Lazy ETL in Action: ETL Technology Dates Scientific Data

Both scientific data and business data have analytical needs. Analysis takes place after a scientific data warehouse is eagerly filled with all data from external data sources (repositories). This is similar to the initial loading stage of Extract, Transform, and Load (ETL) processes that drive business intelligence. ETL can also help scientific data analysis. However, the initial loading is a time and resource consuming operation. It might not be entirely necessary, e.g. if the user is interested in only a subset of the data. We propose to demonstrate Lazy ETL, a technique to lower costs for initial loading. With it, ETL is integrated into the query processing of the scientific data warehouse. For a query, only the required data items are extracted, transformed, and loaded transparently on-the-fly. The demo is built around concrete implementations of Lazy ETL for seismic data analysis. The seismic data warehouse is ready for query processing, without waiting for long initial loading. The audience fires analytical queries to observe the internal mechanisms and modifications that realize each of the steps; lazy extraction, transformation, and loading

Data Vaults: Database Technology for Scientific File Repositories

Current data-management systems and analysis tools fail to meet scientists’ data-intensive needs. A "data vault" approach lets researchers effectively and efficiently explore and analyze information

A New Biometric Template Protection using Random Orthonormal Projection and Fuzzy Commitment

Biometric template protection is one of most essential parts in putting a biometric-based authentication system into practice. There have been many researches proposing different solutions to secure biometric templates of users. They can be categorized into two approaches: feature transformation and biometric cryptosystem. However, no one single template protection approach can satisfy all the requirements of a secure biometric-based authentication system. In this work, we will propose a novel hybrid biometric template protection which takes benefits of both approaches while preventing their limitations. The experiments demonstrate that the performance of the system can be maintained with the support of a new random orthonormal project technique, which reduces the computational complexity while preserving the accuracy. Meanwhile, the security of biometric templates is guaranteed by employing fuzzy commitment protocol.Comment: 11 pages, 6 figures, accepted for IMCOM 201

Instant-on scientific data warehouses: Lazy ETL for data-intensive research

In the dawning era of data intensive research, scientific discovery deploys data analysis techniques similar to those that drive business intelligence. Similar to classical Extract, Transform and Load (ETL) processes, data is loaded entirely from external data sources (repositories) into a scientific data warehouse before it can be analyzed. This process is both, time and resource intensive and may not be entirely necessary if only a subset of the data is of interest to a particular user. To overcome this problem, we propose a novel technique to lower the costs for data loading: Lazy ETL. Data is extracted and loaded transparently on-the-fly only for the required data items. Extensive experiments demonstrate the significant reduction of the time from source data availability to query answer compared to state-of-the-art solutions. In addition to reducing the costs for bootstrapping a scientific data warehouse, our approach also reduces the costs for loading new incoming data

Data Vaults: a Database Welcome to Scientific File Repositories

Efficient management and exploration of high-volume scientific file repositories have become pivotal for advancement in science. We propose to demonstrate the Data Vault, an extension of the database system architecture that transparently opens scientific file repositories for efficient in-database processing and exploration. The Data Vault facilitates science data analysis using high-level declarative languages, such as the traditional SQL and the novel array-oriented SciQL. Data of interest are loaded from the attached repository in a just-in-time manner without need for up-front data ingestion. The demo is built around concrete implementations of the Data Vault for two scientific use cases: seismic time series and Earth observation images. The seismic Data Vault uses the queries submitted by the audience to illustrate the internals of Data Vault functioning by revealing the mechanisms of dynamic query plan generation and on-demand external data ingestion. The image Data Vault shows an application view from the perspective of data mining researchers

TrpA1 Regulates Thermal Nociception in Drosophila

Pain is a significant medical concern and represents a major unmet clinical need. The ability to perceive and react to tissue-damaging stimuli is essential in order to maintain bodily integrity in the face of environmental danger. To prevent damage the systems that detect noxious stimuli are therefore under strict evolutionary pressure. We developed a high-throughput behavioral method to identify genes contributing to thermal nociception in the fruit fly and have reported a large-scale screen that identified the Ca2+ channel straightjacket (stj) as a conserved regulator of thermal nociception. Here we present the minimal anatomical and neuronal requirements for Drosophila to avoid noxious heat in our novel behavioral paradigm. Bioinformatics analysis of our whole genome data set revealed 23 genes implicated in Ca2+ signaling that are required for noxious heat avoidance. One of these genes, the conserved thermoreceptor TrpA1, was confirmed as a bona fide “pain” gene in both adult and larval fly nociception paradigms. The nociceptive function of TrpA1 required expression within the Drosophila nervous system, specifically within nociceptive multi-dendritic (MD) sensory neurons. Therefore, our analysis identifies the channel TRPA1 as a conserved regulator of nociception

Legal and ethical framework for global health information and biospecimen exchange - an international perspective.

BACKGROUND: The progress of electronic health technologies and biobanks holds enormous promise for efficient research. Evidence shows that studies based on sharing and secondary use of data/samples have the potential to significantly advance medical knowledge. However, sharing of such resources for international collaboration is hampered by the lack of clarity about ethical and legal requirements for transfer of data and samples across international borders. MAIN TEXT: Here, the International Clinical Trial Center Network (ICN) reports the legal and ethical requirements governing data and sample exchange (DSE) across four continents. The most recurring requirement is ethical approval, whereas only in specific conditions approval of national health authorities is required. Informed consent is not required in all sharing situations. However, waiver of informed consent is only allowed in certain countries/regions and under certain circumstances. The current legal and ethical landscape appears to be very complex and under constant evolution. Regulations differ between countries/regions and are often incomplete, leading to uncertainty. CONCLUSION: With this work, ICN illuminates the unmet need for a single international collaborative framework to facilitate DSE. Harmonising requirements for global DSE will reduce inefficiency and waste in research. There are many challenges to realising this ambitious vision, including inconsistent terminology and definitions, and heterogeneous and dynamic legal constraints. Here, we identify areas of agreement and significant difference as a necessary first step towards facilitating international collaboration. We propose the establishment of a working group to continue the comparison across jurisdictions, create a standardised glossary and define a set of basic principles and fundamental requirements for DSE

Compact frequency standard based on an intracavity sample of cold cesium atoms

We have demonstrated the possibility for a compact frequency standard based on a sample of cold cesium atoms. In a cylindrical microwave cavity, the atoms are cooled and interrogated during a free expansion and then detected. The operation of this experiment is different from conventional atomic fountains since all the steps are sequentially performed in the same position of space. In this paper we report the analysis of a Ramsey pattern observed to present a (47±5) Hz linewidth and a stability of (5±0.5)x10-13τ-1/2 for an integration time longer than 100 s. Some of the main limitations of the standard are analyzed. This present report demonstrates considerable improvement of our previous work [J. Opt. Soc. Am. B 25, 909 (2008)] where the atoms were in a free space and not inside a microwave cavity.FAPESPCNPqCAPESFAPESP-CNR

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival