bluuebunny/crossref_metadata_2025 huggingface dataset:
Association Analysis of BMD-associated SNPs with Knee Osteoarthritis
Authors: Yerges-Armstrong Laura M , Yau Michelle S , Liu Youfang , Krishnan Subha , Renner Jordan B , Eaton Charles B , Kwoh C Kent , Nevitt Michael C , Duggan David J , Mitchell Braxton D , Jordan Joanne M , Hochberg Marc C , Jackson Rebecca D
Published: December 2013

Osteoarthritis (OA) risk is widely recognized to be heritable but few loci have been identified. Observational studies have identified higher systemic bone mineral density (BMD) to be associated with an increased risk of radiographic knee osteoarthritis. With this in mind, we sought to evaluate whether well-established genetic loci for variance in BMD are associated with risk for radiographic OA in the Osteoarthritis Initiative (OAI) and the Johnston County Osteoarthritis (JoCo) Project. Cases had at least one knee with definite radiographic OA, defined as the presence of definite osteophytes with or without joint space narrowing (Kellgren-Lawrence [KL] grade ≥ 2) and controls were absent for definite radiographic OA in both knees (KL grade ≤ 1 bilaterally). There were 2014 and 658 Caucasian cases, respectively, in the OAI and JoCo Studies, and 953 and 823 controls. Single nucleotide polymorphisms (SNPs) were identified for association analysis from the literature. Genotyping was carried out on Illumina 2.5M and 1M arrays in Genetic Components of Knee OA (GeCKO) and JoCo, respectively and imputation was done. Association analyses were carried out separately in each cohort with adjustments for age, body mass index (BMI), and sex, and then parameter estimates were combined across the two cohorts by meta-analysis. We identified four SNPs significantly associated with prevalent radiographic knee OA. The strongest signal (p = 0.0009; OR = 1.22; 95% CI, 1.08–1.37) maps to 12q3, which contains a gene coding for SP7. Additional loci map to 7p14.1 (TXNDC3), 11q13.2 (LRP5), and 11p14.1 (LIN7C). For all four loci the allele associated with higher BMD was associated with higher odds of OA. A BMD risk allele score was not significantly associated with OA risk. This meta-analysis demonstrates that several genomewide association studies (GWAS)-identified BMD SNPs are nominally associated with prevalent radiographic knee OA and further supports the hypothesis that BMD, or its determinants, may be a risk factor contributing to OA development. © 2014 American Society for Bone and Mineral Research.
LEAP: Highly accurate prediction of protein loop conformations by integrating coarse‐grained sampling and optimized energy scores with all‐atom refinement of backbone and side chains
Authors: Liang Shide , Zhang Chi , Zhou Yaoqi
Published: December 2013

Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is an unsolved problem. Its solution will significantly impact protein homology and template‐based modeling as well as ab initio protein‐structure prediction. Here, we developed a coarse‐grained, optimized scoring function for initial sampling and ranking of loop decoys. The resulting decoys are then further optimized in backbone and side‐chain conformations and ranked by all‐atom energy scoring functions. The final integrated technique called loop prediction by energy‐assisted protocol achieved a median value of 2.1 Å root mean square deviation (RMSD) for 325 12‐residue test loops and 2.0 Å RMSD for 45 12‐residue loops from critical assessment of structure‐prediction techniques (CASP) 10 target proteins with native core structures (backbone and side chains). If all side‐chain conformations in protein cores were predicted in the absence of the target loop, loop‐prediction accuracy only reduces slightly (0.2 Å difference in RMSD for 12‐residue loops in the CASP target proteins). The accuracy obtained is about 1 Å RMSD or more improvement over other methods we tested. The executable file for a Linux system is freely available for academic users at http://sparks‐lab.org. © 2013 Wiley Periodicals, Inc.
Palladium‐mediated oxidative carbonylation reactions for the synthesis of 11C‐radiolabelled ureas
Authors: Kealey Steven , Husbands Stephen M. , Bennacef Idriss , Gee Antony D. , Passchier Jan
Published: December 2013

Palladium(II)‐mediated oxidative carbonylation reactions have been used to synthesize 11C‐radiolabelled ureas via the coupling of amines with [11C]carbon monoxide, in a one‐pot process. Following trapping of 11CO in a solution of copper(I) tris(3,5‐dimethylpyrazolyl)borate, homocoupling reactions of primary aliphatic amines proceed in the presence of Pd(PPh3)2Cl2 to give the corresponding N,N‐disubstituted [11C]ureas. Secondary amines do not produce the corresponding N,N,N,N‐tetrasubsituted [11C]ureas under these conditions. This difference in reactivity allows for the formation of unsymmetrical N,N’,N’‐trisubstituted [11C]ureas using a mixture of a primary amine and a reactive secondary amine. The potential use of this method in positron emission tomography (PET) was demonstrated by the synthesis of the M1 muscarinic acetylcholine receptor radiotracer, [11C‐carbonyl]GSK1034702.
Alternative approaches for PET radiotracer development in Alzheimer's disease: imaging beyond plaque
Authors: Holland Jason P. , Liang Steven H. , Rotstein Benjamin H. , Collier Thomas L. , Stephenson Nickeisha A. , Greguric Ivan , Vasdev Neil
Published: December 2013

Alzheimer's disease (AD) and related dementias show increasing clinical prevalence, yet our understanding of the etiology and pathobiology of disease‐related neurodegeneration remains limited. In this regard, noninvasive imaging with radiotracers for positron emission tomography (PET) presents a unique tool for quantifying spatial and temporal changes in characteristic biological markers of brain disease and for assessing potential drug efficacy. PET radiotracers targeting different protein markers are being developed to address questions pertaining to the molecular and/or genetic heterogeneity of AD and related dementias. For example, radiotracers including [11C]‐PiB and [18F]‐AV‐45 (Florbetapir) are being used to measure the density of Aβ‐plaques in AD patients and to interrogate the biological mechanisms of disease initiation and progression. Our focus is on the development of novel PET imaging agents, targeting proteins beyond Aβ‐plaques, which can be used to investigate the broader mechanism of AD pathogenesis. Here, we present the chemical basis of various radiotracers which show promise in preclinical or clinical studies for use in evaluating the phenotypic or biochemical characteristics of AD. Radiotracers for PET imaging neuroinflammation, metal ion association with Aβ‐plaques, tau protein, cholinergic and cannabinoid receptors, and enzymes including glycogen‐synthase kinase‐3β and monoamine oxidase B amongst others, and their connection to AD are highlighted. Copyright © 2013 John Wiley & Sons, Ltd.
Removal of the insecticide diazinon from liquid media by free and immobilized Streptomyces sp. isolated from agricultural soil
Authors: Briceño Gabriela , Fuentes María S. , Rubilar Olga , Jorquera Milko , Tortella Gonzalo , Palma Graciela , Amoroso María J. , Diez Maria Cristina
Published: December 2013

From an agricultural soil that had received continuous applications of organophosphorus pesticides, 30 actinobacteria strains were isolated. Two strains, identified as Streptomyces sp. AC1‐6 and Streptomyces sp. ISP4, were selected because of their tolerance to diazinon and based on the relationship between diazinon removal and microbial growth. In liquid medium with diazinon at concentrations of 25 and 50 mg L−1, both strains were able to remove approximately 40–50% and 70–90% of the initial diazinon after 24 and 96 h of incubation, respectively. This diazinon removal was accompanied by microbial growth of the strains, an initial pH decrease, and glucose consumption in the liquid medium. Evaluation of the diazinon removal achieved by the free actinobacteria and Streptomyces sp. AC1‐6 immobilized on alginate beads revealed that the immobilized cells exhibited a 60% higher diazinon removal compared with the free cells. The reusability of the encapsulated biomass was confirmed, and a diazinon removal rate of more than 50% was obtained after the second batch. This work constitutes one of the few reports that describe Streptomyces strains as diazinon degraders. Given the high diazinon removal found, the streptomycetes exhibit suitable potential as diazinon‐degrading actinobacteria for elimination of diazinon from liquid residues.
Margin width is not predictive of residual disease on re‐excision in breast conserving therapy
Authors: Hadzikadic Gusic L. , McGuire K.P. , Ozmen T. , Soran A. , Thomas C.R. , McAuliffe P.F. , Diego E.J. , Bonaventura M. , Johnson R.R. , Ahrendt G.M.
Published: December 2013

Background

There is lack of consensus regarding re‐excision in breast‐conserving therapy (BCT) and close margins. We hypothesize that margin width does not predict residual disease.

Methods

The cancer registry was queried from 2003 to 2008 for patients with BCT who underwent re‐excision for <2‐mm margins. Factors associated with additional disease were evaluated.

Results

One thousand eight hundred forty‐three patients underwent BCT. Our re‐excision rate was 42%. Clinicopathologic factors from 228 patients were analyzed. One hundred five patients (46%) had additional disease; of those, 58% had BCT and 42% mastectomy. One hundred twenty‐three (54%) had no additional disease; of those 82% had BCT and 18% mastectomy. Of the 66 patients who underwent mastectomy, 44 (67%) had residual disease; of the 161 who had BCT, 61 (38%) had residual disease (P < 0.01). On univariate analysis, margin width did not correlate with residual disease. Multifocality, non‐invasive histology, increasing number of close margins, and higher grade predicted additional disease (P < 0.05). On multivariate analysis, only number of close margins remained significant.

Conclusions

Margin width does not predict additional disease. This challenges the practice of using this to select re‐excision candidates. Our data suggest that tumor behavior and extent of disease, defined by volume of residual disease and invasiveness of histology, play a more significant role. J. Surg. Oncol. 2014 109:426–430. © 2013 Wiley Periodicals, Inc.
Treatment and outcome of young patients with esophageal cancer in the Netherlands
Authors: van Nistelrooij Anna M.J. , van Steenbergen Liza N. , Spaander Manon C.W. , Tilanus Hugo W. , van Lanschot J. Jan B. , Lemmens Valery E.P.P. , Wijnhoven Bas P.L.
Published: December 2013

Background

Esophageal cancer is increasingly recognized in younger patients. We compared clinicopathological characteristics, treatment, and survival of patients aged ≤50 years with patients aged >50 years diagnosed with esophageal cancer in the Netherlands.

Methods

From the nationwide Netherlands Cancer Registry we identified all patients diagnosed with esophageal cancer between January 2000 and January 2011. Proportions were compared using the χ2 test for categorical variables. Overall and relative survival was calculated.

Results

Eleven percent of the patients (n = 1,466) were aged ≤50 years and adenocarcinoma was the most common tumor type (73.6%). Grade of tumor differentiation was comparable between both age groups (P = 0.460) as well as T‐stage (P = 0.058). Younger patients presented more often with positive lymph nodes (70.1% vs. 66.4%, P = 0.010) and distant metastasis (50.5% vs. 44.7%, P < 0.001) but had surgery more often as compared to older patients: 40.6% versus 37.9%, P = 0.047. There was no significant difference in the 5‐year relative survival between both age groups: 18.1% versus 17.2%, P > 0.05. A subgroup analysis among patients diagnosed with adenocarcinoma revealed similar results.

Conclusions

Young patients with esophageal cancer present with more advanced disease stage and received more often treatment. However, they show comparable relative survival rates with their older counterparts. J. Surg. Oncol. 2014 109:561–566. © 2013 Wiley Periodicals, Inc.
Effect of nickel base superalloy composition on oxidation resistance in SO2 containing, high pO2 environments
Authors: Jalowicka A. , Nowak W. , Naumenko D. , Singheiser L. , Quadakkers W.J.
Published: December 2013

Modern gas turbine materials are subjected to increasing operating temperatures in service environments, which contain high concentrations of gaseous species originating from fuel impurities, e.g. sulfur. In the present study, the oxidation behavior of two commercially available nickel‐base alloys, Rene 80 and PWA 1483, was investigated for up to 500 h duration in synthetic air and synthetic air containing 2% SO2 at 1050 °C. In order to investigate the mechanisms of SO2 attack, specimens of the two alloys after different oxidation times were characterized using a number of surface analytical techniques such as scanning electron microscopy, XRD, and glow discharge optical emission spectrometry. The corrosion reactions in the presence of SO2 were found to be strongly alloy dependent and could not be explained simply in terms of the contents of the main scale‐forming alloying elements, Cr and Al. Severe internal sulfidation was observed underneath the chromium‐rich oxide scale on Rene 80, leading to breakaway oxidation after longer exposure times. For PWA 1483 sub‐scale formation of a near‐continuous alumina occurred, which resulted in substantial suppression of sulfidation. Consequently, no breakaway oxidation of PWA 1483 was observed up to 500 h exposure at 1050 °C in synthetic air with 2% SO2. The formation of a dense alumina sub‐scale on PWA 1483 is believed to be correlated with the Ta‐addition in this material. It is proposed that Ta can tie up Ti by forming a mixed oxide of the type TiTaO4. In this way, it prevents the incorporation of Ti into the chromia scale, which can lead to enhanced scale growth.
Nonvolitional assessment of muscle endurance in idiopathic inflammatory myopathies: There is no relationship between patient‐reported fatigue and muscle fatigability
Authors: Campbell Richard , Gordon Patrick , Ward Katie , Reilly Charles , Scott David L. , Rafferty Gerrard F.
Published: December 2013

Introduction: We investigated whether muscle endurance differs between IIM patients and controls and if a relationship exists between perceived fatigue and poor muscle endurance. Methods: Quadriceps contractility, measured using femoral nerve stimulation (TwQ), and strength, measured using maximal voluntary contraction (MVCQ), were assessed in 20 IIM patients and matched controls. Quadriceps endurance was assessed using repetitive electrical stimulation (3 minutes). Time for force to fall to 70% initial force was determined (T70). Reported fatigue was measured using the FACIT‐F/Fatigue Severity Scales. Results: TwQ and MVCQ were lower and perceived fatigue greater for patients. There was no difference in T70 between groups. No relationships were observed between perceived fatigue and endurance (T70). Conclusions: IIM patients reported more fatigue and were weaker than controls, but there was no difference in muscle endurance. Endurance and strength were unrelated to reported fatigue measures. Mechanisms driving perceived IIM fatigue are likely to be multifactorial. Muscle Nerve 50: 401–406, 2014
Improved upwind discretization of the advection equation
Authors: Erdogan Utku
Published: December 2013

The simplest upwind discretization of the advection equation is only first‐order accurate in time and space and very diffusive. In this article, the first‐order upwind method is improved by changing its basis functions. The resulting scheme, called exponentially fitted, proves to be more accurate in both space and time. In addition, it inherits some qualitative behaviors of the advection equation. The proposed approach is able to be generalized for more complicated problems provided that appropriate relations between the fitting parameters of the method are imposed. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 773–787, 2014
An Augmented Beam Element for Structural Dynamics Using Unit Deflection Shapes Gained on a 2D Finite Element Mesh of the Cross Section
Authors: Müller Gerhard , Kreutz Johannes
Published: December 2013

Wave behaviour of line shaped structures can be analysed if they are simply shaped (beams, rods, etc.) and if the frequency or wavelength is within a range where the underlying theories are still applicable. If the frequencies and wavelengths exceed these limits, the modelling of these line or beam shaped structures is only possible using volume elements which results in considerably high computation time and modelling effort. The idea of this work is to keep the beam like modelling of structures but enhance the solution space such that arbitrary but reasonable deflection shapes of the cross section can be covered. The unit deflection shapes are defined and computed on the basis of a 2D finite element mesh of the beam cross section: warpshapes for primary and secondary torsion and shear forces, Eigenmodes for the problem of a plate in membrane and a plate in bending action, derived warpshapes for in plane shapes and shapes which cover the lateral strains. By this transformation of unknowns the number of system degrees of freedom can be reduced considerably. Expensive pre‐ and postprocessing steps can be done in parallel which opens the gate for massive performance gains. This method was validated in previous publications of the authors and shall now be extended using unit deflection shapes gained from eigenmodes of an infinite Fourier transformed structure obtained by solving a quadratic eigenvalue problem for the wavenumber kx. The results of both methods shall be compared. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Solution of Complementarity Problems via Piecewise Linearization
Authors: Piontkowski Julia , Griewank Andreas
Published: December 2013

My master thesis concerns the solution linear complementarity problems (LCP). The Lemke algorithm, the most commonly used algorithm for solving a LCP until this day, was compared with the piecewise Newton method (PLN algorithm). The piecewise Newton method is an algorithm to solve a piecewise linear system on the basis of damped Newton methods. The linear complementarity problem is formulated as a piecewise linear system for the applicability of the PLN algorithm. Then, different application examples will be presented, solved with the PLN algorithm. As a result of the findings (of my master thesis) it can be assumed that – under the condition of coherent orientation – the PLN‐algorithm requires fewer iterations to solve a linear complementarity problem than the Lemke algorithm. The coherent orientation for piecewise linear problems corresponds for linear complementarity problems to the P‐matrix‐property. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Infinite Penalization for Optimal Control Problems: An infinite‐dimensional optimization method for constrained optimization problems
Authors: Gugat Martin , Herty Michael
Published: December 2013

We present results on a method for infinite dimensional constrained optimization problems. In particular, we are interested in state constrained optimal control problems and discuss an algorithm based on penalization and smoothing. The algorithm contains update rules for the penalty and the smoothing parameter that depend on the constraint violation. Theoretical as well as numerical results are given. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multi‐Fracture Reservoir Simulations for Long Time Physical Processes
Authors: Ostermeyer Georg‐Peter , Srisupattarawanit Tarin
Published: December 2013

Reservoirs with multi‐fracture techniques are developed and frequently used for oil and gas industry. Recently, they are also used for deep geothermal reservoirs especially for Hot Dry Rock (HDR). The analysis of the reservoir is generally interested in long time physical properties (10–100 years), e.g. fluid flow, heat transport etc. Typical CFD simulations are limited in this context. Here we developed a fluid flow and heat transport modeling in a multi‐fracture reservoir based on the so‐called Mixed Dimensional Model (MDM), which describes the different characteristic flows and the heat transport in different dimensions. In the mathematical point of view, these models are discretized based on the Cellular Automaton (CA) method combined with other necessary numerical techniques. The different cases of fluid flow and heat transport in multi‐fracture reservoirs have been simulated and shown physical results very reasonably with less computational time. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An alternative approach to integro‐differential equations
Authors: Trostorff Sascha
Published: December 2013

A class of integro‐differential equations with operator‐valued integral kernels, including equations of neutral type is studied. We show that this class is covered by the framework of evolutionary equations and we derive sufficient conditions on the kernels within this framework in order to show well‐posedness. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Predictions of flow behaviors and entrance pressure drop characteristics of a rubber compound in a capillary die using various rheological models
Authors: Kim J.H. , Lyu M.Y
Published: December 2013

Rubber compounds have highly viscoelastic properties. The viscoelastic behaviors that have been exhibited during die extrusion include die swell and vortices in regions of sudden contraction. In this study, the application of rheological models to the capillary die extrusion process is investigated. Experiments and simulations were conducted using a fluidity tester and finite element analysis, respectively. The velocity distributions, velocity profiles, pressure drops, and vortices at the capillary die entrance were analyzed through computer simulations for various viscoelastic models [i.e., Phan‐Thien and Tanner (PTT), Giesekus, POMPOM, simplified viscoelastic, and generalized Newtonian models]. Different models exhibited different pressure drops and different velocity profiles in the capillary die. Only the full viscoelastic models (PTT, Giesekus, and POMPOM) predicted the vortex at the corner of the reservoir that is the capillary die entrance. However, the simplified viscoelastic and generalized Newtonian models did not predict the vortex. All the viscoelastic models studied in this article predicted the die swells in various ways, and these were compared with the experimental results. The PTT and simplified viscoelastic models exhibited good agreement with the experimental results of the die swells. POLYM. ENG. SCI., 54:2441–2448, 2014. © 2013 Society of Plastics Engineers
Inflammatory cytokines in exhaled breath condensate in children with inflammatory bowel diseases
Authors: Krenke K. , Peradzyńska J. , Lange J. , Banaszkiewicz A. , Łazowska‐Przeorek I. , Grzela K. , Radzikowski A. , Kulus M.
Published: December 2013

Background

Although inflammatory bowel diseases (IBD) affect mainly the gastrointestinal tract, the extra‐intestinal manifestations are not uncommon. Different diagnostic methods have been applied to assess pulmonary involvement in patients with IBD, but majority of these methods show significant limitations in children. The aim of our study was to evaluate the usefulness of exhaled breath condensate (EBC) measurements of pro‐inflammatory cytokines in children with IBD.

Material and Methods

Twenty‐two children with Crohn's disease (CD) (mean age 13.8 ± 3.3 years), 25 with ulcerative colitis (UC) (mean age 14.1 ± 3.3 years) and 37 healthy volunteers (mean age 13.9 ± 3.6 years) were studied. IBD activity was assessed using appropriate scoring systems. None of the patients had signs or symptoms of pulmonary disease. Exhaled breath condensate was collected and EBC concentration of interleukin 6 (IL‐6), tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β), and interleukin 8 (IL‐8) was measured.

Results

The concentrations of all the assessed cytokines were significantly higher in the study group as compared to controls. A negative correlation between IL‐1β and CD activity index was found. There were no significant relationships between TNF‐α, IL‐6, or IL‐8 level and CD activity index as well as between IL‐1β, TNF‐α, IL‐6, IL‐8 and UC activity index. No significant correlation between the concentration of IL‐1β, TNF‐α, IL‐6, IL‐8, and IBD duration or treatment duration was found.

Conclusions

Elevated concentration of pro‐inflammatory cytokines in EBC in children with IBD may suggest the presence of asymptomatic inflammation in the lower airways. Pediatr Pulmonol. 2014; 49:1190–1195. © 2013 Wiley Periodicals, Inc.
Lung function in African infants: A pilot study
Authors: Gray D.M. , Willemse L. , Alberts A. , Simpson S. , Sly P.D. , Hall G.L. , Zar H.J.
Published: December 2013

Background

The burden of childhood respiratory illness is large in low and middle income countries (LMICs). Infant lung function (ILF) testing may provide useful information about lung growth and susceptibility to respiratory disease. However, ILF has not been widely available in LMICs settings where the greatest burden of childhood respiratory disease occurs.

Aim

To implement and evaluate a pilot study of ILF testing in a semi‐rural setting in South Africa.

Method

Infant lung function testing was established at a community hospital in South Africa. All measures were done in unsedated infants during sleep. Measurements, made with the infant quietly breathing through a face mask and bacterial filter, included tidal breathing (TBFVL), exhaled nitric oxide (eNO), and sulphur hexafluoride multiple breath washout (MBW) measures using an ultrasonic flow meter and chemoluminescent NO analyzer.

Results

Twenty infants, mean age of 7.7 (SD 2.9) weeks were tested; 8 (40%) were Black African and 12 (60%) were mixed race. Five (25%) infants were preterm. There were 19 (95%) successful TBFVL and NO tests and 18 (90%) successful MBW tests. The mean tidal volume was 30.5 ml (SD 5.9), respiratory rate 50.2 breaths per minute (SD 8.7), and eNO 10.4 ppb (SD 7.3). The mean MBW measures were: functional residual capacity 71 ml (SD 13) and the lung clearance index 7.6 (SD 0.5). The intra‐subject coefficient of variations (CV) of lung function measures were similar to published normative data for Caucasian European infants.

Conclusion

In this study we demonstrate that unsedated infant lung function measures of tidal breathing, MBW, and eNO are feasible in a semi‐rural African setting with rates comparable to those reported from high income countries. Pediatr Pulmonol. 2015; 50:49–54. © 2013 The Authors. Pediatric Pulmonology published by Wiley Periodicals, Inc.
Long‐term recovery after parapneumonic empyema in children
Authors: Honkinen Maria , Lahti Elina , Svedström Erkki , Jartti Tuomas , Virkki Raimo , Peltola Ville , Ruuskanen Olli
Published: December 2013

Background

The incidence of parapneumonic empyema in children has increased worldwide, but the long‐term anatomical and functional consequences in the lungs after empyema are not known.

Methods

We investigated the long‐term outcome of childhood empyema in 26 patients by physical examination, chest radiograph and magnetic resonance image (MRI) of the lungs, and pulmonary function tests.

Results

At follow‐up 3–19 years (mean 8 years) after empyema, all patients had normal findings in the physical examination. Spirometry was normal in 80% of patients, and evidence of obstructive airway disease was detected in 16%. Thirty‐six percent of patients had abnormal findings in the chest radiograph and 92% in the MRI of the lungs. In six patients, the MRI revealed significant pleural scarring (extension longer than 1 cm). Thirteen patients (50%) reported persistent respiratory symptoms, such as impaired tolerance of physical activity or prolonged cough after a common cold. During the follow‐up four patients suffered a second pneumonia.

Conclusions

The long‐term recovery of children with parapneumonic empyema is good, since most patients subsequently have normal lung function, chest radiograph, and clinical recovery. Half of the patients reported subjective respiratory symptoms and most patients had minor lung abnormalities, mostly pleural scars, detected in the MRI many years after empyema. However, as long‐term impairment of lung function was rarely found, the clinical significance of the anatomical residues seen in the lung MRI seems to be minor. Pediatr Pulmonol. 2014; 49:1020–1027. © 2013 Wiley Periodicals, Inc.
Honokiol inhibits androgen receptor activity in prostate cancer cells
Authors: Hahm Eun‐Ryeong , Karlsson A. Isabella , Bonner Michael Y. , Arbiser Jack L. , Singh Shivendra V.
Published: December 2013

BACKGROUND

We have shown previously that honokiol (HNK), a bioactive component of the medicinal plant Magnolia officinalis, inhibits growth of human prostate cancer cells in vitro and in vivo. However, the effect of HNK on androgen receptor (AR) signaling has not been studied.

METHODS

LNCaP, C4‐2, and TRAMP‐C1 cells were used for various assays. Trypan blue dye exclusion assay or clonogenic assay was performed for determination of cell viability. The effects of HNK and/or its analogs on protein levels of AR and its target gene product prostate specific antigen (PSA) were determined by western blotting. RNA interference of p53 was achieved by transient transfection. Reverse transcription‐polymerase chain reaction was performed for mRNA expression of AR. Nuclear level of AR was visualized by microscopy. Apoptosis was quantified by DNA fragmentation assay or flow cytometry after Annexin V‐propidium iodide staining.

RESULTS

HNK and its dichloroacetate analog (HDCA) were relatively more effective in suppressing cell viability and AR protein level than honokiol epoxide or biseugenol. Nuclear translocation of AR stimulated by a synthetic androgen (R1881) was markedly suppressed in the presence of HNK. Downregulation of AR protein resulting from HNK exposure was attributable to transcriptional repression as well as proteasomal degradation. HNK‐mediated suppression of AR protein was maintained in LNCaP cells after knockdown of p53 protein. HNK‐induced apoptosis was not affected by R1881 treatment.

CONCLUSIONS

The present study demonstrates, for the first time, that HNK inhibits activity of AR in prostate cancer cells regardless of the p53 status. Prostate 74:408–420, 2014. © 2013 Wiley Periodicals, Inc.
Eigen‐analysis of nonlinear PCA with polynomial kernels
Authors: Liang Zhiyu , Lee Yoonkyung
Published: December 2013

There has been growing interest in kernel methods for classification, clustering and dimension reduction. For example, kernel Fisher discriminant analysis, spectral clustering and kernel principal component analysis are widely used in statistical learning and data mining applications. The empirical success of the kernel method is generally attributed to nonlinear feature mapping induced by the kernel, which in turn determines a low dimensional data embedding. It is important to understand the effect of a kernel and its associated kernel parameter(s) on the embedding in relation to data distributions. In this paper, we examine the geometry of the nonlinear embedding for kernel principal component analysis (PCA) when polynomial kernels are used. We carry out eigen‐analysis of the polynomial kernel operator associated with data distributions and investigate the effect of the degree of polynomial. The results provide both insights into the geometry of nonlinear data embedding and practical guidelines for choosing an appropriate degree for dimension reduction with polynomial kernels. We further comment on the effect of centering kernels on the spectral property of the polynomial kernel operator. © 2013 Wiley Periodicals, Inc. Statistical Analysis and Data Mining, 2013
Effects of Ultrasound on the Degassing of Molten Steel in the RH Refining Process
Authors: Xu Minren , Liu Qingcai , Ma Dongran , Wu Guofang , Hu Bin , Ma Lihua
Published: December 2013

RH degasser is an efficient way of degassing in producing high quality products. Moreover, ultrasonic degassing has also been proven to be a reasonably efficient way of degassing. In this paper, an experimental equipment similar to RH degasser combined with ultrasound was built. Parametric studies have been carried out to assess the effectiveness of ultrasonic degassing and to explore the possibility of using ultrasonic vibration to accelerate the degassing process in RH degasser. The results indicate that the degassing process can be accelerated by the use of ultrasound, and makes the RH degassing more efficient.
Investigation of Skull Formation in a Blast Furnace Hearth
Authors: Zhao Yongfu , Fu Dong , Lherbier Louis W. , Chen Yan , Zhou Chenn Q. , Grindey John G.
Published: December 2013

A stable skull layer formed on the inner surface of the hearth could effectively protect the lining and extend blast furnace campaign life. This is the first comprehensive work of using integrated heat transfer, fluid flow dynamics and solidification numerical simulation to investigate skull formation phenomena in a blast furnace hearth. The impact of hearth design and furnace operation parameters on skull formation is examined, including lining property and structure, cooling water temperature and flow rate, hot metal production rate, temperature and viscosity, and cast practice. The findings from this study are compared with operating experience of United States Steel blast furnaces.
Designing guidance for interpreting dynamic visualizations: Generating versus reading explanations
Authors: Ryoo Kihyun , Linn Marcia C.
Published: December 2013

We compared designs of guidance to support students while interacting with dynamic visualizations of complex scientific phenomena in inquiry instruction. Three hundred thirty‐two 7th‐grade students were randomly assigned to either a reading or a generating condition and completed a web‐based inquiry unit focusing on energy concepts in photosynthesis. When students interacted with a dynamic visualization of energy transformation, typical guidance provided text explanations while inquiry‐oriented guidance asked students to generate their own explanations about three key energy transformation concepts. The results showed that both reading and generating explanations helped students interpret the visualization, but generating explanations was more beneficial. Students who generated explanations were better able to extract salient information and distinguish among multiple ideas. In particular, they made more connections between their understanding of energy transformation learned from the visualization to other energy concepts to articulate the process of photosynthesis than those who read instructional explanations. Analyses of log data revealed that students in each condition spent similar amounts of time learning from the visualization but navigated the activities in distinct ways and engaged in different kinds of collaborative discourse. This study builds on previous research showing the value of prompting students to generate explanations by clarifying the effective timing for such guidance and characterizing how it helps students make sense of visualizations. These results show that well‐designed guidance enables students working in pairs to generate useful explanations for learning from visualizations and suggest promising designs for online instruction featuring dynamic visualizations. © 2013 Wiley Periodicals, Inc. J Res Sci Teach 51: 147–174, 2014
Rethinking the Argumentative Essay
Authors: Schneer David
Published: December 2013

This article investigates the construction of the argumentative essay as it is commonly presented in academic writing textbooks and classrooms for English language learners. The author first examines the traditional three‐stage structure (thesis‐argument‐conclusion) and then problematizes it within a genre‐based approach to academic writing. He then describes and discusses authentic samples of argumentative writing using a moves analysis of 50 argumentative opinion blog entries, focusing on the organization of the stages as well as the positioning and articulation of the evaluation move (often referred to as the thesis statement). The authentic texts are then juxtaposed with argumentative essays in academic writing textbooks. The essential finding is that authentic argumentative writing varies considerably and thus presents a challenge to the commonly taught three‐stage model.
Diamagnetic chemical exchange saturation transfer (diaCEST) liposomes: physicochemical properties and imaging applications
Authors: Chan Kannie W.Y. , Bulte Jeff W.M. , McMahon Michael T.
Published: December 2013

Chemical exchange saturation transfer (CEST) is a new type of magnetic resonance imaging (MRI) contrast based on labile spins which rapidly exchange with solvent, resulting in an amplification of signal which allows detection of solute protons at millimolar to micromolar concentrations. An additional feature of these agents is that natural organic and biodegradable compounds can provide strong CEST contrast, allowing the development of diamagnetic CEST (diaCEST) MRI contrast agents. The sensitivity of the CEST approach per unit of agent increases further when diaCEST contrast agents are loaded into liposomes to become diaCEST liposomes. In this review, we will discuss the unique and favorable features of diaCEST liposomes which are well suited for in vivo imaging. diaCEST liposomes are nanocarriers which feature high concentrations of encapsulated contrast material, controlled release of payload, and an adjustable coating for passive or active tumor targeting. These liposomes have water permeable bilayers and both the interior and exterior can be fine‐tuned for many biomedical applications. Furthermore, a number of liposome formulations are used in the clinic including Doxil™, which is an approved product for treating patients with cancer for decades, rapid translation of these materials can be envisaged. diaCEST liposomes have shown promise in imaging of cancer, and monitoring of chemotherapy and cell transplants. The unique features of diaCEST liposomes are discussed to provide an overview of the applications currently envisioned for this new technology and to provide an overall insight of their potential. WIREs Nanomed Nanobiotechnol 2014, 6:111–124. doi: 10.1002/wnan.1246

This article is categorized under:

Diagnostic Tools > Diagnostic Nanodevices

Diagnostic Tools > In Vivo Nanodiagnostics and Imaging

Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
RNA in development: how ribonucleoprotein granules regulate the life cycles of pathogenic protozoa
Authors: Kramer Susanne
Published: December 2013

Ribonucleoprotein (RNP) granules are important posttranscriptional regulators of messenger RNA (mRNA) fate. Several types of RNP granules specifically regulate gene expression during development of multicellular organisms and are commonly referred to as germ granules. The function of germ granules is not entirely understood and probably diverse, but it is generally agreed that one main function is posttranscriptional regulation of gene expression during early development, when transcription is silent. One example is the translational repression of maternally derived mRNAs in oocytes. Here, I hope to show that the need for regulation of gene expression by RNP granules is not restricted to animal development, but plays an equally important role during the development of pathogenic protozoa. Apicomplexa and Trypanosomatidae have complex life cycles with frequent host changes. The need to quickly adapt gene expression to a new environment as well as the ability to suppress translation to survive latencies is critical for successful completion of life cycles. Posttranscriptional gene regulation is not necessarily simpler in protozoa. Apicomplexa surprise with the presence of micro RNA (miRNAs) and upstream open reading frames (µORFs). Trypanosomes have an unusually large repertoire of different RNP granule types. A better understanding of RNP granules in protozoa may help to gain insight into the evolutionary origin of RNP granules: Trypanosomes for example have two types of granules with interesting similarities to animal germ granules. WIREs RNA 2014, 5:263–284. doi: 10.1002/wrna.1207

This article is categorized under:

Translation > Translation Regulation

RNA Export and Localization > RNA Localization

RNA in Disease and Development > RNA in Development
Comparison of systematic roost searches and acoustic detection to determine occupancy of rare forest bats
Authors: Comer Christopher E. , Stuemke Leigh A. , Morrison Michael L. , Maxey Ricky W.
Published: December 2013

Despite recent increases in conservation interest, the distribution, habitat needs, and conservation priorities remain poorly understood for many animal species, including forest bats. In some cases, little quantitative information exists about appropriate survey methods to determine occupancy or abundance of bats in forest systems. We quantitatively compared detection probabilities between 2 commonly used survey techniques for 2 bat species that are closely associated with bottomland hardwood stands in the southeastern United States. Passive acoustic surveys of echolocation calls were more likely than systematic roost searches to detect both Rafinesque's big‐eared bats (Corynorhinus rafinesquii) and southeastern myotis (Myotis austroriparius) at 7 study areas in eastern Texas. Our results confirmed that numerous repeat visits (>15 acoustic‐survey‐nights) are necessary to have high confidence in detecting Rafinesque's big‐eared bats; however, southeastern myotis were easier to detect. Our results emphasize the importance of quantitatively assessing survey methods prior to designing or implementing widespread survey programs for bats. © 2013 The Wildlife Society
Syntheses and Crystal Structures of the Cyclotriphosphate Hydrates Nd(P3O9)·3H2O, Nd(P3O9)·4.5H2O, RE(P3O9)·5H2O (RE = Pr, Nd), and Na3RE(P3O9)2·6H2O (RE = Pr, Nd)
Authors: Daub Michael , Kazmierczak Karolina , Höppe Henning A.
Published: December 2013

Several rare‐earth cyclotriphosphate hydrates were obtained from mixtures of sodium cyclotriphosphates and the respective rare‐earth chlorides. Nd(P3O9)·3H2O [P$\bar{6}$, Z = 3, a = 677.90(9), c = 608.67(9) pm, R1 = 0.016, wR2 = 0.038, 312 data, 36 parameters] was obtained by a solid state reaction and is isotypic with respective rare‐earth phosphate hydrates, while all the others adopt new structure types. Nd(P3O9)·4.5H2O [C2/c, Z = 8, a = 1644.6(3), b = 756.11(15), c = 1856.1(4) pm, β = 97.25(3)°, R1 = 0.032, wR2 = 0.081, 1763 data, 194 parameters], Nd(P3O9)·5H2O [P21/c, Z = 4, a = 773.75(15), b = 1149.1(2), c = 1394.9(3) pm, β = 106.07(3)°, R1 = 0.042, wR2 = 0.082, 1338 data, 194 parameters], Pr(P3O9)·5H2O [P$\bar{1}$, Z = 2, a = 745.64(15), b = 889.07(18), c = 934.55(19) pm, α = 79.00(3), β = 80.25(3), γ = 66.48(3), R1 = 0.059, wR2 = 0.089, 1468 data, 193 parameters], Na3Nd(P3O9)2·6H2O [P21/n, Z = 4, a = 1059.78(18), b = 1207.25(15), c = 1645.7(4) pm, β = 99.742(17), R1 = 0.047, wR2 = 0.119, 1109 data, 351 parameters] and Na3Pr(P3O9)2·6H2O [P21/n, Z = 4, a = 1061.42(16), b = 1209.0(2), c = 1635.5(3) pm, β = 99.841(13), R1 = 0.035, wR2 = 0.062, 1323 data, 350 parameters] were obtained by careful crystallization at room temperature. A thorough structure discussion is given. The infrared spectrum of Nd(P3O9)·4.5H2O is also reported.
Outcome of Negative‐Pressure Wound Therapy for Open Abdomen Treatment After Nontraumatic Lower Gastrointestinal Surgery: Analysis of Factors Affecting Delayed Fascial Closure in 101 Patients
Authors: Bertelsen Claus Anders , Fabricius Rasmus , Kleif Jakob , Kristensen Bent , Gögenur Ismail
Published: December 2013

Background

Few studies have focused on the risk factors for failure to achieve fascial closure after use of negative‐pressure wound therapy (NPWT) in an open abdomen (OA). We aimed at analyzing possible risk factors for failure of fascial closure and the risk of fistulas after nontrauma lower gastrointestinal (GI) tract surgery treated with OA.

Methods

This retrospective study included 101 nontrauma patients treated with OA from 2007 to 2011. Multivariate analyses of risk factors were performed.

Results

Indications for OA were diffuse peritonitis (n = 47), need for second look (n = 26), failure to achieve fascial closure (e.g., bowel edema) at primary laparotomy (n = 24), and fascial necrosis (n = 4). Of the 101 patients, 61 (60 %) were alive at discharge, with one death possibly related to OA (fistula from an iatrogenic perforation). Delayed fascial closure was obtained in 40 (66 %) of the surviving patients, with 80 % when the indications for OA was need for second look and 72 % in cases of diffuse peritonitis. Compared with need for second look [hazard ratio (HR = 1), 95 % CI], proportional HR for failure of delayed fascial closure were peritonitis 1.96 (1.10–3.49) and failure to achieve fascial closure at primary laparotomy 4.70 (2.17–10.2). In the presence of a stoma the HR was 2.02 (1.13–3.63).

Conclusions

OA using NPWT seems to be a safe procedure, with few procedure‐related complications. Failure of fascial closure is related to the indication of OA and the presence of a stoma. Prospective multicenter studies are needed to establish which patients with lower GI surgery benefit from OA.
Effects of leaf zeatin and zeatin riboside induced by different clipping heights on the regrowth capacity of ryegrass
Authors: Wang Xiao‐Ling , Guo Xiao‐Lin , Hou Xiao‐Gai , Zhao Wei , Xu Guo‐Wei , Li Zhen‐Qing
Published: December 2013

The effect of clipping height on ryegrass regrowth was investigated by examining the roles of several plant hormones. Our study consisted of three treatment conditions: (1) darkness over whole plants, (2) darkness only over stubble leaf sheaths, and (3) light over whole plants. Results showed that under darkness over whole plant, low stubble height resulted in low leaf regrowth biomass. Similar leaf regrowth biomass was observed under conditions of darkness only over stubble leaf sheaths as well as light over whole plants. Each unit weight of stubble at different clipping heights has relatively similar potential of providing stored organic substance for leaf regrowth. Therefore, regrowth index, calculated as newly grown leaf biomass divided by unit stubble weight, was used to evaluate regrowth capacity at different clipping heights under minimal influence of organic substances stored in stubbles. Under light over whole plants and single clipping, low stubble height and high stubble height with root thinning resulted in low leaf biomass and high regrowth index. On the other hand, under light over whole plants and frequent clipping high leaf biomass and regrowth index were observed in high stubble height. In addition, we found that leaf zeatin and zeatin riboside (Z + ZR) affected ryegrass regrowth and that roots regulated leaf Z + ZR concentration. Thus, our results indicate that root‐derived cytokinin concentration in leaves influences ryegrass regrowth at different clipping heights.
Ionenkanalerkrankungen des Gehirns – monogene Epilepsien
Authors: Maljevic S. , Hedrich U.B.S. , Lerche H.
Published: December 2013

Die Epilepsien zählen zu den häufigsten neurologischen Erkrankungen. Sie zeichnen sich durch das wiederholte Auftreten von unprovozierten epileptischen Anfällen aus, bei denen spontane synchrone neuronale Entladungen Störungen des Befindens oder Verhaltens auslösen. Etwa ein Drittel aller Epilepsien ist überwiegend genetisch bedingt, darunter insbesondere idiopathische Epilepsien, bei denen sich keine Hinweise auf äußere Ursachen oder Veränderungen des Gehirns finden. Mutationen in Genen, die neuronale Ionenkanäle kodieren, spielen für die Ursache dieser Epilepsien eine zentrale Rolle. In dieser Übersicht werden bekannte mit Epilepsie assoziierte Mutationen in Ionenkanalgenen und deren funktionelle Auswirkungen beschrieben. Die resultierenden Krankheitsmechanismen und die sich daraus ergebenden Konsequenzen für die Behandlung werden diskutiert.