Measuring the promise of open data: Development of the Impact Monitoring Framework

It is a challenge to measure the impact of releasing data to the public since the effects may not be directly linked to particular open data activities or substantial impact may only occur several years after publishing the data. This paper proposes a framework to assess the impact of releasing open data by applying the Social Return on Investment (SROI) approach. SROI was developed for organizations intended to generate social and environmental benefits thus fitting the purpose of most open data initiatives. We link the four steps of SROI (input, output, outcome, impact) with the 14 high-value data categories of the G8 Open Data Charter to create a matrix of open data examples, activities, and impacts in each of the data categories. This Impact Monitoring Framework helps data providers to navigate the impact space of open data laying out the conceptual basis for further research.

Good reproducibility of heart rate variability after orthostatic challenge in patients with a history of acute coronary syndrome

BACKGROUND: Several parameters of heart rate variability (HRV) have been shown to predict the risk of sudden cardiac death (SCD) in cardiac patients. There is consensus that risk prediction is increased when measuring HRV during specific provocations such as orthostatic challenge. For the first time, we provide data on reproducibility of such a test in patients with a history of acute coronary syndrome. METHODS: Sixty male patients (65+/-8years) with a history of acute coronary syndrome on stable medication were included. HRV was measured in supine (5min) and standing (5min) position on 2 occasions separated by two weeks. For risk assessment relevant time-domain [standard deviation of all R-R intervals (SDNN) and root mean squared standard differences between adjacent R-R intervals (RMSSD)], frequency domain [low-frequency power (LF), high-frequency power (HF) and LF/HF power ratio] and short-term fractal scaling component (DF1) were computed. Absolute reproducibility was assessed with the standard errors of the mean (SEM) and 95% limits of random variation, and relative reproducibility by the intraclass correlation coefficient (ICC). RESULTS: We found comparable SEMs and ICCs in supine position and after an orthostatic challenge test. All ICCs were good to excellent (ICCs between 0.636 and 0.869). CONCLUSIONS: Reproducibility of HRV parameters during orthostatic challenge is good and comparable with supine position.

Genetic alterations associated with prostate cancer progression

Prostate cancer is the second most commonly diagnosed cancer among men in the United States. In this study, evidence is presented to support the hypothesis that specific chromosomal aberrations (involving one or more chromosomal regions) are associated with prostate cancer progression from organ-confined to locally advanced tumors and that some aberrations seen in high frequency in metastatic tumors may also be present in a subset of primary tumors. To determine the appropriate approach to address this hypothesis, I have established a modified CGH protocol by microdissection and DOP-PCR for use in detecting chromosomal changes in clinical prostate tumor specimens that is more sensitive and accurate than conventional CGH methods. I have successfully performed the improved CGH protocol to screen for genetic changes of 24 organ confined (pT2) and 21 locally advanced (pT3b) clinical prostate cancer specimens without metastases (N0M0). Comparisons of tumors by stage or Gleason scores following contingency table analysis showed that seven regions of the genome differed significantly between pT2 and pT3b tumors or between low and high Gleason tumors suggesting that these regions may be important in local prostate cancer progression. These included losses on 6p21–25, 6q24–27, 8p, 10q25–26, 15q22–26, and 18cen–q12 as well as gain of 3p13–q13. Multivariate analyses showed that loss of 8p (step1) and loss of 6q25–26 (or 6p21–25 or 10q25–26) (step 2) were predictive of pathologic stage or Gleason groups with 80% accuracy. Additional 5–7 steps in the multivariate model increased the predictive value to 91–95%. Comparison of the CGH data from the primary prostate tumors of this study with those obtained from published literature on metastases and recurrent tumors showed that the clinically more aggressive stage pT3b tumors shared more abnormalities in high frequency with metastases and recurrent tumors than less aggressive stage pT2 tumors. Furthermore, loss of 11cen–q22 was shared only between the primary tumors and metastases while gain of Xcen–q13 and loss of 18cen–q12 were in common between primary and recurrent tumors. These analyses suggest that the multistage model of prostate cancer progression is not linear and that some early primary tumors may be predisposed to metastasize or evolve into recurrent tumors due to the presence of specific genetic alterations. ^

Social cognitive theory and factors associated with Mexican-American parents' beliefs, attitudes and practices regarding communication with their adolescent children about sex

Latinos have the highest teen birth rate nationally. Cameron County, Texas is primarily Latino (Mexican-American). This mixed-method study (n=43) examines Mexican-American parents of adolescents' beliefs, attitudes and practices regarding communication with their adolescent children about sex. Social Cognitive Theory (SCT) constructs self-efficacy, behavioral determinism, environment, outcome expectations and reciprocal determinism can be influences on frequency and quality of parent-adolescent sex communication.^ This study describes Mexican-American parents' of adolescents recollections of their own experiences associated with learning about sexuality. It also examines the attitudes and practices regarding communication about sex and the self-efficacy and behavioral capability of participants to teach their adolescent children about sex and sexually transmitted infections. ^ Negative childhood experiences (shame, lies and trauma) of the parents in this study played a key role in terms of their desire to communicate more comprehensively about sexuality with their own children than did their parents. While participants' reported low self-efficacy and behavioral capability to communicate with their adolescent children about sex, they reported relatively high frequency and quality of communication, with 75% of participants receiving a high quality score and over 44% reporting frequent communication with their adolescent children about sex. A Chi square analysis and Fisher's Exact Score revealed no association between acculturation status, gender or having a child who has mothered/fathered a baby and the frequency or quality of communication about sex with adolescent children. Study participants also gave specific recommendations for method, content and setting of sex education for their children and themselves. Promotora delivery of information and education in a comfortable, culturally appropriate neighborhood setting, as well as parent –child learning sessions were identified as possible approaches to address improve self-efficacy and behavioral capability of parents communicating with their adolescent children about sex.^ The results of this analysis provide public health practitioners and interested community entities data to identify and develop interventions that use a theoretical, evidence-based framework for culturally appropriate interventions to encourage and equip Mexican-American parents to effectively communicate with their adolescent children about sexuality, and ultimately to address the high rates of teen pregnancy in this U.S.-Mexico border community. ^

Functional data analysis approaches for genotype-phenotype association studies from next-generation sequencing

Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^

The role of p53 in skin cancer induction by UV radiation and as a potential tumor antigen in UV-induced murine skin tumors

Carcinoma of the skin is the most common type of human cancer in the United States. Ultraviolet radiation (UVR) present in the sunlight is thought to be the major carcinogen responsible for induction of skin cancer. In UV-associated skin carcinogenesis, mutations in p53 are not only present with very high frequency, but occur early in the course of tumor development. In addition, UV-induced skin tumors in mice exhibit unique immunological characteristics. They are highly antigenic and express both individually-specific tumor transplantation antigens recognized by effector T cells and the UV-associated common antigen recognized by UV-induced suppressor T cells. ^ To examine the hypothesis that p53 plays a critical role in preventing skin cancer induction by UVR, mice constitutively lacking one or two functional p53 alleles were compared to wild-type mice for their susceptibility to UV carcinogenesis. Both p53 +/– and –/– mice showed greater susceptibility to skin cancer induction than wild-type mice, and –/– mice were the most susceptible, Accelerated tumor development in the p53 +/– mice was not associated with loss of the remaining wild-type allele of p53 , but in many cases was associated with UV-induced mutations in p53. Our studies clearly demonstrate the essential role of p53 in protection against UV carcinogenesis, particularly in the eye and epidermis. ^ The role of p53 in the antigenicity of UV-induced murine skin tumors was also addressed. Primary UV-induced tumors from p53 –/–, +/– and +/+ mice were transplanted into both normal and immunosuppressed mice, and rates of tumor rejection were compared. Tumors from mice with only one or no functional p53 alleles were less antigenic than those from mice with two functional p53 alleles. Moreover, tumors with no functional p53 also failed to grow well in chronically UV-irradiated mice. These results indicate that p53 contributes to the strong antigenicity of UV-induced murine skin tumors, and suggest that it may play a critical role in expression of the UV-associated common antigen recognized by suppressor T cells. ^ In this study we also monitored the effect of UVR on the development of lymphoid malignancies in p53 deficient mice. The incidence of lymphoid malignancies in UV-irradiated p53 +/– mice was drastically enhanced compared to that in unirradiated counterparts. The immune responses of the mice were identical and were suppressed to the same extent by UV irradiation regardless of the p53 genotype. These data provide the first experimental evidence that exposure to UVR can contribute to the development of lymphoid neoplasms in genetically susceptible hosts. ^

Varved sediments of the Arabian Sea

The upper Holocene marine section from a kasten core taken from the oxygen minimum zone off Karachi (Pakistan) at water depth 700 m contains continuously laminated sediments with a sedimentation rate of 1.2 mm/yr and a unique record of monsoonal climatic variability covering the past 5000 years. Our chronostratigraphy is based on varve counts verified by conventional and AMS14C dating. Individual hemipelagic varve couplets are about 0.8-1.5 mm thick, with light-colored terrigenous laminae (A) deposited mainly during the winter monsoon alternating with dark-colored laminae (B) rich in marine organic matter, coccoliths, and fish debris that reflect deposition during the high-productivity season of the late summer monsoon (August-October). Precipitation and river runoff appear to control varve thickness and turbidite frequency. We infer that precipitation decreased in the river watershed (indicated by thinning varves) after 3500-4000 yr B.P. This is about the time of increasing aridification in the Near East and Middle East, as documented by decreasing Nile River runoff data and lake-level lowstands between Turkey and northwestern India. This precipitation pattern continued until today with precipitation minima about 2200-1900 yr B.P., 1000 yr B.P., and in the late Middle Ages (700-400 yr B.P.), and precipitation maxima in the intervening periods. As documented by spectral analysis, the thickness of varve couplets responds to the average length of a 250-yr cycle, a 125-yr cycle, the Gleissberg cycle of solar activity (95 yr), and a 56-yr cycle of unknown origin. Higher frequency cycles are also present at 45, 39, 29-31, and 14 yr. The sedimentary gray-value also shows strong variability in the 55-yr band plus a 31-yr cycle. Because high-frequency cyclicity in the ENSO band (ca. 3.5 and 5 yr) is only weakly expressed, our data do not support a straightforward interaction of the Pacific ENSO with the monsoon-driven climate system of the Arabian Sea.

Physical properties of 39 sediment cores from the Bengal Fan and northeast Indian Ocean

We obtained sediment physical properties and geochemical data from 47 piston and gravity cores located in the Bay of Bengal, to study the complex history of the Late Pleistocene run-off from the Ganges and Brahmaputra rivers and its imprint on the Bengal Fan. Grain-size parameters were predicted from core logs of density and velocity to infer sediment transport energy and to distinguish different environments along the 3000-km-long transport path from the delta platform to the lower fan. On the shelf, 27 cores indicate rapidly prograding delta foresets today that contain primarily mud, whereas outer shelf sediment has 25% higher silt contents, indicative of stronger and more stable transport regime, which prevent deposition and expose a Late Pleistocene relic surface. Deposition is currently directed towards the shelf canyon 'Swatch of No Ground', where turbidites are released to the only channel-levee system that is active on the fan during the Holocene. Active growth of the channel-levee system occurred throughout sea-level rise and highstand with a distinct growth phase at the end of the Younger Dryas. Coarse-grained material bypasses the upper fan and upper parts of the middle fan, where particle flow is enhanced as a result of flow-restriction in well-defined channels. Sandier material is deposited mainly as sheet-flow deposits on turbidite-dominated plains at the lower fan. The currently most active part of the fan with 10-40 cm thick turbidites is documented for the central channel including inner levees (e.g., site 40). Site 47 from the lower fan far to the east of the active channel-levee system indicates the end of turbidite sedimentation at 300 ka for that location. That time corresponds to the sea-level lowering during late isotopic stage 9 when sediment supply to the fan increased and led to channel avulsion farther upstream, probably indicating a close relation of climate variability and fan activity. Pelagic deep-sea sites 22 and 28 contain a 630-kyear record of climate response to orbital forcing with dominant 21- and 41-kyear cycles for carbonate and magnetic susceptibility, respectively, pointing to teleconnections of low-latitude monsoonal forcing on the precession band to high-latitude obliquity forcing. Upper slope sites 115, 124, and 126 contain a record of the response to high-frequency climate change in the Dansgaard-Oeschger bands during the last glacial cycle with shared frequencies between 0.75 and 2.5 kyear. Correlation of highs in Bengal Fan physical properties to lows in the d18O record of the GISP2 ice-core suggests that times of greater sediment transport energy in the Bay of Bengal are associated with cooler air temperatures over Greenland. Teleconnections were probably established through moisture and other greenhouse-gas forcing that could have been initiated by instabilities in the methane hydrate reservoir in the oceans.

Late Quaternary geochemical record of sediment core GeoB3375-1

Analyses of terrigenous sediments from the Chilean continental slope off the southern border of the Atacama desert (27.5°S), focusing on illite crystallinity and the Fe:Al ratio of the sediments, reveal a high-frequency variability of the position of the Southern Westerlies, which is very similar to the coeval short-term climatic events known from Greenland ice cores and from North Atlantic sediments. Besides showing dominantly precession-driven variability in precipitation over the Andes, these analyses also reveal rapid changes in weathering intensity along the Chilean Coastal Range during the last 80,000 years. These rapid changes occur at much shorter timescales than the 19-100 kyr orbital forcing of the Milankovitch cycles.

Reconstruction of sea surface temperature and salinity of the Arabian Sea

High-frequency suborbital variations (Dansgaard-Oeschger cycles) characterize the climatic history of the Northern Hemisphere as observed in Greenland ice cores, deep-sea sediments of the North Atlantic, the Californian borderland, the Arabian Sea, the South China Sea, and the Chinese loess area. Paleoceanographic data from core KL126 from the Bay of Bengal in combination with data from the other Asian monsoonal areas indicate that the feedback processes involving snow and dust of the Tibetan Plateau vary the summer monsoon capacity to transport moisture into central South Asia and into the atmosphere. We postulate that the summer monsoon initiates, amplifies, and terminates these cycles in the Northern Hemisphere.

Laboratory investigation of flow structure and resistance of high- and low-angle dunes

A prominent control on the flow over subaqueous dunes is the slope of the downstream leeside. While previous work has focused on steep (~30°), asymmetric dunes with permanent flow separation, little is known about dunes with lower lee-slope angles for which flow separation is absent or intermittent. Here, we present a laboratory investigation where we systematically varied the dune lee-slope, holding other geometric parameters and flow hydraulics constant, to explore effects on the turbulent flow field and flow resistance. Three sets of fixed dunes (lee-slopes of 10°, 20° and 30°) were separately installed in a 15 m long and 1 m wide flume and subjected to 0.20 m deep flow. Measurements consisted of high-frequency, vertical profiles collected with a Laser Doppler Velocimeter (LDV). We show that the temporal and spatial occurrence of flow separation decreases with dune lee-slope. Velocity gradients in the dune leeside depict a free shear layer downstream of the 30° dunes and a weaker shear layer closer to the bed for the 20° and 10° dunes. The decrease in velocity gradients leads to lower magnitude of turbulence production for gentle lee-slopes. Aperiodic, strong ejection events dominate the shear layer, but decrease in strength and frequency for low-angle dunes. Flow resistance of dunes decreases with lee-slope; the transition being non-linear. Over the 10°, 20° and 30° dunes, shear stress is 8%, 33% and 90 % greater than a flat bed, respectively. Our results demonstrate that dune lee-slope plays an important, but often ignored role in flow resistance.

Isotope ratios of osmiun, carbon and oxygen of Miocene sediments and benthic foraminifera

Seawater 187Os/188Os ratios for the Middle Miocene were reconstructed by measuring the 187Os/188Os ratios of metalliferous carbonates from the Pacific (DSDP 598) and Atlantic (DSDP 521) oceans. Atlantic and Pacific 187Os/188Os measurements are nearly indistinguishable and are consistent with previously published Os isotope records from Pacific cores. The Atlantic data reported here provide the first direct evidence that the long-term sedimentary 187Os/188Os record reflects whole-ocean changes in the Os isotopic composition of seawater. The Pacific and the Atlantic Os measurements confirm a long-term 0.01/Myr increase in marine 187Os/188Os ratios that began no later than 16 Ma. The beginning of the Os isotopic increase coincided with a decrease in the rate of increase of marine 87Sr/86Sr ratios at 16 Ma. A large increase of 1? in benthic foraminiferal delta18O values, interpreted to reflect global cooling and ice sheet growth, began approximately 1 million years later at 14.8 Ma, and the long-term shift toward lower bulk carbonate delta13C values began more than 2 Myr later around 13.6 Ma. The post-16 Ma increase in marine 187Os/188Os ratios was most likely forced by weathering of radiogenic materials, either old sediments or sialic crust with a sedimentary protolith. We consider two possible Miocene-specific geologic events that can account for both this increase in marine 187Os/188Os ratios and also nearly constant 87Sr/86Sr ratios: (1) the first glacial erosion of sediment-covered cratons in the Northern Hemisphere; (2) the exhumation of the Australian passive margin-New Guinea arc system. The latter event offers a mechanism, via enhanced availability of soluble Ca and Mg silicates in the arc terrane, for the maintenance of assumed low CO2 levels after 15 Ma. The temporal resolution (three samples/Myr) of the 187Os/188Os record from Site 598, for which a stable isotope stratigraphy was also constructed, is significantly higher than that of previously published records. These high resolution data suggest oscillations with amplitudes of 0.01 to 0.02 and periods of around 1 Myr. Although variations in the 187Os/188Os record of this magnitude can be easily resolved analytically, this higher frequency signal must be verified at other sites before it can be safely interpreted as global in extent. However, the short-term 187Os/188Os variations may correlate inversely with short-term benthic foraminiferal delta18O and bulk carbonate delta13C variations that reflect glacioeustatic events.