bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quasi‐static crack growth simulation based on the singular ES‐FEM
Authors: Nourbakhshnia N. , Liu G. R. 
Published: March 2011

AbstractIn 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

AbstractAlthough 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

AbstractThe 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

AbstractBackgroundOur 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.ProcedureFrom 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.ResultsWith 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.ConclusionsIn 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

AbstractOrganically‐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

AbstractProteomics 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

AbstractThe 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

AbstractThe 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

AbstractTo 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

AbstractObjectiveWe studied patients' experiences with oncology providers regarding communication about sexual issues during and after treatment for cancer.MethodsDuring 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.ResultsMost 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.ConclusionsSexual 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

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

AbstractDespite 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

AbstractIn 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

AbstractImproved 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

AbstractPurpose: 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

AbstractA 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.