72 research outputs found
Chemical data evaluation: General considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report)
The International Union of Pure and Applied Chemistry has a long tradition of supporting the
compilation of chemical data and their evaluation through direct projects, nomenclature and terminology
work, and partnerships with international scientific bodies, government agencies, and other organizations.
The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data has been established to provide
guidance on issues related to the evaluation of chemical data. In this first report, we define the general
principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in
chemistryinfo:eu-repo/semantics/publishedVersio
Best practice guidelines for cetacean tagging
Animal-borne electronic instruments (tags) are valuable tools for collecting information on cetacean physiology, behaviour and ecology, and for enhancing conservation and management policies for cetacean populations. Tags allow researchers to track the movement patterns, habitat use andother aspects of the behaviour of animals that are otherwise difficult to observe. They can even be used to monitor the physiology of a tagged animal within its changing environment. Such tags are ideal for identifying and predicting responses to anthropogenic threats, thus facilitating the development of robust mitigation measures. With the increasing need for data best provided by tagging and the increasing availability of tags, such research is becoming more common. Tagging can, however, pose risks to the health and welfare of cetaceans and to personnel involved in tagging operations. Here we provide ‘best practice’ recommendations for cetacean tag design, deployment and follow-up assessment of tagged individuals, compiled by biologists and veterinarians with significant experience in cetacean tagging. This paper is intended to serve as a resource to assist tag users, veterinarians, ethics committees and regulatory agency staff in the implementation of high standards of practice, and to promote the training of specialists in this area. Standardised terminology for describing tag design and illustrations of tag types and attachment sites are provided, along with protocols for tag testing and deployment (both remote and through capture-release), including training of operators. The recommendations emphasise the importance of ensuring that tagging is ethically and scientifically justified for a particular project and that tagging only be used to address bona fide research or conservation questions that are best addressed with tagging, as supported by an exploration of alternative methods. Recommendations are provided for minimising effects on individual animals (e.g. through careful selection of the individual, tag design and implant sterilisation) and for improving knowledge of tagging effects on cetaceans through increased post-tagging monitoring.Publisher PDFPeer reviewe
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
Fluids and barriers of the CNS: a historical viewpoint
Tracing the exact origins of modern science can be a difficult but rewarding pursuit. It is possible for the astute reader to follow the background of any subject through the many important surviving texts from the classical and ancient world. While empirical investigations have been described by many since the time of Aristotle and scientific methods have been employed since the Middle Ages, the beginnings of modern science are generally accepted to have originated during the 'scientific revolution' of the 16th and 17th centuries in Europe. The scientific method is so fundamental to modern science that some philosophers consider earlier investigations as 'pre-science'. Notwithstanding this, the insight that can be gained from the study of the beginnings of a subject can prove important in the understanding of work more recently completed. As this journal undergoes an expansion in focus and nomenclature from cerebrospinal fluid (CSF) into all barriers of the central nervous system (CNS), this review traces the history of both the blood-CSF and blood-brain barriers from as early as it was possible to find references, to the time when modern concepts were established at the beginning of the 20th century
Global Spatial Risk Assessment of Sharks Under the Footprint of Fisheries
Effective ocean management and conservation of highly migratory species depends on resolving overlap between animal movements and distributions and fishing effort. Yet, this information is lacking at a global scale. Here we show, using a big-data approach combining satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively) and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of high-seas fishing effort. Results demonstrate an urgent need for conservation and management measures at high-seas shark hotspots and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real time, dynamic management
Recommended from our members
State of the California Current 2013-14: El Niño Looming
In 2013, the California current was dominated by
strong coastal upwelling and high productivity. Indices
of total cumulative upwelling for particular coastal
locations reached some of the highest values on record.
Chlorophyll a levels were high throughout spring and
summer. Catches of upwelling-related fish species were
also high. After a moderate drop in upwelling during fall
2013, the California current system underwent a major
change in phase. Three major basin-scale indicators, the
PDO, the NPGO, and the ENSO-MEI, all changed
phase at some point during the winter of 2013/14. The
PDO changed to positive values, indicative of warmer
waters in the North Pacific; the NPGO to negative values,
indicative of lower productivity along the coast; and
the MEI to positive values, indicative of an oncoming
El Niño. Whereas the majority of the California Current
system appears to have transitioned to an El Niño
state by August 2014, based on decreases in upwelling
and chlorophyll a concentration, and increases in SST,
there still remained pockets of moderate upwelling,
cold water, and high chlorophyll a biomass at various central
coast locations, unlike patterns seen during the
more major El Niños (e.g., the 97–98 event). Catches of
rockfish, market squid, euphausiids, and juvenile sanddab
remained high along the central coast, whereas catches
of sardine and anchovy were low throughout the CCS.
2014 appears to be heading towards a moderate El Niño
state, with some remaining patchy regions of upwelling-driven
productivity along the coast. Superimposed on
this pattern, three major regions have experienced possibly
non-El Niño-related warming since winter: the
Bering Sea, the Gulf of Alaska, and offshore of southern
California. It is unclear how this warming may interact
with the predicted El Niño, but the result will likely be
reduced growth or reproduction for many key fisheries
species
- …