SciCombinator

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

Concept: Computing platform

32

Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.

Concepts: Computer, Computational genomics, Impact factor, Capital punishment, Computing, Computing platform, Computing platforms

24

Theranostic nanoplatforms with integrated diagnostic and therapeutic functions, aiming at imaging-guided therapy to improve treatment planning, as well as combination therapy to enhance treatment efficacy, have received tremendous attention in recent years. Among numerous types of functional nanomaterials explored in this field, protein-based nanocarriers with inherent biocompatibility have also been selected as building blocks to construct multifunctional theranostic platforms. In particular, albumin, which has been extensively used as drug-delivery carriers for decades, has shown great new promise in the construction of novel imaging and therapeutic nanoagents, as demonstrated by a number of recent studies. IHere, the motivations of using albumins to build up nanoscale theranostics are discussed, and the latest progress/future perspectives in this direction are summarized.

Concepts: Therapy, Albumin, Efficacy, Construction, Building, Fire protection, Theranostics, Computing platform

19

From the desktop to the laptop to the mobile device, personal computing platforms evolve over time. Moving forward, wearable computing is widely expected to be integral to consumer electronics and beyond. The primary interface between a wearable computer and a user is often a near-eye display. However, current generation near-eye displays suffer from multiple limitations: they are unable to provide fully natural visual cues and comfortable viewing experiences for all users. At their core, many of the issues with near-eye displays are caused by limitations in conventional optics. Current displays cannot reproduce the changes in focus that accompany natural vision, and they cannot support users with uncorrected refractive errors. With two prototype near-eye displays, we show how these issues can be overcome using display modes that adapt to the user via computational optics. By using focus-tunable lenses, mechanically actuated displays, and mobile gaze-tracking technology, these displays can be tailored to correct common refractive errors and provide natural focus cues by dynamically updating the system based on where a user looks in a virtual scene. Indeed, the opportunities afforded by recent advances in computational optics open up the possibility of creating a computing platform in which some users may experience better quality vision in the virtual world than in the real one.

Concepts: Computer, Java, Lens, Personal digital assistant, Wearable computer, User interface, Ubiquitous computing, Computing platform

6

Here we describe the honeycomb maze, a behavioural paradigm for the study of spatial navigation in rats. The maze consists of 37 platforms that can be raised or lowered independently. Place navigation requires an animal to go to a goal platform from any of several start platforms via a series of sequential choices. For each, the animal is confined to a raised platform and allowed to choose between two of the six adjacent platforms, the correct one being the platform with the smallest angle to the goal-heading direction. Rats learn rapidly and their choices are influenced by three factors: the angle between the two choice platforms, the distance from the goal, and the angle between the correct platform and the direction of the goal. Rats with hippocampal damage are impaired in learning and their performance is affected by all three factors. The honeycomb maze represents a marked improvement over current spatial navigation tests, such as the Morris water maze, because it controls the choices of the animal at each point in the maze, provides the ability to assess knowledge of the goal direction from any location, enables the identification of factors influencing task performance and provides the possibility for concomitant single-cell recording.

Concepts: Hippocampus, Learning, Knowledge, Choice, Computing platform

5

HIV Viral Load and Early Infant Diagnosis technologies in many high burden settings are restricted to centralized laboratory testing, leading to long result turnaround times and patient attrition. GeneXpert (Cepheid, CA, USA) is a polyvalent near point-of-care platform and is widely implemented for Xpert MTB/RIF diagnosis. This study sought to evaluate the operational feasibility of integrated HIV VL, EID and MTB/RIF testing in new GeneXpert platforms.

Concepts: Antiretroviral drug, HIV, HIV/AIDS, Viral load, Tuberculosis, Cytomegalovirus, Java, Computing platform

5

The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support.

Concepts: Greek loanwords, Pathogen, Collaboration, Technical support, Tool, Computing platform

4

The impact of a new class of automated digital patient engagement (DPE) platforms on potentially avoidable costs, hospital admissions, and complications after discharge following hip and knee arthroplasties has not been established.

Concepts: Patient, Hospital, Sartorius muscle, Java, Computing platform

3

Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown.

Concepts: Electron, Molecular biology, Atom, Data, Java, Protocol, Height, Computing platform

3

Successful post-operative telerehabilitation following total knee replacement (TKR) has been documented using synchronous (real-time) video. Bandwidth and the need for expensive hardware are cited as barriers to implementation. Web-based asynchronous visual platforms promise to address these problems but have not been evaluated.We performed a randomized control study comparing an asynchronous video-based software platform to in-person outpatient physical therapy visits following TKR.

Concepts: Orthopedic surgery, Java, Knee replacement, Autologous chondrocyte implantation, Computing platform, Computing platforms

3

We present rCGH, a comprehensive aCGH analysis workflow, integrating computational improvements, and functionalities specifically designed for precision medicine. rCGH supports the major microarray platforms, ensures a full traceability, and facilitates profiles interpretation and decision-making through sharable interactive visualizations.

Concepts: Engineering, Computational genomics, Major, Profiles, Nick Mason, Computing platform