Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Nucleic Acids Res 2018 Jan 4; 46(D1):D221-D228

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

No Pie in the (Digital) Sky: Co-Imagining the Food Metaverse

Human behaviour and habits co-evolve with technology, and the metaverse is poised to become a key player in reshaping how we live our everyday life. Given the importance of food in our daily lives, we ask: how will our relationships with food be transformed by the metaverse, and what are the promises and pitfalls of this technology? To answer this, we propose a co-design study that reveals the important elements people value in their daily interactions with food. We then present a speculative catalogue of novel metaverse food experiences, and insights from discussing these ideas with food designers, anthropologists and metaverse experts. Our work aims to provide designers with inspirations for building a metaverse that: provides inclusive opportunities for the future of food; helps re-discover the forgotten or lost knowledge about food; facilitates the exploration, excitement and joy of eating; and reinvigorates the ways that food can soothe and heal

Variation in Detrital Resource Stoichiometry Signals Differential Carbon to Nutrient Limitation for Stream Consumers Across Biomes

Stoichiometric ratios of resources and consumers have been used to predict nutrient limitation across diverse terrestrial and aquatic ecosystems. In forested headwater streams, coarse and fine benthic organic matter (CBOM, FBOM) are primary basal resources for the food web, and the distribution and quality of these organic matter resources may therefore influence patterns of secondary production and nutrient cycling within stream networks or among biomes. We measured carbon (C), nitrogen (N), and phosphorus (P) content of CBOM and FBOM and calculated their stoichiometric ratios (C/N, C/P, N/P) from first- to fourth-order streams from tropical montane, temperate deciduous, and boreal forests, and tallgrass prairie, to compare the magnitude and variability of these resource types among biomes. We then used the ratios to predict nutritional limitations for consumers of each resource type. Across biomes, CBOM had consistently higher %C and %N, and higher and more variable C/N and C/P than FBOM, suggesting that microbial processing results in more tightly constrained elemental composition in FBOM than in CBOM. Biome-specific differences were observed in %P and N/P between the two resource pools; CBOM was lower in %P but higher in N/P than FBOM in the tropical montane and temperate deciduous forest biomes, while CBOM was higher in %P but similar in N/P than FBOM in the grassland and boreal forest biomes. Stable C-13 isotopes suggest that FBOM likely derives from CBOM in tropical and temperate deciduous forest, but that additional non-detrital components may contribute to FBOM in boreal forests and grasslands. Comparisons of stoichiometric ratios of CBOM and FBOM to estimated needs of aquatic detritivores suggest that shredders feeding on CBOM are more likely to experience nutrient (N and/or P) than C limitation, whereas collector-gatherers consuming FBOM are more likely to experience C than N and/or P limitation. Our results suggest that differences in basal resource elemental content and stoichiometric ratios have the potential to affect consumer production and ecosystem rates of C, N, and P cycling in relatively consistent ways across diverse biomes

Disconnecting Mitochondrial Content from Respiratory Chain Capacity in PGC-1-Deficient Skeletal Muscle

The transcriptional coactivators PGC-1α and PGC-1β are widely thought to be required for mitochondrial biogenesis and fiber typing in skeletal muscle. Here, we show that mice lacking both PGC-1s in myocytes do indeed have profoundly deficient mitochondrial respiration but, surprisingly, have preserved mitochondrial content, isolated muscle contraction capacity, fiber-type composition, in-cage ambulation, and voluntary running capacity. Most of these findings are recapitulated in cell culture and, thus, are cell autonomous. Functional electron microscopy reveals normal cristae density with decreased cytochrome oxidase activity. These data lead to the following surprising conclusions: (1) PGC-1s are in fact dispensable for baseline muscle function, mitochondrial content, and fiber typing, (2) endurance fatigue at low workloads is not limited by muscle mitochondrial capacity, and (3) mitochondrial content and cristae density can be dissociated from respiratory capacity

firedrakeproject/tsfc: The Two Stage Form Compiler

<p>This release is specifically created to document the version of tsfc used in a particular set of experiments using Firedrake. Please do not cite this as a general source for Firedrake or any of its dependencies. Instead, refer to https://www.firedrakeproject.org/citing.html</p&gt

AxFoundation/strax: v1.5.4

What's Changed Split compare_metadata into utils.compare_meta by @dachengx in https://github.com/AxFoundation/strax/pull/754 Change endtime - time >= 0 to endtime >= time by @JYangQi00 in https://github.com/AxFoundation/strax/pull/756 Mandatorily wrap _read_chunk in a check_chunk_n decorator by @dachengx in https://github.com/AxFoundation/strax/pull/758 New Contributors @JYangQi00 made their first contribution in https://github.com/AxFoundation/strax/pull/756 Full Changelog: https://github.com/AxFoundation/strax/compare/v1.5.3...v1.5.