Experimental Data Curation at Large Instrument Facilities with Open Source Software

The National Synchrotron Light Source II operating at Brookhaven National Laboratory since 2014 for the US Department of Energy is one of the newest and brightest storage-ring synchrotron facility in the world.  NSLS-II, like other facilities, provides pre-processing of the raw data and some analysis capabilities to its users. We describe the research collaborations and open source infrastructure  developed at large instrument facilities such as NSLS-II for the purpose of curating high value scientific data along the early stages of the data lifecycle.  Data acquisition and curation tasks include storing experiment configuration, detector metadata, raw data acquisition with infrastructure that converts proprietary instrument formats to industry standards.  In addition, we describe a specific effort for discovering sample information at NSLS-II and tracing the provenance of analysis performed on acquired images.  We show that curation tasks must be embedded into software along the data life cycle for effectiveness and ease of use, and that loosely defined collaborations evolve around shared open source tools.  Finally we discuss best practices for experimental metadata capture in such facilities, data access and the new challenges of scale and complexity posed by AI-based discovery for the synthesis of new materials

Experimental Data Curation at Large Instrument Facilities with Open Source Software

The National Synchrotron Light Source II operating at Brookhaven National Laboratory since 2014 for the US Department of Energy is one of the newest and brightest storage-ring synchrotron facility in the world.  NSLS-II, like other facilities, provides pre-processing of the raw data and some analysis capabilities to its users. We describe the research collaborations and open source infrastructure  developed at large instrument facilities such as NSLS-II for the purpose of curating high value scientific data along the early stages of the data lifecycle.  Data acquisition and curation tasks include storing experiment configuration, detector metadata, raw data acquisition with infrastructure that converts proprietary instrument formats to industry standards.  In addition, we describe a specific effort for discovering sample information at NSLS-II and tracing the provenance of analysis performed on acquired images.  We show that curation tasks must be embedded into software along the data life cycle for effectiveness and ease of use, and that loosely defined collaborations evolve around shared open source tools.  Finally we discuss best practices for experimental metadata capture in such facilities, data access and the new challenges of scale and complexity posed by AI-based discovery for the synthesis of new materials

Report of the QCD Tools Working Group

We report on the activities of the ``QCD Tools for heavy flavors and new physics searches'' working group of the Run II Workshop on QCD and Weak Bosons. The contributions cover the topics of improved parton showering and comparisons of Monte Carlo programs and resummation calculations, recent developments in Pythia, the methodology of measuring backgrounds to new physics searches, variable flavor number schemes for heavy quark electro-production, the underlying event in hard scattering processes, and the Monte Carlo MCFM for NLO processes.Comment: LaTeX, 47 pages, 41 figures, 10 tables, uses run2col.sty, to appear in the Proceedings of the Workshop on "QCD and Weak Boson Physics in Run II", Fermilab, March - November 199

Incomplete Polyp Resection During Colonoscopy—Results of the Complete Adenoma Resection (CARE) Study

Although the adenoma detection rate is used as a measure of colonoscopy quality, there are limited data on the quality of endoscopic resection of detected adenomas. We determined the rate of incompletely resected neoplastic polyps in clinical practice.We performed a prospective study on 1427 patients who underwent colonoscopy at 2 medical centers and had at least 1 nonpedunculated polyp (5-20 mm). After polyp removal was considered complete macroscopically, biopsies were obtained from the resection margin. The main outcome was the percentage of incompletely resected neoplastic polyps (incomplete resection rate [IRR]) determined by the presence of neoplastic tissue in post-polypectomy biopsies. Associations between IRR and polyp size, morphology, histology, and endoscopist were assessed by regression analysis. Of 346 neoplastic polyps (269 patients; 84.0% men; mean age, 63.4 years) removed by 11 gastroenterologists, 10.1% were incompletely resected. IRR increased with polyp size and was significantly higher for large (10-20 mm) than small (5-9 mm) neoplastic polyps (17.3% vs 6.8%; relative risk = 2.1), and for sessile serrated adenomas/polyps than for conventional adenomas (31.0% vs 7.2%; relative risk = 3.7). The IRR for endoscopists with at least 20 polypectomies ranged from 6.5% to 22.7%; there was a 3.4-fold difference between the highest and lowest IRR after adjusting for size and sessile serrated histology. Neoplastic polyps are often incompletely resected, and the rate of incomplete resection varies broadly among endoscopists. Incomplete resection might contribute to the development of colon cancers after colonoscopy (interval cancers). Efforts are needed to ensure complete resection, especially of larger lesions

Lymphocyte Cc Chemokine Receptor 9 and Epithelial Thymus-Expressed Chemokine (Teck) Expression Distinguish the Small Intestinal Immune Compartment: Epithelial Expression of Tissue-Specific Chemokines as an Organizing Principle in Regional Immunity

The immune system has evolved specialized cellular and molecular mechanisms for targeting and regulating immune responses at epithelial surfaces. Here we show that small intestinal intraepithelial lymphocytes and lamina propria lymphocytes migrate to thymus-expressed chemokine (TECK). This attraction is mediated by CC chemokine receptor (CCR)9, a chemoattractant receptor expressed at high levels by essentially all CD4+ and CD8+ T lymphocytes in the small intestine. Only a small subset of lymphocytes in the colon are CCR9+, and lymphocytes from other tissues including tonsils, lung, inflamed liver, normal or inflamed skin, inflamed synovium and synovial fluid, breast milk, and seminal fluid are universally CCR9−. TECK expression is also restricted to the small intestine: immunohistochemistry reveals that intense anti-TECK reactivity characterizes crypt epithelium in the jejunum and ileum, but not in other epithelia of the digestive tract (including stomach and colon), skin, lung, or salivary gland. These results imply a restricted role for lymphocyte CCR9 and its ligand TECK in the small intestine, and provide the first evidence for distinctive mechanisms of lymphocyte recruitment that may permit functional specialization of immune responses in different segments of the gastrointestinal tract. Selective expression of chemokines by differentiated epithelium may represent an important mechanism for targeting and specialization of immune responses

Caveolin-2 associates with intracellular chlamydial inclusions independently of caveolin-1

BACKGROUND: Lipid raft domains form in plasma membranes of eukaryotic cells by the tight packing of glycosphingolipids and cholesterol. Caveolae are invaginated structures that form in lipid raft domains when the protein caveolin-1 is expressed. The Chlamydiaceae are obligate intracellular bacterial pathogens that replicate entirely within inclusions that develop from the phagocytic vacuoles in which they enter. We recently found that host cell caveolin-1 is associated with the intracellular vacuoles and inclusions of some chlamydial strains and species, and that entry of those strains depends on intact lipid raft domains. Caveolin-2 is another member of the caveolin family of proteins that is present in caveolae, but of unknown function. METHODS: We utilized a caveolin-1 negative/caveolin-2 positive FRT cell line and laser confocal immunofluorescence techniques to visualize the colocalization of caveolin-2 with the chlamydial inclusions. RESULTS: We show here that in infected HeLa cells, caveolin-2, as well as caveolin-1, colocalizes with inclusions of C. pneumoniae (Cp), C. caviae (GPIC), and C. trachomatis serovars E, F and K. In addition, caveolin-2 also associates with C. trachomatis serovars A, B and C, although caveolin-1 did not colocalize with these organisms. Moreover, caveolin-2 appears to be specifically, or indirectly, associated with the pathogens at the inclusion membranes. Using caveolin-1 deficient FRT cells, we show that although caveolin-2 normally is not transported out of the Golgi in the absence of caveolin-1, it nevertheless colocalizes with chlamydial inclusions in these cells. However, our results also show that caveolin-2 did not colocalize with UV-irradiated Chlamydia in FRT cells, suggesting that in these caveolin-1 negative cells, pathogen viability and very likely pathogen gene expression are necessary for the acquisition of caveolin-2 from the Golgi. CONCLUSION: Caveolin-2 associates with the chlamydial inclusion independently of caveolin-1. The function of caveolin-2, either in the uninfected cell or in the chlamydial developmental cycle, remains to be elucidated. Nevertheless, this second caveolin protein can now be added to the small number of host proteins that are associated with the inclusions of this obligate intracellular pathogen

What is missing in autonomous discovery: Open challenges for the community

Self-driving labs (SDLs) leverage combinations of artificial intelligence, automation, and advanced computing to accelerate scientific discovery. The promise of this field has given rise to a rich community of passionate scientists, engineers, and social scientists, as evidenced by the development of the Acceleration Consortium and recent Accelerate Conference. Despite its strengths, this rapidly developing field presents numerous opportunities for growth, challenges to overcome, and potential risks of which to remain aware. This community perspective builds on a discourse instantiated during the first Accelerate Conference, and looks to the future of self-driving labs with a tempered optimism. Incorporating input from academia, government, and industry, we briefly describe the current status of self-driving labs, then turn our attention to barriers, opportunities, and a vision for what is possible. Our field is delivering solutions in technology and infrastructure, artificial intelligence and knowledge generation, and education and workforce development. In the spirit of community, we intend for this work to foster discussion and drive best practices as our field grows