bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interobserver reproducibility of histologic parameters of melanoma deposits in sentinel lymph nodes
Authors: Murali Rajmohan , Cochran Alistair J. , Cook Martin G. , Hillman Joseph D. , Karim Rooshdiya Z. , Moncrieff Marc , Starz Hans , Thompson John F. , Scolyer Richard A. 
Published: August 2009

AbstractBACKGROUND:Histologic parameters of melanoma deposits in sentinel lymph nodes (SLNs) have been shown to be predictive of clinical outcome and the presence or absence of tumor in non‐SLNs, but assessment of these parameters is prone to interobserver variation.METHODS:Histologic sections of 44 SLNs containing metastatic melanoma were examined by 7 pathologists. Parameters assessed included cross‐sectional area of tumor deposits, cross‐sectional area of SLNs, percentage of SLN area involved by tumor calculated from the 2 previous parameters, estimated percentage of SLN area involved by tumor, tumor penetrative depth, location of tumor within the SLN, and presence of extracapsular spread. Levels of interobserver agreement were measured by using intraclass correlation coefficients (ICC).RESULTS:There was good to excellent interobserver agreement on measurement of quantitative parameters: maximal size of largest tumor deposits, calculated area of 3 largest tumor deposits, percentage of the area of SLN involved by tumor, and tumor penetrative depth (ICC, 0.88, 0.73, 0.68, and 0.83, respectively). There was moderate agreement on the evaluation of subcapsular versus nonsubcapsular location of tumor deposits (ICC = 0.50). Agreement on assessment of extracapsular spread was fair (ICC = 0.39).CONCLUSIONS:Assessment of some of the quantitative parameters was highly reproducible between pathologists. However, evaluation of the location of tumor deposits within SLNs and assessment of extracapsular spread was less reproducible. Clearer definitions and training can be expected to improve the reproducibility of assessment. These results have important implications for reliability and reproducibility of these parameters in staging, prediction of outcome, and clinical management of melanoma patients. Cancer 2009. © 2009 American Cancer Society.
Identification of borderline thyroid tumors by gene expression array analysis
Authors: Arora Nimmi , Scognamiglio Theresa , Lubitz Carrie C. , Moo Tracy A. , Kato Meredith A. , Zhu Baixin , Zarnegar Rasa , Chen Yao‐Tseng , Fahey Thomas J. 
Published: August 2009

AbstractBACKGROUND:A subset of follicular lesions of the thyroid is encapsulated similar to follicular adenomas but with partial nuclear features suggestive of papillary thyroid carcinoma (PTC), raising the possibility of biologically borderline tumors.METHODS:Gene expression profiling and advanced significance analyses were performed on 50 histologically unequivocal benign and malignant tumors, and a list of 61 differentially expressed genes was generated. By using this 61‐gene list, unsupervised hierarchical and K‐means cluster analyses were performed on 40 additional tumors, including 15 histologically borderline tumors, 11 benign tumors, and 14 PTCs.RESULTS:Analysis revealed 3 distinct tumor groups—benign, malignant, and intermediate. Tumors in the intermediate group (n = 15) were mostly histologic borderline tumors and had an expression profile overlapping with the benign and malignant groups. Twenty‐seven genes were expressed differentially between the benign and intermediate groups, including the cyclic AMP response element‐binding protein/p300‐interactivator with glutamic acid/aspartic acid‐rich carboxy‐terminal domain 1 or CITED1 gene and the fibroblast growth factor receptor 2 or FGFR2 gene. Fourteen genes were expressed differentially between the intermediate group and malignant tumors, notably overexpression of the met proto‐oncogene and of the high‐mobility group adenine/thymine‐hook 2 or HMGA2 gene in malignancies. Mutations of the v‐raf murine sarcoma viral oncogene homolog B1 or BRAF gene were identified in 4 of 14 malignant tumors but not in benign or intermediate tumors. Patients who had either histologically or molecularly borderline tumors did not have metastasis or recurrences.CONCLUSIONS:Gene expression profiling supported the finding that encapsulated thyroid follicular lesions with partial nuclear features of PTC are biologically borderline tumors that are distinct molecularly from benign and malignant tumors. Cancer 2009. © 2009 American Cancer Society.
Evaluating color difference equation performance incorporating visual uncertainty
Authors: Shen Shizhe , Berns Roy S. 
Published: August 2009

AbstractFive thousand randomized ellipsoids for each of 19 color centers comprising the RIT‐DuPont dataset were generated based on both the tolerance median (T50) and visual uncertainty (fiducial limits). When plotted as two‐space projections, they provided a qualitative description of the ellipsoid reliability, this reliability was dependent on visual uncertainty. The ellipsoids were considered as local color‐difference equations. STRESS was calculated for each ellipsoid, quantifying the deviation between visual color differences and numerical color differences calculated by the T50‐based ellipsoids, the randomized ellipsoids and three color‐difference equations: CIELAB, CIE94, and CIEDE2000. F‐tests comparing STRESS determined statistical significance between calculated and visual color differences. The percentage of randomized ellipsoids that were beyond the critical F values was used as a metric for determining whether a color difference equation was under‐ or over‐fitting the visual data. A nonellipsoid method and an average standard error method were developed and tested for cases when the dataset may not enable ellipsoid fitting and where uncertainty has been reported only as an average standard error. In the latter case, only equation under‐fitting could be determined. Thus visual uncertainty can be used as a criterion in both equation development and evaluation. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 375–390, 2009
Variability in estimation of suprathreshold small color differences
Authors: Kuehni Rolf G. 
Published: August 2009

AbstractIntraobserver and interobserver variability in perceptual small color difference evaluation are known but are rarely analyzed phenomena. They raise the question if humans are equipped to make reliable and uniform estimates of this kind. Data from two recent well‐controlled studies show that intraobserver and, particularly, interobserver variability are surprisingly large. The use of a gray reference scale in place of a single gray reference pair has a small normative effect on the estimate. A large interobserver variability in the estimated magnitude of chromatic differences compared with achromatic reference pairs remains, with an average ratio between largest and smallest estimate of over 3:1 and ratios for individual observers and sample pairs ranging up to 28:1. No correlation was found between the reliability of judgment and the judged magnitude of difference: highly reliable observer groups are not more consistent. Relative reliability of estimate was found inversely related to magnitude of perceived difference. Consequences of these results for the development of improved color difference formulas are discussed. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 367–374, 2009
Agent‐based simulation of an N‐person game with parabolic payoff functions
Authors: Szilagyi Miklos N. , Somogyi Iren 
Published: August 2009

AbstractWe report computer simulation experiments based on our agent‐based simulation tool to model a new N‐person game based on John Conway's Game of Life. The individual agents may choose between two behavior options: cooperation or defection. The payoff (reward/penalty) functions are given as two parabolas: one for each option. After a certain number of iterations, the behavior of the agents stabilizes to either a constant value or oscillates around such a value. The simulation's goal is to investigate the effects of intermediate behavior on a society of agents. We have performed a systematic investigation of this game for all six possible cases of the mutual positions of parabolic payoff functions crossing each other at two points:x= 0.3 and 0.7 wherexis the ratio of the cooperation choice to the total number of agents in the agent's neighborhood. The global ratiosX(t) of the total number of cooperators in the entire array of agents as functions of time (iterations) and the solutions of the gameXfinalas functions ofX0were observed for each case for Pavlovian, greedy, and conformist agents. The solutions have predictable tendencies only when the neighborhood is the entire array of greedy or conformist agents. In all other cases unexpected properties emerge. © 2009 Wiley Periodicals, Inc. Complexity, 2010
A novel scale for measuring mixed states in bipolar disorder
Authors: Cavanagh Jonathan , Schwannauer Matthias , Power Mick , Goodwin Guy M. 
Published: August 2009

AbstractObjectives: Conventional descriptions of bipolar disorder tend to treat the mixed state as something of an afterthought. There is no scale that specifically measures the phenomena of the mixed state. This study aimed to test a novel scale for mixed state in a clinical and community population of bipolar patients. Methods: The scale included clinically relevant symptoms of both mania and depression in a bivariate scale. Recovered respondents were asked to recall their last manic episode. The scale allowed endorsement of one or more of the manic and depressive symptoms. Internal consistency analyses were carried out using Cronbach alpha. Factor analysis was carried out using a standard Principal Components Analysis followed by Varimax Rotation. A confirmatory factor analytic method was used to validate the scale structure in a representative clinical sample. Results: The reliability analysis gave a Cronbach alpha value of 0.950, with a range of corrected‐item‐total‐scale correlations from 0.546 (weight change) to 0.830 (mood). The factor analysis revealed a two‐factor solution for the manic and depressed items which accounted for 61.2% of the variance in the data. Factor 1 represented physical activity, verbal activity, thought processes and mood. Factor 2 represented eating habits, weight change, passage of time and pain sensitivity. Conclusions: This novel scale appears to capture the key features of mixed states. The two‐factor solution fits well with previous models of bipolar disorder and concurs with the view that mixed states may be more than the sum of their parts. Copyright © 2009 John Wiley & Sons, Ltd.Key Practitioner Message:

There is no clinical scale that specifically measures the phenomena of the bipolar mixed state. This new scale includes clinically relevant symptoms of both mania and depression in a bivariate scale. The scale appears to capture key features of the mixed state and endorses the view that mixed states may be more than the sum of their parts.
Multispot live‐image autofocusing for high‐throughput microscopy of fluorescently stained bacteria
Authors: Zeder M. , Pernthaler J. 
Published: August 2009

AbstractScreening by automated high‐throughput microscopy has become a valuable research tool. An essential component of such systems is the autonomous acquisition of focused images. Here we describe the implementation of a high‐precision autofocus routine for imaging of fluorescently stained bacteria on a commercially available microscope. We integrated various concepts and strategies that together substantially enhance the performance of autonomous image acquisition. These are (i) nested focusing in bright‐field and fluorescence illumination, (ii) autofocusing by continuous life‐image acquisition during movement in z‐direction rather than at distinct z‐positions, (iii) assessment of the quality and topology of a field of view (FOV) by multispot focus measurements, and (iv) acquisition of z‐stacks and application of an extended depth of field algorithm to compensate for FOV unevenness. The freely provided program and documented source code allow ready adaptation of the here presented approach to various platforms and scientific questions. © 2009 International Society for Advancement of Cytometry
Alternative mRNA splicing creates transcripts encoding soluble proteins from most LILR genes
Authors: Jones Des C. , Roghanian Ali , Brown Damien P. , Chang Chiwen , Allen Rachel L. , Trowsdale John , Young Neil T. 
Published: August 2009

AbstractLeucocyte Ig‐like receptors (LILR) are a family of innate immune receptors expressed on myeloid and lymphoid cells that influence adaptive immune responses. We identified a common mechanism of alternative mRNA splicing, which generates transcripts that encode soluble protein isoforms of the majority of human LILR. These alternative splice variants lack transmembrane and cytoplasmic encoding regions, due to the transcription of a cryptic stop codon present in an intron 5′ of the transmembrane encoding exon. The alternative LILR transcripts were detected in cell types that express their membrane‐associated isoforms. Expression of the alternative LILRB1 transcript in transfected cells resulted in the release of a soluble ∼65 Kd LILRB1 protein into culture supernatants. Soluble LILRB1 protein was also detected in the culture supernatants of monocyte‐derived DC. In vitro assays suggested that soluble LILRB1 could block the interaction between membrane‐associated LILRB1 and HLA‐class I. Soluble LILRB1 may act as a dominant negative regulator of HLA‐class I‐mediated LILRB1 inhibition. Soluble isoforms of the other LILR may function in a comparable way.
T cells require Foxo1 to populate the peripheral lymphoid organs
Authors: Gubbels Bupp Melanie R. , Edwards Bonnie , Guo Caiying , Wei Datsen , Chen Gang , Wong Brian , Masteller Emma , Peng Stanford L. 
Published: August 2009

AbstractForkhead transcription factors play critical roles in leukocyte homeostasis. To study further the immunological functions of Foxo1, we generated mice that selectively lack Foxo1 in T cells (Foxo1flox/flox Lck.cre+conditional knockout mice (cKO)). Although thymocyte development appeared relatively normal, Foxo1 cKO mice harbored significantly increased percentages of mature single positive T cells in the thymus as compared with WT mice, yet possessed smaller lymph nodes and spleens that contained fewer T cells. Foxo1 cKO T cells were not more prone to apoptosis, but instead were characterized by a CD62Llo CCR7lo CD44hi surface phenotype, a poorly populated lymphoid compartment in the periphery, and were relatively refractory to TCR stimulation, all of which were associated with reduced expression of Sell, Klf2, Ccr7, and S1pr1. Thus, Foxo1 is critical for naïve T cells to populate the peripheral lymphoid organs by coordinating a molecular program that maintains homeostasis and regulates trafficking.
ULBP6/RAET1L is an additional human NKG2D ligand
Authors: Eagle Robert A. , Traherne James A. , Hair James R. , Jafferji Insiya , Trowsdale John 
Published: August 2009

AbstractTo date five ULBP/RAET (UL16‐binding protein, also known as retinoic acid early transcript) genes, encoded on human chromosome 6q24.2‐q25.3, have been shown to encode ligands of the activating immunoreceptor NKG2D. Here, we show that a sixth gene, ULBP6/RAET1L, is a polymorphic locus that expresses a functional transcript. ULBP6 had a more restricted expression profile in cell lines and primary human tissues than other NKG2D ligands, but expression was detected in several human papillomavirus‐positive cervical carcinoma cell lines and was inducible on infection with human CMV. ULBP6 bound to recombinant NKG2D as well as the human CMV immune evasion molecule UL16. By confocal microscopy we show that UL16 retains ULBP6 inside the cell, preventing it from reaching the cell surface. Expression of ULBP6 on target cells induced a significant increase in NK‐cell killing. Comparison of ULBP6 with ULBP4 and ULBP5 indicated that differences in recombinant NKG2D binding correlated with differences in NK‐cell activation.
Conformationally Restricted Nucleocyclitols: a Study into their Conformational Preferences and Supramolecular Architecture in the Solid State
Authors: Mehta Goverdhan , Talukdar Pinaki , Pullepu Venkatesh , Sen Saikat 
Published: August 2009

AbstractWith the intent of probing the feasibility of employing annulation as a tactic to engender axial rich conformations in nucleoside analogues, two adenine‐derived, “conformationally restricted” nucleocylitols, 9 and 10, have been conceptualized as representatives of a hitherto unexplored class of nucleic acid base‐cyclitol hybrids. A general synthetic strategy, with an inherent scope for diversification, allowed rapid functionalization of indane and tetralin to furnish 9 and 10 respectively in fair yield. Single‐crystal X‐ray diffraction analysis revealed that the two nucleocyclitols under study, though homologous, present completely dissimilar modes of molecular packing, marked, in particular, by the nature of involvement of the adenynyl NH2 group in the supramolecular assembly. In addition, the crystal structures of 9 and 10 also exhibit two different conformations of the functionalized cyclohexane ring. Thus, while the six‐membered carbocycle in cyclopenta‐annulated 9 exists in the expected chair (C) conformation that in cyclohexaannulated 10, which crystallizes as a dihydrate, shows an unusual twist‐boat (TB) conformation. From a close analysis of the 1HNMR spectroscopic data recorded for 9 and 10 in CD3OD, it was possible to put forth a putative explanation for the uncanny conformational preferences of crystalline 9 and 10.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Catalytic hydroprocessing of biomass fast pyrolysis bio‐oil to produce hydrocarbon products
Authors: Elliott Douglas C. , Hart Todd R. , Neuenschwander Gary G. , Rotness Leslie J. , Zacher Alan H. 
Published: August 2009

AbstractCatalytic hydroprocessing has been applied to biomass fast pyrolysis liquid product (bio‐oil) in a bench‐scale continuous‐flow fixed‐bed reactor system. The intent of the research was to develop process technology to convert the bio‐oil into a petroleum refinery feedstock to supplement fossil energy resources and to displace imported feedstock. The project was a cooperative research and development agreement among UOP LLC, the National Renewable Energy Laboratory and the Pacific Northwest National Laboratory (PNNL). This article is focused on the process experimentation and product analysis undertaken at PNNL.This article describes the experimental methods used and relates the results of the product analyses. A range of catalyst formulations were tested over a range of operating parameters including temperature, pressure, and flow rate with bio‐oil derived from several different biomass feedstocks. Effects of liquid hourly space velocity and catalyst bed temperature were assessed. Details of the process results were presented included product yields and hydrogen consumption. Detailed analysis of the products were provided including elemental composition, chemical functional type determined by mass spectrometry, and product descriptors such as density, viscosity, and total acid number. In conclusion, this article provides an understanding of the efficacy of hydroprocessing as applied to bio‐oil. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Thermal pretreatment of lignocellulosic biomass
Authors: Yan Wei , Acharjee Tapas C. , Coronella Charles J. , Vásquez Victor R. 
Published: August 2009

AbstractTorrefaction is a process to convert diverse lignocellulosic biomass feedstocks into an energy dense homogeneous solid, a pretreatment for subsequent thermochemical conversion. Loblolly pine was treated by wet torrefaction (hot compressed water, 200–260°C) and dry torrefaction (nitrogen, 250–300°C), with mass yield of solid product ranging between 57 and 89%, and energy densification to 108–136% of the original feedstock. The solid product has been characterized, including proximate analysis, fiber analysis, ultimate analysis, and equilibrium moisture. In both dry and wet torrefaction, increasing temperature results in decreased mass yield and increased energy densification, and results in a solid with increased carbon content, decreased oxygen content, and decreased volatiles. The biomass is transformed into a fuel similar to a low‐rank coal. Generally, the wet torrefaction process produces a solid with greater energy density than dry torrefaction, with the same mass yield. The fiber analysis indicates that hemicellulose is quickly removed during wet torrefaction, and the solid product contains substantial quantities of aqueous soluble compounds. The equilibrium moisture content of solids produced by both processes is somewhat decreased from that of the biomass feedstock, indicating a hydrophobic solid suitable for storage and transportation. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Equilibrium pricing of contingent claims in tradable permit markets
Authors: Kijima Masaaki , Maeda Akira , Nishide Katsumasa 
Published: August 2009

AbstractWe advance a model of the tradable permit market and derive a pricing formula for contingent claims traded in the market in a general equilibrium framework. It is shown that prices of such contingent claims exhibit significantly different properties from those in the ordinary financial markets. In particular, if the social cost function kinks at some level of abatement, the forward price, as well as the spot price, can be subject to the so‐called price spike. However, this price‐spike phenomenon can be weakened if a system of banking and borrowing is properly introduced. © 2009 Wiley Periodicals, Inc. Jrl Fut Mark 30:559–589, 2010
Design in tunnelling, structural design methods for the inner lining
Authors: Stadelmann Rolf , Pfeffer Alfred , Wei Zhang Qing 
Published: August 2009

AbstractThe following article deals with the design of the inner lining of the Gotthard Base Tunnel and the determination of the design loads. The determination of the loads is based on the geological conditions encountered and takes into account the installed support measures and the deformation, occurring. The observational method also makes a considerable contribution. Together with the criteria stated above, it proved possible to find a definition of the hazard scenarios and the resulting rock pressure in order to optimise the design of the inner lining.Der folgende Beitrag behandelt die Dimensionierung der Innenschale des Gotthard Basistunnels und die Ermittlung der hierfür anzusetzenden Lasten. Die Lastenermittlung basiert auf der angetroffenen Geologie unter Berücksichtigung der eingebauten Sicherungsmittel und der eingetretenen Deformationen. Einen nicht unwesentlichen Beitrag dazu leistete die Beobachtungsmethode. Zusammen mit den vorgenannten Kriterien gelang es, eine Definition der Gefährdungsbilder und den damit gegebenen Gebirgsdrücken zu finden, um schließlich die Dimensionierung der Innenschale zu optimieren.
Performance of hemisphere algorithm for fast form factor calculation
Authors: Yamada Noboru , Shinoda Tomoaki , Takizawa Hiroyuki 
Published: August 2009

AbstractA fast and accurate algorithm is required for carrying out radiative heat transfer simulations designing thermally efficient devices. This paper describes the performance of the hemisphere algorithm, which was originally developed for fast form factor calculation for obtaining photorealistic three‐dimensional computer graphics. We compare the performance of the hemisphere algorithm with that of two conventional algorithms that are widely used for radiative heat transfer simulations. The hemisphere algorithm is found to be significantly faster than the other algorithms, but it has an absolute error of 1.0×10−5. In addition, the result indicates that the hemisphere algorithm is suitable for simulating the trial and error process in the practical analysis of large‐scale models due to its tolerable visualization of form factor distribution. © 2009 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20259