KinImmerse: Macromolecular VR for NMR ensembles

Background  

In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case.     

Tai Chi and vestibular rehabilitation improve vestibulopathic gait via different neuromuscular mechanisms: Preliminary report

Background  

Vestibular rehabilitation (VR) is a well-accepted exercise program intended to remedy balance impairment caused by damage to the peripheral vestibular system. Alternative therapies, such as Tai Chi (TC), have recently gained popularity as a treatment for balance impairment. Although VR and TC can benefit people with vestibulopathy, the degree to which gait improvements may be related to neuromuscular adaptations of the lower extremities for the two different therapies are unknown.     

Multisensory stimulation can induce an illusion of larger belly size in immersive virtual reality

Background

Body change illusions have been of great interest in recent years for the understanding of how the brain represents the body. Appropriate multisensory stimulation can induce an illusion of ownership over a rubber or virtual arm, simple types of out-of-the-body experiences, and even ownership with respect to an alternate whole body. Here we use immersive virtual reality to investigate whether the illusion of a dramatic increase in belly size can be induced in males through (a) first person perspective position (b) synchronous visual-motor correlation between real and virtual arm movements, and (c) self-induced synchronous visual-tactile stimulation in the stomach area.

Methodology

Twenty two participants entered into a virtual reality (VR) delivered through a stereo head-tracked wide field-of-view head-mounted display. They saw from a first person perspective a virtual body substituting their own that had an inflated belly. For four minutes they repeatedly prodded their real belly with a rod that had a virtual counterpart that they saw in the VR. There was a synchronous condition where their prodding movements were synchronous with what they felt and saw and an asynchronous condition where this was not the case. The experiment was repeated twice for each participant in counter-balanced order. Responses were measured by questionnaire, and also a comparison of before and after self-estimates of belly size produced by direct visual manipulation of the virtual body seen from the first person perspective.

Conclusions

The results show that first person perspective of a virtual body that substitutes for the own body in virtual reality, together with synchronous multisensory stimulation can temporarily produce changes in body representation towards the larger belly size. This was demonstrated by (a) questionnaire results, (b) the difference between the self-estimated belly size, judged from a first person perspective, after and before the experimental manipulation, and (c) significant positive correlations between these two measures. We discuss this result in the general context of body ownership illusions, and suggest applications including treatment for body size distortion illnesses.     

Validation of a model-based virtual trials method for tight glycemic control in intensive care

Background  

In-silico virtual patients and trials offer significant advantages in cost, time and safety for designing effective tight glycemic control (TGC) protocols. However, no such method has fully validated the independence of virtual patients (or resulting clinical trial predictions) from the data used to create them. This study uses matched cohorts from a TGC clinical trial to validate virtual patients and in-silico virtual trial models and methods.     

Digit ratios by computer-assisted analysis confirm lack of anatomical evidence of prenatal androgen exposure in clinical phenotypes of polycystic ovary syndrome

Background  

We recently showed that women with four clinical phenotypes of polycystic ovary syndrome (PCOS) do not demonstrate anatomical evidence of elevated prenatal androgen exposure as judged by a lower ratio of the index (2D) to ring (4D) finger. However, those findings conflicted with a previous study where women with PCOS had lower right hand 2D:4D compared to healthy female controls. Both these studies used Vernier calipers to measure finger lengths - a method recently shown to be less reliable at obtaining finger length measurements than computer-assisted analysis.     

Virtual reality as a tool for evaluation of repetitive rhythmic movements in the elderly and Parkinson's disease patients

This work presents an immersive Virtual Reality (VR) system to evaluate, and potentially treat, the alterations in rhythmic hand movements seen in Parkinson's disease (PD) and the elderly (EC), by comparison with healthy young controls (YC). The system integrates the subjects into a VR environment by means of a Head Mounted Display, such that subjects perceive themselves in a virtual world consisting of a table within a room. In this experiment, subjects are presented in 1(st) person perspective, so that the avatar reproduces finger tapping movements performed by the subjects. The task, known as the finger tapping test (FT), was performed by all three subject groups, PD, EC and YC. FT was carried out by each subject on two different days (sessions), one week apart. In each FT session all subjects performed FT in the real world (FT(REAL)) and in the VR (FT(VR)); each mode was repeated three times in randomized order. During FT both the tapping frequency and the coefficient of variation of inter-tap interval were registered. FT(VR) was a valid test to detect differences in rhythm formation between the three groups. Intra-class correlation coefficients (ICC) and mean difference between days for FT(VR) (for each group) showed reliable results. Finally, the analysis of ICC and mean difference between FT(VR) vs FT(REAL), for each variable and group, also showed high reliability. This shows that FT evaluation in VR environments is valid as real world alternative, as VR evaluation did not distort movement execution and detects alteration in rhythm formation. These results support the use of VR as a promising tool to study alterations and the control of movement in different subject groups in unusual environments, such as during fMRI or other imaging studies.     

Molecular and physiological comparison of spoilage wine yeasts

Aims

Dekkera bruxellensis and Pichia guilliermondii are contaminating yeasts in wine due to the production of phenolic aromas. Although the degradation pathway of cinnamic acids, precursors of these phenolic compounds has been described in D. bruxellensis, no such pathway has been described in P. guilliermondii.

Methods and Results

A molecular and physiological characterization of 14 D. bruxellensis and 15 P. guilliermondii phenol‐producing strains was carried out. Both p‐coumarate decarboxylase (CD) and vinyl reductase (VR) activities, responsible for the production of volatile phenols, were quantified and the production of 4‐vinylphenol and 4‐ethylphenol were measured. All D. bruxellensis and some P. guilliermondii strains showed the two enzymatic activities, whilst 11 of the 15 strains of this latter species showed only CD activity and did not produce 4‐EP in the assay conditions. Furthermore, PCR products obtained with degenerated primers showed a low homology with the sequence of the gene for a phenyl acrylic acid decarboxylase activity described in Saccharomyces cerevisiae.

Conclusions

D. bruxellensis and P. guilliermondii may share a similar metabolic pathway for the degradation of cinnamic acids.

Significance and Impact of the Study

This is the first work that analyses the CD and VR activities in P. guilliermondii, and the results suggest that within this species, there are differences in the metabolization of cinnamic acids.     

Cytomegalovirus antibodies in dried blood spots: a minimally invasive method for assessing stress,immune function,and aging

Background  

Cytomegalovirus (CMV) is a prevalent herpesvirus with links to both stress and aging. This paper describes and validates a minimally invasive method for assessing antibodies against CMV in finger stick whole blood spot samples for use as an indirect marker of an aspect of cell-mediated immunity.     

Conservation,diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome

Background  

The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. The comparison of zinc finger proteins in several eukaryotes has shown that there is a lot of lineage specific diversification and expansion. Although the number of characterized plant proteins that carry the classical C2H2 zinc finger motifs is growing, a systematic classification and analysis of a plant genome zinc finger gene set is lacking.     

Diversity and seasonal dynamics of bacterial community in indoor environment

Background  

We spend most of our lives in indoor environments and are exposed to microbes present in these environments. Hence, knowledge about this exposure is important for understanding how it impacts on human health. However, the bacterial flora in indoor environments has been only fragmentarily explored and mostly using culture methods. The application of molecular methods previously utilised in other environments has resulted in a substantial increase in our awareness of microbial diversity.     

RNF122: A novel ubiquitin ligase associated with calcium-modulating cyclophilin ligand

Background  

RNF122 is a recently discovered RING finger protein that is associated with HEK293T cell viability and is overexpressed in anaplastic thyroid cancer cells. RNF122 owns a RING finger domain in C terminus and transmembrane domain in N terminus. However, the biological mechanism underlying RNF122 action remains unknown.     

Usage Position and Virtual Keyboard Design Affect Upper-Body Kinematics,Discomfort, and Usability during Prolonged Tablet Typing

Purpose

The increase in tablet usage allows people to perform computer work in non-traditional office environments. The aim of this study was to assess the effects of changes in tablet keyboard design on postures of the upper extremities and neck, discomfort, and usability under different usage positions during prolonged touch-typing.

Methods

Eighteen healthy participants familiar with touch-screen devices were randomized into three usage positions (desk, lap, and bed) and completed six, 60-minute typing sessions using three virtual keyboard designs (standard, wide, split). Electrogoniometers continuously measured the postures of the wrists, elbow, and neck. Body discomfort and system usability were evaluated by questionnaires before and immediately after each typing session.

Results

Separate linear mixed effects models on various postural measures and subjective ratings are conducted with usage position as the between-subject factors, keyboard design and typing duration as the with-in subject factors were conducted. Using the tablet in bed led to more extended wrists but a more natural elbow flexion than the desk position. The angled split virtual keyboard significantly reduced the extent of wrist ulnar deviation than the keyboard with either standard or wide design. However, little difference was observed across the usage position and keyboard design. When the postural data were compared between the middle and end of typing sessions, the wrists, elbow, and neck all exhibited a substantially increased range of joint movements (13% to 38%). The discomfort rating also increased significantly over time in every upper body region investigated. Additionally, the split keyboard design received a higher usability rating in the bed position, whereas participants had more satisfactory experience while using the wide keyboard in the traditional desk setting.

Conclusions

Prolonged use of tablets in non-traditional office environments may result in awkward postures in the upper body that may expose users to greater risks of developing musculoskeletal symptoms. Adequate virtual keyboard designs show the potential to alleviate some postural effects and improve the user experience without changing the tablet form factors.     

An update on the mouse liver proteome

Background  

Decoding of the liver proteome is subject of intense research, but hampered by methodological constraints. We recently developed an improved protocol for studying rat liver proteins based on 2-DE-MALDI-TOF-MS peptide mass finger printing.     

Development of a new tank-to-wheels methodology for energy use and green house gas emissions analysis based on vehicle fleet modeling

Background, aim and scope  

Tank-to-Wheels (TtW) makes the largest contribution to the total Well-to-Wheels (WtW) energy consumption and greenhouse gas (GHG) emissions from fossil-derived transportation fuels. The most commonly adopted TtW methodologies to obtain vehicle energy consumption, energy efficiency, and GHG emissions used to date all have significant limitations. A new TtW methodology, which combines micro-scale virtual vehicle simulation with macro-scale fleet modeling, is proposed in this paper. The models capabilities are demonstrated using a case study based on data from the passenger car sector in Great Britain.     

Transcription factors Elk-1 and SRF are engaged in IL1-dependent regulation of <Emphasis Type="Italic">ZC3H12A</Emphasis> expression

Background  

MCPIP is a novel CCCH zinc finger protein described as an RNase engaged in the regulation of immune responses. The regulation of expression of the gene coding for MCPIP - ZC3H12A is poorly explored.     

Quantitative genetic analysis of life-history traits of <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> in stressful environments

Background  

Organisms live in environments that vary. For life-history traits that vary across environments, fitness will be maximised when the phenotype is appropriately matched to the environmental conditions. For the free-living nematode Caenorhabditis elegans, we have investigated how two major life-history traits, (i) the development of environmentally resistant dauer larvae and (ii) reproduction, respond to environmental stress (high population density and low food availability), and how these traits vary between lines and the genetic basis of this variation.     

Agile methods in biomedical software development: a multi-site experience report

Background  

Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods.