Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

5-HTTLPR Polymorphism Impacts Task-Evoked and Resting-State Activities of the Amygdala in Han Chinese

Background: Prior research has shown that the amygdala of carriers of the short allele (s) of the serotonin transporter (5-HTT) gene (5-HTTLPR) have a larger response to negative emotional stimuli and higher spontaneous activity during the resting state than non-carriers. However, recent studies have suggested that the effects of 5-HTTLPR may be specific to different ethnic groups. Few studies have been conducted to address this issue. Methodology/Principal Findings: Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) was conducted on thirty-eight healthy Han Chinese subjects (l/l group, n = 19; s/s group, n = 19) during the resting state and during an emotional processing task. Compared with the s/s group, the l/l group showed significantly increased regional homogeneity or local synchronization in the right amygdala during the resting state (|t|.2.028, p,0.05, corrected), but no significant difference was found in the bilateral amygdala in response to negative stimuli in the emotional processing task. Conclusions/Significance: 5-HTTLPR can alter the spontaneous activity of the amygdala in Han Chinese. However, the effect of 5-HTTLPR on the amygdala both in task state and resting state in Asian population was no similar with Caucasians. The

Adding value to under-utilised Irish fish roe: a physico-chemical and sensory comparison of cured Irish pollock (Pollachius pollachius) roe with commercial mullet (Mugil cephalus) and cod (Gadus morhua) products

peer reviewedIrish marine fish roe is generally discarded at sea or processed as low value-added fishmeal and not utilised as nutritious seafood ingredients. Locally sourced pollock roes were salted, air-dried (Mediterranean-style) and compared to similar commercial mullet and cod products for: weight; moisture content; pH; instrumental texture and colour; and sensory attributes. Raw pollock roes averaged 105 g (n = 25). Roes lost on average 3.1% moisture (w/w) after a 2-h salting period and 48.8% weight reduction was observed after an average 105 h air-drying time. The moisture content of pollock was not significantly different to commercial products. Average pH for pollock, mullet and cod products was 5.9, 5.4 and 5.7, respectively (P < 0.05). Pollock and mullet had similar hardness, but cod was significantly harder than both, when measured instrumentally. Total colour difference (ΔE*) between the surface of pollock and cod, and that of pollock and mullet was 7.5 and 3.0, respectively. Sensory assessment of sliced and powdered products, using 9-point hedonic and 5-point just-about-right (JAR) scales, was conducted with 38 consumers. Pollock received the highest scores for overall liking and intention to purchase compared to commercial mullet and cod products, averaging 5.6, 5.6 and 4.9, respectively, for sliced roe products, and 6.3, 5.3 and 6.1 for powdered products. Penalty analysis of JAR showed “overall liking” was impacted by the flavour being “too fishy”. In conclusion, pollock had similar characteristics and acceptable sensory attributes compared to commercial products presenting opportunities to expand the range of value-added roe products (e.g., trout, salmon) available, while also contributing to waste reduction

Patients', radiographers' and radiography students’ experiences of 360° virtual counselling environment for the coronary computed tomography angiography: A qualitative study

Abstract Introduction The aim of this study was to describe patients', radiographers' and radiography students’ experiences of the developed 360° virtual counselling environment (360°VCE) for the coronary computed tomography angiography (cCTA). Methods A descriptive qualitative approach was used. The participants were cCTA patients (n = 10), radiographers (n = 10) and radiography students (n = 10) who used the 360°VCE and visited or worked at a university hospital in Finland. The 360°VCE, resembling the authentic environments of a CT imaging unit, included digital counselling materials in text, image, animation and video formats. Data were gathered through thematic interviews individually to obtain an understanding of participants’ perspectives and analyzed by inductive content analysis. Results Five main categories and 15 categories were identified. Identified benefits of the 360°VCE for patients included improvements in knowledge, spatial and environmental orientation, and senses of security and self-efficacy, with reductions in fear and nervousness. Patients found the counselling materials engaging, and that the 360° technology conveniently provided reassuring familiarity with the environment before their visit. Identified benefits for radiographers and radiography students included improvements in patients' mental preparedness, knowledge, spatial and environmental orientation, and reductions in patients’ fear, which eased procedures and enhanced diagnostic success. The 360°VCE also provided useful information and familiarization with the cCTA unit for students during clinical practice and staff of referring units.  Conclusion It seems that patients', radiographers' and radiography students' experiences of 360°VCE respond to patients’ needs by improved knowledge and reduced fears. Thus, current counselling practices can be usefully complemented with spherical panoramic imaging technology and online information delivery. Implications for practice The results may be used to improve patient counselling and care, thereby optimizing the cCTA examination procedure and reducing fear. However, further research is needed to characterize experiences of the 360° VCE more comprehensively. Keywords Counselling, Patient, Computed tomography, Radiographer, Digital, Virtua

Effectiveness of digital counseling environments on anxiety, depression, and adherence to treatment among patients who are chronically ill:systematic review

Abstract Background: Patients who are chronically ill need novel patient counseling methods to support their self-care at different stages of the disease. At present, knowledge of how effective digital counseling is at managing patients’ anxiety, depression, and adherence to treatment seems to be fragmented, and the development of digital counseling will require a more comprehensive view of this subset of interventions. Objective: This study aims to identify and synthesize the best available evidence on the effectiveness of digital counseling environments at improving anxiety, depression, and adherence to treatment among patients who are chronically ill. Methods: Systematic searches of the EBSCO (CINAHL), PubMed, Scopus, and Web of Science databases were conducted in May 2019 and complemented in October 2020. The review considered studies that included adult patients aged ≥18 years with chronic diseases; interventions evaluating digital (mobile, web-based, and ubiquitous) counseling interventions; and anxiety, depression, and adherence to treatment, including clinical indicators related to adherence to treatment, as outcomes. Methodological quality was assessed using the standardized Joanna Briggs Institute critical appraisal tool for randomized controlled trials or quasi-experimental studies. As a meta-analysis could not be conducted because of considerable heterogeneity in the reported outcomes, narrative synthesis was used to synthesize the results. Results: Of the 2056 records screened, 20 (0.97%) randomized controlled trials, 4 (0.19%) pilot randomized controlled trials, and 2 (0.09%) quasi-experimental studies were included. Among the 26 included studies, 10 (38%) digital, web-based interventions yielded significantly positive effects on anxiety, depression, adherence to treatment, and the clinical indicators related to adherence to treatment, and another 18 (69%) studies reported positive, albeit statistically nonsignificant, changes among patients who were chronically ill. The results indicate that an effective digital counseling environment comprises high-quality educational materials that are enriched with multimedia elements and activities that engage the participant in self-care. Because of the methodological heterogeneity of the included studies, it is impossible to determine which type of digital intervention is the most effective for managing anxiety, depression, and adherence to treatment. Conclusions: This study provides compelling evidence that digital, web-based counseling environments for patients who are chronically ill are more effective than, or at least comparable to, standard counseling methods; this suggests that digital environments could complement standard counseling