SVSBI: Sequence-based virtual screening of biomolecular interactions

Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not available in general but can be obtained from molecular docking. However, current docking accuracy is relatively low, rendering unreliable VS models. We introduce sequence-based virtual screening (SVS) as a new generation of VS models for modeling biomolecular interactions. The SVS model utilizes advanced natural language processing (NLP) algorithms and optimizes deep $K$-embedding strategies to encode biomolecular interactions without invoking 3D structure-based docking. We demonstrate the state-of-art performance of SVS for four regression datasets involving protein-ligand binding, protein-protein, protein-nucleic acid binding, and ligand inhibition of protein-protein interactions and five classification datasets for the protein-protein interactions in five biological species. SVS has the potential to dramatically change the current practice in drug discovery and protein engineering

Sweet Liking Status and PROP Taster Status impact emotional response to sweetened beverage

© 2019 Elsevier Ltd Humans are innately predisposed to enjoy sweetness. However, excessive sugar consumption has been linked to a range of health issues. In order to develop an effective strategy to provide customised products and promote healthy eating, it is important to understand individual variation in sweetness preference. This study investigated how both Sweet Liking Status and PROP Taster Status impact on liking and emotional response to an ice tea product varying in sweetness intensity. One hundred and seventy five consumers were invited to rate liking and sweetness intensity of 5 sucrose solutions and emotional response, liking and sweetness intensity of ice tea samples varying in sweetness concentration (Low, Medium and High), and with sugar type (Sucrose and Sweetener). Cluster analysis followed by validation test within each cluster group has identified 34% High Sweet Likers (HSL), 16% Medium Sweet Likers (MSL), 35% Low Sweet Likers (LSL) and 15% Unclassified group (UN). LSL had an overall heightened sweetness sensitivity than HSL for the sucrose solutions. For ice tea samples, no significant differences on liking and emotional response were observed between the two types of sugar, indicating consumers have a high acceptability when using sweetener as a sugar substitute in beverages. Overall, liking and positive emotions were rated more intensely for the Medium sweetened ice tea, whereas the opposite was found for the Low sweetened ice tea. A significant Sweet Liking Status*Concentration interaction was observed, where for High sweetened ice tea, LSL significantly disliked the sample and associated with lower positive and higher negative emotions, but an opposite trend was observed for HSL. For ideal sweetness, LSL indicated a significant lower ideal sweetness level in ice tea than HSL. Unlike Sweet Liking Status, an overall PROP Taster Status effect on both liking and emotional response was observed, but the effect was found to be independent of sweetness levels. A relative effect of Sweet Liking Status and PROP Taster Status on emotional response was also observed, where the effect of Sweet Liking Status was more pronounced in both pST and pNT group

Measuring consumer emotional response and acceptance to sustainable food products

© 2020 Elsevier Ltd With current global challenges such as population growth, climate change and water scarcity, it is critical to develop sustainable strategies to achieve food security. One way to tackle this is by developing new products that use alternative and more sustainable ingredients. Bambara groundnut is a low-impact African legume as it can be grown on marginal soils and is resistant to high temperatures. The aim of this study was to investigate UK consumer acceptability and emotional response to snack products containing Bambara groundnut flour as an alternative sustainable ingredient. A key objective was to understand the contribution that measuring emotional response would reveal. Additionally the impact of extrinsic information on consumer acceptability and emotional response to snack products was investigated by sharing information concerning Bambara groundnut's sustainability and nutritional credentials. 100 UK participants were recruited to evaluate two biscotti and two cracker products. For each category a standard product made from standard ingredients sourced commercially, and one made replacing some of standard flour with Bambara flour were obtained. For each sample, participants were asked to rate their overall liking and emotional response based on sensory properties of the product (the blind condition). Participants were invited back for a second session, where they were informed about global resource challenges, and the sustainable features and nutritional value of Bambara, and which products contained this as an ingredient (informed condition). Under the blind condition, no significant differences in overall liking were observed between standard and Bambara products, indicating UK consumers accept the sensory properties of products that contain Bambara flour. Interestingly, the extrinsic information shifted consumer emotional response towards more positive emotions and less negative emotions when consuming products containing Bambara flour. It also made them felt less guilty when consuming the Bambara products, suggesting consumers engage with the idea of sustainable ingredients, and that this sustainable ingredient has potential for future new product development. It also highlighted the value of measuring emotional response for novel products to understand what may drive purchase behaviour when products are matched for liking. Food neophobia status did not impact product acceptability and emotional response between Bambara and standard products, however overall a lower emotional response was found for medium neophobic consumers in general who are more likely to evade novel products

CoderEval: A Benchmark of Pragmatic Code Generation with Generative Pre-trained Models

Code generation models based on the pre-training and fine-tuning paradigm have been increasingly attempted by both academia and industry, resulting in well-known industrial models such as Codex, CodeGen, and PanGu-Coder. To evaluate the effectiveness of these models, multiple existing benchmarks are proposed, including only cases of generating a standalone function, i.e., a function that may invoke or access only built-in functions and standard libraries. However, non-standalone functions, which typically are not included in the existing benchmarks, constitute more than 70% of the functions in popular open-source projects, and evaluating models' effectiveness on standalone functions cannot reflect these models' effectiveness on pragmatic code generation scenarios. To help bridge the preceding gap, in this paper, we propose a benchmark named CoderEval, consisting of 230 Python and 230 Java code generation tasks carefully curated from popular real-world open-source projects and a self-contained execution platform to automatically assess the functional correctness of generated code. CoderEval supports code generation tasks from six levels of context dependency, where context refers to code elements such as types, APIs, variables, and consts defined outside the function under generation but within the dependent third-party libraries, current class, file, or project. CoderEval can be used to evaluate the effectiveness of models in generating code beyond only standalone functions. By evaluating three code generation models on CoderEval, we find that the effectiveness of these models in generating standalone functions is substantially higher than that in generating non-standalone functions. Our analysis highlights the current progress and pinpoints future directions to further improve a model's effectiveness by leveraging contextual information for pragmatic code generation

Mutation and Lineage Analysis of DNMT3A in BCR-ABL1-negative Chronic Myeloproliferative Neoplasms

SummaryIn addition to the JAK2 V617F mutation, somatic mutation in DNMT3A has been described in BCL-ABL1-negative myeloproliferative neoplasms (MPNs). We have screened for DNMT3A exon 23 mutations in 130 adult Taiwanese patients with chronic phase myeloproliferative neoplasms. Only one somatic DNMT3A R882H mutation was identified in one JAK2 V617F mutation-positive essential thrombocythemia patient (1/91, 1%). Both mutations were detected in the CD34+-, CD19+-, peripheral blood mononuclear cell- and granulocyte-enriched fractions, but were not detected in the CD3+-enriched fraction by lineage analysis. Our findings suggest that DNMT3A mutation is not prevalent in MPNs, and further study is needed to clarify its role in the molecular pathogenesis of myeloproliferative neoplasms

Learning to recommend descriptive tags for questions in social forums

10.1145/2559157ACM Transactions on Information Systems321-ATIS

Relative effects of sensory modalities and importance of fatty acid sensitivity on fat perception in a real food model

Fat can be perceived through mouthfeel, odour and taste, but the influence of these modalities on fat perception remains undefined. Fatty acids are stimuli. Individual’s sensitivity to fatty acids varies. Studies show association between fatty acid sensitivity, dietary intake and BMI, but results are conflicting. Therefore, this study examined this association, and the effects of modalities on fat perception. Two sub-studies conducted. In Study 1 (n=46), fat intensity was assessed by milk/cream mixtures varying by five fat levels. Fat intensity was rated under four conditions: mouthfeel-odour masked, mouthfeel masked, odour masking and no masking. Mouthfeel masking was achieved using thickener and paraffin, odour masking using nose-clips. Fatty acid sensitivity was measured by 3-AFC-staircase method using milk containing oleic acid (0.31-31.4mM). In Study 2 (n=51), more fat levels were added in fat intensity rating. A 2-AFC discrimination test was used to confirm whether fat levels could be distinguished. In the sensitivity test, a wider range of oleic acid was included. Fat intensity was rated higher without nose-clips (p<0.0001), implying that odour increased fat perception. Samples with mouthfeel-masked were rated higher, showing that increased viscosity and lubricity enhanced fat perception (p<0.0001). Participants could distinguish fat levels based on “taste” in rating tests and 2-AFC-tests. Participants were divided into high/medium/low-sensitivity groups. No significant difference found in fat intensity between groups, however, high-sensitivity group discriminated more fat levels. No association between sensitivity groups, nutrient intake or BMI found

The effect of genotypical and phenotypical variation in taste sensitivity on liking of ice cream and dietary fat intake

Emerging evidence suggests fat can be perceived as a taste. G-protein coupled receptors as well as CD36, a fatty acid translocase, have been proposed to be involved in fat perception. Therefore, differences in number of receptors and genotype of CD36 have both been proposed to influence inter-individual fat taste perception. Fungiform papillae density (FPD) and PROP taster status are phenotypes related to receptor number. Previous authors have proposed an association between such phenotypes and CA6 (gustin) genotype, because the latter influences receptor cell proliferation. The effect of these factors on fat perception, preference and intake, requires further investigation. Therefore, the main aim of this study was to investigate the effects of taste sensitivity, including both genotypic and phenotypic variation, on liking of ice cream and dietary fat intake. Participants (n=136) age 18-55 years were recruited in the UK. Hedonic liking results demonstrated that liking for ice cream was significantly affected by the fat content of the sample, and by demographic factors (gender, ethnicity, age) but not by the consumers CD36 rs1761667 or CA6 rs2274333 genotype, PROP taster status nor FPD. However, categorising taste sensitivity from participant responses to salt taste alone (rather than to salt and PROP) found significant differences, with low salt perceivers liking the high fat (20%) ice cream substantially more than medium- and high salt perceivers. This indicated that increased taste sensitivity reduced liking of high fat. Cluster analysis highlighted that one group of consumers (18%) liked higher fat ice cream, whereas another (30%) liked lower fat ice cream compared to the 52% of consumers that liked ice cream regardless of fat content. There was a significant association between these groups and salt taste sensitivity. Concerning recorded dietary intake, the high-fat liker group were found to have substantially higher dairy product consumption compared to high-fat dislikers. Fat intake as a percentage of total energy intake was significantly related to CA6 genotype, however the minor allele frequency at rs2274333 is too low to draw firm conclusions within this study population

Exploring the effects of genotypical and phenotypical variations in bitter taste sensitivity on perception, liking and intake of brassica vegetables in the UK

Brassicaceous vegetables (BV) have chemoprotective effects and yet consumption of BV in the UK is low. Previous studies suggest perception, liking and intake of BV are influenced by bitter taste sensitivity which this study further explores. Phenotypical taste sensitivity of 136 subjects was classified using propythiouracil (PROP) and sodium chloride and fungiform papillae density (FPD) was measured from tongue images. Polymorphisms of TAS2R38 and gustin (CA6) genes were analysed. Liking and bitterness of four raw vegetables (two BV (broccoli and white cabbage) and two non-BV (spinach and courgette)), as well as habitual consumption, were evaluated. There was a significant association between TAS2R38 genotype and PROP taster status (p<0.0001) and between FPD and PROP taster status (p=0.029). Individuals with greater sensitivity for PROP predominantly had TAS2R38 PAV/PAV genotype and greater FPD. BV were perceived as more bitter than non-BV (p<0.0001) with PAV/PAV subjects perceiving significantly stronger bitter intensity. There was a significant difference in liking for the four vegetables (p=0.002), and between consumers of different TAS2R38 genotype (p=0.0024). Individuals with TAS2R38 AVI/AVI genotype liked BV more. Regarding intake, both PAV/PAV and AVI/AVI individuals consumed more total vegetables and BV than PAV/AVI. Although PROP nontasters tended to consume more vegetables and BV than the other two phenotype groups, liking and vegetable intake were not significantly affected by taste phenotype. Although there was not a significant effect of CA6 genotype on bitterness ratings, there was a significant interaction between CA6 and TAS2R38, and in addition CA6 genotype was significantly associated with BV intake. However, these effects require validation as the proportions of the population with the CA6 G/G genotype was extremely small (7%). Our results confirmed that bitter taste perception in vegetables was influenced by both genotype and phenotype of bitter taste sensitivity. Moreover, our findings demonstrated that neither genotype nor phenotype of taste sensitivity alone accurately predict vegetable liking and intake as demographic factors were found to have a substantial influence

Consumer acceptability and sensory profile of cooked broccoli with mustard seeds added to improve chemoprotective properties

Broccoli, a rich source of glucosinolates, is a commonly consumed vegetable of the Brassica family. Hydrolysis products of glucosinolates, isothiocyanates, have been associated with health benefits and contribute to the flavour of Brassica. However, boiling broccoli causes the myrosinase enzyme needed for hydrolysis to denature. In order to ensure hydrolysis, broccoli must either be mildly cooked or active sources of myrosinase, such as mustard seed powder, can be added post-cooking. In this study, samples of broccoli were prepared in six different ways; standard boiling with and without mustard seeds, sous-vide cooking at low temperature (70 °C) and sous-vide cooking at higher temperature (100 ºC) without mustard and with mustard at two different concentrations. The majority of consumers disliked the mildly cooked broccoli samples (70 ºC, 12 min, sous-vide) which had a hard and stringy texture. The highest mean consumer liking was for standard boiled samples (100 ºC, 7 min). Addition of 1% mustard seed powder developed sensory attributes such as pungency, burning sensation, mustard odour and flavour. One cluster of consumers (32%) found mustard seeds to be a good complement to cooked broccoli, however, the majority disliked the mustard-derived sensory attributes. Where the mustard seeds were partially processed, doubling the addition to 2% led to only the same level of mustard flavour and pungency as 1% unprocessed seeds, and mean consumer liking remained unaltered. This suggests that optimisation of the addition level of partially processed mustard seeds may be a route to enhance bioactivity of cooked broccoli without compromising consumer acceptability