bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding important sites in protein sequences
Authors: Bickel Peter J. , Kechris Katherina J. , Spector Philip C. , Wedemayer Gary J. , Glazer Alexander N.
Published: November 2002

By using sequence information from an aligned protein family, a procedure is exhibited for finding sites that may be functionally or structurally critical to the protein. Features based on sequence conservation within subfamilies in the alignment and associations between sites are used to select the sites. The sites are subject to statistical evaluation correcting for phylogenetic bias in the collection of sequences. This method is applied to two families: the phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptomonads, and the globins that function in oxygen storage and transport. The sites identified by the procedure are located in key structural positions and merit further experimental study.
Explaining the Pleistocene megafaunal extinctions: Models, chronologies, and assumptions
Authors: Brook Barry W. , Bowman David M. J. S.
Published: November 2002

Understanding of the Pleistocene megafaunal extinctions has been advanced recently by the application of simulation models and new developments in geochronological dating. Together these have been used to posit a rapid demise of megafauna due to over-hunting by invading humans. However, we demonstrate that the results of these extinction models are highly sensitive to implicit assumptions concerning the degree of prey naivety to human hunters. In addition, we show that in Greater Australia, where the extinctions occurred well before the end of the last Ice Age (unlike the North American situation), estimates of the duration of coexistence between humans and megafauna remain imprecise. Contrary to recent claims, the existing data do not prove the “blitzkrieg” model of overkill.
The
Coprinus cinereus
adherin Rad9 functions in Mre11-dependent DNA repair, meiotic sister-chromatid cohesion, and meiotic homolog pairing
Authors: Cummings W. Jason , Merino Sandra T. , Young Kevin G. , Li Libo , Johnson Christopher W. , Sierra Elizabeth A. , Zolan Miriam E.
Published: November 2002

Mitotic sister-chromatid cohesion (SCC) is known to depend in part on conserved proteins called adherins, which although necessary for SCC are not themselves localized between sister chromatids. We have examined mitotic DNA-repair and meiotic chromosome behavior in the
Coprinus cinereus
adherin mutant
rad9
-
1
. Genetic pathway analysis established that Rad9 functions in an Mre11-dependent pathway of DNA repair. Using fluorescence
in situ
hybridization, we found that the
rad9
-
1
mutant is defective in the establishment of meiotic homolog pairing at both interstitial and subtelomeric sites but in the maintenance of pairing at only interstitial loci. To determine the role of Rad9 in meiotic SCC, we hybridized nuclear spreads simultaneously with a homolog-specific probe and a probe that recognizes both members of a homologous pair. We found that Rad9 is required for wild-type levels of meiotic SCC, and that nuclei showing loss of cohesion were twice as likely also to fail at homolog pairing. To ask whether the contribution of Rad9 to homolog pairing is solely in the establishment of SCC, we examined a
rad9
-
1
;
msh5
-
22
double mutant, in which premeiotic DNA replication is inhibited. The
msh5
-
22
mutation partially suppressed the deleterious effects of the
rad9
-
1
mutation on homolog pairing; however, pairing in the double mutant still was significantly lower than in the
msh5
-
22
single mutant control. Because the role of Rad9 in homolog pairing is not obviated by the absence of a sister chromatid, we conclude that adherins have one or more early meiotic functions distinct from the establishment of cohesion.
TELEPARALLELIZED AND AFFINE THEORIES OF GRAVITY: NEW PERSPECTIVES FOR MACHIAN AND QUANTUM GRAVITY
Authors: VON BORZESZKOWSKI HORST-HEINO
Published: November 2002

We compare metric theories to theories with teleparallelism and affine theories of gravity in order to discuss perspectives in the canonical quantization of gravity opened by a realization of Mach's principle.
A DYNAMICAL SYSTEM APPROACH TO CRITICAL GRAVITATIONAL COLLAPSE
Authors: DE OLIVEIRA H. P. , DAMIÃO SOARES I.
Published: November 2002

The general dynamics of the spherically symmetric gravitational collapse of a massless scalar field is examined. We apply the Galerkin projection method to transform the partial differential equations ruling the dynamics of the collapse into a finite set of ordinary differential equations for the modal coefficients, after a convenient truncation procedure. We thus generate a dynamical system that not only reproduces the essential features of the dynamics of the gravitational collapse, even for a low order of truncation, but also discloses the structure of the dynamics. Each initial condition in modal space corresponds to a well defined spatial distribution of the scalar field. Numerical experiments with the system show that two main asymptotic configurations are possible: either the formation of a black hole or the dispersion of the scalar field leaving behind flat spacetime. Between the two asymptotic states there is a critical solution represented by a periodic orbit in the modal space with period Δ u ≈ 3.55. This periodic orbit acts as an intermediate attractor for the dynamics, being a limiting configuration for orbits generated from initial conditions in a critical surface of codimension one in the N-dimensional modal space. The compactness and fractality of this surface are briefly discussed.
THE FOCUSING OF VACUUM FLUCTUATIONS
Authors: FORD L. H. , SVAITER N. F.
Published: November 2002

The quantization of the scalar and electromagnetic fields in the presence of a parabolic mirror is developed in the context of a geometric optics approximation. We calculate the mean squared scalar and electric fields near the focal line of a parabolic cylindrical mirror. These quantities are found to grow as inverse powers of the distance from the focus. We give a combination of analytic and numerical results for the mean squared fields. In particular, we find that the mean squared electric field can be either negative or positive, depending upon the choice of parameters. The case of a negative mean squared electric field corresponds to a repulsive Van der Waals force on an atom near the focus, and to a region of negative energy density. Similarly, a positive value corresponds to an attractive force and a possibility of atom trapping in the vicinity of the focus.
Primordial Genetics: Phenotype of the Ribocyte
Authors: Yarus Michael
Published: November 2002

▪ Abstract  The idea that the ancestors of modern cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection-amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modern experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. There are substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modern four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles (<1 attomole) of predominantly inactive random sequences.
Understanding the Function of Actin-Binding Proteins Through Genetic Analysis of Drosophila Oogenesis
Authors: Hudson Andrew M. , Cooley Lynn
Published: November 2002

▪ Abstract  Much of our knowledge of the actin cytoskeleton has been derived from biochemical and cell biological approaches, through which actin-binding proteins have been identified and their in vitro interactions with actin have been characterized. The study of actin-binding proteins (ABPs) in genetic model systems has become increasingly important for validating and extending our understanding of how these proteins function. New ABPs have been identified through genetic screens, and genetic results have informed the interpretation of in vitro experiments. In this review, we describe the molecular and ultrastructural characteristics of the actin cytoskeleton in the Drosophila ovary, and discuss recent genetic analyses of actin-binding proteins that are required for oogenesis.
Genetic Approaches to Molecular and Cellular Cognition: A Focus on LTP and Learning and Memory
Authors: Matynia Anna , Kushner Steven A. , Silva Alcino J.
Published: November 2002

▪ Abstract  Long-term potentiation (LTP) is the predominant experimental model for the synaptic plasticity mechanisms thought to underlie learning and memory. This review is focused on the contributions of genetics to the understanding of the role of LTP in learning and memory. These studies have used a combination of genetics, molecular biology, neurophysiology, and psychology to demonstrate that molecular mechanisms of synaptic plasticity are critical for learning and memory. Because of the large scope of this literature, we focus primarily on genetic studies of hippocampal-dependent learning. Altogether, these findings not only demonstrate a role for plasticity in learning, they also lay down the foundations for the new field of molecular and cellular cognition.
Linear and nonlinear viscoelasticity of carbon black filled elastomers: Use of complementary rheological characterizations
Authors: Barrès C. , Mongruel A. , Cartault M. , Leblanc J. L.
Published: November 2002

The viscoelastic properties of filled elastomers (uncured styrene–butadiene rubber filled with carbon black) were investigated with two shear rheometers specially designed for the characterization of complex polymer systems. A torsional strain‐controlled rheometer [i.e., a rubber process analyzer (RPA)] was used in dynamic and relaxation modes for measuring the storage and loss moduli and the relaxation modulus. A stress‐controlled sliding cylinder rheometer (SCR) was operated for the measurement of the creep compliance. Both devices could be operated on a large scale of imposed strains or stresses ranging from the linear viscoelastic regime to the nonlinear viscoelastic regime, and they were complementary in supporting the original viscoelastic behavior of filled elastomers for a wide experimental time range. Moreover, when the measuring ranges of the two apparatus overlapped, a cross‐check of the material functions obtained with the RPA or SCR could be successfully carried out. This validation of the data was performed not only in the linear domain of viscoelasticity, with the classical approach of a generalized Maxwell model, but also in the nonlinear domain, with a viscoelastic integral model of type K‐BKZ. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 31–41, 2003
Long‐term safety and maintenance of clinical improvement following treatment with anakinra (recombinant human interleukin‐1 receptor antagonist) in patients with rheumatoid arthritis: Extension phase of a randomized, double‐blind, placebo‐controlled trial
Authors: Nuki George , Bresnihan Barry , Bear Moraye B. , McCabe Dorothy
Published: November 2002

Objective

To demonstrate the long‐term efficacy of anakinra, a human recombinant interleukin‐1 receptor antagonist, in patients with rheumatoid arthritis (RA), and to assess the long‐term safety of anakinra at different daily doses.

Methods

The efficacy and safety of anakinra were previously demonstrated in a double‐blind, placebo‐controlled, 24‐week evaluation in 472 patients with active RA. Of 345 patients who completed the placebo‐controlled phase of the study, 309 continued in a 52‐week, multicenter, double‐blind, parallel‐group extension phase of the study. Patients received subcutaneous injections of anakinra (30, 75, or 150 mg) once daily. Efficacy was assessed among the 309 patients for the first 24 weeks of the extension phase (48 weeks total therapy), using the American College of Rheumatology composite score (ACR20), its components, and radiographs of the hands and wrists. Safety was assessed in all 472 patients over the entire 52‐week extension phase (76 weeks total exposure).

Results

A total of 218 patients completed the extension phase. Of the 91 patients who withdrew prematurely, 46 did so following adverse events, and 26 withdrew because of lack of efficacy. Among patients receiving anakinra who entered the extension phase, the level of improvement was maintained for 48 weeks. The ACR20 response was 51% at week 24 and 46% at week 48, and this effect was consistent across all dose groups. The durability of the response to anakinra was further demonstrated in an evaluation of the sustained ACR20 response, which was similar during the first and second 24‐week periods (36% and 42%, respectively). At week 48, ACR50 and ACR70 responses were demonstrated in 18% and 3% of patients, respectively, who continued taking anakinra (all dose groups) and in 20% and 1% of patients, respectively, who were originally receiving placebo and then were randomized to all doses of anakinra. Anakinra was well tolerated for 76 weeks. The only side effects that appeared to be treatment‐related were skin reactions at the injection site. There was no evidence of decreased tolerance, an increased number of withdrawals, or an increased incidence of clinical complications associated with extended anakinra therapy.

Conclusion

The clinical benefits of treatment with daily self‐administered subcutaneous injections of anakinra in a cohort of patients with active RA were maintained for up to 48 weeks. Anakinra was well tolerated over 76 weeks. These observations support the long‐term use of anakinra for the treatment of patients with RA.
Hematopoietic stem cell transplantation for severe and refractory lupus
Authors: Traynor Ann E. , Barr Walter G. , Rosa Robert M. , Rodriguez Julianne , Oyama Yu , Baker Steven , Brush Mary , Burt Richard K.
Published: November 2002

Objective

To determine the safety and long‐term efficacy of immune ablation and autologous hematopoietic stem cell transplantation (HSCT) in severe systemic lupus erythematosus (SLE).

Methods

Fifteen patients with persistently active SLE after intravenous (IV) cyclophosphamide (CYC) therapy underwent HSCT. Stem cells were mobilized with CYC (2.0 gm/m2) and granulocyte colony‐stimulating factor (5 μg/kg/day). Lymphocytes were depleted from the graft by selection of CD34‐positive cells. The conditioning regimen used was CYC (200 mg/kg), antithymocyte globulin (90 mg/kg), and methylprednisolone (3 mg/kg). Outcome was evaluated by the SLE Disease Activity Index (SLEDAI), serum complement levels, serologic features, function of diseased organs, and immunosuppressive medication requirements.

Results

Fifteen patients with persistent, severe SLE, 7 of whom were critically ill, were treated. No deaths occurred following treatment. The median followup after HSCT has been 36 months (range 12–66 months). All patients demonstrated a gradual, but marked, improvement. The SLEDAI score has declined to ≤5 in 12 patients. Complement and anti–double‐stranded DNA levels have normalized and marked improvements in end organ function have occurred in all subjects. Of the 12 patients followed up for >1 year after HSCT, 10 have discontinued immunosuppressive medications, and the prednisone dosage has been tapered to 15 mg/day in 1. Only 2 patients have demonstrated clinical evidence of recurrence of active lupus. One of these patients currently requires no immunosuppressive medication and has a normal performance status. The other patient is currently receiving IV CYC.

Conclusion

In patients experiencing the persistence of organ‐threatening lupus following standard, aggressive therapy, HSCT may be performed safely, with marked improvement and sustained withdrawal of all immunosuppressive medication for most patients. A phase III randomized trial is warranted to determine the relative efficacy and durability of remission of HSCT compared with standard therapies.
Determinants and sequelae associated with utilization of acetaminophen versus traditional nonsteroidal antiinflammatory drugs in an elderly population
Authors: Rahme Elham , Pettitt Dan , LeLorier Jacques
Published: November 2002

Objective

Acetaminophen is recommended as initial therapy for patients with arthritis, particularly those at increased risk of nonsteroidal antiinflammatory drug (NSAID)–induced gastrointestinal (GI) side effects. However, higher doses of acetaminophen inhibit prostaglandin synthesis and have been associated with GI events. This study was undertaken to compare the observed and adjusted rates of GI events (hospitalizations, ulcers, dyspepsia, GI prophylaxis) occurring with higher versus lower doses of acetaminophen.

Methods

This was a retrospective cohort study of subjects ages ≥65 years who received a prescription for acetaminophen or NSAID between 1994 and 1996. Pharmaceutical and medical records were reviewed for 1 year of historical data prior to the index prescription of acetaminophen or non‐aspirin NSAID. Risk factors for GI events were identified based on the historical data. To further control for bias, patients were categorized by propensity score (the likelihood of receiving acetaminophen, given defined risk factor values). Records were then reviewed for the duration of the index prescription or 30 days, whichever was less, to generate data on the occurrence of GI events. Determinants of acetaminophen utilization were identified using logistic regression, and rates of GI events for each therapy were examined using Poisson regression analyses, controlling for duration of exposure, individual risk factors, and propensity scores.

Results

The study included 26,978 patients in the NSAID cohort and 21,207 in the acetaminophen cohort. Determinants of acetaminophen utilization compared with NSAIDs (odds ratio [95% confidence interval]) included recent hospitalization (8.6 [7.7–9.5]), concomitant anticoagulation therapy (3.2 [2.7–3.8]), age >85 years (2.3 [2.1–2.4]), and history of prior GI events, especially those requiring hospitalization (14.6 [11.7–18.7]). Unadjusted rates of GI hospitalization, ulcer, and dyspepsia were higher for patients in the acetaminophen cohort than for those in the NSAID cohort. The occurrence of GI events in acetaminophen‐treated patients was dose dependent, with rate ratios (compared with high‐dose NSAIDs and adjusted for risk susceptibility) ranging from 0.6 (95% confidence interval 0.5–0.7) for ≤650 mg/day to 1.0 (0.9–1.1) for >3,250 mg/day.

Conclusion

In this cohort, acetaminophen utilization is more common in patients at higher risk of GI events. After adjustment for risk susceptibility, patients receiving higher doses of acetaminophen have higher rates of GI events compared with those receiving lower doses.
Increase in expression of receptor activator of nuclear factor κB at sites of bone erosion correlates with progression of inflammation in evolving collagen‐induced arthritis
Authors: Lubberts Erik , Oppers‐Walgreen Birgitte , Pettit Allison R. , Van Den Bersselaar Liduine , Joosten Leo A. B. , Goldring Steven R. , Gravallese Ellen M. , Van Den Berg Wim B.
Published: November 2002

Objective

The receptor activator of nuclear factor κB (RANK)/RANK ligand (RANKL) pathway is critical in osteoclastogenesis and bone resorption and has been implicated in the process of focal bone erosion in arthritis. This study was undertaken to identify in vivo the hitherto‐unknown origin and localization of RANK‐expressing osteoclast precursor cells at sites of bone erosion in arthritis.

Methods

DBA‐1 mice were immunized with bovine type II collagen/Freund's complete adjuvant and were given an intraperitoneal booster injection of type II collagen on day 21. Arthritis was monitored visually, and joint pathology was examined histologically. RANK and RANKL expression were analyzed using specific immunohistochemistry, and tartrate‐resistant acid phosphatase (TRAP) staining was performed. In addition, TRAP and cathepsin K messenger RNA expression were analyzed by in situ hybridization.

Results

A marked increase in the number of cells expressing RANK correlated with the progression of synovial inflammation and clinical disease severity in evolving collagen‐induced arthritis (CIA). Interestingly, RANK expression demonstrated a gradient pattern with increased numbers of RANK‐positive cells within the synovial infiltrate in areas closer to periosteum and cortical bone. Cells expressing RANK included cells in synovial tissue, bone lining cells on the surface of trabecular bone at sites of erosion, and cells in periosteal areas adjacent to synovial inflammation. In areas where RANK‐positive cells were abundant, TRAP‐positive, multinucleated osteoclast‐like cells were also present at sites of focal bone erosion, suggesting differentiation of synovially derived RANK‐positive osteoclast precursor cells into osteoclasts. In addition, TRAP– and cathepsin K–double‐positive osteoclast‐like cells were detected on the synovial side of cortical bone at sites of early and advanced cortical bone erosion. Sites of RANK expression also correlated well with sites of RANKL expression, and there was a close correlation of the temporal expression of the receptor–ligand pair.

Conclusion

Cells expressing RANK increased in abundance with the progression of arthritis in evolving CIA, and sites of RANK‐expressing cells correlated with sites of TRAP‐positive, multinucleated osteoclast‐like cells as well as with sites of RANKL expression. These data support the hypothesis that the RANK/RANKL pathway plays an important role in the process of bone erosion in CIA.
Dehydroepiandrosterone treatment of women with mild‐to‐moderate systemic lupus erythematosus: A multicenter randomized, double‐blind, placebo‐controlled trial
Authors: Chang Deh‐Ming , Lan Joung‐Liang , Lin Hsiao‐Yi , Luo Shue‐Fen
Published: November 2002

Objective

To evaluate the efficacy and tolerability of dehydroepiandrosterone (DHEA) at a dosage of 200 mg/day in adult women with active systemic lupus erythematosus (SLE).

Methods

In a multicenter randomized, double‐blind, placebo‐controlled trial, 120 adult women with active SLE received oral DHEA (200 mg/day; n = 61) or placebo (n = 59) for 24 weeks. The primary end point was the mean change from baseline in the Systemic Lupus Activity Measure (SLAM) score at 24 weeks of therapy. Secondary end points included time to first flare, change in SLE Disease Activity Index (SLEDAI) score, and physician's and patient's global assessment scores at week 24.

Results

The two groups were well balanced for baseline characteristics. Mean reductions in SLAM scores from baseline were similar and were not statistically significantly different between treatment groups (DHEA −2.6 ± 3.4 versus placebo −2.0 ± 3.8, mean ± SD). The number of patients with flares was decreased by 16% in the DHEA group (18.3% of DHEA‐treated patients versus 33.9% of placebo‐treated patients; P = 0.044, based on time to first flare). The mean change in the patient's global assessment was statistically significant between the two groups (DHEA −5.5 versus placebo 5.4; P = 0.005). The number of patients with serious adverse events, most of which were related to SLE flare, was significantly lower in DHEA‐treated patients compared with placebo‐treated patients (P = 0.010). Expected hormonal effects, including increased testosterone levels and increased incidence of acne, were observed. No life‐threatening reactions or serious safety issues were identified during this study.

Conclusion

The overall results confirm that DHEA treatment was well‐tolerated, significantly reduced the number of SLE flares, and improved patient's global assessment of disease activity.
The relative prevalence of disease symptoms for ill persons: evidence from Benin
Authors: Muller Christophe
Published: November 2002

In developing countries, the usual modelling of the correlates of health problems is not a good fit for the health phenomena encountered and the available data. Indeed, three common situations occur: (a) it is often the observed symptoms that are used to determine medical interventions instead of specific disease diagnostics or general health indicators; (b) the ill persons described by the data are often affected by multiple health problems; and (c) the correlates of the full spectrum of all symptoms need to be considered together. In this paper, these issues are dealt with by proposing a statistical approach based on competing scores of symptoms that explain their relative prevalence among the observed ill persons.

Using multinomial logit models, the relative prevalence of four symptoms was estimated for four age classes of ill persons in Benin. Socio‐demographic characteristics, household equipment and consumption behaviour are shown to influence the relative prevalence of symptoms and therefore could be used to decide what treatment to use. Moreover, living standards and economic activities are important and the pattern of symptoms among poor or agricultural ill persons differs from that of the rich or the non‐peasants. The proposed method can be used to assist the definition of target groups and to guide the allocation of scarce resources in poor countries. Copyright © 2000 John Wiley & Sons, Ltd.
NMR assignments of selected bacterial carotenoids
Authors: Lutnaes Bjart Frode , Krane Jostein , Liaaen‐Jensen Synnøve
Published: November 2002

Complete 1H and 13C NMR assignments for selected carotenoids from purple and green phototropic bacteria are reported for the first time. Assignments are made for the all‐E isomers of OH‐rhodopin (1, 1,2,1′,2′‐tetrahydro‐ψ,ψ‐carotene‐1,1′‐diol), rhodovibrin (2, 1′‐methoxy‐3′,4′‐didehydro‐1,2,1′,2′‐tetrahydro‐ψ,ψ‐carotene‐1‐ol), anhydrorhodovibrin (3, 1‐methoxy‐3,4‐didehydro‐1,2‐dihydro‐ψ,ψ‐carotene), 2‐ketorhodovibrin (4, 1′‐hydroxy‐1‐methoxy‐3,4,3′,4′‐tetradehydro‐1,2, 1′,2′‐tetrahydro‐ψ,ψ‐carotene‐2‐one) and chlorobactene (5, ϕ,ψ‐carotene). Copyright © 2002 John Wiley & Sons, Ltd.
19F diffusion NMR analysis of enzyme–inhibitor binding
Authors: Derrick Tiffany S. , Lucas Laura H. , Dimicoli Jean‐Luc , Larive Cynthia K.
Published: November 2002

NMR diffusion measurements are a useful tool for probing molecular interactions, especially ligand–protein binding, because the diffusion coefficient measured for the ligand can reflect the binding affinity. This technique is useful for determining relative affinities of multiple ligands and quantitating binding constants to a specific biomolecular target, such as an enzyme. In this work, binding of two TFA‐derivitized inhibitors to the enzyme elastase was measured by 19F pulsed field gradient NMR spectroscopy. The differing thermodynamic (Kd) and kinetic (chemical exchange) properties of the elastase inhibitors introduced unique challenges to the NMR diffusion analysis. Line broadening due to fast T2 relaxation, differential T1 relaxation on the diffusion time‐scale and chemical exchange severely compromised the spectral signal‐to‐noise ratio and forced the use of extensive signal averaging. The resultant experimental time caused inhibitor hydrolysis to occur on the time‐scale of the measurement. Modulation of resonance intensity in LED spectra measured as a function of the diffusion delay time was explored as a function of the population ratio of the free and bound ligands. The intensity modulation introduced by chemical exchange during the diffusion delay of the LED experiment can be removed by choosing a pulse sequence such as BPPLED that incorporates bipolar gradient pulse pairs separated by 180° pulses that refocus chemical shift evolution. Copyright © 2002 John Wiley & Sons, Ltd.
Computations on historic masonry structures
Authors: Lourenço Paulo B
Published: November 2002

Is modelling and analysis of historical masonry structures necessary? Is the experimental behaviour of historical masonry constructions known? The answers seem to be ‘yes’, and substantial developments have occurred in recent decades in the challenging issues of conservation and restoration. A key issue is what type of analysis should be used. It seems that all methods are of interest, depending on the actual constraints of the engineering problem. In this paper, the possibilities of analysis of historic structures are addressed and a set of guidelines is proposed.
Three-dimensional nonlinear solitary waves in
shallow water generated by an advancing
disturbance
Authors: LI YILE , SCLAVOUNOS PAUL D.
Published: November 2002

The nonlinear long waves generated by a disturbance moving at subcritical, critical
and supercritical speed in unbounded shallow water are investigated. The problem is
formulated by a new modified generalized Boussinesq equation and solved numerically
by an implicit finite-difference algorithm. Three-dimensional upstream solitary waves
with significant amplitude are generated with a periodicity by a pressure distribution
or slender strut advancing on the free surface. The crestlines of these solitons are
almost perfect parabolas with decreasing curvature with respect to time. Behind the
disturbance, a complicated, divergent Kelvin-like wave pattern is formed. It is found
that, unlike the wave breaking phenomena in a narrow channel at Fh [ges ] 1.2, the three-
dimensional upstream solitons form several parabolic water humps and are blocked
ahead of the disturbance at supercritical speed in an unbounded domain for large
time.
Localisation of the hyaluronan receptor CD44 in porcine cumulus cells during in vivo and in vitro maturation
Authors: Yokoo Masaki , Tienthai Paisan , Kimura Naoko , Niwa Koji , Sato Eimei , Rodriguez-Martinez Heriberto
Published: November 2002

Polyspermy is fairly common during porcine in vitro fertilisation (IVF), perhaps due to incomplete in vitro oocyte maturation (IVM). Porcine cumulus cells (CCs) layered around the oocyte produce large amounts of extracellular hyaluronan (HA) when forming an expanding cell cloud during the last phase of oocyte maturation. The specific actions of HA are mediated via HA-binding proteins (HABPs), such as CD44, which act as receptors. In this study using immunocytochemistry and western blotting we investigated the localisation of CD44 in CCs obtained from in vivo-matured pig cumulus-oocyte complexes (COCs) and compared it with that in CCs from immature COCs and of COCs subjected to IVM and IVF procedures. Immunolabelling of CD44 was absent or very weak in CCs from immature COCs but strongly present on the surface of the CCs obtained from in vivo, displaying a similar localisation in the in vitro-matured COCs. In the latter, the labelling decreased but did not disappear in CCs 4 h after sperm co-incubation during IVF. Immunoblotting detected bands of between 73 and 88 kDa, corresponding to CD44, in the protein extract from in vivo CCs collected immediately prior to, or following spontaneous ovulation. The in vitro-matured CCs, however, presented bands ranging from 81 kDa to 88 kDa. Also, the bands found in the in vivo-matured CCs showed a larger variation of intensity and migration among animals than did the batches of in vitro-matured CCs. No CD44 band was detected on aliquots of the frozen-thawed boar spermatozoa used for IVF. The results clearly demonstrate that the specific HA receptor CD44 is present in expanding CCs of in vivo-matured pig COCs, in relation to increasing amounts of inter-CC HA. The subtle differences in molecular weight and migration ability observed between in vivo and in vitro samples may relate to differences in glycosylation and thus explain differences in HA-binding ability, of consequence for optimising in vitro culture conditions.
The novel antagonist 3‐CBW discriminates between kainate receptors expressed on neonatal rat motoneurones and those on dorsal root C‐fibres
Authors: More Julia C A , Troop Helen M , Jane David E
Published: November 2002

The natural product willardiine is a selective AMPA receptor agonist. We report that an N3‐substituted analogue of willardiine, (S)‐3‐(4‐carboxybenzyl)willardiine (3‐CBW), antagonizes AMPA and kainate receptors expressed on motoneurones and dorsal root C‐fibres, respectively.

Reduction of the fast component of the dorsal root‐evoked ventral root potential (fDR‐VRP) has been used as a novel method to compare AMPA receptor antagonists. 3‐CBW, NBQX and GYKI53655 depressed the fDR‐VRP with IC50 values of 10.3±2.4, 0.214±0.043 and 4.03±0.31 μM, respectively. That 3‐CBW depressed the fDR‐VRP by acting at AMPA and not metabotropic glutamate receptors was demonstrated by the lack of effect of LY341495 (100 μM).

The Schild plot for antagonism of responses to (S)‐5‐fluorowillardiine on motoneurones by 3‐CBW had a slope of 1.11±0.13 giving a pA2 value of 4.48. The Schild plot for antagonism of kainate responses on the dorsal root by 3‐CBW had a slope of 1.05±0.05 giving a pA2 value of 4.96.

On neonatal rat motoneurones 3‐CBW (200 μM) almost completely abolished responses to AMPA while responses to NMDA, kainate and DHPG were 101.6±11.6%, 39.4±5.8% and 110.5±9.0% of control, respectively. 3‐CBW can therefore be used to isolate kainate receptor responses from those mediated by AMPA receptors.

3‐CBW antagonized kainate‐induced responses on dorsal root C‐fibres with a pA2 value of 4.96 whereas kainate receptor mediated responses (isolated by including GYKI53655 in the medium) on motoneurones were not completely blocked by 200 μM 3‐CBW, substantiating evidence that kainate receptors on neonatal rat motoneurones differ from those on dorsal root C‐fibres.

British Journal of Pharmacology (2002) 137, 1125–1133. doi:10.1038/sj.bjp.0704957
Unravelling mechanisms underlying ischaemic arrhythmias – the importance of models
Authors: Guppy L J , Walker M J A
Published: November 2002

A new model of regional ischaemia using blood‐perfused isolated rat hearts is reported in this issue. This model has potential value in pharmacology to test the actions of drugs against the arrhythmias that arise early period (0–30 min) after induction of ischaemia. Unfortunately, the severity of arrhythmias in this new model is reduced, when compared to other models, in both the early and the late period (1–4 h) of coronary artery occlusion. This commentary compares the new model with previous models, and comments on the possible mechanisms of arrhythmias induced by ischaemia.

British Journal of Pharmacology (2002) 137, 941–942. doi:10.1038/sj.bjp.0704976
Coordinate regulation of energy transduction modules in
Halobacterium
sp. analyzed by a global systems approach
Authors: Baliga Nitin S. , Pan Min , Goo Young Ah , Yi Eugene C. , Goodlett David R. , Dimitrov Krassen , Shannon Paul , Aebersold Ruedi , Ng Wailap Victor , Hood Leroy
Published: November 2002

The extremely halophilic archaeon
Halobacterium NRC-1
can switch from aerobic energy production (energy from organic compounds) to anaerobic phototrophy (energy from light) by induction of purple membrane biogenesis. The purple membrane is made up of multiple copies of a 1:1 complex of bacterioopsin (Bop) and retinal called bacteriorhodopsin that functions as a light-driven proton pump. A light- and redox-sensing transcription regulator, Bat, regulates critical genes encoding the biogenesis of the purple membrane. To better understand the regulatory network underlying this physiological state, we report a systems approach using global mRNA and protein analyses of four strains of
Halobacterium
sp.: the wild-type,
NRC-1
; and three genetically perturbed strains:
S9
(
bat
+), a purple membrane overproducer, and two purple membrane deficient strains,
SD23
(a
bop
knockout) and
SD20
(a
bat
knockout). The integrated DNA microarray and proteomic data reveal the coordinated coregulation of several interconnected biochemical pathways for phototrophy: isoprenoid synthesis, carotenoid synthesis, and bacteriorhodopsin assembly. In phototrophy, the second major biomodule for ATP production, arginine fermentation, is repressed. The primary systems level insight provided by this study is that two major energy production pathways in
Halobacterium
sp., phototrophy and arginine fermentation, are inversely regulated, presumably to achieve a balance in ATP production under anaerobic conditions.
Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle
Authors: Haslett Judith N. , Sanoudou Despina , Kho Alvin T. , Bennett Richard R. , Greenberg Steven A. , Kohane Isaac S. , Beggs Alan H. , Kunkel Louis M.
Published: November 2002

The primary cause of Duchenne muscular dystrophy (DMD) is a mutation in the dystrophin gene leading to the absence of the corresponding RNA transcript and protein. Absence of dystrophin leads to disruption of the dystrophin-associated protein complex and substantial changes in skeletal muscle pathology. Although the histological pathology of dystrophic tissue has been well documented, the underlying molecular pathways remain poorly understood. To examine the pathogenic pathways and identify new or modifying factors involved in muscular dystrophy, expression microarrays were used to compare individual gene expression profiles of skeletal muscle biopsies from 12 DMD patients and 12 unaffected control patients. Two separate statistical analysis methods were used to interpret the resulting data:
t
test analysis to determine the statistical significance of differential expression and geometric fold change analysis to determine the extent of differential expression. These analyses identified 105 genes that differ significantly in expression level between unaffected and DMD muscle. Many of the differentially expressed genes reflect changes in histological pathology. For instance, immune response signals and extracellular matrix genes are overexpressed in DMD muscle, an indication of the infiltration of inflammatory cells and connective tissue. Significantly more genes are overexpressed than are underexpressed in dystrophic muscle, with dystrophin underexpressed, whereas other genes encoding muscle structure and regeneration processes are overexpressed, reflecting the regenerative nature of the disease.
The lipid phosphatase myotubularin is essential for skeletal muscle maintenance but not for myogenesis in mice
Authors: Buj-Bello Anna , Laugel Vincent , Messaddeq Nadia , Zahreddine Hala , Laporte Jocelyn , Pellissier Jean-François , Mandel Jean-Louis
Published: November 2002

Myotubularin is a ubiquitously expressed phosphatase that acts on phosphatidylinositol 3-monophosphate [PI(3)P], a lipid implicated in intracellular vesicle trafficking and autophagy. It is encoded by the
MTM1
gene, which is mutated in X-linked myotubular myopathy (XLMTM), a muscular disorder characterized by generalized hypotonia and muscle weakness at birth leading to early death of most affected males. The disease was proposed to result from an arrest in myogenesis, as the skeletal muscle from patients contains hypotrophic fibers with centrally located nuclei that resemble fetal myotubes. To understand the physiopathological mechanism of XLMTM, we have generated mice lacking myotubularin by homologous recombination. These mice are viable, but their lifespan is severely reduced. They develop a generalized and progressive myopathy starting at around 4 weeks of age, with amyotrophy and accumulation of central nuclei in skeletal muscle fibers leading to death at 6–14 weeks. Contrary to expectations, we show that muscle differentiation in knockout mice occurs normally. We provide evidence that fibers with centralized myonuclei originate mainly from a structural maintenance defect affecting myotubularin-deficient muscle rather than a regenerative process. In addition, we demonstrate, through a conditional gene-targeting approach, that skeletal muscle is the primary target of murine XLMTM pathology. These mutant mice represent animal models for the human disease and will be a valuable tool for understanding the physiological role of myotubularin.
Multistage carcinogenesis and the incidence of colorectal cancer
Authors: Luebeck E. Georg , Moolgavkar Suresh H.
Published: November 2002

We use general multistage models to fit the age-specific incidence of colorectal cancers in the Surveillance, Epidemiology, and End Results registry, which covers ≈10% of the U.S. population, while simultaneously adjusting for birth cohort and calendar year effects. The incidence of colorectal cancers in the Surveillance, Epidemiology, and End Results registry is most consistent with a model positing two rare events followed by a high-frequency event in the conversion of a normal stem cell into an initiated cell that expands clonally to give rise to an adenomatous polyp. Only one more rare event appears to be necessary for malignant transformation. The two rare events involved in initiation are interpreted to represent the homozygous loss of adenomatous polyposis coli gene function. The subsequent transition of a preinitiated stem cell into an initiated cell capable of clonal expansion via symmetric division is predicted to occur with a frequency too high for a mutational event but may reflect a positional effect in colonic crypts. Our results suggest it is not necessary to invoke genomic instability to explain colorectal cancer incidence rates in human populations. Temporal trends in the incidence of colon cancer appear to be dominated by calendar year effects. The model also predicts that interventions, such as administration of nonsteroidal anti-inflammatory drugs, designed to decrease the growth rate of adenomatous polyps, are very efficient at lowering colon cancer risk substantially, even when begun later in life. By contrast, interventions that decrease the rate of mutations at the adenomatous polyposis coli locus are much less effective in reducing the risk of colon cancer.
A single point mutation in ecdysone receptor leads to increased ligand specificity: Implications for gene switch applications
Authors: Kumar M. B. , Fujimoto T. , Potter D. W. , Deng Q. , Palli S. R.
Published: November 2002

The ecdysone receptor (EcR), a member of the nuclear receptor superfamily, plays an important role in regulating development and reproduction in insects. The EcR binds to ecdysteroids and regulates transcription of genes that contain ecdysone response elements. The EcR has been used to develop inducible gene switches for efficient regulation of foreign genes in applications such as gene therapy, protein production, and functional genomics. An EcR [
Choristoneura fumiferana
EcR (CfEcR)] homology model was constructed, and 17 amino acid residues were identified as critical for 20-hydroxyecdysone binding. Mutation of these amino acids followed by analysis of these mutants in transactivation (in insect and mammalian cells and
in vivo
in mice) and ligand-binding assays identified one particular mutant (A110P) that failed to respond to steroids, but its response to the diacylhydrazine nonsteroidal ligands RG-102240 (GS
TM
E) and RG-102317 was unaffected. This steroid-insensitive EcR mutant has potential gene switch applications in insects and plants that have endogenous ecdysteroids. In addition, this mutant would be also useful for developing orthogonal EcR-ligand pairs for simultaneous regulation of multiple genes in the same cell.
A reassessment of human cranial plasticity: Boas revisited
Authors: Sparks Corey S. , Jantz Richard L.
Published: November 2002

In 1912, Franz Boas published a study demonstrating the plastic nature of the human body in response to changes in the environment. The results of this study have been cited for the past 90 years as evidence of cranial plasticity. These findings, however, have never been critiqued thoroughly for their statistical and biological validity. This study presents a reassessment of Boas' data within a modern statistical and quantitative genetic framework. The data used here consist of head and face measurements on over 8,000 individuals of various European ethnic groups. By using pedigree information contained in Boas' data, narrow sense heritabilities are estimated by the method of maximum likelihood. In addition, a series of
t
tests and regression analyses are performed to determine the statistical validity of Boas' original findings on differentiation between American and European-born children and the prolonged effect of the environment on cranial form. Results indicate the relatively high genetic component of the head and face diameters despite the environmental differences during development. Results point to very small and insignificant differences between European- and American-born offspring, and no effect of exposure to the American environment on the cranial index in children. These results contradict Boas' original findings and demonstrate that they may no longer be used to support arguments of plasticity in cranial morphology.
Mutations in
Mcoln3
associated with deafness and pigmentation defects in varitint-waddler (
Va
) mice
Authors: Di Palma Federica , Belyantseva Inna A. , Kim Hung J. , Vogt Thomas F. , Kachar Bechara , Noben-Trauth Konrad
Published: November 2002

Deafness in spontaneously occurring mouse mutants is often associated with defects in cochlea sensory hair cells, opening an avenue to systematically identify genes critical for hair cell structure and function. The classical semidominant mouse mutant varitint-waddler (
Va
) exhibits early-onset hearing loss, vestibular defects, pigmentation abnormalities, and perinatal lethality. A second allele,

Va
J

, which arose in a cross segregating for
Va
, shows a less severe phenotype. By using a positional cloning strategy, we identify two additional members of the mucolipin gene family (
Mcoln2
and
Mcoln3
) in the 350-kb

Va
J

minimal interval and provide evidence for
Mcoln3
as the gene mutated in varitint-waddler.
Mcoln3
encodes a putative six-transmembrane-domain protein with sequence and motif similarities to the family of nonselective transient-receptor-potential (TRP) ion channels. In the
Va
allele an Ala419Pro substitution occurs in the fifth transmembrane domain of
Mcoln3
, and in

Va
J

, a second sequence alteration (Ile362Thr) occurring in cis partially rescues the
Va
allele. Mcoln3 localizes to cytoplasmic compartments of hair cells and plasma membrane of stereocilia. Hair cell defects are apparent by embryonic day 17.5, assigning
Mcoln3
an essential role during early hair cell maturation. Our data suggest that Mcoln3 is involved in ion homeostasis and acts cell-autonomously. Hence, we identify a molecular link between hair cell physiology and melanocyte function. Last,
MCOLN2
and
MCOLN3
are candidate genes for hereditary and/or sporadic forms of neurosensory disorders in humans.