TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Background: Popular approaches in human tissue-based biomarker discovery include tissue microarrays (TMAs) and DNA Microarrays (DMAs) for protein and gene expression profiling respectively. The data generated by these analytic platforms, together with associated image, clinical and pathological data currently reside on widely different information platforms, making searching and cross-platform analysis difficult. Consequently, there is a strong need to develop a single coherent database capable of correlating all available data types.

Method: This study presents TMAX, a database system to facilitate biomarker discovery tasks. TMAX organises a variety of biomarker discovery-related data into the database. Both TMA and DMA experimental data are integrated in TMAX and connected through common DNA/protein biomarkers. Patient clinical data (including tissue pathological data), computer assisted tissue image and associated analytic data are also included in TMAX to enable the truly high throughput processing of ultra-large digital slides for both TMAs and whole slide tissue digital slides. A comprehensive web front-end was built with embedded XML parser software and predefined SQL queries to enable rapid data exchange in the form of standard XML files.

Results & Conclusion: TMAX represents one of the first attempts to integrate TMA data with public gene expression experiment data. Experiments suggest that TMAX is robust in managing large quantities of data from different sources (clinical, TMA, DMA and image analysis). Its web front-end is user friendly, easy to use, and most importantly allows the rapid and easy data exchange of biomarker discovery related data. In conclusion, TMAX is a robust biomarker discovery data repository and research tool, which opens up the opportunities for biomarker discovery and further integromics research.

Multimodal Biometric Human Recognition for Perceptual Human-Computer Interaction

In this paper, a novel video-based multimodal biometric verification scheme using the subspace-based low-level feature fusion of face and speech is developed for specific speaker recognition for perceptual human--computer interaction (HCI). In the proposed scheme, human face is tracked and face pose is estimated to weight the detected facelike regions in successive frames, where ill-posed faces and false-positive detections are assigned with lower credit to enhance the accuracy. In the audio modality, mel-frequency cepstral coefficients are extracted for voice-based biometric verification. In the fusion step, features from both modalities are projected into nonlinear Laplacian Eigenmap subspace for multimodal speaker recognition and combined at low level. The proposed approach is tested on the video database of ten human subjects, and the results show that the proposed scheme can attain better accuracy in comparison with the conventional multimodal fusion using latent semantic analysis as well as the single-modality verifications. The experiment on MATLAB shows the potential of the proposed scheme to attain the real-time performance for perceptual HCI applications.

Novel system for distant assessment of cataract surgical quality in rural China

BACKGROUND: This study aims to assess the quality of various steps of manual small incision cataract surgery and predictors of quality, using video recordings.
DESIGN: This paper applies a retrospective study.
PARTICIPANTS: Fifty-two trainees participated in a hands-on small incision cataract surgery training programme at rural Chinese hospitals.
METHODS: Trainees provided one video each recorded by a tripod-mounted digital recorder after completing a one-week theoretical course and hands-on training monitored by expert trainers. Videos were graded by two different experts, using a 4-point scale developed by the International Council of Ophthalmology for each of 12 surgical steps and six global factors. Grades ranged from 2 (worst) to 5 (best), with a score of 0 if the step was performed by trainers.
MAIN OUTCOME MEASURES: Mean score for the performance of each cataract surgical step rated by trainers.
RESULTS: Videos and data were available for 49/52 trainees (94.2%, median age 38 years, 16.3% women and 77.5% completing > 50 training cases). The majority (53.1%, 26/49) had performed ≤ 50 cataract surgeries prior to training. Kappa was 0.57∼0.98 for the steps (mean 0.85). Poorest-rated steps were draping the surgical field (mean ± standard deviation = 3.27 ± 0.78), hydro-dissection (3.88 ± 1.22) and wound closure (3.92 ± 1.03), and top-rated steps were insertion of viscoelastic (4.96 ± 0.20) and anterior chamber entry (4.69 ± 0.74). In linear regression models, higher total score was associated with younger age (P = 0.015) and having performed >50 independent manual small incision cases (P = 0.039).
CONCLUSIONS: More training should be given to preoperative draping, which is poorly performed and crucial in preventing infection. Surgical experience improves ratings.© 2015 Royal Australian and New Zealand College of Ophthalmologists.

DOMINANCE OF SHORT-RANGE-ORDER EFFECTS IN LOW-ENERGY ELECTRON-DIFFRACTION INTENSITY SPECTRA

Using low-energy electron-diffraction (LEED) formalism, we demonstrate theoretically that LEED I-V spectra are characterized mainly by short-range order. We also show experimentally that diffuse LEED (DLEED) I-V spectra can be accurately measured from a disordered system using a video-LEED system even at very low coverage. These spectra demonstrate that experimental DLEED I-V spectra from disordered systems may be used to determine local structures. As an example, it is shown that experimental DLEED I-V spectra from K/Co {1010BAR} at potassium coverages of 0.07, 0.1, and 0.13 monolayer closely resemble calculated and experimental LEED I-V spectra for a well-ordered Co{1010BAR}-c(2X2)-K superstructure, leading to the conclusion that at low coverages, potassium atoms are located in the fourfold-hollow sites and that there is no large bond-length change with coverage.

Reconfigurable system-on-a-chip motion estimation architecture for multi-standard video coding

A new domain-specific, reconfigurable system-on-a-chip (SoC) architecture is proposed for video motion estimation. This has been designed to cover most of the common block-based video coding standards, including MPEG-2, MPEG-4, H.264, WMV-9 and AVS. The architecture exhibits simple control, high throughput and relatively low hardware cost when compared with existing circuits. It can also easily handle flexible search ranges without any increase in silicon area and can be configured prior to the start of the motion estimation process for a specific standard. The computational rates achieved make the circuit suitable for high-end video processing applications, such as HDTV. Silicon design studies indicate that circuits based on this approach incur only a relatively small penalty in terms of power dissipation and silicon area when compared with implementations for specific standards. Indeed, the cost/performance achieved exceeds that of existing but specific solutions and greatly exceeds that of general purpose field programmable gate array (FPGA) designs.

How Video Lecture Capture affects Student Engagement in a University Computer Programming Course: Attendance, Video Viewing Behaviours and Student Attitudes

Introduction
The use of video capture of lectures in Higher Education is not a recent occurrence with web based learning technologies including digital recording of live lectures becoming increasing commonly offered by universities throughout the world (Holliman and Scanlon, 2004). However in the past decade the increase in technical infrastructural provision including the availability of high speed broadband has increased the potential and use of videoed lecture capture. This had led to a variety of lecture capture formats including pod casting, live streaming or delayed broadcasting of whole or part of lectures.
Additionally in the past five years there has been a significant increase in the popularity of online learning, specifically via Massive Open Online Courses (MOOCs) (Vardi, 2014). One of the key aspects of MOOCs is the simulated recording of lecture like activities. There has been and continues to be much debate on the consequences of the popularity of MOOCs, especially in relation to its potential uses within established University programmes.
There have been a number of studies dedicated to the effects of videoing lectures.
The clustered areas of research in video lecture capture have the following main themes:
• Staff perceptions including attendance, performance of students and staff workload
• Reinforcement versus replacement of lectures
• Improved flexibility of learning
• Facilitating engaging and effective learning experiences
• Student usage, perception and satisfaction
• Facilitating students learning at their own pace
Most of the body of the research has concentrated on student and faculty perceptions, including academic achievement, student attendance and engagement (Johnston et al, 2012).
Generally the research has been positive in review of the benefits of lecture capture for both students and faculty. This perception coupled with technical infrastructure improvements and student demand may well mean that the use of video lecture capture will continue to increase in frequency in the next number of years in tertiary education. However there is a relatively limited amount of research in the effects of lecture capture specifically in the area of computer programming with Watkins 2007 being one of few studies . Video delivery of programming solutions is particularly useful for enabling a lecturer to illustrate the complex decision making processes and iterative nature of the actual code development process (Watkins et al 2007). As such research in this area would appear to be particularly appropriate to help inform debate and future decisions made by policy makers.
Research questions and objectives
The purpose of the research was to investigate how a series of lecture captures (in which the audio of lectures and video of on-screen projected content were recorded) impacted on the delivery and learning of a programme of study in an MSc Software Development course in Queen’s University, Belfast, Northern Ireland. The MSc is conversion programme, intended to take graduates from non-computing primary degrees and upskill them in this area. The research specifically targeted the Java programming module within the course. It also analyses and reports on the empirical data from attendances and various video viewing statistics. In addition, qualitative data was collected from staff and student feedback to help contextualise the quantitative results.
Methodology, Methods and Research Instruments Used
The study was conducted with a cohort of 85 post graduate students taking a compulsory module in Java programming in the first semester of a one year MSc in Software Development. A pre-course survey of students found that 58% preferred to have available videos of “key moments” of lectures rather than whole lectures. A large scale study carried out by Guo concluded that “shorter videos are much more engaging” (Guo 2013). Of concern was the potential for low audience retention for videos of whole lectures.
The lecturers recorded snippets of the lecture directly before or after the actual physical delivery of the lecture, in a quiet environment and then upload the video directly to a closed YouTube channel. These snippets generally concentrated on significant parts of the theory followed by theory related coding demonstration activities and were faithful in replication of the face to face lecture. Generally each lecture was supported by two to three videos of durations ranging from 20 – 30 minutes.
Attendance
The MSc programme has several attendance based modules of which Java Programming was one element. In order to assess the consequence on attendance for the Programming module a control was established. The control used was a Database module which is taken by the same students and runs in the same semester.
Access engagement
The videos were hosted on a closed YouTube channel made available only to the students in the class. The channel had enabled analytics which reported on the following areas for all and for each individual video; views (hits), audience retention, viewing devices / operating systems used and minutes watched.
Student attitudes
Three surveys were taken in regard to investigating student attitudes towards the videoing of lectures. The first was before the start of the programming module, then at the mid-point and subsequently after the programme was complete.
The questions in the first survey were targeted at eliciting student attitudes towards lecture capture before they had experienced it in the programme. The midpoint survey gathered data in relation to how the students were individually using the system up to that point. This included feedback on how many videos an individual had watched, viewing duration, primary reasons for watching and the result on attendance, in addition to probing for comments or suggestions. The final survey on course completion contained questions similar to the midpoint survey but in summative view of the whole video programme.
Conclusions and Outcomes
The study confirmed findings of other such investigations illustrating that there is little or no effect on attendance at lectures. The use of the videos appears to help promote continual learning but they are particularly accessed by students at assessment periods. Students respond positively to the ability to access lectures digitally, as a means of reinforcing learning experiences rather than replacing them. Feedback from students was overwhelmingly positive indicating that the videos benefited their learning. Also there are significant benefits to part recording of lectures rather than recording whole lectures. The behaviour viewing trends analytics suggest that despite the increase in the popularity of online learning via MOOCs and the promotion of video learning on mobile devices in fact in this study the vast majority of students accessed the online videos at home on laptops or desktops However, in part, this is likely due to the nature of the taught subject, that being programming.
The research involved prerecording the lecture in smaller timed units and then uploading for distribution to counteract existing quality issues with recording entire live lectures. However the advancement and consequential improvement in quality of in situ lecture capture equipment may well help negate the need to record elsewhere. The research has also highlighted an area of potentially very significant use for performance analysis and improvement that could have major implications for the quality of teaching. A study of the analytics of the viewings of the videos could well provide a quick response formative feedback mechanism for the lecturer. If a videoed lecture either recorded live or later is a true reflection of the face to face lecture an analysis of the viewing patterns for the video may well reveal trends that correspond with the live delivery.

A Steganalysis System Utilizing Temporal Pixel Correlation Of HEVC Video

High Efficiency Video Coding (HEVC) is the most recent video codec coming after currently most popular H.264/MPEG4 codecs and has promising compression capabilities. It is conjectured that it will be a substitute for current video compression standards. However, to the best knowledge of the authors, none of the current video steganalysis methods designed or tested with HEVC video. In this paper, pixel domain steganography applied on HEVC video is targeted for the first time. Also, its the first paper that employs accordion unfolding transformation, which merges temporal and spatial correlation, in pixel domain video steganalysis. With help of the transformation, temporal correlation is incorporated into the system. Its demonstrated for three different feature sets that integrating temporal dependency substantially increased the detection accuracy.

Geochronological database and classification system for age uncertainties in Neotropical pollen records.

The newly updated inventory of palaeoecological research in Latin America offers an important overview of sites available for multi-proxy and multi-site purposes. From the collected literature supporting this inventory, we collected all available age model metadata to create a chronological database of 5116 control points (e.g. 14C, tephra, fission track, OSL, 210Pb) from 1097 pollen records. Based on this literature review, we present a summary of chronological dating and reporting in the Neotropics. Difficulties and recommendations for chronology reporting are discussed. Furthermore, for 234 pollen records in northwest South America, a classification system for age uncertainties is implemented based on chronologies generated with updated calibration curves. With these outcomes age models are produced for those sites without an existing chronology, alternative age models are provided for researchers interested in comparing the effects of different calibration curves and age–depth modelling software, and the importance of uncertainty assessments of chronologies is highlighted. Sample resolution and temporal uncertainty of ages are discussed for different time windows, focusing on events relevant for research on centennial- to millennial-scale climate variability. All age models and developed R scripts are publicly available through figshare, including a manual to use the scripts.

The SEMAINE Database: Annotated Multimodal Records of Emotionally Colored Conversations between a Person and a Limited Agent

SEMAINE has created a large audiovisual database as a part of an iterative approach to building Sensitive Artificial Listener (SAL) agents that can engage a person in a sustained, emotionally colored conversation. Data used to build the agents came from interactions between users and an operator simulating a SAL agent, in different configurations: Solid SAL (designed so that operators displayed an appropriate nonverbal behavior) and Semi-automatic SAL (designed so that users' experience approximated interacting with a machine). We then recorded user interactions with the developed system, Automatic SAL, comparing the most communicatively competent version to versions with reduced nonverbal skills. High quality recording was provided by five high-resolution, high-framerate cameras, and four microphones, recorded synchronously. Recordings total 150 participants, for a total of 959 conversations with individual SAL characters, lasting approximately 5 minutes each. Solid SAL recordings are transcribed and extensively annotated: 6-8 raters per clip traced five affective dimensions and 27 associated categories. Other scenarios are labeled on the same pattern, but less fully. Additional information includes FACS annotation on selected extracts, identification of laughs, nods, and shakes, and measures of user engagement with the automatic system. The material is available through a web-accessible database. © 2010-2012 IEEE.