Big Data: Astronomical or Genomical?

Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a "four-headed beast"-it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the "genomical" challenges of the next decade

Sight Distance Standards Based On Observational Data Risk Evaluation Of Passing

The paper presents an application of a reliability analysis for evaluating the risk associated with passing sight distance (PSD) standards in terms of the expected probability of noncompliance. Calculation of PSD is required to determine where drivers can safely execute passing maneuvers. Traditional PSD standards are based on deterministic, theoretical models, which are calibrated with conservative percentile values for uncertain design inputs to account for uncertainty. The PSD standards do not provide information about the risk of deviation from them. Reliability analysis is a technique that is based on limit state design and that accounts for the propagation of variability from input random parameters to the design outputs. A total of 1,098 passing maneuvers were observed on several two-lane highways in Spain; two data collection methodologies were used: external observations and an instrumented vehicle. The most significant factors affecting PSD were impeding-vehicle speed, passing-vehicle acceleration, and head-ways between impeding and passing vehicles. A uniform acceleration model described the passing-vehicle trajectory. The characterized input parameters and the passing model were used to perform a reliability analysis. The results showed the probability of noncompliance in different scenarios, defined as the proportion of cases in which the required PSD would exceed the available sight distance. American and Spanish PSD standards were evaluated. Geometric design standards presented a probability of noncompliance of about 0.15, whereas some marking standards had a probability of noncompliance exceeding 0.85. These standards may be associated with higher risk levels if they are followed by drivers. As well, PSD risk levels were not consistent for different design speeds, since they underestimated operating speed at some locationsThis paper was developed as a result of a mobility study at the University of British Columbia funded by the Erasmus Mundus Program of the European Commission under the Transatlantic Partnership for Excellence in Engineering project. The authors thank the Spanish Ministry of Economy and Competitiveness, which subsidized the research project, and the Spanish Directorate General of Traffic, Spanish Ministry of Public Works, Valencia Regional Department of Transport, and Valencia province road department for their collaboration during the field study.Llorca Garcia, C.; Moreno Chou, AT.; Sayed, T.; García García, A. (2014). Sight Distance Standards Based On Observational Data Risk Evaluation Of Passing. Transportation research record. 2404:18-26. doi:10.3141/2404-03S18262404Ismail, K., & Sayed, T. (2009). Risk-based framework for accommodating uncertainty in highway geometric design. Canadian Journal of Civil Engineering, 36(5), 743-753. doi:10.1139/l08-146Ismail, K., & Sayed, T. (2010). Risk-Based Highway Design. Transportation Research Record: Journal of the Transportation Research Board, 2195(1), 3-13. doi:10.3141/2195-01Richl, L., & Sayed, T. (2006). Evaluating the Safety Risk of Narrow Medians Using Reliability Analysis. Journal of Transportation Engineering, 132(5), 366-375. doi:10.1061/(asce)0733-947x(2006)132:5(366)Harwood, D. W., Gilmore, D. K., & Richard, K. R. (2010). Criteria for Passing Sight Distance for Roadway Design and Marking. Transportation Research Record: Journal of the Transportation Research Board, 2195(1), 36-46. doi:10.3141/2195-05Wang, Y., & Cartmell, M. P. (1998). New Model for Passing Sight Distance on Two-Lane Highways. Journal of Transportation Engineering, 124(6), 536-545. doi:10.1061/(asce)0733-947x(1998)124:6(536)Polus, A., Livneh, M., & Frischer, B. (2000). Evaluation of the Passing Process on Two-Lane Rural Highways. Transportation Research Record: Journal of the Transportation Research Board, 1701(1), 53-60. doi:10.3141/1701-07Llorca, C., & García, A. (2011). Evaluation of Passing Process on Two-Lane Rural Highways in Spain with New Methodology Based on Video Data. Transportation Research Record: Journal of the Transportation Research Board, 2262(1), 42-51. doi:10.3141/2262-05Carlson, P., Miles, J., & Johnson, P. (2006). Daytime High-Speed Passing Maneuvers Observed on Rural Two-Lane, Two-Way Highway: Findings and Implications. Transportation Research Record: Journal of the Transportation Research Board, 1961, 9-15. doi:10.3141/1961-02Llorca, C., Moreno, A. T., García, A., & Pérez-Zuriaga, A. M. (2013). Daytime and Nighttime Passing Maneuvers on a Two-Lane Rural Road in Spain. Transportation Research Record: Journal of the Transportation Research Board, 2358(1), 3-11. doi:10.3141/2358-01Easa, S. M. (1993). Reliability‐Based Design of Intergreen Interval at Traffic Signals. Journal of Transportation Engineering, 119(2), 255-271. doi:10.1061/(asce)0733-947x(1993)119:2(255)Selvanathan, E. A., & Selvanathan, S. (1994). The demand for transport and communication in the United Kingdom and Australia. Transportation Research Part B: Methodological, 28(1), 1-9. doi:10.1016/0191-2615(94)90027-2Easa, S. M. (2000). Reliability Approach to Intersection Sight Distance Design. Transportation Research Record: Journal of the Transportation Research Board, 1701(1), 42-52. doi:10.3141/1701-06Ibrahim, S. E.-B., & Sayed, T. (2011). Developing safety performance functions incorporating reliability-based risk measures. Accident Analysis & Prevention, 43(6), 2153-2159. doi:10.1016/j.aap.2011.06.006Khoury, J. E., & Hobeika, A. G. (2007). Assessing the Risk in the Design of Passing Sight Distances. Journal of Transportation Engineering, 133(6), 370-377. doi:10.1061/(asce)0733-947x(2007)133:6(370)Khoury, J. E., & Hobeika, A. G. (2012). Integrated Stochastic Approach for Risk and Service Estimation: Passing Sight Distance Application. Journal of Transportation Engineering, 138(5), 571-579. doi:10.1061/(asce)te.1943-5436.0000366Kim, S., & Choi, J. (2013). Effects of preceding geometric conditions on operating speed consistency of multilane highways. Canadian Journal of Civil Engineering, 40(6), 528-536. doi:10.1139/cjce-2012-005

Identification and prediction of Parkinson's disease subtypes and progression using machine learning in two cohorts.

The clinical manifestations of Parkinson's disease (PD) are characterized by heterogeneity in age at onset, disease duration, rate of progression, and the constellation of motor versus non-motor features. There is an unmet need for the characterization of distinct disease subtypes as well as improved, individualized predictions of the disease course. We used unsupervised and supervised machine learning methods on comprehensive, longitudinal clinical data from the Parkinson's Disease Progression Marker Initiative (n = 294 cases) to identify patient subtypes and to predict disease progression. The resulting models were validated in an independent, clinically well-characterized cohort from the Parkinson's Disease Biomarker Program (n = 263 cases). Our analysis distinguished three distinct disease subtypes with highly predictable progression rates, corresponding to slow, moderate, and fast disease progression. We achieved highly accurate projections of disease progression 5 years after initial diagnosis with an average area under the curve (AUC) of 0.92 (95% CI: 0.95 ± 0.01) for the slower progressing group (PDvec1), 0.87 ± 0.03 for moderate progressors, and 0.95 ± 0.02 for the fast-progressing group (PDvec3). We identified serum neurofilament light as a significant indicator of fast disease progression among other key biomarkers of interest. We replicated these findings in an independent cohort, released the analytical code, and developed models in an open science manner. Our data-driven study provides insights to deconstruct PD heterogeneity. This approach could have immediate implications for clinical trials by improving the detection of significant clinical outcomes. We anticipate that machine learning models will improve patient counseling, clinical trial design, and ultimately individualized patient care

Ice and pulsed electromagnetic field to reduce pain and swelling after distal radius fractures

Objective: To examine the relative effectiveness of ice therapy and/or pulsed electromagnetic field in reducing pain and swelling after the immobilization period following a distal radius fracture.Methods: A total of 83 subjects were randomly allocated to receive 30 minutes of either ice plus pulsed electromagnetic field (group A); ice plus sham pulsed electromagnetic field (group B); pulsed electromagnetic field alone (group C), or sham pulsed electromagnetic field treatment for 5 consecutive days (group D). All subjects received a standard home exercise programme. A visual analogue scale was used for recording pain; volumetric displacement for measuring the swelling of the forearm; and a hand-held goniometer for measuring the range of wrist motions before treatment on days 1, 3 and 5.Results: At day 5, a significantly greater cumulative reduction in the visual analogue scores as well as ulnar deviation range of motion was found in group A than the other 3 groups. For volumetric measurement and pronation, participants in group A performed better than subjects in group D but not those in group B.Conclusion: The addition of pulsed electromagnetic field to ice therapy produces better overall treatment outcomes than ice alone, or pulsed electromagnetic field alone in pain reduction and range of joint motion in ulnar deviation and flexion for a distal radius fracture after an immobilization period of 6 weeks.<br /

Bone fragility and decline in stem cells in prematurely aging DNA repair deficient trichothiodystrophy mice

Trichothiodystrophy (TTD) is a rare, autosomal recessive nucleotide excision repair (NER) disorder caused by mutations in components of the dual functional NER/basal transcription factor TFIIH. TTD mice, carrying a patient-based point mutation in the Xpd gene, strikingly resemble many features of the human syndrome and exhibit signs of premature aging. To examine to which extent TTD mice resemble the normal process of aging, we thoroughly investigated the bone phenotype. Here, we show that female TTD mice exhibit accelerated bone aging from 39 weeks onwards as well as lack of periosteal apposition leading to reduced bone strength. Before 39 weeks have passed, bones of wild-type and TTD mice are identical excluding a developmental defect. Albeit that bone formation is decreased, osteoblasts in TTD mice retain bone-forming capacity as in vivo PTH treatment leads to increased cortical thickness. In vitro bone marrow cell cultures showed that TTD osteoprogenitors retain the capacity to differentiate into osteoblasts. However, after 13 weeks of age TTD females show decreased bone nodule formation. No increase in bone resorption or the number of osteoclasts was detected. In conclusion, TTD mice show premature bone aging, which is preceded by a decrease in mesenchymal stem cells/osteoprogenitors and a change in systemic factors, identifying DNA damage and repair as key determinants for bone fragility by influencing osteogenesis and bone metabolism