Deep ConvNet: Non-Random Weight Initialization for Repeatable Determinism, Examined with FSGM

A repeatable and deterministic non-random weight initialization method in convolutional layers of neural networks examined with the Fast Gradient Sign Method (FSGM). Using the FSGM approach as a technique to measure the initialization effect with controlled distortions in transferred learning, varying the dataset numerical similarity. The focus is on convolutional layers with induced earlier learning through the use of striped forms for image classification. Which provided a higher performing accuracy in the first epoch, with improvements of between 3–5% in a well known benchmark model, and also ~10% in a color image dataset (MTARSI2), using a dissimilar model architecture. The proposed method is robust to limit optimization approaches like Glorot/Xavier and He initialization. Arguably the approach is within a new category of weight initialization methods, as a number sequence substitution of random numbers, without a tether to the dataset. When examined under the FGSM approach with transferred learning, the proposed method when used with higher distortions (numerically dissimilar datasets), is less compromised against the original cross-validation dataset, at ~31% accuracy instead of ~9%. This is an indication of higher retention of the original fitting in transferred learning.

Bio-informatic Analysis of Missense Single Nucleotide Polymorphisms (SNPs) in Human CD38 Gene Associated with B-Chronic Lymphocytic Leukemia

ABSTRACTBackgroundCLL: Chronic lymphocytic leukemia is a chronic type of haematological malignancies that evoked from lymph proliferative origin of bone marrow and secondary lymphoid tissue, resultant in proliferation and progressive accumulation of distinct monoclonal CD5 /CD19 /CD23 B lymphocytes in the bone marrow, peripheral blood, and lymphatic organs. CD38 is a multifunctional ecto-enzyme, known to be a direct contributor in pathogenesis of CLL by poorly understood mechanism. Even though, it highly expressed in CLL. At specific position of CD38 gene sequence, substitution of single nucleotide may result in change in amino acid that ends by consequent alteration of protein structure.AimTo study CD38 polymorphism and to predict its effect on structure and subsequently function of CD38 molecule.Methodology and ResultThe bioinformatic analysis of CD38 gene had been carried out by using several soft wares. Functional analysis by SIFT, Polyphen2, and PROVEAN reveled 12 deleterious SNPs. These SNPs were further analyzed by SNAP2, SNP@GO. PMut, STRING and other soft wars. Furthermore, Stability analysis was done using I-Mutant and MUpro software where seven SNPs were found to decrease the stability of the protein by I-Mutant, while two SNPs increase it. At the same time, eight SNPs were found to decrease the stability by Mupro software while only one SNP is predicted to increase it. Finally, Physiochemical analysis was done using Project Hope.ConclusionIn summary, CD38 genotype seems to have twelve SNP that possibly will result in deleterious effect on Protein Structure. This genetic variation eventually will lead to alteration in potential molecule functions. Which effect the progression of CLL By the end.

Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping

ABSTRACTHomopolymeric adenosine RNA plays numerous roles in both cells and non-cellular genetic material, and for lack of evidence to the contrary, it is generally accepted to form a random coil under physiological conditions. However, chemical mapping data generated by the Eterna Massive Open Laboratory indicates that a poly (A) sequence of length seven or more, at pH 8.0 and MgCl concentrations of 10 mM, develops unexpected protection to selective 2’-hydroxyl acylation read out by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing. This protection first appears in poly(A) sequences of length 7 and grows to its maximum strength at length ~10. In a long poly(A) sequence, substitution of a single A by any other nucleotide disrupts the protection, but only for the 6 or so nucleotides on the 5’ side of the substitution. The authors are grateful for pre-publication comments; please use https://docs.google.com/document/d/14972Q36IDTYMglwMXTOrqd4P9orQ6-P3bPbCuITdv6A.

Evolutionary assembly patterns of prokaryotic genomes

Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8,228 directional dependencies between genes, and demonstrated that many such dependencies reflect known functional relationships, including, for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.

EFFICIENT PREPROCESSING FOR WEB LOG COMPRESSION

Web log files, storing user activity on a server, may grow at the pace of hundreds of megabytes a day, or even more, on popular sites. They are usually archived, as it enables further analysis, e.g., for detecting attacks or other server abuse patterns. In this work we present a specialized lossless Apache web log preprocessor and test it with combination of several popular general-purpose compressors. Our method works on individual fields of log data (each storing such information like the client’s IP, date/time, requested file or query, download size in bytes, etc.), and utilizes such compression techniques like finding and extracting common prefixes and suffixes, dictionary-based phrase sequence substitution, move-to-front coding, and more. The test results show the proposed transform improves the average compression ratios 2.70 times in case of gzip and 1.86 times in case of bzip2.

Requirements for the Formation of Membrane Pores by the Reovirus Myristoylated μ1N Peptide

ABSTRACT The outer capsid of the nonenveloped mammalian reovirus contains 200 trimers of the μ1 protein, each complexed with three copies of the protector protein σ3. Conformational changes in μ1 following the proteolytic removal of σ3 lead to release of the myristoylated N-terminal cleavage fragment μ1N and ultimately to membrane penetration. The μ1N fragment forms pores in red blood cell (RBC) membranes. In this report, we describe the interaction of recombinant μ1 trimers and synthetic μ1N peptides with both RBCs and liposomes. The μ1 trimer mediates hemolysis and liposome disruption under conditions that promote the μ1 conformational change, and mutations that inhibit μ1 conformational change in the context of intact virus particles also prevent liposome disruption by particle-free μ1 trimer. Autolytic cleavage to form μ1N is required for hemolysis but not for liposome disruption. Pretreatment of RBCs with proteases rescues hemolysis activity, suggesting that μ1N cleavage is not required when steric barriers are removed. Synthetic myristoylated μ1N peptide forms size-selective pores in liposomes, as measured by fluorescence dequenching of labeled dextrans of different sizes. Addition of a C-terminal solubility tag to the peptide does not affect activity, but sequence substitution V13N or L36D reduces liposome disruption. These substitutions are in regions of alternating hydrophobic residues. Their locations, the presence of an N-terminal myristoyl group, and the full activity of a C-terminally extended peptide, along with circular dichroism data that indicate prevalence of β-strand secondary structure, suggest a model in which μ1N β-hairpins assemble in the membrane to form a β-barrel pore.