Overview of the Irish brewing and distilling sector: processing inputs supply and quality requirements

For any brewing and distilling establishment, the supply and quality of processing inputs is a major determinant in its production output. Accessibility and availability of brewing and distilling inputs drives productivity and quality of products. The Irish brewing and distilling sector have shown increased sales and production output, with a growth rate of 4% between 2014 and 2019. The brewing industry in the republic of Ireland has seen a 22% increase in the number of micro-breweries since 2014, and its total output now stands at 8.3 m hectolitres. The distilling industry witnessed an increase from four to thirty-eight in the number of distilleries between 2010 and 2020 with a local and global sales at 2.4 and 20 million nine litre cases, respectively. As a result of the continued growth of the Irish brewing and distilling sector, demand for different processing inputs has increased proportionately. For a sustainable production process, there is need for a steady supply of the right quantity and quality of the major inputs for brewing and distilling. Sustainable growth of the sector requires establishment of a strong base of processing inputs availability and their effective utilisation to minimise environmental impacts. This review, therefore, looks at the current state of the major processing inputs for brewing and distilling in Ireland, as well as their general characteristics and requirements

Review of the Valorization Initiatives of Brewing and Distilling Byproducts

Beer and spirits are two of the most consumed alcoholic beverages in the world, and their production generates enormous amounts of by-product materials. This ranges from spent grain, spent yeast, spent kieselguhr, trub, carbon dioxide, pot ale, and distilled gin spent botanicals. The present circular economy dynamics and increased awareness on resource use for enhanced sustainable production practices have driven changes and innovations in the management practices and utilisation of these by-products. These include food product development, functional food applications, biotechnological applications, and bioactive compounds extraction. As a result, the brewing and distilling sector of the food and drinks industry is beginning to see a shift from conventional uses of byproducts such as animal feed to more innovative applications. This review paper therefore explored some of these valorization initiatives and the current state of the art

Development of FuGO: An ontology for functional genomics investigations

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

BACKGROUND: There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels. DESCRIPTION: SpliceMiner is a web interface for querying Evidence Viewer Database (EVDB). EVDB is a comprehensive, non-redundant compendium of splice variant data for human genes. We constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV). EVDB is based on data obtained from NCBI Entrez Gene and EV. The automated EVDB build process uses only complete coding sequences, which may or may not include partial or complete 5' and 3' UTRs, and filters redundant splice variants. Unlike EV, which supports only one-at-a-time queries, SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format. SpliceMiner maps probes to splice variants, effectively delineating the variants identified by a probe. CONCLUSION: EVDB can be queried by gene symbol, genomic coordinates, or probe sequence via a user-friendly web-based tool we call SpliceMiner (). The EVDB/SpliceMiner combination provides an interface with human splice variant information and, going beyond the very valuable NCBI Evidence Viewer, supports fluent, high-throughput analysis. Integration of EVDB information into microarray analysis and design pipelines has the potential to improve the analysis and bioinformatic interpretation of gene expression data, for both batch and interactive processing. For example, whenever a gene expression value is recognized as important or appears anomalous in a microarray experiment, the interactive mode of SpliceMiner can be used quickly and easily to check for possible splice variant issues

A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies

We conducted a morphological and mtDNA analysis of Cicindela decemnotata Say (Coleoptera: Carabidae: Cicindelinae) populations from throughout its geographic range to determine the extent of variation within the species and to assess the validity of subspecific names. The morphological study included an analysis of traditional subspecific characters including elytral color and maculations. These results provided evidence for the recognition of four subspecies of C. decemnotata, three of which are new: 1. C. d. decemnotata Say usually with green to dark green dorsal coloration and complete elytral maculations; it is widely distributed from Canada south to northern New Mexico and west into southern Utah and Idaho; 2. C. d. meriwetheri n. ssp. is distinguished by its bright green to green dorsal coloration, elytral maculation characterized by a thin middle band, a lack of humeral maculations, and a small number of genal setae; it has a restricted distribution from eastern Washington north to south central British Columbia; 3. C. d. bonnevillensis n. ssp. is distinguished by a combination of green to green-purple dorsal coloration and its greatly reduced elytral maculations; it is restricted to the area of ancient Lake Bonneville in north central Utah; 4. C. d. montevolans n. ssp. is distinguished by a predominately red-purple dorsal color and greatly reduced elytral maculations; its distribution is restricted to high elevations of the Bear River Mountains of northeastern Utah and southeastern Idaho. We also analyzed the mitochondrial haplotypes for cob and cox1 genes for one to six individuals from each of the six populations. This molecular analysis indicated recently diverged but discrete groups within C. decemnotata that are compatible with the subspecies distinctions postulated from morphology. These shallow molecular divergences within C. decemnotata are best explained by rapid phylogenetic radiation in the recent geological past in the wake of postglacial recession

Optimization of Ultrasound Assisted Extraction of Antioxidant Compounds from Marjoram (Origanum majorana L.) Using Response Surface Methodology

The present study optimized the ultrasound assisted extraction (UAE) conditions to maximize the antioxidant activity [Ferric ion Reducing Antioxidant Power (FRAP)], total phenol content (TP) and content of individual polyphenols of extracts from marjoram. Optimal conditions with regard to amplitude of sonication (24.4–61.0 μm) and extraction temperature (15–35 °C) and extraction time (5–15 min) were identified using response surface methodology (RSM). The results showed that the combined treatment conditions of 61 μm, 35 °C and 15 min were optimal for maximizing TP, FRAP, rosmarinic acid, luteolin-7-O-glucoside, apigenin-7-O-glucoside, caffeic acid, carnosic acid and carnosol values of the extracts. The predicted values from the developed quadratic polynomial equation were in close agreement with the actual experimental values with low average mean deviations (E%) ranging from 0.45% to 1.55%. The extraction yields of the optimal UAE were significantly (p \u3c 0.05) higher than solid/liquid extracts. Predicted models were highly significant (p \u3c 0.05) for all the parameters studied with high regression coefficients (R2) ranging from 0.58 to 0.98

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

<p>Abstract</p> <p>Background</p> <p>Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant.</p> <p>Results</p> <p>A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript.</p> <p>Conclusion</p> <p>SpliceCenter <url>http://discover.nci.nih.gov/splicecenter</url> provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists.</p

Are CT-derived muscle measurements prognostic, independent of systemic inflammation in good performance status patients with advanced cancer?

The present study examined the relationships between CT-derived muscle measurements, systemic inflammation, and survival in advanced cancer patients with good performance status (ECOG-PS 0/1). Data was collected prospectively from patients with advanced cancer undergoing anti-cancer therapy with palliative intent. The CT Sarcopenia score (CT-SS) was calculated by combining the CT-derived skeletal muscle index (SMI) and density (SMD). The systemic inflammatory status was determined using the modified Glasgow Prognostic Score (mGPS). The primary outcome of interest was overall survival (OS). Univariate and multivariate Cox regressions were used for survival analysis. Three hundred and seven patients met the inclusion criteria, out of which 62% (n = 109) were male and 47% (n = 144) were ≥65 years of age, while 38% (n = 118) were CT-SS ≥ 1 and 47% (n = 112) of patients with pre-study blood were inflamed (mGPS ≥ 1). The median survival from entry to the study was 11.1 months (1–68.1). On univariate analysis, cancer type (p &lt; 0.05) and mGPS (p &lt; 0.001) were significantly associated with OS. On multivariate analysis, only mGPS (p &lt; 0.001) remained significantly associated with OS. In patients who were ECOG-PS 0, mGPS was significantly associated with CT-SS (p &lt; 0.05). mGPS may dominate the prognostic value of CT-derived sarcopenia in good-performance-status patients with advanced cancer

The relationship between the BMI-adjusted weight loss grading system and quality of life in patients with incurable cancer

Weight loss (WL) has long been recognized as an important factor associated with reduced quality of life (QoL) and reduced survival in patients with cancer. The body mass index (BMI)-adjusted weight loss grading system (WLGS) has been shown to be associated with reduced survival. However, its impact on QoL has not been established. The aim of this study was to assess the relationship between this WLGS and QoL in patients with advanced cancer. A biobank analysis was undertaken of adult patients with advanced cancer. Data collected included patient demographics, Eastern Cooperative Oncology Group performance status, and anthropometric parameters (BMI and %WL). Patients were categorized according to the BMI-adjusted WLGS into one of five distinct WL grades (grades 0-4). QoL was collected using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-C30. The Kruskal-Wallis test and multivariate logistic regression analyses were used to assess the relationship between the WLGS and QoL scores. Overall survival was assessed using Kaplan-Meier curve and Cox proportional hazard models. A total of 1027 patients were assessed (51% male, median age: 66 years). Gastrointestinal cancer was most prevalent (40%), and 87% of patients had metastatic disease. Half (58%) of patients had a WL grade of 0-1, while 12%, 20%, and 10% had WL grades of 2, 3, and 4, respectively. Increasing WL grades were significantly associated with poorer QoL functioning and symptoms scales (all P &lt; 0.05). Physical, role, and emotional functioning decreased by a median of &gt;20 points between WL grade 0 and WL grade 4, while appetite loss, pain, dyspnoea, and fatigue increased by a median score &gt;20 points, indicative of a large clinical significant difference. Increasing WL grades were associated with deteriorating QoL summary score. WL grades 2, 3, and 4 were independently associated with a QoL summary score below the median (&lt;77.7) [odds ratio (OR) 1.69, P = 0.034; OR 2.06, P = 0.001; OR 4.29, P &lt; 0.001, respectively]. WL grades 3 and 4 were independently associated with reduced overall survival [hazard ratio 1.54 (95% confidence interval: 1.22-1.93), P &lt; 0.001 and hazard ratio 1.87 (95% confidence interval: 1.42-2.45), P &lt; 0.001, respectively]. Our findings support that the WLGS is useful in identifying patients at risk of poor QoL that deteriorates with increasing WL grades. WL grade 4 is independently associated with a particularly worse prognosis and increased symptom burden. Identification and early referral to palliative care services may benefit these patients