5,428 research outputs found
High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs
Ptychography is an emerging imaging technique that is able to provide
wavelength-limited spatial resolution from specimen with extended lateral
dimensions. As a scanning microscopy method, a typical two-dimensional image
requires a number of data frames. As a diffraction-based imaging technique, the
real-space image has to be recovered through iterative reconstruction
algorithms. Due to these two inherent aspects, a ptychographic reconstruction
is generally a computation-intensive and time-consuming process, which limits
the throughput of this method. We report an accelerated version of the
multi-mode difference map algorithm for ptychography reconstruction using
multiple distributed GPUs. This approach leverages available scientific
computing packages in Python, including mpi4py and PyCUDA, with the core
computation functions implemented in CUDA C. We find that interestingly even
with MPI collective communications, the weak scaling in the number of GPU nodes
can still remain nearly constant. Most importantly, for realistic diffraction
measurements, we observe a speedup ranging from a factor of to
depending on the data size, which reduces the reconstruction time remarkably
from hours to typically about 1 minute and is thus critical for real-time data
processing and visualization.Comment: work presented in NYSDS 201
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
Self-driving Multimodal Studies at User Facilities
Multimodal characterization is commonly required for understanding materials.
User facilities possess the infrastructure to perform these measurements,
albeit in serial over days to months. In this paper, we describe a unified
multimodal measurement of a single sample library at distant instruments,
driven by a concert of distributed agents that use analysis from each modality
to inform the direction of the other in real time. Powered by the Bluesky
project at the National Synchrotron Light Source II, this experiment is a
world's first for beamline science, and provides a blueprint for future
approaches to multimodal and multifidelity experiments at user facilities.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS
2022). AI4Mat Worksho
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
Meaning behind measurement : self-comparisons affect responses to health related quality of life questionnaires
Purpose The subjective nature of quality of life is particularly pertinent to the domain of health-related quality of
life (HRQOL) research. The extent to which participants’ responses are affected by subjective information and personal reference frames is unknown. This study investigated how an elderly population living with a chronic metabolic bone disorder evaluated self-reported quality of life. Methods Participants (n = 1,331) in a multi-centre randomised controlled trial for the treatment of Paget’s disease completed annual HRQOL questionnaires, including the SF-36, EQ-5D and HAQ. Supplementary questions were added to reveal implicit reference frames used when making HRQOL evaluations. Twenty-one participants (11 male, 10 female, aged 59–91 years) were interviewed retrospectively about their responses to the supplementary questions, using cognitive interviewing techniques and semi-structured topic guides. Results The interviews revealed that participants used complex and interconnected reference frames to promote response shift when making quality of life evaluations. The choice of reference frame often reflected external factors unrelated to individual health. Many participants also stated that they were unclear whether to report general or disease-related HRQOL. Conclusions It is important, especially in clinical trials, to provide instructions clarifying whether ‘quality of life’ refers to disease-related HRQOL. Information on selfcomparison reference frames is necessary for the interpretation of responses to questions about HRQOL.The Chief Scientist Office of the Scottish Government Health Directorates,
The PRISM funding bodies (the Arthritis Research Campaign, the National Association for the Relief of Paget’s disease and the Alliance for Better Bone Health)Peer reviewedAuthor final versio
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
Chemoprevention in BRCA1 mutation carriers (CIBRAC): protocol for an open allocation crossover feasibility trial assessing mechanisms of chemoprevention with goserelin and anastrozole versus tamoxifen and acceptability of treatment
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