Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases

Genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphism (SNP) sites associated with human diseases. In the annotation of human diseases, especially cancers, SNPs, as an important component of genetic factors, have gained increasing attention. Given that most of the SNPs are located in non-coding regions, the functional verification of these SNPs is a great challenge. The key to functional annotation for risk SNPs is to screen SNPs with regulatory activity from thousands of disease associated-SNPs. In this review, we systematically recapitulate the characteristics and functional roles of SNP sites, discuss three parallel reporter screening strategies in detail based on barcode tag classification, and recommend the common in silico strategies to help supplement the annotation of SNP sites with epigenetic activity analysis, prediction of target genes and trans-acting factors. We hope that this review will contribute to this exuberant research field by providing robust activity analysis strategies that can facilitate the translation of GWAS results into personalized diagnosis and prevention measures for human diseases.

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The major enzyme encoded by the glucosinolate biosynthetic gene AOP2 is involved in catalyzing the conversion of glucoiberin (GIB) into sinigrin (SIN) in Brassicaceae crops. The AOP2 proteins have previously been identified in several Brassicaceae species, but not in Tumorous stem mustard. As per this research, the five identified members of the AOP2 family from the whole genome of Brassica juncea named BjuAOP2.1-BjuAOP2.5 were found to be evenly distributed on five chromosomes. The subcellular localization results implied that BjuAOP2 proteins were mainly concentrated in the cytoplasm. Phylogenetic analysis of the AOP2 proteins from the sequenced Brassicaceae species in BRAD showed that BjuAOP2 genes were more closely linked to Brassica carinata and Brassica rapa than Arabidopsis. In comparison with other Brassicaceae plants, the BjuAOP2 members were conserved in terms of gene structures, protein sequences, and motifs. The light response and hormone response elements were included in the BjuAOP2 genes' cis-regulatory elements. The expression pattern of BjuAOP2 genes was influenced by the different stages of development and the type of tissue being examined. The BjuAOP2 proteins were used to perform the heterologous expression experiment. The results showed that all the five BjuAOP2 proteins can catalyze the conversion of GIB to SIN with different catalytic activity. These results provide the basis for further investigation of the functional study of BjuAOP2 in Tumorous stem mustard glucosinolate biosynthesis.

User Experience of the Co-design Research Approach in eHealth: Activity Analysis With the Course-of-Action Framework

Background

The cocreation of eHealth solutions with potential users, or co-design, can help make the solution more acceptable. However, the co-design research approach requires substantial investment, and projects are not always fruitful. Researchers have provided guidelines for the co-design approach, but these are either applicable only in specific situations or not supported by empirical data. Ways to optimize the experience of the co-design process from the point of view of the participants are also missing. Scientific literature in the co-design field generally provides an extrinsic description of the experience of participants in co-design projects.

Objective

We addressed this issue by describing a co-design project and focusing on the participants’ experiences looking at what was significant from their point of view.

Methods

We used a qualitative situated cognitive anthropology approach for this study. Data were collected on a co-design research project that aimed to support the help-seeking process of caregivers of functionally dependent older adults. The methodology was based on the perspective of experience by Dewey and used the course-of-action theoretical and methodological framework. Data collection was conducted in 2 phases: observation of participants and recording of sessions and participant self-confrontation interviews using the session recordings. We interviewed 27% (20/74) of the participants. We analyzed the data through nonexclusive emerging categorization of themes using the constant comparative method.

Results

In total, 5 emerging themes were identified. The perception of extrinsic constraints and the effects of the situation was central and the most important theme, affecting other themes (frustrating interactions with others, learning together, destabilization, and getting personal benefits). Co-occurrences between codes allowed for a visual and narrative understanding of what was significant for the participants during this project. The results highlighted the importance of the role of the research team in preparing and moderating the sessions. They also provided a detailed description of the interactions between participants during the sessions, which is a core aspect of the co-design approach. There were positive and negative aspects of the participants’ experiences during this co-design project. Reflecting on our results, we provided potential affordances to shape the experience of participants in co-design.

Conclusions

Potential users are an essential component of the co-design research approach. Researchers and designers should seek to offer these users a positive and contributory experience to encourage participation in further co-design initiatives. Future research should explore how the proposed affordances influence the success of the intervention.

[The challenges of the professionalization of IPAs in France]

Since the publication of the decree of July 18, 2018, the training of advanced practice nurses, at the master's level, has inevitably come to question the way in which this new profession of care is professionalized, which formalizes the right of nurses to prescribe in France. More precisely, the required alternation between theory and practice questions the construction of their clinical reasoning during their activity and raises discussions about the nursing knowledge to be taught.

[Analysis of Activity and Its Emissions Trend for Construction Equipment in China]

Emissions from non-road equipment are attracting more attention due to their increasing contribution to air pollution. Thus, an accurate estimate of emission inventory for non-road equipment is imperative for air quality management and improvement. Activity data from a large range of construction equipment were collected from multiple sources, including on-site/phone interviews and literature review, and used for further analysis to characterize its operations. Activity analysis of construction equipment included:①activity of construction equipment by type (functionality); ②activity differences by geographical area; and ③activity differences by age. A back-propagation neural network model was developed to estimate the construction equipment population in China from 2018 to 2025. Furthermore, real-world measurements of emissions were made on 47 selected examples of construction equipment using a portable emission measurement system. Population, activity, and emission factors were then combined to develop emission inventories for construction equipment in China from 2015 to 2025. The results showed that activity of construction equipment differs by type or functionality, ranging from 1439 to 4332 hours per year. Furthermore, there are differences in activity by as much as three times due to geographical area differences for the same construction equipment type. In general, activity of construction equipment decreases as it ages by a rate of approximately 140 to 150 hours per year. It is estimated that CO, HC, NO, and PM_2.5 emissions of construction equipment in China in 2015 were approximately 2.099, 0.462, 3.452, and 0.574 million tons, respectively. Compared to 2015, due to the slow growth of the construction equipment population, CO, HC, and PM_2.5 emissions will decrease by 2.4%-33.1% and 7.1%-64.7% by 2020 and 2025, respectively, depending on pollutant. It should be noted that NO emissions appear to increase slightly for the first several years in the future, but then decrease after 2020. As increasingly stringent regulations have been enforced for on-road vehicles, but less has been done regarding non-road equipment, although total emissions from non-road equipment continue to decrease, their contribution to air pollution will continue to increase; they should therefore be one of the focuses for future work.

Deformation Activity Analysis of a Ground Fissure Based on Instantaneous Total Energy

This study proposes a novel instantaneous total energy method to perform an activity analysis of ground fissures deformation, which is calculated by integrating the extreme-point symmetric mode decomposition (ESMD) method and kinetic energy based on the time-series displacement acquired by shape acceleration array (SAA) sensors. The proposed method is tested on the Xiwang Road fissure in Beijing, China. First, to fully monitor the hanging wall and footwall of the monitored ground fissure, a 4 m-long SAA in the vertical direction and an 8 m-long SAA in the horizontal direction were embedded in a ground fissure to obtain an accurate time-series displacement with an accuracy of ±1.5 mm/32 m and a displacement acquisition frequency of once an hour. Second, to improve the accuracy of the activity analysis, the ESMD method and Spearman's rho are applied to perform signal denoising of the original time-series displacement obtained by the SAA sensors. Finally, the instantaneous total energy is obtained to analyze the activity of the monitored ground fissure. The results demonstrate that the proposed method is more reliable to reflect the activity of a monitored ground fissure compared to the time-series displacement.

Validating a Commercial Device for Continuous Activity Measurement in the Older Adult Population for Dementia Management

With the introduction of the large number of fitness devices on the market, there are numerous possibilities for their use in managing chronic diseases in older adults. For example, monitoring people with dementia using commercially available devices that measure heart rate, breathing rate, lung volume, step count, and activity level could be used to predict episodic behavioral and psychological symptoms before they become distressing or disruptive. However, since these devices are designed primarily for fitness assessment, validation of the sensors in a controlled environment with the target cohort population is needed. In this study, we present validation results using a commercial fitness tracker, the Hexoskin sensor vest, with thirty-one participants aged 65 and older. Estimated physiological measures investigated in this study are heart rate, breathing rate, lung volume, step count, and activity level of the participants. Findings indicate that while the processed step count, heart rate, and breathing rate show strong correlations to the clinically accepted gold standard values, lung volume and activity level do not. This indicates the need to proceed cautiously when making clinical decisions using such sensors, and suggests that users should focus on the three strongly correlated parameters for further analysis, at least in the older population. The use of physiological measurement devices such as the Hexoskin may eventually become a non-intrusive way to continuously assess physiological measures in older adults with dementia who are at risk for distressing behavioral and psychological symptoms.

The management of diagnostic uncertainty and decision-making in genetics case conferences

In this paper we examine one type of intraprofessional collaborative activity, namely case conferences in a specialist genetics clinic. Our specific focus is on how clinical geneticists manage decision-making through team talk in the event of diagnostic uncertainty which is mainly attributable to limitations in the current state of genomic knowledge, 'uncertain significances' associated with genetic test results, and a lack of information/ evidence pertaining to cases under discussion. The case conference then becomes a means to minimise the uncertainty and arrive at decisions that optimise the significance of the results in terms of clients' life trajectories. Adopting theme-oriented activity analysis, we examine video-recorded data from five case conferences in Hong Kong. Beginning with a prototypical structural mapping of the case conference activity type, our analysis focuses on what we call 'uncertain cases'. Our findings highlight three discourse types constitutive of team talk: pedagogic talk, diagnostic talk and decisional talk. In paying particular attention to how uncertainty is formulated and negotiated, we suggest that access to and assessment of different kinds of evidence as well as the activity-specific expert role-positions of the participants are crucial with regard to establishing a correct diagnosis and/or striving towards a minimisation of current uncertainties.

Interpreting expressive performance through listener judgments of musical tension

This study examines listener judgments of musical tension for a recording of a Schubert song and its harmonic reduction. Continuous tension ratings collected in an experiment and quantitative descriptions of the piece's musical features, include dynamics, pitch height, harmony, onset frequency, and tempo, were analyzed from two different angles. In the first part of the analysis, the different processing timescales for disparate features contributing to tension were explored through the optimization of a predictive tension model. The results revealed the optimal time windows for harmony were considerably longer (~22 s) than for any other feature (~1–4 s). In the second part of the analysis, tension ratings for the individual verses of the song and its harmonic reduction were examined and compared. The results showed that although the average tension ratings between verses were very similar, differences in how and when participants reported tension changes highlighted performance decisions made in the interpretation of the score, ambiguity in tension implications of the music, and the potential importance of contrast between verses and phrases. Analysis of the tension ratings for the harmonic reduction also provided a new perspective for better understanding how complex musical features inform listener tension judgments.

Linguistic Summarization of Video for Fall Detection Using Voxel Person and Fuzzy Logic

In this paper, we present a method for recognizing human activity from linguistic summarizations of temporal fuzzy inference curves representing the states of a three-dimensional object called voxel person. A hierarchy of fuzzy logic is used, where the output from each level is summarized and fed into the next level. We present a two level model for fall detection. The first level infers the states of the person at each image. The second level operates on linguistic summarizations of voxel person's states and inference regarding activity is performed. The rules used for fall detection were designed under the supervision of nurses to ensure that they reflect the manner in which elders perform these activities. The proposed framework is extremely flexible. Rules can be modified, added, or removed, allowing for per-resident customization based on knowledge about their cognitive and physical ability.