Large deletions in the CFTR gene: clinics and genetics in Swiss patients with CF

Cystic fibrosis (CF) is the most common life-shortening autosomal recessive disorder in Caucasians, and is associated with at least one mutation on each CF transmembrane conductance regulator (CFTR) allele. Some patients, however, with only one identifiable point mutation carry on the other allele, a large deletion that is not detected by conventional screening methods. The overall frequency of large deletions in patients with CF is estimated to be 1-3%. Using the CFTR Multiplex Ligation dependent Probe Amplification Kit (MRC-Holland, Amsterdam, Netherlands) that allows the exact detection of copy numbers from all 27 exons in the CFTR gene, we screened 50 patients with only one identified mutation for large deletions in the CFTR gene. Each detected deletion was confirmed using our real-time polymerase chain reaction (PCR) assay and deletion-specific PCR reactions using junction fragment primers. We detected large deletions in eight patients (16%). These eight CF alleles belong to four different deletion types (CFTRindel2, CFTRdele14b-17b, CFTRdele17a-17b and CFTRdele 2-9) whereof the last is novel. Comparing detailed clinical data of all these patients with CF and the molecular genetic findings, we were able to elaborate criteria for deletion screenings and possible genotype-phenotype associations. In conclusion, we agree with other authors that deletion screenings should be implemented in routine genetic diagnostics of CF.

In vitro differentiation of near-unlimited numbers of functional mouse basophils using conditional Hoxb8

Background: Basophils constitute a rare leukocyte population known for their effector functions in inflammation and allergy, as well as more recently described immunoregulatory roles. Besides their low frequency, functional analysis of basophils is hindered by a short life span, inefficient ex vivo differentiation protocols, and lack of suitable cell models. A method to produce large quantities of basophils in vitro would facilitate basophil research and constitute a sought-after tool for diagnostic and drug testing purposes. Methods: A method is described to massively expand bone marrow–derived basophils in vitro. Myeloid progenitors are conditionally immortalized using Hoxb8 in the presence of interleukin-3 (IL-3) and outgrowing cell lines selected for their potential to differentiate into basophils upon shutdown of Hoxb8 expression. Results: IL-3-dependent, conditional Hoxb8-immortalized progenitor cell lines can be expanded and maintained in culture for prolonged periods. Upon shutdown of Hoxb8 expression, near-unlimited numbers of mature functional basophils can be differentiated in vitro within six days. The cells are end-differentiated and short-lived and express basophil-specific surface markers and proteases. Upon IgE- as well as C5a-mediated activation, differentiated basophils release granule enzymes and histamine and secrete Th2-type cytokines (IL-4, IL-13) and leukotriene C4. IL-3-deprivation induces apoptosis correlating with upregulation of the BH3-only proteins BCL-2-interacting mediator of cell death (BIM) and p53 upregulated modulator of apoptosis (PUMA) and downregulation of proviral integration site for Moloney murine leukemia virus 1 kinase (PIM-1). Conclusion: A novel method is presented to generate quantitative amounts of mouse basophils in vitro, which moreover allows genetic manipulation of conditionally immortalized progenitors. This approach may represent a useful alternative method to isolating primary basophils.

Large deviations for heavy-tailed random elements in convex cones

We prove large deviation results for sums of heavy-tailed random elements in rather general convex cones being semigroups equipped with a rescaling operation by positive real numbers. In difference to previous results for the cone of convex sets, our technique does not use the embedding of cones in linear spaces. Examples include the cone of convex sets with the Minkowski addition, positive half-line with maximum operation and the family of square integrable functions with arithmetic addition and argument rescaling.

Coloured Letters and Numbers (CLaN): A reliable factor-analysis based synaesthesia questionnaire

Synaesthesia is a heterogeneous phenomenon, even when considering one particular sub-type. The purpose of this study was to design a reliable and valid questionnaire for grapheme-colour synaesthesia that captures this heterogeneity. By the means of a large sample of 628 synaesthetes and a factor analysis, we created the Coloured Letters and Numbers (CLaN) questionnaire with 16 items loading on 4 different factors (i.e., localisation, automaticity/attention, deliberate use, and longitudinal changes). These factors were externally validated with tests which are widely used in the field of synaesthesia research. The questionnaire showed good test–retest reliability and construct validity (i.e., internally and externally). Our findings are discussed in the light of current theories and new ideas in synaesthesia research. More generally, the questionnaire is a useful tool which can be widely used in synaesthesia research to reveal the influence of individual differences on various performance measures and will be useful in generating new hypotheses.

Gender differences in colorectal cancer screening and incidence in large nationwide, population-based cohorts

Background. A few studies have reported gender differences along the colorectal cancer (CRC) continuum but none has done so longitudinally to compare a cancer and a non-cancer populations.^ Objectives and Methods. To examine gender differences in colorectal cancer screening (CRCS); to examine trends in gender differences in CRC screening among two groups of patients (Medicare beneficiaries with and without cancer); to examine gender differences in CRC incidence; and to examine for any differences over time. In Paper 1, the study population consisted of men and women, ages 67–89 years, with CRC (73,666) or without any cancer (39,006), residing in 12 U.S. Surveillance Epidemiology and End-Results (SEER) regions. Crude and age-adjusted percentages and odds ratios of receiving fecal occult blood test (FOBT), sigmoidoscopy (SIG), or colonoscopy (COL) were calculated. Multivariable logistic regression was used to assess gender on the odds of receiving CRC screening over time.^ In Paper 2, age-adjusted incidence rates and proportions over time were reported across race, CRC subsite, CRC stage and SEER region for 373,956 patients, ages 40+ years, residing in 9 SEER regions and diagnosed with malignant CRC. ^ Results. Overall, women had higher CRC screening rates than men and screening rates in general were higher in the SEER sample of persons with CRC diagnosis. Significant temporal divergence in FOBT screening was observed between men and women in both cohorts. Although the largest temporal increases in screening rates were found for COL, especially among the cohort with CRC, little change in the gender gap was observed over time. Receipt of FOBT was significantly associated with female gender especially in the period of full Medicare coverage. Receipt of COL was also significantly associated with male gender, especially in the period of limited Medicare coverage.^ Overall, approximately equal numbers of men (187,973) and women (185,983) were diagnosed with malignant CRC. Men had significantly higher age-adjusted CRC incidence rates than women across all categories of age, race, subsite, stage and SEER region even though rates declined in all categories over time. Significant moderate increases in rate difference occurred among 40-59 year olds; significant reductions occurred among patients age 70+, within subsite rectum, unstaged and distant stage CRC, and eastern and western SEER regions. ^ Conclusions. Persistent gender differences in CRC incidence across time may have implications for gender-based interventions that take age into consideration. A shift toward proximal cancer was observed over time for both genders, but the high proportion of men who develop rectal cancer suggests that a greater proportion of men may need to be targeted with newer screening methods such as fecal DNA or COL. Although previous reports have documented higher CRC screening among men, higher incidence of CRC observed among men suggests that higher risk categories of men are probably not being reached. FOBT utilization rates among women have increased over time and the gender gap has widened between 1998 and 2005. COL utilization is associated with male gender but the differences over time are small.^

Performance enhancement of large industrial wastewater stabilization ponds

A 6-month-long, bench-scale simulation of an industrial wastewater stabilization pond (WSP) system was conducted to evaluate responses to several potential performance-enhancing treatments. The industrial WSP system consists of an anaerobic primary (1ry) WSP treating high-strength wastewater, followed by facultative secondary (2ry) and aerobic tertiary (3ry) WSPs in series treating lower-strength wastewater. The 1ry WSP was simulated with four glass aquaria which were fed with wastewater from the actual WSP system. The treatments examined were phosphorus supplementation (PHOS), phosphorus supplementation with pH control (PHOS+ALK), and phosphorus supplementation with pH control and effluent recycle (PHOS+ALK+RCY). The supplementary phosphorus treatment alone did not yield any significant change versus the CONTROL 1ry model pond. The average carbon to phosphorus ratio of the feed wastewater received from the WSP system was already 100:0.019 (i.e., 2,100 mg/l: 0.4 mg/l). The pH-control treatments (PHOS+ALK and PHOS+ALK+RCY) produced significant results, with 9 to 12 percent more total organic carbon (TOC) removal, 43 percent more volatile organic acid (VOA) generation, 78 percent more 2-ethoxyethanol and 14 percent more bis(2-chloroethyl)ether removal, and from 100- to 10,000-fold increases in bacterial enzyme activity and heterotrophic bacterial numbers. Recycling a 10-percent portion of the effluent yielded less variability for certain physicochemical parameters in the PHOS+ALK+RCY 1ry model pond, but overall there was no statistically-detectable improvement in performance versus no recycle. The 2ry and 3ry WSPs were also simulated in the laboratory to monitor the effect and fate of increased phosphorus loadings, as might occur if supplemental phosphorus were added to the 1ry WSP. Noticeable increases in algal growth were observed at feed phosphorus concentrations of 0.5 mg/l; however, there were no significant changes in the monitored physicochemical parameters. The effluent phosphorus concentrations from both the 2ry and 3ry model ponds did increase notably when feed phosphorus concentrations were increased from 0.5 to 1.0 mg/l. ^

Searching for a consensus similarity function for generalized trapezoidal fuzzy numbers

There is controversy regarding the use of the similarity functions proposed in the literature to compare generalized trapezoidal fuzzy numbers since conflicting similarity values are sometimes output for the same pair of fuzzy numbers. In this paper we propose a similarity function aimed at establishing a consensus. It accounts for the different approaches of all the similarity functions. It also has better properties and can easily incorporate new parameters for future improvements. The analysis is carried out on the basis of a large and representative set of pairs of trapezoidal fuzzy numbers.

Numbers and Organization of RNA Polymerases, Nascent Transcripts, and Transcription Units in HeLa Nuclei

Using HeLa cells, we have developed methods to determine 1) the number of RNA polymerases that are active at any moment, 2) the number of transcription sites, and 3) the number of polymerases associated with one transcription unit. To count engaged polymerases, cells were encapsulated in agarose, permeabilized, treated with ribonuclease, and the now-truncated transcripts extended in [32P]uridine triphosphate; then, the number of growing transcripts was calculated from the total number of nucleotides incorporated and the average increment in length of the transcripts. Approximately 15,000 transcripts were elongated by polymerase I, and ∼75,000 were elongated by polymerases II and III. Transcription sites were detected after the cells were grown in bromouridine for <2.5 min, after which the resulting bromo-RNA was labeled with gold particles; electron microscopy showed that most extranucleolar transcripts were concentrated in ∼2400 sites with diameters of ∼80 nm. The number of polymerases associated with a transcription unit was counted after templates were spread over a large area; most extranucleolar units were associated with one elongating complex. These results suggest that many templates are attached in a “cloud” of loops around a site; each site, or transcription “factory,” would contain ∼30 active polymerases and associated transcripts.

Enriching plant diversity in grasslands by large-scale experimental sward disturbance and seed addition along gradients of land-use intensity

Aims The relationship between biodiversity and ecosystem functioning is among the most active areas of ecological research. Furthermore, enhancing the diversity of degraded ecosystems is a major goal in applied restoration ecology. In grasslands, many species may be locally absent due to dispersal or microsite limitation and may therefore profit from mechanical disturbance of the resident vegetation. We established a seed addition and disturbance experiment across several grassland sites of different land use to test whether plant diversity can be increased in these grasslands. Additionally, the experiment will allow us testing the consequences of increased plant diversity for ecosystem processes and for the diversity of other taxa in real-world ecosystems. Here we present details of the experimental design and report results from the first vegetation survey one year after disturbance and seed addition. Moreover, we tested whether the effects of seed addition and disturbance varied among grassland depending on their land use or pre-disturbance plant diversity. Methods A full-factorial experiment was installed in 73 grasslands in three regions across Germany. Grasslands were under regular agricultural use, but varied in the type and the intensity of management, thereby representing the range of management typical for large parts of Central Europe. The disturbance treatment consisted of disturbing the top 10 cm of the sward using a rotavator or rotary harrow. Seed addition consisted of sowing a high-diversity seed mixture of regional plant species. These species were all regionally present, but often locally absent, depending on the resident vegetation composition and richness of each grassland. Important findings One year after sward disturbance it had significantly increased cover of bare soil, seedling species richness and numbers of seedlings. Seed addition had increased plant species richness, but only in combination with sward disturbance. The increase in species richness, when both seed addition and disturbance was applied, was higher at high land-use intensity and low resident diversity. Thus, we show that at least the early recruitment of many species is possible also at high land-use intensity, indicating the potential to restore and enhance biodiversity of species-poor agricultural grasslands. Our newly established experiment provides a unique platform for broad-scale research on the land-use dependence of future trajectories of vegetation diversity and composition and their effects on ecosystem functioning.

The statutes at large; : being a collection of all the laws of Virginia, from the first session of the legislature, in the year 1619. : Published pursuant to an act of the General Assembly of Virginia, passed on the fifth day of February one thousand eight hundred and eight. : Volume I[-XIII]. /

Each volume contains a certification statement and an errata statement, either tipped in or printed on the title page verso.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Large diameter optic nerve axon fibres in Alzheimer's disease

A variety of visual symptoms have been associated with Alzheimer's disease (AD). These include delays in flash visual evoked potentials which indicate a disruption of the integrity of the visual pathway. Examination of the visual cortex has revealed the presence of both senile plaques and neurofibrillary tangles. The purpose of this study was to determine whether there were differences in the number and/or size of optic nerve axons between AD patients and non-demented age-matched controls. Five optic nerves from AD patients and five from age-matched controls were embedded in epon resin and 1 micron sections prepared on a Reichert ultramicrotome. The sections were then stained in toluidine blue and examined at x400 magnification. The numbers of axons were counted in photographs of three fields taken at random from each section. To evaluate the axon diameters, 70 axons were chosen at random from each patient and measured using a calibrated eyepiece graticule. The total axon counts revealed no significant differences between the AD optic nerves and the age-matched controls. However, the frequency distribution of axon diameters was significantly different in the two groups. In particular, there were fewer larger diameter axons in patients with AD as previously reported. Degeneration of the large diameter axons suggests involvement of the magnocellular as opposed to the parvocellular pathways. Hence, there could be differences in visual performance of AD patients compared with normals which could be important in clinical diagnosis.

Adults with dyslexia exhibit large effects of crowding, increased dependence on cues, and detrimental effects of distractors in visual search tasks

Difficulties in visual attention are increasingly being linked to dyslexia. To date, the majority of studies have inferred functionality of attention from response times to stimuli presented for an indefinite duration. However, in paradigms that use reaction times to investigate the ability to orient attention, a delayed reaction time could also indicate difficulties in signal enhancement or noise exclusion once oriented. Thus, in order to investigate attention modulation and visual crowding effects in dyslexia, this study measured stimulus discrimination accuracy to rapidly presented displays. Adults with dyslexia (AwD) and controls discriminated the orientation of a target in an array of different numbers of - and differently spaced - vertically orientated distractors. Results showed that AwD: were disproportionately impacted by (i) close spacing and (ii) increased numbers of stimuli, (iii) did use pre-cues to modulate attention, but (iv) used cues less successfully to counter effects of increasing numbers of distractors. A greater dependence on pre-cues, larger effects of crowding and the impact of increased numbers of distractors all correlated significantly with measures of literacy. These findings extend previous studies of visual crowding of letters in dyslexia to non-complex stimuli. Overall, AwD do not use cues less, but they do use cues less successfully. We conclude that visual attention is an important factor to consider in the aetiology of dyslexia. The results challenge existing theoretical accounts of visual attention deficits, which alone are unable to comprehensively explain the pattern of findings demonstrated here.

Adults with dyslexia demonstrate large effects of crowding and detrimental effects of distractors in a visual tilt discrimination task

Previous research has shown that adults with dyslexia (AwD) are disproportionately impacted by close spacing of stimuli and increased numbers of distractors in a visual search task compared to controls [1]. Using an orientation discrimination task, the present study extended these findings to show that even in conditions where target search was not required: (i) AwD had detrimental effects of both crowding and increased numbers of distractors; (ii) AwD had more pronounced difficulty with distractor exclusion in the left visual field and (iii) measures of crowding and distractor exclusion correlated significantly with literacy measures. Furthermore, such difficulties were not accounted for by the presence of covarying symptoms of ADHD in the participant groups. These findings provide further evidence to suggest that the ability to exclude distracting stimuli likely contributes to the reported visual attention difficulties in AwD and to the aetiology of literacy difficulties. The pattern of results is consistent with weaker and asymmetric attention in AwD.

On the Asymptotic Behavior of the Ratio between the Numbers of Binary Primitive and Irreducible Polynomials

This work was presented in part at the 8th International Conference on Finite Fields and Applications Fq^8 , Melbourne, Australia, 9-13 July, 2007.