Decomposition Methods for Large Scale LP Decoding

When binary linear error-correcting codes are used over symmetric channels, a relaxed version of the maximum likelihood decoding problem can be stated as a linear program (LP). This LP decoder can be used to decode error-correcting codes at bit-error-rates comparable to state-of-the-art belief propagation (BP) decoders, but with significantly stronger theoretical guarantees. However, LP decoding when implemented with standard LP solvers does not easily scale to the block lengths of modern error correcting codes. In this paper we draw on decomposition methods from optimization theory, specifically the Alternating Directions Method of Multipliers (ADMM), to develop efficient distributed algorithms for LP decoding. The key enabling technical result is a "two-slice" characterization of the geometry of the parity polytope, which is the convex hull of all codewords of a single parity check code. This new characterization simplifies the representation of points in the polytope. Using this simplification, we develop an efficient algorithm for Euclidean norm projection onto the parity polytope. This projection is required by ADMM and allows us to use LP decoding, with all its theoretical guarantees, to decode large-scale error correcting codes efficiently. We present numerical results for LDPC codes of lengths more than 1000. The waterfall region of LP decoding is seen to initiate at a slightly higher signal-to-noise ratio than for sum-product BP, however an error floor is not observed for LP decoding, which is not the case for BP. Our implementation of LP decoding using ADMM executes as fast as our baseline sum-product BP decoder, is fully parallelizable, and can be seen to implement a type of message-passing with a particularly simple schedule.Comment: 35 pages, 11 figures. An early version of this work appeared at the 49th Annual Allerton Conference, September 2011. This version to appear in IEEE Transactions on Information Theor

Latent regulatory potential of human-specific repetitive elements

At least half of the human genome is derived from repetitive elements, which are often lineage specific and silenced by a variety of genetic and epigenetic mechanisms. Using a transchromosomic mouse strain that transmits an almost complete single copy of human chromosome 21 via the female germline, we show that a heterologous regulatory environment can transcriptionally activate transposon-derived human regulatory regions. In the mouse nucleus, hundreds of locations on human chromosome 21 newly associate with activating histone modifications in both somatic and germline tissues, and influence the gene expression of nearby transcripts. These regions are enriched with primate and human lineage-specific transposable elements, and their activation corresponds to changes in DNA methylation at CpG dinucleotides. This study reveals the latent regulatory potential of the repetitive human genome and illustrates the species specificity of mechanisms that control it

Comparison of ecosystem processes in a woodland and prairie pond with different hydroperiods

Shallow lakes and ponds constitute a significant number of water bodies worldwide. Many are heterotrophic, indicating that they are likely net contributors to global carbon cycling. Climate change is likely to have important impacts on these waterbodies. In this study, we examined two small Minnesota ponds; a permanent woodland pond and a temporary prairie pond. The woodland pond had lower levels of phosphorus and phytoplankton than the prairie pond. Using the open water oxygen method, we found the prairie pond typically had a higher level of gross primary production (GPP) and respiration (R) than the woodland pond, although the differences between the ponds varied with season. Despite the differences in GPP and R between the ponds the net ecosystem production was similar with both being heterotrophic. Since abundant small ponds may play an important role in carbon cycling and are likely to undergo changes in temperature and hydroperiod associated with climate change, understanding pond metabolism is critical in predicting impacts and designing management schemes to mitigate changes

Probing the centre of the large circumstellar disc in M17

We investigated the nature of the hitherto unresolved elliptical infrared emission in the centre of the ~20000 AU disc silhouette in M 17. We combined high-resolution JHKsL'M' band imaging carried out with NAOS/CONICA at the VLT with [Fe II] narrow band imaging using SOFI at the NTT. The analysis is supported by Spitzer/GLIMPSE archival data and by already published SINFONI/VLT Integral Field Spectroscopy data. For the first time, we resolve the elongated central infrared emission into a point-source and a jet-like feature that extends to the northeast in the opposite direction of the recently discovered collimated H2 jet. They are both orientated almost perpendicular to the disc plane. In addition, our images reveal a curved southwestern emission nebula whose morphology resembles that of the previously detected northeastern one. Both nebulae are located at a distance of 1500 AU from the disc centre. We describe the infrared point-source in terms of a protostar that is embedded in circumstellar material producing a visual extinction of 60 <= Av <= 82. The observed Ks band magnitude is equivalent to a stellar mass range of 2.8 Msun <= Mstar <= 8 Msun adopting conversions for a main-sequence star. Altogether, we suggest that the large M 17 accretion disc is forming an intermediate to high-mass protostar. Part of the accreted material is expelled through a symmetric bipolar jet/outflow.Comment: 6 pages, 3 figures, accepted by MNRAS (16 May 2008

The RMS Survey: Resolving kinematic distance ambiguities towards a sample of compact HII regions using HI absorption

We present high-resolution HI data obtained using the Australia Telescope Compact Array to resolve the near/far distance ambiguities towards a sample of compact HII regions from the Red MSX Source (RMS) survey. The high resolution data are complemented with lower resolution archival HI data extracted from the Southern and VLA Galactic Plane surveys. We resolve the distance ambiguity for nearly all of the 105 sources where the continuum was strong enough to allow analysis of the HI absorption line structure. This represents another step in the determination of distances to the total RMS sample, which with over 1,000 massive young stellar objects and compact HII regions, is the largest and most complete sample of its kind. The full sample will allow the distribution of massive star formation in the Galaxy to be examined.Comment: Accepted by MNRAS. This paper consists of 15 pages and contains 10 figures and 5 table

The Prognostic and Predictive Value of Melanoma-related MicroRNAs Using Tissue and Serum: A MicroRNA Expression Analysis

The overall 5-year survival for melanoma is 91%. However, if distant metastasis occurs (stage IV), cure rates are = 82%) when = 4 miRNAs were expressed. Moreover, the 'MELmiR-7' panel characterised overall survival of melanoma patients better than both serum LDH and S100B (delta log likelihood=11, p < 0.001). This panel was found to be superior to currently used serological markers for melanoma progression, recurrence, and survival; and would be ideally suited to monitor tumour progression in patients diagnosed with early metastatic disease (stages IIIa-c/IV M1a-b) to detect relapse following surgical or adjuvant treatment. (C) 2015 The Authors. Published by Elsevier B. V

Selection effects may account for better outcomes of the German Disease Management Program for type 2 diabetes

<p>Abstract</p> <p>Background</p> <p>The nationwide German disease management program (DMP) for type 2 diabetes was introduced in 2003. Meanwhile, results from evaluation studies were published, but possible baseline differences between DMP and usual-care patients have not been examined. The objective of our study was therefore to find out if patient characteristics as socio-demographic variables, cardiovascular risk profile or motivation for life style changes influence the chance of being enrolled in the German DMP for type 2 diabetes and may therefore account for outcome differences between DMP and usual-care patients.</p> <p>Methods</p> <p>Case control study comparing DMP patients with usual-care patients at baseline and follow up; mean follow-up period of 36 ± 14 months. We used chart review data from 51 GP surgeries. Participants were 586 DMP and 250 usual-care patients with type 2 diabetes randomly selected by chart registry. Data were analysed by multivariate logistic and linear regression analyses. Significance levels were p ≤ 0.05.</p> <p>Results</p> <p>There was a better chance for enrolment if patients a) had a lower risk status for diabetes complications, i.e. non-smoking (odds ratio of 1.97, 95% confidence interval of 1.11 to 3.48) and lower systolic blood pressure (1.79 for 120 mmHg vs. 160 mmHg, 1.15 to 2.81); b) had higher activity rates, i.e. were practicing blood glucose self-monitoring (1.67, 1.03 to 2.76) and had been prescribed a diabetes patient education before enrolment (2.32, 1.29 to 4.19) c) were treated with oral medication (2.17, 1.35 to 3.49) and d) had a higher GP-rated motivation for diabetes education (4.55 for high motivation vs. low motivation, 2.21 to 9.36).</p> <p>Conclusions</p> <p>At baseline, future DMP patients had a lower risk for diabetes complications, were treated more intensively and were more active and motivated in managing their disease than usual-care patients. This finding a) points to the problem that the German DMP may not reach the higher risk patients and b) selection bias may impair the assessment of differences in outcome quality between enrolled and usual-care patients. Suggestions for dealing with this bias in evaluation studies are being made.</p

Cytochrome P450 20A1 in zebrafish: Cloning, regulation and potential involvement in hyperactivity disorders

Cytochrome P450 (CYP) enzymes for which there is no functional information are considered "orphan" CYPs. Previous studies showed that CYP20A1, an orphan, is expressed in human hippocampus and substantia nigra, and in zebrafish (Danio rerio) CYP20A1 maternal transcript occurs in eggs, suggesting involvement in brain and in early development. Moreover, hyperactivity is reported in humans with chromosome 2 microdeletions including CYP20A1. We examined CYP20A1 in zebrafish, including impacts of chemical exposure on expression. Zebrafish CYP20A1 cDNA was cloned, sequenced, and aligned with cloned human CYP20A1 and predicted vertebrate orthologs. CYP20A1s share a highly conserved N-terminal region and unusual sequences in the I-helix and the heme-binding CYP signature motifs. CYP20A1 mRNA expression was observed in adult zebrafish organs including the liver, heart, gonads, spleen and brain, as well as the eye and optic nerve. Putative binding sites in proximal promoter regions of CYP20A1s, and response of zebrafish CYP20A1 to selected nuclear and xenobiotic receptor agonists, point to up-regulation by agents involved in steroid hormone response, cholesterol and lipid metabolism. There also was a dose-dependent reduction of CYP20A1 expression in embryos exposed to environmentally relevant levels of methylmercury. Morpholino knockdown of CYP20A1 in developing zebrafish resulted in behavioral effects, including hyperactivity and a slowing of the optomotor response in larvae. The results suggest that altered expression of CYP20A1 might be part of a mechanism linking methylmercury exposure to neurobehavioral deficits. The expanded information on CYP20A1 brings us closer to "deorphanization" CYP20A1 functions and its roles in health and disease