Four Channels in the Fission of 252Cf

Strutinsky-type calculations indicate that the potential energy favors four channels in the nuclear fission of 252Cf. The connection of this finding with experimental results on the distribution of fragment mass, total kinetic energy, neutron multiplicities, and relative abundances is discussed. Similar calculations for 227Ac, 236U, and 258Fm show that the changing preponderance of the four channels seems to describe striking trends in the fission of the actinides, in particular the dip in the total kinetic energy at symmetrical fission of 236U and the enormously high average kinetic energy of the 258Fm fragments.

Invariant Distributions and Stationary Correlation Functions of One-Dimensional Discrete Processes

The connection between one-dimensional dynamical laws generating discrete processes and their invariant densities as well as their stationary correlaton functions is discussed. In particular the changes occuring under a special equivalence transformation are considered. Correlation functions are used to describe the gradual transition from periodic states to chaotic states via periodic motions with superimposed nonlinearity noise.

Variational Principle for Linear Relaxation Relations

A variational principle for linear relaxation phenomena is considered. I t connects relaxation with anti-relaxation. The latter one is governed by the transposed transport matrix and, in addition, by the diffusion matrix, which drops if Onsager-symmetry holds. This generalizes an earlier result by L. Waldmann

Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis

MOTIVATION

High-throughput experiments such as microarray hybridizations often yield long lists of genes found to share a certain characteristic such as differential expression. Exploring Gene Ontology (GO) annotations for such lists of genes has become a widespread practice to get first insights into the potential biological meaning of the experiment. The standard statistical approach to measuring overrepresentation of GO terms cannot cope with the dependencies resulting from the structure of GO because they analyze each term in isolation. Especially the fact that annotations are inherited from more specific descendant terms can result in certain types of false-positive results with potentially misleading biological interpretation, a phenomenon which we term the inheritance problem.

RESULTS

We present here a novel approach to analysis of GO term overrepresentation that determines overrepresentation of terms in the context of annotations to the term's parents. This approach reduces the dependencies between the individual term's measurements, and thereby avoids producing false-positive results owing to the inheritance problem. ROC analysis using study sets with overrepresented GO terms showed a clear advantage for our approach over the standard algorithm with respect to the inheritance problem. Although there can be no gold standard for exploratory methods such as analysis of GO term overrepresentation, analysis of biological datasets suggests that our algorithm tends to identify the core GO terms that are most characteristic of the dataset being analyzed.

Simultaneous alignment and annotation of cis-regulatory regions

MOTIVATION

Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the results in the end. If the site descriptions are weak or the sequence similarity is low, the local gap structure of the alignment poses a problem in detecting the conserved sites. It is therefore desirable to have an approach that is able to simultaneously consider the alignment as well as possibly matching site locations.

RESULTS

With SimAnn we have developed a tool that serves exactly this purpose. By combining the annotation step and the alignment of the two sequences into one algorithm, it detects conserved sites more clearly. It has the additional advantage that all parameters are calculated based on statistical considerations. This allows for its successful application with any binding site model of interest. We present the algorithm and the approach for parameter selection and compare its performance with that of other, non-simultaneous methods on both simulated and real data.

AVAILABILITY

A command-line based C++ implementation of SimAnn is available from the authors upon request. In addition, we provide Perl scripts for calculating the input parameters based on statistical considerations.

The role of toxicokinetics in xylene-induced ototoxicity in the rat and guinea pig

In the rat, some aromatic solvents cause a high level of ototoxicity that is characterized by damage to outer hair cells in the cochlea, which results in irreversible hearing loss. However, there is a vast difference in their potency. Among the three isomers of xylene, only para-xylene has been shown to be ototoxic in the rat. Moreover, all the species do not show the same susceptibility to ototoxic solvents, the rat being the most susceptible and the guinea pig seeming resistant to this ototoxic effect. The objective of the study was to determine whether toxicokinetic factors could explain the differences in ototoxicity observed among the three isomers of xylene in the rat and the species-dependent ototoxicity in the rat and the guinea pig. Blood and brain concentrations of each isomer were monitored in Sprague-Dawley rats treated orally by gastric intubation with a single dose or a 10 day-repeated treatment of 8.47 mmol/kg (an ototoxic dosage for para-xylene) of each isomer. Moreover, histology of the cochlea was carried out and the toxicokinetics of meta-xylene was monitored in rats treated with a single dose or a 10 day-repeated treatment of 16.94 mmol/kg meta-xylene, a non-ototoxic isomer. Similarly, histology of the cochlea was carried out and the toxicokinetics of para-xylene was followed in guinea pigs treated by gavage with a single dose or a 10 day-repeated treatment of 8.47 mmol/kg para-xylene. Finally, the blood and brain concentrations of para-xylene were measured in both the rats and the guinea pigs after a 4-h exposure to 1800 ppm of para-xylene. Among the three isomers studied, para-xylene yielded the highest blood and brain concentrations in the acutely and repeatedly exposed rats. When given a high dosage of meta-xylene (16.94 mmol/kg), the rats showed blood and brain concentrations of meta-xylene in the same order as those obtained with 8.47 mmol/kg para-xylene, but no outer hair cell loss was observed. No outer hair cell loss was observed in the guinea pigs treated with para-xylene. Whatever the exposure pattern, the blood and brain concentrations of para-xylene in the rats were 3.1-9.5 times higher than those measured in the guinea pigs. These results indicate that toxicokinetic factors cannot explain the differences in ototoxicity observed with the three isomers in the rat. However, they suggest that the differences in susceptibility to para-xylene observed between the rats and the guinea pigs might be due to toxicokinetic factors.

‘Treatise on the Spinal Marrow and its Diseases’ (Anatomy, functions and general considerations on its diseases) by Ollivier d’ Angers CP (1796–1845)

STUDY DESIGN

Collecting and analyzing all possible documents by internet, and consulting medical libraries in different countries.

OBJECTIVE

To focus on the work of Ollivier d'Angers who, in the beginning of the 19th century, spent most of his professional life studying the spinal cord, marrow (SM), or medulla spinalis, and publishing the first comprehensive treatise on the subject in 1824.

SETTING

ParaDoc database, Swiss Paraplegic-Centre, 6207 Nottwil, Switzerland, in collaboration with Paul Dollfus, ISCoS/Paradoc, Mulhouse, France.

RESULTS

Some of d'Angers's clinical descriptions, observations and also pathologic findings, described in the successive editions of his treatise, were very much in advance of his time.

CONCLUSIONS

To our knowledge, this was the first comprehensive treatise, in 1824, at least in France. It gave a clear picture on the matter of the SM and in that period of medical history.

Rap1A-deficient T and B cells show impaired integrin-mediated cell adhesion

Studies in tissue culture cells have demonstrated a role for the Ras-like GTPase Rap1 in the regulation of integrin-mediated cell-matrix and cadherin-mediated cell-cell contacts. To analyze the function of Rap1 in vivo, we have disrupted the Rap1A gene by homologous recombination. Mice homozygous for the deletion allele are viable and fertile. However, primary hematopoietic cells isolated from spleen or thymus have a diminished adhesive capacity on ICAM and fibronectin substrates. In addition, polarization of T cells from Rap1-/- cells after CD3 stimulation was impaired compared to that of wild-type cells. Despite this, these defects did not result in hematopoietic or cell homing abnormalities. Although it is possible that the relatively mild phenotype is a consequence of functional complementation by the Rap1B gene, our genetic studies confirm a role for Rap1A in the regulation of integrins.

A new statistical model to select target sequences bound by transcription factors

Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding to a sequence is a main task in computational biology. Although many methods have been proposed to tackle this problem, the statistical significance of the prediction is still not solved. We propose an approach to give a good approximation for the potential of a sequence to be bound by a TF. Instead of assessing distinct binding sites, we motivate to focus on the number of binding sites. Based on a suitable statistical model, probabilities for scoring are approximated for a TF to bind to a sequence. Two examples show the necessity of such a model as well as the superiority of the proposed method compared to standard approaches.

T-Reg Comparator: an analysis tool for the comparison of position weight matrices

T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position weight matrices. The user inputs a set of such weight matrices or binding site sequences and our program matches them against the T-Reg database, which is presently built on data from the Transfac [E. Wingender (2004) In Silico Biol., 4, 55-61] and Jaspar [A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman and B. Lenhard (2004) Nucleic Acids Res., 32, D91-D94]. Our tool delivers a detailed report on similarities between user-supplied motifs and motifs in the database. Apart from simple one-to-one relationships, T-Reg Comparator is also able to detect similarities between submatrices. In addition, we provide a user interface to a program for sequence scanning with weight matrices. Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de.

Comparative promoter region analysis powered by CORG

Background

Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG , a framework for studying upstream regions including untranslated exons (5' UTR).

Description

The automated annotation of promoter regions integrates information of two kinds. First, statistically significant cross-species conservation within upstream regions of orthologous genes is detected. Pairwise as well as multiple sequence comparisons are computed. Second, binding site descriptions (position-weight matrices) are employed to predict conserved regulatory elements with a novel approach. Assembled EST sequences and verified transcription start sites are incorporated to distinguish exonic from other sequences.

As of now, we have included 5 species in our analysis pipeline (man, mouse, rat, fugu and zebrafish). We characterized promoter regions of 16,127 groups of orthologous genes. All data are presented in an intuitive way via our web site. Users are free to export data for single genes or access larger data sets via our DAS server . The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set.

Conclusion

The CORG platform is a versatile tool to support analyses of gene regulation in vertebrate promoter regions. Applications for CORG cover a broad range from studying evolution of DNA binding sites and promoter constitution to the discovery of new regulatory sequence elements (e.g. microRNAs and binding sites).

Determination of short-term exposure with a direct reading photoionization detector

The use of a direct reading photoionization detector (PID) to determine short-term solvent exposures is described in the present paper. To assess the relevance of such a total exposure evaluation it was necessary to compare it with the real concentration of pollutants. This comparison was made by measuring in parallel with the PID determination the concentration of each pollutant using a standard technique, i.e. sampling on charcoal tubes and subsequent analysis by gas chromatography. Laboratory tests showed that the linearity of the answer of the PID is good for many compounds and for a mixture of these compounds. Similar tests were carried out for painters in workplaces with the same good correlations (determination coefficient r2 close to 1) between the PID response and the real concentration of the pollutants measured on the sampling tubes. The use of PID also allowed determination of the exposure profile of the workers and comparison of the short-term exposure to the corresponding limit values. Many cases of the short-term limit values being exceeded were revealed by use of the PID, although very few cases of the long-term limit values have been found by the usual sampling (charcoal tube) and analytical (gas chromatography) methods.

Differential association of polymorphisms in the TNFalpha region with psoriatic arthritis but not psoriasis

OBJECTIVE

To investigate the potential association of tumour necrosis factor alpha (TNFalpha) microsatellite and promoter alleles with psoriatic arthritis (PsA).

METHODS

DNA from 89 white patients with PsA, 65 patients with psoriasis, and 99 healthy white controls was investigated for two TNFalpha promoter (-238 and -308) and three microsatellite polymorphisms (TNFa, c, and d). Patients had previously been studied by serology for HLA class I antigens and by sequence-specific polymerase chain reaction for DRB1* alleles. In addition, TNFalpha production of Ficoll separated peripheral blood mononuclear cells (PBMC) into culture supernatants after stimulation with lipopolysaccharide, alphaCD3 antibodies, phytohaemagglutinin, and streptococcal superantigen C was determined.

RESULTS

A significant, HLA class I independent increase of the TNFa6c1d3 haplotype was found in the group with PsA but not among patients with psoriasis (32% v. 8%, pc<0.008; relative risk (RR)=5.3). In addition, patients with PsA showed a marked decrease of the TNF308A promoter allele (6% v. 18%; pc<0.008; RR=3.5) compared with healthy controls, which was independent of the increased frequency of the -238A polymorphism in this group. PBMC from patients with PsA secreted significantly less TNFalpha than cells from patients without arthritis. In particular, the TNFa6 microsatellite was associated with decreased TNFalpha production.

CONCLUSION

These data indicate that allelic variations at the TNFalpha locus influence susceptibility to PsA. Decreased production of TNFalpha is at least in part genetically determined and might be related to the development of arthritis. However, the association of the TNF308G allele with the disease also points to other disease related haplotypes with still unknown susceptibility genes.

Thermal convection for large Prandtl numbers

The Rayleigh-Bénard theory by Grossmann and Lohse [J. Fluid Mech. 407, 27 (2000)] is extended towards very large Prandtl numbers Pr. The Nusselt number Nu is found here to be independent of Pr. However, for fixed Rayleigh numbers Ra a maximum in the Nu(Pr) dependence is predicted. We moreover offer the full functional dependences of Nu(Ra,Pr) and Re(Ra,Pr) within this extended theory, rather than only give the limiting power laws as done in J. Fluid. Mech. 407, 27 (2000). This enables us to more realistically describe the transitions between the various scaling regimes.

Dementia in rural primary care practices in Lake County, Oregon

Procedures used in assessing patients with dementia in rural settings are little studied. Among all patients aged 65 years and older in the four primary care practices in Lake County, Oregon, dementia cases were identified from computerized office databases using preselected International Classification of Diseases, Ninth Edition, codes. A semi-structured chart review determined (1) a dementia diagnosis, (2) cognitive and functional domains assessed, and (3) diagnostic studies performed. Of 1540 available records, 30 had dementia. Nineteen of them met National Institute of Neurological and Communicative Diseases and Stroke-Alzheimer's Disease and Related Disorders Association criteria for Alzheimer's disease (AD). Cognitive impairment was documented in 73% of the 51 identified charts and all with AD. Laboratory studies were recorded in 33% overall and in 42% with AD. Neuroimaging was documented in 18% overall and in 16% with AD. The prevalence of documented dementia in these rural practices may be low, possibly because cases of mild dementia may not be labeled as such. Laboratory studies were performed in a minority of cases of dementia.

Scaling hypothesis leading to extended self-similarity in turbulence

A scaling hypothesis leading to extended self-similarity (ESS) for structure functions (the qth order moments of the magnitude of the longitudinal component velocity differences) in isotropic, homogeneous turbulence is proposed. This is done by generalizing the scale variable r to rg(r/L), with a crossover function g. By extending the refined self-similarity, it is shown that the presented scaling also leads to ESS for structure functions of the energy dissipation rate fluctuations, and to ESS bridging relations between velocity and dissipation rate moments. Extended self-similarity on the basis of a universal crossover function g strictly holds toward the outer scale (L) range only. Yet we find at least approximate ESS toward the viscous, inner scale (l) range. Furthermore, the probability densities for the velocity differences and the energy dissipation rate fluctuations which are compatible with this ESS are offered.

Different transcriptional activity and in vitro TNF-alpha production in psoriasis patients carrying the TNF-alpha 238A promoter polymorphism

Genes encoded on chromosome 6 within the major histocompatibility complex region are thought to play an important role in the pathogenesis of psoriasis. A potential candidate gene is tumor necrosis factor alpha. The tumor necrosis factor alpha promoter contains several polymorphisms including two G-->A transitions at position -308 and -238, which are the most common in Caucasian populations. The TNF238.2 (-238A) allele has been strongly associated with psoriasis. We have investigated the effect of the -238 and -308 variants on transcription of the tumor necrosis factor alpha gene in luciferase reporter gene assays. In addition, peripheral blood mononuclear cells of 47 patients with psoriasis and 43 controls were stimulated with different antigens and mitogens (streptococcal sonicate and superantigen, lipopolysaccharide, phorbol-12-myristate, phytohemagglutinin, CD3 antibodies) and tumor necrosis factor alpha production was measured in supernatants by enzyme-linked immunosorbent assay. The psoriasis-associated tumor necrosis factor alpha promoter allele TNF238.2 showed a significantly decreased transcriptional activity. Peripheral blood mononuclear cells carrying this allele produced significantly less tumor necrosis factor alpha after stimulation with T cell mitogens and streptococcal antigens in comparison to controls. The promoter allele TNF238.2 seems to influence tumor necrosis factor alpha production; a possible role in the pathogenesis of psoriasis has to be further evaluated.

Multiscale correlations and conditional averages in numerical turbulence

The equations of motion for the nth order velocity differences raise the interest in correlation functions containing both large and small scales simultaneously. We consider the scaling of such objects and also their conditional average representation with emphasis on the question of whether they behave differently in the inertial or the viscous subranges. The turbulent flow data are obtained by Navier-Stokes solutions on a 60(3) grid with periodic boundary conditions and Re lambda = 70. Our results complement previous high Re data analysis based on measured data [A. L. Fairhall, V. S. L'vov, and I. Procaccia, Europhys. Lett 43, 277 (1998)] whose preference were the larger scales, and the analysis of both experimental and synthetic turbulence data by [R. Benzi and co-workers, Phys. Rev. Lett. 80, 3244 (1998); Phys. Fluids 11, 2215 (1999)]. The inertial range fusion rule is confirmed and insight is obtained for the conditional averages (the local dissipation rate conditioned on the velocity fluctuations).

Continued fraction representation of temporal multiscaling in turbulence

It was shown recently that the anomalous scaling of simultaneous correlation functions in turbulence is intimately related to the breaking of temporal scale invariance, which is equivalent to the appearance of infinitely many times scales in the time dependence of time-correlation functions. In this paper we derive a continued fraction representation of turbulent time correlation functions which is exact and in which the multiplicity of time scales is explicit. We demonstrate that this form yields precisely the same scaling laws for time derivatives and time integrals as the "multi-fractal" representation that was used before. Truncating the continued fraction representation yields the "best" estimates of time correlation functions if the given information is limited to the scaling exponents of the simultaneous correlation functions up to a certain, finite order. It is worth noting that the derivation of a continued fraction representation obtained here for a time evolution operator which is not Hermitian or anti-Hermitian may be of independent interest.

[Future occupational plans of patients after orthopedic rehabilitation: how are they expressed? What influences them?]

Perceptions about one's occupational future are regarded as the initial phase in an ongoing process of occupational resettlement towards achieving gainful activity. Actual gainful activity, however, tends to be increasingly dependent on a number of labour market variables. At the end of an orthopaedic rehabilitation measure, 341 patients with pain syndromes of the locomotor system were interviewed concerning their vocational perspectives and notions, and the data obtained were studied in association with anamnestic and psychosocial factors. It is assumed that both plain expectations (such as returning, or not returning, to work) and multi-layered statements alike (such as the dual message of returning and of not returning to work, at first glance incompatible) will frequently be masked in the interview. Distinct, differing patterns were nevertheless found for the various patient groups regarding pain description, pain course, subjective disablement by pain, subjective job burden, subjective well-being, rehab expectations, and judgement of therapy outcome. Similar differences were stated for the social situation, indicated inter alia by (in)capacity for work, or application for benefit award (severely disabled person status, invalidity pension). Pain drawings, pain severity scaling, differentiated description of various pain qualities, the Pain Disability Index, all emerged as useful and practical additional tools in elucidating these patterns.

Maxwell's Demon at work: Two types of Bose condensate fluctuations in power-law traps

After discussing the idea underlying the Maxwell's Demon ensemble, we employ this ensemble for calculating fluctuations of ideal Bose gas condensates in traps with power-law single-particle energy spectra. Two essentially different cases have to be distinguished. If the heat capacity is continuous at the condensation point, the fluctuations of the number of condensate particles vanish linearly with temperature, independent of the trap characteristics. In this case, microcanonical and canonical fluctuations are practically indistinguishable. If the heat capacity is discontinuous, the fluctuations vanish algebraically with temperature, with an exponent determined by the trap, and the micro-canonical fluctuations are lower than their canonical counterparts.

Bacterial Standing Stock, Activity, and Carbon Production during Formation and Growth of Sea Ice in the Weddell Sea, Antarctica

Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 × 10 8 to 3 × 10 8 liter -1 , were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [ 3 H]leucine incorporation into proteins to [ 3 H]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day -1 indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained lower than in open water. Bacterial concentrations of up to 2.8 × 10 9 cells liter -1 along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 μg of C liter -1 h -1 . In thick ice, bacterial secondary production exceeded primary production of microalgae.

Bacterial activity in sea ice and open water of the Weddell Sea, Antarctica: A microautoradiographic study

Metabolic activity of bacteria was investigated in open water, newly forming sea ice, and successive stages of pack ice in the Weddell Sea. Microautoradiography, using [(3)H]leucine as substrate, was compared with incorporation rates of [(3)H]leucine into proteins. Relation of [(3)H]leucine incorporation to the biomass of active bacteria provides information about changes of specific metabolic activity of cells. During a phytoplankton bloom in an ice-free, stratified water column, total numbers of bacteria in the euphotic zone averaged 2.3 × 10(5) ml(-1), but only about 13% showed activity via leucine uptake. Growth rate of the active bacteria was estimated as 0.3-0.4 days(-1). Total cell concentration of bacteria in 400 m depth was 6.6 × 10(4) ml(-1). Nearly 50% of these cells were active, although biomass production and specific growth rate were only about one-tenth that of the surface populations. When sea ice was forming in high concentrations of phytoplankton, bacterial biomass in the newly formed ice was 49.1 ng C ml(-1), exceeding that in open water by about one order of magnitude. Attachment of large bacteria to algal cells seems to cause their enrichment in the new ice, since specific bacterial activity was reduced during ice formation, and enrichment of bacteria was not observed when ice formed at low algal concentration. During growth of pack ice, biomass of bacteria increased within the brine channel system. Specific activity was still reduced at these later stages of ice development, and percentages of active cells were as low as 3-5%. In old, thick pack ice, bacterial activity was high and about 30% of cells were active. However, biomass-specific activity of bacteria remained significantly lower than that in open water. It is concluded that bacterial assemblages different to those of open water developed within the ice and were dominated by bacteria with lower average metabolic activity than those of ice-free water.

[Osteonecrosis following short-term, high-dosage steroid therapy]

Osteonecrosis of the femoral head is one of many well documented side effects of long term steroid (glucocorticoid) use. Studies have reported on the skeletal effects of short term, high dose steroid therapy. This paper illustrates that short term (up to 6 weeks), high dose steroid therapy, utilized in neurotraumatology or central nervous system disease, can lead to necrosis of bone at multiple sites. This retrospective review of 6 patients supports the 18 previously reported cases: there were 5 male and one female patient, with a mean age of 32.2 years. The patients received an average dose of 5100 mg methylprednisolone for 23 days. The average interval between steroid administration and the onset of symptoms was 28 months. There was radiographic evidence of osteonecrosis of both femoral heads in all 6 patients. The female patient also had osteonecrosis of both humeral heads and both femoral condyles. Five of twelve hip joints were healed by intertrochanteric osteotomy and revascularization. One patient underwent total hip replacement. We were unable to find risk factors in these 6 patients which would make them susceptible to belated osteonecrosis of the femoral head. It is reasonable to conclude that there is a substantial risk of osteonecrosis in patients treated with high dose steroids even on a short term basis.