Source File Set Search for Clone-and-Own Reuse Analysis

Clone-and-own approach is a natural way of source code reuse for software developers. To assess how known bugs and security vulnerabilities of a cloned component affect an application, developers and security analysts need to identify an original version of the component and understand how the cloned component is different from the original one. Although developers may record the original version information in a version control system and/or directory names, such information is often either unavailable or incomplete. In this research, we propose a code search method that takes as input a set of source files and extracts all the components including similar files from a software ecosystem (i.e., a collection of existing versions of software packages). Our method employs an efficient file similarity computation using b-bit minwise hashing technique. We use an aggregated file similarity for ranking components. To evaluate the effectiveness of this tool, we analyzed 75 cloned components in Firefox and Android source code. The tool took about two hours to report the original components from 10 million files in Debian GNU/Linux packages. Recall of the top-five components in the extracted lists is 0.907, while recall of a baseline using SHA-1 file hash is 0.773, according to the ground truth recorded in the source code repositories.Comment: 14th International Conference on Mining Software Repositorie

Scanning Probe Microscopy of Poly(p-phenylene benzobisthiazole) Lamellar Crystal

Rigid polymer, poly(p-phenylene benzobisthiazole), formed lamellar crystals where the molecular chains were oriented perpendicular to the lamellae. It was supposed that, because of wide distribution in the chain length, the lamellar surface bristled with the chain cilia among which many voids were included. Crystallographically, this region afforded us a transitional structure from full to deficient packings of chains. The structure was analyzed using the scanning probe microscope. In the course the method for imaging one molecular chain end was developed. From the images it was concluded that an isolated long cilius did not move so violently at room temperature

Differential Scanning Calorimetric Studies on the Melting Behavior of Water in Stratum Corneum

The melting behavior of water in human stratum corneum (s. corneum) has been studied by sing differential scanning calorimetry (DSC) in the temperature range from -40° to 20°C. The DSC thermogram was analyzed in terms of the amount of about water and the melting temperature of water in s. corneum. Extraction of the s. corneum with the mixed solvent of chloroform: methanol (2:1, v/v) or 0.5% sodium dodecyl sulfate aqueous solution decreased the bound water content, whereas extraction with water did not change the bound water content. The melting temperature of water in the s. corneum was lowered as the water contents decreased. Extraction of the water-soluble components from the s. corneum increased the melting temperature of water when the water contents were constant. The results suggest that 20–30% of water in the s. corneum is bound water interacting strongly with the protein or lipids in the s. corneum, and the excess of water over the bound water content is unbound water solubilizing the water-soluble components such as amino acids and urea in the s. corneum. The thermodynamic theory for freezing-point depression is favourably applied to the melting temperature change of the unbound water, which implies that the water-soluble components are present as an aqueous solution in the s. corneum. Measurements of the melting-point depression of water in s. corneum provides us the quantitative information on the amount of water-soluble components in the s. corneum. This technique is a sensitive and useful tool to evaluate the hydration behavior of s. corneum

Role of piRNA biogenesis and its neuronal function in the development of neurodegenerative diseases

Neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), are caused by neuronal loss and dysfunction. Despite remarkable improvements in our understanding of these pathogeneses, serious worldwide problems with significant public health burdens are remained. Therefore, new efficient diagnostic and therapeutic strategies are urgently required. PIWI-interacting RNAs (piRNAs) are a major class of small non-coding RNAs that silence gene expression through transcriptional and post-transcriptional processes. Recent studies have demonstrated that piRNAs, originally found in the germ line, are also produced in non-gonadal somatic cells, including neurons, and further revealed the emerging roles of piRNAs, including their roles in neurodevelopment, aging, and neurodegenerative diseases. In this review, we aimed to summarize the current knowledge regarding the piRNA roles in the pathophysiology of neurodegenerative diseases. In this context, we first reviewed on recent updates on neuronal piRNA functions, including biogenesis, axon regeneration, behavior, and memory formation, in humans and mice. We also discuss the aberrant expression and dysregulation of neuronal piRNAs in neurodegenerative diseases, such as AD, PD, and ALS. Moreover, we review pioneering preclinical studies on piRNAs as biomarkers and therapeutic targets. Elucidation of the mechanisms underlying piRNA biogenesis and their functions in the brain would provide new perspectives for the clinical diagnosis and treatment of AD and various neurodegenerative diseases

Single-photon generation from a neodymium ion in optical fiber at room temperature

The realization of single-photon generation is important for implementing various quantum information technologies. The use of rare-earth ions in an optical fiber is a promising single photon generation method due to its ability to operate at room temperature as well as the low cost involved. Neodymium ions are especially interesting because the ions are one of the most commercially affordable rare-earth materials in the current industry. The neodymium ion also has the advantage of having a rich energy level structure, which offers several possible wavelengths for emitted single photons from visible to near-telecommunication wavelengths. In this paper, we experimentally demonstrated single-photon generation using an isolated single neodymium ion in tapered silica fiber at room temperature. Our results have significant implications as a platform for low-cost wavelength-selectable single-photon sources and photonic quantum applications.Comment: 7 pages, 5figure

The structure of sperm Izumo1 reveals unexpected similarities with Plasmodium invasion proteins.

Fertilization, the culminating event in sexual reproduction, occurs when haploid sperm and egg recognize each other and fuse to form a diploid zygote. In mammals this process critically depends on the interaction between Izumo1, a protein exposed on the equatorial segment of acrosome-reacted sperm, and the egg plasma-membrane-anchored receptor Juno [1,2]. The molecular mechanism triggering gamete fusion is unresolved because both Izumo1 and Juno lack sequence similarity to known membrane fusogens. Here we report the crystal structure of Izumo1, which reveals a membrane distal region composed of a four-helix bundle connected to a carboxy-terminal immunoglobulin (Ig)-like domain through a β-hairpin stabilized by disulfide bonds. Remarkably, different regions of Izumo1 display significant structural similarities to two proteins expressed by the invasive sporozoite stage of Plasmodium parasites: SPECT1, which is essential for host cell traversal and hepatocyte invasion [3]; and TRAP, which is necessary for gliding motility and invasion [4]. These observations suggest a link between the molecular mechanisms underlying host cell invasion by the malaria parasite and gamete membrane fusion at fertilization. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved