BamView: viewing mapped read alignment data in the context of the reference sequence

Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features

Structural tuning of color chromaticity through nonradiative energy transfer by interspacing CdTe nanocrystal monolayers

Cataloged from PDF version of article.We proposed and demonstrated architectural tuning of color chromaticity by controlling photoluminescence decay kinetics through nonradiative Forster resonance energy transfer in the heterostructure of layer-by-layer spaced CdTe nanocrystal (NC) solids. We achieved highly sensitive tuning by precisely adjusting the energy transfer efficiency from donor NCs to acceptor NCs via controlling interspacing between them at the nanoscale. By modifying decay lifetimes of donors from 12.05 to 2.96 ns and acceptors from 3.68 to 14.57 ns, we fine-tuned chromaticity coordinates from (x,y)=(0.575,0.424) to (0.632, 0.367). This structural adjustment enabled a postsynthesis color tuning capability, alternative or additive to using the size, shape, and composition of NCs

Unenhanced helical computed tomography vs intravenous urography in patients with acute flank pain: accuracy and economic impact in a randomized prospective trial

Abstract.: Unenhanced helical computed tomography (UHCT) has evolved into a well-accepted alternative to intravenous urography (IVU) in patients with acute flank pain and suspected ureterolithiasis. The purpose of our randomized prospective study was to analyse the diagnostic accuracy of UHCT vs IVU in the normal clinical setting with special interest on economic impact, applied radiation dose and time savings in patient management. A total of 122 consecutive patients with acute flank pain suggestive of urolithiasis were randomized for UHCT (n=59) or IVU (n=63). Patient management (time, contrast media), costs and radiation dose were analysed. The films were independently interpreted by four radiologists, unaware of previous findings, clinical history and clinical outcome. Alternative diagnoses if present were assessed. Direct costs of UHCT and IVU are nearly identical (310/309 Euro). Indirect costs are much lower for UHCT because it saves examination time and when performed immediately initial abdominal plain film (KUB) and sonography are not necessary. Time delay between access to the emergency room and start of the imaging procedure was 32h 7min for UHCT and 36h 55min for IVU. The UHCT took an average in-room time of 23min vs 1h 21min for IVU. Mild to moderate adverse reactions for contrast material were seen in 3 (5%) patients. The UHCT was safe, as no contrast material was needed. The mean applied radiation dose was 3.3mSv for IVU and 6.5mSv for UHCT. Alternative diagnoses were identified in 4 (7%) UHCT patients and 3 (5%) IVU patients. Sensitivity and specificity of UHCT and IVU was 94.1 and 94.2%, and 85.2 and 90.4%, respectively. In patients with suspected renal colic KUB and US may be the least expensive and most easily accessable modalities; however, if needed and available, UHCT can be considered a better alternative than IVU because it has a higher diagnostic accuracy and a better economic impact since it is more effective, faster, less expensive and less risky than IVU. In addition, it also has the capability of detecting various additional renal and extrarenal pathologie

Integration of external and internal dosimetry in Switzerland

Individual monitoring regulations in Switzerland are based on the ICRP60 recommendations. The annual limit of 20 mSv for the effective dose applies to the sum of external and internal radiation. External radiation is monitored monthly or quarterly with TLD, DIS or CR-39 dosemeters by 10 approved external dosimetry services and reported as Hp(10) and Hp(0.07). Internal monitoring is done in two steps. At the workplace, simple screening measurements are done frequently in order to recognise a possible incorporation. If a nuclide dependent activity threshold is exceeded then one of the seven approved dosimetry services for internal radiation does an incorporation measurement to assess the committed effective dose E50. The dosimetry services report all the measured or assessed dose values to the employer and to the National Dose Registry. The employer records the annually accumulated dose values into the individual dose certificate of the occupationally exposed person, both the external dose Hp(10) and the internal dose E50 as well as the total effective dose E = Hp(10)+E50. Based on the national dose registry an annual report on the dosimetry in Switzerland is published which contains the statistics for the total effective dose, as well as separate statistics for external and internal exposur

Physical activity in children with Juvenile Idiopathic Arthritis compared to controls

BACKGROUND: To compare physical activity (PA) in children with juvenile idiopathic arthritis (JIA) with controls and to analyse the effect of disease specific factors on PA in children with JIA treated according to current treatment regimes. METHODS: PA was measured with a 7-day activity diary and expressed as physical activity level (PAL). Moderate to vigorous physical activity (MVPA) (hours/day) and sedentary time (hours/day) was determined. In children with JIA, medication, the number of swollen and/or painful joints, disease activity, functional ability, pain and well-being was determined. Multivariate regression analysis was performed to analyze differences in PA between JIA and controls, adjusted for influences of age, gender, season, Body Mass Index (BMI) and to analyze predictors of PA in JIA patients. RESULTS: Seventy-six children with JIA (26 boys and 50 girls, mean ± SD age 10.0 ± 1.4 years) and 131 controls (49 boys and 82 girls, mean ± SD age 10.4 ± 1.2 years) participated in this study. Children with JIA had a significantly lower PAL (0.10, p = 0.01) corrected for age, BMI, gender and season. They spent less time in MVPA (0.41 h/day, p = 0.06) and had a significantly higher mean time spent in sedentary activities (0.59 h/day, p 0.02) compared to controls. The activity level of children with JIA was related to age, gender, season, feeling of well-being and pain. CONCLUSION: Children with JIA have a lower PAL, spent less time in MVPA and spent more time on sedentary activities compared to controls despite current medical treatment and PA encouragement. TRIAL REGISTRATION: Data of the children with JIA are from the Rheumates@work study ISRCTN92733069

The Swiss Systemic lupus erythematosus Cohort Study (SSCS) - cross-sectional analysis of clinical characteristics and treatments across different medical disciplines in Switzerland.

OBJECTIVES: To describe disease characteristics and treatment modalities in a multidisciplinary cohort of systemic lupus erythematosus (SLE) patients in Switzerland. METHODS: Cross-sectional analysis of 255 patients included in the Swiss SLE Cohort and coming from centres specialised in Clinical Immunology, Internal Medicine, Nephrology and Rheumatology. Clinical data were collected with a standardised form. Disease activity was assessed using the Safety of Estrogens in Lupus Erythematosus National Assessment-SLE Disease Activity Index (SELENA-SLEDAI), an integer physician's global assessment score (PGA) ranging from 0 (inactive) to 3 (very active disease) and the erythrocyte sedimentation rate (ESR). The relationship between SLE treatment and activity was assessed by propensity score methods using a mixed-effect logistic regression with a random effect on the contributing centre. RESULTS: Of the 255 patients, 82% were women and 82% were of European ancestry. The mean age at enrolment was 44.8 years and the median SLE duration was 5.2 years. Patients from Rheumatology had a significantly later disease onset. Renal disease was reported in 44% of patients. PGA showed active disease in 49% of patients, median SLEDAI was 4 and median ESR was 14 millimetre/first hour. Prescription rates of anti-malarial drugs ranged from 3% by nephrologists to 76% by rheumatologists. Patients regularly using anti-malarial drugs had significantly lower SELENA-SLEDAI scores and ESR values. CONCLUSION: In our cohort, patients in Rheumatology had a significantly later SLE onset than those in Nephrology. Anti-malarial drugs were mostly prescribed by rheumatologists and internists and less frequently by nephrologists, and appeared to be associated with less active SLE

Mutation, selection, and ancestry in branching models: a variational approach

We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated genealogical tree is viewed both in the forward and the backward direction of time. The stationary type distribution of the reversed process, the so-called ancestral distribution, turns out as a key for the study of mutation-selection balance. This balance can be expressed in the form of a variational principle that quantifies the respective roles of reproduction and mutation for any possible type distribution. It shows that the mean growth rate of the population results from a competition for a maximal long-term growth rate, as given by the difference between the current mean reproduction rate, and an asymptotic decay rate related to the mutation process; this tradeoff is won by the ancestral distribution. Our main application is the quasispecies model of sequence evolution with mutation coupled to reproduction but independent across sites, and a fitness function that is invariant under permutation of sites. Here, the variational principle is worked out in detail and yields a simple, explicit result.Comment: 45 pages,8 figure

Motor development in children 0-2 years pre- and post-LTX, a prospective study

To determine prospectively gross and fine motor development of childre

Shunting operations at flat yards : retrieving freight railcars from storage tracks

In this paper, we study the railcar retrieval problem (RRT) where specified numbers of certain types of railcars have to be withdrawn from the storage tracks of a flat yard. This task arises in the daily operations of workshop yards for railcar maintenance. The objective is to minimize the total cost of shunting via methods such as minimizing the usage of shunting engines. We describe the RRT formally, present a mixed-integer program formulation, and prove the general case to be NP-hard. For some special cases, exact algorithms with polynomial runtimes are proposed. We also analyze several intuitive heuristic solution approaches motivated by observed real-world planning routines. We evaluate their average performances in simulations with different scenarios and provide their worst-case performance guarantee. We show that although the analyzed heuristics result in much better solutions than the naive planning approach, they are still on average 30%-50% from the optimal objective value and may result in up to 14 times higher costs in the worst case. Therefore, we conclude that optimization should be implemented in practice in order to save valuable resources. Furthermore, we analyze the impacts of yard layout and the widespread organizational routine of presorting on the railcar retrieval cost

Quintessence Restrictions on Negative Power and Condensate Potentials

We study the cosmological evolution of scalar fields that arise from a phase transition at some energy scale \Lm_c. We focus on negative power potentials given by V=c\Lm_c^{4+n}\phi^{-n} and restrict the cosmological viable values of \Lm_c and $n$. We make a complete analysis of $V$ and impose $SN1a$ conditions on the different cosmological parameters. The cosmological observations ruled out models where the scalar field has reached its attractor solution. For models where this is not the case, the analytic approximated solutions are not good enough to determine whether a specific model is phenomenologically viable or not and the full differential equations must be numerically solved. The results are not fine tuned since a change of 45% on the initial conditions does not spoil the final results. We also determine the values of $N_c, N_f$ that give a condensation scale \Lm_c consistent with gauge coupling unification, leaving only four models that satisfy unification and SN1a constraints.Comment: 15 pages, LaTeX, 8 Figures. Minor changes in text, a discussion on initial conditions added (accepted in Phys.Rev.D