicopy suppresors the pmp1+ gene was identified. Pmp1 is a dual specificity phosphatase that negatively regulates the Pmk1 mitogen-activated protein kinase (MAPK) cell integrity pathway. Accordingly, elimination of Pmk1 MAPK partially rescued rho1-596 thermosensitivity, corroborating the unexpected antagonistic functional relationship of these genes. We found that rho1-596 cells displayed increased basal activation of the cell integrity MAPK pathway and therefore were hypersensitive to MgCl2 and FK506. Moreover, the absence of calcineurin was lethal for rho1-596. We found a higher level of calcineurin activity in rho1-596 than in wild-type cells, and overexpression of constitutively active calcineurin partially rescued rho1-596 thermosensitivity. All together our results suggest that loss of Rho1 function causes an increase in the cell integrity MAPK activity, which is detrimental to the cells and turns calcineurin activity essential.