SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: File system

395

The timely detection of viremia in HIV-infected patients receiving antiviral treatment is key to ensuring effective therapy and preventing the emergence of drug resistance. In high HIV burden settings, the cost and complexity of diagnostics limit their availability. We have developed a novel complementary metal-oxide semiconductor (CMOS) chip based, pH-mediated, point-of-care HIV-1 viral load monitoring assay that simultaneously amplifies and detects HIV-1 RNA. A novel low-buffer HIV-1 pH-LAMP (loop-mediated isothermal amplification) assay was optimised and incorporated into a pH sensitive CMOS chip. Screening of 991 clinical samples (164 on the chip) yielded a sensitivity of 95% (in vitro) and 88.8% (on-chip) at >1000 RNA copies/reaction across a broad spectrum of HIV-1 viral clades. Median time to detection was 20.8 minutes in samples with >1000 copies RNA. The sensitivity, specificity and reproducibility are close to that required to produce a point-of-care device which would be of benefit in resource poor regions, and could be performed on an USB stick or similar low power device.

Concepts: Antiretroviral drug, HIV, Viral load, Type I and type II errors, Integrated circuit, Transistor, CMOS, File system

28

Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics.

Concepts: Future, Hadoop, Cloud computing, Grid computing, Linux, Google, File system, MapReduce

28

The purpose of this study was to determine the shaping ability of 3 nickel-titanium (NiTi) endodontic file systems by measuring canal transportation.

Concepts: River, Transport, Canal, File system, Canal+

26

The aim of this study was to evaluate the effect of glide path preparation on the surface topography changes of WaveOne and OneShape single files using atomic force microscopy analysis. Two commercially available brands of single file systems were analyzed, including 15 specimens/brand as following: Group I; WaveOne 0.08/25 (Dentsply Maillefer, Ballaigues, Switzerland) and Group II; OneShape 0.06/25 (Micro Mega, Besançon, France). In each group, 3 new files were subjected to AFM analysis as received from manufacturer, and 12 files were analyzed after preparation of root canals. A total of 20 human maxillary molar teeth were selected. In each group, 12 files were divided into 4 subgroups according to instruments that were used in one or three root canals with or without a previous glide path (n = 3). After preparation the surface analysis of single files was performed on 11 different points located along a 3-mm section starting at the tip of each file using AFM. Root mean square (RMS) values were recorded to investigate the surface features of endodontic files. The differences between RMS values were tested by one-way ANOVA. There was no statistically significant difference between the groups (p > 0.05). Creation of a glide path did not affect the surface topography of single file systems. SCANNING 9999:XX-XX, 2014. © 2014 Wiley Periodicals, Inc.

Concepts: Statistics, Statistical significance, Analysis of variance, Posterior superior alveolar artery, Molar, Root mean square, File system, Filename

26

Forensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP.

Concepts: Computer program, E-mail, File format, File system, Filename extension, Computer file, Trace evidence, Digital traces

25

To compare the effect of the TF Adaptive, ProTaper Next, OneShape, WaveOne, Reciproc, (SAF) on the reduction of E. faecalis in experimentally infected root canals.

Concepts: Iron, Redox, File system, Computer file

17

Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability.

Concepts: Sequence, Star Trek: The Next Generation, Star Trek: First Contact, Brent Spiner, File format, File system, Filename extension, Computer file

14

Efficient storage and retrieval of digital data is the focus of much commercial and academic attention. With personal computers, there are two main ways to retrieve files: hierarchical navigation and query-based search. In navigation, users move down their virtual folder hierarchy until they reach the folder in which the target item is stored. When searching, users first generate a query specifying some property of the target file (e.g., a word it contains), and then select the relevant file when the search engine returns a set of results. Despite advances in search technology, users prefer retrieving files using virtual folder navigation, rather than the more flexible query-based search. Using fMRI we provide an explanation for this phenomenon by demonstrating that folder navigation results in activation of the posterior limbic (including the retrosplenial cortex) and parahippocampal regions similar to that previously observed during real-world navigation in both animals and humans. In contrast, search activates the left inferior frontal gyrus, commonly observed in linguistic processing. We suggest that the preference for navigation may be due to the triggering of automatic object finding routines and lower dependence on linguistic processing. We conclude with suggestions for future computer systems design.

Concepts: Hierarchy, Cerebrum, Computer, Search engine optimization, Inferior frontal gyrus, Personal computer, Information retrieval, File system

12

The authors have developed a simple device for computer-aided design/computer-aided manufacturing (CAD-CAM) that uses an image-guided system to define a cutting tool path that is shared with a surgical machining system for drilling bone. Information from 2D images (obtained via CT and MRI) is transmitted to a processor that produces a 3D image. The processor generates code defining an optimized cutting tool path, which is sent to a surgical machining system that can drill the desired portion of bone. This tool has applications for bone removal in both cranial and spine neurosurgical approaches. Such applications have the potential to reduce surgical time and associated complications such as infection or blood loss. The device enables rapid removal of bone within 1 mm of vital structures. The validity of such a machining tool is exemplified in the rapid (< 3 minutes machining time) and accurate removal of bone for transtemporal (for example, translabyrinthine) approaches.

Concepts: Definition, Skull, Computer graphics, 2D computer graphics, Cutting, File system, Drilling, New York City Subway

6

On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several widely used genome browsers, can already be used to manipulate and visualize these formats “out-of-the-box.” We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation, including the detailed file format specifications and example files, are accessible at http://www.psidev.info/probam and at http://www.psidev.info/probed .

Concepts: Genomics, Proteome, Computer program, File format, File system, Computer file formats, Computer file, Human Proteome Organization