bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth plate abnormalities in pediatric cancer patients undergoing phase 1 anti‐angiogenic therapy: A report from the children's oncology group phase I consortium
Authors: Voss Stephan D. , Glade‐Bender Julia , Spunt Sheri L. , DuBois Steven G. , Widemann Brigitte C. , Park Julie R. , Leary Sarah E. S. , Nelson Marvin D. , Adamson Peter C. , Blaney Susan M. , Weigel Brenda 
Published: September 2014

BackgroundPre‐clinical studies suggest that anti‐angiogenic agents may be toxic to the developing growth plate. The purpose of this study was to evaluate the incidence of growth plate abnormalities in children with refractory cancer undergoing anti‐angiogenic therapy.ProcedureTargeted radiographic studies from 53 subjects enrolled on six separate Children's Oncology Group Phase 1 and Pilot Consortium clinical trials evaluating new anti‐cancer agents interfering with angiogenesis were reviewed. Subjects received tyrosine kinase inhibitors with anti‐angiogenic effects (n = 35), monoclonal antibodies targeting vascular endothelial growth factor (VEGF) (n = 13), or angiopoietin (n = 5). Radiographs of their distal femur/proximal tibia were obtained at baseline. Follow‐up radiographs were obtained after odd‐numbered treatment cycles in patients with open growth plates who did not experience disease progression prior to cycle 3.ResultsBaseline and follow‐up growth plate radiographs were acquired in 48/53 (90%) of patients. Five patients (9.4%), all of whom received a specific VEGF/VEGFR blocking agent (sunitinib [n = 1] or pazopanib [n = 4]), had growth plate abnormalities. Four patients had growth plate widening that was apparent on at least two successive radiographs, but was not confirmed by MRI. The fifth patient had progressive growth plate widening and evidence of physeal cartilage hypertrophy on MRI. Subsequent off treatment radiographs showed that the growth plate changes were reversible.ConclusionGrowth plate abnormalities occur in a small, but relevant number of patients undergoing anti‐angiogenic therapy. These results support the need for growth plate monitoring in children with open growth plates who are receiving anti‐angiogenic therapy, and for improved methods to assess toxicity of anti‐angiogenic agents to the developing skeleton. Pediatr Blood Cancer 2015;62:45–51. © 2014 Wiley Periodicals, Inc.
Second malignancies in patients with neuroblastoma: The effects of risk‐based therapy
Authors: Applebaum Mark A. , Henderson Tara O. , Lee Sang Mee , Pinto Navin , Volchenboum Samuel L. , Cohn Susan L. 
Published: September 2014

BackgroundTo investigate the incidence of second malignant neoplasms (SMN) for patients with neuroblastoma, we analyzed patients from the SEER database according to three treatment eras (Era 1: 1973–1989, Era 2: 1990–1996, and Era 3: 1997–2006) corresponding to the introduction of multi‐agent chemotherapy, risk‐based treatment, and stem cell transplant.ProceduresThe SEER database was mined for all patients with neuroblastoma or ganglioneuroblastoma. Cumulative incidence of SMN was calculated with death as a competing risk. A poisson regression model was used to estimate incidence rate ratios and 95% confidence intervals to compare the rates of SMN between patients in different Eras.ResultsThe analytic cohort included 2,801 patients. Thirty‐four patients developed a SMN, accounting for 1.2% of all patients. Of the patients who developed a SMN, 47.1% received radiation for their primary neuroblastoma. Fourteen of the SMN were carcinomas, and 10 were hematologic malignancies, with six cases of acute myelogenous leukemia. There was no difference in the incidence of SMN in Era 1 compared to Era 3 (P = 0.48). The cumulative incidence of SMN at 30 years for high‐risk patients was 10.44% (95% CI 3.98–20.52%) compared to 3.57% (95% CI 1.87–6.12%) for non‐high‐risk patients (P < 0.001).ConclusionsThis study showed no increase in the incidence of SMNs for children treated in the most recent treatment era as compared to earlier Eras. However, as the risk for developing SMN does not plateau, the number of SMNs will likely continue to rise in the cohort of patients treated after 1996. Comprehensive follow‐up care for these survivors will be important. Pediatr Blood Cancer 2015;62:128–133. © 2014 Wiley Periodicals, Inc.
Structure of a partially unfolded form of Escherichia coli dihydrofolate reductase provides insight into its folding pathway
Authors: Kasper Joseph R. , Liu Pei‐Fen , Park Chiwook 
Published: September 2014

AbstractProteins frequently fold via folding intermediates that correspond to local minima on the conformational energy landscape. Probing the structure of the partially unfolded forms in equilibrium under native conditions can provide insight into the properties of folding intermediates. To elucidate the structures of folding intermediates of Escherichia coli dihydrofolate reductase (DHFR), we investigated transient partial unfolding of DHFR under native conditions. We probed the structure of a high‐energy conformation susceptible to proteolysis (cleavable form) using native‐state proteolysis. The free energy for unfolding to the cleavable form is clearly less than that for global unfolding. The dependence of the free energy on urea concentration (m‐value) also confirmed that the cleavable form is a partially unfolded form. By assessing the effect of mutations on the stability of the partially unfolded form, we found that native contacts in a hydrophobic cluster formed by the F‐G and Met‐20 loops on one face of the central β‐sheet are mostly lost in the partially unfolded form. Also, the folded region of the partially unfolded form is likely to have some degree of structural heterogeneity. The structure of the partially unfolded form is fully consistent with spectroscopic properties of the near‐native kinetic intermediate observed in previous folding studies of DHFR. The findings suggest that the last step of the folding of DHFR involves organization in the structure of two large loops, the F‐G and Met‐20 loops, which is coupled with compaction of the rest of the protein.
Effects of active site cleft residues on oligosaccharide binding, hydrolysis, and glycosynthase activities of rice BGlu1 and its mutants
Authors: Pengthaisong Salila , Ketudat Cairns James R. 
Published: September 2014

AbstractRice BGlu1 (Os3BGlu7) is a glycoside hydrolase family 1 β‐glucosidase that hydrolyzes cellooligosaccharides with increasing efficiency as the degree of polymerization (DP) increases from 2 to 6, indicating six subsites for glucosyl residue binding. Five subsites have been identified in X‐ray crystal structures of cellooligosaccharide complexes with its E176Q acid‐base and E386G nucleophile mutants. X‐ray crystal structures indicate that cellotetraose binds in a similar mode in BGlu1 E176Q and E386G, but in a different mode in the BGlu1 E386G/Y341A variant, in which glucosyl residue 4 (Glc4) interacts with Q187 instead of the eliminated phenolic group of Y341. Here, we found that the Q187A mutation has little effect on BGlu1 cellooligosaccharide hydrolysis activity or oligosaccharide binding in BGlu1 E176Q, and only slight effects on BGlu1 E386G glycosynthase activity. X‐ray crystal structures showed that cellotetraose binds in a different position in BGlu1 E176Q/Y341A, in which it interacts directly with R178 and W337, and the Q187A mutation had little effect on cellotetraose binding. Mutations of R178 and W337 to A had significant and nonadditive effects on oligosaccharide hydrolysis by BGlu1, pNPGlc cleavage and cellooligosaccharide inhibition of BGlu1 E176Q and BGlu1 E386G glycosynthase activity. Hydrolysis activity was partially rescued by Y341 for longer substrates, suggesting stacking of Glc4 on Y341 stabilizes binding of cellooligosaccharides in the optimal position for hydrolysis. This analysis indicates that complex interactions between active site cleft residues modulate substrate binding and hydrolysis.
Effect of nitrogen mole fraction on hydrogenated amorphous silicon nitride deposited by DC magnetron sputtering: transition between metallic and reactive sputtering
Authors: Mokeddem Kamel , Kechouane Mohamed 
Published: September 2014

AbstractThe hydrogenated amorphous silicon nitride thin films are deposited by DC magnetron sputtering in argon, molecular hydrogen and nitrogen plasma mixture. The films are deposited at 150 °C and at 130 W sputtering power with wide range of nitrogen mole fraction. The plasma is characterized by the target voltage measurement. The samples are characterized by the optical transmission measurements and the physicochemical structure is studied by the FTIR absorption spectroscopy. When the nitrogen mole fraction increases from 0.075 to 0.24 the target voltage decrease from 413 to 325 V and increases suddenly to 450 V when nitrogen mole fraction increases to 0.69. The decrease of target voltage may be due to the transition from metallic to reactive sputtering process and its increase can be explained by the implantation of reactive ions in the target. Sputtering rate and refractive index decrease respectively from 8.33 to 1.73 Å/sec and from 2.52 to 1.68 with nitrogen mole fraction. The value of refractive index at critical nitrogen mole fraction is about 1.8. When the nitrogen mole fraction increases the frequency related to Si‐H band, on FTIR spectrum, shift from 2097 cm‐1 to reach 2209 cm‐1 at the critical nitrogen mole fraction. Thereafter it varies sharply to 2190 cm‐1 and remains constant. A sudden change is observed on the sputtering rate, on the intensity of the band attributed to the stretching vibration of N‐H and Si‐H bonds. From these results we believe that the stoichiometric composition is reached at the critical nitrogen mole fraction and beyond this the deposited films are rich of nitrogen and hydrogen. This is consistent with the explanation given of the variation of the target voltage. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Distal regeneration involves the age dependent activity of branchial sac stem cells in the ascidian Ciona intestinalis
Authors: Jeffery William R. 
Published: September 2014

AbstractTunicates have high capacities for regeneration but the underlying mechanisms and their relationship to life cycle progression are not well understood. Here we investigate the regeneration of distal structures in the ascidian tunicate Ciona intestinalis. Analysis of regenerative potential along the proximal−distal body axis indicated that distal organs, such as the siphons, their pigmented sensory organs, and the neural complex, could only be replaced from body fragments containing the branchial sac. Distal regeneration involves the formation of a blastema composed of cells that undergo cell proliferation prior to differentiation and cells that differentiate without cell proliferation. Both cell types originate in the branchial sac and appear in the blastema at different times after distal injury. Whereas the branchial sac stem cells are present in young animals, they are depleted in old animals that have lost their regeneration capacity. Thus Ciona adults contain a population of age‐related stem cells located in the branchial sac that are a source of precursors for distal body regeneration.
Pupillometry
Authors: Sirois Sylvain , Brisson Julie 
Published: September 2014

Pupillometry is the study of changes in the diameter of the pupil as a function of cognitive processing. This review paper provides a brief historical overview of the study of pupillometry in cognitive science. The physiology of pupillary responses is introduced, leading to an outline of early pupillometry work, which began with the seminal work of Hess and Polt in the 1960s. The paper then presents a broad review of contemporary research in cognitive sciences that relies on pupillometry. This review is organized around five general domains, namely perception, language processing, memory and decision making, emotion and cognition, and cognitive development. In order to illustrate the nature of the method, and the challenges of analysis, the next section of the review details the process of compiling, processing, and analyzing data from a simple, typical pupillometry study. WIREs Cogn Sci 2014, 5:679–692. doi: 10.1002/wcs.1323This article is categorized under:

Psychology > Attention
Psychology > Perception and Psychophysics
Psychology > Theory and Methods
Biplots: quantitative data
Authors: Gower John C. , Le Roux Niël J. , Gardner‐Lubbe Sugnet 
Published: September 2014

AbstractBiplots provide visualizations of two things, usually, but not necessarily, in two dimensions. This paper deals exclusively with biplots for quantitative data X; qualitative data or data in the form of counts will be addressed in a subsequent paper. Data X may represent either (1) a matrix with n rows representing samples/cases and columns representing p quantitative variables or (2) a two‐way table whose rows and columns both represent classifying variables. Data sets of both types (1) and (2) are considered. Plotting symbols are usually points (typically for samples and distinguished by shape and/or color) and lines (typically for variables which may be calibrated or treated as arrowed vectors). Furthermore, variables may be nonlinear in both regularity of calibration and/or curvature. Interpretation is through distance, inner‐products, and sometimes area. Biplots may be improved by judicious shifts of axes, by scaling and by rotation. Nearly always, biplots give approximations to X and measures, incorporated in the biplot, expressing the degree of approximation are discussed. These aspects are illustrated with reference to examples from principal component analysis, nonlinear biplots, biplots for biadditive models, canonical variate analysis and the analysis of distance between grouped samples. WIREs Comput Stat 2015, 7:42–62. doi: 10.1002/wics.1338This article is categorized under:

Statistical Learning and Exploratory Methods of the Data Sciences > Clustering and Classification
Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Statistical and Graphical Methods of Data Analysis > Statistical Graphics and Visualization
Hydrogen Bonds directed 2D→3D Interdigitated Silver(I) Coordination Polymer: Synthesis, Structure, and Catalytic Property
Authors: Liu Haiyan , Ji Shujing , Hao Yunhui 
Published: September 2014

Abstract A new silver(I) compound, namely [Ag(MA)(FA)0.5]n (1) (MA = melamine, H2FA = fumaric acid), was synthesized via the reactions of AgNO3, MA, and H2FA. Single crystal X‐ray diffraction analysis reveals that compound 1 is 2D undulated layer, which further extended into a 2D→3D interdigitated supramolecular framework by intermolecular hydrogen bonds. In addition, the catalytic property on degradation of methyl orange for compound 1 in a Fenton‐like process was also investigated.
Bi2Pt(hP9) by Low‐Temperature Reduction of Bi13Pt3I7: Reinvestigation of the Crystal Structure and Chemical Bonding Analysis
Authors: Kaiser Martin , Baranov Alexey I. , Ruck Michael 
Published: September 2014

AbstractBi2Pt(hP9) or γ‐Bi2Pt is a high‐temperature modification, which is metastable below 420 °C. We obtained Bi2Pt(hP9) by reducing the layered bismuth subiodide Bi13Pt3I7with a high excess ofn‐butyllithium at 70 °C. The crystals endure the heterogeneous reaction and the enormous mass loss. X‐ray diffraction on a small single‐crystal revealed that Bi2Pt(hP9) crystallizes in the acentric trigonal space groupP31m(no. 157) witha= 657.30(7) pm andc= 616.65(7) pm. Although structure and stacking of the layers of edge‐sharing [PtBi6/3] octahedra resemble the 1H‐polytype of CdI2, Pt–Pt bonding interactions cause distortions that introduce polarity to the structure. Quantum chemical calculations followed by real‐space bonding analysis reveal polar covalent bonding between bismuth and platinum atoms that is not limited to nearest neighbor atoms but is essentially delocalized. The Pt–Pt bond strength in Bi2Pt(hP9) is not much weaker than in the element.
Formalizing provable anonymity in Isabelle/HOL
Authors: Li Yongjian , Pang Jun 
Published: September 2014

Abstract
We formalize in a theorem prover the notion of provable anonymity. Our formalization relies on inductive definitions of message distinguishing ability and observational equivalence on traces observed by the intruder. Our theory differs from its original proposal and essentially boils down to the inductive definition of distinguishing messages with respect to a knowledge set for the intruder. We build our theory in Isabelle/HOL to achieve a mechanical framework for the analysis of anonymity protocols. Its feasibility is illustrated through two case studies of the Crowds and Onion Routing protocols.
Implementation of a Standardized HIPEC Protocol Improves Outcome for Peritoneal Malignancy
Authors: Kuijpers Anke M. J. , Aalbers Arend G. J. , Nienhuijs Simon W. , de Hingh Ignace H. J. T. , Wiezer Marinus J. , van Ramshorst Bert , van Ginkel Robert J. , Havenga Klaas , Heemsbergen Wilma D. , Hauptmann Michael , Verwaal Victor J. 
Published: September 2014

AbstractBackgroundExperience with Cytoreductive Surgery (CRS) and Hyperthermic Intraperitoneal Chemotherapy (HIPEC) in a pioneer hospital resulted in a treatment protocol that has become the standard in the Netherlands. Outcome of CRS and HIPEC was reviewed to assure differences between the pioneer phase and the period wherein the Dutch HIPEC protocol was clinically implemented.MethodsThe first consecutive 100 CRS and HIPEC procedures performed in the Netherlands were included as pioneer cohort (1995–1999). Two‐hundred and seventy‐two procedures that were performed in three participating HIPEC centres after the implementation of the Dutch HIPEC protocol were included as the implementation cohort (2005–2012). Another 100 recent patients of the first centre were included as a control group (2009–2011). Indications for the CRS and HIPEC treatment were peritoneal carcinomatosis (PC) from colorectal carcinoma and pseudomyxoma peritonei (PMP).ResultsOf the 472 included procedures, 327 (69 %) procedures were performed for PC from colorectal carcinoma and 145 for PMP (31 %). Compared with the implementation phase, the pioneer phase was characterized by more affected abdominal regions (mean 4.3 vs. 3.5, p < 0.001), more resections (mean 3.8 vs. 3.4, p < 0.001), less macroscopic radical cytoreductions (66 vs. 86 %, p < 0.001) and more patients with major morbidity (grade III–V) (64 vs. 32 %, p < 0.001). Other determinants of morbidity were high tumour load and multiple organ resections. Outcome of the implementation phase was similar to the control group.ConclusionsThis study determined that outcome had improved ever since the Dutch HIPEC protocol has been implemented based on completeness of cytoreduction and decreasing morbidity.
Transplanting native woody legumes: a suitable option for the revegetation of coastal dunes
Authors: Rodríguez‐Echeverría Susana , Roiloa Sergio R. , de la Peña Eduardo , Crisóstomo João A. , Nabais Cristina 
Published: September 2014

AbstractAcacia longifolia is an invasive woody legume in many coastal sand dunes ecosystems around the world. A useful option to aid in the restoration of invaded areas after acacia removal is the revegetation of the newly open areas using appropriate native dune plants. A field experiment was performed to determine whether two shrubby legumes native to European Atlantic coastal dunes, Cytisus grandiflorus (Brot.) DC. and Ulex europaeus europaeus subsp. latebracteatus (Mariz) Rothm., are suitable to revegetate areas formerly invaded by A. longifolia. Plants of both species were grown for 5 months in a greenhouse and subsequently transplanted to three sites in a coastal dune ecosystem. We monitored survival and growth during 21 months. The effect of soil fertility at the nursery and of root nodulation on the performance of these species in the field was also analyzed. Soil fertility and nodulation had a significant effect on plant growth at the nursery, but only the symbiosis with root nodulating bacteria had a significant positive effect on the survival of both native legumes in the field and on final plant height of U. europaeus plants. We conclude that (1) both native legumes can successfully establish on sites where A. longifolia has been previously removed, thus providing a suitable tool to help in the restoration of invaded areas, and (2) the symbiosis with root nodulating bacteria is crucial for plant performance in the field.
Barriers to energy efficiency in shipping
Authors: Johnson Hannes , Andersson Karin 
Published: September 2014

Abstract
The shipping industry shows potential for improvements in energy efficiency. Nonetheless, shipping companies appear reluctant to adopt these seemingly cost-efficient technical and operational measures aiming at reducing energy costs. Such phenomenon is not specific to the shipping industry and is commonly referred to as the energy efficiency gap. Decades of research in other sectors have contributed to the development of taxonomy of economic, organizational and psychological barriers that determine energy efficiency gaps through the use of a variety of research frameworks. This article aims to apply this research in the shipping context through interviews and review of existing literature and applications from other industries, with the objective of providing useful insight for shipping managers. The article discusses examples of barriers that are typical to shipping and that are related to information asymmetries and power structures within organizations. Managers of shipping firms are encouraged to look through their organizations in search of principal agent problems and power structures among the possible causes for energy efficiency gaps in their companies’ operations and possibly strive towards organizational change.
EU protection is inadequate for a declining flyway population of Black-tailed GodwitLimosa limosa: mismatch between future core breeding areas and existing Special Protection Areas
Authors: VAN DER VLIET ROLAND E. , OQUIÑENA VALLUERCA IMANOL , VAN DIJK JERRY , WASSEN MARTIN J. 
Published: September 2014

SummaryThis study analyses whether effective conservation of Black-tailed GodwitLimosa limosabreeding populations in the Netherlands can be achieved through the EU network of Special Protection Areas (SPAs). An internationally important number of pairs of Black-tailed Godwit breeds in the Netherlands but the breeding population is declining steeply and is, in effect, unprotected, as the Netherlands has not designated SPAs for it. To contribute to firmer and more efficient protection of the Black-tailed Godwit, we set out to identify the core areas in the Netherlands where this species is expected to breed in 2020. On the basis of an optimal combination of three main habitat requirements (groundwater level, land-use and openness of the landscape) we identified five core areas in lower-lying (western) Netherlands: Zuidwest Friesland, Waterland, the IJssel delta area, Arkemheen and Eem polders, and Groene Hart. Because these areas are currently not designated for the breeding period of Black-tailed Godwit within the SPA network, the protection of this flagship species of Dutch meadows could be at risk. It seems likely that the Black-tailed Godwit population will continue to decline, with the result that the Netherlands will breach several policy commitments for the conservation of this species.