Construction of correlation networks with explicit time-slices using time-lagged, variable interval standard and partial correlation coefficients

The construction of gene regulatory models from microarray time-series data has received much attention. Here we propose a method that extends standard correlation networks to incorporate explicit time-slices. The method is applied to a time-series dataset of a study on gene expression in the developmental phase of zebrafish. Results show that the method is able to distinguish real relations between genes from the data. These relations are explicitly placed in time, allowing for a better understanding of gene regulation. The method and data normalisation procedure have been implemented using the R statistical language and are available from http://zebrafish.liacs.nl/supplements.html

Frequent Episode Mining to support Pattern Analysis in Developmental Biology

Computer Systems, Imagery and Medi

Atmospheric Fragmentation of the Gold Basin Meteoroid as Constrained from Cosmogenic Nuclides

Since the discovery of the Gold Basin L4 chondrite shower almost ten years ago in the northwestern corner of Arizona, many thousands of L-chondrite specimens have been recovered from an area of approx.22 km long and approx.10 km wide. Concentrations of cosmogenic 14C and 10Be in a number of these samples indicated a terrestrial age of approx.15,000 years and a large pre-atmospheric size [1]. Additional measurements of cosmogenic Be-10, Al-26, Cl-36, and Ca-41 in the metal and stone fractions of fifteen Gold Basin samples constrained the pre-atmospheric radius to 3-5 m [2]. This implies that Gold Basin is by far the largest stone meteorite in the present meteorite collection, providing us with an opportunity to study the fragmentation process of a large chondritic object during atmospheric entry. Knowledge about the fragmentation process provides information about the mechanical strength of large meteoroids, which is important for the evaluation of future hazards of small asteroid impacts on Earth and possible defensive scenarios to avoid those impacts

Early development of rostrum saw-teeth in a fossil ray tests classical theories of the evolution of vertebrate dentitions

In classical theory, teeth of vertebrate dentitions evolved from co-option of external skin denticles into the oral cavity. This hypothesis predicts that ordered tooth arrangement and regulated replacement in the oral dentition were also derived from skin denticles. The fossil batoid ray Schizorhiza stromeri (Chondrichthyes; Cretaceous) provides a test of this theory. Schizorhiza preserves an extended cartilaginous rostrum with closely spaced, alternating saw-teeth, different from sawfish and sawsharks today. Multiple replacement teeth reveal unique new data from micro-CT scanning, showing how the 'cone-in-cone' series of ordered saw-teeth sets arrange themselves developmentally, to become enclosed by the roots of pre-existing saw-teeth. At the rostrum tip, newly developing saw-teeth are present, as mineralized crown tips within a vascular, cartilaginous furrow; these reorient via two 90° rotations then relocate laterally between previously formed roots. Saw-tooth replacement slows mid-rostrum where fewer saw-teeth are regenerated. These exceptional developmental data reveal regulated order for serial self-renewal, maintaining the saw edge with ever-increasing saw-tooth size. This mimics tooth replacement in chondrichthyans, but differs in the crown reorientation and their enclosure directly between roots of predecessor saw-teeth. Schizorhiza saw-tooth development is decoupled from the jaw teeth and their replacement, dependent on a dental lamina. This highly specialized rostral saw, derived from diversification of skin denticles, is distinct from the dentition and demonstrates the potential developmental plasticity of skin denticles

Acquiescence and Extremity in Cross-National Surveys: Domain Dependence and Country-Level Correlates

Likert-type rating scales are susceptible to response styles, such as acquiescence and extremity scoring. Although it is widely acknowledged that response styles can seriously invalidate findings of cross-cultural research, their theoretical underpinnings are hardly explored. The current study analyzed domain-dependency and country differences in acquiescence and extremity scoring in a large dataset of the International Social Survey Program. The hypothesis that response styles are more likely in domains with a high personal relevance compared to domains with a low personal relevance was tentatively confirmed. Correlations with various cultural, psychological, and economic variables were investigated. We found that acquiescence was negatively related to affluence, individualism, and well-being, while extremity was only negatively related to well-being. Positive associations were found between uncertainty avoidance and both acquiescence and extremity

A randomized multicenter study of the outcome of brachial-basilic arteriovenous fistula and prosthetic brachial-antecubital forearm loop as vascular access for hemodialysis

BackgroundVascular access is a necessity for patients with end-stage renal disease who need chronic intermittent hemodialysis. According to Kidney Disease Outcomes Quality Initiative (KDOQI) guidelines, radial-cephalic (RC) and brachial-cephalic (BC) arteriovenous fistulas (AVF) are the first and second choice for vascular access, respectively. If these options are not possible, an autogenous brachial-basilic fistula in the upper arm (BBAVF) or a prosthetic brachial-antecubital forearm loop (PTFE loop) may be considered. Until now, it was not clear which access type was preferable. We have performed a randomized study comparing BBAVF and prosthetic implantation in patients without the possibility for RCAVF or BCAVF.MethodsPatients with failed primary/secondary access or inadequate arterial and/or venous vessels were randomized for either BBAVF or PTFE loop creation. The numbers of complications and interventions were recorded. Kaplan-Meier method was used to calculate primary, assisted-primary and secondary patency rates. The patency rates were compared with the log-rank test. Complication and intervention rates were compared with the Mann-Whitney test.ResultsA total of 105 patients were randomized for a BBAVF or PTFE loop (52 vs 53, respectively). Primary and assisted-primary 1-year patency rates were significantly higher in the BBAVF group: 46% ± 7.4% vs 22% ± 6.1% (P = .005) and 87% ± 5.0% vs 71% ± 6.7% (P = .045) for the BBAVF and PTFE group, respectively. Secondary patencies were comparable for both groups; 89% ± 4.6% vs 85% ± 5.2% for the BBAVF and PTFE group, respectively. The incidence rate of complications was 1.6 per patient-year in the BBAVF group vs 2.7 per patient-year in the PTFE group. Patients in the BBAVF group needed a total of 1.7 interventions per patient-year vs 2.7 per patient-year for the PTFE group.ConclusionThese data show a significantly better primary and assisted-primary patency in the BBAVF group compared with the PTFE group. Furthermore, in the BBAVF group, fewer interventions were needed. Therefore, we conclude that BBAVF is the preferred choice for vascular access if RCAVF or BCAVF creation is impossible, or when these types of access have already failed

A Complex Exposure History of the Gold Basin L4-Chondrite Shower from Cosmogenic Radionuclides and Noble Gases

Gold Basin is a large L4 chondrite shower, that was recently discovered in the Mojave Desert, Arizona [1]. Based on {sup 109}Be and {sup 14}C concentrations in several fragments, the pre-atmospheric radius of this shower was estimated to be 3-4 meters [2]. Among chondrites, Gold Basin is one of the largest, thus providing a unique opportunity for comparing measured cosmogenic nuclide concentrations with model calculations for large objects. Noble gas measurements combined with {sup 10}Be data of most Gold Basin samples suggest a single-stage exposure of 15-30 Myr, although a few samples may require a complex exposure history [3]. We selected eight samples of the Gold Basin shower that were analyzed for noble gases; these samples represent a wide range of shielding depths

Supervised exercise therapy for intermittent claudication in a community-based setting is as effective as clinic-based

ObjectiveThis cohort study was conducted to determine the effect on walking distances of supervised exercise therapy provided in a community-based setting.MethodsThe study included all consecutive patients presenting at the vascular outpatient clinic with intermittent claudication, diagnosed by a resting ankle brachial index <0.9, who had no previous peripheral vascular intervention for peripheral arterial disease, no major amputation, and sufficient command of the Dutch language. The exclusion criterion was the inability to walk the baseline treadmill test for a minimum of 10 m. The intervention was a supervised exercise therapy in a community-based setting. A progressive treadmill test at baseline and at 1, 3, and 6 months of follow-up measured initial claudication distance and absolute claudication distance. Changes were calculated using the mean percentages of change.ResultsFrom January through October 2005, 93 consecutive patients with claudication were eligible. Overall, 37 patients discontinued the supervised exercise therapy program. Eleven stopped because of intercurrent diseases, whereas for 10, supervised exercise therapy did not lead to adequate improvement and they underwent a vascular intervention. Three patients quit the program, stating that they were satisfied with the regained walking distance and did not require further supervised exercise therapy. Ten patients were not motivated sufficiently to continue the program, and in three patients, a lack of adequate insurance coverage was the reason for dropping out. Data for 56 patients were used and showed a mean percentage increase in initial claudication distance of 187% after 3 months and 240% after 6 months. The mean percentage of the absolute claudication distance increased 142% after 3 months and 191% after 6 months.ConclusionSupervised exercise therapy in a community-based setting is a promising approach to providing conservative treatment for patients with intermittent claudication