bluuebunny/crossref_metadata_2025 huggingface dataset:
Finite element analysis of the mouse tibia: Estimating endocortical strain during three‐point bending in SAMP6 osteoporotic mice
Authors: Silva Matthew J. , Brodt Michael D. , Hucker William J.
Published: March 2005

To support future studies of tibial bending in a murine model of senile osteoporosis (SAMP6), we sought to determine the relationship between applied external bending force and peak endocortical strain in the tibiae of SAMP6 and control SAMR1 mice. The lower hindlimbs of mice were loaded by three‐point bending in the lateral‐medial plane with a support length of 10 mm. Force‐periosteal strain relations were first determined using standard strain gauge methods. Finite‐element analysis (FEA) models of the tibia‐fibula were generated based on microcomputed tomography images. After choosing appropriate boundary conditions, FEA predictions of periosteal strains were within 15% of measured values. FEA revealed a narrow (3–4 mm) region of the central tibia with well‐developed bending strains (tension medially, compression laterally); outside this region, we observed high shear strains. Both the strain gauge data and the finite‐element simulations indicated that the tibia of the SAMP6 mouse was 20–25% stiffer than the SAMR1 tibia, consistent with a larger moment of inertia and higher cortical bone modulus. Thus, higher levels of force are required to produce the same target values of strain in the SAMP6 tibia. The ratio of periosteal to endocortical strain in the region of interest was similar for the two mouse strains (1.5–1.6). Based on these ratios, we scaled the strain gauge data to estimate the force‐endocortical strain relations for the two mouse strains. In conclusion, FEA, with supporting strain gauge measurements, has provided unique insight regarding the strain environment throughout the tibia during three‐point bending in mice. © 2005 Wiley‐Liss, Inc.
Australopithecus anamensis: A finite‐element approach to studying the functional adaptations of extinct hominins
Authors: Macho Gabriele A. , Shimizu Daisuke , Jiang Yong , Spears Iain R.
Published: March 2005

Australopithecus anamensis is the stem species of all later hominins and exhibits the suite of characters traditionally associated with hominins, i.e., bipedal locomotion when on the ground, canine reduction, and thick‐enameled teeth. The functional consequences of its thick enamel are, however, unclear. Without appropriate structural reinforcement, these thick‐enameled teeth may be prone to failure. This article investigates the mechanical behavior of A. anamensis enamel and represents the first in a series that will attempt to determine the functional adaptations of hominin teeth. First, the microstructural arrangement of enamel prisms in A. anamensis teeth was reconstructed using recently developed software and was compared with that of extant hominoids. Second, a finite‐element model of a block of enamel containing one cycle of prism deviation was reconstructed for Homo, Pan, Gorilla, and A. anamensis and the behavior of these tissues under compressive stress was determined. Despite similarities in enamel microstructure between A. anamensis and the African great apes, the structural arrangement of prismatic enamel in A. anamensis appears to be more effective in load dissipation under these compressive loads. The findings may imply that this hominin species was well adapted to puncture crushing and are in some respects contrary to expectations based on macromorphology of teeth. Taking together, information obtained from both finite‐element analyses and dental macroanatomy leads us to suggest that A. anamensis was probably adapted for habitually consuming a hard‐tough diet. However, additional tests are needed to understand the functional adaptations of A. anamensis teeth fully. © 2005 Wiley‐Liss, Inc.
Glucocorticoids inhibit osteocalcin transcription in osteoblasts by suppressing Egr2/Krox20‐binding enhancer
Authors: Leclerc Nathalie , Noh Tommy , Khokhar Arvinder , Smith Elisheva , Frenkel Baruch
Published: March 2005

Objective

Glucocorticoids are widely used for the management of rheumatoid arthritis. Osteoporosis is a major side effect of glucocorticoid therapy and is attributable to inhibition of bone formation. We developed an osteoblast culture system in which glucocorticoids strongly inhibit development of the osteoblast phenotype, including expression of the bone‐specific osteocalcin (OC) gene. Using this gene as a model, the goal of this study was to discover glucocorticoid‐sensitive transcriptional mechanisms in osteoblasts.

Methods

Dexamethasone (DEX; 1 μM) was administered to murine MC3T3‐E1 osteoblastic cultures under conditions that inhibit mineralized extracellular matrix formation and OC messenger RNA levels by >10‐fold. Because standard (short‐term) transient transfection assays with OC promoter‐reporter constructs did not recapitulate the strong DEX‐mediated repression, mapping of OC negative glucocorticoid response elements (GREs) was performed initially by stable transfection and then with long‐term transient transfection assays. Transcription factor binding to the OC negative GRE was studied by electrophoretic mobility shift assays.

Results

Several‐fold repression of OC–luciferase constructs was recapitulated in stable and long‐term transient transfection assays, in which the transfected cells were allowed to progress to a sufficiently advanced developmental stage. Analysis of a 5′ promoter deletion series mapped an OC negative GRE to a 15‐bp G/C‐rich motif (−161/−147) located just upstream of the binding site for the osteoblast master transcription factor Runx2. Oligonucleotides encompassing this element and MC3T3‐E1 cell extracts formed a protein–DNA complex that contained an Egr/Krox family member(s). Complex formation was competed by either an oligonucleotide containing 2 consensus Egr motifs or by anti‐Egr2/Krox20 antibodies. Three copies of this Krox‐binding element conferred 20‐fold transcriptional activation on the 147‐bp basal OC promoter in osteoblasts, and the enhancer activity was inhibited by DEX. Enhancer activity was not observed in 10T1/2 fibroblasts unless these cells were cotransfected with Runx2.

Conclusion

An Egr2/Krox20‐binding site located immediately upstream of the Runx2 site of the mouse OC promoter was identified as an enhancer in osteoblasts, whose activity is repressed by glucocorticoids. Sequence similarity suggests that such a mechanism is likely operative in both murine and human cells. Because glucocorticoids inhibit Egr2/Krox20 expression in osteoblasts, and because trabecular bone formation is arrested in Egr2/Krox20‐knockout mice, the inhibition of Egr2/Krox20 activity likely contributes to glucocorticoid‐induced osteoporosis.
Joint inflammation and chondrocyte death become independent of Fcγ receptor type III by local overexpression of interferon‐γ during immune complex–mediated arthritis
Authors: Nabbe K. C. A. M. , Boross P. , Holthuysen A. E. M. , Sloëtjes A. W. , Kolls J. K. , Verbeek S. , Van Lent P. L. E. M. , Van Den Berg W. B.
Published: March 2005

Objective

It has previously been shown that the onset and the degree of joint inflammation during immune complex (IC)–mediated arthritis depend on Fcγ receptor type III (FcγRIII). Local adenoviral overexpression of interferon‐γ (IFNγ) in the knee joint prior to onset of IC‐mediated arthritis aggravated severe cartilage destruction. In FcγRI−/− mice, however, chondrocyte death was not enhanced by IFNγ, whereas matrix metalloproteinase (MMP)–mediated aggrecan breakdown was markedly elevated, suggesting a role for the activating FcγRIII in the latter process. We undertook this study to determine the role of FcγRIII in joint inflammation and severe cartilage destruction in IFNγ‐stimulated IC‐mediated arthritis, using FcγRIII−/− mice.

Methods

FcγRIII−/− and wild‐type (WT) mice were injected in the knee joint with recombinant adenovirus encoding murine IFNγ (AdIFNγ) or with adenovirus encoding enhanced green fluorescent protein 1 day prior to induction of IC‐mediated arthritis. Histologic sections were obtained 3 days after arthritis onset to study inflammation and cartilage damage. MMP‐mediated expression of the VDIPEN neoepitope was detected by immunolocalization. Chemokine and FcγR expression levels were determined in synovial washouts and synovium, respectively.

Results

Injection of AdIFNγ in naive knee joints markedly increased levels of messenger RNA for FcγRI, FcγRII, and FcγRIII. Upon IFNγ overexpression prior to induction of IC‐mediated arthritis, joint inflammation was similar in FcγRIII−/− and WT mice. The percentage of macrophages in the knee joint was increased, which correlated with high concentrations of the macrophage attractant macrophage inflammatory protein 1α. Furthermore, IFNγ induced 2‐fold and 3‐fold increases in chondrocyte death in WT controls and FcγRIII−/− mice, respectively. Notably, VDIPEN expression also remained high in FcγRIII−/− mice.

Conclusion

IFNγ bypasses the dependence on FcγRIII in the development of IC‐mediated arthritis. Furthermore, both FcγRI and FcγRIII can mediate MMP‐dependent cartilage matrix destruction.
Expression of interleukin‐21 receptor in epidermis from patients with systemic sclerosis
Authors: Distler Jörg H. W. , Jüngel Astrid , Kowal‐Bielecka Otylia , Michel Beat A. , Gay Renate E. , Sprott Haiko , Matucci‐Cerinic Marco , Chilla Meike , Reich Kristian , Kalden Joachim R. , Müller‐Ladner Ulf , Lorenz Hanns M. , Gay Steffen , Distler Oliver
Published: March 2005

Objective

To examine the expression and regulation of interleukin‐21 (IL‐21) and IL‐21 receptor (IL‐21R) in patients with systemic sclerosis (SSc; scleroderma).

Methods

Skin biopsy specimens were obtained from 23 patients with SSc and 15 healthy controls. IL‐21/IL‐21R messenger RNA (mRNA) was quantified using real‐time polymerase chain reaction (PCR). The expression pattern of IL‐21/IL‐21R was analyzed by in situ hybridization and Western blotting. Stimulation experiments were performed with cultured dermal fibroblasts from patients with SSc and healthy controls as well as with keratinocytes, using IL‐1β, platelet‐derived growth factor BB, monocyte chemoattractant protein 1, transforming growth factor β, and IL‐21. The SCID‐hu skin mouse model was used for in vivo experiments.

Results

IL‐21R mRNA was detected in all biopsy specimens from patients with SSc and controls, with a 4.7‐fold increase observed in SSc samples. In situ hybridization and immunohistochemical analysis showed an up‐regulation of IL‐21R in samples of epidermis from SSc patients, whereas no signal was detected in skin specimens from healthy controls. These results were confirmed in vitro, in that cultured keratinocytes expressed significant levels of IL‐21R, whereas no signal was observed in fibroblasts. Interestingly, mRNA for IL‐21 could not be detected by real‐time PCR and in situ hybridization. Various concentrations of key cytokines in the pathogenesis of SSc did not stimulate the expression of IL‐21R mRNA in cultured keratinocytes and dermal fibroblasts. In the SCID mouse transplantation model, the overexpression of IL‐21R mRNA in SSc keratinocytes remained unchanged after transplantation.

Conclusion

The up‐regulation of IL‐21R in keratinocytes indicates that, similar to fibroblasts and endothelial cells, the expression pattern is altered in SSc. Moreover, the expression of IL‐21R appears to be independent of key cytokines that are operant in SSc.
Induction of cartilage damage by overexpression of T cell interleukin‐17A in experimental arthritis in mice deficient in interleukin‐1
Authors: Koenders Marije I. , Lubberts Erik , Oppers‐Walgreen Birgitte , van den Bersselaar Liduine , Helsen Monique M. , Kolls Jay K. , Joosten Leo A. B. , van den Berg Wim B.
Published: March 2005

Objective

To examine the capacity of T cell interleukin‐17A (IL‐17A; referred to hereinafter as IL‐17) to induce cartilage damage during experimental arthritis in the absence of IL‐1.

Methods

Local IL‐17 gene transfer was performed in the knee joint of IL‐1–deficient mice and wild‐type controls during streptococcal cell wall (SCW)–induced arthritis. Knee joints were isolated at various time points for histologic analysis of cartilage proteoglycan (PG) depletion. Expression of messenger RNA for inducible nitric oxide synthase, matrix metalloproteinases (MMPs) 3, 9, and 13, and ADAMTS‐4 was determined by quantitative polymerase chain reaction analysis. VDIPEN staining was analyzed to study MMP‐mediated cartilage damage. In addition, systemic anti–IL‐1α/β antibody treatment was performed in mice immunized with type II collagen and injected locally with an adenoviral vector expressing IL‐17 or with control adenovirus. Knee joints were isolated and analyzed for cartilage PG depletion, chondrocyte death, and cartilage surface erosion.

Results

During SCW‐induced arthritis, local T cell IL‐17 gene transfer turned this acute, macrophage‐driven joint inflammation into a severe, chronic arthritis accompanied by aggravated cartilage damage. Of high interest, the IL‐1 dependency of cartilage PG depletion was fully abrogated when IL‐17 was locally overexpressed in the joint. Moreover, local IL‐17 gene transfer increased MMP expression without the need for IL‐1, although IL‐1 remained essential for part of the cartilage VDIPEN expression. Furthermore, when IL‐17 was overexpressed in the knee joints of mice with collagen‐induced arthritis, anti–IL‐1 treatment did not reduce the degree of chondrocyte death or cartilage surface erosion.

Conclusion

These data show the capacity of IL‐17 to replace the catabolic function of IL‐1 in cartilage damage during experimental arthritis.
Acetabular dysplasia predicts incident osteoarthritis of the hip: The Rotterdam study
Authors: Reijman M. , Hazes J. M. W. , Pols H. A. P. , Koes B. W. , Bierma‐Zeinstra S. M. A.
Published: March 2005

Objective

To investigate the association between acetabular dysplasia and the incidence of radiographic osteoarthritis (OA) of the hip in a population‐based sample of elderly subjects.

Methods

Radiographs of the hip at baseline and at followup (mean followup time 6.6 years) were evaluated in 835 men and women (age ≥55 years) from the Rotterdam Study. Subjects with a baseline Kellgren/Lawrence grade of 0 or 1 in both hips were included in the study. Incident radiographic OA of the hip was defined as a decrease of joint space width of the hip (≥1.0 mm) at followup. Acetabular dysplasia was assessed using the center‐edge angle and the acetabular depth. The association between acetabular dysplasia and incident radiographic hip OA was assessed by calculating odds ratios using multivariate regression analysis.

Results

In this study population with a mean ± SD age of 65.6 ± 6.5 years, 9.3% developed incident radiographic hip OA. Subjects with acetabular dysplasia (center‐edge angle <25°) had a 4.3‐fold increased risk for incident radiographic OA of the hip (95% confidence interval 2.2–8.7) compared with subjects without acetabular dysplasia. These associations were independent of known determinants of hip OA such as age, sex, and body mass index (BMI), but tended to be enhanced by female sex, heavy mechanical load, and low BMI.

Conclusion

In a study population age ≥55 years, acetabular dysplasia is still a strong independent determinant of incident radiographic hip OA.
A serum proteomic approach to gauging the state of remission in Wegener's granulomatosis
Authors: Stone John H. , Rajapakse Vinodh N. , Hoffman Gary S. , Specks Ulrich , Merkel Peter A. , Spiera Robert F. , Davis John C. , St.Clair E. William , McCune Joseph , Ross Sally , Hitt Ben A. , Veenstra Timothy D. , Conrads Thomas P. , Liotta Lance A. , Petricoin Emanuel F. ,   Wegener's Granulomatosis Etanercept Trial (WGET) Research Group
Published: March 2005

Objective

To identify serum ion patterns that distinguish remission from active disease in patients with Wegener's granulomatosis (WG).

Methods

Using sera collected in the WG Etanercept Trial, we selected samples from patients who either were undergoing a period of extended disease remission or had recent flares of active WG. Unfractionated samples were randomized into sets for training and testing, such that remission sera and active disease sera could be analyzed without batch bias. Molecular species within the sera were ionized by high‐resolution, matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. We then used a bioinformatics pattern‐recognition tool to identify optimal combinations of ions. During the training stage, the clinical data (remission versus active disease) were provided in association with the spectral data from each sample. In the testing stage, we performed blinded testing on a previously unexamined set of samples.

Results

The most robust model, trained on a total of 82 samples (42 remission, 40 active disease), included 7 key ions with mass:charge ratios of 803.239, 2,171.672, 2,790.574, 3,085.237, 5,051.726, 5,833.989, and 6,630.465. The combined relative amplitudes of these 7 ions identified 5 distinct clusters of either remission or active disease samples during the training stage. In the testing stage, this model segregated 72 samples into the same 5 clusters, including 1 large remission cluster (n = 28) and another large active disease cluster (n = 32). Three smaller clusters of active disease or remission samples were also identified, with remission clusters populated by 2 samples in one cluster and 8 in another, and an active disease cluster populated by 2 samples. The model categorized 35 of 37 remission samples correctly (sensitivity 95%, 95% confidence interval [95% CI] 82.1–99.4) and 32 of 35 active disease samples correctly (specificity 91%, 95% CI 78.1–98.1).

Conclusion

This serum proteomic profiling approach appears to be useful in distinguishing between states of stable clinical remission and active disease. Further validation and refinement of this strategy may help clinicians apply immunosuppressive therapies more judiciously among their patients, thereby avoiding morbidity and mortality from excessive treatment. Identification of the most robust and clinically useful combinations of ions will permit the rational selection of molecules for sequencing and analysis.
Electroencephalography in the assessment of neuropsychiatric manifestations in antiphospholipid syndrome and systemic lupus erythematosus
Authors: Lampropoulos Christos E. , Koutroumanidis Michael , Reynolds Piero P. M. , Manidakis Ioannis , Hughes Graham R. V. , D'Cruz David P.
Published: March 2005

Objective

To describe the prevalence and clinical associations of abnormalities on electroencephalography (EEG) in patients with antiphospholipid syndrome (APS) and/or systemic lupus erythematosus (SLE) who have neuropsychiatric symptoms.

Methods

The study group comprised 57 patients (age ≤50 years) with manifestations of neuropsychiatric illness. Patients with stroke, epilepsy, or other encephalopathies were excluded. Fourteen patients had APS, 24 patients were positive for antiphospholipid antibodies (aPL), and 19 patients had SLE without aPL. All patients underwent EEG and brain magnetic resonance imaging (MRI) while they were awake.

Results

Abnormal EEG findings (showing mainly bitemporal slow activity) were recorded in 37 of 57 patients (65%). Abnormal EEG findings were observed in all patients with APS and in 17 of 24 aPL‐positive patients (71%), compared with 6 of 19 patients with SLE (32%) (P < 0.001 and P < 0.05, respectively). There was an association between abnormal EEG findings and the frequency of aPL positivity (at least 2 positive results) (P = 0.002). Three EEG recordings showed potentially epileptiform activity. Results of brain MRI were abnormal in 18 (31.6%) of 57 patients: 8 in the APS group (57.1%), 7 in the aPL‐positive group (29.2%), and 3 in the SLE group (15.8%). None of the patients with normal EEG findings had abnormal MRI results. Thus, brain MRI findings were normal in the majority of patients. Patients with abnormal EEG results were more likely to report memory problems (P < 0.001).

Conclusion

Our findings suggest that EEG abnormalities are common and correlate with the presence of aPL even in the absence of brain abnormalities on MRI. EEG should be considered in aPL‐positive patients with neuropsychiatric symptoms, because use of antiaggregants or anticoagulation may need to be considered.
PEGylated interferon alfa‐2b and ribavirin treatment in patients with hepatitis C virus–related systemic vasculitis
Authors: Cacoub Patrice , Saadoun David , Limal Nicolas , Sene Damien , Lidove Olivier , Piette Jean‐Charles
Published: March 2005

Objective

Type II mixed cryoglobulinemia (MC) is a systemic vasculitis usually associated with hepatitis C virus (HCV), which may involve the skin, kidneys, and nervous system. Molecular evidence of antigen‐driven B cell proliferation is definitively provided in HCV‐associated type II MC, and HCV appears to be the key trigger. The present trial was established to investigate the efficacy of therapy with PEGylated interferon alfa‐2b (PEG–IFN alfa‐2b) plus ribavirin in patients with HCV‐related MC vasculitis.

Methods

Nine consecutive patients with HCV‐related MC received PEG–IFN alfa‐2b (1.5 μg/kg/week) subcutaneously plus oral ribavirin (800–1,200 mg/day) for at least 6 months. The response to treatment was analyzed by comparing clinical, immunologic, and virologic parameters at the initial evaluation with those observed during followup.

Results

The mean ± SD duration of therapy with PEG–IFN alfa‐2b plus ribavirin was 13.5 ± 2.8 months. After a mean period of 18.6 months following discontinuation of treatment, all 9 patients are alive. Seven patients (78%) had a sustained virologic response and were complete clinical responders. Serum cryoglobulin disappeared in 5 of 9 patients (56%), and complement levels normalized in 80% of the patients. One patient had a partial virologic response with a complete clinical response. In another patient, a clinical relapse of MC vasculitis occurred in association with the reappearance of HCV RNA. Treatment was well tolerated, and no patient had side effects for which discontinuation of therapy was required.

Conclusion

Treatment with PEG–IFN alfa‐2b plus ribavirin can achieve a complete clinical response in most patients with HCV‐related MC vasculitis. Complete clinical response correlates with the eradication of HCV and requires a shorter treatment period than that previously reported for IFNα plus ribavirin.
Amelioration of acute inflammation by systemic administration of a cell‐permeable peptide inhibitor of NF‐κB activation
Authors: di Meglio Paola , Ianaro Angela , Ghosh Sankar
Published: March 2005

Objective

We used an experimental model of inflammation in mice, carrageenan‐induced paw edema, to study the antiinflammatory effects of the NEMO‐binding domain (NBD) peptide, which blocks activation of the inducible transcription factor NF‐κB.

Methods

Paw edema was induced by subplantar injection of 1% λ‐carrageenan into the mouse left hind paw. Test agents were given intraperitoneally immediately after carrageenan injection. The increase in footpad thickness was considered to be edema. In some experiments, the mice were killed and the paws were removed for histologic and molecular biology analysis. NF‐κB DNA binding activity was evaluated in nuclear extracts by electrophoretic mobility shift assays. The expression levels of NF‐κB–regulated cyclooxygenase 2 (COX‐2) protein and tumor necrosis factor α (TNFα) messenger RNA (mRNA) were evaluated by immunoblot analysis and polymerase chain reaction amplification of reverse‐transcribed mRNA, respectively.

Results

We found that systemically administered NBD peptide significantly inhibited edema formation and cellular infiltration in inflamed mouse paws. This antiinflammatory activity was most likely due to inhibition of expression of proinflammatory mediators, such as TNFα and COX‐2, in inflamed tissues.

Conclusion

These studies further establish NF‐κB as a target for antiinflammatory therapy and provide support for the use of the NBD peptide as a possible therapeutic agent for inflammatory diseases.
Recruitment of topoisomerase I (Scl‐70) to nucleoplasmic proteasomes in response to xenobiotics suggests a role for altered antigen processing in scleroderma
Authors: Chen Min , Dittmann Assemgul , Kuhn Annegret , Ruzicka Thomas , Mikecz Anna von
Published: March 2005

Objective

Scleroderma, also known as systemic sclerosis (SSc), is a chronic, life‐threatening autoimmune disease characterized by a wide spectrum of manifestations and a variable evolution. The presence of particular antinuclear antibodies is often predictive of the clinical expression and prognosis of the disease, but the molecular mechanisms of the immune responses remain unclear. Recently, we have shown xenobiotic‐induced recruitment of nuclear autoantigens to proteasomes in the cell nucleus in cell culture and in animal models in correlation with a unique autoantibody response. In this study, we attempted to validate our findings in patients with SSc.

Methods

Using indirect immunofluorescence microscopy, run‐on replication and transcription assays, immunoblotting, and proteasome activity assays, we analyzed the nuclear structure, function, and proteasomal proteolysis in HEp‐2 cells treated with xenobiotics or left untreated. Blood dendritic cells (DCs) were isolated from 30 patients with SSc and age‐ and sex‐matched control subjects to determine the subcellular localization of SSc autoantigens in relation to proteasomes.

Results

Xenobiotics induced a relocation of the SSc autoantigen DNA topoisomerase I (Scl‐70, topo I) to nucleoplasmic clusters, where proteasomes degrade topo I. Colocalization of topo I with proteasomes occurred exclusively in DCs from patients with SSc who developed antibodies against this autoantigen. Neither centromeres nor other SSc autoantigens colocalized with proteasomes in DCs from patients with SSc or from control subjects.

Conclusion

Alteration of nuclear structure and function by xenobiotics induces recruitment of the nuclear autoantigen topo I for proteasomal processing. This event may, in turn, lead to subsequent presentation of the resulting peptides on the cell surface and the autoimmune responses against topo I in SSc.
Protein name tagging guidelines: lessons learned
Authors: Mani Inderjeet , Hu Zhangzhi , Jang Seok Bae , Samuel Ken , Krause Matthew , Phillips Jon , Wu Cathy H.
Published: March 2005

Interest in information extraction from the biomedical literature is motivated by the need to speed up the creation of structured databases representing the latest scientific knowledge about specific objects, such as proteins and genes. This paper addresses the issue of a lack of standard definition of the problem of protein name tagging. We describe the lessons learned in developing a set of guidelines and present the first set of inter‐coder results, viewed as an upper bound on system performance. Problems coders face include: (a) the ambiguity of names that can refer to either genes or proteins; (b) the difficulty of getting the exact extents of long protein names; and (c) the complexity of the guidelines. These problems have been addressed in two ways: (a) defining the tagging targets as protein named entities used in the literature to describe proteins or protein‐associated or ‐related objects, such as domains, pathways, expression or genes, and (b) using two types of tags, protein tags and long‐form tags, with the latter being used to optionally extend the boundaries of the protein tag when the name boundary is difficult to determine. Inter‐coder consistency across three annotators on protein tags on 300 MEDLINE abstracts is 0.868 F‐measure. The guidelines and annotated datasets, along with automatic tools, are available for research use. Copyright © 2005 John Wiley & Sons, Ltd.
Genomic analyses of transport proteins inRalstonia metallidurans
Authors: von Rozycki Torsten , Nies Dietrich H. , Saier Milton H.
Published: March 2005

Ralstonia (Wautersia, Cupriavidus) metallidurans(Rme) is better able to withstand high concentrations of heavy metals than any other well‐studied organism. This fact renders it a potential agent of bioremediation as well as an ideal model organism for understanding metal resistance phenotypes. We have analysed the genome of Rme for genes encoding homologues of established and putative transport proteins; 13% of all genes in Rme encode such homologues. Nearly one‐third of the transporters identified (32%) appear to function in inorganic ion transport with three‐quarters of these acting on cations. Transporters specific for amino acids outnumber sugar transporters nearly 3 : 1, and this fact plus the large number of uptake systems for organic acids indicates the heterotrophic preferences of these bacteria. Putative drug efflux pumps comprise 10% of the encoded transporters, but numerous efflux pumps for heavy metals, metabolites and macromolecules were also identified. The results presented should facilitate genetic manipulation and mechanistic studies of transport in this remarkable bacterium. Copyright © 2005 John Wiley & Sons, Ltd.
Ontology‐based interactive information extraction from scientific abstracts
Authors: Milward David , Bjäreland Marcus , Hayes William , Maxwell Michelle , Öberg Lisa , Tilford Nick , Thomas James , Hale Roger , Knight Sylvia , Barnes Julie
Published: March 2005

Over recent years, there has been a growing interest in extracting information automatically or semi‐automatically from the scientific literature. This paper describes a novel ontology‐based interactive information extraction (OBIIE) framework and a specific OBIIE system. We describe how this system enables life scientists to make ad hoc queries similar to using a standard search engine, but where the results are obtained in a database format similar to a pre‐programmed information extraction engine. We present a case study in which the system was evaluated for extracting co‐factors from EMBASE and MEDLINE. Copyright © 2005 John Wiley & Sons, Ltd.
Monastrol, a selective inhibitor of the mitotic kinesin Eg5, induces a distinctive growth profile of dendrites and axons in primary cortical neuron cultures
Authors: Yoon Seung Yong , Choi Jung Eun , Huh Jae‐Wan , Hwang Onyou , Lee Hui Sun , Hong Hea Nam , Kim Donghou
Published: March 2005

Various factors including some motor proteins regulate microtubule (MT) transport and influence the formation of neuronal processes. Eg5, a slow and non‐processive (+)‐end directed motor molecule, is expressed in developing and differentiated neurons. However, how Eg5 works in neurons is still elusive. Thus, we treated primary rat cortical neuron cultures with monastrol, a specific inhibitor of Eg5, to investigate its role in neurons. Immature neurons treated with monastrol extended longer processes than control within a few hours. After 3 days, immature neurons treated with monastrol had longer dendrites but slightly shorter axons than control. This difference in growth between dendrites and axons became more prominent as the cells differentiated until 5 days. Interestingly, MT distributions in the cell bodies of monastrol‐treated neurons appeared somewhat circular surrounding the nucleus, while MTs in the cell bodies of control neurons were primarily distributed in the MT organizing center (MTOC) just beside the nucleus. In mature neurons, monastrol treatment induced the axonal clusters of tubulins, grossly not affecting dendrites. Taken together, we conclude that Eg5 acts distinctively on dendrites and axons in neurons and suggest a putative model of how Eg5 works distinctively on dendrites and axons. Cell Motil. Cytoskeleton 60:181–190, 2005. © 2005 Wiley‐Liss, Inc.
Preparing to move: Assembly of the MSP amoeboid motility apparatus during spermiogenesis in Ascaris
Authors: Rodriguez Maria Antonia , LeClaire Lawrence L. , Roberts Thomas M.
Published: March 2005

We exploited the rapid, inducible conversion of non‐motile Ascaris spermatids into crawling spermatozoa to examine the pattern of assembly of the MSP motility apparatus that powers sperm locomotion. In live sperm, the first detectable motile activity is the extension of spikes and, later, blebs from the cell surface. However, examination of cells by EM revealed that the formation of surface protrusions is preceded by assembly of MSP filament tails on the membranous organelles in the peripheral cytoplasm. These organelle‐associated filament meshworks assemble within 30 sec after induction of spermiogenesis and persist until the membranous organelles are sequestered into the cell body when the lamellipod extends. The filopodia‐like spikes, which are packed with bundles of filaments, extend and retract rapidly but last only a few seconds before giving way to, or converting into, blebs. Coalescence of these blebs, each supported by a dense mesh of filaments, often initiates lamellipod extension, which culminates in the formation of the robust, dynamic MSP fiber complexes that generate sperm motility. The same membrane phosphoprotein that orchestrates assembly of the fiber complexes at the leading edge of the lamellipod of mature sperm is also found at all sites of filament assembly during spermiogenesis. The orderly progression of steps that leads to construction of a functional motility apparatus illustrates the precise spatio‐temporal control of MSP filament assembly in the developing cell and highlights the remarkable similarity in organization and plasticity shared by the MSP cytoskeleton and the actin filament arrays in conventional crawling cells. Cell Motil. Cytoskeleton 60:191–199, 2005 © 2005 Wiley‐Liss, Inc.
Through versus Cross Electron Delocalization in Polytriacetylene Oligomers: A Computational Analysis
Authors: Bruschi Maurizio , Giuffreda Maria Grazia , Lüthi Hans Peter
Published: March 2005

Herein, we report a systematic theoretical investigation of the molecular and electronic properties of unsubstituted polytriacetylene (PTA) and iso‐polytriacetylene (iso‐PTA) oligomers, which are characterized by through and cross π‐conjugation pathways, respectively. The goal of the study is to compare through versus cross conjugation on the basis of the computed molecular geometries of the neutral, anionic, and cationic species, the electron affinities, ionization potentials, excitation energies, and nonlinear optical properties for oligomers up to the nonamer. Differences in the effective conjugation length are directly related to electron delocalization in cross‐ and through‐conjugated pathways. As in the through‐conjugated oligomers, that is, the PTAs, the frontier orbitals of the iso‐PTA oligomers are delocalized along the entire carbon backbone, suggesting that π‐delocalization can extend through cross‐linked carbon atoms. However, in contrast to the PTA oligomers, the bond lengths remain strictly constant and the reduction of the energy gap beyond the trimer is completely due to the correlation contribution. On the other hand, in the anions and cations, the bond lengths do change significantly with increasing chain length. Therefore, oxidation or reduction of the iso‐PTA oligomer appears to switch on delocalization through cross‐linked carbon atoms. Obviously, the effective conjugation length is specific and depends on the observable considered.
Pressure Effects on Friedel–Crafts Alkylation Reactions in Supercritical Difluoromethane
Authors: Abbott Andrew P. , Corr Stuart , Durling Nicola E. , Hope Eric G.
Published: March 2005

Dielectrometry is used as a novel technique for following the rate of a Friedel–Crafts alkylation reaction in supercritical (sc) difluoromethane. Although the process was not optimized, good product yields were obtained and reaction rates were found to be larger than in CO2 at comparable conditions. The reaction order is determined using the initial rate method and the reaction is shown to be first‐order with respect to both anisole and t‐butyl chloride. The reaction rate constant is unaffected by pressures above 120 bar but close to the critical pressure the value decreases with increasing pressure. It is also shown that the product distribution for the alkylation of anisole shows significant pressure dependence with substitution at the ortho‐position being favored at lower pressures, which is ascribed to hydrogen bonding. This pressure dependency is not observed in sc CO2 or using toluene as a substrate, which supports the idea that hydrogen bonding may be important in the reaction mechanism. The effect of the different reagents and temperature on the rate of the alkylation reaction was also determined.
Focal‐Point Conformational Analysis of Ethanol, Propanol, and Isopropanol
Authors: Kahn Kalju , Bruice Thomas C.
Published: March 2005

Conformational analysis of three small alcohols—ethanol, propanol, and isopropanol—was carried out by systematically improving the basis set and the level of electron correlation. Correlation energy contributions to conformational energies are strongly basis‐set‐dependent but accurate energy contributions can be obtained by extrapolation to the basis‐set limit. At the basis‐set limit, second‐ and third‐order electron correlation effects play a significant role for rotations around the CCOH, HCCO, and CCCO bonds. Specifically, second‐ and third‐order correlation effects strongly stabilize structures in which the hydroxylic hydrogen eclipses with the adjacent carbon; a lesser stabilization is present in structures where the CCOH moiety is in the gauche form. Fourth‐order correlation effects to the CCOH rotation are small due to a partial cancellation of the singles, doubles, and quadruples contribution by the triples contribution. Electron correlation significantly lowers barriers for methyl‐group rotations in ethanol and isopropanol, and in these cases the fourth‐order correlation effects are noticeable. The relatively large overall importance of third‐order correlation energy contributions raises a concern that the inability to accurately estimate this slowly converging contribution may become a limiting factor when highly accurate conformational energies in larger molecules are sought.
Simultaneous AFM Manipulation and Fluorescence Imaging of Single DNA Strands
Authors: Hards Andrew , Zhou Chunqing , Seitz Markus , Bräuchle Christoph , Zumbusch Andreas
Published: March 2005

We report combined atomic force and far‐field fluorescence microscopic experiments which allow the simultaneous atomic force manipulation and optical observation of individual dye‐labeled DNA molecules. A detailed understanding of the binding properties of DNA to different transparent surfaces is prerequisite for these investigations. Atomic force spectroscopy and fluorescence microscopy of single DNA strands yielded detailed insight into two different types of DNA binding onto transparent polylysine‐coated and silanized glass surfaces. We subsequently demonstrate how the different binding can be exploited to perform two types of nanomanipulation experiments: On polylysine, strong electrostatic interactions over the whole length of the DNA strand enable the writing of micrometer‐sized patterns. By contrast, the strong pointwise attachment of DNA to silanized surfaces allows horizontal stretching of single DNA strands to lengths exceeding 1.6 times the contour length of the DNA strand. With this new approach it is possible to directly observe the rupture of the strongly bonded DNA strand.
MLL is fused to EB1 (MAPRE1), which encodes a microtubule‐associated protein, in a patient with acute lymphoblastic leukemia
Authors: Fu Jen‐Fen , Hsu Hui‐Chin , Shih Lee‐Yung
Published: March 2005

We have shown that the EB1 (MAPRE1) gene, at 20q11.2, is fused to MLL in an adult patient with pro‐B acute lymphoblastic leukemia. Southern blot analysis indicated that a rearrangement of the MLL gene was involved in the chromosomal abnormality. cDNA panhandle polymerase chain reaction (PCR) identified the fusion transcript, in which MLL exon 6 was fused in‐frame with EB1 exon 5. The presence of the MLL–EB1 and the reciprocal EB1–MLL fusion transcripts was verified by reverse‐transcription PCR. EB1 is the first gene on chromosome 20 found to fuse with MLL. The genomic break junctions of MLL–EB1 and EB1–MLL were amplified by long‐distance PCR. Sequencing of the break junctions revealed that multiple DNA breaks had occurred and that the DNA fragments flanked by these breaks had been duplicated, deleted, or inverted. Nontemplate DNA segments of 2 bp also were detected at the breakpoints on derivative chromosomes 11 and 20. These features indicate that this translocation likely resulted from the DNA damage‐repair pathway. EB1 is a microtubule‐associated protein that interacts with the colorectal adenomatous polyposis coli tumor‐suppressor protein and plays important roles in regulating microtubule dynamics, cell polarity, and chromosome stability. Immunofluorescence staining demonstrated that the MLL–EB1 fusion proteins were localized in the nuclei. © 2005 Wiley‐Liss, Inc.
Ductal breast carcinoma develops through different patterns of chromosomal evolution
Authors: Molist Romain , Gerbault‐Seureau Michele , Sastre‐Garau Xavier , Sigal‐Zafrani Brigitte , Dutrillaux Bernard , Muleris Martine
Published: March 2005

In a previous study that used comparative genomic hybridization (CGH) to analyze 43 ductal breast carcinomas selected for hyperdiploidy, we proposed the existence of two distinct pathways of chromosomal evolution. In the present study, in which we reassessed our cytogenetic findings on 158 ductal breast carcinomas selected for having a modal number of chromosomes of fewer than 60, we confirmed the existence of two subtypes of tumors. Along with the great majority of tumors (142 of 158) that evolved through structural rearrangements with no or very few whole‐chromosome gains, we found that a minor subset (16 of 158) evolved through progressive gains of whole chromosomes with no or only a few associated rearrangements. In this article, we describe the karyotypes of these 16 tumors together with data from CGH, which was performed for 10 of them. Chromosomes 5, 7, 8, and 20 were the most frequently gained. Our findings support the evidence of a new pathway of chromosomal evolution in a small subset of ductal breast carcinomas characterized by numerical chromosome aberrations. © 2005 Wiley‐Liss, Inc.
Genetic and epigenetic alterations of the candidate tumor‐suppressor gene MYO18B, on chromosome arm 22q, in colorectal cancer
Authors: Nakano Tetsuhiro , Tani Masachika , Nishioka Michiho , Kohno Takashi , Otsuka Ayaka , Ohwada Susumu , Yokota Jun
Published: March 2005

Allelic imbalance (AI) on chromosome arm 22q has been detected in 20%–40% of colorectal cancers, suggesting that this chromosome arm has a tumor‐suppressor gene involved in colorectal carcinogenesis. Recently, we isolated a candidate tumor‐suppressor gene, MYO18B, at 22q12.1, that is deleted, mutated, and hypermethylated in more than 50% of lung cancers. In the present study, we analyzed genetic and epigenetic alterations of the MYO18B gene in colorectal cancers. AI at the MYO18B locus was detected in 16 of 43 (40%) informative cases. Mutations of the MYO18B gene were detected in 2 of 11 (18%) cell lines and 1 of 47 (2%) surgical specimens. Nine of 11 (82%) cell lines showed reduced MYO18B expression, which was restored in all 9 by treatment with 5‐aza‐2′‐deoxycytidine and/or trichostatin A (TSA). Although hypermethylation of the promoter CpG island for MYO18B was not detected, a significant correlation was observed between the level of MYO18B expression and the level of acetylation of histones H3 and H4 in 6 cell lines with and without TSA treatment. Thus, it was suggested that MYO18B is inactivated in a considerable fraction of colorectal cancers by several mechanisms, especially silencing by histone deacetylation and/or AI. Furthermore, restoration of MYO18B expression in colorectal cancer cell lines HT29 and DLD‐1 suppressed anchorage‐independent growth, whereas it did not affect the growth rate in vitro. These results suggest that genetic and epigenetic inactivation of the MYO18B gene play an important role in colorectal carcinogenesis. © 2005 Wiley‐Liss, Inc.
NY‐ESO‐1/LAGE‐1 coexpression with MAGE‐A cancer/testis antigens: A tissue microarray study
Authors: Bolli Martin , Schultz‐Thater Elke , Zajac Paul , Guller Ulrich , Feder Chantal , Sanguedolce Francesca , Carafa Vincenza , Terracciano Luigi , Hudolin Tvrtko , Spagnoli Giulio C. , Tornillo Luigi
Published: March 2005

The characterization of the expression pattern of different families of cancer/testis (C/T) antigens in different tumors, at the protein level, might be of relevance in the development of multiantigen vaccine preparations for active specific immunotherapy. We have used tissue microarray (TMA) technology to explore in large numbers of tumor specimens the expression of NY‐ESO‐1/LAGE‐1 C/T antigens and its correlation with MAGE‐A expression by using D8.38 and 57B monoclonal antibodies (MAb). The epitopes recognized by these reagents in C/T antigens were identified by molecular mapping by using a bacterial expression system. Out of 2,052 samples, 119 (5.8%) scored positive upon staining with D8.38 NY‐ESO‐1/LAGE‐1‐specific MAb. Expression in >10% of cases was detectable in melanoma and basalioma (31.6 and 18.2%, respectively), large cell carcinomas and adenocarcinomas of the lung (17.8 and 10.5%, respectively), stomach adenocarcinomas of the intestinal type (13.2%), pT2‐4 bladder TCC (18.2%), nonseminomatous carcinomas of the testis (10.4%) and liposarcomas (15.4%). Simultaneous expression of NY‐ESO‐1/LAGE‐1 and MAGE‐A C/T antigens was then addressed in a TMA where 101/845 and 73/845 samples (12 and 8.6%, respectively) showed evidence of MAGE‐A or NY‐ESO‐1/LAGE‐1 specific staining, respectively. In 35/845 specimens (4.1%) concomitant expression of MAGE‐A and NY‐ESO‐1/LAGE‐1 was observed (p = 0.0002). Discrepancies in the expression of NY‐ESO‐1/LAGE‐1 and MAGE‐A were conspicuously detectable in squamous cell carcinomas of the skin (MAGE‐A positive but NY‐ESO‐1/LAGE‐1 negative) and in liposarcomas (NY‐ESO‐1/LAGE‐1 positive, but MAGE‐A negative). Taken together, these data suggest novel areas of application of C/T antigens targeted active specific immunotherapy possibly based on multiantigen vaccine preparations. © 2005 Wiley‐Liss, Inc.
Estimation of the absolute internal‐rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations
Authors: Darian Eva , Hnizdo Vladimir , Fedorowicz Adam , Singh Harshinder , Demchuk Eugene
Published: March 2005

A method of statistical estimation is applied to the problem of evaluating the absolute entropy of internal rotation in a molecule with two torsional degrees of freedom. The configurational part of the entropy is obtained as that of the joint probability density of an arbitrary form represented by a two‐dimensional Fourier series, the coefficients of which are statistically estimated using a sample of the torsional angles of the molecule obtained by a stochastic simulation. The internal rotors in the molecule are assumed to be attached to a common frame, and their reduced moments of inertia are initially calculated as functions of the two torsional angles, but averaged over all the remaining internal degrees of freedom using the stochastic‐simulation sample of the atomic configurations of the molecule. The torsional‐angle dependence of the reduced moments of inertia can be also averaged out, and the absolute internal‐rotation entropy of the molecule is obtained in a good approximation as the sum of the configurational entropy and a kinetic contribution fully determined by the averaged reduced moments of inertia. The method is illustrated using Monte Carlo simulations of isomers of stilbene and halogenated derivatives of propane. The two torsional angles in cis‐stilbene are found to be much more strongly correlated than those in trans‐stilbene, while the degree of the angular correlation in propane increases strongly on substitution of hydrogen atoms with chlorine. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 651–660, 2005