Staircase Codes With 6% to 33% Overhead Zhang, Lei M.; Kschischang, Frank R.
Journal of lightwave technology,
05/2014, Letnik:
32, Številka:
10
Journal Article
Recenzirano
Odprti dostop
We design staircase codes with overheads between 6.25% and 33.3% for high-speed optical transport networks. Using a reduced-complexity simulation of staircase coded transmission over the BSC, we ...select code candidates from within a limited parameter space. Software simulations of coded BSC transmission are performed with algebraic component code decoders. The net coding gain of the best code designs are competitive with the best known hard-decision decodable codes over the entire range of overheads. At 20% overhead, staircase codes are within 0.92 dB of BSC capacity at a bit error-rate of <inline-formula><tex-math>10^{-15}</tex-math></inline-formula>. Decoding complexity and latency of the new staircase codes are also significantly reduced from existing hard-decision decodable schemes.
As a saturable absorption material, the heterostructure with the van der Waals structure has been paid much attention in material science. In general, the heterogeneous combination is able to ...neutralize, or even exceed, the individual material's advantages in some aspects. In this paper, which describes the magnetron sputtering deposition method, the tapered fiber is coated by the MoS2-WS2 heterostructure, and the MoS2-WS2 heterostructure saturable absorber (SA) is fabricated. The modulation depth of the prepared MoS2-WS2 heterostructure SA is measured to be 19.12%. Besides, the theoretical calculations for the band gap and carrier mobility of the MoS2-WS2 heterostructure are provided. By employing the prepared SA, a stable and passively erbium-doped fiber laser is implemented. The generated pulse duration of 154 fs is certified to be the shortest among all fiber lasers based on transition mental dichalcogenides. Results in this paper provide the new direction for the fabrication of ultrafast photon modulation devices.
Abstract
Background
Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or ...implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable.
Results
We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform:
github.com/hippo-yf/MUREN
and on the conda platform:
anaconda.org/hippo-yf/r-muren
.
Conclusions
MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.
Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer ...representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter.
We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads.
RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser . The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.
Crucial to the correctness of a genome assembly is the accuracy of the underlying scaffolds that specify the orders and orientations of contigs together with the gap distances between contigs. The ...current methods construct scaffolds based on the alignments of 'linking' reads against contigs. We found that some 'optimal' alignments are mistaken due to factors such as the contig boundary effect, particularly in the presence of repeats. Occasionally, the incorrect alignments can even overwhelm the correct ones. The detection of the incorrect linking information is challenging in any existing methods.
In this study, we present a novel scaffolding method RegScaf. It first examines the distribution of distances between contigs from read alignment by the kernel density. When multiple modes are shown in a density, orientation-supported links are grouped into clusters, each of which defines a linking distance corresponding to a mode. The linear model parameterizes contigs by their positions on the genome; then each linking distance between a pair of contigs is taken as an observation on the difference of their positions. The parameters are estimated by minimizing a global loss function, which is a version of trimmed sum of squares. The least trimmed squares estimate has such a high breakdown value that it can automatically remove the mistaken linking distances. The results on both synthetic and real datasets demonstrate that RegScaf outperforms some popular scaffolders, especially in the accuracy of gap estimates by substantially reducing extremely abnormal errors. Its strength in resolving repeat regions is exemplified by a real case. Its adaptability to large genomes and TGS long reads is validated as well.
RegScaf is publicly available at https://github.com/lemontealala/RegScaf.git.
Supplementary data are available at Bioinformatics online.
In the phase II multicohort CheckMate 142 study, nivolumab plus low-dose (1 mg/kg) ipilimumab provided robust and durable clinical benefit with a manageable safety profile in previously treated ...patients with microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) metastatic colorectal cancer (mCRC) at 13.4- and 25.4-month median follow-up (Overman MJ, Lonardi S, Wong KYM et al. Durable clinical benefit with nivolumab plus ipilimumab in DNA mismatch repair-deficient/microsatellite instability-high metastatic colorectal cancer. J Clin Oncol. 2018;36:773-779. Overman MJ, Lonardi S, Wong KYM, et al. Nivolumab plus low-dose ipilimumab in previously treated patients with microsatellite instability-high/mismatch repair deficient metastatic colorectal cancer: long-term follow-up. J Clin Oncol. 2019;37:635). Here, we present results from the 4-year follow-up of these patients.
Patients received nivolumab (3 mg/kg) plus low-dose (1 mg/kg) ipilimumab every 3 weeks (four doses) followed by nivolumab (3 mg/kg) every 2 weeks until disease progression. Primary endpoint was investigator-assessed objective response rate (ORR; as per RECIST version 1.1).
A total of 119 patients were treated; 76% had ≥2 prior lines of therapy. Median follow-up was 50.9 months (range 46.9-62.7 months). Median duration of therapy was 24.9 months 95% confidence interval (CI) 15.8-33.2 months. Investigator-assessed ORR increased from 55% (95% CI 45% to 64%) at 13.4 months to 65% (95% CI 55% to 73%) at 50.9 months with a disease control rate of 81% (95% CI 72% to 87%). The complete response rate increased from 3% at 13.4 months to 13% at 50.9 months. Partial responses were observed in 52% of patients; 21% had stable disease, and 12% had progressive disease. Median time to response was 2.8 months (range 1.1-37.1 months), and median duration of response was not reached (range 1.4+ to 58.0+ months). At data cut-off, 37 (48%) patients had ongoing responses. Median progression-free survival was not reached 95% CI 38.4 months-not estimable (NE), and median overall survival was not reached (95% CI NE). Grade 3-4 treatment-related adverse events (TRAEs) were observed in 32% of patients; 13% of patients had any-grade TRAEs leading to discontinuation.
The results confirm long-term benefit of nivolumab plus low-dose ipilimumab for previously treated patients with MSI-H/dMMR mCRC. The safety profile was manageable with no new safety signals.
•In previously treated MSI-H/dMMR mCRC, nivolumab plus ipilimumab showed durable benefit with 4 years of follow-up.•ORR was 65%. The 48-month rates of progression-free survival and overall survival were 53% and 71%, respectively.•Significant and clinically meaningful improvements in quality of life were largely maintained with continuous treatment.•No new safety signals were identified, with a low rate (13% of patients) of any-grade TRAEs leading to discontinuation.•These results show the long-term benefit of nivolumab plus low-dose ipilimumab in previously treated MSI-H/dMMR mCRC.
Pancreatic islet failure is a key characteristic of type 2 diabetes besides insulin resistance. To get molecular insights into the pathology of islets in type 2 diabetes, we developed a computational ...approach to integrating expression profiles of Goto-Kakizaki and Wistar rat islets from a designed experiment with those of the human islets from an observational study. A principal gene-eigenvector in the expression profiles characterized by up-regulated angiogenesis and down-regulated oxidative phosphorylation was identified conserved across the two species. In the case of Goto-Kakizaki versus Wistar islets, such alteration in gene expression can be verified directly by the treatment-control tests over time, and corresponds to the alteration of alpha/beta-cell distribution obtained by quantifying the islet micrographs. Furthermore, the correspondence between the dual sample- and gene-eigenvectors unveils more delicate structures. In the case of rats, the up- and down-trend of insulin mRNA levels before and after week 8 correspond respectively to the top two principal eigenvectors. In the case of human, the top two principal eigenvectors correspond respectively to the late and early stages of diabetes. According to the aggregated expression signature, a large portion of genes involved in the hypoxia-inducible factor signaling pathway, which activates transcription of angiogenesis, were significantly up-regulated. Furthermore, top-ranked anti-angiogenic genes THBS1 and PEDF indicate the existence of a counteractive mechanism that is in line with thickened and fragmented capillaries found in the deteriorated islets. Overall, the integrative analysis unravels the principal transcriptional alterations underlying the islet deterioration of morphology and insulin secretion along type 2 diabetes progression.
Abstract Introduction Transport of glucose from maternal blood across the placental trophoblastic tissue barrier is critical to sustain fetal growth. The mechanism by which GLUTs are regulated in ...trophoblasts in response to ischemic hypoxia encountered with intrauterine growth restriction (IUGR) has not been suitably investigated. Objective To investigate placental expression of GLUT1, GLUT3 and GLUT4 and possible mechanisms of GLUT regulation in idiopathic IUGR. Methods We analyzed clinical, biochemical and histological data from placentas collected from women affected by idiopathic full-term IUGR ( n = 10) and gestational age-matched healthy controls ( n = 10). Results We found increased GLUT3 protein expression in the trophoblast (cytotrophoblast greater than syncytiotrophoblast) on the maternal aspect of the placenta in IUGR compared to normal placenta, but no differences in GLUT1 or GLUT4 were found. No differential methylation of the GLUT3 promoter between normal and IUGR placentas was observed. Increased GLUT3 expression was associated with an increased nuclear concentration of HIF-1α, suggesting hypoxia may play a role in the up-regulation of GLUT3. Discussion Further studies are needed to elucidate whether increased GLUT3 expression in IUGR is a marker for defective villous maturation or an adaptive response of the trophoblast in response to chronic hypoxia. Conclusions Patients with IUGR have increased trophoblast expression of GLUT3, as found under the low-oxygen conditions of the first trimester.
The effect of calorie restriction (CR) on life span extension, demonstrated in organisms ranging from yeast to mice, may involve the down-regulation of pathways, including Tor, Akt, and Ras. Here, we ...present data suggesting that yeast Tor1 and Sch9 (a homolog of the mammalian kinases Akt and S6K) is a central component of a network that controls a common set of genes implicated in a metabolic switch from the TCA cycle and respiration to glycolysis and glycerol biosynthesis. During chronological survival, mutants lacking SCH9 depleted extracellular ethanol and reduced stored lipids, but synthesized and released glycerol. Deletion of the glycerol biosynthesis genes GPD1, GPD2, or RHR2, among the most up-regulated in long-lived sch9Delta, tor1Delta, and ras2Delta mutants, was sufficient to reverse chronological life span extension in sch9Delta mutants, suggesting that glycerol production, in addition to the regulation of stress resistance systems, optimizes life span extension. Glycerol, unlike glucose or ethanol, did not adversely affect the life span extension induced by calorie restriction or starvation, suggesting that carbon source substitution may represent an alternative to calorie restriction as a strategy to delay aging.
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