bluuebunny/crossref_metadata_2025 huggingface dataset:
The crystal structures of semi‐synthetic aequorins
Authors: Toma Sachiko , Chong Khoon Tee , Nakagawa Atsushi , Teranishi Katsunori , Inouye Satoshi , Shimomura Osamu
Published: January 2005

The photoprotein aequorin emits light by an intramolecular reaction in the presence of a trace amount of Ca2+. Semi‐synthetic aequorins, produced by replacing the coelenterazine moiety in aequorin with the analogues of coelenterazine, show widely different sensitivities to Ca2+. To understand the structural basis of the Ca2+‐sensitivity, we determined the crystal structures of four semi‐synthetic aequorins (cp‐, i‐, br‐ and n‐aequorins) at resolutions of 1.6–1.8 Å. In general, the protein structures of these semi‐synthetic aequorins are almost identical to native aequorin. Of the four EF‐hand domains in the molecule, EF‐hand II does not bind Ca2+, and the loop of EF‐hand IV is clearly deformed. It is most likely that the binding of Ca2+ with EF‐hands I and III triggers luminescence. Although little difference was found in the overall structures of aequorins investigated, some significant differences were found in the interactions between the substituents of coelenterazine moiety and the amino acid residues in the binding pocket. The coelenterazine moieties in i‐, br‐, and n‐aequorins have bulky 2‐substitutions, which can interfere with the conformational changes of protein structure that follow the binding of Ca2+ to aequorin. In cp‐aequorin, the cyclopentylmethyl group that substitutes for the original 8‐benzyl group does not interact hydrophobically with the protein part, giving the coelenterazine moiety more conformational freedom to promote the light‐emitting reaction. The differences of various semi‐synthetic aequorins in Ca2+‐sensitivity and reaction rate are explained by the capability of the involved groups and structures to undergo conformational changes in response to the Ca2+‐binding.
Sequence swapping does not result in conformation swapping for the β4/β5 and β8/β9 β‐hairpin turns in human acidic fibroblast growth factor
Authors: Kim Jaewon , Lee Jihun , Brych Stephen R. , Logan Timothy M. , Blaber Michael
Published: January 2005

The β‐turn is the most common type of nonrepetitive structure in globular proteins, comprising ∼25% of all residues; however, a detailed understanding of effects of specific residues upon β‐turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF‐1) is a member of the β‐trefoil superfold and contains a total of five β‐hairpin structures (antiparallel β‐sheets connected by a reverse turn). β‐Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the β4/β5 and β8/β9 turns, were subjected to both sequence‐swapping and poly‐glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild‐type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence‐swapping and glycine substitution mutagenesis. The results indicate that the β‐turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.
EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV
Authors: Kinch Lisa N. , Cheek Sara , Grishin Nick V.
Published: January 2005

Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary‐based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA‐man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically significant sequence similarity detected by PSI‐BLAST; “closed structural grouping” using DALI Z‐scores (each protein inside a group finds all other group members with scores higher than those to proteins outside the group) that includes only these proteins sharing a unique α‐helical hairpin at the C‐terminus and excludes all other proteins with similar topology; similar domain fusions connect Dak and DegV, and genomic neighborhood organizations connect Dak and EIIA‐man. Finally, both Dak and EIIA‐man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV‐like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown.
Crystal structures of RsbQ, a stress‐response regulator in Bacillus subtilis
Authors: Kaneko Tomonori , Tanaka Nobuo , Kumasaka Takashi
Published: January 2005

Growth‐limiting stresses in bacteria induce the general stress response to protect the cells against future stresses. Energy stress caused by starvation conditions in Bacillus subtilis is transmitted to the σB transcription factor by stress‐response regulators. RsbP, a positive regulator, is a phosphatase containing a PAS (Per‐ARNT‐Sim) domain and requires catalytic function of a putative α/β hydrolase, RsbQ, to be activated. These two proteins have been found to interact with each other. We determined the crystal structures of RsbQ in native and inhibitor‐bound forms to investigate why RsbP requires RsbQ. These structures confirm that RsbQ belongs to the α/β hydrolase superfamily. Since the catalytic triad is buried inside the molecule due to the closed conformation, the active site is constructed as a hydrophobic cavity that is nearly isolated from the solvent. This suggests that RsbQ has specificity for a hydrophobic small compound rather than a macromolecule such as RsbP. Moreover, structural comparison with other α/β hydrolases demonstrates that a unique loop region of RsbQ is a likely candidate for the interaction site with RsbP, and the interaction might be responsible for product release by operating the hydrophobic gate equipped between the cavity and the solvent. Our results support the possibility that RsbQ provides a cofactor molecule for the mature functionality of RsbP.
Myristoyl moiety of HIV Nef is involved in regulation of the interaction with calmodulin in vivo
Authors: Matsubara Mamoru , Jing Tao , Kawamura Kumi , Shimojo Naoshi , Titani Koiti , Hashimoto Keiichiro , Hayashi Nobuhiro
Published: January 2005

Human immunodeficiency virus Nef is a myristoylated protein expressed early in infection by HIV. In addition to the well known down‐regulation of the cell surface receptors CD4 and MHCI, Nef is able to alter T‐cell signaling pathways. The ability to alter the cellular signaling pathways suggests that Nef can associate with signaling proteins. In the present report, we show that Nef can interact with calmodulin, the major intracellular receptor for calcium. Coimmunoprecipitation analyses with lysates from the NIH3T3 cell line constitutively expressing the native HIV‐1 Nef protein revealed the presence of a stable Nef‐calmodulin complex. When lysates from NIH3T3 cells were incubated with calmodulin‐agarose beads in the presence of CaCl2 or EGTA, calcium ion drastically enhanced the interaction between Nef and calmodulin, suggesting that the binding is under the influence of Ca2+ signaling. Glutathione S‐transferase‐Nef fusion protein bound directly to calmodulin with high affinity. Using synthetic peptides based on the N‐terminal sequence of Nef, we determined that within a 20‐amino‐acid N‐terminal basic domain was sufficient for calmodulin binding. Furthermore, the myristoylated peptide bound to calmodulin with higher affinity than nonmyris‐toylated form. Thus, the N‐terminal myristoylation domain of Nef plays an important role in interacting with calmodulin. This domain is highly conserved in several HIV‐1 Nef variants and resembles the N‐terminal domain of NAP‐22/CAP23, a myristoylated calmodulin‐binder. These results for the interaction between HIV Nef and calmodulin in the cells suggested that the Nef might interfere with intracellular Ca2+ signaling through calmodulin‐mediated interactions in infected cells.
Comparative study of otolith organs between two species of upside‐down swimming catfish Synodontis nigriventris showing converse swimming postures
Authors: Ohnishi Ken , Ogawa Yoichi , Takahashi Akihisa , Yamashita Masayuki , Ohnishi Takeo
Published: January 2005

To clarify whether the unique postural control of the upside‐down swimming catfish (Synodontis nigriventris, family Mochokidae) is related to the histological characteristics of the otolith organs, we performed light microscopic observation of the utricle, the saccule and the lagena. The histological aspects of the otolith organs were compared between S. nigriventris and Synodontis multipunctatus, which belong to the same genus. S. multipunctatus usually shows upside‐up swimming posture except for feeding behaviour near water surface. As controls, we additionally used a miniature catfish, Corydoras paleatus and goldfish, Carassius auratus, which shows upside‐up swimming posture. We concluded that the structural aspects of the otolith organs did not cause the unique postural control of S. nigriventris. Light microscopic observation clarified the following aspects: (1) The utricle of S. nigriventris was located at the anterior region of the otocyst and under the semicircular canals, and the saccule and the lagena were located at the posteroventral region of the otocyst like those of S. multipunctatus and the other two fishes. (2) The hair cells of the utricle were arranged on the horizontal plane of the fishes with a variation in cell size at the ventral and ventrolateral sites in S. nigriventris, S. multipunctatus and the other two fishes. (3) The hair cells of the saccule and lagena of S. nigriventris, S. multipunctatus and C. auratus presented perpendicular to the horizontal plane of the fish. (4) Region‐specific differences in the size and shape of the hair cells of S. nigriventris were observed along the three‐dimensional axes of the otolith organs like those of S. multipunctatus and the other two fishes. It is unlikely that the unique postural control of upside‐down catfish is related to the localization of the utricle, the saccule and the lagena and the distribution of the different types of hair cell of the otolith organs. Furthermore, the distribution of the hair cells suggests that the otolith organs in S. nigriventris can detect three‐dimensional postural changes like the organs of other fishes showing generally observed upside‐up swimming posture.
Comparison of Coronary Flow Velocities Between Patients with Obstructive and Nonobstructive Type Hypertrophic Cardiomyopathy: Noninvasive Assessment by Transthoracic Doppler Echocardiography
Authors: Celik Seden , Dagdeviren Bahadir , Yildirim Aydin , Uslu Nevzat , Soylu Ozer , Gorgulu Sevket , Gurol Tayfun , Eren Mehmet , Tezel Tuna
Published: January 2005

Background: We aimed to compare coronary flow velocity (CFV) measurements of patients with nonobstructive (NHCM) and obstructive hypertrophic cardiomyopathy (HOCM) by using transthoracic Doppler echocardiography (TTDE). Methods and Results: In 11 patients with NHCM and 26 with HOCM, CFV in the distal left anterior descending (LAD) coronary was measured by TTDE (3.5 MHz) under the guidance of color Doppler flow mapping in addition to standard 2D and Doppler echocardiography. The results were compared with 24 normal participants who had no evidence of cardiac disease. Peak diastolic velocity of LAD was also higher in NHCM and HOCM than controls (52 ± 14 cm/sec and 54 ± 20 cm/sec vs 41 ± 11 cm/sec, respectively, P < 0.01). The analysis of systolic velocities revealed abnormal flow patterns in 16 (61%) patients with HOCM (12 systolic‐reversal flow and 4 no systolic flow) and 6 (54%) (5 reversal flow and 1 zero flow) patients with NHCM (−11 ± 30 cm/sec and −13 ± 38 cm/sec, vs 24 ± 9 cm/sec, respectively, P < 0.001). Linear regression analysis demonstrated no correlation between intraventricular pressure gradient and coronary flow velocities in HOCM patients. However, there were significant positive and negative correlations between septal thickness and diastolic and systolic velocities, respectively (r = 0.50, P < 0.002, and r =−0.43, P < 0.005). Conclusion: We conclude that the coronary flow velocity abnormalities are independent from the type of hypertrophic cardiomyopathy.
Histological Characterization of Microlesions Induced by Myocardial Contrast Echocardiography
Authors: Miller Douglas L. , Li Peng , Gordon David , Armstrong William F.
Published: January 2005

Background: Myocardial contrast echocardiography (MCE) has been shown to have a potential for apparently reversible side effects related to the interaction of ultrasound with the contrast microbubbles, including premature ventricular contractions and microvascular leakage. We investigated the potential for high‐dose MCE to induce histologically definable microlesions. Methods: Myocardial contrast echocardiography with 1:4 end‐systolic triggering was performed at 1.5 MHz and 1.7 mechanical index in a short axis view of the left ventricle in rats. Two high doses (500 μl/kg) of Optison® agent were given 5 minutes apart during 10 minutes of echocardiography. For histology, the hearts were perfused and fixed in 10% neutral‐buffered formalin. Slides from rats sacrificed 1 day after MCE were scored blind by a pathologist, and, in addition, photomicrographs in the anterior half were evaluated by digital image analysis. Results: In rats sacrificed 10 minutes after MCE, microvascular leakage and petechiae were highly significant. However, lesions displaying necrotic debris associated with inflammatory infiltrates were not histologically evident at this time. Heart samples 24 hours after MCE showed microlesions with inflammatory infiltrates scattered primarily over the anterior half of the sections. Pathologically, there was inflammatory cell infiltration in areas of 0.6 ± 0.5% for shams and 3.6 ± 3.6% for MCE (P < 0.01). Analysis of photographs from the anterior wall found microlesion areas of 0.5 ± 0.8% for shams and 7.4 ± 5.0% for MCE (P < 0.02). For rats sacrificed 1 week and 6 weeks after MCE, the microlesions healed to form small fibrous regions interspersed with normal myocytes. Conclusion: High‐dose MCE has a potential for causing microscale lesions in the myocardium and the possibility of therapeutic applications.
Traumatic Aortic Transection
Authors: Zissimopoulos Iraklis , Tsoukas Athanasios , Koliandris Ioannis , Christakos Stamatios
Published: January 2005

We report three cases of patients with blunt thoracic trauma, who underwent transesophageal echocardiography (TEE) because of high index of clinical suspicion for acute traumatic aortic syndrome. TEE revealed three different locations of aortic injury one of which was not diagnosed with aortography.
The use of patient diaries in an intensive care unit
Authors: Combe Denise
Published: January 2005

• Many patients experience posttraumatic stress disorder following a stay in intensive care; this can be due to a lack of recall of their stay

• Retrospective patient diaries (n = 8) with follow‐up have been used to try and help patients’ recovery but have been found to be impersonal

• Prospective diaries (n = 35) were implemented and trialled with follow‐up at 2, 6 and 12 months postdischarge

• Patients’ and relatives’ initial feedback regarding diaries is extremely positive. Benefits included better understanding of the events of the critical illness, helping with more realistic goal setting during the recovery period, improving communication within families through discussion of the diary and providing a source of comfort for the bereaved

• More formal audit of these diaries is required and is currently being undertaken
Relevance of post‐methionine homocysteine and lipoprotein (a) in evaluating the cardiovascular risk in young CAD patients
Authors: Marcucci R. , Brunelli T. , Fedi S. , Pepe G. , Giusti B. , Gori A. M. , Prisco D. , Falai M. , Margheri M. , Abbate R. , Gensini G. F.
Published: January 2005

Background  Aims of our study were to evaluate the prevalence of high lipoprotein (a) [Lp(a)] and homocysteine levels – both in the fasting state (FHcy) and post‐methionine (PMHcy) – in young coronary artery disease (CAD) patients, and to investigate the role of genetic and environmental factors for hyperhomocysteinaemia.

Materials and methods  We studied 140 patients with angiographically documented CAD (24 women ≤ 55 years and 116 men ≤ 50 years) and 140 healthy subjects as controls.

Results  Both FHcy [13·2 (5·4–45·8) vs. 9·0 (5·1–24) µmol L−1); P < 0·0001] and PMHcy [(39·4 (9·0–66·4) vs. 25·2 (16·4–33·9); P < 0·0001] were significantly higher in patients than in controls. Lp(a) levels were significantly higher in patients than in controls (200 (3–1486) mg L−1 vs. 97 (10–412) mg L−1; P < 0·0001). At the multivariate analysis, adjusted for the classical cardiovascular risk factors and creatinine levels, the OR (95% CI) for CAD at young age significantly increased in the fourth quartile of the distribution of FHcy, PMHcy and Lp(a) levels [FHcy: 14·9 (4·1–58), P < 0·0001; PMHcy: 19·2 (4·0–86·3); P < 0·0001; Lp(a): 19·6 (4·7–78·6): < 0·0001]. Vitamin deficiencies were detected in 28/140 (20%) patients. The prevalence of the homozygous C677T (+/+) methylenetetrahydrofolatereductase genotype was higher, but not significantly different, in patients (22·8%) than in controls (18·6%). The allele frequency of the 844ins68 insertion variant in the cystathionine beta‐synthase gene was 0·08 in the control group and 0·06 in the patient group.

Conclusions  Results of the present study indicate the usefulness of including fasting and post‐methionine Hcy, and Lp(a) determination in the diagnostic panels of young CAD patients, in order to obtain a better assessment of their cardiovascular risk profile.
Identification of fatty acid oxidation disorder patients with lowered acyl‐CoA thioesterase activity in human skin fibroblasts
Authors: Hunt M. C. , Ruiter J. , Mooyer P. , Van Roermond C. W. T. , Ofman R. , Ijlst L. , Wanders R. J. A.
Published: January 2005

Background  Acyl‐CoA thioesterases are enzymes that hydrolyze acyl‐CoAs to the free fatty acid and coenzyme A (CoASH). These enzymes have been identified in several cellular compartments and are thought to regulate intracellular levels of acyl‐CoAs, free fatty acids and CoASH. However, to date no patients deficient in acyl‐CoA thioesterases have been identified.

Design  Acyl‐CoA thioesterase activity was measured in human skin fibroblasts. Western‐blot analysis was used to determine Type‐II acyl‐CoA thioesterase protein levels in patients.

Results  Acyl‐CoA thioesterase activity was found in human fibroblasts with all saturated acyl‐CoAs from C4‐CoA to C18‐CoA, with highest activity detected with lauroyl‐CoA and myristoyl‐CoA (C12‐CoA and C14‐CoA). An antibody that recognizes the major isoforms of Type‐II acyl‐CoA thioesterases precipitated the majority of acyl‐CoA thioesterase activity in fibroblasts, showing that the main thioesterase activity detected in fibroblasts is catalyzed by Type‐II thioesterases. Measurement of acyl‐CoA thioesterase activity from fibroblasts of 34 patients with putative fatty acid oxidation disorders resulted in the identification of three patients with lowered Type‐II acyl‐CoA thioesterase activity in fibroblasts. These patients also had lowered expression of Type‐II acyl‐CoA thioesterase protein in fibroblasts as judged by Western‐blot analysis. However, mutation analysis failed to identify any mutation in the coding sequences for the mitochondrial acyl‐CoA thioesterase II (MTE‐II) or the cytosolic acyl‐CoA thioesterase II (CTE‐II).

Conclusions  We have described three patients with lowered Type‐II acyl‐CoA thioesterase protein and activity in human skin fibroblasts, which is the first description of patients with a putative defect in acyl‐CoA thioesterases.
Admixed sexual and facultatively asexual aphid lineages at mating sites
Authors: HALKETT F. , PLANTEGENEST M. , PRUNIER‐LETERME N. , MIEUZET L. , DELMOTTE F. , SIMON J. C.
Published: January 2005

Cyclically parthenogenetic organisms may have facultative asexual counterparts. Such organisms, including aphids, are therefore interesting models for the study of ecological and genetic interactions between lineages differing in reproductive mode. Earlier studies on aphids have revealed major differences in the genetic outcomes of populations that are possibly resulting mostly either from sexual or from asexual reproduction. Besides, notable gene flow between sexual and asexual derivatives has been suspected, which could lead to the emergence of new asexual lineages. The present study examines the interplay between these lineages and is based on analyses of population structure of individuals that may contribute to the pool of sexual reproductive forms in the host alternating aphidRhopalosiphum padi. Using a Bayesian assignment method, we first show that the sexual forms ofR. padion mating sites encompass two genetically distinct clusters of individuals in the western part of France. The first cluster included unique genotypes of sexual lineages, while the second cluster included facultatively asexual lineages in numerous copies, the reproductive mode of the two clusters being confirmed by reference clones. Sexual reproductive forms produced by sexual and facultatively asexual lineages are thus admixed at mating sites which gives a large opportunity for the two clusters to mate with each other. Nevertheless, this study also highlights, as previously demonstrated, that the two clusters retained high genetic differentiation. Possible explanations for the inferred limited genetic exchanges are advanced in the discussion, but further dedicated investigations are required to solve this paradox.
Evaluating mixed samples as a source of error in non‐invasive genetic studies using microsatellites
Authors: ROON DAVID A. , THOMAS MIRANDA E. , KENDALL KATHERINE C. , WAITS LISETTE P.
Published: January 2005

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error‐checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.
Genetic monitoring of wild and repatriated populations of endangered razorback sucker (Xyrauchen texanus, Catostomidae, Teleostei) in Lake Mohave, Arizona‐Nevada
Authors: DOWLING T. E. , MARSH P. C. , KELSEN A. T. , A. TIBBETS C.
Published: January 2005

The Native Fishes Work Group, formed in 1991, developed and implemented a protocol to enhance the dwindling razorback sucker population in Lake Mohave, Arizona‐Nevada. This large, genetically diverse population is severely reduced in size as a result of recruitment failure associated with predation on larvae. To circumvent this problem, wild larvae are captured, reared in protective custody until they are large enough to escape predation, and then released back into the lake. We present results of a monitoring program designed to assess the effectiveness of the sampling design in transmitting the high genetic diversity found in wild adults. Variation in a fragment from the mitochondrial DNA gene cytochrome b was examined by analysis of single‐stranded polymorphisms and direct sequencing. Samples were characterized from three life history stages. Characterization of wild adults verified previous results that identified considerable diversity and provided baseline data. Samples of larvae from several temporal collections from throughout the spawning season and four geographical areas were characterized for 7 years (1997–2003) to assess the transmission of genetic variation from wild adults to larvae. Several analyses identified significant differences among temporal collections, resulting from sampling errors associated with finite number of females spawning at a given time and place. Comparisons among areas and years failed to identify significant variation, indicating that pooled collections for each year possess the same levels and patterns of genetic variation. Examination of repatriates representing 11 years (1992–2002) also failed to identify significant differences among cohorts; however, some sample sizes were small and the amova may lack sufficient power to detect differences. Contrasts of wild adults, larvae, and repatriates identified statistically significant differences among collections within these three groups; however, levels of variation are small and not biologically meaningful. More importantly, this analysis failed to detect significant differences among adults, larvae, and repatriates indicating that the program has been achieving its goal of transmitting variation from adults through the larvae and into the repatriate population. The reproductive capability of repatriates has not been examined, so it is unknown if the program will maintain genetic variation found in the original adult population. This will be most easily achieved by periodic monitoring of genetic variation in larval samples. If levels of variation become reduced in repatriates, levels and patterns of diversity in larvae are also expected to become reduced, and deviations in estimates of genetic diversity may become larger and more frequent. If this is the case, intervention may be necessary to ensure that certain individuals are not over‐represented in the repatriate population.
Prophylaxis and treatment of gastrointestinal complications following transplantation
Authors: Helderman J Harold
Published: January 2005

AbstractMost transplant recipients will experience some type of gastrointestinal (GI) complication. These effects often are caused by infectious damage induced by a variety of opportunistic organisms, but they also may be due to mechanical injury during surgery or to metabolic or organ toxicity associated with immunosuppressive regimens. Although some of these GI complications can substantially impair quality of life or even carry significant mortality risk, many of them can be prevented, and most of them can be treated medically without the need to stop immunosuppression and expose the patient to the risk of rejection. Limiting the use of steroids, giving prophylactic antiviral and antifungal agents (particularly to patients at risk) and adopting a low threshold for endoscopy are among the most important measures that can be used to avoid GI complications after transplantation.
Prediction of Onset of Corrosion in Concrete Bridge Decks Using Neural Networks and Case‐Based Reasoning
Authors: Morcous G. , Lounis Z.
Published: January 2005

Abstract:  This article proposes a methodology for predicting the time to onset of corrosion of reinforcing steel in concrete bridge decks while incorporating parameter uncertainty. It is based on the integration of artificial neural network (ANN), case‐based reasoning (CBR), mechanistic model, and Monte Carlo simulation (MCS). A probabilistic mechanistic model is used to generate the distribution of the time to corrosion initiation based on statistical models of the governing parameters obtained from field data. The proposed ANN and CBR models act as universal functional mapping tools to approximate the relationship between the input and output of the mechanistic model. These tools are integrated with the MCS technique to generate the distribution of the corrosion initiation time using the distributions of the governing parameters. The proposed methodology is applied to predict the time to corrosion initiation of the top reinforcing steel in the concrete deck of the Dickson Bridge in Montreal. This study demonstrates the feasibility, adequate reliability, and computational efficiency of the proposed integrated ANN‐MCS and CBR‐MCS approaches for preliminary project‐level and also network‐level analyses.
Model Identification of Bridges Using Measurement Data
Authors: Robert‐Nicoud Y. , Raphael B. , Burdet O. , Smith I. F. C.
Published: January 2005

Abstract:  Measurements are increasingly used to augment traditional assessments of structural state. Measurements of deflections, rotations, and strain provide indications of damages as well as changes in the values of parameters such as Young's modulus. Finite‐element model‐updating methods have been developed in the 1990s for identifying structural state from measurements. Currently most methods aim to determine the values of stiffness coefficients that result in measured responses. In the present work, a model calibration method identifies causes of structural behavior such as support conditions and material properties. Static measurement data are employed for model calibration. A case study of the Lutrive Bridge in Switzerland illustrates the methodology. Candidate models whose responses reasonably match measured data are identified. These models are then examined to determine whether the calibrated values are physically possible. Such examinations lead to either model rejection or further measurements.
‘The Mighty Pillar of the Family’: Young People's Vocabularies on Household Gender Arrangements in the Asia‐Pacific Region
Authors: Bulbeck Chilla
Published: January 2005

In the light of women's increased labour force participation and the demands of western feminism for men's participation in housework and childcare, this article analyses vocabularies on these issues among young people in Australia, USA and Canada and seven countries in Asia. While very few young people in any of the samples use explicitly feminist justifications for their statements, there is high support for sharing housework when both partners are in paid work. By contrast, the strong support for role reversal — for men being ‘house husbands’— is confined to the western samples. The article explores reasons for these differences based in respondents’ domestic experiences and national family policies. Where many of the western respondents rely on equality or individualism, the Asian respondents are more likely to understand the role of the husband and wife in the context of their duties to each other and the nation or to assert the existence of gender differences between men and women.
The relation between the absolute level of parenting and differential parental treatment with adolescent siblings’ adjustment
Authors: Tamrouti‐Makkink Ilse D. , Dubas Judith Semon , Gerris Jan R.M. , van Aken Marcel A.G.
Published: January 2005

Background:  The present study extends existing studies on the role of differential parental treatment in explaining individual differences in adolescent problem behaviors above the absolute level of parenting and clarifies the function of gender of the child, birth rank and gender constellation of the sibling dyads.

Method:  The absolute level of parenting practices and differential treatment were examined in a sample of 288 Dutch families consisting of two parents and two adolescents. Parents reported on adolescent internalizing and externalizing problem behavior and adolescents reported on parental warmth and coercive control.

Results:  Parenting dimensions were related to problem behavior for same‐ and mixed‐gender sibling pairs, with coercive control as the strongest predictor. No direct association was found between differential parental treatment and child outcomes above the absolute levels of parenting in same‐gender sibling pairs. However, differential maternal and paternal control was related to internalizing behavior of girls and differential paternal warmth was linked to externalizing behavior of the older siblings in mixed‐gender sibling pairs.

Conclusion:  Differential parental treatment is uniquely associated with child problem behavior above the absolute level of parenting for girls and early‐born children in mixed‐gender sibling pairs. Any examination of the effects of differential treatment should not be undertaken without considering the gender and birth rank of the sibling pairs.
Perceived support in sibling relationships and adolescent adjustment
Authors: Branje Susan J.T. , van Lieshout Cornelis F.M. , van Aken Marcel A.G. , Haselager Gerbert J.T.
Published: January 2005

Background:  Siblings may support each other, but also reveal fierce rivalry and mutual aggression. Supportive sibling relationships have been linked to the development of psychosocial competence of children. In the present longitudinal study, we will focus on the development of perceived support in sibling dyads and on the influence of sibling support and sibling problem behavior on psychosocial adjustment in adolescence.

Method:  In a three‐wave longitudinal sample of 285 Dutch families with two adolescent children (11‐ to 15‐year‐olds), these two siblings judged the support perceived from each other. In addition, they themselves and their parents judged their internalizing and externalizing problem behaviors. The relation of sibling support and sibling problem behavior with internalizing and externalizing problem behaviors was examined while controlling for support from parents and friends and, over time, controlling for the autoregressive effects of problem behavior.

Results:  Support perceived from a sibling is mostly negatively related to externalizing problems; sibling problem behavior is strongly related to internalizing problems. Differential developmental trajectories of adolescents’ adjustment are associated with siblings’ support and problem behavior.

Conclusion:  The results indicate that adolescents’ relationships with both older and younger siblings are characterized by modeling processes.
Gait Impairments in a Group of Patients With Incomplete Spinal Cord Injury and Their Relevance Regarding Therapeutic Approaches Using Functional Electrical Stimulation
Authors: Van Der Salm Arjan , Nene Anand V. , Maxwell Douglas J. , Veltink Peter H. , Hermens Hermie J. , IJzerman Maarten J.
Published: January 2005

Abstract:  The purpose of this study is to determine the most important impairments affecting the gait pattern of the incomplete spinal cord injury (SCI) patient and the potential impact of their treatment. The study consists of two parts. Firstly, a survey amongst 16 professionals was done to find out the impact of the impairments in incomplete‐SCI patients. Secondly, gait data from 21 individuals were analyzed to determine the most common impairments. Frequently observed and relevant impairments were: inadequate hip extension (occurrence 76%), limited hip flexion (52%), limited knee flexion (71%), excess of plantar flexion (76%), and impaired foot contact (52%). In conclusion, for gait improvement in incomplete spinal cord injured patients not only ankle movements must be treated, which is done frequently, but also hip extension/flexion and knee flexion are important for gait restoration. The impact on the gait and potential solutions of these impairments are discussed.
An Overview of Complete Artificial Fixed Dentition Supported by Endosseous Implants
Authors: Flanagan Dennis
Published: January 2005

Abstract:  The construction of a complete restoration of the dentition by the surgical placement of endosseous titanium implants that support a fixed prosthesis in each jaw is possible. The positionings of the implants and teeth in the prostheses are important factors for a successful long‐term result. Distribution of the occlusal biting forces over as many implants as possible is important. Off‐axial occlusal biting forces should be diverted to the anterior jaws where the forces are not as great. The posterior teeth should be designed with flat occlusal surfaces that separate during excursionary mandibular chewing movements. Medial mandibular flexure caused by the contraction of the medial pterygoid muscle can be addressed by constructing the prosthesis in segments, so as not to have a rigid entity encased in flexing bone that may induce stress in the bone, potentially leading to loss of implant integration and failure. Segmenting also ensures an appropriate fit of the prosthesis with respect to casting and porcelain firing distortion. Lip support by means of a flange in the prosthesis may be necessary when there has been a large amount of bone loss from edentulous resorption. Cleaning and routine maintenance of the prostheses every 3–6 months is essential.
Quantification of the Secondary Flow in a Radial Coupled Centrifugal Blood Pump Based on Particle Tracking Velocimetry
Authors: Watanabe Nobuo , Masuda Takaya , Iida Tomoya , Kataoka Hiroyuki , Fujimoto Tetsuo , Takatani Setsuo
Published: January 2005

Abstract:  Secondary flow in the centrifugal blood pump helps to enhance the washout effect and to minimize thrombus formation. On the other hand, it has an adverse effect on pump efficiency. Excessive secondary flow may induce hemolytic effects. Understanding the secondary flow is thus important to the design of a compact, efficient, biocompatible blood pump. This study examined the secondary flow in a radial coupled centrifugal blood pump based on a simple particle tracking velocimetry (PTV) technique. A radial magnetically coupled centrifugal blood pump has a bell‐shaped narrow clearance between the impeller inner radius and the pump casing. In order to vary the flow levels through the clearance area, clearance widths of 0.25 mm and 0.50 mm and impeller washout holes with diameters of 0 mm, 2.5 mm, and 4 mm were prepared. A high‐speed video camera (2000 frames per second) was used to capture the particle images from which radial flow components were derived. The flow in the space behind the impeller was assumed to be laminar and Couette type. The larger the inner clearance or diameter of washout hole, the greater was the secondary flow rate. Without washout holes, the flow behind the impeller resulted in convection. The radial flow through the washout holes of the impeller was conserved in the radial as well as in the axial direction behind the impeller. The increase in the secondary flow reduced the net pump efficiency. Simple PTV was successful in quantifying the flow in the space behind the impeller. The results verified the hypothesis that the flow behind the impeller was theoretically Couette along the circumferential direction. The convection flow observed behind the impeller agreed with the reports of other researchers. Simple PTV was effective in understanding the fluid dynamics to help improve the compact, efficient, and biocompatible centrifugal blood pump  for  safe  clinical  applications.
The Kuiper Belt and the Solar System's Comet Disk
Authors: Gladman Brett
Published: January 2005

Our planetary system is embedded in a small-body disk of asteroids and comets, vestigial remnants of the original planetesimal population that formed the planets. Once formed, those planets dispersed most of the remaining small bodies. Outside of Neptune, this process has left our Kuiper belt and built the Oort cloud, as well as emplacing comets into several other identifiable structures. The orbits in these structures indicate that our outer solar system's comet disk was shaped by a variety of different physical processes, which teach us about how the giant planets formed. Recent work has shown that the scattered disk is the most likely source of short-period comets. Moreover, a growing body of evidence indicates that the sculpting of the Kuiper belt region may have involved large-scale planetary migration, the presence of other rogue planetary objects in the disk, and/or the close passage of other stars in the Sun's birth cluster.
Vesicle Endocytosis Requires Dynamin-Dependent GTP Hydrolysis at a Fast CNS Synapse
Authors: Yamashita Takayuki , Hige Toshihide , Takahashi Tomoyuki
Published: January 2005

Molecular dependence of vesicular endocytosis was investigated with capacitance measurements at the calyx of Held terminal in brainstem slices. Intraterminal loading of botulinum toxin E revealed that the rapid capacitance transient implicated as “kiss-and-run” was unrelated to transmitter release. The release-related capacitance change decayed with an endocytotic time constant of 10 to 25 seconds, depending on the magnitude of exocytosis. Presynaptic loading of the nonhydrolyzable guanosine 5′-triphosphate (GTP) analog GTPgS or dynamin-1 proline-rich domain peptide abolished endocytosis. These compounds had no immediate effect on exocytosis, but caused a use-dependent rundown of exocytosis. Thus, the guanosine triphosphatase dynamin-1 is indispensable for vesicle endocytosis at this fast central nervous system (CNS) synapse.
Normalization of Tumor Vasculature: An Emerging Concept in Antiangiogenic Therapy
Authors: Jain Rakesh K.
Published: January 2005

Solid tumors require blood vessels for growth, and many new cancer therapies are directed against the tumor vasculature. The widely held view is that these antiangiogenic therapies should destroy the tumor vasculature, thereby depriving the tumor of oxygen and nutrients. Here, I review emerging evidence supporting an alternative hypothesis—that certain antiangiogenic agents can also transiently “normalize” the abnormal structure and function of tumor vasculature to make it more efficient for oxygen and drug delivery. Drugs that induce vascular normalization can alleviate hypoxia and increase the efficacy of conventional therapies if both are carefully scheduled. A better understanding of the molecular and cellular underpinnings of vascular normalization may ultimately lead to more effective therapies not only for cancer but also for diseases with abnormal vasculature, as well as regenerative medicine, in which the goal is to create and maintain a functionally normal vasculature.
Persistence of Animal and Human Glycopeptide-Resistant Enterococci on Two Norwegian Poultry Farms Formerly Exposed to Avoparcin Is Associated with a Widespread Plasmid-Mediated
vanA
Element within a Polyclonal
Enterococcus faecium
Population
Authors: Johnsen P. J. , Østerhus J. I. , Sletvold H. , Sørum M. , Kruse H. , Nielsen K. , Simonsen G. S. , Sundsfjord A.
Published: January 2005

The evolutionary processes responsible for the long-term persistence of glycopeptide-resistant
Enterococcus faecium
(GREF) in nonselective environments were addressed by genetic analyses of
E. faecium
populations in animals and humans on two Norwegian poultry farms that were previously exposed to avoparcin. A total of 222 fecal GREF (
n
= 136) and glycopeptide-susceptible (
n
= 86)
E. faecium
(GSEF) isolates were obtained from farmers and poultry on three separate occasions in 1998 and 1999. Pulsed-field gel electrophoresis (PFGE) and plasmid DNA analyses discerned 22 GREF and 32 GSEF PFGE types within shifting polyclonal animal and human
E. faecium
populations and indicated the presence of transferable plasmid-mediated
vanA
resistance, respectively. Examples of dominant, persistent GREF PFGE types supported the notion that environmentally well-adapted GREF types may counteract the reversal of resistance. PFGE analyses, sequencing of the
purK
housekeeping gene, and partial typing of
vanA
-containing Tn
1546
suggested a common animal and human reservoir of glycopeptide resistance. Inverse PCR amplification and sequence analyses targeting the right end of the Tn
1546
-plasmid junction fragment strongly indicated the presence of a common single Tn
1546
-plasmid-mediated element in 20 of 22 GREF PFGE types. This observation was further strengthened by
vanY-vanZ
hybridization analyses of plasmid DNAs as well as the finding of a physical linkage between Tn
1546
and a putative postsegregation killing system for seven GREF PFGE types. In conclusion, our observations suggest that the molecular unit of persistence of glycopeptide resistance is a common mobile plasmid-mediated
vanA
-containing element within a polyclonal GREF population that changes over time. In addition, we propose that “plasmid addiction systems” may contribute to the persistence of GREF in nonselective environments.
Phenotypic Screening of
Escherichia coli
K-12 Tn
5
Insertion Libraries, Using Whole-Genome Oligonucleotide Microarrays
Authors: Winterberg Kelly M. , Luecke John , Bruegl Amanda S. , Reznikoff William S.
Published: January 2005

Complete genome sequences in combination with global screening methods allow parallel analysis of multiple mutant loci to determine the requirement for specific genes in different environments. In this paper we describe a high-definition microarray approach for investigating the growth effects of Tn
5
insertions in
Escherichia coli
K-12. Libraries of insertion mutants generated by a unique Tn
5
mutagenesis system were grown competitively in defined media. Biotin-labeled runoff RNA transcripts were generated in vitro from transposon insertions in each population of mutants. These transcripts were then hybridized to custom-designed oligonucleotide microarrays to detect the presence of each mutant in the population. By using this approach, the signal associated with 25 auxotrophic insertions in a 50-mutant pool was not detectable following nine generations of growth in glucose M9 minimal medium. It was found that individual insertion sites could be mapped to within 50 bp of their genomic locations, and 340 dispensable regions in the
E. coli
chromosome were identified. Tn
5
insertions were detected in 15 genes for which no previous insertions have been reported. Other applications of this method are discussed.
Methods To Increase Fidelity of Repetitive Extragenic Palindromic PCR Fingerprint-Based Bacterial Source Tracking Efforts
Authors: Hassan Wail M. , Wang Shiao Y. , Ellender Rudolph D.
Published: January 2005

The goal of the study was to determine which similarity coefficient and statistical method to use to produce the highest rate of correct assignment (RCA) in repetitive extragenic palindromic PCR-based bacterial source tracking. In addition, the use of standards for deciding whether to accept or reject source assignments was investigated. The use of curve-based coefficients Cosine Coefficient and Pearson's Product Moment Correlation yielded higher RCAs than the use of band-based coefficients Jaccard, Dice, Jeffrey's x, and Ochiai. When enterococcal and
Escherichia coli
isolates from known sources were used in a blind test, the use of maximum similarity produced consistently higher RCAs than the use of average similarity. We also found that the use of a similarity value threshold and/or a quality factor threshold (the ratio of the average fingerprint similarity within a source to the average similarity of this source's isolates to an unknown) to decide whether to accept source assignments of unknowns increases the reliability of source assignments. Applying a similarity value threshold improved the overall RCA (ORCA) by 15 to 27% when enterococcal fingerprints were used and 8 to 29% when
E. coli
fingerprints were used. Applying the quality factor threshold resulted in a 22 to 32% improvement in the ORCA, depending on the fingerprinting technique used. This increase in reliability was, however, achieved at the expense of decreased numbers of isolates that were assigned a source.