bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical properties of some BEDT‐TTF cation radical salts with polymeric anions
Authors: Graja Andrzej , Dyachenko Oleg A.
Published: March 2011

The most intensively examined and promising organic materials to show superconducting properties are ion‐radical salts in which a molecule of bis(ethylenedithio)tetrathiafulvalene (BEDT‐TTF or shorter ET) serves as an electron donor. ET is capable of creating salts with various anions. The search for an anion species for ET‐based organic superconductors is one of the approaches towards making progress in the design of these materials. Polymeric anions, which form a stable layer structure, are especially useful for this purpose.

Conducting properties of the organic superconductors are determined mainly by ET packing, but the role of anions is also important. The thickness of anion layers, which effectively alters the interlayer transfer interactions of ET molecules, depends upon the anion organization. Since critical temperature of the organic superconductor increases with the decrease of the magnitude of the anisotropy of the intra‐ and interlayer interaction, the change of the layer thickness gives an opportunity to affect the Tc of the superconductor.

In this paper we present characteristic structures of selected ET salts, give a survey of the anions, especially polymerized anions, review some more common structural types observed, and describe some physical properties of the ET‐based organic superconductors containing polymerized anions.
Melting Pressure Curves of Concentrated Peroxide Solutions up to 3 kbar
Authors: Berbée Otto , Buback Michael , Fischer Bart , Vögele Hans Peter
Published: March 2011

The crystallization of peroxide/solvent mixtures with peroxide contents from 10 to 65 wt.‐% is studied between −50 and +30 °C up to 3 000 bar for di‐tert‐butylperoxide, tert‐butyl peroxyacetate, tert‐butyl peroxypivalate, tert‐butyl peroxy‐2‐ethylhexanoate, and bis(tert‐butyl) peroxybutanoate with decane, octane, isododecane, isooctane, and isopar H as solvents. The liquid/solid phase behavior indicates miscibility in the liquid and immiscibility in the solid phase. With tert‐butyl peroxyacetate/isododecane, in addition, liquid/liquid immiscibility occurs. A few melting pressure curves are presented for ternary systems containing either two solvents or two peroxides.

magnified image
Fast MR parameter mapping using k‐t principal component analysis
Authors: Petzschner Frederike H. , Ponce Irene P. , Blaimer Martin , Jakob Peter M. , Breuer Felix A.
Published: March 2011

Quantification of magnetic resonance parameters plays an increasingly important role in clinical applications, such as the detection and classification of neurodegenerative diseases. The major obstacle that remains for its widespread use in clinical routine is the long scanning times. Therefore, strategies that allow for significant decreases in scan time are highly desired. Recently, the k‐t principal component analysis method was introduced for dynamic cardiac imaging to accelerate data acquisition. This is done by undersampling k‐t space and constraining the reconstruction of the aliased data based on the k‐t Broad‐use Linear Acquisition Speed‐up Technique (BLAST) concept and predetermined temporal basis functions. The objective of this study was to investigate whether the k‐t principal component analysis concept can be adapted to parameter quantification, specifically allowing for significant acceleration of an inversion recovery fast imaging with steady state precession (TrueFISP) acquisition. We found that three basis functions and a single training data line in central k‐space were sufficient to achieve up to an 8‐fold acceleration of the quantification measurement. This allows for an estimation of relaxation times T1 and T2 and spin density in one slice with sub‐millimeter in‐plane resolution, in only 6 s. Our findings demonstrate that the k‐t principal component analysis method is a potential candidate to bring the acquisition time for magnetic resonance parameter mapping to a clinically acceptable level. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Analytic expressions for the ultimate intrinsic signal‐to‐noise ratio and ultimate intrinsic specific absorption rate in MRI
Authors: Kopanoglu E. , Erturk V. B. , Atalar E.
Published: March 2011

The ultimate intrinsic signal‐to‐noise ratio is the highest possible signal‐to‐noise ratio, and the ultimate intrinsic specific absorption rate provides the lowest limit of the specific absorption rate for a given flip angle distribution. Analytic expressions for ultimate intrinsic signal‐to‐noise ratio and ultimate intrinsic specific absorption rate are obtained for arbitrary sample geometries. These expressions are valid when the distance between the point of interest and the sample surface is smaller than the wavelength, and the sample is homogeneous. The dependence on the sample permittivity, conductivity, temperature, size, and the static magnetic field strength is given in analytic form, which enables the easy evaluation of the change in signal‐to‐noise ratio and specific absorption rate when the sample is scaled in size or when any of its geometrical or electrical parameters is altered. Furthermore, it is shown that signal‐to‐noise ratio and specific absorption rate are independent of the permeability of the sample. As a practical case and a solution example, a uniform, circular cylindrically shaped sample is studied. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Simultaneous dual‐nuclei imaging for motion corrected detection and quantification of 19F imaging agents
Authors: Keupp Jochen , Rahmer Jürgen , Grässlin Ingmar , Mazurkewitz Peter C. , Schaeffter Tobias , Lanza Gregory M. , Wickline Samuel A. , Caruthers Shelton D.
Published: March 2011

Fluorine MRI offers broad potential for specific detection and quantification of molecularly targeted agents in diagnosis and therapy planning or monitoring. Because non‐proton MRI applications lack morphological information, accompanying proton images are needed to elucidate the spatial tissue context. Furthermore, low concentrations typical of targeted molecular imaging agents require long examinations for signal averaging during which physiological motion may lead to blurring, underestimation in signal quantification, and erroneous localization of the agent distribution. Novel methods for truly simultaneous acquisition of dual‐nuclei MR data are presented that offer efficient and precise anatomical localization of fluorine signals using accurate motion correction based on contemporaneous proton signals. The feasibility of simultaneous dual‐nuclei MRI motion correction and corresponding dual‐resolution reconstruction, providing nuclei‐specific spatial resolution to retrospectively optimize the balance between signal‐to‐noise ratio and resolution, is shown on a clinical 3 T MR system. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Evidence‐based guideline: Treatment of painful diabetic neuropathy—report of the american association of neuromuscular and electrodiagnostic medicine, the american academy of neurology, and the american academy of physical medicine & rehabilitation
Authors: Bril Vera , England John D. , Franklin Gary M. , Backonja Miroslav , Cohen Jeffrey A. , Del Toro David R. , Feldman Eva L. , Iverson Donald J. , Perkins Bruce , Russell James W. , Zochodne Douglas W.
Published: March 2011

The objective of this report was to develop a scientifically sound and clinically relevant evidence‐based guideline for the treatment of painful diabetic neuropathy (PDN). The basic question that was asked was: “What is the efficacy of a given treatment (pharmacological: anticonvulsants, antidepressants, opioids, others; non‐pharmacological: electrical stimulation, magnetic field treatment, low‐intensity laser treatment, Reiki massage, others) to reduce pain and improve physical function and quality of life (QOL) in patients with PDN?” A systematic review of literature from 1960 to August 2008 was performed, and studies were classified according to the American Academy of Neurology classification of evidence scheme for a therapeutic article. Recommendations were linked to the strength of the evidence. The results indicate that pregabalin is established as effective and should be offered for relief of PDN (Level A). Venlafaxine, duloxetine, amitriptyline, gabapentin, valproate, opioids (morphine sulfate, tramadol, and oxycodone controlled‐release), and capsaicin are probably effective and should be considered for treatment of PDN (Level B). Other treatments have less robust evidence, or the evidence is negative. Effective treatments for PDN are available, but many have side effects that limit their usefulness. Few studies have sufficient information on their effects on function and QOL. Muscle Nerve, 2011.
Factor of safety in a partially saturated slope inferred from hydro‐mechanical continuum modeling
Authors: Borja Ronaldo I. , White Joshua A. , Liu Xiaoyu , Wu Wei
Published: March 2011

Rainfall weakens an earth slope and triggers mass movement. Relevant triggering mechanisms are complex and include reduction of capillary pressure due to increased saturation and frictional drag on the sediment induced by fluid flow. Physics‐based continuum models utilizing modern computational tools are useful for understanding the mechanisms of deformation in partially saturated slopes; however, they do not provide a scalar indicator called ‘factor of safety’ that measures the potential of a given slope for mass movement. In the present work, we employ sequential calculations consisting of a physics‐based finite element model that couples solid deformation with fluid flow to quantify the stress and deformation fields in a steep hillside slope subjected to rainfall infiltration. This is followed by a limit‐equilibrium calculation based on the method of slices that evaluates the desired factor of safety. The field condition investigated is similar to the steep experimental catchment CB1 near Coos Bay, Oregon, which failed as a large debris flow from heavy rainfall. Copyright © 2011 John Wiley & Sons, Ltd.
Content validation of the patient‐reported outcomes measurement information system (PROMIS) framework in women with urinary incontinence
Authors: Sung Vivian W. , Marques Felisha , Rogers Rebecca R. , Williams David A. , Myers Deborah L. , Clark Melissa A.
Published: March 2011

Aims

To assess whether the existing National Institutes of Health (NIH) Patient Reported Outcomes Measurement Information System (PROMIS) conceptual framework and item banks sufficiently capture the concerns of women with urinary incontinence (UI).

Methods

Thirty‐five women with UI were recruited between February‐April 2009 for 4 structured focus groups to develop and assess the content validity of a conceptual framework for the impact of UI. This framework included domains from the NIH PROMIS framework and item banks including broad domains of physical and social function and mental health. All sessions were transcribed, coded, and qualitatively and quantitatively analyzed using analytic induction and deductive analysis to identify new themes and domains relevant to women with UI.

Results

The focus groups provided information that confirmed the relevance of existing PROMIS domains and identified new outcome domains that are important to this patient population. The groups confirmed the relevance of the physical and social functioning, and mental health domains. Additional themes that emerged included the distinction between ability versus participation and satisfaction, role functioning, external mediators, re‐calibration/coping, cognitive function and new possibilities. Participants also felt strongly that not all domains and items apply to all women with UI and an option to tailor questionnaires and skip non‐relevant items was important.

Conclusions

The PROMIS framework domains are relevant to women with UI, but additional patient‐important themes are identified that may improve the comprehensiveness of this assessment framework for measuring outcomes important to women with UI. These results will inform future item content development for UI. 30:503–509, 2011. © 2011 Wiley‐Liss, Inc.
A confidence paradigm for classification systems
Authors: Leap Nathan J. , Bauer Kenneth W.
Published: March 2011

There is no universally accepted methodology to determine how much confidence one should place in the output of a classification system. In this article, we develop a confidence paradigm. This is a theoretical framework that attempts to unite the viewpoints of the classification system developer (or engineer) and the classification system user (or warfighter). The developer designs and tests the classification system at a macro‐level. The user fields the system in an environment often quite different than the environment used to develop the system. The user operates at a micro‐level and is interested in the indications as they are made by the system. The paradigm is based on the assumptions that the system confidence acts like or can be modelled as value, and that indication confidence can be modelled as a function of the posterior probability estimates. The viewpoints of the developer and the user are unified through the fundamental proposition that the expected value of the user's confidence should be approximately equal to the developer's confidence. This paradigm provides a direct link between traditional decision analysis techniques and traditional pattern recognition techniques. This methodology is applied to an automatic target recognition data set, and the results demonstrate the sort of behavior that would be expected from a rational confidence measure. © 2011 Wiley Periodicals, Inc. Naval Research Logistics, 2011
A process for anticipating and shaping adversarial behavior
Authors: McKay Shawn C. , Chaturvedi Alok , Adams Douglas E.
Published: March 2011

A new approach for anticipating and shaping adversarial behavior is developed and demonstrated. The approach extends the notion of prediction, which is a forecast of the future from a third party point of view, to anticipation, which is a forecast from the perspective of an entity having partial control in a domain. Shaping utilizes the models developed for anticipation to determine actions that influence another influential entity (e.g., an enemy) and actions to direct the emergent phenomena of a domain according to an entity's objectives. The approach is developed using principles of control theory and demonstrated in the southeastern region of Afghanistan. A key capability demonstrated by this approach is its ability to handle proactive adversaries when actionable intelligence is nonexistent. In the demonstration, Taliban (Red) combat actions are anticipated from the perspective of the coalition forces (Blue) across time, across space, and by the current state of the region and then shaped to Blue's desires. Shaping identifies periods of time that simultaneous or alternating Blue combat actions in different regions help meet Blue's military and nonmilitary objectives. © 2011 Wiley Periodicals, Inc. Naval Research Logistics, 2011
Image‐based tissue engineering of a total intervertebral disc implant for restoration of function to the rat lumbar spine
Authors: Bowles Robby D. , Gebhard Harry H. , Dyke Jonathan P. , Ballon Douglas J. , Tomasino Andre , Cunningham Matthew E. , Härtl Roger , Bonassar Lawrence J.
Published: March 2011

Nonbiological total disc replacement is currently being used for the treatment of intervertebral disc (IVD) disease and injury, but these implants are prone to mechanical wear, tear and possible dislodgement. Recently, tissue‐engineered total disc replacement (TE‐TDR) has been investigated as a possible alternative to more fully replicate the native IVD properties. However, the performance of TE‐TDRs has not been studied in the native disc space. In this study, MRI and microcomputed tomography imaging of the rat spine were used to design a collagen (annulus fibrosus)/alginate (nucleus pulposus) TE‐TDR to a high degree of geometric accuracy, with less than 10% difference between TE‐TDR and the native disc dimensions. Image‐based TE‐TDR implants were then inserted into the L4/L5 disc space of athymic rats (n = 5) and maintained for 16 weeks. The disc space was fully or partially maintained in three of five animals and proteoglycan and collagen histology staining was similar in composition to the native disc. In addition, good integration was observed between TE‐TDR and the vertebral bodies, as well as remnant native IVD tissue. Overall, this study provides evidence that TE‐TDR strategies may yield a clinically viable treatment for diseased or injured IVD. Copyright © 2011 John Wiley & Sons, Ltd.
B0 field inhomogeneity considerations in pseudo‐continuous arterial spin labeling (pCASL): effects on tagging efficiency and correction strategy
Authors: Jahanian Hesamoddin , Noll Douglas C. , Hernandez‐Garcia Luis
Published: March 2011

Pseudo‐continuous arterial spin labeling (pCASL) is a very powerful technique to measure cerebral perfusion, which circumvents the problems affecting other continuous arterial spin labeling schemes, such as magnetization transfer and duty cycle. However, some variability in the tagging efficiency of the pCASL technique has been reported. This article investigates the effect of B0 field inhomogeneity on the tagging efficiency of the pCASL pulse sequence as a possible cause of this variability. Both theory and simulated data predict that the efficiency of pseudo‐continuous labeling pulses can be degraded in the presence of off‐resonance effects. These findings are corroborated by human in vivo measurements of tagging efficiency. On the basis of this theoretical framework, a method utilizing B0 field map information is proposed to correct for the possible loss in tagging efficiency of the pCASL pulse sequence. The efficiency of the proposed correction method is evaluated using numerical simulations and in vivo implementation. The data show that the proposed method can effectively recover the lost tagging efficiency and signal‐to‐noise ratio of pCASL caused by off‐resonance effects. Copyright © 2011 John Wiley & Sons, Ltd.
Rapid determination of biosynthetic pathways using fractional isotope enrichment and high‐resolution dynamic nuclear polarization enhanced NMR
Authors: Bowen Sean , Sekar Giridhar , Hilty Christian
Published: March 2011

Carbon‐13 NMR has traditionally been a method of choice for the determination of metabolic pathways. Through fractional labeling, 13C spectra allow the identification of fragments incorporated as a unit into a biosynthesized molecule. The low sensitivity of 13C spectroscopy is an impediment to such studies, especially if compounded with an often limited availability of biosynthesized molecules. Dynamic nuclear polarization (DNP) can increase the signal‐to‐noise ratio in magnetic resonance by several orders of magnitude, and in combination with high‐resolution spectroscopy has the potential to increase the reach of this technique for metabolic profiling. Here, we present an application of high‐resolution DNP enhanced NMR to the study of the biosynthetic pathways for membrane lipids. We show that fatty acid methyl esters are readily hyperpolarized in organic solvent. The resulting spectra resolve the various structural features of the chains, including atoms near the termini, as well as unsaturated and cyclopropyl groups. Peak patterns observed in fractionally labeled samples are explained by the way feed molecules are incorporated into fatty acid chains during synthesis. Differences in multiplet intensity between samples made from glucose and acetate feedstock mixtures further reveal metabolic preferences for these precursors in the biosynthesis of the product. In addition to the present study of lipid biosynthesis, high‐resolution DNP‐NMR of fractionally 13C‐labeled metabolites may present itself for the rapid determination of biosynthetic pathways in various biomedical applications, especially in cases of limited availability of the products of interest. Copyright © 2011 John Wiley & Sons, Ltd.
A convected particle domain interpolation technique to extend applicability of the material point method for problems involving massive deformations
Authors: Sadeghirad A. , Brannon R. M. , Burghardt J.
Published: March 2011

A new algorithm is developed to improve the accuracy and efficiency of the material point method for problems involving extremely large tensile deformations and rotations. In the proposed procedure, particle domains are convected with the material motion more accurately than in the generalized interpolation material point method. This feature is crucial to eliminate instability in extension, which is a common shortcoming of most particle methods. Also, a novel alternative set of grid basis functions is proposed for efficiently calculating nodal force and consistent mass integrals on the grid. Specifically, by taking advantage of initially parallelogram‐shaped particle domains, and treating the deformation gradient as constant over the particle domain, the convected particle domain is a reshaped parallelogram in the deformed configuration. Accordingly, an alternative grid basis function over the particle domain is constructed by a standard 4‐node finite element interpolation on the parallelogram. Effectiveness of the proposed modifications is demonstrated using several large deformation solid mechanics problems. Copyright © 2011 John Wiley & Sons, Ltd.
A quasi‐static crack growth simulation based on the singular ES‐FEM
Authors: Nourbakhshnia N. , Liu G. R.
Published: March 2011

In the edge‐based smoothed finite element method (ES‐FEM), one needs only the assumed displacement values (not the derivatives) on the boundary of the edge‐based smoothing domains to compute the stiffness matrix of the system. Adopting this important feature, a five‐node crack‐tip element is employed in this paper to produce a proper stress singularity near the crack tip based on a basic mesh of linear triangular elements that can be generated automatically for problems with complicated geometries. The singular ES‐FEM is then formulated and used to simulate the crack propagation in various settings, using a largely coarse mesh with a few layers of fine mesh near the crack tip. The results demonstrate that the singular ES‐FEM is much more accurate than X‐FEM and the existing FEM. Moreover, the excellent agreement between numerical results and the reference observations shows that the singular ES‐FEM offers an efficient and high‐quality solution for crack propagation problems. Copyright © 2011 John Wiley & Sons, Ltd.
Supporting mothering: Service providers' perspectives of mothers and young children affected by intimate partner violence
Authors: Letourneau Nicole , Young Catherine , Secco Loretta , Stewart Miriam , Hughes Jean , Critchley Kim
Published: March 2011

Although negative outcomes from intimate partner violence (IPV) are not inevitable, IPV is recognized to have profound negative effects on child development. We conducted a qualitative descriptive study of service providers' understandings of the impact of IPV on mothers, young children (birth to 36 months), and mother–infant/child relationships, and of the support needs of these mothers and young children. Service providers suggested that IPV negatively influenced caregiving and identified a pressing need for information and strategies to help mothers promote and protect their young children's development. Although service providers struggled to articulate ideal forms of assistance to promote maternal–infant/child relationships, they agreed that mothers and young children experiencing IPV required more support than is currently available. © 2011 Wiley Periodicals, Inc. Res Nurs Health 34:192–203, 2011
Exploring the dynamics of policy interaction: Feedback among and impacts from multiple, concurrently applied policy approaches for promoting collaboration
Authors: Fuller Boyd W. , Vu Khuong Minh
Published: March 2011

The prisoner's dilemma and stag hunt games, as well as the apparent benefits of collaboration, have motivated governments to promote more frequent and effective collaboration through a variety of policy approaches. Sometimes, multiple kinds of policies are applied concurrently, and yet little is understood about how these policies might interact with each other. This study uses a simulation approach to examine one such case, when policies focused on increasing collaboration competence interact with those that motivate parties to collaborate based on payoff and non‐payoff incentives. Theoretically, our findings suggest seven testable hypotheses for future, rigorous research. Practically, our initial findings suggest that increasing competency generally improves the performance of incentive‐based policies, but not always. Exhortation policies can go too far and may be more prone to doing so when the target population's competency is higher. This means that decision makers are more at risk of applying too much exhortation effort, especially if they are also concurrently applying a competency‐building approach. © 2011 by the Association for Public Policy Analysis and Management.
No advantage of a rotational continuation phase in acute lymphoblastic leukemia in childhood treated with a BFM back‐bone therapy
Authors: Felice Maria S. , Rossi Jorge G. , Gallego Marta S. , Alfaro Elizabeth M. , Zubizarreta Pedro A. , Fraquelli Lidia E. , Alonso Cristina N. , Guitter Myriam R. , Scopinaro Marcelo J.
Published: March 2011

Background

Our aim was to compare two different schedules of maintenance in pediatric acute lymphoblastic leukemia (ALL) treated with a BFM‐based therapy, in a randomized study: an Arm with 6‐MP + MTX (with or without vincristine and dexamethasone pulses) versus a more intensive continuation phase.

Procedure

From January 1996 to November 2002, 429 eligible children with ALL were enrolled in a protocol with BFM‐based back‐bone, followed by a randomized continuation phase in standard (SRG) and intermediate (IRG) risk groups. Patients were randomized between Arms A and B for SRG and B or C for IRG. Arms A and C consisted of 6‐MP and MTX and in Arm C, six pulses of VCR and dexamethasone were added. Arm B combined four pairs of drugs rotated weekly. All risk‐groups received maintenance until completing 2 years of therapy from diagnosis.

Results

With a median follow‐up of 138 (range: 96–178) months, the overall pEFS (SE) was 72 (6)% for all patients and the different risk groups showed: SRG: 85 (3)%, IRG: 71 (1)%, and HRG: 42 (7)% (P‐value ≤0.0001). The pDFS (SE) according to the assigned arm of maintenance was, for Arm A: 89 (3)% and for Arm B: 85 (4)% in SRG, and, for Arm B: 77 (4)% and for Arm C: 75 (4)% in IRG, at 10 years follow‐up. There were no statistically significant differences in outcome between arms of maintenance for both risk groups.

Conclusions

In protocols with initial BFM‐based strategy, a more intensive continuation phase did not benefit any risk group of patients. Pediatr Blood Cancer 2011;57:47–55. © 2011 Wiley‐Liss, Inc.
Effect of blend composition and organoclay loading on the nanocomposite structure and properties of miscible poly(methyl methacrylate)/poly(styrene‐co‐acrylonitrile) blends
Authors: Tiwari Rajkiran R. , Natarajan Upendra
Published: March 2011

Organically‐modified montmorillonite clay nanocomposites of poly(styrene‐co‐acrylonitrile) (SAN), poly(methyl methacrylate) (PMMA) and SAN/PMMA miscible blend are investigated. Structure characteristics at the nanoscale and microscale and thermal and tensile properties are studied as a function of polymer blend composition and filler loading fraction. Blend miscibility and Tg are unaffected by up to 10% by wt. organoclay. Thermal degradation stability increases with SAN content and exhibits an optimum value of clay loading. Stiffness shows significant improvement. Tensile strength and elongation‐at‐break suffer as a result of nanocomposite formation. Modulus shows a maximum enhancement of 57% (5 ± 0.06 GPa at 10 wt% filler, 20/80 SAN/PMMA) and varies linearly with clay fraction for all compositions of matrix phase. Predictions of Halpin–Tsai composite model are in excellent agreement with the experimental behavior over full range of polymer blend composition. Fundamental aspects of a polymer blend–clay nanocomposite are clarified, such as lack of additional synergy between clay platelets and matrix, and tensile ductility reduction, compared with polymer–clay system. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
A posteriori quality control for the curation and reuse of public proteomics data
Authors: Foster Joseph M. , Degroeve Sven , Gatto Laurent , Visser Matthieu , Wang Rui , Griss Johannes , Apweiler Rolf , Martens Lennart
Published: March 2011

Proteomics is a rapidly expanding field encompassing a multitude of complex techniques and data types. To date much effort has been devoted to achieving the highest possible coverage of proteomes with the aim to inform future developments in basic biology as well as in clinical settings. As a result, growing amounts of data have been deposited in publicly available proteomics databases. These data are in turn increasingly reused for orthogonal downstream purposes such as data mining and machine learning. These downstream uses however, need ways to a posteriori validate whether a particular data set is suitable for the envisioned purpose. Furthermore, the (semi‐)automatic curation of repository data is dependent on analyses that can highlight misannotation and edge conditions for data sets. Such curation is an important prerequisite for efficient proteomics data reuse in the life sciences in general. We therefore present here a selection of quality control metrics and approaches for the a posteriori detection of potential issues encountered in typical proteomics data sets. We illustrate our metrics by relying on publicly available data from the Proteomics Identifications Database (PRIDE), and simultaneously show the usefulness of the large body of PRIDE data as a means to derive empirical background distributions for relevant metrics.
Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome
Authors: Specht Michael , Stanke Mario , Terashima Mia , Naumann‐Busch Bianca , Janßen Ingrid , Höhner Ricarda , Hom Erik F. Y. , Liang Chun , Hippler Michael
Published: March 2011

The use and development of post‐genomic tools naturally depends on large‐scale genome sequencing projects. The usefulness of post‐genomic applications is dependent on the accuracy of genome annotations, for which the correct identification of intron–exon borders in complex genomes of eukaryotic organisms is often an error‐prone task. Although automated algorithms for predicting intron–exon structures are available, supporting exon evidence is necessary to achieve comprehensive genome annotation. Besides cDNA and EST support, peptides identified via MS/MS can be used as extrinsic evidence in a proteogenomic approach. We describe an improved version of the Genomic Peptide Finder (GPF), which aligns de novo predicted amino acid sequences to the genomic DNA sequence of an organism while correcting for peptide sequencing errors and accounting for the possibility of splicing. We have coupled GPF and the gene finding program AUGUSTUS in a way that provides automatic structural annotations of the Chlamydomonas reinhardtii genome, using highly unbiased GPF evidence. A comparison of the AUGUSTUS gene set incorporating GPF evidence to the standard JGI FM4 (Filtered Models 4) gene set reveals 932 GPF peptides that are not contained in the Filtered Models 4 gene set. Furthermore, the GPF evidence improved the AUGUSTUS gene models by altering 65 gene models and adding three previously unidentified genes.
Shotgun proteomics of human bile in hilar cholangiocarcinoma
Authors: Farid Shahid G. , Craven Rachel A. , Peng Jianhe , Bonney Glenn K. , Perkins David N. , Selby Peter J. , Rajendra Prasad K. , Banks Rosamonde E.
Published: March 2011

The need to find biomarkers for hepatobiliary diseases including cholangiocarcinoma (CCA) has led to an interest in using bile as a proximal fluid in biomarker discovery experiments, although there are inherent challenges both in its acquisition and analysis. The study described here greatly extends previous studies that have started to characterise the bile proteome. Bile from four patients with hilar CCA was depleted of albumin and immunoglobulin G and analysed by GeLC‐MS/MS. The number of proteins identified per bile sample was between 378 and 741. Overall, the products of 813 unique genes were identified, considerably extending current knowledge of the malignant bile proteome. Of these, 268 were present in at least 3 out of 4 patients. This data set represents the largest catalogue of bile proteins to date and together with other studies in the literature constitutes an important prelude to the potential promise of expression proteomics and subsequent validation studies in CCA biomarker discovery.
Synthesis and micellization of new biodegradable phosphorylcholine‐capped polyurethane
Authors: Wang Zhigao , Wan Pengjun , Ding Mingming , Yi Xuan , Li Jiehua , Fu Qiang , Tan Hong
Published: March 2011

To obtain controllable and biocompatible drug carriers, a series of amphiphilic biodegradable multiblock polyurethanes end‐capped by phosphorylcholine were designed and synthesized using L‐lysine ethyl ester diisocyanate (LDI), poly(lactic acid)‐poly(ethylene glycol)‐poly(lactic acid) (PLA‐PEG‐PLA), 1,4‐butanediol (BDO), and 4‐hydroxy butyl phosphorylcholine (BPC) was used as end‐capper to improve their biocompatibility and provide them with tailored micellization characteristics. The resulting polyurethanes were fully characterized with proton nuclear magnetic resonance spectroscopy (1H NMR), Fourier transform infrared spectroscopy (FT‐IR), gel permeation chromatograph (GPC), and differential scanning calorimetry (DSC). More importantly, these phosphorylcholine‐capped polyurethanes can self assemble into micelles that are smaller than 100 nm in diameter. Their particle sizes, size distributions, and zeta potentials can also be tailored by varying the phosphorylcholine content. The incorporation of phosphorylcholine into these polyurethanes has significantly affected their degree of microphase separation, bulk and micelle degradation rates. This work provides a new and facile approach to prepare amphiphilic block copolymer micelles with controllable performances, which could be useful for drug delivery and bioimaging applications. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Patient experiences with communication about sex during and after treatment for cancer
Authors: Flynn Kathryn E. , Reese Jennifer Barsky , Jeffery Diana D. , Abernethy Amy P. , Lin Li , Shelby Rebecca A. , Porter Laura S. , Dombeck Carrie B. , Weinfurt Kevin P.
Published: March 2011

Objective

We studied patients' experiences with oncology providers regarding communication about sexual issues during and after treatment for cancer.

Methods

During development of the Patient‐Reported Outcomes Measurement Information System (PROMIS®) Sexual Function measure, we collected focus group and survey data on communication with oncology professionals about sexual problems. We conducted 16 focus groups with patients and survivors (n = 109) and analyzed the discussions for major themes, including experiences discussing sex during oncology visits. During testing of the PROMIS Sexual Function measure, we assessed experiences discussing sexual problems with oncology professionals (n = 819) and measured bivariate associations between asking for information from clinicians and sexual function and satisfaction with sex life.

Results

Most patients and survivors (74%) thought that discussions with oncology professionals about sexual problems were important, but whether they had ever received information about sexual function from a provider varied by cancer type (23% lung, 29% breast, 39% colorectal, and 79% prostate). Those who had asked an oncology professional about sexual problems had significantly greater interest in sexual activity as well as more sexual dysfunction.

Conclusions

Sexual problems are a widespread concern among patients and survivors, but there is much variation in experiences of communication about sexual issues, and many patients do not receive the information they need from their oncology providers. There are large differences in sexual function between patients who do and do not ask providers about sexual problems. Sexual health has yet to be fully integrated into oncology care, even for cancers involving sex organs.

Copyright © 2011 John Wiley & Sons, Ltd.
‘The end of treatment is not the end’: parents' experiences of their child's transition from treatment for childhood cancer
Authors: Mckenzie Sian E. , Curle Christine
Published: March 2011

Objective

This study explores parents' experiences of the end of treatment (EOT) for childhood cancer and aims to develop a theoretical understanding of this transition.

Method

The study used a grounded theory design to develop a theory from 11 semi‐structured interviews with parents of children who had finished their cancer treatment. These were transcribed verbatim and analysed.

Results

The core theme of ‘the end of treatment is not the end’ emerged and reflected the continued process of role and identity changes that parents faced. The results suggest that the active treatment phase and post treatment phases are interlinked and inseparable for parents. The main process identified during treatment was ‘getting through’ to the EOT and this was managed through parents ‘adjusting’ and an ‘increase in support’. These core processes continued to mediate the process of ‘managing the unknown’ after treatment, and parents were left with a sense of ‘balancing their emotions’ between, ‘life is very normal’ and ‘it's not going to go away’.

Conclusions

Across all themes the process of managing identity changes emerged as a key issue for parents, which needs to be considered. During treatment, health professionals have an opportunity to discuss the impact of finishing treatment and prepare parents for this transition and the challenges that they may face.

Copyright © 2011 John Wiley & Sons, Ltd.
A roadmap for successful applications of clinical proteomics
Authors: Ioannidis John P. A.
Published: March 2011

Despite over 30 000 publications on proteomics in the last decade, and the accumulation of extensive interesting information on the human proteome in diverse observations, the clinical translation of proteomics to‐date has had major setbacks. I review here a roadmap for improving the success rate of clinical proteomics. The roadmap includes steps for improvements that need to be made in analytical tools, discovery, validation, clinical application, and post‐clinical application appraisal. It is likely that most if not all of the components that are necessary for clinical success are either readily available, or should be possible to put in place with more rigorous research standards and concerted efforts of the research community, clinicians, and health agencies. Enthusiasm for the clinical impact of proteomics may need to be tempered currently until robust evidence can be obtained, but some clinical successes should eventually be feasible.
Is the time ripe for kidney tissue proteomics?
Authors: Charonis Aristidis , Luider Theo , Baumann Marc , Schanstra Joost P.
Published: March 2011

In this viewpoint article, the importance of renal tissue proteomics in health and disease is explored. The analysis of the urinary proteome and the potential clinical application of these findings are progressing. However, additional benefit would be gained from a detailed parallel exploration of the proteome of the renal parenchyma, both in models and clinical samples. With this aim, we will briefly summarize the existing literature, compare the findings and propose future tasks. Special emphasis is placed on the importance of studying specific cellular compartments and cell types within the kidney. Recent technical advances are also discussed. It is anticipated that the combination of such technologies, especially proteomic analysis of material extracted by laser capture microdissection from paraffin embedded tissue or direct mass spectrometrical tissue imaging, will revolutionize the field.
Profiling the proteome in renal transplantation
Authors: Sigdel Tara K. , Lee Sangho , Sarwal Minnie M.
Published: March 2011

Improved monitoring of transplanted solid organs is one of the next crucial steps leading to an increase in both patient and allograft survival. This can be facilitated through one or a set of surrogate biomarker molecules that accurately and precisely indicate the health status of the transplanted organ. Recent developments in the field of high throughput “omic” methods including genomics and proteomics have facilitated robust and comprehensive analysis of genes and proteins. This development has stimulated efforts in the identification of effective and clinically applicable gene and protein biomarkers in solid organ transplantation, including kidney transplantation. Some achievements have been made through proteomics in terms of profiling proteins and identification of potential biomarkers. However, the road to a successful biomarker discovery and its clinical implementation has proved to be challenging, requiring a number of key issues to be addressed. Such issues are: the lack of widely accepted protocols, difficulty in sample processing and transportation and a lack of collaborative efforts to achieve significant sample sizes in clinical studies. In this review using our area of expertise, we describe the current strategies used for proteomic‐based biomarker discovery in renal transplantation, discuss inherent issues associated with these efforts and propose better strategies for successful biomarker discovery.
Mapping of molecular pathways, biomarkers and drug targets for diabetic nephropathy
Authors: Fechete Raul , Heinzel Andreas , Perco Paul , Mönks Konrad , Söllner Johannes , Stelzer Gil , Eder Susanne , Lancet Doron , Oberbauer Rainer , Mayer Gert , Mayer Bernd
Published: March 2011

Purpose: For diseases with complex phenotype such as diabetic nephropathy (DN), integration of multiple Omics sources promises an improved description of the disease pathophysiology, being the basis for novel diagnostics and therapy, but equally important personalization aspects.

Experimental design: Molecular features on DN were retrieved from public domain Omics studies and by mining scientific literature, patent text and clinical trial specifications. Molecular feature sets were consolidated on a human protein interaction network and interpreted on the level of molecular pathways in the light of the pathophysiology of the disease and its clinical context defined as associated biomarkers and drug targets.

Results: About 1000 gene symbols each could be assigned to the pathophysiological description of DN and to the clinical context. Direct feature comparison showed minor overlap, whereas on the level of molecular pathways, the complement and coagulation cascade, PPAR signaling, and the renin–angiotensin system linked the disease descriptor space with biomarkers and targets.

Conclusion and clinical relevance: Only the combined molecular feature landscapes closely reflect the clinical implications of DN in the context of hypertension and diabetes. Omics data integration on the level of interaction networks furthermore provides a platform for identification of pathway‐specific biomarkers and therapy options.
Preparation, Crystal Structure and Explosive Properties of Copper(II) Perchlorate Complex with 4‐Amino‐1,2,4‐Triazole and Water
Authors: Cudziło Stanisław , Trzciński Waldemar , Nita Marcin , Michalik Sławomir , Krompiec Stanisław , Kruszyński Rafał , Kusz Joachim
Published: March 2011

A complex from copper(II) perchlorate with 4‐amino‐1,2,4‐triazole (4‐AT, C2H4N4) was synthesized, and elemental composition, molecular structure, and explosive properties were determined. To this end, elemental and X‐ray analyses were carried out, sensitivity to mechanical and thermal stimuli was measured, mechanism of thermal decomposition was investigated, and kinetic parameters of decomposition were determined. In the next step measurements of heat of combustion and detonation velocity were performed. Detonation parameters were also calculated. It was stated that the complex has slightly distorted square bipyramidal (4+2) coordination. The four basal bonds are formed by nitrogen atoms of four 4‐AT molecules. The coordination of the metal is completed by two axial oxygen atoms, one of the perchlorate ion, and one of the water molecule. With respect to explosive properties, tetrakis(4‐AT)copper(II) perchlorate monohydrate belongs to the group of sensitive secondary explosives.
Complying with OSHA's RNEP, CNEP, and VPP RAGAGEP
Authors: Patschke Chad
Published: March 2011

The OSHA Refinery National Emphasis Program (RNEP) and OSHA Voluntary Protection Program incorporate specific questions relative to many recognized and generally accepted good engineering practices (RAGAGEP). Many of the same RAGAGEP can be expected to be used in the OSHA Chemicals NEP as well. To comply with OSHA's process safety management (PSM) regulation and improve process safety at their sites, chemical industry personnel should be aware of what RAGAGEP OSHA is recognizing and inspecting against and their key requirements. This article will discuss: (1) OSHA's expectations for compliance with RAGAGEP, including some of the RAGAGEP OSHA references in compliance directives, instructions, and citations, (2) some citations issued by OSHA involving RAGAGEP, and (3) common RAGAGEP compliance issues ABSG Consulting observes when conducting PSM audits and assessments throughout the petrochemical and related industries. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Burn injury caused by mixing incompatible chemicals with sodium permanganate
Authors: Ogle Russell A. , Morrison Delmar “Trey”
Published: March 2011

This article discusses the investigation of an incident caused by the mixing of incompatible chemicals: a strong oxidizing agent with a reducing agent. The exact mixture and sequence of mixing was unknown, but the materials included an aqueous solution of 40% sodium permanganate and either solid sodium thiosulfate or solid sodium metabisulfite. These chemicals were part of a new technology being pilot‐tested for remediating contaminated groundwater. Throughout the pilot test, excess waste permanganate was transported by hand in 5‐gallon pails from the injection area to a designated nearby area for reduction. During one such transfer, a worker was seriously burned when a pail of sodium permanganate solution erupted onto him. The liquid splashed onto and ignited his clothing. A puzzling feature of this accident was the apparent time delay between chemical addition and the subsequent reaction.

Various chemical addition scenarios were evaluated by thermodynamic calculations, followed by laboratory, pilot, and full‐scale tests. The test results revealed that while some chemical addition scenarios resulted in a prompt exothermic reaction with the generation of steam; other scenarios resulted in a similar but delayed reaction. The time delay was caused by mass transfer limitations associated with the solids dissolution process. This case study serves as a reminder that the hazardous result of mixing incompatible chemicals may be delayed and may occur when least expected. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011