Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

BACKGROUND: Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear. RESULTS: We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation. CONCLUSION: The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation

Potential for Liquefaction Due to Construction Blasting

A method based on laboratory cyclic triaxial and torsional tests of undisturbed soil samples has been developed to predict the potential for liquefaction due to buried charges, such as those used in construction blasting. The results of a test blasting program conducted at a construction site are presented. The case history yielded data on particle velocities and blast induced porewater pressure changes

The Minimum Effective Training Dose Required for 1RM Strength in Powerlifters

The aim of this multi-experiment paper was to explore the concept of the minimum effective training dose (METD) required to increase 1-repetition-maximum (1RM) strength in powerlifting (PL) athletes. The METD refers to the least amount of training required to elicit meaningful increases in 1RM strength. A series of five studies utilising mixed methods, were conducted using PL athletes & coaches of all levels in an attempt to better understand the METD for 1RM strength. The studies of this multi-experiment paper are: an interview study with elite PL athletes and highly experienced PL coaches (n = 28), an interview and survey study with PL coaches and PL athletes of all levels (n = 137), two training intervention studies with intermediate-advanced PL athletes (n = 25) and a survey study with competitive PL athletes of different levels (n = 57). PL athletes looking to train with a METD approach can do so by performing ~3–6 working sets of 1–5 repetitions each week, with these sets spread across 1–3 sessions per week per powerlift, using loads above 80% 1RM at a Rate of Perceived Exertion (RPE) of 7.5–9.5 for 6–12 weeks and expect to gain strength. PL athletes who wish to further minimize their time spent training can perform autoregulated single repetition sets at an RPE of 9–9.5 though they should expect that strength gains will be less likely to be meaningful. However, the addition of 2–3 back-off sets at ~80% of the single repetitions load, may produce greater gains over 6 weeks while following a 2-3-1 squat-bench press-deadlift weekly training frequency. When utilizing accessory exercises in the context of METD, PL athletes typically utilize 1–3 accessory exercises per powerlift, at an RPE in the range of 7–9 and utilize a repetition range of ~6–10 repetitions

Genome Abnormalities Precede Prostate Cancer and Predict Clinical Relapse

The prediction of prostate cancer clinical outcome remains a major challenge after the diagnosis, even with improved early detection by prostate-specific antigen (PSA) monitoring. To evaluate whether copy number variation (CNV) of the genomes in prostate cancer tumor, in benign prostate tissues adjacent to the tumor (AT), and in the blood of patients with prostate cancer predicts biochemical (PSA) relapse and the kinetics of relapse, 241 samples (104 tumor, 49 matched AT, 85 matched blood, and 3 cell lines) were analyzed using Affymetrix SNP 6.0 chips. By using gene-specific CNV from tumor, the genome model correctly predicted 73% (receiver operating characteristic P = 0.003) cases for relapse and 75% (P < 0.001) cases for short PSA doubling time (PSADT, <4 months). The gene-specific CNV model from AT correctly predicted 67% (P = 0.041) cases for relapse and 77% (P = 0.015) cases for short PSADT. By using median-sized CNV from blood, the genome model correctly predicted 81% (P < 0.001) cases for relapse and 69% (P = 0.001) cases for short PSADT. By using median-sized CNV from tumor, the genome model correctly predicted 75% (P < 0.001) cases for relapse and 80% (P < 0.001) cases for short PSADT. For the first time, our analysis indicates that genomic abnormalities in either benign or malignant tissues are predictive of the clinical outcome of a malignancy

A decision support framework for the discrimination of children with controlled epilepsy based on EEG analysis

This work was supported in part by the EC-IST project Biopattern, contract no: 508803, by the EC ICT project TUMOR, contract no: 247754, by the University of Malta grant LBA-73-695, by an internal grant from the Technical University of Crete, ELKE# 80037 and by the Academy of Finland, project nos: 113572, 118355, 134767 and 213462.Background: In this work we consider hidden signs (biomarkers) in ongoing EEG activity expressing epileptic tendency, for otherwise normal brain operation. More specifically, this study considers children with controlled epilepsy where only a few seizures without complications were noted before starting medication and who showed no clinical or electrophysiological signs of brain dysfunction. We compare EEG recordings from controlled epileptic children with age-matched control children under two different operations, an eyes closed rest condition and a mathematical task. The aim of this study is to develop reliable techniques for the extraction of biomarkers from EEG that indicate the presence of minor neurophysiological signs in cases where no clinical or significant EEG abnormalities are observed. Methods: We compare two different approaches for localizing activity differences and retrieving relevant information for classifying the two groups. The first approach focuses on power spectrum analysis whereas the second approach analyzes the functional coupling of cortical assemblies using linear synchronization techniques. Results: Differences could be detected during the control (rest) task, but not on the more demanding mathematical task. The spectral markers provide better diagnostic ability than their synchronization counterparts, even though a combination (or fusion) of both is needed for efficient classification of subjects. Conclusions: Based on these differences, the study proposes concrete biomarkers that can be used in a decision support system for clinical validation. Fusion of selected biomarkers in the Theta and Alpha bands resulted in an increase of the classification score up to 80% during the rest condition. No significant discrimination was achieved during the performance of a mathematical subtraction task.peer-reviewe

Spectroscopic parameters for silacyclopropynylidene, SiC2_2, from extensive astronomical observations toward CW Leo (IRC +10216) with the Herschel satellite

A molecular line survey has been carried out toward the carbon-rich asymptotic giant branch star CW Leo employing the HIFI instrument on board of the Herschel satellite. Numerous features from 480 GHz to beyond 1100 GHz could be assigned unambiguously to the fairly floppy SiC$_2$ molecule. However, predictions from laboratory data exhibited large deviations from the observed frequencies even after some lower frequency data from this survey were incorporated into a fit. Therefore, we present a combined fit of all available laboratory data together with data from radio-astronomical observations.Comment: 7 pages, 1 figure, J. Mol. Spectrosc., appeared; CDMS links corrected (version 2; current version: 3; may be updated later this year

Development of Advanced Traffic Flow Models and Implementation in Parallel Processing, Phase II (9/15/92-9/15/93)

In this report, five high-order continuum traffic flow models are compared: Payne's model; Papageorgiou's model; the semi-viscous model and the viscous model as well as a proposed high-order model, and the simple continuum model. The stability of the high-order models is analyzed and the shock structure investigated in all models. In addition, the importance of the proper choice of finite-difference method is addressed. For this reason, three explicit finite-difference methods for numerical implementation, namely, the Lax method, the explicit Euler method and the upwind scheme with flux vector splitting, are discussed. The test with hypothetical data and the comparison of numerical results with field data suggest that high-order models implemented through the upwind method are better than the simple continuum model. The proposed high-order model appears to be more accurate than the other high-order models

Conditional Genetic Elimination of Hepatocyte Growth Factor in Mice Compromises Liver Regeneration after Partial Hepatectomy

Hepatocyte growth factor (HGF) has been shown to be indispensable for liver regeneration because it serves as a main mitogenic stimulus driving hepatocytes toward proliferation. We hypothesized that ablating HGF in adult mice would have a negative effect on the ability of hepatocytes to regenerate. Deletion of the HGF gene was achieved by inducing systemic recombination in mice lacking exon 5 of HGF and carrying the Mx1-cre or Cre-ERT transgene. Analysis of liver genomic DNA from animals 10 days after treatment showed that a majority (70-80%) of alleles underwent cre-induced genetic recombination. Intriguingly, however, analysis by RT-PCR showed the continued presence of both unrecombined and recombined forms of HGF mRNA after treatment. Separation of liver cell populations into hepatocytes and non-parenchymal cells showed equal recombination of genomic HGF in both cell types. The presence of the unrecombined form of HGF mRNA persisted in the liver in significant amounts even after partial hepatectomy (PH), which correlated with insignificant changes in HGF protein and hepatocyte proliferation. The amount of HGF produced by stellate cells in culture was indirectly proportional to the concentration of HGF, suggesting that a decrease in HGF may induce de novo synthesis of HGF from cells with residual unrecombined alleles. Carbon tetrachloride (CCl4)-induced regeneration resulted in a substantial decrease in preexisting HGF mRNA and protein, and subsequent PH led to a delayed regenerative response. Thus, HGF mRNA persists in the liver even after genetic recombination affecting most cells; however, PH subsequent to CCl4 treatment is associated with a decrease in both HGF mRNA and protein and results in compromised liver regeneration, validating an important role of this mitogen in hepatic growth. © 2013 Nejak-Bowen et al

Macroscopic Dynamics of Multi-Lane Traffic

We present a macroscopic model of mixed multi-lane freeway traffic that can be easily calibrated to empirical traffic data, as is shown for Dutch highway data. The model is derived from a gas-kinetic level of description, including effects of vehicular space requirements and velocity correlations between successive vehicles. We also give a derivation of the lane-changing rates. The resulting dynamic velocity equations contain non-local and anisotropic interaction terms which allow a robust and efficient numerical simulation of multi-lane traffic. As demonstrated by various examples, this facilitates the investigation of synchronization patterns among lanes and effects of on-ramps, off-ramps, lane closures, or accidents.Comment: For related work see http://www.theo2.physik.uni-stuttgart.de/helbing.htm