Assessment of transcript reconstruction methods for RNA-seq.

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.

An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim  Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.Location  World-wide.Methods  Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.Results  Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.Main conclusions  By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

Rehabilitation of Concrete Pavements Utilizing Rebblization and Crack and Seat Methods, June 2005

Deterioration in portland cement concrete (PCC) pavements can occur due to distresses caused by a combination of traffic loads and weather conditions. Hot mix asphalt (HMA) overlay is the most commonly used rehabilitation technique for such deteriorated PCC pavements. However, the performance of these HMA overlaid pavements is hindered due to the occurrence of reflective cracking, resulting in significant reduction of pavement serviceability. Various fractured slab techniques, including rubblization, crack and seat, and break and seat are used to minimize reflective cracking by reducing the slab action. However, the design of structural overlay thickness for cracked and seated and rubblized pavements is difficult as the resulting structure is neither a “true” rigid pavement nor a “true” flexible pavement. Existing design methodologies use the empirical procedures based on the AASHO Road Test conducted in 1961. But, the AASHO Road Test did not employ any fractured slab technique, and there are numerous limitations associated with extrapolating its results to HMA overlay thickness design for fractured PCC pavements. The main objective of this project is to develop a mechanistic-empirical (ME) design approach for the HMA overlay thickness design for fractured PCC pavements. In this design procedure, failure criteria such as the tensile strain at the bottom of HMA layer and the vertical compressive strain on the surface of subgrade are used to consider HMA fatigue and subgrade rutting, respectively. The developed ME design system is also implemented in a Visual Basic computer program. A partial validation of the design method with reference to an instrumented trial project (IA-141, Polk County) in Iowa is provided in this report. Tensile strain values at the bottom of the HMA layer collected from the FWD testing at this project site are in agreement with the results obtained from the developed computer program.

Evaluation of Transverse Joint Forming Methods for PCC Pavement, January 2006

The members of the Iowa Concrete Paving Association, the National Concrete Pavement Technology Center Research Committee, and the Iowa Highway Research Board commissioned a study to examine alternative ways of developing transverse joints in portland cement concrete pavements. The present study investigated six separate variations of vertical metal strips placed above and below the dowels in conventional baskets. In addition, the study investigated existing patented assemblies and a new assembly developed in Spain and used in Australia. The metal assemblies were placed in a new pavement and allowed to stay in place for 30 days before the Iowa Department of Transportation staff terminated the test by directing the contractor to saw and seal the joints. This report describes the design, construction, testing, and conclusions of the project.

Opioid antagonist detoxification under anaesthesia versus traditional clonidine detoxification combined with an additional week of psychosocial support: a randomised clinical trial.

BACKGROUND: While detoxification under anaesthesia accelerates the detoxification procedure, there is a lack of randomised clinical trials evaluating its effectiveness compared to traditional detoxification procedures, and a lack of data on long-term abstinence. METHODS: Prospective randomised clinical trial. Analysis by intention to treat and per protocol. Setting: Specialised substance abuse unit in a psychiatric teaching hospital and an intensive care unit of a general hospital. Participants: Seventy patients with opiate mono-dependence requesting detoxification: 36 randomised to RODA (treatment as allocated received by 26) and 34 randomised to classical clonidine detoxification (treatment as allocated received by 21). Main outcome measures: Successful detoxification, safety and self-reported abstinence at 3, 6 and 12 months after detoxification. RESULTS: Socio-demographics were similar in both groups at baseline. No complications were reported during or after anaesthesia. According to the intention to treat analysis, 28/36 (78%) RODA patients and 21/34 (62%) of the clonidine group successfully completed the detoxification process (p=0.14). In the intention to treat analysis, 30% of RODA patients were abstinent after 3 months compared to 14% in the clonidine group (p=0.11). No difference was found at 6 and 12 months (both groups showed less than 5% abstinence after 12 months). The per-protocol analysis showed similar results with no statistical differences either for ASI mean scores or for the SF36 questionnaire. CONCLUSION: Although the detoxification success rate and abstinence after 3 months were slightly better for the RODA procedure compared to clonidine treatment, these differences were not statistically significant and disappeared completely after 6 and 12 months.

Are There Classical Business Cycles?

The aim of this paper is to test formally the classical business cycle hypothesis, using data from industrialized countries for the time period since 1960. The hypothesis is characterized by the view that the cyclical structure in GDP is concentrated in the investment series: fixed investment has typically a long cycle, while the cycle in inventory investment is shorter. To check the robustness of our results, we subject the data for 15 OECD countries to a variety of detrending techniques. While the hypothesis is not confirmed uniformly for all countries, there is a considerably high number for which the data display the predicted pattern. None of the countries shows a pattern which can be interpreted as a clear rejection of the classical hypothesis.

Progress in cardiovascular anastomoses: will the vascular join replace Carrel's technique?

BACKGROUND: Vascular reconstructions are becoming challenging due to the comorbidity of the aging population and since the introduction of minimally invasive approaches. Many sutureless anastomosis devices have been designed to facilitate the cardiovascular surgeon's work and the vascular join (VJ) is one of these. We designed an animal study to assess its reliability and long-term efficacy. METHODS: VJ allows the construction of end-to-end and end-to-side anastomoses. It consists of two metallic crowns fixed to the extremity of the two conduits so that vessel edges are joined layer by layer. There is no foreign material exposed to blood. In adult sheep both carotid arteries were prepared and severed. End-to-end anastomoses were performed using the VJ device on one side and the classical running suture technique on the other side. Animals were followed-up with Duplex-scan every 3 months and sacrificed after 12 months. Histopathological analysis was carried out. RESULTS: In 20 animals all 22 sutureless anastomoses were successfully completed in less than 2 min versus 6 +/- 3 min for running suture. Duplex showed the occlusion of three controls and one sutureless anastomosis. Two controls and one sutureless had stenosis >50%. Histology showed very thin layer of myointimal hyperplasia (50 +/- 10 microm) in the sutureless group versus 300 +/- 27 microm in the control. No significant inflammatory reaction was detected. CONCLUSIONS: VJ provides edge-to-edge vascular repair that can be considered the most physiological way to restore vessel continuity. For the first time, in healthy sheep, an anastomotic device provided better results than suture technique.

Evaluation of U.S. and European Concrete Pavement Noise Reduction Methods, July 2006

Highway noise is one of the most pressing of the surface characteristics issues facing the concrete paving industry. This is particularly true in urban areas, where not only is there a higher population density near major thoroughfares, but also a greater volume of commuter traffic (Sandberg and Ejsmont 2002; van Keulen 2004). To help address this issue, the National Concrete Pavement Technology Center (CP Tech Center) at Iowa State University (ISU), Federal Highway Administration (FHWA), American Concrete Pavement Association (ACPA), and other organizations have partnered to conduct a multi-part, seven-year Concrete Pavement Surface Characteristics Project. This document contains the results of Part 1, Task 2, of the ISU-FHWA project, addressing the noise issue by evaluating conventional and innovative concrete pavement noise reduction methods. The first objective of this task was to determine what if any concrete surface textures currently constructed in the United States or Europe were considered quiet, had long-term friction characteristics, could be consistently built, and were cost effective. Any specifications of such concrete textures would be included in this report. The second objective was to determine whether any promising new concrete pavement surfaces to control tire-pavement noise and friction were in the development stage and, if so, what further research was necessary. The final objective was to identify measurement techniques used in the evaluation.

Integrative Review: Concepts And Methods Used In Nursing


Integrative review (IR) has an international reputation in nursing research and evidence-based practice. This IR aimed at identifying and analyzing the concepts and methods recommended to undertaking IR in nursing. Nine information resources,including electronic databases and grey literature were searched. Seventeen studies were included. The results indicate that: primary studies were mostly from USA; it is possible to have several research questions or hypotheses and include primary studies in the review from different theoretical and methodological approaches; it is a type of review that can go beyond the analysis and synthesis of findings from primary studies allowing exploiting other research dimensions, and that presents potentialities for the development of new theories and new problems for research. Conclusion: IR is understood as a very complex type of review and it is expected to be developed using standardized and systematic methods to ensure the required rigor of scientific research and therefore the legitimacy of the established evidence.


Segmental copy number variation shapes tissue transcriptomes.

Copy number variation (CNV) is a key source of genetic diversity, but a comprehensive understanding of its phenotypic effect is only beginning to emerge. We have generated a CNV map in wild mice and classical inbred strains. Genome-wide expression data from six major organs show not only that expression of genes within CNVs tend to correlate with copy number changes, but also that CNVs influence the expression of genes in their vicinity, an effect that extends up to half a megabase. Genes within CNVs show lower expression and more specific spatial expression patterns than genes mapping elsewhere. Our analyses reveal differential constraint on copy number changes of genes expressed in different tissues. Dosage alterations of brain-expressed genes are less frequent than those of other genes and are buffered by tighter transcriptional regulation. Our study provides initial evidence that CNVs shape tissue transcriptomes on a global scale.

Use of flow cytometric methods for single-cell analysis in environmental microbiology

Flow cytometry (FCM) is emerging as an important tool in environmental microbiology. Although flow cytometry applications have to date largely been restricted to certain specialized fields of microbiology, such as the bacterial cell cycle and marine phytoplankton communities, technical advances in instrumentation and methodology are leading to its increased popularity and extending its range of applications. Here we will focus on a number of recent flow cytometry developments important for addressing questions in environmental microbiology. These include (i) the study of microbial physiology under environmentally relevant conditions, (ii) new methods to identify active microbial populations and to isolate previously uncultured microorganisms, and (iii) the development of high-throughput autofluorescence bioreporter assays