Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

Governor's Youth Race and Detention Task Force; Full Force, May 2009

This report, the Full Report, is the culmination of the Task Force’s responsibilities as set out in Executive Order 5, dated October 30, 2007. The Executive Order specifies a number of goals and report requirements.There is a commonly held perception that the use of detention may serve as a deterrent to future delinquency. Data in this report reflect that approximately 40% of youth detained in 2006 were re-detained in 2006. Research conducted by national experts indicates that, particularly for low risk/low level offenders, that the use of detention is not neutral, and may increase the likelihood of recidivism. Comparable data for Iowa are not available (national data studied for this report provide level of risk, but risk level related to detention is not presently available for Iowa). The Task Force finds no evidence suggesting that recidivism levels (as related to detention risk) in Iowa should be different than found in other states. Data in this report also suggest that detention is one of the juvenile justice system’s more costly sanctions ($257 - $340 per day). Other sites and local jurisdictions have been able to redirect savings from the reduced use of juvenile detention to support less costly, community-based detention alternatives without compromising public safety.

A novel technique for the reconstruction of infected full-thickness chest wall defects.

BACKGROUND: Chest wall resection and reconstruction can be performed with minimal mortality and excellent functional and cosmetic results using synthetic meshes, methylmethacrylate, or other substitutes. However, these techniques are less easily applicable if chest wall resections have to be performed for infections. METHODS: We report a novel technique for this purpose using a modified latissimus dorsi flap harvested in continuity with the thoracolumbar fascia. The vascularized fascia was sutured into the chest wall defect, providing a stable base for the muscular component of the flap. Three patients requiring large full-thickness resections of the anterolateral chest wall for chronic infections were treated accordingly, two presenting with chronic radionecrosis and osteomyelitis and one with chest wall invasion by pulmonary aspergillosis. RESULTS: There were no intraoperative or postoperative complications and immediate extubation was possible in all 3 patients without the need for postoperative ventilation or tracheotomy. Healing of the infected chest wall was observed in all 3 patients. Postoperative cinemagnetic resonance imaging revealed concordant movements of the replaced segments without evidence of paradoxical motion during inspiration and expiration. CONCLUSIONS: This technique is easy and safe. It allows a stable and satisfactory reconstruction after large anterolateral full-thickness chest wall resections of infected, previously irradiated tissues, using only well-vascularized autologous tissue.

Instrumental leadership: An extension of the Full-Range Leadership Theory

From a theoretical perspective, an extension to the Full Range leadership Theory (FRLT) seems needed. In this paper, we explain why instrumental leadership--a class of leadership includes leader behaviors focusing on task and strategic aspects that are neither values nor exchange oriented--can fulfill this extension. Instrument leadership is composed of four factors: environmental monitoring, strategy formulation and implementation, path-goal facilitation and outcome monitoring; these aspects of leadership are currently not included in any of the FRLT's nine leadership scales (as measured by the MLQ--Multifactor Leadership Questionnaire). We present results from two empirical studies using very large samples from a wide array of countries (N > 3,000) to examine the factorial, discriminant and criterion-related validity of the instrumental leadership scales. We find support for a four-factor instrumental leadership model, which explains incremental variance in leader outcomes in over and above transactional and transformational leadership.

Source-wavelet estimation during full-waveform inversion of ground-penetrating radar data

A major issue in the application of waveform inversion methods to crosshole ground-penetrating radar (GPR) data is the accurate estimation of the source wavelet. Here, we explore the viability and robustness of incorporating this step into a recently published time-domain inversion procedure through an iterative deconvolution approach. Our results indicate that, at least in non-dispersive electrical environments, such an approach provides remarkably accurate and robust estimates of the source wavelet even in the presence of strong heterogeneity of both the dielectric permittivity and electrical conductivity. Our results also indicate that the proposed source wavelet estimation approach is relatively insensitive to ambient noise and to the phase characteristics of the starting wavelet. Finally, there appears to be little to no trade-off between the wavelet estimation and the tomographic imaging procedures.

Full-waveform inversion of cross-hole ground-penetrating radar data to characterize a gravel aquifer close to the Thur River, Switzerland

Cross-hole radar tomography is a useful tool for mapping shallow subsurface electrical properties viz. dielectric permittivity and electrical conductivity. Common practice is to invert cross-hole radar data with ray-based tomographic algorithms using first arrival traveltimes and first cycle amplitudes. However, the resolution of conventional standard ray-based inversion schemes for cross-hole ground-penetrating radar (GPR) is limited because only a fraction of the information contained in the radar data is used. The resolution can be improved significantly by using a full-waveform inversion that considers the entire waveform, or significant parts thereof. A recently developed 2D time-domain vectorial full-waveform crosshole radar inversion code has been modified in the present study by allowing optimized acquisition setups that reduce the acquisition time and computational costs significantly. This is achieved by minimizing the number of transmitter points and maximizing the number of receiver positions. The improved algorithm was employed to invert cross-hole GPR data acquired within a gravel aquifer (4-10 m depth) in the Thur valley, Switzerland. The simulated traces of the final model obtained by the full-waveform inversion fit the observed traces very well in the lower part of the section and reasonably well in the upper part of the section. Compared to the ray-based inversion, the results from the full-waveform inversion show significantly higher resolution images. At either side, 2.5 m distance away from the cross-hole plane, borehole logs were acquired. There is a good correspondence between the conductivity tomograms and the natural gamma logs at the boundary of the gravel layer and the underlying lacustrine clay deposits. Using existing petrophysical models, the inversion results and neutron-neutron logs are converted to porosity. Without any additional calibration, the values obtained for the converted neutron-neutron logs and permittivity results are very close and similar vertical variations can be observed. The full-waveform inversion provides in both cases additional information about the subsurface. Due to the presence of the water table and associated refracted/reflected waves, the upper traces are not well fitted and the upper 2 m in the permittivity and conductivity tomograms are not reliably reconstructed because the unsaturated zone is not incorporated into the inversion domain.

Mental imagery for full and upper human bodies: common right hemisphere activations and distinct extrastriate activations.

The processing of human bodies is important in social life and for the recognition of another person's actions, moods, and intentions. Recent neuroimaging studies on mental imagery of human body parts suggest that the left hemisphere is dominant in body processing. However, studies on mental imagery of full human bodies reported stronger right hemisphere or bilateral activations. Here, we measured functional magnetic resonance imaging during mental imagery of bilateral partial (upper) and full bodies. Results show that, independently of whether a full or upper body is processed, the right hemisphere (temporo-parietal cortex, anterior parietal cortex, premotor cortex, bilateral superior parietal cortex) is mainly involved in mental imagery of full or partial human bodies. However, distinct activations were found in extrastriate cortex for partial bodies (right fusiform face area) and full bodies (left extrastriate body area). We propose that a common brain network, mainly on the right side, is involved in the mental imagery of human bodies, while two distinct brain areas in extrastriate cortex code for mental imagery of full and upper bodies.

Value of positron emission tomography in full-thickness chest wall resections for malignancies.

Preoperative imaging for resection of chest wall malignancies is generally performed by computed tomography (CT). We evaluated the role of (18)F-fluorodeoxyglucose (FDG) positron emission tomography (PET) in planning full-thickness chest wall resections for malignancies. We retrospectively included 18 consecutive patients operated from 2004 to 2006 at our institution. Tumor extent was measured by CT and PET, using the two largest perpendicular tumor extensions in the chest wall plane to compute the tumor surface assuming an elliptical shape. Imaging measurements were compared to histopathology assessment of tumor borders. CT assessment consistently overestimated the tumor size as compared to PET (+64% vs. +1%, P<0.001). Moreover, PET was significantly better than CT at defining the size of lesions >24 cm(2) corresponding to a mean diameter >5.5 cm or an ellipse of >4 cm x 7.6 cm (positive predictive value 80% vs. 44% and specificity 93% vs. 64%, respectively). Metabolic PET imaging was superior to CT for defining the extent of chest wall tumors, particularly for tumors with a diameter >5.5 cm. PET can complement CT in planning full-thickness chest wall resection for malignancies, but its true value remains to be determined in larger, prospective studies.

ABCtoolbox: a versatile toolkit for approximate Bayesian computations.

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

Feasibility Study of Dynamic Overload and Ultimate Load Tests of Full-Scale Highway Bridges, HR-160, 1973

As a result of the construction of the Saylorville Dam and Reservoir on the Des Moines River, six highway bridges are scheduled for removal. Five of these are old high-truss single-lane bridges, each bridge having several simple spans. The other bridge is a fairly modern (1955) double 4-span continuous beam-and-slab composite highway bridge. The availability of these bridges affords an unusual opportunity for study of the behavior of full-scale bridges. Because of the magnitude of the potential testing program, a feasibility study was initiated and the results are presented in this two-part final report. Part I summarizes the findings and Part II presents the supporting detailed information.

Ultimate Load Behavior of Full-Scale Highway Truss Bridges, Summary Report, HR-169, 1975

As a result of the construction of the Saylorville Dam and Reservoir on the Des Moines River, six highway bridges crossing the river were scheduled for removal. One of these, an old pin-connected, high-truss, single-lane bridge, was selected for a comprehensive testing program which included ultimate load tests, service load tests, and a supplementary test program. A second bridge was used for a limited service load test program. The results of the research are detailed in two interim reports. The first interim report outlines the ultimate load tests and the second interim report details the results of the service load and supplementary test program. This report presents a summary of these findings along with recommendations for implementation of the findings.

Full-genome sequence of the plant growth-promoting bacterium Pseudomonas protegens CHA0.

We report the complete genome sequence of the free-living bacterium Pseudomonas protegens (formerly Pseudomonas fluorescens) CHA0, a model organism used in plant-microbe interactions, biological control of phytopathogens, and bacterial genetics.

Issue review : state of Iowa full-time-equivalent positions and personnel costs.

This issue review provides background on the establishment of full-time-equivalent, or FTE, positions and examines how FTE positions are used in the state's budgeting process. This issue review also provides historical information regarding FTE positions and personnel costs and the current status and outlook of FTE positions and salary expenditures for fiscal year 2011. In addition, this issue review outlines the new requirements included in Senate File 2088, Government Reorganization Efficiency Act, that will impact FTE levels and expenditure of salary dollars for fiscal 2011.

Validity of the acoustic approximation in full-waveform seismic crosshole tomography

Acoustic waveform inversions are an increasingly popular tool for extracting subsurface information from seismic data. They are computationally much more efficient than elastic inversions. Naturally, an inherent disadvantage is that any elastic effects present in the recorded data are ignored in acoustic inversions. We investigate the extent to which elastic effects influence seismic crosshole data. Our numerical modeling studies reveal that in the presence of high contrast interfaces, at which P-to-S conversions occur, elastic effects can dominate the seismic sections, even for experiments involving pressure sources and pressure receivers. Comparisons of waveform inversion results using a purely acoustic algorithm on synthetic data that is either acoustic or elastic, show that subsurface models comprising small low-to-medium contrast (?30%) structures can be successfully resolved in the acoustic approximation. However, in the presence of extended high-contrast anomalous bodies, P-to-S-conversions may substantially degrade the quality of the tomographic images. In particular, extended low-velocity zones are difficult to image. Likewise, relatively small low-velocity features are unresolved, even when advanced a priori information is included. One option for mitigating elastic effects is data windowing, which suppresses later arriving seismic arrivals, such as shear waves. Our tests of this approach found it to be inappropriate because elastic effects are also included in earlier arriving wavetrains. Furthermore, data windowing removes later arriving P-wave phases that may provide critical constraints on the tomograms. Finally, we investigated the extent to which acoustic inversions of elastic data are useful for time-lapse analyses of high contrast engineered structures, for which accurate reconstruction of the subsurface structure is not as critical as imaging differential changes between sequential experiments. Based on a realistic scenario for monitoring a radioactive waste repository, we demonstrated that acoustic inversions of elastic data yield substantial distortions of the tomograms and also unreliable information on trends in the velocity changes.