Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses

Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference databases that only contain proteins (originating from the UniProtKB resource) associated with a predetermined list of taxa. This improves both the taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By limiting the proteins present in a reference database, it is also possible to perform (meta)proteogenomics analyses. Since the protein reference database resides on the user's local machine, they have complete control over the database used during an analysis. Data no longer need to be transmitted over the Internet, decreasing the time required for an analysis and better safeguarding privacy-sensitive data. As a proof of concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using different targeted databases based on matched 16S rRNA gene sequencing data.

mHealth Interventions for Treatment Adherence and Outcomes of Care for Cardiometabolic Disease Among Adults Living With HIV: Systematic Review

BACKGROUND

The success of antiretroviral therapy has led to an increase in life expectancy and an associated rise in the risk of cardiometabolic diseases (CMDs) among people living with HIV.

OBJECTIVE

Our aim was to conduct a systematic review to synthesize the existing literature on the patterns of use and effects of mobile health (mHealth) interventions for improving treatment adherence and outcomes of care for CMD among people living with HIV.

METHODS

A systematic search of multiple databases, including PubMed-MEDLINE, Embase, CINAHL, Scopus, Web of Science, African Journals online, ClinicalTrials.gov, and the World Health Organization Global Index Medicus of peer-reviewed articles, was conducted with no date or language restrictions. Unpublished reports on mHealth interventions for treatment adherence and outcomes of care for CMD among adults living with HIV were also included in this review. Studies were included if they had at least 1 component that used an mHealth intervention to address treatment adherence or 1 or more of the stated outcomes of care for CMD among people living with HIV.

RESULTS

Our search strategy yielded 1148 unique records. In total, 10 articles met the inclusion criteria and were included in this review. Of the 10 studies, only 4 had published results. The categories of mHealth interventions ranged from short messaging, telephone calls, and wearable devices to smartphone and desktop web-based mobile apps. Across the different categories of interventions, there were no clear patterns in terms of consistency in the use of a particular intervention, as most studies (9/10, 90%) assessed a combination of mHealth interventions. Short messaging and telephone calls were however the most common interventions. Half of the studies (5/10, 50%) reported on outcomes that were indirectly linked to CMD, and none of them provided reliable evidence for evaluating the effectiveness of mHealth interventions for treatment adherence and outcomes of care for CMD among people living with HIV.

CONCLUSIONS

Due to the limited number of studies and the heterogeneity of interventions and outcome measures in the studies, no definitive conclusions could be drawn on the patterns of use and effects of mHealth interventions for treatment adherence and outcomes of care for CMD among people living with HIV. We therefore recommend that future trials should focus on standardized outcomes for CMD. We also suggest that future studies should consider having a longer follow-up period in order to determine the long-term effects of mHealth interventions on CMD outcomes for people living with HIV.

TRIAL REGISTRATION

PROSPERO International Prospective Register of Systematic Reviews CRD42018086940; https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42018086940.

Virtual Reality in Anatomy: A Pilot Study Evaluating Different Delivery Modalities

Technologies such as virtual reality are used in higher education to develop virtual learning resources (VLRs). These VLRs can be delivered in multiple modalities, from truly immersive involving wearable devices to less immersive modalities such as desktop. However, research investigating perceptions of VLRs in anatomy has mainly focused on a single delivery modality and a limited-demographic participant cohort, warranting a comparison of different modalities and a consideration of different cohorts. This pilot study aimed to compare perceptions of highly immersive and less immersive VLR deliveries among anatomy students and tutors and evaluate the impact of prior university experience on students' perceptions of VLRs. A skull anatomy VLR was developed using the Unity^® gaming platform and participants were voluntarily recruited to assess highly immersive stereoscopic and less immersive desktop deliveries of the VLR. A validated survey tool was used to gather perceptions of both deliveries. Most participants agreed that both VLR deliveries were interesting and engaging and provided an immersive experience. Anatomy students perceived the stereoscopic delivery to be significantly more useful for understanding (P = 0.013), while anatomy tutors perceived the desktop delivery as more useful. A degree of physical discomfort and disorientation was reported by some participants for both deliveries, although to a greater extent for the stereoscopic delivery. The stereoscopic delivery was also found to be more mentally taxing than desktop delivery. These results suggest that desktop VLR delivery may minimize the risk of discomfort and disorientation associated with more immersive modalities while still providing a valuable learning experience.

Desktop VR Is Better Than Non-ambulatory HMD VR for Spatial Learning

Use of virtual reality (VR) technology is proliferating for designing and upgrading entertainment devices, and creating virtual environments that could be used for research and training. VR is becoming a strong research tool by providing a tighter control on the experimental environment and by allowing almost limitless possibilities of creating ecologically valid stimuli. However, the enhanced fidelity between the real and virtual worlds that VR provides does not always benefit human performance. For a better understanding, and increasing VR's usability, we need to identify the relevant constituent components of immersive technologies, and differentiate their roles, for example, how visual and interaction fidelity differentially improves human performance. We conducted an experiment to examine how two common VR display modes, head mounted display (HMD) and desktop (DT), would affect spatial learning when we restrict ambulatory locomotion in HMD. This manipulation allowed examining the role of varying visual fidelity with low interaction fidelity. We used a between-group design with 40 naïve participants. They explored a virtual environment and later drew its sketch-map. Our results showed participants spent more time and perceived less motion-sickness and task effort using desktop than HMD VR. With reduced interaction fidelity, the high visual fidelity of HMD as compared to desktop resulted in similar or poorer performance on different spatial learning tasks after accounting for motion-sickness and workload effort. Participants were better in recalling spatial components related to junction and cyclic order of the navigated virtual space in desktop vs. HMD VR, and performed equally well on components related to street segments and object associations. We explain these results in terms of deficient idiothetic information in non-ambulatory HMD and lesser sensory conflicts in desktop mode. Overall, our results highlight the differential effect of visual vs. interaction fidelity on human performance based on using immersive technologies, how such an effect depends on the nature of cognitive and functional behavior users employ, and the higher usability of traditional desktop VR. These results are relevant for developing customized and sustainable virtual reality based human-computer interactions.

Allergens on desktop surfaces in preschools and elementary schools of urban children with asthma

Desktop dust has been studied as a source of food allergen, but not as a source of potential aeroallergen exposure. Thirty-six wiped samples from desktop surfaces were collected from preschools and schools. Samples were analyzed for detectable levels of common aeroallergens including Alternaria, cockroach, dog, dust mite, cat, mouse, and rat allergens by immunoassay. Mouse allergen was the most prevalent, detectable in 97.2% of samples. Cat allergen was detectable in 80.6% of samples, and dog allergen was detectable in 77.8% of samples. Other allergens were not as prevalent. Mouse was the only allergen that was highly correlated with settled floor dust collected from the same rooms (r = 0.721, P < 0.001). This is the first study to detect aeroallergens on desktop surfaces by using moist wipes. Allergens for mouse, cat, and dog were highly detectable in wipes with mouse desktop surface levels correlating with levels in vacuumed floor dust.