Database computing in HEP. Progress report

The major SSC experiments are expected to produce up to 1 Petabyte of data per year each. Once the primary reconstruction is completed by farms of inexpensive processors. I/O becomes a major factor in further analysis of the data. We believe that the application of database techniques can significantly reduce the I/O performed in these analyses. We present examples of such I/O reductions in prototype based on relational and object-oriented databases of CDF data samples

Characterization of the phenolic ripening development of "BRS Vitoria" seedless table grapes using HPLC-DAD-ESI-MS/MS.

Determining the harvest date of table grapes is very important to achieve high-quality bunches with adequate soluble solids content, low titratable acidity, and high concentrations of polyphenols. Table grape consumption has increased worldwide due to its phenolic compound content and its beneficial effects on human health. Thus, this study aimed to characterize the phenolic ripening of ?BRS Vitoria? seedless table grapes at different ripening stages using HPLC?DAD?ESI-MS/MS. For this purpose, a trial was carried out during 2016 in a commercial vineyard of ?BRS Vitoria? seedless grape located in Marialva, state of Parana (Southern Brazil). Berry samples were assessed weekly, starting at v ́eraison until full ripeness. At each ripening stage, the berries were analyzed to determine their physicochemical characteristics and polyphenolic profile. It was observed that ?BRS Vitoria? grapes can be harvested approximately 28 days after v ́eraison, when the berries reach soluble solids content higher than 15◦Brix and low titratable acidity. The grapes presented a typical anthocyanin profile of hybrid grapes, composed of 3-glucoside and 3,5-diglucoside derivatives. In addition, pelargonidin traces were also observed, and this aglycone is rarely detected in grapes. The total anthocyanin concentration, as malvidin-3,5- diglucoside equivalents, is close to 596.9 mg k

Requirements for a system to analyze HEP events using database computing

We describe the requirements for the design and prototyping of an object-oriented database designed to analyze data in high energy physics. Our goal is to satisfy the data processing and analysis needs of a generic high energy physics experiment to be proposed for the Superconducting SuperCollider (SSC), and requires the collection and analysis of between 10 and 100 million sets of vectors (events), each approximately one megabyte in length. We sketch how this analysis would proceed using an object-oriented database which support the basic data types used in HEP

Electric toothbrush application is a reliable and valid test for differentiating temporomandibular disorders pain patients from controls

<p>Abstract</p> <p>Background</p> <p>Current methods for identifying patients with pain hypersensitivity are sufficiently complex to limit their widespread application in clinical settings. We assessed the reliability and validity of a simple multi-modal vibrotactile stimulus, applied using an electric toothbrush, to evaluate its potential as a screening tool for central sensitization.</p> <p>Methods</p> <p>Fourteen female temporomandibular disorders (TMD) subjects with myofascial pain (RDC/TMD Ia or Ib) and arthralgia (RDC/TMD IIIa) were compared to 13 pain-free controls of matched age and gender. Vibrotactile stimulus was performed with an electric toothbrush, applied with 1 pound pressure for 30 seconds in four locations: over the lateral pole of the temporomandibular joint, masseter, temporalis, and mid-ventral surface of forearm. Pain intensity (0–10) was recorded following the stimulus at 0, 15, 30, and 60 seconds. Test-retest reliability was assessed with measurements from 8 participants, taken 2–12 hours apart. Case versus control differentiation involved comparison of area under the curve (AUC). A receiver operating characteristic (ROC) curve was used to determine cutoff AUC scores for maximum sensitivity and specificity for this multi-modal vibrotactile stimulus.</p> <p>Results</p> <p>Test-retest reliability resulted in an ICC of 0.87 for all 4 pooled sites. ROC-determined AUC cutoff scores resulted in a sensitivity of 57% and specificity of 92% for all 4 pooled sites.</p> <p>Conclusion</p> <p>The electric toothbrush stimulus had excellent test-retest reliability. Validity of the scores was demonstrated with modest sensitivity and good specificity for differentiating TMD pain patients from controls, which are acceptable properties for a screening test.</p

Delivering 21st century Antarctic and Southern Ocean science

The Antarctic Roadmap Challenges (ARC) project identified critical requirements to deliver high priority Antarctic research in the 21st century. The ARC project addressed the challenges of enabling technologies, facilitating access, providing logistics and infrastructure, and capitalizing on international co-operation. Technological requirements include: i) innovative automated in situ observing systems, sensors and interoperable platforms (including power demands), ii) realistic and holistic numerical models, iii) enhanced remote sensing and sensors, iv) expanded sample collection and retrieval technologies, and v) greater cyber-infrastructure to process ‘big data’ collection, transmission and analyses while promoting data accessibility. These technologies must be widely available, performance and reliability must be improved and technologies used elsewhere must be applied to the Antarctic. Considerable Antarctic research is field-based, making access to vital geographical targets essential. Future research will require continent- and ocean-wide environmentally responsible access to coastal and interior Antarctica and the Southern Ocean. Year-round access is indispensable. The cost of future Antarctic science is great but there are opportunities for all to participate commensurate with national resources, expertise and interests. The scope of future Antarctic research will necessitate enhanced and inventive interdisciplinary and international collaborations. The full promise of Antarctic science will only be realized if nations act together

Current clinical practice and outcome of neoadjuvant chemotherapy for early breast cancer: analysis of individual data from 94,638 patients treated in 55 breast cancer centers

Neoadjuvant chemotherapy (NACT) is frequently used in patients with early breast cancer. Randomized controlled trials have demonstrated similar survival after NACT or adjuvant chemotherapy (ACT). However, certain subtypes may benefit more when NACT contains regimes leading to high rates of pathologic complete response (pCR) rates. In this study we analyzed data using the OncoBox research from 94,638 patients treated in 55 breast cancer centers to describe the current clinical practice of and outcomes after NACT under routine conditions. These data were compared to patients treated with ACT. 40% of all patients received chemotherapy. The use of NACT increased over time from 5% in 2007 up to 17.3% in 2016. The proportion of patients receiving NACT varied by subtype. It was low in patients with HR-positive/HER2-negative breast cancer (5.8%). However, 31.8% of patients with triple-negative, 31.9% with HR-negative/HER2-positive, and 26.5% with HR-positive/HER2-positive breast cancer received NACT. The rates of pCR were higher in patients with HR-positive/HER2-positive, HR negative/HER2-positive and triple-negative tumors (36, 53 and 38%) compared to HR-positive/HER2-negative tumors (12%). PCR was achieved more often in HER2-positive and triple-negative tumors over time. This is the largest study on use and effects of NACT in German breast cancer centers. It demonstrates the increased use of NACT based on recommendations in current clinical guidelines. An improvement of pCR was shown in particular in HER2-positive and triple-negative breast cancer, which is consistent with data from randomized controlled trails

Experience with a run file archive using database technology

High Energy Physics experiments are known for their production of large amounts of data. Even small projects may have to manage several Giga Byte of event information. One possible solution for the management of this data is to use today`s technology to archive the raw data files in tertiary storage and build on-line catalogs which reference interesting data. This approach has been taken by the Gammas, Electrons and Muons (GEM) Collaboration for their evaluation of muon chamber technologies at the Superconducting Super Collider Laboratory (SSCL). Several technologies were installed and tested during a 6 month period. Events produced were first recorded in the UNIX filesystem of the data acquisition system and then migrated to the Physics Detector Simulation Facility (PDSF) for long term storage. The software system makes use of a commercial relational database management system (SYBASE) and the Data Management System (DMS), a tape archival system developed at the SSCL. The components are distributed among several machines inside and outside PDSF. A Motif-based graphical user interface (GUI) enables physicists to retrieve interesting runs from the archive using the on-line database catalog