Database Infrastructure Research Articles

The protective effect of different dialysis types on residual renal function in patients with maintenance hemodialysis: A systematic review and meta-analysis.

Residual renal function (RRF) is an important determinant of mortality and morbidity in patients undergoing hemodialysis. Different dialysis types may have different effects on RRF. We therefore conducted this meta-analysis to examine the RRF protective effect of different dialysis types for hemodialysis patients. A systematic search was performed on PubMed, EMbase, Web of Science, Chinese Biomedical Literature Database, Wanfang database, and China National Knowledge Infrastructure for randomized controlled trials and cohort studies. Dialysis types included low-flux hemodialysis (LFHD), high-flux hemodialysis (HFHD), hemodiafiltration (HDF), and hemodialysis and hemoperfusion (HD+HP). The mean of endogenous creatinine clearance rate (CCR) and urea clearance rate (Curea), or urine volume was used to estimate RRF [95% confidence interval (95% CI), 6.05-16.80]. There were 12 articles involving 1224 patients, including 11 random controlled trials and 1 cohort study. Meta-analysis showed that the RRF protective effect of HFHD [mean difference (MD) = 1.48, 95% CI (2.11 to 0.86), P < .01] and HD+HP [MD = 0.41, 95% CI (0.69 to 0.12), P = .005] was better than that of LFHD, and the RRF decline rate was the lowest in HFHD group [MD = 0.13, 95% CI (0.17 to 0.09), P < .01]. Descriptive analysis showed that HDF could better protect RRF when compared with LFHD. However, there was no consistency among other interventions when removing LFHD due to limited data. For patients undergoing maintenance hemodialysis, the HFHD, HD+HP and HDF may better protect RRF, compared with LFHD.

The impact of informing diagnosis on quality of life in patients with cancer: A protocol of systematic review and meta-analysis.

Cancer is the second leading cause of death globally. More millions new cancer cases are diagnosed, and millions persons died due to cancer each year. There are different attitudes on disclosure of diagnosis to the patients with cancer. The current systematic reviews are qualitative, and indicate that there is limited evidence on the association between awareness of diagnosis and quality of life in patients with cancer. In this study, we aim to evaluate the effect of awareness of diagnosis on quality of life in patients with cancer by conducting a systematic review and meta-analysis. We will perform a comprehensive electronic search in the databases below: MEDLINE (via PubMed), EMBASE, Cochrane Central Register of Controlled Trials, PsycINFO, WEB OF SCIENCE, Chinese Biomedical Literature database, WANFANG database, and China National Knowledge Infrastructure. The cohort studies focusing on the association between awareness of diagnosis and quality of life in patients with cancer will be included. The risk of bias for the included studies will be appraised using the Newcastle-Ottawa Scale tool for cohort study. We will pool the effect estimates from the included studies to quantitatively present the strength of the association of interest. This study will present pooled effect estimates regarding the impact of informing diagnosis on quality of life in patients with cancer. This is the first quantitative systematic review which tends to provide modest evidence on the association between informing diagnosis and quality of life in patients with cacner. CRD42017060073.

Epistemic Harvest

&#x0D; &#x0D; &#x0D; The following discussion of computational capital takes the electronic database, an infrastructure for storing information, as vantage point. Following a brief look into how database systems serve information desires, the notion of ‘database as discourse’ by Mark Poster is explored and further developed. Database as discourse establishes a machinic agency, directed towards the individual in a specific mode of hailing. This mode of hailing in turn leads to a scatteredform of subjectivity, that is identified with Manuela Ott and Gerald Raunig as dividual. How does dividualization emerge from database infrastructure? What is the specificquality of data, that is produced by and being harvested from in/dividuals into databases, and what are the consequences of such ashifted view?&#x0D; &#x0D; &#x0D;

Prevalence of Internet addiction disorder in Chinese university students: A comprehensive meta-analysis of observational studies

Background and aimsInternet addiction disorder (IAD) is common in university students. A number of studies have examined the prevalence of IAD in Chinese university students, but the results have been inconsistent. This is a meta-analysis of the prevalence of IAD and its associated factors in Chinese university students.MethodsBoth English (PubMed, PsycINFO, and Embase) and Chinese (Wan Fang Database and Chinese National Knowledge Infrastructure) databases were systematically and independently searched from their inception until January 16, 2017.ResultsAltogether 70 studies covering 122,454 university students were included in the meta-analysis. Using the random-effects model, the pooled overall prevalence of IAD was 11.3% (95% CI: 10.1%–12.5%). When using the 8-item Young Diagnostic Questionnaire, the 10-item modified Young Diagnostic Questionnaire, the 20-item Internet Addiction Test, and the 26-item Chen Internet Addiction Scale, the pooled prevalence of IAD was 8.4% (95% CI: 6.7%–10.4%), 9.3% (95% CI: 7.6%–11.4%), 11.2% (95% CI: 8.8%–14.3%), and 14.0% (95% CI: 10.6%–18.4%), respectively. Subgroup analyses revealed that the pooled prevalence of IAD was significantly associated with the measurement instrument (Q = 9.41, p = .024). Male gender, higher grade, and urban abode were also significantly associated with IAD. The prevalence of IAD was also higher in eastern and central of China than in its northern and western regions (10.7% vs. 8.1%, Q = 4.90, p = .027).ConclusionsIAD is common among Chinese university students. Appropriate strategies for the prevention and treatment of IAD in this population need greater attention.

Practical use of aggregator data quality metrics in a collection scenario

The recent incorporation of standardized data quality metrics into the GBIF, iDigBio, and ALA portal infrastructures enables data providers with useful information they can use to clean or augment Darwin Core data at the source based on these recommendations. Numerous taxonomic and geographic based metrics provide useful information on the quality of various Darwin Core fields in this realm, while also providing input on Darwin Core compliance for others. As a provider/data manager for the Biodiversity Institute, University of Kansas, and having spent some time evaluating their efficacy and reliability, this presentation will highlight some of the positive and negative aspects of my experience with specific examples while highlighting concerns regarding the user experience and standardization of these metrics across the aggregator landscape. These metrics have indicated both data and publishing issues that have increased the utility and cleanliness of our data while also highlighting batch processing challenges and issues with the process of inferring "bad" data. The integration of these metrics into source database infrastructure will also be postulated, with Specify Software as an example.

Prognostic Value of MUC2 Expression in Colorectal Cancer: A Systematic Review and Meta-Analysis.

Background The reliability of MUC2 as a prognostic marker in colorectal cancer (CRC) is controversial. This study evaluated the association between MUC2 expression levels in CRC tissues and prognosis. Methods The PubMed, Web of Science, Embase, Cochrane Library, China Biology Medicine disc (CBMdisc), Wanfang Database, and China National Knowledge Infrastructure (CNKI) databases were searched to identify studies exploring the relationship between MUC2 expression in CRC tissues and overall survival (OS). Pooled hazard ratios (HRs) and risk ratios (RRs) with 95% confidence intervals (CIs) were used to evaluate the associations between MUC2 expression levels and prognosis and MUC2 expression levels and CRC clinicopathological characteristics, respectively. Results The meta-analysis included 11 studies (2619 patients). Low MUC2 expression level was significantly associated with poor OS (HR, 1.67; 95% CI, 1.43–1.94; P < 0.00001) and disease-free survival (DFS)/recurrence-free survival (RFS) (HR, 1.60; 95% CI, 1.21–2.12; P = 0.001) in patients with CRC. Low MUC2 expression level was associated with advanced TNM stage (RR, 1.42; 95% CI, 1.26–1.60; P < 0.00001), lymph node metastasis (RR, 1.41; 95% CI, 1.25–1.60; P < 0.00001), lymphatic invasion (RR,1.64; 95% CI, 1.26–2.12; P = 0.0002), rectal tumor site (RR, 1.26; 95% CI, 1.09–1.46; P = 0.001), and large tumor size (RR,1.32; 95% CI, 1.02–1.70; P = 0.03). There were no associations between low MUC2 expression level and gender, histological grade, depth of invasion, and distant metastasis. Conclusion The low levels of MUC2 in CRC tissues are poor prognostic factor independent of stage or other well-recognized markers of later-stage disease. Large well-designed cohort studies are required to validate MUC2 as a biomarker for poor prognosis in CRC.

2324 A community-academic partnership to understand the correlates of successful aging in place (year 2)

OBJECTIVES/SPECIFIC AIMS: Objective: The Rockefeller University Center for Clinical and Translational Science (RU-CCTS), Clinical Directors Network (CDN), and Carter Burden Network (CBN), a multisite senior services organization serving East Harlem, NY, formed a community-academic partnership to examine the use of a simple validated surrogate measure of overall health status and frailty in this population. Many CBN seniors are racial/ethnic minorities, low-income, and suffer from multiple chronic conditions, depression and food insecurity. Multiple biological, musculoskeletal, psychosocial and nutritional factors contribute to frailty, which has been defined variously in senior health outcomes research. The CTSA-funded Pilot Project aims to: (1) Engage CBN seniors and stakeholders in priority-setting, joint protocol development, research conduct, analysis, and dissemination; (2) Characterize the health status of the CBN seniors using validated measures; (3) Establish database infrastructure for current and future research; (4) Understand how health and senior activities information can be used to create programs to improve senior health. METHODS/STUDY POPULATION: Methods: (1) CEnR-Navigation, a collaborative program/process that consists of semistructured meetings and activities facilitated by expert Navigators, was used for partnership development and to engage Carter Burden seniors to refine priorities and research questions, provide feedback on study design and conduct, and analyze and disseminate results. (2) Standard physical measurements and validated survey instruments were used to collect health information; target enrollment is 240 seniors across 2 sites (1 hosted within a subsidized housing facility and Social Model Adult Day Program). (3) A REDCap-based platform was designed for data capture and import. Individual attendance at senior activities for the prior year was extracted from existing records. The primary outcome is frailty, as measured by validated walk/balance tests (Short Physical Performance Battery). Secondary outcomes include measures of engagement, and association of use of services/activities with the primary outcome. RESULTS/ANTICIPATED RESULTS: (1) In total, 29 residents and 14 other stakeholders engaged in partnership-building, study design and implementation. (2) From May to November 2017, 98 participants were enrolled from site 1 (a residential site). Enrollment at site 2 (a senior center), begun in November, is projected for February completion. Characteristics of site 1 participants: median age=63.6 years; Hispanic, 44.90% (44); White, 13.89% (10), Black, 62.50% (45); Asian, 4.17% (3); American Indian or Alaskan Native, 2.78% (2), and Other, 16.67% (12). Educational attainment: 51.04% (49) had not completed high school; 19.79% (19) were high school graduates; 18.75% (18) completed some college, and 10.42% (10) were college graduates. For the 85 participants reporting annual income: 64.71% (55) reported &lt;$10,000; 28.24% (24) reported $10,000–$15,000; 7.06% (6) were among the ranges from $15,000 to $50,000. The average body mass index (BMI) was 30, which is obese. For 83.67% (82) of site 1 participants, the BMI was in the range of overweight or obese. Half of participants (49) reported health literacy barriers in the Single Item Health Literacy Survey. Demographics and Frailty assessments (walk and balance tests) for participants enrolled at both sites will be reported. (3) Activity participation data for July 2016–November 2017 were recovered for 507 sessions at site 1 and are being analyzed. DISCUSSION/SIGNIFICANCE OF IMPACT: Here we report progress in developing a sustainable community-academic partnership, infrastructure and research capacity with the CBN senior services organization, and characterizing this at-risk population, of whom 71% have a high school education or less, 93% live in extreme poverty, and 84% are overweight or obese. A simple validated frailty measure in seniors will enable the acceleration of community-based translational research addressing senior health, and examine changes in this measure in relationship to the utilization of senior services.

Comparison of Epithelium-Off Versus Transepithelial Corneal Collagen Cross-Linking for Keratoconus: A Systematic Review and Meta-Analysis.

To systematically compare standard epithelium-off corneal collagen cross-linking (SCXL) and transepithelial corneal collagen cross-linking (TECXL) for treating keratoconus. PubMed, EMBASE, the Cochrane Library, the US trial registry (ClinicalTrials.gov), VIP Database, Wanfang Databse, and China National Knowledge Infrastructure searches up to February 2017 were conducted. Primary outcomes were changes at 1 year in uncorrected distance visual acuity, maximum keratometry (Kmax), and mean keratometry (mean K). Secondary outcomes were changes at 1 year in corrected distance visual acuity, mean refractive spherical equivalent, central corneal thickness, endothelial cell density, and the occurrence of adverse events. Eight studies with a total of 455 eyes were included. For primary outcomes, SCXL showed a greater reduction in mean K [standardized mean difference (SMD) 0.28; 95% confidence interval (CI), 0.03-0.53; P = 0.03] compared with TECXL. Subgroup analysis indicated that SCXL had a comparable effect on reducing mean K with TECXL protocols using chemical enhancers (SMD 0.05; 95% CI, -0.36 to 0.45; P = 0.82) but a greater reduction in mean K compared with TECXL with current iontophoretic protocols (SMD 0.43; 95% CI, 0.10-0.75; P = 0.01). For the other outcomes, there were no statistically significant differences. With the exception of less reduction in mean K with current iontophoretic protocols, analysis of the limited number of comparative studies available seems to demonstrate that SCXL and TECXL have a comparable effect on visual, refractive, pachymetric, and endothelial parameters at 1 year after surgery. Further follow-up is required to determine whether these techniques are comparable in the long-term.

Levodopa/carbidopa/entacapone versus levodopa/dopa-decarboxyiase inhibitor for the treatment of Parkinson's disease: systematic review, meta-analysis, and economic evaluation.

AimsTo review the evidence for efficacy, safety, and cost-effectiveness of levodopa/carbidopa/entacapone (LCE) compared with levodopa/dopa-decarboxyiase inhibitor (DDCI) for Parkinson’s disease (PD).MethodsPubMed, Embase, the Cochrane Library, and Chinese databases WangFang Data, Chinese Sci-tech Journals Database and China National Knowledge Infrastructure, as well as ClinicalTrials.gov, were searched for randomized controlled trials with “levodopa/carbidopa/entacapone” as keywords. The search period was from inception to August 2017. We conducted meta-analyses to synthesize the evidence quantitatively.ResultsA total of 5,693 records were obtained. We included seven randomized controlled trials and one cost-effectiveness study after the screening process. Compared with levodopa–DDCI, LCE improved patient Unified Parkinson’s Disease Rating Scale (UPDRS) II score (mean difference [MD] −1.17, 95% CI −1.64 to −0.71), UPDRS III score (MD −1.55, 95% CI −2.29 to −0.81), and Schwab and England daily activity rating (MD 2.05, 95% CI 0.85–3.26). There was no statistically significant difference in the risk of serious adverse events (AEs) or discontinuation due to AEs in patients with LCE, and the risk of total AEs was higher in the LCE group (risk ratio [RR] 1.33, 95% CI 1.05–1.70). The incremental cost-effectiveness ratio of LCE was £3,105 per quality-adjusted life-year (QALY) gained in the UK.ConclusionLCE can improve PD patients’ motor symptoms and daily living functioning when compared with levodopa/DDCI.

A database infrastructure to implement real-time solar and wind power generation intra-hour forecasts

This paper presents a simple forecasting database infrastructure implemented using the open-source database management system MySQL. This proposal aims at advancing the myriad of solar and wind forecast models present in the literature into a production stage. The paper gives all relevant details necessary to implement a MySQL infra-structure that collects the raw data, filters unrealistic values, classifies the data, and produces forecasts automatically and without the assistance of any other computational tools. The performance of this methodology is demonstrated by creating intra-hour power output forecasts for a 1 MW photovoltaic installation in Southern California and a 10 MW wind power plant in Central California. Several machine learning forecast models are implemented (persistence, auto-regressive and nearest neighbors) and tested. Both point forecasts and prediction intervals are generated with this methodology. Quantitative and qualitative analyses of solar and wind power forecasts were performed for an extended testing period (4 years and 6 years, respectively). Results show an acceptable and robust performance for the proposed forecasts.

Prevalence of sleep disturbances in Chinese university students: a comprehensive meta-analysis.

This is a meta-analysis of the pooled prevalence of sleep disturbances and its associated factors in Chinese university students. English (PubMed, PsycINFO, Embase) and Chinese (SinoMed, Wan Fang Database and Chinese National Knowledge Infrastructure) databases were systematically and independently searched from inception until 16 August 2016. The prevalence of sleep disturbances was pooled using random-effects model. Altogether 76 studies involving 112939 university students were included. The overall pooled prevalence of sleep disturbances was 25.7% (95% CI: 22.5-28.9%). When using the screening scales Pittsburgh Sleep Quality Index, Athens Insomnia Scale and Self-Rating Sleeping State Scale, and the diagnostic criteria of the Chinese Classification of Mental Disorders (Second Edition), the pooled prevalence of sleep disturbances was 24.1% (95% CI: 21.0-27.5%) and 18.1% (95% CI: 16.4-20.0%), respectively. The percentages of students dissatisfied with sleep quality and those suffering from insomnia symptoms were 20.3% (95% CI: 13.0-30.3%) and 23.6% (95% CI: 18.9-29.0%), respectively. Subgroup analyses revealed that medical students were more vulnerable to sleep disturbances than other student groups. There was no significant difference between males and females, and across geographic locations. Sleep disturbances are common in Chinese university students. Appropriate strategies for prevention and treatment of sleep disturbances in this population need greater attention.

Towards efficiently supporting database as a service with QoS guarantees

Quality of Service (QoS) is at the core of the vision of Database as a Service (DBaaS), which provides guarantees to database users on the usability of database services, even when the underlying database infrastructure is shared by multiple users. When QoS guarantees are necessitated, traditional approaches in DBaaS often have to reserve computation resources (e.g. CPU and memory) for tenants according to their performance Service Level Objectives (SLOs), so that the database engine always possesses sufficient resources to accomplish the expected workloads under any circumstance. Such resource reservation schemes inevitably result in poor resource utilization, as the actual workloads of tenants are usually below their maximal workload expectation described in their SLOs.In this paper, we propose a novel scheme called FrugalDB to further improve resource utilization and thus reduce operational cost for DBaaS systems with QoS guarantees. FrugalDB accommodates two independent database engines, an in-memory engine for heavy workloads with tight SLOs, and a disk-based engine for light workloads with loose SLOs. The in-memory database is leveraged to migrate temporary heavy workloads from the disk-based database, when the latter itself does not suffice to handle all active tenants’ workloads, and thus it could be relieved of the tremendous data serving pressure yielded by those heavy workloads, and focus on processing massive numbers of light workloads. When the heavy workloads fade out, FrugalDB reversely migrates a tenant’s workload from the in-memory database into the disk-based database, so that the occupied memory resources could be recollected for subsequent workload migrations. By an effective workload estimation method and an efficient migration schedule algorithm, FrugalDB tries to minimize workload migration cost incurred in moving workloads between the two engines. By allocating each tenant’s workload to an appropriate engine via workload migration, this dual-engine scheme can substantially save computation resources, and thus consolidate more tenants on a single database server. We evaluate FrugalDB with extensive experiments, which show that it has a higher tenant consolidation rate with performance SLO guarantees and fewer performance SLO violations than the existing systems, as well as with acceptable response latency.

MINDMAP: establishing an integrated database infrastructure for research in ageing, mental well-being, and the urban environment

BackgroundUrbanization and ageing have important implications for public mental health and well-being. Cities pose major challenges for older citizens, but also offer opportunities to develop, test, and implement policies, services, infrastructure, and interventions that promote mental well-being. The MINDMAP project aims to identify the opportunities and challenges posed by urban environmental characteristics for the promotion and management of mental well-being and cognitive function of older individuals.MethodsMINDMAP aims to achieve its research objectives by bringing together longitudinal studies from 11 countries covering over 35 cities linked to databases of area-level environmental exposures and social and urban policy indicators. The infrastructure supporting integration of this data will allow multiple MINDMAP investigators to safely and remotely co-analyse individual-level and area-level data.Individual-level data is derived from baseline and follow-up measurements of ten participating cohort studies and provides information on mental well-being outcomes, sociodemographic variables, health behaviour characteristics, social factors, measures of frailty, physical function indicators, and chronic conditions, as well as blood derived clinical biochemistry-based biomarkers and genetic biomarkers. Area-level information on physical environment characteristics (e.g. green spaces, transportation), socioeconomic and sociodemographic characteristics (e.g. neighbourhood income, residential segregation, residential density), and social environment characteristics (e.g. social cohesion, criminality) and national and urban social policies is derived from publically available sources such as geoportals and administrative databases.The linkage, harmonization, and analysis of data from different sources are being carried out using piloted tools to optimize the validity of the research results and transparency of the methodology.DiscussionMINDMAP is a novel research collaboration that is combining population-based cohort data with publicly available datasets not typically used for ageing and mental well-being research. Integration of various data sources and observational units into a single platform will help to explain the differences in ageing-related mental and cognitive disorders both within as well as between cities in Europe, the US, Canada, and Russia and to assess the causal pathways and interactions between the urban environment and the individual determinants of mental well-being and cognitive ageing in older adults.

Association between hypertensive disorders of pregnancy and risk of autism in offspring: a systematic review and meta-analysis of observational studies.

BackgroundAutism spectrum disorder (ASD) is a common severe pervasive neurodevelopmental disorder of undetermined etiology. Environmental exposures, especially pregnancy complications, have been increasingly recognized as a potential risk factor for ASD. Our aim was to (1) systematically evaluate the association between hypertensive disorders of pregnancy (HDP) and the risk of ASD in offspring, (2) specifically draw a subgroup analysis of disease severity in patients with HDP to achieve more sufficient evidence on this issue.ResultsA total of 21 studies were identified with more than 6.5 million participants, including 31,027 ASD probands. A comparative meta-analysis established that offspring born premature to HDP were significantly associated with ASD than matched controls (OR = 1.42, 95% CI: 1.34–1.50). Subgroup analysis of clinical classification include: (1) gestational hypertension, (2) pre-eclampsia, (3) chronic hypertension complicating pregnancy (CHP). The offspring of mothers with pre-eclampsia and CHP have slightly higher risk (OR = 1.43; OR = 1.48, respectively) of ASD than those of mothers with gestational hypertension (OR = 1.37). In consistence with most previous researches, higher ASD prevalence was observed in male than female (OR = 1.38), indicating a potential role for gender in the pathophysiology of ASD.Materials and MethodsWe conducted a systematic literature search on PubMed, EMBASE, Web of Science, PsycINFO database and China National Knowledge Infrastructure up to Jun. 2017. Statistical analysis was performed using Stata 10.0.ConclusionsThis meta-analysis implies a possible link between HDP and the risk of ASD in offspring. However, further investigation should be conducted to confirm this conclusion, and intensive prenatal surveillance and early prediction for ASD is needed.

Phylogenetic Classification of Seed Plants of Taiwan

BackgroundBiological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/), the national portal website that integrates Taiwan’s biodiversity information databases, angiosperms are arranged according to Cronquist’s System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55–70, 2011)’s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan.ResultsThe Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized.ConclusionsThe adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation’s biodiversity information databases.

Digital pathology in nephrology clinical trials, research, and pathology practice.

In this review, we will discuss (i) how the recent advancements in digital technology and computational engineering are currently applied to nephropathology in the setting of clinical research, trials, and practice; (ii) the benefits of the new digital environment; (iii) how recognizing its challenges provides opportunities for transformation; and (iv) nephropathology in the upcoming era of kidney precision and predictive medicine. Recent studies highlighted how new standardized protocols facilitate the harmonization of digital pathology database infrastructure and morphologic, morphometric, and computer-aided quantitative analyses. Digital pathology enables robust protocols for clinical trials and research, with the potential to identify previously underused or unrecognized clinically useful parameters. The integration of digital pathology with molecular signatures is leading the way to establishing clinically relevant morpho-omic taxonomies of renal diseases. The introduction of digital pathology in clinical research and trials, and the progressive implementation of the modern software ecosystem, opens opportunities for the development of new predictive diagnostic paradigms and computer-aided algorithms, transforming the practice of renal disease into a modern computational science.

XRootD popularity on hadoop clusters

Performance data and metadata of the computing operations at the CMS experiment are collected through a distributed monitoring infrastructure, currently relying on a traditional Oracle database system. This paper shows how to harness Big Data architectures in order to improve the throughput and the efficiency of such monitoring. A large set of operational data - user activities, job submissions, resources, file transfers, site efficiencies, software releases, network traffic, machine logs - is being injected into a readily available Hadoop cluster, via several data streamers. The collected metadata is further organized running fast arbitrary queries; this offers the ability to test several Map&Reduce-based frameworks and measure the system speed-up when compared to the original database infrastructure. By leveraging a quality Hadoop data store and enabling an analytics framework on top, it is possible to design a mining platform to predict dataset popularity and discover patterns and correlations.

First use of LHC Run 3 Conditions Database infrastructure for auxiliary data files in ATLAS

Processing of the large amount of data produced by the ATLAS experiment requires fast and reliable access to what we call Auxiliary Data Files (ADF). These files, produced by Combined Performance, Trigger and Physics groups, contain conditions, calibrations, and other derived data used by the ATLAS software. In ATLAS this data has, thus far for historical reasons, been collected and accessed outside the ATLAS Conditions Database infrastructure and related software. For this reason, along with the fact that ADF are effectively read by the software as binary objects, this class of data appears ideal for testing the proposed Run 3 conditions data infrastructure now in development. This paper describes this implementation as well as the lessons learned in exploring and refining the new infrastructure with the potential for deployment during Run 2.

Functional tests of a prototype for the CMS-ATLAS common non-event data handling framework

Since 2014 the ATLAS and CMS experiments share a common vision on the database infrastructure for the handling of the non-event data in forthcoming LHC runs. The wide commonality in the use cases has allowed to agree on a common overall design solution that is meeting the requirements of both experiments. A first prototype has been completed in 2016 and has been made available to both experiments. The prototype is based on a web service implementing a REST api with a set of functions for the management of conditions data. In this contribution, we describe this prototype architecture and the tests that have been performed within the CMS computing infrastructure, with the aim of validating the support of the main use cases and of suggesting future improvements.

Acquisition of Seismic, Hydroacoustic, and Infrasonic Data with Hadoop and Accumulo

ABSTRACT Recent developments in distributed data systems now allow faster ingestion and processing of larger quantities of time‐series data than available in current seismic, hydroacoustic, and infrasonic analysis platforms. However, the data model and storage architecture of these systems are significantly different than those in use today. We developed a data acquisition and signal analysis platform using a relatively inexpensive cluster of commodity computing hardware running a Hadoop Distributed File System, an Accumulo database infrastructure, and the Zeppelin web‐based analytics tool suite. The Accumulo data model allows individual waveform samples and their associated metadata to be stored as discrete rows in the database. This is a significant departure from traditional storage practices, in which continuous waveform segments are stored with their associated metadata as a single entity. Our design allows for rapid table scans of large data archives within the Accumulo database for locating, retrieving, and analyzing specific waveform segments directly. The system infrastructure is horizontally scalable, which allows additional data acquisition and processing resources to be added simply through the addition of new data nodes. Easy scalability permits the system to accommodate the ingestion and analysis of new data as the network of seismic, hydroacoustic, and infrasonic sensors grows. The barrier of entry for establishing a functional data acquisition system is relatively low for which a proof of concept prototype can be developed on a limited budget and later scaled as storage and processing requirements dictate.