SDAR: a practical tool for graphical analysis of two-dimensional data

ABSTRACT: BACKGROUND: Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in Java with a user-friendly interface are rare. RESULTS: We have developed SDAR, a Java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the Java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. CONCLUSION: Since SDAR is implemented in Java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://www.structuralchemistry.org/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.     

Super-Memorizers Are Not Super-Recognizers

Humans have a natural expertise in recognizing faces. However, the nature of the interaction between this critical visual biological skill and memory is yet unclear. Here, we had the unique opportunity to test two individuals who have had exceptional success in the World Memory Championships, including several world records in face-name association memory. We designed a range of face processing tasks to determine whether superior/expert face memory skills are associated with distinctive perceptual strategies for processing faces. Superior memorizers excelled at tasks involving associative face-name learning. Nevertheless, they were as impaired as controls in tasks probing the efficiency of the face system: face inversion and the other-race effect. Super memorizers did not show increased hippocampal volumes, and exhibited optimal generic eye movement strategies when they performed complex multi-item face-name associations. Our data show that the visual computations of the face system are not malleable and are robust to acquired expertise involving extensive training of associative memory.     

Task placement for crowd recognition in edge-cloud based urban intelligent video systems

Recently, edge-cloud has attracted much attention by its promising prospect in terms of facilitating the benefits of edge and cloud together. It is promising for urban video systems that require efficient and effective processing for their intelligent monitoring drives on various ends, like sky drones and land cameras. For instance, to support crowd recognition for public safety, the tasks to crowd recognition need to be placed into all processing nodes in the video systems for processing effectively. This is a challenging problem to facilitate the edge-cloud orchestrated scenarios. However, the variability of tasks based on their complexities is not considered fully in existing strategies. In this regard, we model and analyse task placement for crowd recognition in edge-cloud intelligent video systems. Then, our strategies are proposed which are referred to Node-Graph based Task Placement (NGTP) and Cluster-Graph based Task Placement (CGTP). Specifically, with the help of data dependencies, NGTP utilises the greedy approach with node graphs in the centralised way for general scenarios. Comparatively, CGTP utilises data dependency and similarity for task placing in the decentralised way for emergency scenarios. The experiments demonstrate the superior and effectiveness performance in forming tasks cost and running time of our proposed approaches.

     

DBToolkit: processing protein databases for peptide-centric proteomics

SUMMARY: DBToolkit is a user-friendly, easily extensible tool that allows the processing of protein sequence databases to peptide-centric sequence databases. This processing is primarily aimed at enhancing the useful information content of these databases for use as optimized search spaces for efficient identification of peptide fragmentation spectra obtained by mass spectrometry. In addition, DBToolkit can be used to reliably solve a range of other typical tasks in processing sequence databases. AVAILABILITY: DBToolkit is open source under the GNU GPL license. The source code, full user and developer documentation and cross-platform binaries are freely downloadable from the project website at http://genesis.UGent.be/dbtoolkit/ CONTACT: lennart.martens@UGent.be     

A microcomputer interface for a digital audio processor-based data recording system.

An inexpensive interface is described that performs direct transfer of digitized data from the digital audio processor and video cassette recorder based data acquisition system designed by Bezanilla (1985, Biophys. J., 47:437-441) to an IBM PC/XT microcomputer. The FORTRAN callable software that drives this interface is capable of controlling the video cassette recorder and starting data collection immediately after recognition of a segment of previously collected data. This permits piecewise analysis of long intervals of data that would otherwise exceed the memory capability of the microcomputer.     

A digital signal processing system for EEG frequency analysis

This paper describes the digital signal processing work of a research project for studying children's cognitive processes by analyzing EEG signals during school-related tasks. The EEG being analyzed involves two homologous channels (left and right parietal area), and is recorded on magnetic tapes. The objective of the analysis is to determine if, by examining the alpha band of the ongoing EEG, different school tasks and correct vs incorrect responses can be detected. Analysis of alpha-band calls for the determination of signal power in the 7-12 Hz frequency band (adjusted for the age of the subjects) for each channel as well as correlation between the channels. A digital signal processing scheme implemented on an Apple II microcomputer was developed for such an analysis. The results obtained are discussed.     

Object-Oriented Design of QoS Multicast Communications

Multicast (group) communications have been widely recognized by current research and industry. Multicast is very useful for various network applications such as distributed (replicated) database, video/audio conference, information distribution and server locations, etc. But design and implementation of such multicast communication systems in networks are complicated tasks, especially when quality of services (QoS) of applications such as real-time and reliability are desired. To quick design and implement multicast communication, good tools are crucial and must be facilitated. This paper presents a novel object-oriented (O-O) QoS driven approach for the quick design and prototyping of multicast communication systems under certain QoS requirements for multicast message transmission and receptions such as real-time, total ordering, atomicity and fault-tolerance, etc.     

Analysis of functional brain connections for positive–negative emotions using phase locking value

In this study, we investigate the brain networks during positive and negative emotions for different types of stimulus (audio only, video only and audio + video) in \(\alpha , \beta\), and \(\gamma\) bands in terms of phase locking value, a nonlinear method to study functional connectivity. Results show notable hemispheric lateralization as phase synchronization values between channels are significant and high in right hemisphere for all emotions. Left frontal electrodes are also found to have control over emotion in terms of functional connectivity. Besides significant inter-hemisphere phase locking values are observed between left and right frontal regions, specifically between left anterior frontal and right mid-frontal, inferior-frontal and anterior frontal regions; and also between left and right mid frontal regions. ANOVA analysis for stimulus types show that stimulus types are not separable for emotions having high valence. PLV values are significantly different only for negative emotions or neutral emotions between audio only/video only and audio only/audio + video stimuli. Finding no significant difference between video only and audio + video stimuli is interesting and might be interpreted as that video content is the most effective part of a stimulus.     

Comparison of the Expectation of Caregivers and Children with Type 1 Diabetes Mellitus Doe Independence in Diabetes Care-Related Tasks

ObjectiveChildren who are given unsupervised responsibility for their diabetes care prior to developmental and/or emotional readiness may have poorer glycemic control. The purpose of this study was to assess the age-related expectations of children and caregivers for independence in diabetes care-related tasks.MethodsA total of 150 participants with type 1 diabetes mellitus (T1DM) receiving multiple daily injections (MDI) or continuous subcutaneous insulin infusion (CSII) were enrolled in this study. All caregivers and participants older than 10 years of age completed questionnaires evaluating the expected age of independence for different diabetes care-related tasks.ResultsThe participants expected independence with no direct supervision in most diabetes care-related tasks at a younger age than their caregivers (P < .05). The difference was more prominent for those on CSII compared to MDI (P < .01). There was a positive correlation between the age when caregivers expect independence for most of the diabetes-related tasks and the age at diagnosis, regardless of the use of MDI or CSII (P < .01).ConclusionChildren with T1DM expect to assume independence at a younger age than their caregivers do. The younger the children are at diagnosis, the younger they are expected by their caregivers to be independent, especially those on CSII. (Endocr Pract. 2014;20:629-637)     

Analyse de mouvement : une revue

Image sequence analysis has been a major topic for years. It allows accessing important information on the objects of interest for detection, estimation, tracking and recognition tasks. Many applications are concerned from video to weather forecasting, robotics to in-door monitoring up to medicine. The place that it has today and the diversity of the problems to address have motivated this state-of-the-art. A generic approach has been adopted in order to provide a full view on the recent advances reported in the literature at the methodological level. After introducing the key elements to be considered (objects, observations, objectives), three main classes of methods are analysed and discussed: the differential approaches, the Bayesian techniques and the matching methods. A last section is focused on the links with medical imaging with the aim to emphasize the special features to deal with.     

Chemical derivatization of compact disc polycarbonate surfaces for SNPs detection

Compact discs have been proposed as an efficient analytical platform, with potential to develop high-throughput affinity assays for genomics, proteomics, clinics, and health monitoring. Chemical derivatization of CD surfaces is one of the keys to developing highly efficient microarraying-based assays on discs. Approaches for mild chemical modification of polycarbonate (PC) disc surface based on nitration, reduction, and chloromethylation reactions have been developed. Derivatized surfaces as amino and thiol are obtained for PC, maintaining unchanged the mechanical and optical properties of the discs. Studies of covalent attachment of oligonucleotide probes (5' Cy5-labeled, 3' NH 2-ended) on the modified surfaces have been performed to develop microarraying assays based on hybridization of cDNA strands and single nucleotide polymorphism discrimination (SNPs). A demonstration of the applicability to the compact disc audio/video technology for its use as analytical system is performed, including the employment of a commercial CD player to read the results on disc.     

Video-based image collection for quantitative histopathology

Obtaining histologic images for computer-based morphometric analysis is associated with a number of standardization problems, which must be solved if reproducible data collection is expected. These problems include tissue processing, sectioning and staining, standardizing and calibrating the video camera and determining the appropriate sampling rate (pixels/micron). Suggested solutions for these problems are presented for a specific image analysis system, but are applicable to other systems with similar capabilities. Biologic variability is not eliminated by computer-assisted analysis, so it is important to minimize data-collection artifacts by parallel processing of experimental and control material, as in other investigative work.     

SWEET-HOME ICT technologies for the assessment of elderly subjects

Functional assessments are designed to ascertain a person's ability to perform activities of daily living (ADL) and provide valuable diagnostic as well as care-planning information. Currently, the gold standard for the assessment of functional ability involves clinical rating scales. However, scales are often limited in their ability to provide objective and sensitive information. In contrast, information and communication technologies (ICT) may overcome these limitations by capturing more fully the functional, as well as behavioral and cognitive disturbances associated with Alzheimer disease (AD). In this context, the ANR Tec San 2009 SWEET-HOME project aims at building an innovative framework for modeling ADL. The first result of the SWEET-HOME project has been the installation in a classical consultation setting of a specific room equipped with audio and video sensors. This leads to the following results: (1) physical activity recognition done by patients, (e.g., balance test, repeated transfers between sitting and standing): the monitoring system is able to detect the full set of activities with a detection rate varying from 96.9% to 100% (true positive rate); (2) activity of daily living: the monitoring system had an average sensitivity of 90% and an average precision of 83.51%. Using a functional score it is possible to differentiate AD patients from healthy controls; (3) acceptability of the system: results of the survey (all the 64 participants who accepted to be assessed using the system) indicated that the assessment has been perceived as pleasant (83%).     

The difference is in the start: impact of timing and start procedure on sprint running performance

The difference is in the start: impact of timing and start procedure on sprint running performance. The purpose of this study was to compare different sprint start positions and to generate correction factors between popular timing triggering methods on 40-m/40-yd sprint time. Fourteen female athletes (17 ± 1 years), personal best 100 m: 13.26 (±0.68) seconds and 11 male athletes (20 ± 5 years), personal best 100 m: 11.58 (±0.74) seconds participated. They performed 2 series of 3 40-m sprints in randomized order: (a) start from the block, measured by means of Brower audio sensor (BAS) and Dartfish video timing (DVT), (b) 3-point start, measured by using hand release pod (HR) and DVT, and (c) standing start, triggered by both photocell across starting line (SFC), and foot release (FR) plus DVT. Video analysis was performed by 2 independent observers and averaged. Simultaneous measurements at national athletics competitions demonstrated that DVT and BAS were equivalent to Omega Timing within the limits of precision of video timing (±0.01 seconds). Hand and floor timer triggering showed small but significant biases compared with movement captured from video (0.02-0.04 seconds), presumably because of sensitivity of pressure thresholds. Coefficient of variation for test-retest timing using different starting positions ranged from 0.7 to 1.0%. Compared with block starts reacting to gunfire, HR, SFC, and FR starts yielded 0.17 ± 0.09, 0.27 ± 0.12, and 0.69 ± 0.11 second faster times, respectively, over 40 m (all p < 0.001) because of inclusion or exclusion of reaction time, plus momentum, and body position differences at trigger moment. Correction factors for the conversion of 40 m/40 yd and 40 yd/40 m were 0.92 and 1.08, respectively. The correction factors obtained from this study may facilitate more meaningful comparisons of published sprint performances.     

A method to synchronise video cameras using the audio band

This paper proposes and evaluates a novel method for synchronisation of video cameras using the audio band. The method consists in generating and transmitting an audio signal through radio frequency for receivers connected to the microphone input of the cameras and inserting the signal in the audio band. In a software environment, the phase differences among the video signals are calculated and used to interpolate the synchronous 2D projections of the trajectories. The validation of the method was based on: (1) Analysis of the phase difference changes as a function of time of two video signals. (2) Comparison between the values measured with an oscilloscope and by the proposed method. (3) Estimation of the improvement in the accuracy in the measurements of the distance between two markers mounted on a rigid body during movement applying the method. The results showed that the phase difference changes in time slowly (0.150 ms/min) and linearly, even when the same model of cameras are used. The values measured by the proposed method and by oscilloscope showed equivalence (R2=0.998), the root mean square of the difference between the measurements was 0.10 ms and the maximum difference found was 0.31 ms. Applying the new method, the accuracy of the 3D reconstruction had a statistically significant improvement. The accuracy, simplicity and wide applicability of the proposed method constitute the main contributions of this work.     

Centralized data analysis of a large interlaboratory proteomics project: a feasibility study

The human Plasma Proteome Project (PPP) is a large-scale collaboration between many laboratories. One of the most demanding tasks in the PPP involved the analysis of very large amounts of raw MS/MS data produced by the participants. The main approach for managing this task was letting the participants analyze their own data and submit the results to the central PPP repository as lists of identified proteins and peptides. To complement this distributed approach, we also performed centralized analysis of the raw MS/MS data provided by the participants. Due to the data redundancy inherent in such a project, centralized analysis has the potential to reduce the computational effort by reducing redundancy before the analysis. Centralized analysis can also unify the process and take advantage of data sharing among laboratories to improve protein identification and validation. The process we employed included removing low-quality spectra, clustering spectra by mutual similarity, and applying uniform peptide and protein identification procedures. To demonstrate the process, we analyzed 5.28 million MS/MS spectra derived by eight laboratories from tryptic peptides of serum and plasma proteins.     

Oral health behaviour and socio-demographic profile of subjects with Alzheimer's disease as reported by their family caregivers

Objective: To evaluate the oral health care provided to subjects with Alzheimer's disease (AD) as reported by their family caregivers. Method: Structured interviews were performed with 56 Alzheimer caregivers from the Group of relatives and friends of subjects with AD of the Hospital de Clínicas de Porto Alegre. Spearman and Pearson correlations were performed. Results: The mean age of the subjects with AD was 76.09 (±7.76) years, 53.6% were female and 58.9% were in the advanced stage of AD. The mean number of teeth present was 11.66 (±10.94), and oral hygiene was performed 2.21 (±1.04) times/day. The provision of oral health care to subjects with AD was carried out by caregivers in 85.7%. Oral hygiene was provided by the caregivers to the subjects with AD with the aid of a toothbrush and/or gauze embedded with non‐fluoridated mouthwash in the majority of the cases. Complete dental prostheses were cleaned with the aid of mouthwashes instead of denture brushes by 44% of the subjects/caregivers. There was a significant association between the number of teeth in the subjects with AD and the number of oral hygiene procedures performed per day and current smoking. Conclusion: Oral health care planning for subjects with AD should take into account caregivers’ perceptions and knowledge about oral health and hygiene as caregivers represent the primary providers to these patients when the disease progresses from early to more advanced stages.     

A Bioinformatician's Guide to Metagenomics

Summary: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.     

Caspase-1 activation and mature interleukin-1&beta; release are uncoupled events in monocytes

AIM: To investigate whether caspase-1 activation/intracellular processing of pro-interleukin-1β (pro-IL-1β) and extracellular release of mature IL-1β from activated monocytes are separable events. METHODS: All experiments were performed on fresh or overnight cultured human peripheral blood monocytes (PBMCs) that were isolated from healthy donors. PBMCs were activated by lipopolysaccharide (LPS) stimulation before being treated with Adenosine triphosphate (ATP, 1 mmol/L), human α-defensin-5 (HD-5, 50 μg/mL), and/or nigericin (Nig, 30 μmol/L). For each experiment, the culture supernatants were collected separately from the cells. Cell lysates and supernatants were both subject to immunoprecipitation with anti-IL-1β antibodies followed by western blot analysis with anti-caspase-1 and anti-IL-1β antibodies. RESULTS: We found that pro-IL-1β was processed to mature IL-1β in LPS-activated fresh and overnight cultured human monocytes in response to ATP stimulation. In the presence of HD-5, this release of IL-1β, but not the processing of pro-IL-1β to IL-1β, was completely inhibited. Similarly, in the presence of HD-5, the release of IL-1β, but not the processing of IL-1β, was significantly inhibited from LPS-activated monocytes stimulated with Nig. Finally, we treated LPS-activated monocytes with ATP and Nig and collected the supernatants. We found that both ATP and Nig stimulation could activate and release cleaved caspase-1 from the monocytes. Interestingly, and contrary to IL-1β processing and release, caspase-1 cleavage and release was not blocked by HD-5. All images are representative of three independent experiments. CONCLUSION: These data suggest that caspase-1 activation/processing of pro-IL-1β by caspase-1 and the release of mature IL-1β from human monocytes are distinct and separable events.     

Experimental measurements and design guidelines for real-time software encryption in multimedia wireless LANs

To secure interactive multimedia applications in wireless LANs (WLANs), it is pertinent to implement real time cryptographic services. In this paper we evaluate the use of software based encryption algorithms that are implemented in the layer service provider as defined by WinSock 2 for Windows 95/NT. Our measurements show that software implementation of various encryptors can sustain the throughput requirements of interactive multimedia applications for WLANs such as telephone-quality audio, video conferencing, and MPEG video. We present a design methodology that includes guidelines for a secure multimedia system design in terms of the encryption method chosen as a function of required application throughput, system configuration, protocol layers overhead and wireless LAN throughput. This revised version was published online in July 2006 with corrections to the Cover Date.