bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matched study of three methods for palliation of malignant pyloroduodenal obstruction
Authors: Mittal A , Windsor J , Woodfield J , Casey P , Lane M 
Published: January 2004

Abstract

Background
The traditional management of pyloroduodenal obstruction is open gastrojejunostomy (OGJ). More recently laparoscopic gastrojejunostomy (LGJ) and endoscopic stenting (ES) have been introduced. The aim of this study was to evaluate the three approaches to the palliation of malignant pyloroduodenal obstruction.

Methods
All patients who underwent surgery (open and laparoscopic) for malignant pyloroduodenal obstruction at Auckland City Hospital between 1989 and 2002 inclusive were identified from International Classification of Diseases (ICD) 10 codes and from the Otago Surgical Audit Database. Patients who had an endoscopic stent were identified from the Endoscribe database. A review of medical records was conducted and data recorded in a structured pro forma. There were 181 patients with malignant pyloroduodenal obstruction of whom 56 patients had OGJ, 14 had LGJ and 16 had ES. Patients in the LGJ and ES groups were matched with those who underwent OGJ with respect to American Society of Anesthesiologists (ASA) grade (I–V), age (within 10 years) and level of obstruction (pylorus, first part of duodenum D1, D2, D3 and D4). The primary outcomes compared between the groups were time to starting free oral fluids and light diet, length of stay and survival.

Results
There were no significant differences in age, sex, ASA grade and level of obstruction between the matched OGJ (n = 16), LGJ (n = 14) and ES (n = 16) groups. There was a significant reduction in time to starting free oral fluids and light diet, and length of stay after the procedure, in the ES group. Patients who underwent surgical palliation of the obstruction had significantly more complications than those who underwent stenting (P = 0·016). There were no significant differences in requirement for biliary drainage either before or after the procedure between the three groups. Survival was shortest in the ES group.

Conclusion
This matched study showed significant advantages for ES compared with OGJ and LGJ in the palliation of malignant pyloroduodenal obstruction.
Carcinoma showing thymic-like elements—a rare malignancy of the thyroid gland
Authors: Roka S , Kornek G , Schüller J , Ortmann E , Feichtinger J , Armbruster C 
Published: January 2004

Abstract

Background
Carcinoma showing thymic-like elements (CASTLE) is a rare tumour of the thyroid of thymic origin. The histological appearance of this tumour may be similar to that of squamous cell carcinoma of the thyroid, but outcome associated with CASTLE is more favourable.

Methods
A systematic literature review was conducted for case reports on CASTLE. A text word search of the Medline database was made with a manual search of the citations from these references. Twenty-two case reports were found.

Results
In five patients with tumour-negative lymph nodes no local or distant recurrence was observed. Seventeen patients had unknown or involved lymph nodes. Two patients were excluded from further study: one had no follow-up and one was treated by irradiation only. Of the remaining 15, six had local, three had distant and two had local and distant recurrence. In patients with involved or unknown lymph node status, local recurrence was noted in one of five patients treated by surgery and irradiation, and in seven of ten patients treated by surgery alone. Irradiation or systemic chemotherapy was given to four patients with recurrent tumours, with variable response.

Conclusion
CASTLE with tumour-negative lymph nodes has a low risk of recurrence and surgery without adjuvant therapy is sufficient. Radiotherapy seems indicated when lymph nodes are tumour positive and can be effective for recurrent tumours. In selected patients surgery for recurrent tumour can improve quality of life and outcome.
Construction of an Artificial Receptor Protein (“Anticalin”) Based on the Human Apolipoprotein D
Authors: Vogt Martin , Skerra Arne 
Published: January 2004

AbstractHuman apolipoprotein D (ApoD) is a prominent member of the lipocalin family of proteins and transports arachidonic acid and progesterone in various body fluids. Lipocalins share a structurally conserved β barrel as their central folding unit, which supports a set of four hypervariable loops that form the entrance to the ligand pocket. Based on this structural pattern ApoD was employed as a scaffold for the combinatorial design of artificial receptor proteins termed anticalins. After randomization of 24 amino acids located within the loop region, several ApoD variants were selected against hemoglobin, a biochemically well‐characterized model target, by using bacterial phagemid display and colony screening. One variant, dubbed HbgA, was further investigated by surface plasmon resonance interaction analysis and found to complex hemoglobin specifically and with a dissociation constant of about 2 μM. While our previous work on the structurally related insect bilin‐binding protein was focused on the generation of binding activity towards low‐molecular‐weight ligands, this study demonstrates for the first time that a lipocalin can also be tailored to recognize a protein target. The fact that even a human member of this protein family has now been successfully recruited for anticalin construction opens the possibility for future application of such engineered lipocalins as target‐recognition vehicles in medical therapy.
Addressing the Challenge of Changing the Specificity of RNase T1 with Rational and Evolutionary Approaches
Authors: Struhalla Marc , Czaja Rico , Hahn Ulrich 
Published: January 2004

AbstractAlthough ribonuclease T1 (RNase T1) is one of the best‐characterized proteins with respect to structure and enzymatic action, numerous attempts at altering the specificity of the enzyme to cleave single‐stranded RNA at the 3′‐side of adenylic instead of guanylic residues by rational approaches have failed so far. Recently we generated and characterized the RNase T1 variant RV with a 7200‐fold increase in adenylyl‐3′,5′‐cytidine (ApC)/guanylyl‐3′,5′‐cytidine (GpC) preference, with the guanine‐binding loop changed from 41‐KYNNYE‐46 (wt) to 41‐EFRNWN‐46. Now we have introduced the asparagine residue at position 46 of the wild‐type enzyme as a single‐point mutation in variant E46N and in combination with the Y45W exchange also occurring in RV. Both variants show an improved ApC/GpC preference with a 1450‐fold increase for E46N and a 2100‐fold increase for Y45W/E46N in comparison to wild‐type activity. We also addressed the challenge of altering enzyme specificity with an evolutionary approach. We have randomly introduced point mutations into the RNase T1 wild‐type gene and into the gene of the variant RV with different mutation rates. Altogether we have screened about 100 000 individual clones for activity on RNase indicator plates; 533 of these clones were active. A significant change in substrate specificity towards an ApC preference could not be observed for any of these active variants; this demonstrated the magnitude of the challenge to alter the specificity of this evolutionary perfected enzyme.
Learning from Directed Evolution: Theoretical Investigations into Cooperative Mutations in Lipase Enantioselectivity
Authors: Bocola Marco , Otte Nikolaj , Jaeger Karl‐Erich , Reetz Manfred T. , Thiel Walter 
Published: January 2004

AbstractMolecular modeling with classical force‐fields has been used to study the reactant complex and the tetrahedral intermediate in lipase‐catalyzed ester hydrolysis in 20 enzyme/substrate combinations. The R and S enantiomers of α‐methyldecanoic acid ester served as substrates for the wild‐type lipase from Pseudomonas aeruginosa and nine selected mutants. After suitable preparation of initial structures from an available wild‐type crystal structure, each system was subjected to 1 ns CHARMM force‐field molecular dynamics simulations. The resulting geometric and energetic changes allow interpretation of some experimentally observed effects of mutations, particularly with regard to the “hot spots” at residues 155 and 162. The replacement S155F enhances S enantiopreference through a steric relay involving Leu162. The double mutation S53P + L162G improves S enantioselectivity by creating a new binding pocket for the S enantiomer with an additional stabilizing hydrogen bond to His83. The simulations provide insight into remote and cooperative effects of mutations.
Modulating Functional Loop Movements: The Role of Highly Conserved Residues in the Correlated Loop Motions
Authors: Gunasekaran Kannan , Nussinov Ruth 
Published: January 2004

AbstractLoop flexibility in enzymes plays a vital role in correctly positioning catalytically important residues. This strong relationship between enzyme flexibility and function provides an opportunity to engineer new substrates and inhibitors. It further allows the design of site‐directed mutagenesis experiments to explore enzymatic activity through the control of flexibility of a functional loop. Earlier, we described a novel mechanism in which a small loop triggers the motions of a functional loop in three enzymes (β‐1,4‐galactosyltransferase, lipase, and enolase) unrelated in sequence, structure, or function. Here, we further address the question of how the interactions between various flexible loops modulate the movements of the functional loop. We examine β‐1,4‐galactosyltransferase as a model system in which a Long loop undergoes a large conformational change (moves in space up to 20 Å) upon substrate binding in addition to a small loop (Trp loop) that shows a considerably smaller conformational change. Our molecular‐dynamics simulations carried out in implicit and explicit solvent show that, in addition to these two loops, two other neighboring loops are also highly flexible. These loops are in contact with either the Long loop or the Trp loop. Analysis of the covariance of the spatial displacement of the residues reveals that coupled motions occur only in one of these two loops. Sequence analysis indicates that loops correlated in their motions also have highly conserved residues involved in the loop–loop interactions. Further, analysis of crystal structures and simulations in explicit water open the possibility that the Trp loop that triggers the movement of the Long loop in the unbound conformation may also play the same role in the substrate‐bound conformation through its contact with the conserved and correlated third loop. Our proposition is supported by the observation that four of the five conserved positions in the third loop are at the interface with the Trp loop. Evolution appears to select residues that drive the functional Long loop to a large conformational change. These observations suggest that altering selected loop–loop interactions might modulate the movements of the functional loop.
Adaptation of Class‐13 α‐Amylases to Diverse Living Conditions
Authors: Linden Anni , Wilmanns Matthias 
Published: January 2004

AbstractThere are currently 35 available nonredundant molecular structures of class‐13 α‐amylases (EC 3.2.1.1), mostly from microbial organisms living under a wide range of environmental conditions. One of the most recent additions has been the first α‐amylase structure of a hyperthermophilic archaeon [Linden et al., J. Biol. Chem. 2003, 278, 9875–9884]. The structure has been used for comparative analyses with a representative set of three α‐amylases from thermophilic, mesophilic and psychrophilic sources to identify molecular parameters for environmental adaptation. Our analysis supports generally observed trends such as an increase in structural compactness as well as an increase in salt bridges in order to cope with high‐temperature conditions. The two representative thermophilic structures used in this comparative study have independently evolved di‐metal centres—not present in the mesophilic and psychrophilic structures—in the vicinity of the active site. These observations may provide impetus for the design of α‐amylases with improved molecular properties to enhance their utility in biotechnological processes.
Lipase‐Specific Foldases
Authors: Rosenau Frank , Tommassen Jan , Jaeger Karl‐Erich 
Published: January 2004

AbstractLipases represent the most important class of enzymes used in biotechnology. Many bacteria produce and secrete lipases but the enzymes originating from Pseudomonas and Burkholderia species seem to be particularly useful for a wide variety of different biocatalytic applications. These enzymes are usually encoded in an operon together with a second gene which codes for a lipase‐specific foldase, Lif, which is necessary to obtain enzymatically active lipase. A detailed analysis based on amino acid homology has suggested the classification of Lif proteins into four different families and also revealed the presence of a conserved motif, Rx1x2FDY(F/C)L(S/T)A. Recent experimental evidence suggests that Lifs are so‐called steric chaperones, which exert their physiological function by lowering energetic barriers during the folding of their cognate lipases, thereby providing essential steric information needed to fold lipases into their enzymatically active conformation.
Consensus Design of Repeat Proteins
Authors: Forrer Patrik , Binz H. Kaspar , Stumpp Michael T. , Plückthun Andreas 
Published: January 2004

AbstractConsensus design is a valuable protein‐engineering method that is based on statistical information derived from sequence alignments of homologous proteins. Recently, consensus design was adapted to repeat proteins. We discuss the potential of this novel repeat‐based approach for the design of consensus repeat proteins and repeat protein libraries and summarize recent results from such experiments.
A new method for computing optimum weights for calculating CIE tristimulus values
Authors: Li C. J. , Luo M. R. , Rigg B. 
Published: January 2004

AbstractWeighing tables are widely used for calculating CIE tristimulus values. In this article, a direct method for computing optimum weighing tables for any illuminant and observer combination is developed. A comprehensive set of 1‐nm reflectance functions based upon Munsell samples is used to test various methods. Four types of weighing tables are compared. They are ASTM E308 Tables 5 and 6, ASTM E2022, and new tables proposed by this study. The results clearly show that the newly developed optimum tables outperform the other three types of tables. The new method is simple and avoids the iterative process used by Venable and adopted by ASTM for some of its tables. It may be used for calculating weighing tables for any combination of illuminant and observer. A detailed procedure and a worked example are given in the article. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 91–103, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10229
The principal components of reflectances
Authors: Fairman Hugh S. , Brill Michael H. 
Published: January 2004

AbstractThere are practical reasons to represent a set of reflectance spectra by a limited basis‐function expansion. Such an expansion is most tractable in color technology applications when it is homogenous. However, more often a true principal‐component analysis (PCA) is performed, which involves an offset of the expansion by a mean spectrum. In deference to custom, we discuss and exercise the traditional PCA on reflectances. We review the method of calculation and present tables of the principal components of 3,534 object‐color samples from three color‐order systems. Next, we describe two kinds of principal‐component coordinates of a measured reflectance spectrum, one obtained by least‐square best fit and the other by tristimulus match under one or more specified lights. Finally, we show illustrative examples, and propose some possible new uses for principal‐component analysis of reflectances. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 104–110, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10230
Museum lighting: Optimizing the illuminant
Authors: Scuello Michael , Abramov Israel , Gordon James , Weintraub Steven 
Published: January 2004

AbstractMuseums must choose illumination that will optimize observers' aesthetic experiences without compromising preservation of the artworks. Typical lighting is 3000 K at 200 lux. We examined the effects of color temperature by comparing the same “artwork” under several different illuminants (in side‐by‐side miniature museum rooms); for each painting, observers rated the preference for seeing it under one of the two illuminants; this was repeated for all pairings of illuminants. Our observers preferred higher color temperatures at about 3600 K. Between viewing trials observers' visual systems were adapted to a specific illuminant. This had no effect on preferred illumination of an artwork. To explore a wider range of artworks, we developed a set of numerical scales that could be applied directly to individual pictures; these were viewed, one at a time, in a single simulated room illuminated by one of a series of illuminants. Again, observers preferred a color temperature of about 3600 K. In both studies there was a small interaction between illuminant and color gamut of a given painting. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 121–127, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10231
Quantifying variations in personal color spaces: Are there sex differences in color vision?
Authors: Bimler David L. , Kirkland John , Jameson Kimberly A. 
Published: January 2004

AbstractWe report a search for group differences in color experience between male and female subjects, focusing on the relative prominence of the axes of color space. Dissimilarity data were collected in the form of triadic (odd‐one‐out) judgments, made with the caps of the D‐15 color deficiency test, with lighting conditions controlled. Multidimensional scaling reduced these judgments to a small number of dimensional‐weight parameters, describing each subject's sensitivity to color axes, i.e., how much each axis contributes to the inter‐color dissimilarities perceived by each subject. Normal trichromatic subjects in two age bands were examined, teenagers and university students, and in both cases males placed significantly less weight on a ‘red‐green’ axis, and more on ‘lightness’. We consider the implications and possible explanations. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 128–134, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10232
Spectrophotometric error in colour coordinates introduced by fluorescence of white calibration tile
Authors: Pons Alicia , Campos Joaquín 
Published: January 2004

AbstractFluorescence has been detected in some white standard tiles intended for the calibration of spectrophotometers for colour measurements. The problem is that usually no warning is given to the user about it, giving raise to errors if they are calibrated using conventional spectrophotometric techniques. This work analyzes the differences on the colour coordinates of one of these standards measured with a polychromatic illumination spectrophotometer and with a monochromatic illumination one. This work also analyzes the colour coordinates error obtained when other coloured standards are calibrated against one of these white fluorescent standards, when reflectance measurement is done with a polychromatic illumination spectrophotometer as well as with a monochromatic illumination instrument. These are the two most typical situations found in practice where the use of fluorescent standards may produce errors. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 111–114, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10233
Proposal of an opponent‐colors system based on color‐appearance and color‐vision studies
Authors: Nayatani Yoshinobu 
Published: January 2004

AbstractA new theoretical color order system is proposed on the basis of various studies on color appearance and color vision. It has three orthogonal opponent‐colors axes and an improved chromatic strength of each hue. The system has color attributes whiteness w, blackness bk, grayness gr, chroma C, and hue H. A method is given for determining Munsell notations of any colors on any equi‐hue planes in the system. A method is also given for determining grayness regions and grayness values on hue‐chroma planes in the system. It is concluded that colors with the same color attributes [w, gr, bk, C] but with different hues in the theoretical space have approximately the same perceived lightness, the same degree of vividness (“azayakasa” in Japanese), and also the same color tone. The tone concept, for example used in the Practical Color Coordinate System (PCCS), is clarified perceptually. The proposed system is a basic and latent color‐order system to PCCS. In addition, the concept of veiling grayness by a pure color with any hue is introduced. Further, relationships are clarified between generalized chroma c(gen) and grayness. © 2004 Wiley Periodicals, Inc. Col Res Appl, 29, 135–150, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10234
Growth of Thin Films of Molybdenum and Tungsten Oxides by Combustion CVD Using Aqueous Precursor Solutions
Authors: Davis M.J. , Benito G. , Sheel D.W. , Pemble M.E. 
Published: January 2004

AbstractUsing combustion (C) CVD, layers of molybdenum and tungsten oxides have been deposited on glass and silicon at low temperatures. Inexpensive ammonium salts of molybdate and metatungstate ions were used as precursors and were delivered to the coating flame as an aqueous solution using a nebulizer. The resulting films were analyzed by scanning electron microscopy (SEM), energy‐dispersive analysis of X‐rays (EDAX), Rutherford backscattering (RBS), X‐ray photoelectron spectroscopy (XPS), and X‐ray diffraction (XRD). These indicated that the films were continuous, moderately smooth, and consisted of amorphous, disordered molybdenum and tungsten trioxides.
Deposition of Antimony and Antimony Oxides by MOCVD
Authors: Myers C.P. , Haycock P.W. , Pichot M. , Horley G.A. , Molloy K.C. , Rushworth S.A. , Smith L.M. 
Published: January 2004

AbstractThin films of antimony and antimony oxides have been deposited by metal–organic (MO) CVD from a variety of metal–organic precursors at temperatures in the range 150–650 °C under both atmospheric and reduced pressure. Below 400 °C, uniform films of pure senarmontite (Sb2O3) with a microstructure and crystal texture that was strongly dependent on the deposition temperature, were deposited. Above 400 °C, mixed phase material was produced, with isolated crystallites of pure antimony becoming the dominant phase as the temperature was increased. The maximum temperature at which pure senarmontite could be formed was higher for larger precursor ligands. Addition of oxygen to the precursor flow led to the production of higher antimony oxidation states.
Analysis of amino acids in individual human erythrocytes by capillary electrophoresis with electroporation for intracellular derivatization and laser‐induced fluorescence detection
Authors: Zhang Hua , Jin Wenrui 
Published: January 2004

AbstractA method for monitoring amino acids in single erythrocytes is described. For intracellular derivatization, reagent fluorescein isothiocyanate (FITC) was introduced into living cells by electroporation. For an 8 μm erythrocyte, the analytes were diluted by a factor of only 1.6. After completion of the derivatization reaction, a single cell was injected into the separation capillary tip and lysed there. The derivatized amino acids were separated by capillary electrophoresis, followed by laser‐induced fluorescence detection. Nine amino acids were quantitatively determined, with amounts of amino acids ranging from 3.8–32 amol/single cell.