bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphometrical Analysis on Cut Marks Using a 3D Digital Microscope
Authors: Boschin F. , Crezzini J. 
Published: September 2011

ABSTRACTMicroscopic analysis represents a powerful tool for understanding taphonomy. Our work, as in other studies, aims to identify the origin of different kinds of marks on bones. In this paper, we test the application of a HIROX Digital Microscope KH‐7700. This microscope captures 3D images of the bone surface, thus bringing into focus the whole section of striations. This enables the direct observation of their shape from several points of view and the relatively rapid procurement of a variety of measurements (e.g. depth, breadth, angles). This technology has been applied to several butchery experiments, in which both stone and metal tools have been used to produce cut marks on skeletal elements. The morphometrical parameters presented in this paper enabled the correct identification of the different origins of experimental striations and were further tested on two archaeological sets of cut marks inflicted by both metal blades and flint flakes or tools. Therefore, the obtained experimental records constitute a useful database for archaeological remains. The morphometrical parameters developed and implemented in this study represent objective criteria for identifying the origin of cut marks which can be processed through statistical analysis. Copyright © 2011 John Wiley & Sons, Ltd.
The Diagnosis and Context of a Facial Deformity from an Anglo‐Saxon Cemetery at Spofforth, North Yorkshire
Authors: Craig E. , Craig G. 
Published: September 2011

ABSTRACTAn individual aged between 6 and 7 years at death from a 7th to 9th century cemetery at Village Farm, Spofforth, North Yorkshire, presented significant pathological swelling to the left facial bones. The ectocranial surface was bulbous and uneven, and the expanded diploë was densely packed with a mass of thick trabeculae. Radiographic and histological analysis, in combination with the macroscopically observed pathological changes, supported the differential diagnosis of fibrous dysplasia. The skeletal changes to the left face and jaw would have resulted in a significant facial deformity. Examples of individuals with physical impairments or disfigurements from Anglo‐Saxon cemeteries are rare. Nevertheless, it seems that a significant proportion are afforded unusual burial practices more often associated with deviancy, for example, at the edge of cemeteries or on a reversed orientation, seemingly indicating that their diminished physical capabilities or altered physical appearance had a detrimental effect on their social status. The child from Spofforth was, however, buried in a normative manner, extended, supine and in a plain earth‐cut grave, with no indication that their facial deformity had prompted unusual funerary provision. This example of facial disfigurement contributes to a growing corpus of potentially disabled individuals from early medieval England. Copyright © 2011 John Wiley & Sons, Ltd.
Voluntary environmental programs: A comparative perspective
Authors: Prakash Aseem , Potoski Matthew 
Published: September 2011

AbstractVoluntary environmental programs (VEPs) are institutions for inducing firms to produce environmental goods beyond legal requirements. A comparative perspective on VEPs shows how incentives to sponsor and participate in VEPs vary across countries in ways that reveal their potential and limitations. Our brief survey examines conditions under which VEPs emerge, attract participants, and improve participants' environmental performance. We focus on the costs and bene‐fits for actors seeking to supply (or sponsor) these governance mechanisms as well as the costs and benefits for firms who are considering joining VEPs and adhering to their program obligations. © 2011 by the Association for Public Policy Analysis and Management.
Sorafenib and cisplatin/doxorubicin (PLADO) in pediatric hepatocellular carcinoma
Authors: Schmid Irene , Häberle Beate , Albert Michael H. , Corbacioglu Selim , Fröhlich Birgit , Graf Norbert , Kammer Birgit , Kontny Udo , Leuschner Ivo , Scheel‐Walter Hans‐Gerhard , Scheurlen Wolfram , Werner Sebastian , Wiesel Thomas , von Schweinitz Dietrich 
Published: September 2011

AbstractPurposeOverall survival is poor in children with primary unresectable hepatocellular carcinoma. Sorafenib has been shown to significantly improve progression‐free survival in adult hepatocellular carcinoma (HCC) patients. We evaluated the experience of PLADO (cisplatin 80 mg/m2/day, doxorubicin 2 × 30 mg/m2/day) in combination with sorafenib in pediatric HCC patients.Patients and MethodsClinical data of 12 patients (7–16 years), 7 with unresectable tumor, were retrospectively assessed.ResultsIn total 6/12 (50%) patients are in complete remission after a median follow‐up of 20 months (4 with PLADO/sorafenib/resection, 2 with liver transplantation after local relapse). Of the seven patients with unresectable tumor, PLADO/sorafenib resulted in partial response (PR) in four, stable disease (SD) in two, and progression in one. Three are alive in CR after complete resection after 12 (alternative therapy after two cycles PLADO/sorafenib), 12 and 18 months (six cycles PLADO/sorafenib), respectively. All four patients with elevated alpha‐fetoprotein levels had a marked drop after two cycles. Of the five patients with primary complete tumor resection one is alive disease‐free at 27 months. Four had local or metastatic relapses (13, 7, 12, and 13 months), two of whom were rescued by liver transplantation (CR after 25 and 32 months). The main toxicity attributable to sorafenib was a hand–foot skin reaction (HFSR) in seven patients.ConclusionSorafenib in combination with PLADO may be a promising approach in pediatric HCC; HFSR was the most important toxicity. Data based on prospective studies are needed to evaluate pharmacokinetics, resectability rates, and survival in pediatric HCC treated with sorafenib. Pediatr Blood Cancer 2012; 58: 539–544. © 2011 Wiley Periodicals, Inc.
Durable complete response to chemotherapy in an infant with a clival chordoma
Authors: Al‐Rahawan Mohamad M. , Siebert James D. , Mitchell Craig S. , Smith Stephen D. 
Published: September 2011

AbstractChordomas are rare bone tumors of notochord remnants that may occur anywhere within the axial skeleton. The standard of care is complete surgical removal. Proton beam irradiation is commonly used when the tumor is inaccessible or has recurred. Chemotherapy has been used in the treatment of patients at relapse but it has been generally proven ineffective. We report a 7‐month‐old infant with a clival chordoma who responded to combination chemotherapy consisting of cycles of vincristine/cyclophosphamide/doxorubicin alternating with etoposide/ifosfamide. She has been off chemotherapy for 2 years and is well at age 5. Pediatr Blood Cancer 2012;59:323–325. © 2011 Wiley Periodicals, Inc.
Incidence, clinical features, and risk factors of idiopathic pneumonia syndrome following hematopoietic stem cell transplantation in children
Authors: Sakaguchi Hirotoshi , Takahashi Yoshiyuki , Watanabe Nobuhiro , Doisaki Sayoko , Muramatsu Hideki , Hama Asahito , Shimada Akira , Yagasaki Hiroshi , Kudo Kazuko , Kojima Seiji 
Published: September 2011

AbstractBackgroundIdiopathic pneumonia syndrome (IPS) is a severe complication that can occur after hematopoietic stem cell transplantation (HSCT) and is often associated with a fatal outcome despite intensive supportive care.ProcedureTo assess the incidence and risk factors of IPS, we reviewed 251 consecutive patients (median age, 7.0 years) who received HSCT at the Department of Pediatrics, Nagoya University Hospital, between January 1990 and July 2009.ResultsTwenty of 251 (cumulative incidence of IPS at 2 years after HSCT, 8.0%; 95% confidence interval (CI), 5.1–12.4%) patients developed IPS. The median duration from HSCT to diagnosis of IPS was 67 days (range, 12–486 days). Patients with IPS had significantly higher 5‐year transplant‐related mortality compared to patients without IPS (52% (95% CI, 19–77%) vs. 13% (95% CI, 5–25%), P < 0.001), and the probability of 5‐year overall survival was significantly worse for patients with IPS (42% (95% CI, 25–64%) vs. 68% (95% CI, 59–76%), P = 0.01). By multivariate analysis, high risk in underlying disease (HR, 2.5; 95% CI, 1.0–6.7; P = 0.05) and a busulfan‐containing regimen (HR, 3.5; 95% CI, 1.3–9.9; P < 0.01) were identified as the independent risk factors for developing IPS.ConclusionThe prophylactic strategies for IPS in patients with these risk factors were warranted. Pediatr Blood Cancer 2012; 58: 780–784. © 2011 Wiley Periodicals, Inc.
Neuroblastoma progress on many fronts: The neuroblastoma research symposium
Authors: Wylie Luke , Philpott Anna 
Published: September 2011

AbstractNeuroblastoma (NBL) is a pediatric tumor of infancy derived from precursor cells of the sympathetic nervous system. Clinicians and researchers in developmental biology and genetics recently met to facilitate meaningful crosstalk and to discuss considerable progress made in the clinical treatment and basic biology of NBL. For instance, discoveries in familial NBL have identified genetic aberrations in Phox2b and Alk that predispose to NBL, while advances in epigenetics and MYCN regulation have also offered insight into NBL pathogenesis and future treatment. Moreover, novel therapeutic avenues are also being explored, including targeted immunotherapies, and innovative radiotherapeutic and chemotherapeutic approaches. This multi‐disciplinary meeting was convened to aid the transfer of new biological findings into the clinic and to use clinical advances to inform the basic biological understanding of this devastating disease. Pediatr Blood Cancer 2012; 58: 649–651. © 2011 Wiley Periodicals, Inc.
Frequency and determinants of potential drug‐drug interactions in an elderly population receiving regular home visits by GPs ‐ results of the home medication review in the AGnES‐studies
Authors: Hoffmann Wolfgang , van den Berg Neeltje , Thyrian Jochen René , Fiss Thomas 
Published: September 2011

ABSTRACTPurposeThere is limited knowledge about prevalence and determinants of potential drug‐drug‐interactions (pDDI) in the ambulatory health care setting. In this manuscript we analysed the prevalence and determinants of pDDI in the AGnES home visit population (GP‐supporting, community‐based, e‐health‐assisted, systemic intervention).Methods779 Home‐dwelling patients received an IT‐supported home medication review (HMR). The interaction monographs of the ABDA‐database were used to identify pDDI. A binary multivariate logistic regression model was used to analyse determinants for occurrence of moderate and serious pDDI, respectively.ResultsPatients (mean age f: 79.8 yrs; m: 76.2 yrs) took a mean number of 6.8 active substances (SD = 3.3) regularly. 626 patients (80.4%) with an HMR had at least one pDDI (mean = 4.8; SD = 4.4). In 454 patients (58.3%) we found at least one pDDI with moderate or serious relevance (mean = 2.9; SD = 2.8). The most frequent moderate pDDI was the combination of potassium excretion diuretics (e.g. hydrochlorothiazide) with anti‐inflammatory drugs (e.g. ibuprofen; n = 258 patients). Adjusted for age and gender, multiple binary logistic regression showed significant results for the number of taken active substances (continuous variable; OR = 1.48; 95%‐CI 1.382‐1.585), metabolic diseases (OR = 1.52; 95%‐CI 1.039‐2.223), a diagnose of a muscular‐skeletal disease (OR = 1.741; 95%‐CI 1.204‐2.517), infectious disease (OR = 0.127; 95%‐CI 0.021‐0.783), and gastro‐intestinal disease (OR = 0.538; 95%‐CI 0.322‐0.899).ConclusionUsing a comprehensive, computer‐assisted HMR in an ambulatory care setting we have identified a high proportion of pDDI of moderate or serious clinical relevance. These pDDI require an intervention from intensified monitoring to a change in medication. Further investigations should focus on clinical outcome of pDDI. Copyright © 2011 John Wiley & Sons, Ltd.
Well‐defined diblock copolymers possessing fluorescent and metal chelating functionalities as novel macromolecular sensors for amines and metal ions
Authors: Demetriou Maria , Krasia‐Christoforou Theodora 
Published: September 2011

AbstractThe amino‐ and metal‐ion sensing capability of a novel type of well‐defined block copolymers based on 9‐anthrylmethyl methacrylate (AnMMA; hydrophobic, fluorescent) and 2‐(acetoacetoxy)ethyl methacrylate (AEMA; hydrophobic, metal chelating) has been investigated in organic media. AEMAx‐b‐AnMMAy diblock copolymers were prepared for the first time using reversible addition‐fragmentation chain transfer (RAFT) polymerization. All polymers were characterized in terms of molecular weights, polydispersity indices and compositions by size exclusion chromatography and 1H NMR spectroscopy, respectively. The glass transition (Tg) temperatures of the AEMAx and AnMMAx homopolymers and the AEMAx‐b‐AnMMAy diblock copolymers were determined using differential scanning calorimetry. These systems were evaluated toward their ability to act as effective dual chemosensors (i.e., amino‐ and metal‐ion sensors) in an organic solvent (chloroform). More precisely, the fluorescence intensity of both the AnMMAx homopolymers and the AnMMAx‐b‐AEMAy diblock copolymers in solution exhibited a significant decrease in the presence of triethylamine. Moreover, the presence of iron (III) cations were also found to significantly affect the fluorescence signal of the anthracene moieties when those were combined in a block copolymer structure with the AEMA units, due to complex formation occurring between the β‐ketoester groups of the AEMAx segment and the cations. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Micromechanical models of young's modulus of NR/organoclay nanocomposites
Authors: Lowe David J. , Chapman Andrew V. , Cook Stuart , Busfield James J. C. 
Published: September 2011

AbstractSmall strain Young's moduli of natural rubber (NR)/organoclay nanocomposites were estimated using the Guth–Gold, Halpin–Tsai (HT), and Krieger–Dougherty (KD) models, and compared with experimental measurements of NR vulcanizates containing organo‐montmorillonite (OM) or organo‐sepiolite (OS). To account for the effect on modulus of the NR matrix of the vulcanization‐active modifier in the organoclay, a matrix modulus correction (MMC) term was derived from the vulcanization parameters of the nanocomposites. The KD model gave a better empirical fit with the experimental data than the Guth–Gold model, with both giving good agreement with particle shape factors estimated from transmission electron microscope (TEM) images. The HT model gave the best fit with experiment for both types of nanocomposite, and use of the MMC term meant that the empirical shape factor was sufficiently close to that estimated from TEM images that the model could potentially be used to accurately predict the Young's moduli of NR/OM and NR/OS nanocomposites. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1621–1627, 2011
Ghrelin receptor as a novel imaging target for prostatic neoplasms
Authors: Lu Chen , McFarland Mark S. , Nesbitt Rae‐Lynn , Williams Andrew K. , Chan Susanne , Gomez‐Lemus Jose , Autran‐Gomez Anna Maria , Al‐Zahrani Ali , Chin Joseph L. , Izawa Jonathan I. , Luyt Leonard G. , Lewis John D. 
Published: September 2011

AbstractBACKGROUNDGhrelin is a natural growth hormone secretagogue (GHS) that is co‐expressed with its receptor GHSR in human prostate cancer (PCa) cells. Imaging probes that target receptors for ghrelin may delineate PCas from benign disease. The specificity of a novel ghrelin‐imaging probe for PCa over normal tissue or benign disease was assessed.METHODSA fluorescein‐bearing ghrelin analogue was synthesized (fluorescein‐ghrelin(1–18)), and its application for imaging was evaluated in a panel of PCa cell lines and human prostate tissue. Prostate core biopsy samples were collected from fresh surgery specimens of 13 patients undergoing radical prostatectomy. Ghrelin probe signal was detected and quantified in each sample using a hapten amplification technique and associated with pathological features.RESULTSThe ghrelin probe was taken up by GHSR‐expressing LNCaP and PC‐3 cells, and not in BPH cells that express low levels of GHSR. Binding was blocked by competition with excess unlabeled probe. The ghrelin probe signal was 4.7 times higher in PCa compared to benign hyperplasia tissue (P = 0.0027) and normal tissue (P = 0.0093). Furthermore, while the ghrelin probe signal was 1.9‐fold higher in PIN compared to benign hyperplasia (P = 0.0022) and normal tissue (P = 0.0047), there was no significant difference in the signal of benign hyperplasia compared to normal tissue.CONCLUSIONThe imaging probe fluorescein‐ghrelin(1–18) is specific for PCa, and did not associate significantly with benign hyperplasia or normal prostate tissue. This data suggests that ghrelin analogues may be useful as molecular imaging probes for prostatic neoplasms in both localized and metastatic disease. Prostate 72:825–833, 2012. © 2011 Wiley Periodicals, Inc.
On the use of distance constraints in protein–protein docking computations
Authors: Shih Edward S. C. , Hwang Ming‐Jing 
Published: September 2011

AbstractProtein–protein docking (PPD) is a computational process that predicts the structure of a complex of two interacting proteins from their unbound structures. The accuracy of PPD predictions is low, but can be greatly enhanced if experimentally determined distance data are available for incorporation into the prediction. However, the specific effects of distance constraints on PPD predictions are largely uncharacterized. In this study, we systematically simulated the effects of using distance constraints both on a new distance constraint‐driven PPD approach, called DPPD, and also, by re‐ranking, on a well‐established grid‐based global search approach. Our results for a PPD benchmark dataset of 84 protein complexes of known structures showed that near 100% docking success rates could be obtained when the number of distance constraints exceeded six, the degrees of freedom of the system, but the success rate was significantly reduced by long distance constraints, large binding‐induced conformational changes, and large errors in the distance data. Our results also showed that, under most conditions simulated, even two or three distance constraints were sufficient to achieve a much better success rate than those using a sophisticated physicochemical function to re‐rank the results of the global search. Our study provides guidelines for the practical incorporation of experimental distance data to aid PPD predictions. Proteins 2012;. © 2011 Wiley Periodicals, Inc.
Template‐based protein structure modeling using TASSERVMT
Authors: Zhou Hongyi , Skolnick Jeffrey 
Published: September 2011

AbstractTemplate‐based protein structure modeling is commonly used for protein structure prediction. Based on the observation that multiple template‐based methods often perform better than single template‐based methods, we further explore the use of a variable number of multiple templates for a given target in the latest variant of TASSER, TASSERVMT. We first develop an algorithm that improves the target‐template alignment for a given template. The improved alignment, called the SP3alternative alignment, is generated by a parametric alignment method coupled with short TASSER refinement on models selected using knowledge‐based scores. The refined top model is then structurally aligned to the template to produce the SP3alternative alignment. Templates identified using SP3threading are combined with the SP3alternative and HHEARCH alignments to provide target alignments to each template. These template models are then grouped into sets containing a variable number of template/alignment combinations. For each set, we run short TASSER simulations to build full‐length models. Then, the models from all sets of templates are pooled, and the top 20–50 models selected using FTCOM ranking method. These models are then subjected to a single longer TASSER refinement run for final prediction. We benchmarked our method by comparison with our previously developed approach, pro‐sp3‐TASSER, on a set with 874 easy and 318 hard targets. The average GDT‐TS score improvements for the first model are 3.5 and 4.3% for easy and hard targets, respectively. When tested on the 112 CASP9 targets, our method improves the average GDT‐TS scores as compared to pro‐sp3‐TASSER by 8.2 and 9.3% for the 80 easy and 32 hard targets, respectively. It also shows slightly better results than the top ranked CASP9 Zhang‐Server, QUARK and HHpredA methods. The program is available for download athttp://cssb.biology.gatech.edu/. © 2011 Wiley Periodicals, Inc.
Progress in the prediction of pKavalues in proteins
Authors: Alexov Emil , Mehler Ernest L. , Baker Nathan , M. Baptista António , Huang Yong , Milletti Francesca , Erik Nielsen Jens , Farrell Damien , Carstensen Tommy , Olsson Mats H. M. , Shen Jana K. , Warwicker Jim , Williams Sarah , Word J. Michael 
Published: September 2011

AbstractThe pKa‐cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pKavalues and protein electrostatics in general. The first round of the pKa‐cooperative, which challenged computational labs to carry out blind predictions against pKas experimentally determined in the laboratory of Bertrand Garcia‐Moreno, was completed and results discussed at the Telluride meeting (July 6–10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue ofPROTEINS: Structure, Function and Bioinformatics. Here, we briefly outline existing approaches for pKacalculations, emphasizing methods that were used by the participants in calculating the blind pKavalues in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pKacalculations. Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 target classification
Authors: Kinch Lisa N. , Shi Shuoyong , Cheng Hua , Cong Qian , Pei Jimin , Mariani Valerio , Schwede Torsten , Grishin Nick V. 
Published: September 2011

AbstractThe Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain‐based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence‐related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds. Proteins 2011; © 2011 Wiley‐Liss, Inc.