Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait.

PubMed

Dubé, M P; Mlodzienski, M A; Kibar, Z; Farlow, M R; Ebers, G; Harper, P; Kolodny, E H; Rouleau, G A; Figlewicz, D A

1997-03-01

Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity.

Describing the linkages of the immigration, refugees and citizenship Canada permanent resident data and vital statistics death registry to Ontario's administrative health database.

PubMed

Chiu, Maria; Lebenbaum, Michael; Lam, Kelvin; Chong, Nelson; Azimaee, Mahmoud; Iron, Karey; Manuel, Doug; Guttmann, Astrid

2016-10-21

Ontario, the most populous province in Canada, has a universal healthcare system that routinely collects health administrative data on its 13 million legal residents that is used for health research. Record linkage has become a vital tool for this research by enriching this data with the Immigration, Refugees and Citizenship Canada Permanent Resident (IRCC-PR) database and the Office of the Registrar General's Vital Statistics-Death (ORG-VSD) registry. Our objectives were to estimate linkage rates and compare characteristics of individuals in the linked versus unlinked files. We used both deterministic and probabilistic linkage methods to link the IRCC-PR database (1985-2012) and ORG-VSD registry (1990-2012) to the Ontario's Registered Persons Database. Linkage rates were estimated and standardized differences were used to assess differences in socio-demographic and other characteristics between the linked and unlinked records. The overall linkage rates for the IRCC-PR database and ORG-VSD registry were 86.4 and 96.2 %, respectively. The majority (68.2 %) of the record linkages in IRCC-PR were achieved after three deterministic passes, 18.2 % were linked probabilistically, and 13.6 % were unlinked. Similarly the majority (79.8 %) of the record linkages in the ORG-VSD were linked using deterministic record linkage, 16.3 % were linked after probabilistic and manual review, and 3.9 % were unlinked. Unlinked and linked files were similar for most characteristics, such as age and marital status for IRCC-PR and sex and most causes of death for ORG-VSD. However, lower linkage rates were observed among people born in East Asia (78 %) in the IRCC-PR database and certain causes of death in the ORG-VSD registry, namely perinatal conditions (61.3 %) and congenital anomalies (81.3 %). The linkages of immigration and vital statistics data to existing population-based healthcare data in Ontario, Canada will enable many novel cross-sectional and longitudinal studies to be conducted. Analytic techniques to account for sub-optimal linkage rates may be required in studies of certain ethnic groups or certain causes of death among children and infants.

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps

PubMed Central

Jacobs, Guy S.; Sluckin, Timothy J.; Kivisild, Toomas

2016-01-01

During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly’s ZnS and ωmax) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly’s ZnS offers high power, but is outperformed by a novel statistic that we test, which we call Zα. We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics—ωmax, Kelly’s ZnS, and Zα—are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While ωmax replicates most candidates when recombination map data are not available, the ZnS and Zα statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available. PMID:27516617

The sumLINK statistic for genetic linkage analysis in the presence of heterogeneity.

PubMed

Christensen, G B; Knight, S; Camp, N J

2009-11-01

We present the "sumLINK" statistic--the sum of multipoint LOD scores for the subset of pedigrees with nominally significant linkage evidence at a given locus--as an alternative to common methods to identify susceptibility loci in the presence of heterogeneity. We also suggest the "sumLOD" statistic (the sum of positive multipoint LOD scores) as a companion to the sumLINK. sumLINK analysis identifies genetic regions of extreme consistency across pedigrees without regard to negative evidence from unlinked or uninformative pedigrees. Significance is determined by an innovative permutation procedure based on genome shuffling that randomizes linkage information across pedigrees. This procedure for generating the empirical null distribution may be useful for other linkage-based statistics as well. Using 500 genome-wide analyses of simulated null data, we show that the genome shuffling procedure results in the correct type 1 error rates for both the sumLINK and sumLOD. The power of the statistics was tested using 100 sets of simulated genome-wide data from the alternative hypothesis from GAW13. Finally, we illustrate the statistics in an analysis of 190 aggressive prostate cancer pedigrees from the International Consortium for Prostate Cancer Genetics, where we identified a new susceptibility locus. We propose that the sumLINK and sumLOD are ideal for collaborative projects and meta-analyses, as they do not require any sharing of identifiable data between contributing institutions. Further, loci identified with the sumLINK have good potential for gene localization via statistical recombinant mapping, as, by definition, several linked pedigrees contribute to each peak.

The Myocardial Ischaemia National Audit Project (MINAP)

PubMed Central

Smeeth, Liam; Walker, Lynne; Weston, Clive

2010-01-01

Aims of MINAP To audit the quality of care of patients with acute coronary syndrome and provide a resource for academic research. Quality of care interventions Feedback to hospitals, ambulance services and cardiac networks regarding benchmarking of performance against national standards and targets. Setting All 230 acute hospitals in England and Wales. Years: 2000-present. Population Consecutive patients, unconsented. Current number of records: 735 000. Startpoints Any acute coronary syndrome, including non-ST-elevation myocardial infarction, ST-elevation myocardial infarction and unstable angina. Baseline data 123 fields covering demographic factors, co-morbid conditions and treatment in hospital. No blood resource. Data capture Manual entry by clerks, nurses or doctors onto Lotus Notes; non-financial incentives at hospital level. Data quality Hospitals perform an annual data validation study, where data are re-entered from the case notes in 20 randomly selected records that are held on the server. In 2008 data were >90% complete for 20 key fields, with >80% completeness for all but four of the remaining fields. Endpoints and linkages to other data All-cause mortality is obtained through linkage with Office for National Statistics. No other linkages exist at present. Access to data Available for research and audit by application to the MINAP Academic Group. http://www.rcplondon.ac.uk/CLINICAL-STANDARDS/ORGANISATION/PARTNERSHIP/Pages/MINAP-.aspx. PMID:20659944

Ultra-low frequency vertical vibration isolator based on LaCoste spring linkage.

PubMed

Li, G; Hu, H; Wu, K; Wang, G; Wang, L J

2014-10-01

For the applications in precision measurement such as absolute gravimeter, we have designed and built an ultra-low frequency vertical vibration isolator based on LaCoste spring linkage. In the system, an arm with test mass is suspended by a mechanical extension spring, and one end of the arm is connected to the frame with flexible pivots. The displacement of the arm is detected by an optical reflection method. With the displacement signal, a feedback control force is exerted on the arm to keep it at the balance position. This method can also correct the systematic drift caused by temperature change. In order to study the vibration isolation performance of the system, we analyze the dynamic characteristics of the spring linkage in the general case, and present key methods to adjust the natural oscillating period of the system. With careful adjustment, the system can achieve a steady oscillation with a natural period up to 32 s. This isolator has been tested based on the T-1 absolute gravimeter. A statistical uncertainty of 2 μGal has been achieved within a typical 12 h measurement. The experimental results verify that the isolator has significant vibration isolation performance, and it is very suitable for applications in high precision absolute gravity measurement.

Ultra-low frequency vertical vibration isolator based on LaCoste spring linkage

NASA Astrophysics Data System (ADS)

Li, G.; Hu, H.; Wu, K.; Wang, G.; Wang, L. J.

2014-10-01

For the applications in precision measurement such as absolute gravimeter, we have designed and built an ultra-low frequency vertical vibration isolator based on LaCoste spring linkage. In the system, an arm with test mass is suspended by a mechanical extension spring, and one end of the arm is connected to the frame with flexible pivots. The displacement of the arm is detected by an optical reflection method. With the displacement signal, a feedback control force is exerted on the arm to keep it at the balance position. This method can also correct the systematic drift caused by temperature change. In order to study the vibration isolation performance of the system, we analyze the dynamic characteristics of the spring linkage in the general case, and present key methods to adjust the natural oscillating period of the system. With careful adjustment, the system can achieve a steady oscillation with a natural period up to 32 s. This isolator has been tested based on the T-1 absolute gravimeter. A statistical uncertainty of 2 μGal has been achieved within a typical 12 h measurement. The experimental results verify that the isolator has significant vibration isolation performance, and it is very suitable for applications in high precision absolute gravity measurement.

A systematic review and meta-analysis of community and facility-based approaches to address gaps in HIV testing and linkage in sub-Saharan Africa

PubMed Central

Sharma, Monisha; Ying, Roger; Tarr, Gillian; Barnabas, Ruanne

2016-01-01

HIV testing and counselling is the first crucial step for linkage to HIV treatment and prevention. However, despite high HIV burden in sub-Saharan Africa, testing coverage is low, particularly among young adults and men. Community-based HIV testing and counselling (testing outside of health facilities) has the potential to reduce coverage gaps, but the relative impact of different modalities is not well assessed. We conducted a systematic review of HIV testing and counselling modalities, characterizing facility and community (home, mobile, index, key populations, campaign, workplace and self-testing) approaches by population reached, HIV-positivity, CD4 count at diagnosis and linkage. Of 2,520 abstracts screened, 126 met eligibility criteria. Community HIV testing had high coverage and uptake and identified HIV-positive individuals at higher CD4 counts than facility testing. Mobile HIV testing reached the highest proportion of men of all modalities examined (50%, 95% CI = 47–54%) and home with self-testing reached the highest proportion of young adults (66%, 95% CI = 65–67%). Few studies evaluated HIV testing and counselling for key populations (commercial sex workers and men who have sex with men), but these interventions yielded high HIV positivity (38%, 95% CI = 19–62%) combined with the highest proportion of first-time testers (78%, 95% CI = 63–88%), indicating service gaps. Facilitated linkage (for example, counsellor follow-up to support linkage) achieved high linkage to care (95%, 95% CI = 87–98%) and ART initiation (75%, 95% CI = 68–82%). Expanding mobile HIV testing, self-testing and outreach to key populations with facilitated linkage can increase the proportion of men, young adults and high-risk individuals linked to HIV treatment and prevention. PMID:26633769

Distribution of lod scores in oligogenic linkage analysis.

PubMed

Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

2001-01-01

In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

Integrating statistical and clinical research elements in intervention-related grant applications: summary from an NIMH workshop.

PubMed

Sherrill, Joel T; Sommers, David I; Nierenberg, Andrew A; Leon, Andrew C; Arndt, Stephan; Bandeen-Roche, Karen; Greenhouse, Joel; Guthrie, Donald; Normand, Sharon-Lise; Phillips, Katharine A; Shear, M Katherine; Woolson, Robert

2009-01-01

The authors summarize points for consideration generated in a National Institute of Mental Health (NIMH) workshop convened to provide an opportunity for reviewers from different disciplines-specifically clinical researchers and statisticians-to discuss how their differing and complementary expertise can be well integrated in the review of intervention-related grant applications. A 1-day workshop was convened in October, 2004. The workshop featured panel presentations on key topics followed by interactive discussion. This article summarizes the workshop and subsequent discussions, which centered on topics including weighting the statistics/data analysis elements of an application in the assessment of the application's overall merit; the level of statistical sophistication appropriate to different stages of research and for different funding mechanisms; some key considerations in the design and analysis portions of applications; appropriate statistical methods for addressing essential questions posed by an application; and the role of the statistician in the application's development, study conduct, and interpretation and dissemination of results. A number of key elements crucial to the construction and review of grant applications were identified. It was acknowledged that intervention-related studies unavoidably involve trade-offs. Reviewers are helped when applications acknowledge such trade-offs and provide good rationale for their choices. Clear linkage among the design, aims, hypotheses, and data analysis plan and avoidance of disconnections among these elements also strengthens applications. The authors identify multiple points to consider when constructing intervention-related grant applications. The points are presented here as questions and do not reflect institute policy or comprise a list of best practices, but rather represent points for consideration.

The acceptability of conducting data linkage research without obtaining consent: lay people's views and justifications.

PubMed

Xafis, Vicki

2015-11-17

A key ethical issue arising in data linkage research relates to consent requirements. Patients' consent preferences in the context of health research have been explored but their consent preferences regarding data linkage specifically have been under-explored. In addition, the views on data linkage are often those of patient groups. As a result, little is known about lay people's views and their preferences about consent requirements in the context of data linkage. This study explores lay people's views and justifications regarding the acceptability of conducting data linkage research without obtaining consent. A qualitative study explored lay people's views regarding consent requirements in data linkage via four hypothetical data linkage scenarios of increasing complexity. Prior to considering the scenarios, participants were provided with information regarding best practice data linkage processes via discussion and a diagrammatic representation of the process. Lay people were able to understand the intricate processes involved in data linkage and the key protections afforded within a short amount of time. They were supportive of data linkage research and, on the whole, believed it should be conducted without consent provided a data linkage organization de-identifies the data used so that researchers do not handle identifiable data. Many thought that de-identified data holds a different status to identifiable data and should be used without specific consent in research that aims to benefit society. In weighing up conflicting values and interests, participants shifted consent preferences before arriving at their final consent preference for each scenario and provided justifications for their choices. They considered the protection of people's information, societal benefits, and the nature and constraints of research and recognized that these need to be balanced. With some exposure to the features of data linkage, lay people have the capacity to understand the processes sufficiently in order to consider ethical issues associated with consent preferences. Shifts in views reveal the complexity of such decisions. While privacy protection remained an important consideration for most participants, adequate protection measures adopted in best practice data linkage were viewed by most as protection enough for data linkage to proceed without specific individual consent.

Significant linkage to airway responsiveness on chromosome 12q24 in families of children with asthma in Costa Rica.

PubMed

Celedón, Juan C; Soto-Quiros, Manuel E; Avila, Lydiana; Lake, Stephen L; Liang, Catherine; Fournier, Eduardo; Spesny, Mitzi; Hersh, Craig P; Sylvia, Jody S; Hudson, Thomas J; Verner, Andrei; Klanderman, Barbara J; Freimer, Nelson B; Silverman, Edwin K; Weiss, Scott T

2007-01-01

Although asthma is a major public health problem in certain Hispanic subgroups in the United States and Latin America, only one genome scan for asthma has included Hispanic individuals. Because of small sample size, that study had limited statistical power to detect linkage to asthma and its intermediate phenotypes in Hispanic participants. To identify genomic regions that contain susceptibility genes for asthma and airway responsiveness in an isolated Hispanic population living in the Central Valley of Costa Rica, we conducted a genome-wide linkage analysis of asthma (n = 638) and airway responsiveness (n = 488) in members of eight large pedigrees of Costa Rican children with asthma. Nonparametric multipoint linkage analysis of asthma was conducted by the NPL-PAIR allele-sharing statistic, and variance component models were used for the multipoint linkage analysis of airway responsiveness as a quantitative phenotype. All linkage analyses were repeated after exclusion of the phenotypic data of former and current smokers. Chromosome 12q showed some evidence of linkage to asthma, particularly in nonsmokers (P < 0.01). Among nonsmokers, there was suggestive evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 2.33 at 146 cM). After genotyping 18 additional short-tandem repeat markers on chromosome 12q, there was significant evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 3.79 at 144 cM), with a relatively narrow 1.5-LOD unit support interval for the observed linkage peak (142-147 cM). Our results suggest that chromosome 12q24.31 contains a locus (or loci) that influence a critical intermediate phenotype of asthma (airway responsiveness) in Costa Ricans.

Tests for linkage and association in nuclear families.

PubMed Central

Martin, E R; Kaplan, N L; Weir, B S

1997-01-01

The transmission/disequilibrium test (TDT) originally was introduced to test for linkage between a genetic marker and a disease-susceptibility locus, in the presence of association. Recently, the TDT has been used to test for association in the presence of linkage. The motivation for this is that linkage analysis typically identifies large candidate regions, and further refinement is necessary before a search for the disease gene is begun, on the molecular level. Evidence of association and linkage may indicate which markers in the region are closest to a disease locus. As a test of linkage, transmissions from heterozygous parents to all of their affected children can be included in the TDT; however, the TDT is a valid chi2 test of association only if transmissions to unrelated affected children are used in the analysis. If the sample contains independent nuclear families with multiple affected children, then one procedure that has been used to test for association is to select randomly a single affected child from each sibship and to apply the TDT to those data. As an alternative, we propose two statistics that use data from all of the affected children. The statistics give valid chi2 tests of the null hypothesis of no association or no linkage and generally are more powerful than the TDT with a single, randomly chosen, affected child from each family. PMID:9311750

Estimation and test for linkage between markers: a comparison of lod score and χ (2) test in a linkage study of maritime pine (Pinus pinaster Ait.).

PubMed

Gerber, S; Rodolphe, F

1994-06-01

The first step in the construction of a linkage map involves the estimation and test for linkage between all possible pairs of markers. The lod score method is used in many linkage studies for the latter purpose. In contrast with classical statistical tests, this method does not rely on the choice of a first-type error level. We thus provide a comparison between the lod score and a χ (2) test on linkage data from a gymnosperm, the maritime pine. The lod score appears to be a very conservative test with the usual thresholds. Its severity depends on the type of data used.

Developing the design of a continuous national health survey for New Zealand

PubMed Central

2013-01-01

Background A continuously operating survey can yield advantages in survey management, field operations, and the provision of timely information for policymakers and researchers. We describe the key features of the sample design of the New Zealand (NZ) Health Survey, which has been conducted on a continuous basis since mid-2011, and compare to a number of other national population health surveys. Methods A number of strategies to improve the NZ Health Survey are described: implementation of a targeted dual-frame sample design for better Māori, Pacific, and Asian statistics; movement from periodic to continuous operation; use of core questions with rotating topic modules to improve flexibility in survey content; and opportunities for ongoing improvements and efficiencies, including linkage to administrative datasets. Results and discussion The use of disproportionate area sampling and a dual frame design resulted in reductions of approximately 19%, 26%, and 4% to variances of Māori, Pacific and Asian statistics respectively, but at the cost of a 17% increase to all-ethnicity variances. These were broadly in line with the survey’s priorities. Respondents provided a high degree of cooperation in the first year, with an adult response rate of 79% and consent rates for data linkage above 90%. Conclusions A combination of strategies tailored to local conditions gives the best results for national health surveys. In the NZ context, data from the NZ Census of Population and Dwellings and the Electoral Roll can be used to improve the sample design. A continuously operating survey provides both administrative and statistical advantages. PMID:24364838

Key practices for implementing geospatial technologies for a planning and environment linkages (PEL) approach

DOT National Transportation Integrated Search

2008-07-01

This report presents three case studies that illustrate how geographic information systems (GIS) have been used to implement the Federal Highway Administrations (FHWA) Planning and Environment Linkages (PEL) approach. The PEL approach provides inf...

Tracking linkage to HIV care for former prisoners

PubMed Central

Montague, Brian T.; Rosen, David L.; Solomon, Liza; Nunn, Amy; Green, Traci; Costa, Michael; Baillargeon, Jacques; Wohl, David A.; Paar, David P.; Rich, Josiah D.; Study Group, on behalf of the LINCS

2012-01-01

Improving testing and uptake to care among highly impacted populations is a critical element of Seek, Test, Treat and Retain strategies for reducing HIV incidence in the community. HIV disproportionately impacts prisoners. Though, incarceration provides an opportunity to diagnose and initiate therapy, treatment is frequently disrupted after release. Though model programs exist to support linkage to care on release, there is a lack of scalable metrics with which to assess adequacy of linkage to care after release. The linking data from Ryan White program Client Level Data (CLD) files reported to HRSA with corrections release data offers an attractive means of generating these metrics. Identified only by use of a confidential encrypted Unique Client Identifier (eUCI) these CLD files allow collection of key clinical indicators across the system of Ryan White funded providers. Using eUCIs generated from corrections release data sets as a linkage tool, the time to the first service at community providers along with key clinical indicators of patient status at entry into care can be determined as measures of linkage adequacy. Using this strategy, high and low performing sites can be identified and best practices can be identified to reproduce these successes in other settings. PMID:22561157

Introductory Guide to the Statistics of Molecular Genetics

ERIC Educational Resources Information Center

Eley, Thalia C.; Rijsdijk, Fruhling

2005-01-01

Background: This introductory guide presents the main two analytical approaches used by molecular geneticists: linkage and association. Methods: Traditional linkage and association methods are described, along with more recent advances in methodologies such as those using a variance components approach. Results: New methods are being developed all…

Rural Resources.

ERIC Educational Resources Information Center

Novak, Kathy

Designed as a resource for rural adult basic education (ABE) program planners, this guidebook describes model linkage strategies between ABE and job placement as well as ABE and job training services that are targeted to rural Americans. The following topics are addressed in the guide: key linkage strategies (community advisory councils,…

Joint QTL linkage mapping for multiple-cross mating design sharing one common parent

USDA-ARS?s Scientific Manuscript database

Nested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present th...

Developments in Transnational Research Linkages: Evidence from U.S. Higher-Education Activity

ERIC Educational Resources Information Center

Koehn, Peter H.

2014-01-01

In our knowledge-driven era, multiple and mutual benefits accrue from transnational research linkages. The article identifies important directions in transnational research collaborations involving U.S. universities revealed by key dimensions of 369 projects profiled on a U.S. higher-education association's database. Project initiators, principal…

Evaluating privacy-preserving record linkage using cryptographic long-term keys and multibit trees on large medical datasets.

PubMed

Brown, Adrian P; Borgs, Christian; Randall, Sean M; Schnell, Rainer

2017-06-08

Integrating medical data using databases from different sources by record linkage is a powerful technique increasingly used in medical research. Under many jurisdictions, unique personal identifiers needed for linking the records are unavailable. Since sensitive attributes, such as names, have to be used instead, privacy regulations usually demand encrypting these identifiers. The corresponding set of techniques for privacy-preserving record linkage (PPRL) has received widespread attention. One recent method is based on Bloom filters. Due to superior resilience against cryptographic attacks, composite Bloom filters (cryptographic long-term keys, CLKs) are considered best practice for privacy in PPRL. Real-world performance of these techniques using large-scale data is unknown up to now. Using a large subset of Australian hospital admission data, we tested the performance of an innovative PPRL technique (CLKs using multibit trees) against a gold-standard derived from clear-text probabilistic record linkage. Linkage time and linkage quality (recall, precision and F-measure) were evaluated. Clear text probabilistic linkage resulted in marginally higher precision and recall than CLKs. PPRL required more computing time but 5 million records could still be de-duplicated within one day. However, the PPRL approach required fine tuning of parameters. We argue that increased privacy of PPRL comes with the price of small losses in precision and recall and a large increase in computational burden and setup time. These costs seem to be acceptable in most applied settings, but they have to be considered in the decision to apply PPRL. Further research on the optimal automatic choice of parameters is needed.

Normalization Ridge Regression in Practice II: The Estimation of Multiple Feedback Linkages.

ERIC Educational Resources Information Center

Bulcock, J. W.

The use of the two-stage least squares (2 SLS) procedure for estimating nonrecursive social science models is often impractical when multiple feedback linkages are required. This is because 2 SLS is extremely sensitive to multicollinearity. The standard statistical solution to the multicollinearity problem is a biased, variance reduced procedure…

Preliminary evidence for linkage to chromosome 1q31-32, 10q23.3, and 16p13.3 in a South African cohort with bipolar disorder.

PubMed

Savitz, Jonathan; Cupido, Cinda-Lee; Ramesar, Raj Kumar

2007-04-05

Although the genetic variants predisposing to the development of bipolar disorder (BPD) have yet to be conclusively identified, replicated reports of linkage to particular chromosomal regions have been encouraging. Here we carried out a non-parametric linkage analysis of nine of these candidate loci in a unique South African sample of 47 BPD pedigrees (N = 350). Three polymorphic markers per region of interest (3 x 9) were typed in a Caucasian cohort of Afrikaner and British origin. Statistically significant evidence for linkage was obtained at 1q31-32, 10q23.3, and 16p13.3 with maximum NPL scores of 2.52, 2.01, and 1.84, respectively. Our results add to the growing evidence that these chromosomal regions harbor genetic variants that play a role in the development of bipolar spectrum illness. Negative results were obtained for the remaining six candidate loci, possibly due to limited statistical power. (c) 2006 Wiley-Liss, Inc.

Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

USDA-ARS?s Scientific Manuscript database

A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

THE LINK NURSE ROLE IN END OF LIFE CARE IN AGED CARE.

PubMed

Rosenberg, John

2016-08-01

The care of older people at the end of life is a key element of primary and community care. The Decision Assist -- Palliative Care Linkages project aimed to improve end of life care given to older Australians through establishing linkages between aged care and specialist palliative care services.

Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families.

PubMed

Bailey-Wilson, Joan E; Childs, Erica J; Cropp, Cheryl D; Schaid, Daniel J; Xu, Jianfeng; Camp, Nicola J; Cannon-Albright, Lisa A; Farnham, James M; George, Asha; Powell, Isaac; Carpten, John D; Giles, Graham G; Hopper, John L; Severi, Gianluca; English, Dallas R; Foulkes, William D; Mæhle, Lovise; Møller, Pål; Eeles, Rosalind; Easton, Douglas; Guy, Michelle; Edwards, Steve; Badzioch, Michael D; Whittemore, Alice S; Oakley-Girvan, Ingrid; Hsieh, Chih-Lin; Dimitrov, Latchezar; Stanford, Janet L; Karyadi, Danielle M; Deutsch, Kerry; McIntosh, Laura; Ostrander, Elaine A; Wiley, Kathleen E; Isaacs, Sarah D; Walsh, Patrick C; Thibodeau, Stephen N; McDonnell, Shannon K; Hebbring, Scott; Lange, Ethan M; Cooney, Kathleen A; Tammela, Teuvo L J; Schleutker, Johanna; Maier, Christiane; Bochum, Sylvia; Hoegel, Josef; Grönberg, Henrik; Wiklund, Fredrik; Emanuelsson, Monica; Cancel-Tassin, Geraldine; Valeri, Antoine; Cussenot, Olivier; Isaacs, William B

2012-06-19

Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.

Correlation between quantitative traits and correlation between corresponding LOD scores: detection of pleiotropic effects.

PubMed

Ulgen, Ayse; Han, Zhihua; Li, Wentian

2003-12-31

We address the question of whether statistical correlations among quantitative traits lead to correlation of linkage results of these traits. Five measured quantitative traits (total cholesterol, fasting glucose, HDL cholesterol, blood pressure, and triglycerides), and one derived quantitative trait (total cholesterol divided by the HDL cholesterol) are used for phenotype correlation studies. Four of them are used for linkage analysis. We show that although correlation among phenotypes partially reflects the correlation among linkage analysis results, the LOD-score correlations are on average low. The most significant peaks found by using different traits do not often overlap. Studying covariances at specific locations in LOD scores may provide clues for further bivariate linkage analyses.

Role of University-Industry-Government Linkages in the Innovation Processes of a Small Catching-Up Economy

ERIC Educational Resources Information Center

Varblane, Urmas; Mets, Tonis; Ukrainski, Kadri

2008-01-01

During the transformation process from a command economy, the extraordinary statist university-industry-government (UIG) linkages model was replaced by an extreme version of laissez-faire relationships. A more modern interaction-based UIG model could be implemented only by changing the whole national innovation system of catching-up economies. The…

Development Co-operation and Linkages in Higher Education: Key Issues Concerning Policy and Organisation

NASA Astrophysics Data System (ADS)

van Audenhove, Leo

1998-09-01

The term linkage is used to indicate co-operation between an institution in the North and an institution in the South. Donor organisations have generally used linkages to support the development of higher education and research in developing countries. Over time, there has been a trend away from co-operation on individual academic projects towards broader development co- operation and concentration on selected institutions. This shift raises questions about organisation, procedures and support mechanisms, and about the mandate and capabilities of universities in the North, given the frequently asymmetrical relationship between Northern institutions with their own research agendas and Southern beneficiaries. The recent restructuring of Canadian, Dutch, Norwegian and Swedish support for higher education and research is the result of a search for new, more appropriate models of co-operation. This paper examines the evolution of key issues of policy and organisation within the international donor community.

Delivering proportionate governance in the era of eHealth

PubMed Central

Sethi, Nayha; Laurie, Graeme T.

2013-01-01

This article advances a principled proportionate governance model (PPGM) that overcomes key impediments to using health records for research. Despite increasing initiatives for maximising benefits of data linkage, significant challenges remain, including a culture of caution around data sharing and linkage, failure to make use of flexibilities within the law and failure to incorporate intelligent iterative design. The article identifies key issues for consideration and posits a flexible and accessible governance model that provides a robust and efficient means of paying due regard to both privacy and the public interests in research. We argue that proportionate governance based on clear guiding principles accurately gauges risks associated with data uses and assigns safeguards accordingly. This requires a clear articulation of roles and responsibilities at all levels of decision-making and effective training for researchers and data custodians. Accordingly, the PPGM encourages and supports defensible judgements about data linkage in the public interest. PMID:24634569

An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

PubMed

Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

2006-08-01

Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

Detecting temporal change in freshwater fisheries surveys: statistical power and the important linkages between management questions and monitoring objectives

USGS Publications Warehouse

Wagner, Tyler; Irwin, Brian J.; James R. Bence,; Daniel B. Hayes,

2016-01-01

Monitoring to detect temporal trends in biological and habitat indices is a critical component of fisheries management. Thus, it is important that management objectives are linked to monitoring objectives. This linkage requires a definition of what constitutes a management-relevant “temporal trend.” It is also important to develop expectations for the amount of time required to detect a trend (i.e., statistical power) and for choosing an appropriate statistical model for analysis. We provide an overview of temporal trends commonly encountered in fisheries management, review published studies that evaluated statistical power of long-term trend detection, and illustrate dynamic linear models in a Bayesian context, as an additional analytical approach focused on shorter term change. We show that monitoring programs generally have low statistical power for detecting linear temporal trends and argue that often management should be focused on different definitions of trends, some of which can be better addressed by alternative analytical approaches.

31. VIEW NORTHEAST OF OPERATING MACHINERY. GEAR 'C5' IS AT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

31. VIEW NORTHEAST OF OPERATING MACHINERY. GEAR 'C5' IS AT LOWER LEFT AND EMERGENCY BRAKE MECHANISM ON PEDESTAL AT CENTER. NOTE LOWER EQUALIZING LINKAGE FOR COUNTERWEIGHT AT LEFT CENTER OF PHOTOGRAPH - THIS WAS A KEY COMPONENT OF STRAUSS' PATENT PARALLOGRAM LINKAGE - Tomlinson Bridge, Spanning Quinnipiac River at Forbes Street (U.S. Route 1), New Haven, New Haven County, CT

Evaluating Health Outcomes of Criminal Justice Populations Using Record Linkage: The Importance of Aliases

ERIC Educational Resources Information Center

Larney, Sarah; Burns, Lucy

2011-01-01

Individuals in contact with the criminal justice system are a key population of concern to public health. Record linkage studies can be useful for studying health outcomes for this group, but the use of aliases complicates the process of linking records across databases. This study was undertaken to determine the impact of aliases on sensitivity…

Links between Home and School among Low-Income Mexican-American and European-American Families. Educational Practice Report: 9.

ERIC Educational Resources Information Center

Azmitia, Margarita; And Others

This report shows that, in low-income Mexican-American and European-American families, children's everyday learning activities at home and aspirations of parents for their children's future are key elements in home-school linkages. Two models of home-school linkages are reviewed: the cultural match/mismatch model and the two-way partnership…

Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families

PubMed Central

2012-01-01

Background Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. Methods Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. Results Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2–3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. Conclusions Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2–3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region. PMID:22712434

Allele-sharing models: LOD scores and accurate linkage tests.

PubMed

Kong, A; Cox, N J

1997-11-01

Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

Allele-sharing models: LOD scores and accurate linkage tests.

PubMed Central

Kong, A; Cox, N J

1997-01-01

Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested. PMID:9345087

Systematic Parameterization of Lignin for the CHARMM Force Field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg

Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization formore » emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between disparate feedstocks, and guide further lignin engineering efforts.« less

[A network to promote health systems based on primary health care in the Region of the Americas].

PubMed

Herrera Vázquez, María Magdalena; Rodríguez Avila, Nuria; Nebot Adell, Carme; Montenegro, Hernán

2007-05-01

To identify the relational components of an international network of organizations that provide technical and financial assistance to promote the development of health systems based on primary health care in the countries of the Region of the Americas; to analyze the linkages that would allow the collaborating partners of the Pan American Health Organization (PAHO) to work together on health issues; and to determine the basic theoretical elements that can help to develop action strategies that support advocacy efforts by a network. This was a qualitative and quantitative cross-sectional study based on identifying key informants and on analyzing social networks. Ethnographic and relational information from 46 international organizations was collected through a self-administered semistructured questionnaire. From 46 international health cooperation organizations, 29 decision makers from 29 organizations participated (63.0% response rate). The structure and the strength of the network was evaluated in terms of density, closeness, clustering, and centralization. The statistical analysis was done using computer programs that included UCINET, Pajek, and Microsoft Access. We found a structurally centralized theoretical network, whose nodes were clustered into four central subgroups linked by a shared vision. The leadership, influence, and political interests reflected the formal and technical-cooperation linkages, the formal support for health systems based on primary health care, and the flow of resources being more often technical ones than financial ones. The interorganizational relational components and the social-action ties that were identified could help in the development and consolidation of a thematic network for advocacy and for the management of technical and financial assistance that supports primary health care in the Americas. The linkages for joint action that were identified could advance international cooperation in developing health systems based on primary health care, once PAHO formulates clear implementation strategies and takes a leadership position in mobilizing financial resources and in creating informal and interpersonal linkages for action.

Robust LOD scores for variance component-based linkage analysis.

PubMed

Blangero, J; Williams, J T; Almasy, L

2000-01-01

The variance component method is now widely used for linkage analysis of quantitative traits. Although this approach offers many advantages, the importance of the underlying assumption of multivariate normality of the trait distribution within pedigrees has not been studied extensively. Simulation studies have shown that traits with leptokurtic distributions yield linkage test statistics that exhibit excessive Type I error when analyzed naively. We derive analytical formulae relating the deviation from the expected asymptotic distribution of the lod score to the kurtosis and total heritability of the quantitative trait. A simple correction constant yields a robust lod score for any deviation from normality and for any pedigree structure, and effectively eliminates the problem of inflated Type I error due to misspecification of the underlying probability model in variance component-based linkage analysis.

Linkage analysis of chromosome 22q12-13 in a United Kingdom/Icelandic sample of 23 multiplex schizophrenia families

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalsi, G.; Read, T.; Butler, R.

A possible linkage to a genetic subtype of schizophrenia and related disorders has been reported on the long arm of chromosome 22 at q12-13. However formal statistical tests in a combined sample could not reject homogeneity and prove that there was linked subgroup of families. We have studied 23 schizophrenia pedigrees to test whether some multiplex schizophrenia families may be linked to the microsatellite markers D22S274 and D22S283 which span the 22q12-13 region. Two point followed by multipoint lod and non-parametric linkage analyses under the assumption of heterogeneity provided no evidence for linkage over the relevant region. 16 refs., 4more » tabs.« less

A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

PubMed

Boyd, James H; Guiver, Tenniel; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Anderson, Phil; Dickinson, Teresa

2016-05-17

Record linkage techniques allow different data collections to be brought together to provide a wider picture of the health status of individuals. Ensuring high linkage quality is important to guarantee the quality and integrity of research. Current methods for measuring linkage quality typically focus on precision (the proportion of incorrect links), given the difficulty of measuring the proportion of false negatives. The aim of this work is to introduce and evaluate a sampling based method to estimate both precision and recall following record linkage. In the sampling based method, record-pairs from each threshold (including those below the identified cut-off for acceptance) are sampled and clerically reviewed. These results are then applied to the entire set of record-pairs, providing estimates of false positives and false negatives. This method was evaluated on a synthetically generated dataset, where the true match status (which records belonged to the same person) was known. The sampled estimates of linkage quality were relatively close to actual linkage quality metrics calculated for the whole synthetic dataset. The precision and recall measures for seven reviewers were very consistent with little variation in the clerical assessment results (overall agreement using the Fleiss Kappa statistics was 0.601). This method presents as a possible means of accurately estimating matching quality and refining linkages in population level linkage studies. The sampling approach is especially important for large project linkages where the number of record pairs produced may be very large often running into millions.

Genetic Alterations in Familial Breast Cancer: Mapping and Cloning Genes Other Than BRCAl

DTIC Science & Technology

1997-09-01

predisposition to breast cancer in families. The gene PTEN was successfully cloned by this project, and simultaneously by others (for a different ...with germline translocations’and breast cancer for the identification of tumor suppressor genes. 14. SUBJECT TERMS Breast cancer 17. SECURITY...would limit the statistical power of linkage analysis. Therefore, we decided to integrate linkage analysis with the analysis of germline chromosomal

Possible connections of the opposite trends in Arctic and Antarctic sea-ice cover.

PubMed

Yu, Lejiang; Zhong, Shiyuan; Winkler, Julie A; Zhou, Mingyu; Lenschow, Donald H; Li, Bingrui; Wang, Xianqiao; Yang, Qinghua

2017-04-05

Sea ice is an important component of the global climate system and a key indicator of climate change. A decreasing trend in Arctic sea-ice concentration is evident in recent years, whereas Antarctic sea-ice concentration exhibits a generally increasing trend. Various studies have investigated the underlying causes of the observed trends for each region, but possible linkages between the regional trends have not been studied. Here, we hypothesize that the opposite trends in Arctic and Antarctic sea-ice concentration may be linked, at least partially, through interdecadal variability of the Pacific Decadal Oscillation (PDO) and the Atlantic Multidecadal Oscillation (AMO). Although evaluation of this hypothesis is constrained by the limitations of the sea-ice cover record, preliminary statistical analyses of one short-term and two long-term time series of observed and reanalysis sea-ice concentrations data suggest the possibility of the hypothesized linkages. For all three data sets, the leading mode of variability of global sea-ice concentration is positively correlated with the AMO and negatively correlated with the PDO. Two wave trains related to the PDO and the AMO appear to produce anomalous surface-air temperature and low-level wind fields in the two polar regions that contribute to the opposite changes in sea-ice concentration.

Cardiac registers: the adult cardiac surgery register.

PubMed

Bridgewater, Ben

2010-09-01

AIMS OF THE SCTS ADULT CARDIAC SURGERY DATABASE: To measure the quality of care of adult cardiac surgery in GB and Ireland and provide information for quality improvement and research. Feedback of structured data to hospitals, publication of named hospital and surgeon mortality data, publication of benchmarked activity and risk adjusted clinical outcomes through intermittent comprehensive database reports, annual screening of all hospital and individual surgeon risk adjusted mortality rates by the professional society. All NHS hospitals in England, Scotland and Wales with input from some private providers and hospitals in Ireland. 1994-ongoing. Consecutive patients, unconsented. Current number of records: 400000. Adult cardiac surgery operations excluding cardiac transplantation and ventricular assist devices. 129 fields covering demographic factors, pre-operative risk factors, operative details and post-operative in-hospital outcomes. Entry onto local software systems by direct key board entry or subsequent transcription from paper records, with subsequent electronic upload to the central cardiac audit database. Non-financial incentives at hospital level. Local validation processes exist in the hospitals. There is currently no external data validation process. All cause mortality is obtained through linkage with Office for National Statistics. No other linkages exist at present. Available for research and audit by application to the SCTS database committee at http://www.scts.org.

Possible connections of the opposite trends in Arctic and Antarctic sea-ice cover

PubMed Central

Yu, Lejiang; Zhong, Shiyuan; Winkler, Julie A.; Zhou, Mingyu; Lenschow, Donald H.; Li, Bingrui; Wang, Xianqiao; Yang, Qinghua

2017-01-01

Sea ice is an important component of the global climate system and a key indicator of climate change. A decreasing trend in Arctic sea-ice concentration is evident in recent years, whereas Antarctic sea-ice concentration exhibits a generally increasing trend. Various studies have investigated the underlying causes of the observed trends for each region, but possible linkages between the regional trends have not been studied. Here, we hypothesize that the opposite trends in Arctic and Antarctic sea-ice concentration may be linked, at least partially, through interdecadal variability of the Pacific Decadal Oscillation (PDO) and the Atlantic Multidecadal Oscillation (AMO). Although evaluation of this hypothesis is constrained by the limitations of the sea-ice cover record, preliminary statistical analyses of one short-term and two long-term time series of observed and reanalysis sea-ice concentrations data suggest the possibility of the hypothesized linkages. For all three data sets, the leading mode of variability of global sea-ice concentration is positively correlated with the AMO and negatively correlated with the PDO. Two wave trains related to the PDO and the AMO appear to produce anomalous surface-air temperature and low-level wind fields in the two polar regions that contribute to the opposite changes in sea-ice concentration. PMID:28378830

High-frequency stock linkage and multi-dimensional stationary processes

NASA Astrophysics Data System (ADS)

Wang, Xi; Bao, Si; Chen, Jingchao

2017-02-01

In recent years, China's stock market has experienced dramatic fluctuations; in particular, in the second half of 2014 and 2015, the market rose sharply and fell quickly. Many classical financial phenomena, such as stock plate linkage, appeared repeatedly during this period. In general, these phenomena have usually been studied using daily-level data or minute-level data. Our paper focuses on the linkage phenomenon in Chinese stock 5-second-level data during this extremely volatile period. The method used to select the linkage points and the arbitrage strategy are both based on multi-dimensional stationary processes. A new program method for testing the multi-dimensional stationary process is proposed in our paper, and the detailed program is presented in the paper's appendix. Because of the existence of the stationary process, the strategy's logarithmic cumulative average return will converge under the condition of the strong ergodic theorem, and this ensures the effectiveness of the stocks' linkage points and the more stable statistical arbitrage strategy.

Linkage mapping of beta 2 EEG waves via non-parametric regression.

PubMed

Ghosh, Saurabh; Begleiter, Henri; Porjesz, Bernice; Chorlian, David B; Edenberg, Howard J; Foroud, Tatiana; Goate, Alison; Reich, Theodore

2003-04-01

Parametric linkage methods for analyzing quantitative trait loci are sensitive to violations in trait distributional assumptions. Non-parametric methods are relatively more robust. In this article, we modify the non-parametric regression procedure proposed by Ghosh and Majumder [2000: Am J Hum Genet 66:1046-1061] to map Beta 2 EEG waves using genome-wide data generated in the COGA project. Significant linkage findings are obtained on chromosomes 1, 4, 5, and 15 with findings at multiple regions on chromosomes 4 and 15. We analyze the data both with and without incorporating alcoholism as a covariate. We also test for epistatic interactions between regions of the genome exhibiting significant linkage with the EEG phenotypes and find evidence of epistatic interactions between a region each on chromosome 1 and chromosome 4 with one region on chromosome 15. While regressing out the effect of alcoholism does not affect the linkage findings, the epistatic interactions become statistically insignificant. Copyright 2003 Wiley-Liss, Inc.

The centrality of laboratory services in the HIV treatment and prevention cascade: The need for effective linkages and referrals in resource-limited settings.

PubMed

Alemnji, George; Fonjungo, Peter; Van Der Pol, Barbara; Peter, Trevor; Kantor, Rami; Nkengasong, John

2014-05-01

Strong laboratory services and systems are critical for delivering timely and quality health services that are vital to reduce patient attrition in the HIV treatment and prevention cascade. However, challenges exist in ensuring effective laboratory health systems strengthening and linkages. In particular, linkages and referrals between laboratory testing and other services need to be considered in the context of an integrated health system that includes prevention, treatment, and strategic information. Key components of laboratory health systems that are essential for effective linkages include an adequate workforce, appropriate point-of-care (POC) technology, available financing, supply chain management systems, and quality systems improvement, including accreditation. In this review, we highlight weaknesses of and gaps between laboratory testing and other program services. We propose a model for strengthening these systems to ensure effective linkages of laboratory services for improved access and retention in care of HIV/AIDS patients, particularly in low- and middle-income countries.

The HepHIV 2017 Conference in Malta: joining forces for the earlier diagnosis of HIV and viral hepatitis.

PubMed

Raben, D; Hoekstra, M; Sperle, I; Amato Gauci, A J; Gauci, C; West, B; Sullivan, A; Lazarus, J V; Platteau, T; Rockstroh, J K

2018-02-01

The objective of the article is to provide an overview of the results of the HepHIV 2017 Conference organized by the HIV in Europe initiative under the Maltese EU Presidency in January 2017. A thourough review of all conference presentations (oral and poster presentations) was performed to retrieve the key outcomes of the conference. The key result from the conference was a call to action summarising key priorities in HIV and viral hepatitis testing and linkage to care. This included improving monitoring of viral hepatitis and HIV, mixing testing strategies and ensuring policy support. The important contribution and outcomes of EU funded projects OptTEST and EuroHIVEdat was highlighted. An integrated approach to earlier testing and linkage to care across diseases is needed in Europe and the HepHIV conferences create an important forum to reach this aim. © 2018 British HIV Association.

A procedure for linking psychosocial job characteristics data to health surveys.

PubMed Central

Schwartz, J E; Pieper, C F; Karasek, R A

1988-01-01

A system is presented for linking information about psychosocial characteristics of job situations to national health surveys. Job information can be imputed to individuals on surveys that contain three-digit US Census occupation codes. Occupational mean scores on psychosocial job characteristics-control over task situation (decision latitude), psychological work load, physical exertion, and other measures-for the linkage system are derived from US national surveys of working conditions (Quality of Employment Surveys 1969, 1972, and 1977). This paper discusses a new method for reducing the biases in multivariate analyses that are likely to arise when utilizing linkage systems based on mean scores. Such biases are reduced by modifying the linkage system to adjust imputed individual scores for demographic factors such as age, education, race, marital status and, implicitly, sex (since men and women have separate linkage data bases). Statistics on the linkage system's efficiency and reliability are reported. All dimensions have high inter-survey reproducibility. Despite their psychosocial nature, decision latitude and physical exertion can be more efficiently imputed with the linkage system than earnings (a non-psychosocial job characteristic). The linkage system presented here is a useful tool for initial epidemiological studies of the consequences of psychosocial job characteristics and constitutes the methodological basis for the subsequent paper. PMID:3389426

Relative Linkages of Chlorophyll-a with the Hydroclimatic and Biogeochemical Variables across the Continental U.S. (CONUS)

NASA Astrophysics Data System (ADS)

Ahmed, M. H.; Abdul-Aziz, O. I.

2017-12-01

Chlorophyll-a (Chl-a) is a key indicator for stream water quality and ecological health. The characterization of interplay between Chl-a and its numerous hydroclimatic and biogeochemical drivers is complex, and often involves multicollinear datasets. A systematic data analytics methodology was employed to determine the relative linkages of stream Chl-a with its dynamic environmental drivers at 50 stream water quality monitoring stations across the continental U.S. Multivariate statistical techniques of principal component analysis (PCA) and factor analysis (FA), in concert with Pearson correlation analysis, were applied to evaluate interrelationships among hydroclimatic, biogeochemical, and biological variables. Power-law based partial least square regression (PLSR) models were developed with a bootstrap Monte Carlo procedure (1000 iterations) to reliably estimate the comparative linkages of Chl-a by resolving multicollinearity in the data matrices (Nash-Sutcliff efficiency = 0.50-87). The data analytics suggested four environmental regimes of stream Chl-a, as dominated by nutrient, climate, redox, and hydro-atmospheric contributions, respectively. Total phosphorous (TP) was the most dominant driver of stream Chl-a in the nutrient controlled regime. Water temperature demonstrated the strongest control of Chl-a in the climate-dominated regime. Furthermore, pH and stream flow were found to be the most important drivers of Chl-a in the redox and hydro-atmospheric component dominated regimes, respectively. The research led to a significant reduction of dimensionality in the large data matrices, providing quantitative and qualitative insights on the dynamics of stream Chl-a. The findings would be useful to manage stream water quality and ecosystem health in the continental U.S. and around the world under a changing climate and environment.

Beyond Metrics? The Role of Hydrologic Baseline Archetypes in Environmental Water Management.

PubMed

Lane, Belize A; Sandoval-Solis, Samuel; Stein, Eric D; Yarnell, Sarah M; Pasternack, Gregory B; Dahlke, Helen E

2018-06-22

Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics. Here we propose the additional use of high-resolution dimensionless archetypes of regional stream classes to improve understanding of baseline hydrologic conditions and inform regional environmental flows assessments. In an application to California, we describe the development and analysis of hydrologic baseline archetypes to characterize patterns of flow variability within and between stream classes. We then assess the utility of archetypes to provide context for common flow metrics and improve understanding of linkages between aquatic patterns and processes and their hydrologic controls. Results indicate that these archetypes may offer a distinct and complementary tool for researching mechanistic flow-ecology relationships, assessing regional patterns for streamflow management, or understanding impacts of changing climate.

Joint multi-population analysis for genetic linkage of bipolar disorder or "wellness" to chromosome 4p.

PubMed

Visscher, P M; Haley, C S; Ewald, H; Mors, O; Egeland, J; Thiel, B; Ginns, E; Muir, W; Blackwood, D H

2005-02-05

To test the hypothesis that the same genetic loci confer susceptibility to, or protection from, disease in different populations, and that a combined analysis would improve the map resolution of a common susceptibility locus, we analyzed data from three studies that had reported linkage to bipolar disorder in a small region on chromosome 4p. Data sets comprised phenotypic information and genetic marker data on Scottish, Danish, and USA extended pedigrees. Across the three data sets, 913 individuals appeared in the pedigrees, 462 were classified, either as unaffected (323) or affected (139) with unipolar or bipolar disorder. A consensus linkage map was created from 14 microsatellite markers in a 33 cM region. Phenotypic and genetic data were analyzed using a variance component (VC) and allele sharing method. All previously reported elevated test statistics in the region were confirmed with one or both analysis methods, indicating the presence of one or more susceptibility genes to bipolar disorder in the three populations in the studied chromosome segment. When the results from both the VC and allele sharing method were considered, there was strong evidence for a susceptibility locus in the data from Scotland, some evidence in the data from Denmark and relatively less evidence in the data from the USA. The test statistics from the Scottish data set dominated the test statistics from the other studies, and no improved map resolution for a putative genetic locus underlying susceptibility in all three studies was obtained. Studies reporting linkage to the same region require careful scrutiny and preferably joint or meta analysis on the same basis in order to ensure that the results are truly comparable. (c) 2004 Wiley-Liss, Inc.

Establishing a process for conducting cross-jurisdictional record linkage in Australia.

PubMed

Moore, Hannah C; Guiver, Tenniel; Woollacott, Anthony; de Klerk, Nicholas; Gidding, Heather F

2016-04-01

To describe the realities of conducting a cross-jurisdictional data linkage project involving state and Australian Government-based data collections to inform future national data linkage programs of work. We outline the processes involved in conducting a Proof of Concept data linkage project including the implementation of national data integration principles, data custodian and ethical approval requirements, and establishment of data flows. The approval process involved nine approval and regulatory bodies and took more than two years. Data will be linked across 12 datasets involving three data linkage centres. A framework was established to allow data to flow between these centres while maintaining the separation principle that serves to protect the privacy of the individual. This will be the first project to link child immunisation records from an Australian Government dataset to other administrative health datasets for a population cohort covering 2 million births in two Australian states. Although the project experienced some delays, positive outcomes were realised, primarily the development of strong collaborations across key stakeholder groups including community engagement. We have identified several recommendations and enhancements to this now established framework to further streamline the process for data linkage studies involving Australian Government data. © 2015 Public Health Association of Australia.

Data Linkage: A powerful research tool with potential problems

PubMed Central

2010-01-01

Background Policy makers, clinicians and researchers are demonstrating increasing interest in using data linked from multiple sources to support measurement of clinical performance and patient health outcomes. However, the utility of data linkage may be compromised by sub-optimal or incomplete linkage, leading to systematic bias. In this study, we synthesize the evidence identifying participant or population characteristics that can influence the validity and completeness of data linkage and may be associated with systematic bias in reported outcomes. Methods A narrative review, using structured search methods was undertaken. Key words "data linkage" and Mesh term "medical record linkage" were applied to Medline, EMBASE and CINAHL databases between 1991 and 2007. Abstract inclusion criteria were; the article attempted an empirical evaluation of methodological issues relating to data linkage and reported on patient characteristics, the study design included analysis of matched versus unmatched records, and the report was in English. Included articles were grouped thematically according to patient characteristics that were compared between matched and unmatched records. Results The search identified 1810 articles of which 33 (1.8%) met inclusion criteria. There was marked heterogeneity in study methods and factors investigated. Characteristics that were unevenly distributed among matched and unmatched records were; age (72% of studies), sex (50% of studies), race (64% of studies), geographical/hospital site (93% of studies), socio-economic status (82% of studies) and health status (72% of studies). Conclusion A number of relevant patient or population factors may be associated with incomplete data linkage resulting in systematic bias in reported clinical outcomes. Readers should consider these factors in interpreting the reported results of data linkage studies. PMID:21176171

Using Object Oriented Bayesian Networks to Model Linkage, Linkage Disequilibrium and Mutations between STR Markers

PubMed Central

Kling, Daniel; Egeland, Thore; Mostad, Petter

2012-01-01

In a number of applications there is a need to determine the most likely pedigree for a group of persons based on genetic markers. Adequate models are needed to reach this goal. The markers used to perform the statistical calculations can be linked and there may also be linkage disequilibrium (LD) in the population. The purpose of this paper is to present a graphical Bayesian Network framework to deal with such data. Potential LD is normally ignored and it is important to verify that the resulting calculations are not biased. Even if linkage does not influence results for regular paternity cases, it may have substantial impact on likelihood ratios involving other, more extended pedigrees. Models for LD influence likelihoods for all pedigrees to some degree and an initial estimate of the impact of ignoring LD and/or linkage is desirable, going beyond mere rules of thumb based on marker distance. Furthermore, we show how one can readily include a mutation model in the Bayesian Network; extending other programs or formulas to include such models may require considerable amounts of work and will in many case not be practical. As an example, we consider the two STR markers vWa and D12S391. We estimate probabilities for population haplotypes to account for LD using a method based on data from trios, while an estimate for the degree of linkage is taken from the literature. The results show that accounting for haplotype frequencies is unnecessary in most cases for this specific pair of markers. When doing calculations on regular paternity cases, the markers can be considered statistically independent. In more complex cases of disputed relatedness, for instance cases involving siblings or so-called deficient cases, or when small differences in the LR matter, independence should not be assumed. (The networks are freely available at http://arken.umb.no/~dakl/BayesianNetworks.) PMID:22984448

Significant Linkage for Tourette Syndrome in a Large French Canadian Family

PubMed Central

Mérette, Chantal; Brassard, Andrée; Potvin, Anne; Bouvier, Hélène; Rousseau, François; Émond, Claudia; Bissonnette, Luc; Roy, Marc-André; Maziade, Michel; Ott, Jurg; Caron, Chantal

2000-01-01

Family and twin studies provide strong evidence that genetic factors are involved in the transmission of Gilles de la Tourette syndrome (TS) and related psychiatric disorders. To detect the underlying susceptibility gene(s) for TS, we performed linkage analysis in one large French Canadian family (127 members) from the Charlevoix region, in which 20 family members were definitely affected by TS and 20 others showed related tic disorders. Using model-based linkage analysis, we observed a LOD score of 3.24 on chromosome 11 (11q23). This result was obtained in a multipoint approach involving marker D11S1377, the marker for which significant linkage disequilibrium with TS recently has been detected in an Afrikaner population. Altogether, 25 markers were studied, and, for level of significance, we derived a criterion that took into account the multiple testing arising from the use of three phenotype definitions and three modes of inheritance, a procedure that yielded a LOD score of 3.18. Hence, even after adjustment for multiple testing, the present study shows statistically significant evidence for genetic linkage with TS. PMID:10986045

Transmission-Ratio Distortion and Allele Sharing in Affected Sib Pairs: A New Linkage Statistic with Reduced Bias, with Application to Chromosome 6q25.3

PubMed Central

Lemire, Mathieu; Roslin, Nicole M.; Laprise, Catherine; Hudson, Thomas J.; Morgan, Kenneth

2004-01-01

We studied the effect of transmission-ratio distortion (TRD) on tests of linkage based on allele sharing in affected sib pairs. We developed and implemented a discrete-trait allele-sharing test statistic, Sad, analogous to the Spairs test statistic of Whittemore and Halpern, that evaluates an excess sharing of alleles at autosomal loci in pairs of affected siblings, as well as a lack of sharing in phenotypically discordant relative pairs, where available. Under the null hypothesis of no linkage, nuclear families with at least two affected siblings and one unaffected sibling have a contribution to Sad that is unbiased, with respect to the effects of TRD independent of the disease under study. If more distantly related unaffected individuals are studied, the bias of Sad is generally reduced compared with that of Spairs, but not completely. Moreover, Sad has higher power, in some circumstances, because of the availability of unaffected relatives, who are ignored in affected-only analyses. We discuss situations in which it may be an efficient use of resources to genotype unaffected relatives, which would give insights for promising study designs. The method is applied to a sample of pedigrees ascertained for asthma in a chromosomal region in which TRD has been reported. Results are consistent with the presence of transmission distortion in that region. PMID:15322985

A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16.

PubMed

Asherson, P; Zhou, K; Anney, R J L; Franke, B; Buitelaar, J; Ebstein, R; Gill, M; Altink, M; Arnold, R; Boer, F; Brookes, K; Buschgens, C; Butler, L; Cambell, D; Chen, W; Christiansen, H; Feldman, L; Fleischman, K; Fliers, E; Howe-Forbes, R; Goldfarb, A; Heise, A; Gabriëls, I; Johansson, L; Lubetzki, I; Marco, R; Medad, S; Minderaa, R; Mulas, F; Müller, U; Mulligan, A; Neale, B; Rijsdijk, F; Rabin, K; Rommelse, N; Sethna, V; Sorohan, J; Uebel, H; Psychogiou, L; Weeks, A; Barrett, R; Xu, X; Banaschewski, T; Sonuga-Barke, E; Eisenberg, J; Manor, I; Miranda, A; Oades, R D; Roeyers, H; Rothenberger, A; Sergeant, J; Steinhausen, H-C; Taylor, E; Thompson, M; Faraone, S V

2008-05-01

As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage was observed on the most established ADHD-linked genomic regions of 5p and 17p. We found suggestive linkage signals on chromosomes 9 and 16, respectively, with the highest multipoint nonparametric linkage signal on chromosome 16q23 at 99 cM (log of the odds, LOD=3.1) overlapping data published from the previous UCLA (University of California, Los Angeles) (LOD>1, approximately 95 cM) and Dutch (LOD>1, approximately 100 cM) studies. The second highest peak in this study was on chromosome 9q22 at 90 cM (LOD=2.13); both the previous UCLA and German studies also found some evidence of linkage at almost the same location (UCLA LOD=1.45 at 93 cM; German LOD=0.68 at 100 cM). The overlap of these two main peaks with previous findings suggests that loci linked to ADHD may lie within these regions. Meta-analysis or reanalysis of the raw data of all the available ADHD linkage scan data may help to clarify whether these represent true linked loci.

[Detection of underlying causes of death among the deceased of Yusho patients by linkage to the national vital statistics data].

PubMed

Kaneko, S; Yoshimura, T; Ikeda, M; Nishisaka, K

2001-05-01

As of January 31, 1996, 292 deaths among registered patients of Yusho were identified by three follow-up studies conducted in 1986, 1990, and 1996. In this study, we attempted to identify underlying causes of death by linkage of the registered data to the National Vital Statistics Data provided by the Management and Coordination Agency of Japan, which included 15 million deaths between 1978 and 1996. The two datasets were linked by matching for six variables; birth year/month/day, death year/month, and sex, along with a variable of death day or death place, or both. The matched cases were 203 among 235 deaths between 1978 and 1996 (matching rate was 86%). Among the 203 deaths, 58 underlying causes of death were newly identified, 146 causes of death were already grasped by the follow-up studies, and 31 deaths did not have matching pair in the National Vital Statistics data. Among the 146 deaths, 110 causes of death were concordant with each other, however, 35 causes of death were completely discord. The reason of the discordance and the unmatched deaths might be due to difference in information of the matching variables in the two datasets. In order to conduct an efficient follow-up study of Yusho patients, identification of underlying causes of death by linkage to the National Vital Statistics Date is evitable. For that, we need to substitute basic information in the Yusho database to those compatible to the National civil registration system.

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

PubMed

Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

2017-07-05

The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

Comparing the National Death Index and the Social Security Administration's Death Master File to ascertain death in HIV surveillance.

PubMed

Hanna, David B; Pfeiffer, Melissa R; Sackoff, Judith E; Selik, Richard M; Begier, Elizabeth M; Torian, Lucia V

2009-01-01

New York City (NYC) maintains a population-based registry of people with human immunodeficiency virus (HIV) infection to monitor the epidemic and inform resource allocation. We evaluated record linkages with the National Death Index (NDI) and the Social Security Administration's Death Master File (SSDMF) to find deaths occurring from 2000 through 2004. We linked records from 32,837 people reported with HIV and not previously known to be dead with deaths reported in the NDI and the SSDMF. We calculated the kappa statistic to assess agreement between data sources. We performed subgroup analyses to assess differences within demographic and transmission risk subpopulations. We quantified the benefit of linkages with each data source beyond prior death ascertainment from local vital statistics data. We discovered 1,926 (5.87%) deaths, which reduced the HIV prevalence estimate in NYC by 2.03%, from 1.19% to 1.16%. Of these, 458 (23.78%) were identified only from NDI, and 305 (15.84%) only from SSDMF. Agreement in ascertainment between sources was substantial (kappa = [K] 0.74, 95% confidence interval [CI] 0.72, 0.76); agreement was lower among Hispanic people (K = 0.65, 95% CI 0.62, 0.69) and people born outside the U.S. (K = 0.60, 95% CI 0.52, 0.68). We identified an additional 13.62% of deaths to people reported with HIV in NYC; white people and men who have sex with men were disproportionately likely to be underascertained without these linkages (p < 0.0001). Record linkages with national databases are essential for accurate prevalence estimates from disease registries, and the SSDMF is an inexpensive means to supplement linkages with the NDI to maximize death ascertainment.

The power to detect linkage in complex disease by means of simple LOD-score analyses.

PubMed Central

Greenberg, D A; Abreu, P; Hodge, S E

1998-01-01

Maximum-likelihood analysis (via LOD score) provides the most powerful method for finding linkage when the mode of inheritance (MOI) is known. However, because one must assume an MOI, the application of LOD-score analysis to complex disease has been questioned. Although it is known that one can legitimately maximize the maximum LOD score with respect to genetic parameters, this approach raises three concerns: (1) multiple testing, (2) effect on power to detect linkage, and (3) adequacy of the approximate MOI for the true MOI. We evaluated the power of LOD scores to detect linkage when the true MOI was complex but a LOD score analysis assumed simple models. We simulated data from 14 different genetic models, including dominant and recessive at high (80%) and low (20%) penetrances, intermediate models, and several additive two-locus models. We calculated LOD scores by assuming two simple models, dominant and recessive, each with 50% penetrance, then took the higher of the two LOD scores as the raw test statistic and corrected for multiple tests. We call this test statistic "MMLS-C." We found that the ELODs for MMLS-C are >=80% of the ELOD under the true model when the ELOD for the true model is >=3. Similarly, the power to reach a given LOD score was usually >=80% that of the true model, when the power under the true model was >=60%. These results underscore that a critical factor in LOD-score analysis is the MOI at the linked locus, not that of the disease or trait per se. Thus, a limited set of simple genetic models in LOD-score analysis can work well in testing for linkage. PMID:9718328

The power to detect linkage in complex disease by means of simple LOD-score analyses.

PubMed

Greenberg, D A; Abreu, P; Hodge, S E

1998-09-01

Maximum-likelihood analysis (via LOD score) provides the most powerful method for finding linkage when the mode of inheritance (MOI) is known. However, because one must assume an MOI, the application of LOD-score analysis to complex disease has been questioned. Although it is known that one can legitimately maximize the maximum LOD score with respect to genetic parameters, this approach raises three concerns: (1) multiple testing, (2) effect on power to detect linkage, and (3) adequacy of the approximate MOI for the true MOI. We evaluated the power of LOD scores to detect linkage when the true MOI was complex but a LOD score analysis assumed simple models. We simulated data from 14 different genetic models, including dominant and recessive at high (80%) and low (20%) penetrances, intermediate models, and several additive two-locus models. We calculated LOD scores by assuming two simple models, dominant and recessive, each with 50% penetrance, then took the higher of the two LOD scores as the raw test statistic and corrected for multiple tests. We call this test statistic "MMLS-C." We found that the ELODs for MMLS-C are >=80% of the ELOD under the true model when the ELOD for the true model is >=3. Similarly, the power to reach a given LOD score was usually >=80% that of the true model, when the power under the true model was >=60%. These results underscore that a critical factor in LOD-score analysis is the MOI at the linked locus, not that of the disease or trait per se. Thus, a limited set of simple genetic models in LOD-score analysis can work well in testing for linkage.

Genetics of recurrent early-onset major depression (GenRED): significant linkage on chromosome 15q25-q26 after fine mapping with single nucleotide polymorphism markers.

PubMed

Levinson, Douglas F; Evgrafov, Oleg V; Knowles, James A; Potash, James B; Weissman, Myrna M; Scheftner, William A; Depaulo, J Raymond; Crowe, Raymond R; Murphy-Eberenz, Kathleen; Marta, Diana H; McInnis, Melvin G; Adams, Philip; Gladis, Madeline; Miller, Erin B; Thomas, Jo; Holmans, Peter

2007-02-01

The authors studied a dense map of single nucleotide polymorphism (SNP) DNA markers on chromosome 15q25-q26 to maximize the informativeness of genetic linkage analyses in a region where they previously reported suggestive evidence for linkage of recurrent early-onset major depressive disorder. In 631 European-ancestry families with multiple cases of recurrent early-onset major depressive disorder, 88 SNPs were genotyped, and multipoint allele-sharing linkage analyses were carried out. Marker-marker linkage disequilibrium was minimized, and a simulation study with founder haplotypes from these families suggested that linkage scores were not inflated by linkage disequilibrium. The dense SNP map increased the information content of the analysis from around 0.7 to over 0.9. The maximum evidence for linkage was the Z likelihood ratio score statistic of Kong and Cox (Z(LR))=4.69 at 109.8 cM. The exact p value was below the genomewide significance threshold. By contrast, in the genome scan with microsatellite markers at 9 cM spacing, the maximum Z(LR) for European-ancestry families was 3.43 (106.53 cM). It was estimated that the linked locus or loci in this region might account for a 20% or less populationwide increase in risk to siblings of cases. This region has produced modestly positive evidence for linkage to depression and related traits in other studies. These results suggest that DNA sequence variations in one or more genes in the 15q25-q26 region can increase susceptibility to major depression and that efforts are warranted to identify these genes.

A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics.

PubMed

Pare, Guillaume; Mao, Shihong; Deng, Wei Q

2016-06-08

Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD). We now propose a novel method, LD Adjusted Regional Genetic Variance (LARGV), to estimate phenotypic variance explained by regional associations using summary statistics while accounting for LD. Our method is asymptotically equivalent to a multiple linear regression model when no interaction or haplotype effects are present. It has several applications, such as ranking of genetic regions according to variance explained or comparison of variance explained by two or more regions. Using height and BMI data from the Health Retirement Study (N = 7,776), we show that most genetic variance lies in a small proportion of the genome and that previously identified linkage peaks have higher than expected regional variance.

A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics

PubMed Central

Pare, Guillaume; Mao, Shihong; Deng, Wei Q.

2016-01-01

Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD). We now propose a novel method, LD Adjusted Regional Genetic Variance (LARGV), to estimate phenotypic variance explained by regional associations using summary statistics while accounting for LD. Our method is asymptotically equivalent to a multiple linear regression model when no interaction or haplotype effects are present. It has several applications, such as ranking of genetic regions according to variance explained or comparison of variance explained by two or more regions. Using height and BMI data from the Health Retirement Study (N = 7,776), we show that most genetic variance lies in a small proportion of the genome and that previously identified linkage peaks have higher than expected regional variance. PMID:27273519

Assessing the role of mini-applications in predicting key performance characteristics of scientific and engineering applications

DOE PAGES

Barrett, R. F.; Crozier, P. S.; Doerfler, D. W.; ...

2014-09-28

Computational science and engineering application programs are typically large, complex, and dynamic, and are often constrained by distribution limitations. As a means of making tractable rapid explorations of scientific and engineering application programs in the context of new, emerging, and future computing architectures, a suite of miniapps has been created to serve as proxies for full scale applications. Each miniapp is designed to represent a key performance characteristic that does or is expected to significantly impact the runtime performance of an application program. In this paper we introduce a methodology for assessing the ability of these miniapps to effectively representmore » these performance issues. We applied this methodology to four miniapps, examining the linkage between them and an application they are intended to represent. Herein we evaluate the fidelity of that linkage. This work represents the initial steps required to begin to answer the question, ''Under what conditions does a miniapp represent a key performance characteristic in a full app?''« less

Economic and Physical Linkages of the Information and Communication Technology (ICT) Service Industry to Key Industries of the Economy: An Ad Hoc Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, David M.; Hoffman, Michael G.; Niemeyer, Jackie M.

This report examines the information and communications technology (ICT) services industry in response to an inquiry by the Department of Energy’s (DOE’s) Office of Energy Policy and Systems Analysis. The report answers several key questions: •How has the reliance on ICT services evolved in recent years for key infrastructure services such as air travel, freight transport, electricity and natural gas distribution, financial services, and critical health care, and for the household sector? •What ICT industry trends explain continued strong linkage to and reliance upon ICT? •What is the ICT industry’s reliance on grid-supplied power, uninterruptible power supplies, emergency generators andmore » back-up energy storage technologies? •What are the observed direct effects of ICT disruptions induced by electrical system failures in recent history and how resilient are the components of the ICT industry?« less

Male-to-male transmission in extended pedigrees with multiple cases of autism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hallmayer, J.; Spiker, D.; Lotspeich, L.

Despite strong genetic influences in autism, the true mode of inheritance remains unknown. Sex differences in autism have been described in both singleton and multiplex families: boys outnumber girls by 3 or 4 to 1, and so a sex-linked mode of transmission must also be considered. The key characteristic of X-linkage is that all sons of affected men are unaffected (no male-to-male transmission). In the present study, which is part of an ongoing linkage project in autism, we describe 77 multiplex autism families, 11 of who are affected cousin or half-sibling families. By using these families, it is possible tomore » trace the path of genetic transmission and observe whether the hypothesis of X-linkage is tenable. Of 11 extended pedigrees from 77 multiplex families, six show male-to-male transmission; in these families, X-linkage can be excluded as the genetic basis for their autism. The data from the other five families are compatible with either an autosomal or an X-linked mode of transmission. The key point to emerge, then, is that autism cannot be exclusively an X-linked disorder; there must be an autosomal mode of transmission at least in some families. Thus we must consider the alternative hypotheses that autism is either entirely autosomal, or it is genetically heterogeneous, involving at least one autosomal locus with gender-specific expression, as well as a possible locus on the X-chromosome. 28 refs., 1 fig.« less

History of the Rochester Epidemiology Project: Half a Century of Medical Records Linkage in a US Population

PubMed Central

Rocca, Walter A.; Yawn, Barbara P.; St. Sauver, Jennifer L.; Grossardt, Brandon R.; Melton, L. Joseph

2012-01-01

The Rochester Epidemiology Project (REP) has maintained a comprehensive medical records linkage system for nearly half a century for almost all persons residing in Olmsted County, Minnesota. Herein, we provide a brief history of the REP before and after 1966, the year in which the REP was officially established. The key protagonists before 1966 were Henry Plummer, Mabel Root, and Joseph Berkson, who developed a medical records linkage system at Mayo Clinic. In 1966, Leonard Kurland established collaborative agreements with other local health care providers (hospitals, physician groups, and clinics [primarily Olmsted Medical Center]) to develop a medical records linkage system that covered the entire population of Olmsted County, and he obtained funding from the National Institutes of Health to support the new system. In 1997, L. Joseph Melton III addressed emerging concerns about the confidentiality of medical record information by introducing a broad patient research authorization as per Minnesota state law. We describe how the key protagonists of the REP have responded to challenges posed by evolving medical knowledge, information technology, and public expectation and policy. In addition, we provide a general description of the system; discuss issues of data quality, reliability, and validity; describe the research team structure; provide information about funding; and compare the REP with other medical information systems. The REP can serve as a model for the development of similar research infrastructures in the United States and worldwide. PMID:23199802

Linkage studies on chromosome 22 in familial schizophrenia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vallada, H.P.; Gill, M.; Sham, P.

1995-04-24

As part of a systematic search for a major genetic locus for schizophrenia we have examined chromosome 22 using 14 highly polymorphic markers in 23 disease pedigrees. The markers were distributed at an average distance of 6.6 cM, covering 70-80% of the chromosome. We analyzed the data by the lod score method using five plausible genetic models ranging from dominant to recessive, after testing the power of our sample under the same genetic parameters. The most positive lod score found was 1.51 under a recessive model for the marker D22S278, which is insufficient to conclude linkage. However, an excess ofmore » shared alleles in affected siblings (P < .01) was found for both D22S278 and D22S283. For D22S278, the A statistic was equal to the lod score (1.51) and therefore did not provide additional evidence for linkage allowing for heterogeneity, but the Liang statistic was more significant (P = .002). Our results suggest the possibility that the region around D22S278 and D22S283 contains a gene which contributes to the etiology of schizophrenia. 60 refs., 1 fig., 5 tabs.« less

Localization of Usher syndrome type II to chromosome 1q.

PubMed

Kimberling, W J; Weston, M D; Möller, C; Davenport, S L; Shugart, Y Y; Priluck, I A; Martini, A; Milani, M; Smith, R J

1990-06-01

Usher syndrome is characterized by congenital hearing loss, progressive visual impairment due to retinitis pigmentosa, and variable vestibular problems. The two subtypes of Usher syndrome, types I and II, can be distinguished by the degree of hearing loss and by the presence or absence of vestibular dysfunction. Type I is characterized by a profound hearing loss and totally absent vestibular responses, while type II has a milder hearing loss and normal vestibular function. Fifty-five members of eight type II Usher syndrome families were typed for three DNA markers in the distal region of chromosome 1q: D1S65 (pEKH7.4), REN (pHRnES1.9), and D1S81 (pTHH33). Statistically significant linkage was observed for Usher syndrome type II with a maximum multipoint lod score of 6.37 at the position of the marker THH33, thus localizing the Usher type II (USH2) gene to 1q. Nine families with type I Usher syndrome failed to show linkage to the same three markers. The statistical test for heterogeneity of linkage between Usher syndrome types I and II was highly significant, thus demonstrating that they are due to mutations at different genetic loci.

A Test of Outreach and Drop-in Linkage Versus Shelter Linkage for Connecting Homeless Youth to Services.

PubMed

Slesnick, Natasha; Feng, Xin; Guo, Xiamei; Brakenhoff, Brittany; Carmona, Jasmin; Murnan, Aaron; Cash, Scottye; McRee, Annie-Laurie

2016-05-01

Outreach and service linkage are key for engaging marginalized populations, such as homeless youth, in services. Research to date has focused primarily on engaging individuals already receiving some services through emergency shelters, clinics, or other programs. Less is known about those who are not connected to services and, thus, likely the most vulnerable and in need of assistance. The current study sought to engage non-service-connected homeless youth (N = 79) into a strengths-based outreach and advocacy intervention. Youth were randomly assigned to receive 6 months of advocacy that focused on linking youth to a drop-in center (n = 40) or to a crisis shelter (n = 39). All youth were assessed at baseline and 3, 6, and 9 months post-baseline. Findings indicated that youth prefer drop-in center services to the shelter. Also, the drop-in center linkage condition was associated with more service linkage overall (B = 0.34, SE = 0.04, p < 0.01) and better alcohol-l [B = -0.39, SE = 0.09, t(75) = -4.48, p < 0.001] and HIV-related outcomes [B = 0.62, SE = 0.10, t(78) = 6.34, p < 0.001] compared to the shelter linkage condition. Findings highlight the importance of outreach and service linkage for reconnecting service-marginalized youth, and drop-in centers as a primary service option for homeless youth.

Composite Bloom Filters for Secure Record Linkage.

PubMed

Durham, Elizabeth Ashley; Kantarcioglu, Murat; Xue, Yuan; Toth, Csaba; Kuzu, Mehmet; Malin, Bradley

2014-12-01

The process of record linkage seeks to integrate instances that correspond to the same entity. Record linkage has traditionally been performed through the comparison of identifying field values ( e.g., Surname ), however, when databases are maintained by disparate organizations, the disclosure of such information can breach the privacy of the corresponding individuals. Various private record linkage (PRL) methods have been developed to obscure such identifiers, but they vary widely in their ability to balance competing goals of accuracy, efficiency and security. The tokenization and hashing of field values into Bloom filters (BF) enables greater linkage accuracy and efficiency than other PRL methods, but the encodings may be compromised through frequency-based cryptanalysis. Our objective is to adapt a BF encoding technique to mitigate such attacks with minimal sacrifices in accuracy and efficiency. To accomplish these goals, we introduce a statistically-informed method to generate BF encodings that integrate bits from multiple fields, the frequencies of which are provably associated with a minimum number of fields. Our method enables a user-specified tradeoff between security and accuracy. We compare our encoding method with other techniques using a public dataset of voter registration records and demonstrate that the increases in security come with only minor losses to accuracy.

Genomewide scan for gout in taiwanese aborigines reveals linkage to chromosome 4q25.

PubMed

Cheng, Li Shu-Chuan; Chiang, Shang-Lun; Tu, Hung-Pin; Chang, Shun-Jen; Wang, Tsu-Nai; Ko, Allen Min-Jen; Chakraborty, Ranajit; Ko, Ying-Chin

2004-09-01

Gout is a disorder of uric-acid metabolism. The Pacific Austronesian population, including Taiwanese aborigines, has a remarkably high prevalence of hyperuricemia and gout, which suggests a founder effect across the Pacific region. We report here a genomewide linkage study of 21 multiplex pedigrees with gout from an aboriginal tribe in Taiwan. From observations of familial clustering, early onset of gout, and clinically severe manifestations, we hypothesized that a major gene plays a role in this trait. Using 382 random polymorphic markers spread across 22 autosomes, we demonstrated a highly significant linkage for gout at marker D4S2623 on chromosome 4q25 (P=.0002 by nonparametric linkage [the NPL(all) statistic]; empirical P=.0006; LOD=4.3, P=4.4x10-6 by logistic regression). When alcohol consumption was included as a covariate in the model, the LOD score increased to 5.66 (P=1.3x10-6). Quantitative traits, including serum uric acid and creatinine, also showed a moderate linkage to this region. To our knowledge, this is the first genome-scan report to identify a genetic locus harboring a gout-susceptibility gene.

Composite Bloom Filters for Secure Record Linkage

PubMed Central

Durham, Elizabeth Ashley; Kantarcioglu, Murat; Xue, Yuan; Toth, Csaba; Kuzu, Mehmet; Malin, Bradley

2014-01-01

The process of record linkage seeks to integrate instances that correspond to the same entity. Record linkage has traditionally been performed through the comparison of identifying field values (e.g., Surname), however, when databases are maintained by disparate organizations, the disclosure of such information can breach the privacy of the corresponding individuals. Various private record linkage (PRL) methods have been developed to obscure such identifiers, but they vary widely in their ability to balance competing goals of accuracy, efficiency and security. The tokenization and hashing of field values into Bloom filters (BF) enables greater linkage accuracy and efficiency than other PRL methods, but the encodings may be compromised through frequency-based cryptanalysis. Our objective is to adapt a BF encoding technique to mitigate such attacks with minimal sacrifices in accuracy and efficiency. To accomplish these goals, we introduce a statistically-informed method to generate BF encodings that integrate bits from multiple fields, the frequencies of which are provably associated with a minimum number of fields. Our method enables a user-specified tradeoff between security and accuracy. We compare our encoding method with other techniques using a public dataset of voter registration records and demonstrate that the increases in security come with only minor losses to accuracy. PMID:25530689

Linkage design effect on the reliability of surface-micromachined microengines driving a load

NASA Astrophysics Data System (ADS)

Tanner, Danelle M.; Peterson, Kenneth A.; Irwin, Lloyd W.; Tangyunyong, Paiboon; Miller, William M.; Eaton, William P.; Smith, Norman F.; Rodgers, M. Steven

1998-09-01

The reliability of microengines is a function of the design of the mechanical linkage used to connect the electrostatic actuator to the drive. We have completed a series of reliability stress tests on surface micromachined microengines driving an inertial load. In these experiments, we used microengines that had pin mechanisms with guides connecting the drive arms to the electrostatic actuators. Comparing this data to previous results using flexure linkages revealed that the pin linkage design was less reliable. The devices were stressed to failure at eight frequencies, both above and below the measured resonance frequency of the microengine. Significant amounts of wear debris were observed both around the hub and pin joint of the drive gear. Additionally, wear tracks were observed in the area where the moving shuttle rubbed against the guides of the pin linkage. At each frequency, we analyzed the statistical data yielding a lifetime (t50) for median cycles to failure and (sigma) , the shape parameter of the distribution. A model was developed to describe the failure data based on fundamental wear mechanisms and forces exhibited in mechanical resonant systems. The comparison to the model will be discussed.

Linking stressors and ecological responses

USGS Publications Warehouse

Gentile, J.H.; Solomon, K.R.; Butcher, J.B.; Harrass, M.; Landis, W.G.; Power, M.; Rattner, B.A.; Warren-Hicks, W.J.; Wenger, R.; Foran, Jeffery A.; Ferenc, Susan A.

1999-01-01

To characterize risk, it is necessary to quantify the linkages and interactions between chemical, physical and biological stressors and endpoints in the conceptual framework for ecological risk assessment (ERA). This can present challenges in a multiple stressor analysis, and it will not always be possible to develop a quantitative stressor-response profile. This review commences with a conceptual representation of the problem of developing a linkage analysis for multiple stressors and responses. The remainder of the review surveys a variety of mathematical and statistical methods (e.g., ranking methods, matrix models, multivariate dose-response for mixtures, indices, visualization, simulation modeling and decision-oriented methods) for accomplishing the linkage analysis for multiple stressors. Describing the relationships between multiple stressors and ecological effects are critical components of 'effects assessment' in the ecological risk assessment framework.

Common variants of the EPDR1 gene and the risk of Dupuytren’s disease.

PubMed

Dębniak, T; Żyluk, A; Puchalski, P; Serrano-Fernandez, P

2013-10-01

The object of this study was the investigation of 3 common variants of single nucleotide polymorphisms of the ependymin-related gene 1 and its association with the occurrence of Dupuytren's disease. DNA samples were obtained from the peripheral blood of 508 consecutive patients. The control group comprised 515 healthy adults who were age-matched with the Dupuytren's patients. 3 common variants were analysed using TaqMan® genotyping assays and sequencing. The differences in the frequencies of variants of single nucleotide polymorphisms in patients and the control group were statistically tested. Additionally, haplotype frequency and linkage disequilibrium were analysed for these variants. A statistically significant association was noted between rs16879765_CT, rs16879765_TT and rs13240429_AA variants and Dupuytren's disease. 2 haplotypes: rs2722280_C+rs13240429_A+rs16879765_C and rs2722280_C+rs13240429_G+rs16879765_T were found to be statistically significantly associated with Dupuytren's disease. Moreover, we found that rs13240429 and rs16879765 variants were in strong linkage disequilibrium, while rs2722280 was only in moderate linkage disequilibrium. No significant differences were found in the frequencies of the variants of the gene between the groups with a positive and negative familial history of Dupuytren's disease. In conclusion, results of this study suggest that EPDR1 gene can be added to a growing list of genes associated with Dupuytren's disease development. © Georg Thieme Verlag KG Stuttgart · New York.

Avoiding false discoveries in association studies.

PubMed

Sabatti, Chiara

2007-01-01

We consider the problem of controlling false discoveries in association studies. We assume that the design of the study is adequate so that the "false discoveries" are potentially only because of random chance, not to confounding or other flaws. Under this premise, we review the statistical framework for hypothesis testing and correction for multiple comparisons. We consider in detail the currently accepted strategies in linkage analysis. We then examine the underlying similarities and differences between linkage and association studies and document some of the most recent methodological developments for association mapping.

Vertical variability and effect of stability on turbulence characteristics down to the floor of a pine forest

NASA Astrophysics Data System (ADS)

Launiainen, Samuli; Vesala, Timo; Mölder, Meelis; Mammarella, Ivan; Smolander, Sampo; Rannik, Üllar; Kolari, Pasi; Hari, Pertti; Lindroth, Anders; Katul, Gabriel G.

2007-11-01

Among the fundamental problems in canopy turbulence, particularly near the forest floor, remain the local diabatic effects and linkages between turbulent length scales and the canopy morphology. To progress on these problems, mean and higher order turbulence statistics are collected in a uniform pine forest across a wide range of atmospheric stability conditions using five 3-D anemometers in the subcanopy. The main novelties from this experiment are: (1) the agreement between second-order closure model results and measurements suggest that diabatic states in the layer above the canopy explain much of the modulations of the key velocity statistics inside the canopy except in the immediate vicinity of the trunk space and for very stable conditions. (2) The dimensionless turbulent kinetic energy in the trunk space is large due to a large longitudinal velocity variance but it is inactive and contributes little to momentum fluxes. (3) Near the floor layer, a logarithmic mean velocity profile is formed and vertical eddies are strongly suppressed modifying all power spectra. (4) A spectral peak in the vertical velocity near the ground commensurate with the trunk diameter emerged at a moderate element Reynolds number consistent with Strouhal instabilities describing wake production.

Key concepts regarding the genetics of hypertension in humans.

PubMed

Williams, R R

1991-11-01

More and more, genetic research is being used to investigate the problem of hypertension, especially as hypertension appears to be a population-wide phenomenon. This article discusses such key concepts as phenotypic variation within the hypertensive subpopulation, the importance of a family history for hypertension in predicting hypertension, the development of hypertension in youth, environmental considerations (nature v nurture), and gene linkage.

Facilitators and Barriers to Linkage to HIV Care among Female Sex Workers Receiving HIV Testing Services at a Community-Based Organization in Periurban Uganda: A Qualitative Study

PubMed Central

Kintu, Betty N.

2016-01-01

Introduction. While four in ten female sex workers (FSWs) in sub-Saharan Africa are infected with HIV, only a small proportion is enrolled in HIV care. We explored facilitators and barriers to linkage to HIV care among FSWs receiving HIV testing services at a community-based organization in periurban Uganda. Methods. The cross-sectional qualitative study was conducted among 28 HIV positive FSWs from May to July 2014. Key informant interviews were conducted with five project staff and eleven peer educators. Data were collected on facilitators for and barriers to linkage to HIV care and manually analyzed following a thematic framework approach. Results. Facilitators for linkage to HIV care included the perceived good quality of health services with same-day results and immediate initiation of treatment, community peer support systems, individual's need to remain healthy, and having alternative sources of income. Linkage barriers included perceived stigma, fear to be seen at outreach HIV clinics, fear and myths about antiretroviral therapy, lack of time to attend clinic, and financial constraints. Conclusion. Linkage to HIV care among FSWs is influenced by good quality friendly services and peer support. HIV service delivery programs for FSWs should focus on enhancing these and dealing with barriers stemming from stigma and misinformation. PMID:27493826

Quantifying the Correctness, Computational Complexity, and Security of Privacy-Preserving String Comparators for Record Linkage

PubMed Central

Durham, Elizabeth; Xue, Yuan; Kantarcioglu, Murat; Malin, Bradley

2011-01-01

Record linkage is the task of identifying records from disparate data sources that refer to the same entity. It is an integral component of data processing in distributed settings, where the integration of information from multiple sources can prevent duplication and enrich overall data quality, thus enabling more detailed and correct analysis. Privacy-preserving record linkage (PPRL) is a variant of the task in which data owners wish to perform linkage without revealing identifiers associated with the records. This task is desirable in various domains, including healthcare, where it may not be possible to reveal patient identity due to confidentiality requirements, and in business, where it could be disadvantageous to divulge customers' identities. To perform PPRL, it is necessary to apply string comparators that function in the privacy-preserving space. A number of privacy-preserving string comparators (PPSCs) have been proposed, but little research has compared them in the context of a real record linkage application. This paper performs a principled and comprehensive evaluation of six PPSCs in terms of three key properties: 1) correctness of record linkage predictions, 2) computational complexity, and 3) security. We utilize a real publicly-available dataset, derived from the North Carolina voter registration database, to evaluate the tradeoffs between the aforementioned properties. Among our results, we find that PPSCs that partition, encode, and compare strings yield highly accurate record linkage results. However, as a tradeoff, we observe that such PPSCs are less secure than those that map and compare strings in a reduced dimensional space. PMID:22904698

Quantifying the Correctness, Computational Complexity, and Security of Privacy-Preserving String Comparators for Record Linkage.

PubMed

Durham, Elizabeth; Xue, Yuan; Kantarcioglu, Murat; Malin, Bradley

2012-10-01

Record linkage is the task of identifying records from disparate data sources that refer to the same entity. It is an integral component of data processing in distributed settings, where the integration of information from multiple sources can prevent duplication and enrich overall data quality, thus enabling more detailed and correct analysis. Privacy-preserving record linkage (PPRL) is a variant of the task in which data owners wish to perform linkage without revealing identifiers associated with the records. This task is desirable in various domains, including healthcare, where it may not be possible to reveal patient identity due to confidentiality requirements, and in business, where it could be disadvantageous to divulge customers' identities. To perform PPRL, it is necessary to apply string comparators that function in the privacy-preserving space. A number of privacy-preserving string comparators (PPSCs) have been proposed, but little research has compared them in the context of a real record linkage application. This paper performs a principled and comprehensive evaluation of six PPSCs in terms of three key properties: 1) correctness of record linkage predictions, 2) computational complexity, and 3) security. We utilize a real publicly-available dataset, derived from the North Carolina voter registration database, to evaluate the tradeoffs between the aforementioned properties. Among our results, we find that PPSCs that partition, encode, and compare strings yield highly accurate record linkage results. However, as a tradeoff, we observe that such PPSCs are less secure than those that map and compare strings in a reduced dimensional space.

History of the Rochester Epidemiology Project: half a century of medical records linkage in a US population.

PubMed

Rocca, Walter A; Yawn, Barbara P; St Sauver, Jennifer L; Grossardt, Brandon R; Melton, L Joseph

2012-12-01

The Rochester Epidemiology Project (REP) has maintained a comprehensive medical records linkage system for nearly half a century for almost all persons residing in Olmsted County, Minnesota. Herein, we provide a brief history of the REP before and after 1966, the year in which the REP was officially established. The key protagonists before 1966 were Henry Plummer, Mabel Root, and Joseph Berkson, who developed a medical records linkage system at Mayo Clinic. In 1966, Leonard Kurland established collaborative agreements with other local health care providers (hospitals, physician groups, and clinics [primarily Olmsted Medical Center]) to develop a medical records linkage system that covered the entire population of Olmsted County, and he obtained funding from the National Institutes of Health to support the new system. In 1997, L. Joseph Melton III addressed emerging concerns about the confidentiality of medical record information by introducing a broad patient research authorization as per Minnesota state law. We describe how the key protagonists of the REP have responded to challenges posed by evolving medical knowledge, information technology, and public expectation and policy. In addition, we provide a general description of the system; discuss issues of data quality, reliability, and validity; describe the research team structure; provide information about funding; and compare the REP with other medical information systems. The REP can serve as a model for the development of similar research infrastructures in the United States and worldwide. Copyright © 2012 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Statistics on continuous IBD data: Exact distribution evaluation for a pair of full(half)-sibs and a pair of a (great-) grandchild with a (great-) grandparent

PubMed Central

Stefanov, Valeri T

2002-01-01

Background Pairs of related individuals are widely used in linkage analysis. Most of the tests for linkage analysis are based on statistics associated with identity by descent (IBD) data. The current biotechnology provides data on very densely packed loci, and therefore, it may provide almost continuous IBD data for pairs of closely related individuals. Therefore, the distribution theory for statistics on continuous IBD data is of interest. In particular, distributional results which allow the evaluation of p-values for relevant tests are of importance. Results A technology is provided for numerical evaluation, with any given accuracy, of the cumulative probabilities of some statistics on continuous genome data for pairs of closely related individuals. In the case of a pair of full-sibs, the following statistics are considered: (i) the proportion of genome with 2 (at least 1) haplotypes shared identical-by-descent (IBD) on a chromosomal segment, (ii) the number of distinct pieces (subsegments) of a chromosomal segment, on each of which exactly 2 (at least 1) haplotypes are shared IBD. The natural counterparts of these statistics for the other relationships are also considered. Relevant Maple codes are provided for a rapid evaluation of the cumulative probabilities of such statistics. The genomic continuum model, with Haldane's model for the crossover process, is assumed. Conclusions A technology, together with relevant software codes for its automated implementation, are provided for exact evaluation of the distributions of relevant statistics associated with continuous genome data on closely related individuals. PMID:11996673

Systematic search for major genes in schizophrenia: Methodological issues and results from chromosome 12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, E.; Powell, J.F.; Sham, P.

1995-10-09

We describe a method of systematically searching for major genes in disorders of unknown mode of inheritance, using linkage analysis. Our method is designed to minimize the probability of missing linkage due to inadequate exploration of data. We illustrate this method with the results of a search for a locus for schizophrenia on chromosome 12 using 22 highly polymorphic markers in 23 high density pedigrees. The markers span approximately 85-90% of the chromosome and are on average 9.35 cM apart. We have analysed the data using the most plausible current genetic models and allowing for the presence of genetic heterogeneity.more » None of the markers was supportive of linkage and the distribution of the heterogeneity statistics was in accordance with the null hypothesis. 53 refs., 2 figs., 4 tabs.« less

Latitudinal variability of the dynamic linkage between temperature and atmospheric carbon dioxide concentrations - Latitudinal variability

NASA Astrophysics Data System (ADS)

Triacca, Umberto; Di Iorio, Francesca

2018-06-01

In this paper, a novel data-driven approach is used to investigate the presence of spatial differences in the dynamic linkage between temperature and atmospheric carbon dioxide concentrations. This linkage seems to be latitude dependent. The main findings of the study are as follows. In the latitude belts surrounding the equator (0°- 24° N and 0°- 24° S), the link seems very similar. On the opposite, the patterns of the temperature CO2 link in the Arctic is very distant from those concerning the equatorial regions and other latitude bands in the South Hemisphere. This big distance is consistent with the so-called Arctic amplification phenomenon. Further, it is important to underline that this observational data-based analysis provides an independent statistical confirmation of the results from global circulation modelling.

A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

PubMed

Livingstone, Donald; Stack, Conrad; Mustiga, Guiliana M; Rodezno, Dayana C; Suarez, Carmen; Amores, Freddy; Feltus, Frank A; Mockaitis, Keithanne; Cornejo, Omar E; Motamayor, Juan C

2017-01-01

Cacao ( Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families.

PubMed

Liu, Yong-Jun; Rocha-Sanchez, Sonia M S; Liu, Peng-Yuan; Long, Ji-Rong; Lu, Yan; Elze, Leo; Recker, Robert R; Deng, Hong-Wen

2004-04-13

Genetic variations in the leptin receptor (LEPR) gene have been conceived to affect body weight in general populations. In this study, using the tests implemented in the statistical package QTDT, we evaluated association and/or linkage of the LEPR gene with obesity phenotypes in a large sample comprising 1,873 subjects from 405 Caucasian nuclear families. Obesity phenotypes tested include body mass index (BMI), fat mass, percentage fat mass (PFM), and lean mass, with the latter three measured by dual-energy X-ray absorptiometry (DXA). Three single nucleotide polymorphisms (SNPs), namely Lys109Arg (A/G), Lys656Asn (G/C), Pro1019Pro (G/A), in the LEPR gene were analyzed. Significant linkage disequilibrium (0.394 < or = |D'| < or = 0.688, P < 0.001) was observed between pairs of the three SNPs. No significant population stratification was found for any SNP/phenotype. In single-locus analyses, evidence of association was observed for Lys656Asn with lean mass (P = 0.002) and fat mass (P = 0.015). The contribution of this polymorphism to the phenotypic variation of lean mass and fat mass was 2.63% and 1.15%, respectively. Subjects carrying allele G at the Lys656Asn site had, on average, 3.16% higher lean mass and 2.71% higher fat mass than those without it. In the analyses for haplotypes defined by the three SNPs, significant associations were detected between haplotype GCA (P = 0.005) and lean mass. In addition, marginally significant evidence of association was observed for this haplotype with fat mass (P = 0.012). No statistically significant linkage was found, largely due to the limited power of the linkage approach to detect small genetic effects in our data sets. Our results suggest that the LEPR gene polymorphisms contribute to variation in obesity phenotypes.

Patient Perspectives on the Experience of Being Newly Diagnosed with HIV in the Emergency Department/Urgent Care Clinic of a Public Hospital

PubMed Central

Christopoulos, Katerina A.; Massey, Amina D.; Lopez, Andrea M.; Hare, C. Bradley; Johnson, Mallory O.; Pilcher, Christopher D.; Fielding, Hegla; Dawson-Rose, Carol

2013-01-01

We sought to understand patient perceptions of the emergency department/urgent care (ED/UC) HIV diagnosis experience as well as factors that may promote or discourage linkage to HIV care. We conducted in-depth interviews with patients (n=24) whose HIV infection was diagnosed in the ED/UC of a public hospital in San Francisco at least six months prior and who linked to HIV care at the hospital HIV clinic. Key diagnosis experience themes included physical discomfort and limited functionality, presence of comorbid diagnoses, a wide spectrum of HIV risk perception, and feelings of isolation and anxiety. Patients diagnosed with HIV in the ED/UC may not have their desired emotional supports with them, either because they are alone or they are with family members or friends to whom they do not want to immediately disclose. Other patients may have no one they can rely on for immediate support. Nearly all participants described compassionate disclosure of test results by ED/UC providers, although several noted logistical issues that complicated the disclosure experience. Key linkage to care themes included the importance of continuity between the testing site and HIV care, hospital admission as an opportunity for support and HIV education, and thoughtful matching by linkage staff to a primary care provider. ED/UC clinicians and testing programs should be sensitive to the unique roles of sickness, risk perception, and isolation in the ED/UC diagnosis experience, as these things may delay acceptance of HIV diagnosis. The disclosure and linkage to care experience is crucial in forming patient attitudes towards HIV and HIV care, thus staff involved in disclosure and linkage activities should be trained to deliver compassionate, informed, and thoughtful care that bridges HIV testing and treatment sites. PMID:23991214

Mars Design Reference Architecture 5.0 Study: Executive Summary

NASA Technical Reports Server (NTRS)

Drake, Bret G.

2008-01-01

The NASA Mars Design Reference Architecture 5.0 Study seeks to update its long term goals and objective for human exploration missions; flight and surface systems for human missions and supporting infrastructure; operational concept for human and robotic exploration of Mars; key challenges including risk and cost drivers; and, its development schedule options. It additionally seeks to assess strategic linkages between lunar and Mars strategies and develop and understanding of methods for reducing the cost/risk of human Mars missions through investment in research, technology development, and synergy with other exploration plans. Recommendations are made regarding conjunction class (long-stay) missions which are seen as providing the best balance of cost, risk, and performance. Additionally, this study reviews entry, descent, and landing challenges; in-space transportation systems; launch vehicle and Orion assessments; risk and risk mitigation; key driving requirements and challenges; and, lunar linkages.

Linkage to HIV care after home-based HIV counselling and testing in sub-Saharan Africa: a systematic review.

PubMed

Ruzagira, Eugene; Baisley, Kathy; Kamali, Anatoli; Biraro, Samuel; Grosskurth, Heiner

2017-07-01

Home-based HIV counselling and testing (HBHCT) has the potential to increase HIV testing uptake in sub-Saharan Africa (SSA), but data on linkage to HIV care after HBHCT are scarce. We conducted a systematic review of linkage to care after HBHCT in SSA. Five databases were searched for studies published between 1st January 2000 and 19th August 2016 that reported on linkage to care among adults newly identified with HIV infection through HBHCT. Eligible studies were reviewed, assessed for risk of bias and findings summarised using the PRISMA guidelines. A total of 14 studies from six countries met the eligibility criteria; nine used specific strategies (point-of-care CD4 count testing, follow-up counselling, provision of transport funds to clinic and counsellor facilitation of HIV clinic visit) in addition to routine referral to facilitate linkage to care. Time intervals for ascertaining linkage ranged from 1 week to 12 months post-HBHCT. Linkage ranged from 8.2% [95% confidence interval (CI), 6.8-9.8%] to 99.1% (95% CI, 96.9-99.9%). Linkage was generally lower (<33%) if HBHCT was followed by referral only, and higher (>80%) if additional strategies were used. Only one study assessed linkage by means of a randomised trial. Five studies had data on cotrimoxazole (CTX) prophylaxis and 12 on ART eligibility and initiation. CTX uptake among those eligible ranged from 0% to 100%. The proportion of persons eligible for ART ranged from 16.5% (95% CI, 12.1-21.8) to 77.8% (95% CI, 40.0-97.2). ART initiation among those eligible ranged from 14.3% (95% CI, 0.36-57.9%) to 94.9% (95% CI, 91.3-97.4%). Additional linkage strategies, whilst seeming to increase linkage, were not associated with higher uptake of CTX and/or ART. Most of the studies were susceptible to risk of outcome ascertainment bias. A pooled analysis was not performed because of heterogeneity across studies with regard to design, setting and the key variable definitions. Only few studies from SSA investigated linkage to care among adults newly diagnosed with HIV through HBHCT. Linkage was often low after routine referral but higher if additional interventions were used to facilitate it. The effectiveness of linkage strategies should be confirmed through randomised controlled trials. © 2017 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Markov chain Monte Carlo linkage analysis: effect of bin width on the probability of linkage.

PubMed

Slager, S L; Juo, S H; Durner, M; Hodge, S E

2001-01-01

We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

Introductory guide to the statistics of molecular genetics.

PubMed

Eley, Thalia C; Rijsdijk, Frühling

2005-10-01

This introductory guide presents the main two analytical approaches used by molecular geneticists: linkage and association. Traditional linkage and association methods are described, along with more recent advances in methodologies such as those using a variance components approach. New methods are being developed all the time but the core principles of linkage and association remain the same. The basis of linkage is the transmission of a marker along with a disease within families, whereas association is based on the comparison of marker frequencies in case and control groups. It is becoming increasingly clear that effect sizes of individual markers on diseases and traits are likely to be very small. As such, much greater power is needed, and correspondingly greater sample sizes. Although non-replication is still a problem, molecular genetic studies in some areas such as attention deficit/hyperactivity disorder (ADHD) are starting to show greater convergence. Epidemiologists and other researchers with large well-characterized samples will be well placed to use these methods. Inter-disciplinary studies can then ask far more interesting questions such as those relating to developmental, multivariate and gene-environment interaction hypotheses.

A novel metadata management model to capture consent for record linkage in longitudinal research studies.

PubMed

McMahon, Christiana; Denaxas, Spiros

2017-11-06

Informed consent is an important feature of longitudinal research studies as it enables the linking of the baseline participant information with administrative data. The lack of standardized models to capture consent elements can lead to substantial challenges. A structured approach to capturing consent-related metadata can address these. a) Explore the state-of-the-art for recording consent; b) Identify key elements of consent required for record linkage; and c) Create and evaluate a novel metadata management model to capture consent-related metadata. The main methodological components of our work were: a) a systematic literature review and qualitative analysis of consent forms; b) the development and evaluation of a novel metadata model. We qualitatively analyzed 61 manuscripts and 30 consent forms. We extracted data elements related to obtaining consent for linkage. We created a novel metadata management model for consent and evaluated it by comparison with the existing standards and by iteratively applying it to case studies. The developed model can facilitate the standardized recording of consent for linkage in longitudinal research studies and enable the linkage of external participant data. Furthermore, it can provide a structured way of recording consent-related metadata and facilitate the harmonization and streamlining of processes.

Familial isolated hyperparathyroidism is linked to a 1.7 Mb region on chromosome 2p13.3–14

PubMed Central

Warner, J; Nyholt, D R; Busfield, F; Epstein, M; Burgess, J; Stranks, S; Hill, P; Perry‐Keene, D; Learoyd, D; Robinson, B; Teh, B T; Prins, J B; Cardinal, J W

2006-01-01

Bachground Familial isolated hyperparathyroidism (FIHP) is an autosomal dominantly inherited form of primary hyperparathyroidism. Although comprising only about 1% of cases of primary hyperparathyroidism, identification and functional analysis of a causative gene for FIHP is likely to advance our understanding of parathyroid physiology and pathophysiology. Methods A genome‐wide screen of DNA from seven pedigrees with FIHP was undertaken in order to identify a region of genetic linkage with the disorder. Results Multipoint linkage analysis identified a region of suggestive linkage (LOD score 2.68) on chromosome 2. Fine mapping with the addition of three other families revealed significant linkage adjacent to D2S2368 (maximum multipoint LOD score 3.43). Recombination events defined a 1.7 Mb region of linkage between D2S2368 and D2S358 in nine pedigrees. Sequencing of the two most likely candidate genes in this region, however, did not identify a gene for FIHP. Conclusions We conclude that a causative gene for FIHP lies within this interval on chromosome 2. This is a major step towards eventual precise identification of a gene for FIHP, likely to be a key component in the genetic regulation of calcium homeostasis. PMID:16525030

Parent-Of-Origin Effects in Autism Identified through Genome-Wide Linkage Analysis of 16,000 SNPs

PubMed Central

Fradin, Delphine; Cheslack-Postava, Keely; Ladd-Acosta, Christine; Newschaffer, Craig; Chakravarti, Aravinda; Arking, Dan E.; Feinberg, Andrew; Fallin, M. Daniele

2010-01-01

Background Autism is a common heritable neurodevelopmental disorder with complex etiology. Several genome-wide linkage and association scans have been carried out to identify regions harboring genes related to autism or autism spectrum disorders, with mixed results. Given the overlap in autism features with genetic abnormalities known to be associated with imprinting, one possible reason for lack of consistency would be the influence of parent-of-origin effects that may mask the ability to detect linkage and association. Methods and Findings We have performed a genome-wide linkage scan that accounts for potential parent-of-origin effects using 16,311 SNPs among families from the Autism Genetic Resource Exchange (AGRE) and the National Institute of Mental Health (NIMH) autism repository. We report parametric (GH, Genehunter) and allele-sharing linkage (Aspex) results using a broad spectrum disorder case definition. Paternal-origin genome-wide statistically significant linkage was observed on chromosomes 4 (LODGH = 3.79, empirical p<0.005 and LODAspex = 2.96, p = 0.008), 15 (LODGH = 3.09, empirical p<0.005 and LODAspex = 3.62, empirical p = 0.003) and 20 (LODGH = 3.36, empirical p<0.005 and LODAspex = 3.38, empirical p = 0.006). Conclusions These regions may harbor imprinted sites associated with the development of autism and offer fruitful domains for molecular investigation into the role of epigenetic mechanisms in autism. PMID:20824079

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamer, D.H.; Hu, S.; Magnuson, V.L.

The role of genetics in male sexual orientation was investigated by pedigree and linkage analyses on 114 families of homosexual men. Increased rates of same-sex orientation were found in the maternal uncles and male cousins of these subjects, but not in their fathers or paternal relatives, suggesting the possibility of sex-linked transmission in a portion of the population. DNA linkage analysis of a selected group of 40 families in which there were two gay brothers and no indication of nonmaternal transmission revealed a correlation between homosexual orientation and the inheritance of polymorphic markers on the X chromosome in approximately 64more » percent of the sib-pairs tested. The linkage to markers on Xq28, the subtelomeric region of the long arm of the sex chromosome, had a multipoint lod score of 4.0(P = 10[sup [minus]5]), indicating a statistical confidence level of more than 99 percent that at least one subtype of male sexual orientation is genetically influenced.« less

Reginald Crundall Punnett: first Arthur Balfour Professor of Genetics, Cambridge, 1912.

PubMed

Edwards, A W F

2012-09-01

R. C. Punnett, the codiscoverer of linkage with W. Bateson in 1904, had the good fortune to be invited to be the first Arthur Balfour Professor of Genetics at Cambridge University, United Kingdom, in 1912 when Bateson, for whom it had been intended, declined to leave his new appointment as first Director of the John Innes Horticultural Institute. We here celebrate the centenary of the first professorship dedicated to genetics, outlining Punnett's career and his scientific contributions, with special reference to the discovery of "partial coupling" in the sweet pea (later "linkage") and to the diagram known as Punnett's square. His seeming reluctance as coauthor with Bateson to promote the reduplication hypothesis to explain the statistical evidence for linkage is stressed, as is his relationship with his successor as Arthur Balfour Professor, R. A. Fisher. The background to the establishment of the Professorship is also described.

A Larger Chocolate Chip—Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps

PubMed Central

Livingstone, Donald; Stack, Conrad; Mustiga, Guiliana M.; Rodezno, Dayana C.; Suarez, Carmen; Amores, Freddy; Feltus, Frank A.; Mockaitis, Keithanne; Cornejo, Omar E.; Motamayor, Juan C.

2017-01-01

Cacao (Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance. PMID:29259608

Quantification of NSW Ambulance Record Linkages with Multiple External Datasets.

PubMed

Carroll, Therese; Muecke, Sandy; Simpson, Judy; Irvine, Katie; Jenkins, André

2015-01-01

This study has two aims: 1) to describe linkage rates between ambulance data and external datasets for "episodes of care" and "patient only" linkages in New South Wales (NSW), Australia; and 2) to detect and report any systematic issues with linkage that relate to patients, and operational or clinical variables that may introduce bias in subsequent studies if not adequately addressed. During 2010-11, the Centre for Health Record Linkage (CHeReL) in NSW, linked the records for patients attended by NSW Ambulance paramedics for the period July 2006 to June 2009, with four external datasets: Emergency Department Data Collection; Admitted Patient Data Collection; NSW Registry of Births, Deaths and Marriages death registration data; and the Australian Bureau of Statistics mortality data. This study reports linkage rates in terms of those "expected" to link and those who were "not expected" to link with external databases within 24 hours of paramedic attendance. Following thorough data preparation processes, 2,041,728 NSW Ambulance care episodes for 1,116,509 patients fulfilled the inclusion criteria. The overall episode-specific hospital linkage rate was 97.2%. Where a patient was not transported to hospital following paramedic care, 8.6% of these episodes resulted in an emergency department attendance within 24 hours. For all care episodes, 5.2% linked to a death record at some time within the 3-year period, with 2.4% of all death episodes occurring within 7 days of a paramedic encounter. For NSW Ambulance episodes of care that were expected to link to an external dataset but did not, nonlinkage to hospital admission records tended to decrease with age. For all other variables, issues relating to rates of linkage and nonlinkage were more indiscriminate. This quantification of the limitations of this large linked dataset will underpin the interpretation and results of ensuing studies that will inform future clinical and operational policies and practices at NSW Ambulance.

Methods of analysis and resources available for genetic trait mapping.

PubMed

Ott, J

1999-01-01

Methods of genetic linkage analysis are reviewed and put in context with other mapping techniques. Sources of information are outlined (books, web sites, computer programs). Special consideration is given to statistical problems in canine genetic mapping (heterozygosity, inbreeding, marker maps).

Experimental Approaches to Systematic Discovery and Development of Reproductive Adverse Outcome Pathways in Fish

EPA Science Inventory

Adverse outcome pathways (AOPs) are conceptual frameworks that portray causal and predictive linkages between key events at multiple scales of biological organization that connect molecular initiating events and early cellular perturbations (e.g., initiation of toxicity pathways)...

Exploring evidence-policy linkages in health research plans: A case study from six countries

PubMed Central

Syed, Shamsuzzoha B; Hyder, Adnan A; Bloom, Gerald; Sundaram, Sandhya; Bhuiya, Abbas; Zhenzhong, Zhang; Kanjilal, Barun; Oladepo, Oladimeji; Pariyo, George; Peters, David H

2008-01-01

The complex evidence-policy interface in low and middle income country settings is receiving increasing attention. Future Health Systems (FHS): Innovations for Equity, is a research consortium conducting health systems explorations in six Asian and African countries: Bangladesh, India, China, Afghanistan, Uganda, and Nigeria. The cross-country research consortium provides a unique opportunity to explore the research-policy interface. Three key activities were undertaken during the initial phase of this five-year project. First, key considerations in strengthening evidence-policy linkages in health system research were developed by FHS researchers through workshops and electronic communications. Four key considerations in strengthening evidence-policy linkages are postulated: development context; research characteristics; decision-making processes; and stakeholder engagement. Second, these four considerations were applied to research proposals in each of the six countries to highlight features in the research plans that potentially strengthen the research-policy interface and opportunities for improvement. Finally, the utility of the approach for setting research priorities in health policy and systems research was reflected upon. These three activities yielded interesting findings. First, developmental consideration with four dimensions – poverty, vulnerabilities, capabilities, and health shocks – provides an entry point in examining research-policy interfaces in the six settings. Second, research plans focused upon on the ground realities in specific countries strengthens the interface. Third, focusing on research prioritized by decision-makers, within a politicized health arena, enhances chances of research influencing action. Lastly, early and continued engagement of multiple stakeholders, from local to national levels, is conducive to enhanced communication at the interface. The approach described has four main utilities: first, systematic analyses of research proposals using key considerations ensure such issues are incorporated into research proposals; second, the exact meaning, significance, and inter-relatedness of these considerations can be explored within the research itself; third, cross-country learning can be enhanced; and finally, translation of evidence into action may be facilitated. Health systems research proposals in low and middle income countries should include reflection on transferring research findings into policy. Such deliberations may be informed by employing the four key considerations suggested in this paper in analyzing research proposals. PMID:18331651

Linking databases on perinatal health: a review of the literature and current practices in Europe

PubMed Central

Szamotulska, K.; Hindori-Mohangoo, A.D.; Blondel, B.; Macfarlane, A.J.; Dattani, N.; Barona, C.; Berrut, S.; Zile, I.; Wood, R.; Sakkeus, L.; Gissler, M.; Zeitlin, J.

2016-01-01

Background: International comparisons of perinatal health indicators are complicated by the heterogeneity of data sources on pregnancy, maternal and neonatal outcomes. Record linkage can extend the range of data items available and thus can improve the validity and quality of routine data. We sought to assess the extent to which data are linked routinely for perinatal health research and reporting. Methods: We conducted a systematic review of the literature by searching PubMed for perinatal health studies from 2001 to 2011 based on linkage of routine data (data collected continuously at various time intervals). We also surveyed European health monitoring professionals about use of linkage for national perinatal health surveillance. Results: 516 studies fit our inclusion criteria. Denmark, Finland, Norway and Sweden, the US and the UK contributed 76% of the publications; a further 29 countries contributed at least one publication. Most studies linked vital statistics, hospital records, medical birth registries and cohort data. Other sources were specific registers for: cancer (70), congenital anomalies (56), ART (19), census (19), health professionals (37), insurance (22) prescription (31), and level of education (18). Eighteen of 29 countries (62%) reported linking data for routine perinatal health monitoring. Conclusion: Research using linkage is concentrated in a few countries and is not widely practiced in Europe. Broader adoption of data linkage could yield substantial gains for perinatal health research and surveillance. PMID:26891058

Predictors of locating women six to eight years after contact: internet resources at recruitment may help to improve response rates in longitudinal research

PubMed Central

Cadarette, Suzanne M; Dickson, Leigh; Gignac, Monique AM; Beaton, Dorcas E; Jaglal, Susan B; Hawker, Gillian A

2007-01-01

Background The ability to locate those sampled has important implications for response rates and thus the success of survey research. The purpose of this study was to examine predictors of locating women requiring tracing using publicly available methods (primarily Internet searches), and to determine the additional benefit of vital statistics linkages. Methods Random samples of women aged 65–89 years residing in two regions of Ontario, Canada were selected from a list of those who completed a questionnaire between 1995 and 1997 (n = 1,500). A random sample of 507 of these women had been searched on the Internet as part of a feasibility pilot in 2001. All 1,500 women sampled were mailed a newsletter and information letter prior to recruitment by telephone in 2003 and 2004. Those with returned mail or incorrect telephone number(s) required tracing. Predictors of locating women were examined using logistic regression. Results Tracing was required for 372 (25%) of the women sampled, and of these, 181 (49%) were located. Predictors of locating women were: younger age, residing in less densely populated areas, having had a web-search completed in 2001, and listed name identified on the Internet prior to recruitment in 2003. Although vital statistics linkages to death records subsequently identified 41 subjects, these data were incomplete. Conclusion Prospective studies may benefit from using Internet resources at recruitment to determine the listed names for telephone numbers thereby facilitating follow-up tracing and improving response rates. Although vital statistics linkages may help to identify deceased individuals, these may be best suited for post hoc response rate adjustment. PMID:17577404

Predictors of locating women six to eight years after contact: internet resources at recruitment may help to improve response rates in longitudinal research.

PubMed

Cadarette, Suzanne M; Dickson, Leigh; Gignac, Monique A M; Beaton, Dorcas E; Jaglal, Susan B; Hawker, Gillian A

2007-06-18

The ability to locate those sampled has important implications for response rates and thus the success of survey research. The purpose of this study was to examine predictors of locating women requiring tracing using publicly available methods (primarily Internet searches), and to determine the additional benefit of vital statistics linkages. Random samples of women aged 65-89 years residing in two regions of Ontario, Canada were selected from a list of those who completed a questionnaire between 1995 and 1997 (n = 1,500). A random sample of 507 of these women had been searched on the Internet as part of a feasibility pilot in 2001. All 1,500 women sampled were mailed a newsletter and information letter prior to recruitment by telephone in 2003 and 2004. Those with returned mail or incorrect telephone number(s) required tracing. Predictors of locating women were examined using logistic regression. Tracing was required for 372 (25%) of the women sampled, and of these, 181 (49%) were located. Predictors of locating women were: younger age, residing in less densely populated areas, having had a web-search completed in 2001, and listed name identified on the Internet prior to recruitment in 2003. Although vital statistics linkages to death records subsequently identified 41 subjects, these data were incomplete. Prospective studies may benefit from using Internet resources at recruitment to determine the listed names for telephone numbers thereby facilitating follow-up tracing and improving response rates. Although vital statistics linkages may help to identify deceased individuals, these may be best suited for post hoc response rate adjustment.

Genetic linkage study of bipolar disorder and the serotonin transporter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelsoe, J.R.; Morison, M.; Mroczkowski-Parker, Z.

1996-04-09

The serotonin transporter (HTT) is an important candidate gene for the genetic transmission of bipolar disorder. It is the site of action of many antidepressants, and plays a key role in the regulation of serotonin neurotransmission. Many studies of affectively ill patients have found abnormalities in serotonin metabolism, and dysregulation of the transporter itself. The human serotonin transporter has been recently cloned and mapped to chromosome 17. We have identified a PstI RFLP at the HTT locus, and here report our examination of this polymorphism for possible linkage to bipolar disorder. Eighteen families were examined from three populations: the Oldmore » Order Amish, Iceland, and the general North American population. In addition to HTT, three other microsatellite markers were examined, which span an interval known to contain HTT. Linkage analyses were conducted under both dominant and recessive models, as well as both narrow (bipolar only) and broad (bipolar + recurrent unipolar) diagnostic models. Linkage could be excluded to HTT under all models examined. Linkage to the interval spanned by the microsatellites was similarly excluded under the dominant models. In two individual families, maximum lod scores of 1.02 and 0.84 were obtained at D17S798 and HTT, respectively. However, these data overall do not support the presence of a susceptibility locus for bipolar disorder near the serotonin transporter. 20 refs., 2 tabs.« less

Analysis of quantitative lipid traits in the genetics of NIDDM (GENNID) study.

PubMed

Malhotra, Alka; Wolford, Johanna K

2005-10-01

Coronary heart disease (CHD) is the leading cause of death among individuals with type 2 diabetes. Dyslipidemia contributes significantly to CHD in diabetic patients, in whom lipid abnormalities include hypertriglyceridemia, low HDL cholesterol, and increased levels of small, dense LDL particles. To identify genes for lipid-related traits, we performed genome-wide linkage analyses for levels of triglycerides and HDL, LDL, and total cholesterol in Caucasian, Hispanic, and African-American families from the Genetics of NIDDM (GENNID) study. Most lipid traits showed significant estimates of heritability (P < 0.001) with the exception of triglycerides and the triglyceride/HDL ratio in African Americans. Variance components analysis identified linkage on chromosome 3p12.1-3q13.31 for the triglyceride/HDL ratio (logarithm of odds [LOD] = 3.36) and triglyceride (LOD = 3.27) in Caucasian families. Statistically significant evidence for linkage was identified for the triglyceride/HDL ratio (LOD = 2.45) on 11p in Hispanic families in a region that showed suggestive evidence for linkage (LOD = 2.26) for triglycerides in this population. In African Americans, the strongest evidence for linkage (LOD = 2.26) was found on 19p13.2-19q13.42 for total cholesterol. Our findings provide strong support for previous reports of linkage for lipid-related traits, suggesting the presence of genes on 3p12.1-3q13.31, 11p15.4-11p11.3, and 19p13.2-19q13.42 that may influence traits underlying lipid abnormalities associated with type 2 diabetes.

"Epidemiological criminology": coming full circle.

PubMed

Akers, Timothy A; Lanier, Mark M

2009-03-01

Members of the public health and criminal justice disciplines often work with marginalized populations: people at high risk of drug use, health problems, incarceration, and other difficulties. As these fields increasingly overlap, distinctions between them are blurred, as numerous research reports and funding trends document. However, explicit theoretical and methodological linkages between the 2 disciplines remain rare. A new paradigm that links methods and statistical models of public health with those of their criminal justice counterparts is needed, as are increased linkages between epidemiological analogies, theories, and models and the corresponding tools of criminology. We outline disciplinary commonalities and distinctions, present policy examples that integrate similarities, and propose "epidemiological criminology" as a bridging framework.

Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

2008-02-01

The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

Parametric and nonparametric Granger causality testing: Linkages between international stock markets

NASA Astrophysics Data System (ADS)

De Gooijer, Jan G.; Sivarajasingham, Selliah

2008-04-01

This study investigates long-term linear and nonlinear causal linkages among eleven stock markets, six industrialized markets and five emerging markets of South-East Asia. We cover the period 1987-2006, taking into account the on-set of the Asian financial crisis of 1997. We first apply a test for the presence of general nonlinearity in vector time series. Substantial differences exist between the pre- and post-crisis period in terms of the total number of significant nonlinear relationships. We then examine both periods, using a new nonparametric test for Granger noncausality and the conventional parametric Granger noncausality test. One major finding is that the Asian stock markets have become more internationally integrated after the Asian financial crisis. An exception is the Sri Lankan market with almost no significant long-term linear and nonlinear causal linkages with other markets. To ensure that any causality is strictly nonlinear in nature, we also examine the nonlinear causal relationships of VAR filtered residuals and VAR filtered squared residuals for the post-crisis sample. We find quite a few remaining significant bi- and uni-directional causal nonlinear relationships in these series. Finally, after filtering the VAR-residuals with GARCH-BEKK models, we show that the nonparametric test statistics are substantially smaller in both magnitude and statistical significance than those before filtering. This indicates that nonlinear causality can, to a large extent, be explained by simple volatility effects.

Linkages Between Patient-centered Medical Homes and Addiction Treatment Organizations: Results From a National Survey.

PubMed

D'Aunno, Thomas; Pollack, Harold; Chen, Qixuan; Friedmann, Peter D

2017-04-01

To meet their aims of providing comprehensive and coordinated care, patient-centered medical homes (PCMHs) need to coordinate services for individuals with substance use disorders. Yet, the 14,000 addiction treatment (AT) organizations across the United States that provide services for more than 1 million individuals daily are generally ill-prepared to work with PCMHs (eg, AT organizations often lack electronic health records). To examine the extent to which AT organizations have formal linkages through contracts with PCMHs; to identify key dimensions of linkages between PCMHs and AT organizations (eg, shared use of electronic health records); to identify characteristics of AT organizations and their environments associated with these linkages. We draw on data from a 2014 nationally representative survey of directors and clinical supervisors from 695 AT organizations (n=1390 survey respondents). Thirty-eight percent of patients across the nation are receiving treatment in AT organizations linked by contracts to PCMHs. This number increases to 51% in states that expanded Medicaid (vs. only 6.2% of patients in non-Medicaid expansion states). Yet, the great majority of linkages are relatively weak; they do not include the exchange of patient information. Results from multivariable analyses show that larger, nonprofit and publicly owned AT organizations, as well as those located in the northeast and in states that expanded Medicaid coverage, are more likely to have contracts with PCMHs. Without stronger linkages between AT organizations and PCMHs or the development of other models that integrate services, individuals with substance abuse disorders may continue to receive uncoordinated care.

Some methods for blindfolded record linkage.

PubMed

Churches, Tim; Christen, Peter

2004-06-28

The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects - a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy.

Some methods for blindfolded record linkage

PubMed Central

Churches, Tim; Christen, Peter

2004-01-01

Background The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. Methods A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. Results The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Conclusion Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy. PMID:15222890

Data linkage between existing healthcare databases to support hospital epidemiology.

PubMed

García Álvarez, L; Aylin, P; Tian, J; King, C; Catchpole, M; Hassall, S; Whittaker-Axon, K; Holmes, A

2011-11-01

Enhancing the use of existing datasets within acute hospitals will greatly facilitate hospital epidemiology, surveillance, the monitoring of a variety of processes, outcomes and risk factors, and the provision of alert systems. Multiple overlapping data systems exist within National Health Service (NHS) hospitals in the UK, and many duplicate data recordings take place because of the lack of linkage and interfaces. This results in hospital-collected data not being used efficiently. The objective was to create an inventory of all existing systems, including administrative, management, human resources, microbiology, patient care and other platforms, to describe the data architecture that could contribute valuable information for a hospital epidemiology unit. These datasets were investigated as to how they could be used to generate surveillance data, key performance indicators and risk information that could be shared at board, clinical programme group, specialty and ward level. An example of an output of this integrated data platform and its application in influenza resilience planning and responsiveness is described. The development of metrics for staff absence and staffing levels may also be used as key indicators for risk-monitoring for infection prevention. This work demonstrates the value of such a data inventory and linkage and the importance of more sophisticated uses of existing NHS data, and innovative collaborative approaches to support clinical care, quality improvement, surveillance, emergency planning and research. Copyright © 2011 The Healthcare Infection Society. All rights reserved.

The Anthropocene and the international law of the sea.

PubMed

Vidas, Davor

2011-03-13

The current law of the sea provides a framework for various specific issues, but is incapable of responding adequately to the overall challenges facing humankind, now conceivably already living in the Anthropocene. The linkages between the development of the law of the sea and the current process towards formal recognition of an Anthropocene epoch are twofold. First, there is a linkage of origin. The ideological foundations of the law of the sea facilitated the emergence of forces that were to lead to the Industrial Revolution and, eventually, to levels of development entailing ever-greater human impacts on the Earth System. Second, there are linkages in interaction. Geological information has prompted key developments in the law of the sea since the introduction of the continental shelf concept in the mid-twentieth century. With the formalization of the Anthropocene epoch, geology might again act as a trigger for new developments needed in the law of the sea. This article explores those two aspects of linkages and examines prospects for further development of the law of the sea framework, through concepts such as the responsibility for the seas as well as those related to new approaches to global sustainability such as the 'planetary boundaries'.

Assessing National Data on Education.

ERIC Educational Resources Information Center

Plisko, Valena White; And Others

This paper applies questions of coverage, quality and linkages to the current collection of national statistics on education at the preprimary, elementary/secondary, and higher education levels. The main questions raised at the preprimary level pertain to availability of programs, standards, and family-school interaction. At the…

Detecting local haplotype sharing and haplotype association

USDA-ARS?s Scientific Manuscript database

A novel haplotype association method is presented, and its power is demonstrated. Relying on a statistical model for linkage disequilibrium (LD), the method first infers ancestral haplotypes and their loadings at each marker for each individual. The loadings are then used to quantify local haplotype...

Generalising Ward's Method for Use with Manhattan Distances.

PubMed

Strauss, Trudie; von Maltitz, Michael Johan

2017-01-01

The claim that Ward's linkage algorithm in hierarchical clustering is limited to use with Euclidean distances is investigated. In this paper, Ward's clustering algorithm is generalised to use with l1 norm or Manhattan distances. We argue that the generalisation of Ward's linkage method to incorporate Manhattan distances is theoretically sound and provide an example of where this method outperforms the method using Euclidean distances. As an application, we perform statistical analyses on languages using methods normally applied to biology and genetic classification. We aim to quantify differences in character traits between languages and use a statistical language signature based on relative bi-gram (sequence of two letters) frequencies to calculate a distance matrix between 32 Indo-European languages. We then use Ward's method of hierarchical clustering to classify the languages, using the Euclidean distance and the Manhattan distance. Results obtained from using the different distance metrics are compared to show that the Ward's algorithm characteristic of minimising intra-cluster variation and maximising inter-cluster variation is not violated when using the Manhattan metric.

Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan

PubMed Central

Geesaman, Bard J.; Benson, Erica; Brewster, Stephanie J.; Kunkel, Louis M.; Blanché, Hélène; Thomas, Gilles; Perls, Thomas T.; Daly, Mark J.; Puca, Annibale A.

2003-01-01

We previously reported a genomewide linkage study for human longevity using 308 long-lived individuals (LLI) (centenarians or near-centenarians) in 137 sibships and identified statistically significant linkage within chromosome 4 near microsatellite D4S1564. This interval spans 12 million bp and contains ≈50 putative genes. To identify the specific gene and gene variants impacting lifespan, we performed a haplotype-based fine-mapping study of the interval. The resulting genetic association study identified a haplotype marker within microsomal transfer protein as a modifier of human lifespan. This same variant was tested in a second cohort of LLI from France, and although the association was not replicated, there was evidence for statistical distortion in the form of Hardy–Weinberg disequilibrium. Microsomal transfer protein has been identified as the rate-limiting step in lipoprotein synthesis and may affect longevity by subtly modulating this pathway. This study provides proof of concept for the feasibility of using the genomes of LLI to identify genes impacting longevity. PMID:14615589

Development of an adverse outcome pathway for acetylcholinesterase inhibition leading to acute mortality

EPA Science Inventory

Adverse outcome pathways (AOPs) are designed to describe linkages of key events (KEs) within a biological pathway that result in an adverse outcome associated with chemical perturbation of a well-defined molecular initiating event (MIE). Risk assessors have traditionally relied ...

A new method of linkage analysis using LOD scores for quantitative traits supports linkage of monoamine oxidase activity to D17S250 in the Collaborative Study on the Genetics of Alcoholism pedigrees.

PubMed

Curtis, David; Knight, Jo; Sham, Pak C

2005-09-01

Although LOD score methods have been applied to diseases with complex modes of inheritance, linkage analysis of quantitative traits has tended to rely on non-parametric methods based on regression or variance components analysis. Here, we describe a new method for LOD score analysis of quantitative traits which does not require specification of a mode of inheritance. The technique is derived from the MFLINK method for dichotomous traits. A range of plausible transmission models is constructed, constrained to yield the correct population mean and variance for the trait but differing with respect to the contribution to the variance due to the locus under consideration. Maximized LOD scores under homogeneity and admixture are calculated, as is a model-free LOD score which compares the maximized likelihoods under admixture assuming linkage and no linkage. These LOD scores have known asymptotic distributions and hence can be used to provide a statistical test for linkage. The method has been implemented in a program called QMFLINK. It was applied to data sets simulated using a variety of transmission models and to a measure of monoamine oxidase activity in 105 pedigrees from the Collaborative Study on the Genetics of Alcoholism. With the simulated data, the results showed that the new method could detect linkage well if the true allele frequency for the trait was close to that specified. However, it performed poorly on models in which the true allele frequency was much rarer. For the Collaborative Study on the Genetics of Alcoholism data set only a modest overlap was observed between the results obtained from the new method and those obtained when the same data were analysed previously using regression and variance components analysis. Of interest is that D17S250 produced a maximized LOD score under homogeneity and admixture of 2.6 but did not indicate linkage using the previous methods. However, this region did produce evidence for linkage in a separate data set, suggesting that QMFLINK may have been able to detect a true linkage which was not picked up by the other methods. The application of model-free LOD score analysis to quantitative traits is novel and deserves further evaluation of its merits and disadvantages relative to other methods.

Near-Earth Object Orbit Linking with the Large Synoptic Survey Telescope

NASA Astrophysics Data System (ADS)

Vereš, Peter; Chesley, Steven R.

2017-07-01

We have conducted a detailed simulation of the ability of the Large Synoptic Survey Telescope (LSST) to link near-Earth and main belt asteroid detections into orbits. The key elements of the study were a high-fidelity detection model and the presence of false detections in the form of both statistical noise and difference image artifacts. We employed the Moving Object Processing System (MOPS) to generate tracklets, tracks, and orbits with a realistic detection density for one month of the LSST survey. The main goals of the study were to understand whether (a) the linking of near-Earth objects (NEOs) into orbits can succeed in a realistic survey, (b) the number of false tracks and orbits will be manageable, and (c) the accuracy of linked orbits would be sufficient for automated processing of discoveries and attributions. We found that the overall density of asteroids was more than 5000 per LSST field near opposition on the ecliptic, plus up to 3000 false detections per field in good seeing. We achieved 93.6% NEO linking efficiency for H< 22 on tracks composed of tracklets from at least three distinct nights within a 12 day interval. The derived NEO catalog was comprised of 96% correct linkages. Less than 0.1% of orbits included false detections, and the remainder of false linkages stemmed from main belt confusion, which was an artifact of the short time span of the simulation. The MOPS linking efficiency can be improved by refined attribution of detections to known objects and by improved tuning of the internal kd-tree linking algorithms.

Teacher-Principal Relationships: Exploring Linkages between Empowerment and Interpersonal Trust

ERIC Educational Resources Information Center

Moye, Melinda J.; Henkin, Alan B.; Egley, Robert J.

2005-01-01

Purpose: To investigate relationships between teacher empowerment and interpersonal level trust in the principal. Design/methodology/approach: Trust is a fundamental element in well-functioning organizations. Studies of empowerment, a motivational construct, have suggested that empowering employees is a key factor in managerial and organizational…

X-chromosome STR markers data in a Cabo Verde immigrant population of Lisboa.

PubMed

Afonso Costa, Heloísa; Morais, Paulo; Vieira da Silva, Cláudia; Matos, Sara; Marques Santos, Rodolfo; Espinheira, Rosa; Costa Santos, Jorge; Amorim, António

2014-01-01

Population genetic data of 12 X chromosomal short tandem repeats markers (DXS10074, DXS10079, DXS10101, DXS10103, DXS10134, DXS10135, DXS10146, DXS10148, DXS7132, DXS7423, DXS8378 and HPRTB) were analysed in 54 females and 95 males of an immigrant population from Cabo Verde living in Lisboa. The obtained results for forensic statistical parameters such as observed heterozigosity, polymorphism information content, power of discrimination and mean exclusion chance, based on single allele frequencies, reveal that this multiplex system is highly informative and can represent an important tool for genetic identification purposes in the immigrant population of Cabo Verde. Since the studied short tandem repeats genetic markers are distributed on four linkage groups, that can provide independent genotype information, we studied those groups as haploytes. The forensic efficiency parameters for the linked groups were all higher than 0.97, with linkage group I being the most polymorphic and linkage group III the less informative.

The lod score method.

PubMed

Rice, J P; Saccone, N L; Corbett, J

2001-01-01

The lod score method originated in a seminal article by Newton Morton in 1955. The method is broadly concerned with issues of power and the posterior probability of linkage, ensuring that a reported linkage has a high probability of being a true linkage. In addition, the method is sequential, so that pedigrees or lod curves may be combined from published reports to pool data for analysis. This approach has been remarkably successful for 50 years in identifying disease genes for Mendelian disorders. After discussing these issues, we consider the situation for complex disorders, where the maximum lod score (MLS) statistic shares some of the advantages of the traditional lod score approach but is limited by unknown power and the lack of sharing of the primary data needed to optimally combine analytic results. We may still learn from the lod score method as we explore new methods in molecular biology and genetic analysis to utilize the complete human DNA sequence and the cataloging of all human genes.

Meta-analysis of genome-wide linkage studies in BMI and obesity.

PubMed

Saunders, Catherine L; Chiodini, Benedetta D; Sham, Pak; Lewis, Cathryn M; Abkevich, Victor; Adeyemo, Adebowale A; de Andrade, Mariza; Arya, Rector; Berenson, Gerald S; Blangero, John; Boehnke, Michael; Borecki, Ingrid B; Chagnon, Yvon C; Chen, Wei; Comuzzie, Anthony G; Deng, Hong-Wen; Duggirala, Ravindranath; Feitosa, Mary F; Froguel, Philippe; Hanson, Robert L; Hebebrand, Johannes; Huezo-Dias, Patricia; Kissebah, Ahmed H; Li, Weidong; Luke, Amy; Martin, Lisa J; Nash, Matthew; Ohman, Miina; Palmer, Lyle J; Peltonen, Leena; Perola, Markus; Price, R Arlen; Redline, Susan; Srinivasan, Sathanur R; Stern, Michael P; Stone, Steven; Stringham, Heather; Turner, Stephen; Wijmenga, Cisca; Collier, David A

2007-09-01

The objective was to provide an overall assessment of genetic linkage data of BMI and BMI-defined obesity using a nonparametric genome scan meta-analysis. We identified 37 published studies containing data on over 31,000 individuals from more than >10,000 families and obtained genome-wide logarithm of the odds (LOD) scores, non-parametric linkage (NPL) scores, or maximum likelihood scores (MLS). BMI was analyzed in a pooled set of all studies, as a subgroup of 10 studies that used BMI-defined obesity, and for subgroups ascertained through type 2 diabetes, hypertension, or subjects of European ancestry. Bins at chromosome 13q13.2- q33.1, 12q23-q24.3 achieved suggestive evidence of linkage to BMI in the pooled analysis and samples ascertained for hypertension. Nominal evidence of linkage to these regions and suggestive evidence for 11q13.3-22.3 were also observed for BMI-defined obesity. The FTO obesity gene locus at 16q12.2 also showed nominal evidence for linkage. However, overall distribution of summed rank p values <0.05 is not different from that expected by chance. The strongest evidence was obtained in the families ascertained for hypertension at 9q31.1-qter and 12p11.21-q23 (p < 0.01). Despite having substantial statistical power, we did not unequivocally implicate specific loci for BMI or obesity. This may be because genes influencing adiposity are of very small effect, with substantial genetic heterogeneity and variable dependence on environmental factors. However, the observation that the FTO gene maps to one of the highest ranking bins for obesity is interesting and, while not a validation of this approach, indicates that other potential loci identified in this study should be investigated further.

A Locus for Autosomal Dominant Hereditary Spastic Ataxia, SAX1, Maps to Chromosome 12p13

PubMed Central

Meijer, I. A.; Hand, C. K.; Grewal, K. K.; Stefanelli, M. G.; Ives, E. J.; Rouleau, G. A.

2002-01-01

The hereditary spastic ataxias (HSA) are a group of clinically heterogeneous neurodegenerative disorders characterized by lower-limb spasticity and generalized ataxia. HSA was diagnosed in three unrelated autosomal dominant families from Newfoundland, who presented mainly with severe leg spasticity, dysarthria, dysphagia, and ocular-movement abnormalities. A genomewide scan was performed on one family, and linkage to a novel locus for HSA on chromosome 12p13, which contains the as-yet-unidentified gene locus SAX1, was identified. Fine mapping confirmed linkage in the two large families, and the third, smaller family showed LOD scores suggestive of linkage. Haplotype construction by use of 13 polymorphic markers revealed that all three families share a disease haplotype, which key recombinants and overlapping haplotypes refine to ∼5 cM, flanked by markers D12S93 and GATA151H05. SAX1 is the first locus mapped for autosomal dominant HSA. PMID:11774073

Solution- and solid-phase parallel synthesis of 4-alkoxy-substituted pyrimidines with high molecular diversity.

PubMed

Font, David; Heras, Montserrat; Villalgordo, José M

2003-01-01

A simple and straightforward methodology toward the synthesis of novel 2,6-disubstituted-4-alkoxypyrimidine derivatives of type 16 and 19 has been developed. This methodology, initially developed in solution, can be perfectly adapted to the solid support under analogous conditions, taking full advantage of automated parallel synthesis systems. This successful methodology benefits from the key role played by the thioether linkage placed at the 2-position in 3, 9, or 13 in a double manner: on one side, the steric effect exerted by the thioether linkage is likely to be responsible for the very high observed selectivity toward the formation of the O-alkylation products. On the other side, this sulfur linkage can serve not only as a robust point of attachment for the heterocycle, stable to a number of reaction conditions, but also as a means of introducing a new element of diversity through activation to the corresponding sulfone (safety-catch linker concept) and subsequent ipso-substitution reaction with a variety of different N-nucleophiles.

Involvement of polyubiquitin chains via specific chain linkages in stress response in mammalian cells.

PubMed

Fujimuro, Masahiro; Nishiya, Tadashi; Nomura, Yasuyuki; Yokosawa, Hideyoshi

2005-12-01

Polyubiquitination plays key roles in various proteasome-dependent and independent cellular events. To elucidate roles in stress response of polyubiquitin chains formed via specific chain linkages in mammalian cells, we established NIH3T3 stable cell lines that are capable of conditionally expressing K29R, K48R and K63R ubiquitin mutants, in which the Lys29, Lys48 and Lys63 residues of ubiquitin had been changed to Arg, and we examined the effects of various stresses on their cell viabilities. The expression of K63R ubiquitin mutant decreased viability of the cells post-exposed to ethanol, H(2)O(2) and methyl methanesulfonate (MMS), while that of K48R mutant decreased viability of the cells post-exposed to heat shock as well as ethanol, H(2)O(2) and MMS. Thus, these results suggest that polyubiquitin chains formed via specific chain linkages are involved in the respective stress responses in mammalian cells.

Barriers and facilitators of linkage to HIV care among HIV-infected young Chinese men who have sex with men: a qualitative study.

PubMed

Li, Haochu; Wei, Chongyi; Tucker, Joseph; Kang, Dianmin; Liao, Meizhen; Holroyd, Eleanor; Zheng, Jietao; Qi, Qian; Ma, Wei

2017-03-16

The Four Free and One Care Policy (HIV/AIDS-related free services) has been in place in China since 2004. However, linkage to human immunodeficiency virus (HIV) care is not yet achieved very well among people living with HIV. We conducted a qualitative study to explore individual and contextual factors that may influence a linkage to HIV care from the perspective of young HIV-infected men who have sex with men (MSM) in a highly centralized HIV care context of China. Purposive sampling was used to recruit 21 HIV-infected MSM in Shandong Province, with in-depth interviews conducted between March and July 2015. Thematic content analysis was subsequently used for data analysis. Key barriers and facilitators related to a linkage to HIV care emerged from participants' narratives. The barriers included perceived healthy status, low health literacy, and stigma associated with receiving HIV care. The facilitators included an awareness of responsibility, knowledge associated with health literacy, social support, and trusting and relying on services provided by the Center for Disease Control and Prevention (CDC) and the government. These were related to the quality of current HIV counselling and testing, service promotion, and the cost and placement of these HIV services. In order to improve the MSM linkage to HIV care in China, it is imperative to improve the quality of the current on-going counselling and testing. Further critical linkage support includes increasing supportive services among local CDC systems, designated hospitals and community-based organizations (CBOs), and more financial support for HIV/AIDS related testing, medical checkups and treatments.

Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations-significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes Research Group.

PubMed

Malhotra, Alka; Igo, Robert P; Thameem, Farook; Kao, W H Linda; Abboud, Hanna E; Adler, Sharon G; Arar, Nedal H; Bowden, Donald W; Duggirala, Ravindranath; Freedman, Barry I; Goddard, Katrina A B; Ipp, Eli; Iyengar, Sudha K; Kimmel, Paul L; Knowler, William C; Kohn, Orly; Leehey, David; Meoni, Lucy A; Nelson, Robert G; Nicholas, Susanne B; Parekh, Rulan S; Rich, Stephen S; Chen, Yii-Der I; Saad, Mohammed F; Scavini, Marina; Schelling, Jeffrey R; Sedor, John R; Shah, Vallabh O; Taylor, Kent D; Thornley-Brown, Denyse; Zager, Philip G; Horvath, Amanda; Hanson, Robert L

2009-11-01

Previous studies have shown that in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations. Phenotypic and genotypic data were obtained from African American (AA; total number of individuals [N] = 1004), American Indian (AI; N = 883), European American (EA; N = 537), and Mexican American (MA; N = 1634) individuals from the Family Investigation of Nephropathy and Diabetes. Non-parametric linkage analysis, using an average of 4404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM. Statistically significant evidence for linkage was observed on chromosome 4q21.1 (LOD = 3.13; genome-wide p = 0.04) in AA. In addition, a total of 11 regions showed suggestive evidence for linkage (estimated at LOD > 1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD = 2.02) and 22q12.3 (LOD = 2.38) in AA, 2p11.1 (LOD = 2.23) in AI, 6p12.3 (LOD = 2.77) in EA, and 13q21.1 (LOD = . 2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD > 1.71 have been identified in previously published studies. The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA; 6p in EA; 2p in AI; and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population.

On computation of p-values in parametric linkage analysis.

PubMed

Kurbasic, Azra; Hössjer, Ola

2004-01-01

Parametric linkage analysis is usually used to find chromosomal regions linked to a disease (phenotype) that is described with a specific genetic model. This is done by investigating the relations between the disease and genetic markers, that is, well-characterized loci of known position with a clear Mendelian mode of inheritance. Assume we have found an interesting region on a chromosome that we suspect is linked to the disease. Then we want to test the hypothesis of no linkage versus the alternative one of linkage. As a measure we use the maximal lod score Z(max). It is well known that the maximal lod score has asymptotically a (2 ln 10)(-1) x (1/2 chi2(0) + 1/2 chi2(1)) distribution under the null hypothesis of no linkage when only one point (one marker) on the chromosome is studied. In this paper, we show, both by simulations and theoretical arguments, that the null hypothesis distribution of Zmax has no simple form when more than one marker is used (multipoint analysis). In fact, the distribution of Zmax depends on the number of families, their structure, the assumed genetic model, marker denseness, and marker informativity. This means that a constant critical limit of Zmax leads to tests associated with different significance levels. Because of the above-mentioned problems, from the statistical point of view the maximal lod score should be supplemented by a p-value when results are reported. Copyright (c) 2004 S. Karger AG, Basel.

Genomewide significant linkage to recurrent, early-onset major depressive disorder on chromosome 15q.

PubMed

Holmans, Peter; Zubenko, George S; Crowe, Raymond R; DePaulo, J Raymond; Scheftner, William A; Weissman, Myrna M; Zubenko, Wendy N; Boutelle, Sandra; Murphy-Eberenz, Kathleen; MacKinnon, Dean; McInnis, Melvin G; Marta, Diana H; Adams, Philip; Knowles, James A; Gladis, Madeleine; Thomas, Jo; Chellis, Jennifer; Miller, Erin; Levinson, Douglas F

2004-06-01

A genome scan was performed on the first phase sample of the Genetics of Recurrent Early-Onset Depression (GenRED) project. The sample consisted of 297 informative families containing 415 independent affected sibling pairs (ASPs), or, counting all possible pairs, 685 informative affected relative pairs (555 ASPs and 130 other pair types). Affected cases had recurrent major depressive disorder (MDD) with onset before age 31 years for probands or age 41 years for other affected relatives; the mean age at onset was 18.5 years, and the mean number of depressive episodes was 7.3. The Center for Inherited Disease Research genotyped 389 microsatellite markers (mean spacing of 9.3 cM). The primary linkage analysis considered allele sharing in all possible affected relative pairs with the use of the Z(lr) statistic computed by the ALLEGRO program. A secondary logistic regression analysis considered the effect of the sex of the pair as a covariate. Genomewide significant linkage was observed on chromosome 15q25.3-26.2 (Zlr=4.14, equivalent LOD = 3.73, empirical genomewide P=.023). The linkage was not sex specific. No other suggestive or significant results were observed in the primary analysis. The secondary analysis produced three regions of suggestive linkage, but these results should be interpreted cautiously because they depended primarily on the small subsample of 42 male-male pairs. Chromosome 15q25.3-26.2 deserves further study as a candidate region for susceptibility to MDD.

77 FR 6803 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-09

...) 1999- 2010 Birth Certificate Linkage Study--Pregnant Women--New--National Center for Health Statistics... and ask permission to link their data to the child's birth certificate data, for the birth that... about the pregnant women at the time of interview. Having information on their children's birth...

“Epidemiological Criminology”: Coming Full Circle

PubMed Central

Lanier, Mark M.

2009-01-01

Members of the public health and criminal justice disciplines often work with marginalized populations: people at high risk of drug use, health problems, incarceration, and other difficulties. As these fields increasingly overlap, distinctions between them are blurred, as numerous research reports and funding trends document. However, explicit theoretical and methodological linkages between the 2 disciplines remain rare. A new paradigm that links methods and statistical models of public health with those of their criminal justice counterparts is needed, as are increased linkages between epidemiological analogies, theories, and models and the corresponding tools of criminology. We outline disciplinary commonalities and distinctions, present policy examples that integrate similarities, and propose “epidemiological criminology” as a bridging framework. PMID:19150901

Linking HIV-Negative Youth to Prevention Services in 12 U.S. Cities: Barriers and Facilitators to Implementing the HIV Prevention Continuum.

PubMed

Doll, Mimi; Fortenberry, J Dennis; Roseland, Denise; McAuliff, Kathleen; Wilson, Craig M; Boyer, Cherrie B

2018-04-01

Linkage of HIV-negative youth to prevention services is increasingly important with the development of effective pre-exposure prophylaxis that complements behavioral and other prevention-focused interventions. However, effective infrastructure for delivery of prevention services does not exist, leaving many programs to address HIV prevention without data to guide program development/implementation. The objective of this study was to provide a qualitative description of barriers and facilitators of linkage to prevention services among high-risk, HIV-negative youth. Thematic analysis of structured interviews with staff implementing linkage to prevention services programs for youth aged 12-24 years. Twelve adolescent medicine HIV primary care programs as part of larger testing research program focused on young sexual minority men of color. The study included staff implementing linkage to prevention services programs along with community-based HIV testing programs. The main outcomes of the study were key barriers/facilitators to linkage to prevention services. Eight themes summarized perspectives on linkage to prevention services: (1) relationships with community partners, (2) trust between providers and youth, (3) youth capacity to navigate prevention services, (4) pre-exposure prophylaxis specific issues, (5) privacy issues, (6) gaps in health records preventing tailored services, (7) confidentiality of care for youth accessing services through parents'/caretakers' insurance, and (8) need for health-care institutions to keep pace with models that prioritize HIV prevention among at-risk youth. Themes are discussed in the context of factors that facilitated/challenged linkage to prevention services. Several evidence-based HIV prevention tools are available; infrastructures for coordinated service delivery to high-risk youth have not been developed. Implementation of such infrastructures requires attention to community-, provider-, and youth-related issues. Copyright © 2017 The Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

A reference linkage map for Eucalyptus

PubMed Central

2012-01-01

Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research. PMID:22702473

Titin is a candidate gene for stroke volume response to endurance training: the HERITAGE Family Study.

PubMed

Rankinen, Tuomo; Rice, Treva; Boudreau, Anik; Leon, Arthur S; Skinner, James S; Wilmore, Jack H; Rao, D C; Bouchard, Claude

2003-09-29

A genome-wide linkage scan for endurance training-induced changes in submaximal exercise stroke volume (DeltaSV50) in the HERITAGE Family Study revealed two chromosomal regions (2q31-q32 and 10p11.2) with at least suggestive evidence of linkage among white families. Here we report a further characterization of the quantitative trait locus (QTL) in chromosome 2q31 and provide evidence that titin (TTN) is likely a candidate gene involved. The original linkage was detected with two markers (D2S335 and D2S1391), and the QTL covered approximately 25 million base pairs (Mb). We added 12 microsatellite markers resulting in an average marker density of one marker per 2.3 Mb. The evidence of linkage increased from P = 0.006 to P = 0.0002 and 0.00002 in the multi- and single-point analyses, respectively. The strongest evidence of linkage was seen with two markers in and near the TTN gene. Transmission/disequilibrium test (TDT) with the same marker set provided evidence for association with one of the TTN markers (D2S385; P = 0.004). TTN is a major contributor to the elasticity of cardiomyocytes and a key regulator of the Frank-Starling mechanism. Since TTN is the largest gene in the human genome, the challenge is to identify the DNA sequence variants contributing to the interindividual differences in cardiac adaptation to endurance training.

Quantitative AOP-based predictions for two aromatase inhibitors evaluating the influence of bioaccumulation on prediction accuracy

EPA Science Inventory

The adverse outcome pathway (AOP) framework can be used to support the use of mechanistic toxicology data as a basis for risk assessment. For certain risk contexts this includes defining, quantitative linkages between the molecular initiating event (MIE) and subsequent key events...

Discovering regions of the bovine genome associated with variation in the immune response

USDA-ARS?s Scientific Manuscript database

Infectious disease of livestock continues to be a cause of substantial economic loss and adverse welfare. Breeding for disease resistant livestock could improve both the economic burden and animal welfare. Using genetic linkage and association methods, we aim to identify key genes and pathways that ...

Fiber Optics and Library Technology.

ERIC Educational Resources Information Center

Koenig, Michael

1984-01-01

This article examines fiber optic technology, explains some of the key terminology, and speculates about the way fiber optics will change our world. Applications of fiber optics to library systems in three major areas--linkage of a number of mainframe computers, local area networks, and main trunk communications--are highlighted. (EJS)

Holocene Glacier Fluctuations in the Peruvian Andes Indicate Northern Climate Linkages

NASA Astrophysics Data System (ADS)

Licciardi, Joseph M.; Schaefer, Joerg M.; Taggart, Jean R.; Lund, David C.

2009-09-01

The role of the tropics in triggering, transmitting, and amplifying interhemispheric climate signals remains a key debate in paleoclimatology. Tropical glacier fluctuations provide important insight on regional paleoclimatic trends and forcings, but robust chronologies are scarce. Here, we report precise moraine ages from the Cordillera Vilcabamba (13°20‧S) of southern Peru that indicate prominent glacial events and associated climatic shifts in the outer tropics during the early Holocene and late in the “Little Ice Age” period. Our glacier chronologies differ from the New Zealand record but are broadly correlative with well-dated glacial records in Europe, suggesting climate linkages between the tropics and the North Atlantic region.

The linkage disequilibrium pattern of the angiotensin converting enzyme gene in Arabic and Asian population groups.

PubMed

Kharrat, Najla; Abdelmouleh, Wafa; Abdelhedi, Rania; Alfadhli, Suad; Rebai, Ahmed

2012-01-01

DNA variations within the Angiotensin-Converting Enzyme (ACE) gene have been shown to be involved in the aetiology of several common diseases and the therapeutic response. This study reports a comparison of haplotype analysis of five SNPs in the ACE gene region using a sample of 100 healthy subjects derived from five different populations (Tunisian, Iranian, Kuwaiti, Bahraini and Indian). Strong linkage disequilibrium was found among all SNPs studied for all populations. Two SNPs (rs1800764 and rs4340) were identified as key SNPs for all populations. These SNPs will be valuable for future effective association studies of the ACE gene polymorphisms in Arab and Asian populations.

[Analysis of HLA haplotype frequency and linkage disequilibrium in patients with acute lymphoblastic leukemia from Northern Chinese Han].

PubMed

Gao, Su-qing; Cheng, Liang-hong; Lu, Liang; Jing, Shi-zheng; Cheng, Xi; Zhang, Yin-ze; Zou, Hong-yan; Deng, Zhi-hui

2009-02-01

To analyze the difference between the frequencies of HLA-A-B, B-DRB1 and A-B-DRB1 haplotype, as well as their linkage disequilibrium pattern in patients with acute lymphoblastic leukemia(ALL) and healthy controls from Northern Chinese Han. The frequencies of HLA-A-B, B-DRB1, A-B-DR haplotypes and linkage disequilibrium were estimated by Expectation Maximization method based on the genotypes of 643 patients with ALL and 2 0359 unrelated healthy donors, and the statistical significance between the two groups were estimated by chi-square test. Linkage disequilibrium was analyzed with population genetic methods. The most common HLA-A-B, B-DRB1, and A-B-DR haplotypes were A30-B13, A2-B46, A33-B58, B13-DR7, B46-DR9, B52-DR15, B58-DR17, A30-B13-DR7, A33-B58-DR17 and A1-B37-DR10 in both groups. The frequencies of A30-B13, A2-B46, A33-B44, B13-DR7, A30-B13-DR7 and A2-B46-DR9 haplotypes and linkage disequilibrium value were significantly decreased (P<0.05) in the patient group than that in the control group. On the other hand, the frequencies of A2-B52, A31-B61, A24- B8, B60-DR9, B27-DR4, B52-DR14, B44-DR17, B27-DR12 and A11-B27-DR12 haplotypes and linkage disequilibrium value were significantly increased (P<0.05) in the patient group than that in the control group. There are some common and positive linkage disequilibrium haplotypes in both the ALL patients and the healthy donors in Northern Chinese Han. Interestingly, some haplotypes and their linkage disequilibrium patterns had significantly different distributions between the two groups. The study provided basic data for the relationship of ALL and HLA haplotype and for finding the HLA-A, B, DR matching donors.

Food-Web Structure in Relation to Environmental Gradients and Predator-Prey Ratios in Tank-Bromeliad Ecosystems

PubMed Central

Dézerald, Olivier; Leroy, Céline; Corbara, Bruno; Carrias, Jean-François; Pélozuelo, Laurent; Dejean, Alain; Céréghino, Régis

2013-01-01

Little is known of how linkage patterns between species change along environmental gradients. The small, spatially discrete food webs inhabiting tank-bromeliads provide an excellent opportunity to analyse patterns of community diversity and food-web topology (connectance, linkage density, nestedness) in relation to key environmental variables (habitat size, detrital resource, incident radiation) and predators:prey ratios. We sampled 365 bromeliads in a wide range of understorey environments in French Guiana and used gut contents of invertebrates to draw the corresponding 365 connectance webs. At the bromeliad scale, habitat size (water volume) determined the number of species that constitute food-web nodes, the proportion of predators, and food-web topology. The number of species as well as the proportion of predators within bromeliads declined from open to forested habitats, where the volume of water collected by bromeliads was generally lower because of rainfall interception by the canopy. A core group of microorganisms and generalist detritivores remained relatively constant across environments. This suggests that (i) a highly-connected core ensures food-web stability and key ecosystem functions across environments, and (ii) larger deviations in food-web structures can be expected following disturbance if detritivores share traits that determine responses to environmental changes. While linkage density and nestedness were lower in bromeliads in the forest than in open areas, experiments are needed to confirm a trend for lower food-web stability in the understorey of primary forests. PMID:23977128

RECOGNIZING AND IDENTIFYING PEOPLE: A neuropsychological review

PubMed Central

Barton, Jason J S; Corrow, Sherryse L

2016-01-01

Recognizing people is a classic example of a cognitive function that involves multiple processing stages and parallel routes of information. Neuropsychological data have provided important evidence for models of this process, particularly from case reports; however, the quality and extent of the data varies widely between studies. In this review we first discuss the requirements and logical basis of the types of neuropsychological evidence to support conclusions about the modules in this process. We then survey the adequacy of the current body of reports to address two key issues. First is the question of which cognitive operation generates a sense of familiarity: the current debate revolves around whether familiarity arises in modality-specific recognition units or later amodal processes. Key evidence on this point comes from the search for dissociations between familiarity for faces, voices and names. The second question is whether lesions can differentially affect the abilities to link diverse sources of person information (e.g. face, voice, name, biographic data). Dissociations of these linkages may favour a distributed-only model of the organization of semantic knowledge, whereas a ‘person-hub’ model would predict uniform impairments of all linkages. While we conclude that there is reasonable evidence for dissociations in name, voice and face familiarity in regards to the first question, the evidence for or against dissociated linkages between information stores in regards to the second is tenuous at best. We identify deficiencies in the current literature that should motivate and inform the design of future studies. PMID:26773237

A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas.

PubMed

Hippolyte, Isabelle; Bakry, Frederic; Seguin, Marc; Gardes, Laetitia; Rivallan, Ronan; Risterucci, Ange-Marie; Jenny, Christophe; Perrier, Xavier; Carreel, Françoise; Argout, Xavier; Piffanelli, Pietro; Khan, Imtiaz A; Miller, Robert N G; Pappas, Georgios J; Mbéguié-A-Mbéguié, Didier; Matsumoto, Takashi; De Bernardinis, Veronique; Huttner, Eric; Kilian, Andrzej; Baurens, Franc-Christophe; D'Hont, Angélique; Cote, François; Courtois, Brigitte; Glaszmann, Jean-Christophe

2010-04-13

The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent. We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.

Effect of Linkage Disequilibrium on the Identification of Functional Variants

PubMed Central

Thomas, Alun; Abel, Haley J; Di, Yanming; Faye, Laura L; Jin, Jing; Liu, Jin; Wu, Zheyan; Paterson, Andrew D

2011-01-01

We summarize the contributions of Group 9 of Genetic Analysis Workshop 17. This group addressed the problems of linkage disequilibrium and other longer range forms of allelic association when evaluating the effects of genotypes on phenotypes. Issues raised by long-range associations, whether a result of selection, stratification, possible technical errors, or chance, were less expected but proved to be important. Most contributors focused on regression methods of various types to illustrate problematic issues or to develop adaptations for dealing with high-density genotype assays. Study design was also considered, as was graphical modeling. Although no method emerged as uniformly successful, most succeeded in reducing false-positive results either by considering clusters of loci within genes or by applying smoothing metrics that required results from adjacent loci to be similar. Two unexpected results that questioned our assumptions of what is required to model linkage disequilibrium were observed. The first was that correlations between loci separated by large genetic distances can greatly inflate single-locus test statistics, and, whether the result of selection, stratification, possible technical errors, or chance, these correlations seem overabundant. The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium. PMID:22128051

Genetic mapping of the gene for Usher syndrome: linkage analysis in a large Samaritan kindred.

PubMed

Bonné-Tamir, B; Korostishevsky, M; Kalinsky, H; Seroussi, E; Beker, R; Weiss, S; Godel, V

1994-03-01

Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness were studied in 10 related sibships. DNA samples from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed.

Genetic heterogeneity of Usher syndrome type II.

PubMed Central

Pieke Dahl, S; Kimberling, W J; Gorin, M B; Weston, M D; Furman, J M; Pikus, A; Möller, C

1993-01-01

Usher syndrome is an autosomal recessive disorder characterised by retinitis pigmentosa and congenital sensorineural hearing loss. A gene for Usher syndrome type II (USH2) has been localised to chromosome 1q32-q41. DNA from a family with four of seven sibs affected with clinical characteristics of Usher syndrome type II was genotyped using markers spanning the 1q32-1q41 region. These included D1S70 and D1S81, which are believed to flank USH2. Genotypic results and subsequent linkage analysis indicated non-linkage of this family to these markers. The A test analysis for heterogeneity with this family and 32 other Usher type II families was statistically significant at p < 0.05. Further clinical evaluation of this family was done in light of the linkage results to determine if any phenotypic characteristics would allow for clinical identification of the unlinked type. No clear phenotypic differences were observed; however, this unlinked family may represent a previously unreported subtype of Usher type II characterised by a milder form of retinitis pigmentosa and mild vestibular abnormalities. Heterogeneity of Usher syndrome type II complicates efforts to isolate and clone Usher syndrome genes using linkage analysis and limits the use of DNA markers in early detection of Usher type II. Images PMID:7901420

Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests

PubMed Central

Li, Hui; Wang, Xugao; Liang, Chao; Hao, Zhanqing; Zhou, Lisha; Ma, Sam; Li, Xiaobin; Yang, Shan; Yao, Fei; Jiang, Yong

2015-01-01

Understanding ecological linkages between above- and below-ground biota is critical for deepening our knowledge on the maintenance and stability of ecosystem processes. Nevertheless, direct comparisons of plant-microbe diversity at the community level remain scarce due to the knowledge gap between microbial ecology and plant ecology. We compared the α- and β- diversities of plant and soil bacterial communities in two temperate forests that represented early and late successional stages. We documented different patterns of aboveground-belowground diversity relationships in these forests. We observed no linkage between plant and bacterial α-diversity in the early successional forest, and even a negative correlation in the late successional forest, indicating that high bacterial α-diversity is not always linked to high plant α-diversity. Beta-diversity coupling was only found at the late successional stage, while in the early successional forest, the bacterial β-diversity was closely correlated with soil property distances. Additionally, we showed that the dominant competitive tree species in the late successional forest may play key roles in driving forest succession by shaping the soil bacterial community in the early successional stage. This study sheds new light on the potential aboveground-belowground linkage in natural ecosystems, which may help us understand the mechanisms that drive ecosystem succession. PMID:26184121

The apolipoprotein E/CI/CII gene cluster and late-onset Alzheimer disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Chang-En; Nemens, E.; Olson, J.M.

1994-04-01

The chromosome 19 apolipoprotein E/CI/CII gene cluster was examined for evidence of linkage to a familial Alzheimer disease (FAD) locus. The family groups studied were Volga German (VG), early-onset non-VG (ENVG; mean age at onset <60 years), and late-onset families. A genetic association was observed between apolipoprotein E (ApoE) allele E4 and FAD in late-onset families; the E4 allele frequency was .51 in affected subjects, .37 in at-risk subjects, .11 in spouses, and .19 in unrelated controls. The differences between the E4 frequencies in affected subjects versus controls and in at-risk subjects versus controls were highly significant. No association betweenmore » the E4 allele and FAD was observed in the ENVG or VG groups. A statistically significant allelic association between E4 and AD was also observed in a group of unrelated subjects; the E4 frequency was .26 in affected subjects, versus .19 in controls (Z[sub SND] = 2.20, P < .03). Evidence of linkage of ApoE and ApoCII to FAD was examined by maximum-likelihood methods, using three models and assuming autosomal dominant inheritance: (1) age-dependent penetrance, (2) extremely low (1%) penetrance, and (3) age-dependent penetrance corrected for sporadic Alzheimer disease (AD). For ApoCII in late-onset families, results for close linkage were negative, and only small positive lod-score-statistic (Z) values were obtained. For ApoE in late-onset kindreds, positive Z values were obtained when either allele frequencies from controls or allele frequencies from the families were used. When linkage disequilibrium was incorporated into the analysis, the Z values increased. For the ENVG group, results for ApoE and ApoCII were uniformly negative. Affected-pedigree-member analysis gave significant results for the late-onset kindreds, for ApoE, when control allele frequencies were used but not when allele frequencies were derived from the families. 58 refs., 6 tabs.« less

HIV service delivery models towards 'Zero AIDS-related Deaths': a collaborative case study of 6 Asia and Pacific countries.

PubMed

Fujita, Masami; Poudel, Krishna C; Green, Kimberly; Wi, Teodora; Abeyewickreme, Iyanthi; Ghidinelli, Massimo; Kato, Masaya; Vun, Mean Chhi; Sopheap, Seng; San, Khin Ohnmar; Bollen, Phavady; Rai, Krishna Kumar; Dahal, Atul; Bhandari, Durga; Boas, Peniel; Yaipupu, Jessica; Sirinirund, Petchsri; Saonuam, Pairoj; Duong, Bui Duc; Nhan, Do Thi; Thu, Nguyen Thi Minh; Jimba, Masamine

2015-04-24

In the Asia-Pacific region, limited systematic assessment has been conducted on HIV service delivery models. Applying an analytical framework of the continuum of prevention and care, this study aimed to assess HIV service deliveries in six Asia and Pacific countries from the perspective of service availability, linking approaches and performance monitoring for maximizing HIV case detection and retention. Each country formed a review team that provided published and unpublished information from the national HIV program. Four types of continuum were examined: (i) service linkages between key population outreach and HIV diagnosis (vertical-community continuum); (ii) chronic care provision across HIV diagnosis and treatment (chronological continuum); (iii) linkages between HIV and other health services (horizontal continuum); and (iv) comprehensive care sites coordinating care provision (hub and heart of continuum). Regarding the vertical-community continuum, all districts had voluntary counselling and testing (VCT) in all countries except for Myanmar and Vietnam. In these two countries, limited VCT availability was a constraint for referring key populations reached. All countries monitored HIV testing coverage among key populations. Concerning the chronological continuum, the proportion of districts/townships having antiretroviral treatment (ART) was less than 70% except in Thailand, posing a barrier for accessing pre-ART/ART care. Mechanisms for providing chronic care and monitoring retention were less developed for VCT/pre-ART process compared to ART process in all countries. On the horizontal continuum, the availability of HIV testing for tuberculosis patients and pregnant women was limited and there were sub-optimal linkages between tuberculosis, antenatal care and HIV services except for Cambodia and Thailand. These two countries indicated higher HIV testing coverage than other countries. Regarding hub and heart of continuum, all countries had comprehensive care sites with different degrees of community involvement. The analytical framework was useful to identify similarities and considerable variations in service availability and linking approaches across the countries. The study findings would help each country critically adapt and adopt global recommendations on HIV service decentralization, linkages and integration. Especially, the findings would inform cross-fertilization among the countries and national HIV program reviews to determine county-specific measures for maximizing HIV case detection and retention.

Limited Evidence for Classic Selective Sweeps in African Populations

PubMed Central

Granka, Julie M.; Henn, Brenna M.; Gignoux, Christopher R.; Kidd, Jeffrey M.; Bustamante, Carlos D.; Feldman, Marcus W.

2012-01-01

While hundreds of loci have been identified as reflecting strong-positive selection in human populations, connections between candidate loci and specific selective pressures often remain obscure. This study investigates broader patterns of selection in African populations, which are underrepresented despite their potential to offer key insights into human adaptation. We scan for hard selective sweeps using several haplotype and allele-frequency statistics with a data set of nearly 500,000 genome-wide single-nucleotide polymorphisms in 12 highly diverged African populations that span a range of environments and subsistence strategies. We find that positive selection does not appear to be a strong determinant of allele-frequency differentiation among these African populations. Haplotype statistics do identify putatively selected regions that are shared across African populations. However, as assessed by extensive simulations, patterns of haplotype sharing between African populations follow neutral expectations and suggest that tails of the empirical distributions contain false-positive signals. After highlighting several genomic regions where positive selection can be inferred with higher confidence, we use a novel method to identify biological functions enriched among populations’ empirical tail genomic windows, such as immune response in agricultural groups. In general, however, it seems that current methods for selection scans are poorly suited to populations that, like the African populations in this study, are affected by ascertainment bias and have low levels of linkage disequilibrium, possibly old selective sweeps, and potentially reduced phasing accuracy. Additionally, population history can confound the interpretation of selection statistics, suggesting that greater care is needed in attributing broad genetic patterns to human adaptation. PMID:22960214

Basics of Bayesian methods.

PubMed

Ghosh, Sujit K

2010-01-01

Bayesian methods are rapidly becoming popular tools for making statistical inference in various fields of science including biology, engineering, finance, and genetics. One of the key aspects of Bayesian inferential method is its logical foundation that provides a coherent framework to utilize not only empirical but also scientific information available to a researcher. Prior knowledge arising from scientific background, expert judgment, or previously collected data is used to build a prior distribution which is then combined with current data via the likelihood function to characterize the current state of knowledge using the so-called posterior distribution. Bayesian methods allow the use of models of complex physical phenomena that were previously too difficult to estimate (e.g., using asymptotic approximations). Bayesian methods offer a means of more fully understanding issues that are central to many practical problems by allowing researchers to build integrated models based on hierarchical conditional distributions that can be estimated even with limited amounts of data. Furthermore, advances in numerical integration methods, particularly those based on Monte Carlo methods, have made it possible to compute the optimal Bayes estimators. However, there is a reasonably wide gap between the background of the empirically trained scientists and the full weight of Bayesian statistical inference. Hence, one of the goals of this chapter is to bridge the gap by offering elementary to advanced concepts that emphasize linkages between standard approaches and full probability modeling via Bayesian methods.

The Conceptualization and Measurement of Equity in School Finance in Virginia.

ERIC Educational Resources Information Center

Verstegen, Deborah A.; Salmon, Richard G.

1989-01-01

Employed various statistical techniques to measure fiscal equity in Virginia. The new state aid system for financing education was unable to mitigate large and increasing disparities in education revenues between more and less affluent localities and a strong and growing linkage between revenue and wealth. Includes 34 footnotes. (MLH)

Symptoms versus Impairment: The Case for Respecting "DSM-IV"'s Criterion D

ERIC Educational Resources Information Center

Gordon, Michael; Antshel, Kevin; Faraone, Stephen; Barkley, Russell; Lewandowski, Larry; Hudziak, James J.; Biederman, Joseph; Cunningham, Charles

2006-01-01

Diagnosing ADHD based primarily on symptom reports assumes that the number/frequency of symptoms is tied closely to the impairment imposed on an individual's functioning. That presumed linkage encourages diagnosis more by "Diagnostic and Statistical Manual of Mental Disorders" (4th ed.) style symptom lists than well-defined,…

Understanding the behavioral linkages needed for designing effective interventions to increase fruit and vegetable intake in diverse populations

USDA-ARS?s Scientific Manuscript database

The design of interventions to increase fruit and vegetable consumption in a population (e.g. all men, all elementary school students) requires an underlying model that organizes the relevant literatures and provides an audience. The mediating-moderating variable model is a statistical analysis tech...

Testing the Self-Efficacy-Performance Linkage of Social-Cognitive Theory.

ERIC Educational Resources Information Center

Harrison, Allison W.; Rainer, R. Kelly, Jr.; Hochwarter, Wayne A.; Thompson, Kenneth R.

1997-01-01

Briefly reviews Albert Bandura's Self-Efficacy Performance Model (ability to perform a task is influenced by an individual's belief in their capability). Tests this model with a sample of 776 university employees and computer-related knowledge and skills. Results supported Bandura's thesis. Includes statistical tables and a discussion of related…

Tests for a disease-susceptibility locus allowing for an inbreeding coefficient (F).

PubMed

Song, Kijoung; Elston, Robert C

2003-11-01

We begin by discussing the false positive test results that arise because of cryptic relatedness and population substructure when testing a disease susceptibility locus. We extend and evaluate the Hardy-Weinberg disequilibrium (HWD) method, allowing for an inbreeding coefficient (F) in a similar way that Devlin and Roeder (1999) allowed for inbreeding in a case-control study. Then we compare the HWD measure and the common direct measure of linkage disequilibrium, both when there is no population substructure (F = 0) and when there is population substructure (F not = 0), for a single marker. The HWD test statistic gives rise to false positives caused by population stratification. These false positives can be controlled by adjusting the test statistic for the amount of variance inflation caused by the inbreeding coefficient (F). The power loss for the HWD test that arises when controlling for population structure is much less than that which arises for the common direct measure of linkage disequilibrium. However, in the multiplicative model, the HWD test has virtually no power even when allowing for non-zero F.

Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians, Lurs, Kurds and Azeris.

PubMed

Poulsen, L; Farzad, M Sharafi; Børsting, C; Tomas, C; Pereira, V; Morling, N

2015-07-01

A total of 255 individuals (Persians, Lurs, Kurds and Azeris) from Iran were typed for three sets of forensic genetic markers with the NGM SElect™, DIPplex(®) and Argus X-12 kits. Statistically significant deviations (P≤0.002) from Hardy-Weinberg expectations were observed for the insertion-deletion markers HLD97 and HLD93 after Holm-Šidák correction. Statistically significant (P<0.05) levels of linkage disequilibrium were observed between markers within two of the four studied X-chromosomal linkage groups. AMOVA analyses of the three sets of markers did not show population structure when the individuals were grouped according to their ethnic group. The Iranian population grouped closely to populations living geographically near to Iran based on pairwise FST distances. The matching probabilities ranged from 1 in 3.2×10(7) males by using haplotype frequencies of four X-chromosomal haplogroups to 1 in 3.4×10(21) individuals for the 16 autosomal STRs. Copyright © 2015. Published by Elsevier Ireland Ltd.

Structural Equation Modeling of Knowledge Content Improvement Using Inquiry Based Instruction

ERIC Educational Resources Information Center

Reeves, Christopher Gonwa; Fostvedt, Luke; Laugerman, Marcia; Baenziger, Joan; Shelley, Mack; Hand, Brian; Therrien, William

2013-01-01

A key element in science education is establishing and maintaining linkages between teachers and researchers that can eventuate in enhanced student outcomes. Determining when and where a new educational program or intervention results in an enhanced outcome can be sensitive to many different forces that the researcher must carefully manage. The…

Development of Relative Importance Values as Contribution Weights for Evaluating Human Wellbeing: An Ecosystem Services Example

EPA Science Inventory

The dependence of society on the flows, valuation and provisioning of various capital driven services is key to understanding and developing linkages to human wellbeing. By extension, decision makers need knowledge and an array of products that allow them to think more broadly a...

Rural Job Creation--A Study of CETA Linkage with Economic Development.

ERIC Educational Resources Information Center

Bruno, A. Lee; Wright, L. M., Jr.

This study examines how jobs are created in rural areas by or with the help of Comprehensive Employment and Training Act (CETA) programs involved with local economic development activities. It consists of five chapters. Chapter 1 reviews literature pertinent to the historical perspective and key elements of economic development, economic…

Needs and Beliefs in Construct Accessibility: Keys to New Understanding.

ERIC Educational Resources Information Center

Culbertson, Hugh M.; Denbow, Carl J.; Stempel, Guido H., III

1998-01-01

Surveyed 390 Ohioans who rated five concepts as to closeness of linkage with osteopathic medicine. Finds, as suggested by the storage-bin concept in construct accessibility theory, that those who had experience with these concepts were most apt to use them in assessing osteopathic medicine--this held even though most respondents reported no…

Catch a Raindrop! Science Makes Sense Integrating across the Curriculum.

ERIC Educational Resources Information Center

Gleason, Donna; Watten, Cynthia

A thematic approach provides the best opportunity for children to discover the linkage among science, mathematics, and language arts. This document explores the water cycle. Investigations are divided into six key areas: (1) comparing the size of raindrops; (2) learning to measure rain; (3) making rainbows; (4) exploring the principles of…

What Drives Crude Oil Prices?

EIA Publications

2017-01-01

An assessment of the various factors that may influence oil prices - physical market factors as well as those related to trading and financial markets. The analysis describes seven key factors that could influence oil markets and explores possible linkages between each factor and oil prices. Regularly updated graphs are included to illustrate aspects of those relationships.

What Are the Key Statistics about Brain and Spinal Cord Cancers?

MedlinePlus

... Brain and Spinal Cord Tumors in Adults Key Statistics for Brain and Spinal Cord Tumors The American ... Cord Tumors . Visit the American Cancer Society’s Cancer Statistics Center for more key statistics. Written by References ...

LOD significance thresholds for QTL analysis in experimental populations of diploid species

PubMed

Van Ooijen JW

1999-11-01

Linkage analysis with molecular genetic markers is a very powerful tool in the biological research of quantitative traits. The lack of an easy way to know what areas of the genome can be designated as statistically significant for containing a gene affecting the quantitative trait of interest hampers the important prediction of the rate of false positives. In this paper four tables, obtained by large-scale simulations, are presented that can be used with a simple formula to get the false-positives rate for analyses of the standard types of experimental populations with diploid species with any size of genome. A new definition of the term 'suggestive linkage' is proposed that allows a more objective comparison of results across species.

Contextualizing Embodied Resources in Global Food Trade

NASA Astrophysics Data System (ADS)

MacDonald, G. K.; Brauman, K. A.; Sun, S.; West, P. C.; Carlson, K. M.; Cassidy, E. S.; Gerber, J. S.; Ray, D. K.

2014-12-01

Trade in agricultural commodities has created increasingly complex linkages between resource use and food supplies across national borders. Understanding the degree to which food production and consumption relies on trade is vital to understanding how to sustainably meet growing food demands across scales. We use detailed bilateral trade statistics and data on agricultural management to examine the land use and water consumption embodied in agricultural trade, which we relate to basic nutritional indicators to show how trade contributes to food availability worldwide. Agricultural trade carries enough calories to provide >1.7 billion people a basic diet each year. We identify key commodities and producer-consumer relationships that disproportionately contribute to embodied resource use and flows of food nutrition at the global scale. For example, just 15 disproportionately large soybean trades comprised ~10% the total harvested area embodied in export production. We conclude by framing these results in terms of the fraction of each country's food production and consumption that is linked to international trade. These findings help to characterize how countries allocate resources to domestic versus foreign food demand.

Genetic analysis of prolactin gene in Pakistani cattle.

PubMed

Uddin, Raza Mohy; Babar, Masroor Ellahi; Nadeem, Asif; Hussain, Tanveer; Ahmad, Shakil; Munir, Sadia; Mehboob, Riffat; Ahmad, Fridoon Jawad

2013-10-01

Prolactin (PRL) is a polypeptide hormone, secreted mainly by the anterior pituitary gland. It is involved in many endocrine activities. The key functions of PRL are related to reproduction and lactation in mammals. To ascertain the presence of polymorphisms in the bovine PRL gene (bPRL), the bPRL gene was sequenced. Five mutations were identified in exonic region and eleven in associated intronic regions in 100 cattle from four Pakistani cattle breeds. Haplotype of predicted amino acid changes represent a common alteration at codon 222 from R-Arginine into K-Lysine in all four breeds. Significant statistical variations were observed in the distribution of single nucleotide polymorphism (SNP) in various cattle populations. However, on basis of present study, an association of these SNPs with milk performance traits in four Pakistani cow breeds cannot be truly replicated but at least can be effective DNA markers for some of the breeds studied. Linkage analysis between these SNPs on larger populations can be useful for the association with milk production traits. Furthermore, present study may be used for marker-assisted selection and management in cattle breeding program in local cattle breeds.

Extending the Fellegi-Sunter probabilistic record linkage method for approximate field comparators.

PubMed

DuVall, Scott L; Kerber, Richard A; Thomas, Alun

2010-02-01

Probabilistic record linkage is a method commonly used to determine whether demographic records refer to the same person. The Fellegi-Sunter method is a probabilistic approach that uses field weights based on log likelihood ratios to determine record similarity. This paper introduces an extension of the Fellegi-Sunter method that incorporates approximate field comparators in the calculation of field weights. The data warehouse of a large academic medical center was used as a case study. The approximate comparator extension was compared with the Fellegi-Sunter method in its ability to find duplicate records previously identified in the data warehouse using different demographic fields and matching cutoffs. The approximate comparator extension misclassified 25% fewer pairs and had a larger Welch's T statistic than the Fellegi-Sunter method for all field sets and matching cutoffs. The accuracy gain provided by the approximate comparator extension grew as less information was provided and as the matching cutoff increased. Given the ubiquity of linkage in both clinical and research settings, the incremental improvement of the extension has the potential to make a considerable impact.

The millennium development goals and road traffic injuries: exploring the linkages in South Asia.

PubMed

Hyder, Adnan A; Ghaffar, Abdul

2004-12-01

In a major summit of the members of the United Nations (UN) in 2000, a Millennium Declaration was adopted which called for making the elimination of poverty and promotion of sustainable development a global priority. A road map was agreed upon to operationalize the declaration, and the Millennium Development Goals (MDG) were integrated within the document. The MDGs are now increasingly being used to assess the performance of countries, institutions and the global community. WHO declares that the MDGs provide "a set of outcomes that are relevant to the development of national health policy frameworks". It also states that although MDGs do not cover all the components of public health, when broadly interpreted "the goals provide an opportunity to address important cross-cutting issues and key constraints to health". Consistent with WHO's call for a broad interpretation of the MDGs, and building on the health linkages identified by WHO, this paper explores the linkages between the MDGs and the impact of road traffic injuries (RTI). This is done in the context of South Asia, one of the poorest and populated regions of the developing world.

Measuring anxiety after spinal cord injury: Development and psychometric characteristics of the SCI-QOL Anxiety item bank and linkage with GAD-7.

PubMed

Kisala, Pamela A; Tulsky, David S; Kalpakjian, Claire Z; Heinemann, Allen W; Pohlig, Ryan T; Carle, Adam; Choi, Seung W

2015-05-01

To develop a calibrated item bank and computer adaptive test to assess anxiety symptoms in individuals with spinal cord injury (SCI), transform scores to the Patient Reported Outcomes Measurement Information System (PROMIS) metric, and create a statistical linkage with the Generalized Anxiety Disorder (GAD)-7, a widely used anxiety measure. Grounded-theory based qualitative item development methods; large-scale item calibration field testing; confirmatory factor analysis; graded response model item response theory analyses; statistical linking techniques to transform scores to a PROMIS metric; and linkage with the GAD-7. Setting Five SCI Model System centers and one Department of Veterans Affairs medical center in the United States. Participants Adults with traumatic SCI. Spinal Cord Injury-Quality of Life (SCI-QOL) Anxiety Item Bank Seven hundred sixteen individuals with traumatic SCI completed 38 items assessing anxiety, 17 of which were PROMIS items. After 13 items (including 2 PROMIS items) were removed, factor analyses confirmed unidimensionality. Item response theory analyses were used to estimate slopes and thresholds for the final 25 items (15 from PROMIS). The observed Pearson correlation between the SCI-QOL Anxiety and GAD-7 scores was 0.67. The SCI-QOL Anxiety item bank demonstrates excellent psychometric properties and is available as a computer adaptive test or short form for research and clinical applications. SCI-QOL Anxiety scores have been transformed to the PROMIS metric and we provide a method to link SCI-QOL Anxiety scores with those of the GAD-7.

The linkage between geopotential height and monthly precipitation in Iran

NASA Astrophysics Data System (ADS)

Shirvani, Amin; Fadaei, Amir Sabetan; Landman, Willem A.

2018-04-01

This paper investigates the linkage between large-scale atmospheric circulation and monthly precipitation during November to April over Iran. Canonical correlation analysis (CCA) is used to set up the statistical linkage between the 850 hPa geopotential height large-scale circulation and monthly precipitation over Iran for the period 1968-2010. The monthly precipitation dataset for 50 synoptic stations distributed in different climate regions of Iran is considered as the response variable in the CCA. The monthly geopotential height reanalysis dataset over an area between 10° N and 60° N and from 20° E to 80° E is utilized as the explanatory variable in the CCA. Principal component analysis (PCA) as a pre-filter is used for data reduction for both explanatory and response variables before applying CCA. The optimal number of principal components and canonical variables to be retained in the CCA equations is determined using the highest average cross-validated Kendall's tau value. The 850 hPa geopotential height pattern over the Red Sea, Saudi Arabia, and Persian Gulf is found to be the major pattern related to Iranian monthly precipitation. The Pearson correlation between the area averaged of the observed and predicted precipitation over the study area for Jan, Feb, March, April, November, and December months are statistically significant at the 5% significance level and are 0.78, 0.80, 0.82, 0.74, 0.79, and 0.61, respectively. The relative operating characteristic (ROC) indicates that the highest scores for the above- and below-normal precipitation categories are, respectively, for February and April and the lowest scores found for December.

Alternative Natural Resource Monitoring Strategies in the Mexican States of Jalisco and Colima

Treesearch

Cele Aguirre-Bravo; Hans Schreuder

2005-01-01

This paper presents a strategy for inventorying and monitoring the natural resources in the Mexican states of Jalisco and Colima. The strategy emphasizes a strong linkage between remote sensing with field sampling design to produce statistical summaries and spatial estimates at multiple scales and resolution levels. Outputs derived from this strategy are expected to...

Representing Micro-Macro Linkages by Actor-Based Dynamic Network Models

ERIC Educational Resources Information Center

Snijders, Tom A. B.; Steglich, Christian E. G.

2015-01-01

Stochastic actor-based models for network dynamics have the primary aim of statistical inference about processes of network change, but may be regarded as a kind of agent-based models. Similar to many other agent-based models, they are based on local rules for actor behavior. Different from many other agent-based models, by including elements of…

Using Sieving and Unknown Sand Samples for a Sedimentation-Stratigraphy Class Project with Linkage to Introductory Courses

ERIC Educational Resources Information Center

Videtich, Patricia E.; Neal, William J.

2012-01-01

Using sieving and sample "unknowns" for instructional grain-size analysis and interpretation of sands in undergraduate sedimentology courses has advantages over other techniques. Students (1) learn to calculate and use statistics; (2) visually observe differences in the grain-size fractions, thereby developing a sense of specific size…

Linking Data for Mothers and Babies in De-Identified Electronic Health Data.

PubMed

Harron, Katie; Gilbert, Ruth; Cromwell, David; van der Meulen, Jan

2016-01-01

Linkage of longitudinal administrative data for mothers and babies supports research and service evaluation in several populations around the world. We established a linked mother-baby cohort using pseudonymised, population-level data for England. Retrospective linkage study using electronic hospital records of mothers and babies admitted to NHS hospitals in England, captured in Hospital Episode Statistics between April 2001 and March 2013. Of 672,955 baby records in 2012/13, 280,470 (42%) linked deterministically to a maternal record using hospital, GP practice, maternal age, birthweight, gestation, birth order and sex. A further 380,164 (56%) records linked using probabilistic methods incorporating additional variables that could differ between mother/baby records (admission dates, ethnicity, 3/4-character postcode district) or that include missing values (delivery variables). The false-match rate was estimated at 0.15% using synthetic data. Data quality improved over time: for 2001/02, 91% of baby records were linked (holding the estimated false-match rate at 0.15%). The linked cohort was representative of national distributions of gender, gestation, birth weight and maternal age, and captured approximately 97% of births in England. Probabilistic linkage of maternal and baby healthcare characteristics offers an efficient way to enrich maternity data, improve data quality, and create longitudinal cohorts for research and service evaluation. This approach could be extended to linkage of other datasets that have non-disclosive characteristics in common.

Statistical aspects of evolution under natural selection, with implications for the advantage of sexual reproduction.

PubMed

Crouch, Daniel J M

2017-10-27

The prevalence of sexual reproduction remains mysterious, as it poses clear evolutionary drawbacks compared to reproducing asexually. Several possible explanations exist, with one of the most likely being that finite population size causes linkage disequilibria to randomly generate and impede the progress of natural selection, and that these are eroded by recombination via sexual reproduction. Previous investigations have either analysed this phenomenon in detail for small numbers of loci, or performed population simulations for many loci. Here we present a quantitative genetic model for fitness, based on the Price Equation, in order to examine the theoretical consequences of randomly generated linkage disequilibria when there are many loci. In addition, most previous work has been concerned with the long-term consequences of deleterious linkage disequilibria for population fitness. The expected change in mean fitness between consecutive generations, a measure of short-term evolutionary success, is shown under random environmental influences to be related to the autocovariance in mean fitness between the generations, capturing the effects of stochastic forces such as genetic drift. Interaction between genetic drift and natural selection, due to randomly generated linkage disequilibria, is demonstrated to be one possible source of mean fitness autocovariance. This suggests a possible role for sexual reproduction in reducing the negative effects of genetic drift, thereby improving the short-term efficacy of natural selection. Copyright © 2017 Elsevier Ltd. All rights reserved.

The promise of record linkage for assessing the uptake of health services in resource constrained settings: a pilot study from South Africa.

PubMed

Kabudula, Chodziwadziwa W; Clark, Benjamin D; Gómez-Olivé, Francesc Xavier; Tollman, Stephen; Menken, Jane; Reniers, Georges

2014-05-24

Health and Demographic Surveillance Systems (HDSS) have been instrumental in advancing population and health research in low- and middle- income countries where vital registration systems are often weak. However, the utility of HDSS would be enhanced if their databases could be linked with those of local health facilities. We assess the feasibility of record linkage in rural South Africa using data from the Agincourt HDSS and a local health facility. Using a gold standard dataset of 623 record pairs matched by means of fingerprints, we evaluate twenty record linkage scenarios (involving different identifiers, string comparison techniques and with and without clerical review) based on the Fellegi-Sunter probabilistic record linkage model. Matching rates and quality are measured by their sensitivity and positive predictive value (PPV). Background characteristics of matched and unmatched cases are compared to assess systematic bias in the resulting record-linked dataset. A hybrid approach of deterministic followed by probabilistic record linkage, and scenarios that use an extended set of identifiers including another household member's first name yield the best results. The best fully automated record linkage scenario has a sensitivity of 83.6% and PPV of 95.1%. The sensitivity and PPV increase to 84.3% and 96.9%, respectively, when clerical review is undertaken on 10% of the record pairs. The likelihood of being linked is significantly lower for females, non-South Africans and the elderly. Using records matched by means of fingerprints as the gold standard, we have demonstrated the feasibility of fully automated probabilistic record linkage using identifiers that are routinely collected in health facilities in South Africa. Our study also shows that matching statistics can be improved if other identifiers (e.g., another household member's first name) are added to the set of matching variables, and, to a lesser extent, with clerical review. Matching success is, however, correlated with background characteristics that are indicative of the instability of personal attributes over time (e.g., surname in the case of women) or with misreporting (e.g., age).

The promise of record linkage for assessing the uptake of health services in resource constrained settings: a pilot study from South Africa

PubMed Central

2014-01-01

Background Health and Demographic Surveillance Systems (HDSS) have been instrumental in advancing population and health research in low- and middle- income countries where vital registration systems are often weak. However, the utility of HDSS would be enhanced if their databases could be linked with those of local health facilities. We assess the feasibility of record linkage in rural South Africa using data from the Agincourt HDSS and a local health facility. Methods Using a gold standard dataset of 623 record pairs matched by means of fingerprints, we evaluate twenty record linkage scenarios (involving different identifiers, string comparison techniques and with and without clerical review) based on the Fellegi-Sunter probabilistic record linkage model. Matching rates and quality are measured by their sensitivity and positive predictive value (PPV). Background characteristics of matched and unmatched cases are compared to assess systematic bias in the resulting record-linked dataset. Results A hybrid approach of deterministic followed by probabilistic record linkage, and scenarios that use an extended set of identifiers including another household member’s first name yield the best results. The best fully automated record linkage scenario has a sensitivity of 83.6% and PPV of 95.1%. The sensitivity and PPV increase to 84.3% and 96.9%, respectively, when clerical review is undertaken on 10% of the record pairs. The likelihood of being linked is significantly lower for females, non-South Africans and the elderly. Conclusion Using records matched by means of fingerprints as the gold standard, we have demonstrated the feasibility of fully automated probabilistic record linkage using identifiers that are routinely collected in health facilities in South Africa. Our study also shows that matching statistics can be improved if other identifiers (e.g., another household member’s first name) are added to the set of matching variables, and, to a lesser extent, with clerical review. Matching success is, however, correlated with background characteristics that are indicative of the instability of personal attributes over time (e.g., surname in the case of women) or with misreporting (e.g., age). PMID:24884457

Roles and challenges of outreach workers in HIV clinical and support programs serving young racial/ethnic minority men who have sex with men.

PubMed

Hidalgo, Julia; Coombs, Elizabeth; Cobbs, Will O; Green-Jones, Monique; Phillips, Gregory; Wohl, Amy Rock; Smith, Justin C; Ramos, Albert Daniel; Fields, Sheldon D

2011-08-01

The federal government has established rapid identification, linkage, and engagement in medical care of HIV-positive individuals as a high priority. Outreach workers and other linkage coordinators are identified as key personnel in implementing this policy. Young racial/ethnic minority men who have sex with men (MSM) have relatively high and growing rates of HIV infection and would benefit from the services of outreach workers. In this article, we describe the characteristics of outreach workers employed by eight demonstration sites participating in the federal Special Projects of National Significance (SPNS) Young MSM of Color Initiative, the linkage and retention models used by the sites, and the number of outreach/ linkage contacts and individuals referred to HIV care. We summarize rates of retention of outreach workers in employment, factors associated with worker turnover, and costs associated with their replacement. We also summarize the experiences of demonstration sites in employing and retaining outreach workers and improving their performance. The insights of outreach workers are reported regarding the challenges they experienced while conducting outreach. Recommendations from demonstration site project managers and outreach workers are offered to improve workplace performance and job retention. Outreach and retention strategies, as well as lessons learned in employing outreach workers, are useful to programs serving young racial/ethnic minority MSM and other HIV-positive groups.

Children and Young People at Risk of Social Exclusion: Links between Homelessness, Child Protection and Juvenile Justice. Data Linkage Series. Number 13

ERIC Educational Resources Information Center

Aalders, Rachel

2012-01-01

Current research demonstrates relationships between child abuse and neglect, homelessness and criminal activity. This report presents key findings from analysis of a data set linking three community-sector data collections: Supported Accommodation Assistance Program (SAAP), juvenile justice supervision, and child protection notifications and…

New Jersey Case Report: A Managed Market Approach.

ERIC Educational Resources Information Center

Richardson, Richard C., Jr.

This report describes key policy decisions that have shaped the New Jersey system of higher education during the past third of a century. The study was part of a larger study that aimed at understanding the linkages between policy decisions and higher education performance through comparative case studies of two states in the United States and two…

Parental School Involvement in Relation to Children's Grades and Adaptation to School

ERIC Educational Resources Information Center

Tan, Edwin T.; Goldberg, Wendy A.

2008-01-01

From an ecological perspective, it is important to examine linkages among key settings in the child's life. The current study focuses on parents' involvement in children's education both at school and at home. Ninety-one families with school-aged children (91 fathers and 91 mothers) participated in a survey study assessing the levels of parental…

Missing lynx and trophic cascades in food webs: A reply to Ripple et al.

Treesearch

John R. Squires; Nicholas J. DeCesare; Mark Hebblewhite; Joel Berger

2012-01-01

Ripple et al. (2011) proposed a hypothesis that the recovery of gray wolves (Canis lupus) may positively affect the viability of threatened Canada lynx (Lynx canadensis) populations in the contiguous United States through indirect species interactions. Ripple et al. (2011) proposed 2 key trophic linkages connecting wolf restoration with lynx recovery. First, recovering...

LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies

PubMed Central

Bulik-Sullivan, Brendan K.; Loh, Po-Ru; Finucane, Hilary; Ripke, Stephan; Yang, Jian; Patterson, Nick; Daly, Mark J.; Price, Alkes L.; Neale, Benjamin M.

2015-01-01

Both polygenicity (i.e., many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size. PMID:25642630

Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results

PubMed Central

Dorfman, Ruslan; Li, Weili; Sun, Lei; Lin, Fan; Wang, Yongqian; Sandford, Andrew; Paré, Peter D.; McKay, Karen; Kayserova, Hana; Piskackova, Tereza; Macek, Milan; Czerska, Kamila; Sands, Dorota; Tiddens, Harm; Margarit, Sonia; Repetto, Gabriela; Sontag, Marci K.; Accurso, Frank J.; Blackman, Scott; Cutting, Garry R.; Tsui, Lap-Chee; Corey, Mary; Durie, Peter; Zielenski, Julian; Strug, Lisa J.

2010-01-01

Cystic fibrosis (CF) is a monogenic disease due to mutations in the CFTR gene. Yet, variability in CF disease presentation is presumed to be affected by modifier genes, such as those recently demonstrated for the pulmonary aspect. Here, we conduct a modifier gene study for meconium ileus (MI), an intestinal obstruction that occurs in 16–20% of CF newborns, providing linkage and association results from large family and case–control samples. Linkage analysis of modifier traits is different than linkage analysis of primary traits on which a sample was ascertained. Here, we articulate a source of confounding unique to modifier gene studies and provide an example of how one might overcome the confounding in the context of linkage studies. Our linkage analysis provided evidence of a MI locus on chromosome 12p13.3, which was segregating in up to 80% of MI families with at least one affected offspring (HLOD = 2.9). Fine mapping of the 12p13.3 region in a large case–control sample of pancreatic insufficient Canadian CF patients with and without MI pointed to the involvement of ADIPOR2 in MI (p = 0.002). This marker was substantially out of Hardy–Weinberg equilibrium in the cases only, and provided evidence of a cohort effect. The association with rs9300298 in the ADIPOR2 gene at the 12p13.3 locus was replicated in an independent sample of CF families. A protective locus, using the phenotype of no-MI, mapped to 4q13.3 (HLOD = 3.19), with substantial heterogeneity. A candidate gene in the region, SLC4A4, provided preliminary evidence of association (p = 0.002), warranting further follow-up studies. Our linkage approach was used to direct our fine-mapping studies, which uncovered two potential modifier genes worthy of follow-up. PMID:19662435

Barriers Influencing Linkage to Hypertension Care in Kenya: Qualitative Analysis from the LARK Hypertension Study.

PubMed

Naanyu, Violet; Vedanthan, Rajesh; Kamano, Jemima H; Rotich, Jackson K; Lagat, Kennedy K; Kiptoo, Peninah; Kofler, Claire; Mutai, Kennedy K; Bloomfield, Gerald S; Menya, Diana; Kimaiyo, Sylvester; Fuster, Valentin; Horowitz, Carol R; Inui, Thomas S

2016-03-01

Hypertension, the leading global risk factor for mortality, is characterized by low treatment and control rates in low- and middle-income countries. Poor linkage to hypertension care contributes to poor outcomes for patients. However, specific factors influencing linkage to hypertension care are not well known. To evaluate factors influencing linkage to hypertension care in rural western Kenya. Qualitative research study using a modified Health Belief Model that incorporates the impact of emotional and environmental factors on behavior. Mabaraza (traditional community assembly) participants (n = 242) responded to an open invitation to residents in their respective communities. Focus groups, formed by purposive sampling, consisted of hypertensive individuals, at-large community members, and community health workers (n = 169). We performed content analysis of the transcripts with NVivo 10 software, using both deductive and inductive codes. We used a two-round Delphi method to rank the barriers identified in the content analysis. We selected factors using triangulation of frequency of codes and themes from the transcripts, in addition to the results of the Delphi exercise. Sociodemographic characteristics of participants were summarized using descriptive statistics. We identified 27 barriers to linkage to hypertension care, grouped into individual (cognitive and emotional) and environmental factors. Cognitive factors included the asymptomatic nature of hypertension and limited information. Emotional factors included fear of being a burden to the family and fear of being screened for stigmatized diseases such as HIV. Environmental factors were divided into physical (e.g. distance), socioeconomic (e.g. poverty), and health system factors (e.g. popularity of alternative therapies). The Delphi results were generally consistent with the findings from the content analysis. Individual and environmental factors are barriers to linkage to hypertension care in rural western Kenya. Our analysis provides new insights and methodological approaches that may be relevant to other low-resource settings worldwide.

EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

PubMed Central

2010-01-01

Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species. PMID:20712870

Analyzing the Relative Linkages of Land Use and Hydrologic Variables with Urban Surface Water Quality using Multivariate Techniques

NASA Astrophysics Data System (ADS)

Ahmed, S.; Abdul-Aziz, O. I.

2015-12-01

We used a systematic data-analytics approach to analyze and quantify relative linkages of four stream water quality indicators (total nitrogen, TN; total phosphorus, TP; chlorophyll-a, Chla; and dissolved oxygen, DO) with six land use and four hydrologic variables, along with the potential external (upstream in-land and downstream coastal) controls in highly complex coastal urban watersheds of southeast Florida, U.S.A. Multivariate pattern recognition techniques of principle component and factor analyses, in concert with Pearson correlation analysis, were applied to map interrelations and identify latent patterns of the participatory variables. Relative linkages of the in-stream water quality variables with their associated drivers were then quantified by developing dimensionless partial least squares (PLS) regression model based on standardized data. Model fitting efficiency (R2=0.71-0.87) and accuracy (ratio of root-mean-square error to the standard deviation of the observations, RSR=0.35-0.53) suggested good predictions of the water quality variables in both wet and dry seasons. Agricultural land and groundwater exhibited substantial controls on surface water quality. In-stream TN concentration appeared to be mostly contributed by the upstream water entering from Everglades in both wet and dry seasons. In contrast, watershed land uses had stronger linkages with TP and Chla than that of the watershed hydrologic and upstream (Everglades) components for both seasons. Both land use and hydrologic components showed strong linkages with DO in wet season; however, the land use linkage appeared to be less in dry season. The data-analytics method provided a comprehensive empirical framework to achieve crucial mechanistic insights into the urban stream water quality processes. Our study quantitatively identified dominant drivers of water quality, indicating key management targets to maintain healthy stream ecosystems in complex urban-natural environments near the coast.

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts

PubMed Central

Shirasawa, Kenta; Hand, Melanie L.; Henderson, Steven T.; Okada, Takashi; Johnson, Susan D.; Taylor, Jennifer M.; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M. G.

2015-01-01

Background and Aims Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. Methods RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. Key Results A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. Conclusions A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. PMID:25538115

Lods, wrods, and mods: the interpretation of lod scores calculated under different models.

PubMed

Hodge, S E; Elston, R C

1994-01-01

In this paper we examine the relationships among classical lod scores, "wrod" scores (lod scores calculated under the wrong genetic model), and "mod" scores (lod scores maximized over genetic model parameters). We compare the behavior of these scores when the state of nature is linkage to their behavior when the state of nature is no linkage. We describe sufficient conditions for mod scores to be valid and discuss their use to determine the correct genetic model. We show that lod scores represent a likelihood-ratio test for independence. We explain the "ascertainment-assumption-free" aspect of using mod scores to determine mode of inheritance and we set this aspect into a well-established statistical framework. Finally, we summarize practical guidelines for the use of mod scores.

Extended Intermarker Linkage Disequilibrium in the Afrikaners

PubMed Central

Hall, Diana; Wijsman, Ellen M.; Roos, J. Louw; Gogos, Joseph A.; Karayiorgou, Maria

2002-01-01

In this study we conducted an investigation of the background level of linkage disequilibrium (LD) in the Afrikaner population to evaluate the appropriateness of this genetic isolate for mapping complex traits. We analyzed intermarker LD in 62 nuclear families using microsatellite markers covering extended chromosomal regions. The markers were selected to allow the first direct comparison of long-range LD in the Afrikaners to LD in other demographic groups. Using several statistical measures, we find significant evidence for LD in the Afrikaners extending remarkably over a 6-cM range. In contrast, LD decays significantly beyond 3-cM distances in the other founder and outbred populations examined. This study strongly supports the appropriateness of the Afrikaner population for genome-wide scans that exploit LD to map common, multigenic disorders. PMID:12045148

Extended intermarker linkage disequilibrium in the Afrikaners.

PubMed

Hall, Diana; Wijsman, Ellen M; Roos, J Louw; Gogos, Joseph A; Karayiorgou, Maria

2002-06-01

In this study we conducted an investigation of the background level of linkage disequilibrium (LD) in the Afrikaner population to evaluate the appropriateness of this genetic isolate for mapping complex traits. We analyzed intermarker LD in 62 nuclear families using microsatellite markers covering extended chromosomal regions. The markers were selected to allow the first direct comparison of long-range LD in the Afrikaners to LD in other demographic groups. Using several statistical measures, we find significant evidence for LD in the Afrikaners extending remarkably over a 6-cM range. In contrast, LD decays significantly beyond 3-cM distances in the other founder and outbred populations examined. This study strongly supports the appropriateness of the Afrikaner population for genome-wide scans that exploit LD to map common, multigenic disorders.

The role of the GABRA2 polymorphism in multiplex alcohol dependence families with minimal comorbidity: within-family association and linkage analyses.

PubMed

Matthews, Abigail G; Hoffman, Eric K; Zezza, Nicholas; Stiffler, Scott; Hill, Shirley Y

2007-09-01

The genes encoding the gamma-aminobutyric acid(A) (GABA(A)) receptor have been the focus of several recent studies investigating the genetic etiology of alcohol dependence. Analyses of multiplex families found a particular gene, GABRA2, to be highly associated with alcohol dependence, using within-family association tests and other methods. Results were confirmed in three case-control studies. The objective of this study was to investigate the GABRA2 gene in another collection of multiplex families. Analyses were based on phenotypic and genotypic data available for 330 individuals from 65 bigenerational pedigrees with a total of 232 alcohol-dependent subjects. A proband pair of same-sex siblings meeting Diagnostic and Statistical Manual of Mental Disorders, Third Edition, criteria for alcohol dependence was required for entry of a family into the study. One member of the proband pair was identified while in treatment for alcohol dependence. Linkage and association of GABRA2 and alcohol dependence were evaluated using SIBPAL (a nonparametric linkage package) and both the Pedigree Disequilibrium Test and the Family-Based Association Test, respectively. We find no evidence of a relationship between GABRA2 and alcohol dependence. Linkage analyses exhibited no linkage using affected/affected, affected/unaffected, and unaffected/unaffected sib pairs (all p's < .13). There was no evidence of a within-family association (all p's > .39). Comorbidity may explain why our results differ from those in the literature. The presence of primary drug dependence and/or other psychiatric disorders is minimal in our pedigrees, although several of the other previously published multiplex family analyses exhibit a greater degree of comorbidity.

Genome-wide linkage scan for loci of musical aptitude in Finnish families: evidence for a major locus at 4q22

PubMed Central

Pulli, K; Karma, K; Norio, R; Sistonen, P; Göring, H H H; Järvelä, I

2008-01-01

Background: Music perception and performance are comprehensive human cognitive functions and thus provide an excellent model system for studying human behaviour and brain function. However, the molecules involved in mediating music perception and performance are so far uncharacterised. Objective: To unravel the biological background of music perception, using molecular and statistical genetic approaches. Methods: 15 Finnish multigenerational families (with a total of 234 family members) were recruited via a nationwide search. The phenotype of all family members was determined using three tests used in defining musical aptitude: a test for auditory structuring ability (Karma Music test; KMT) commonly used in Finland, and the Seashore pitch and time discrimination subtests (SP and ST respectively) used internationally. We calculated heritabilities and performed a genome-wide variance components-based linkage scan using genotype data for 1113 microsatellite markers. Results: The heritability estimates were 42% for KMT, 57% for SP, 21% for ST and 48% for the combined music test scores. Significant evidence of linkage was obtained on chromosome 4q22 (LOD 3.33) and suggestive evidence of linkage at 8q13-21 (LOD 2.29) with the combined music test scores, using variance component linkage analyses. The major contribution of the 4q22 locus was obtained for the KMT (LOD 2.91). Interestingly, a positive LOD score of 1.69 was shown at 18q, a region previously linked to dyslexia (DYX6) using combined music test scores. Conclusion: Our results show that there is a genetic contribution to musical aptitude that is likely to be regulated by several predisposing genes or variants. PMID:18424507

Understanding Local Spatial Variation Along the Care Continuum: The Potential Impact of Transportation Vulnerability on HIV Linkage to Care and Viral Suppression in High-Poverty Areas, Atlanta, Georgia.

PubMed

Goswami, Neela D; Schmitz, Michelle M; Sanchez, Travis; Dasgupta, Sharoda; Sullivan, Patrick; Cooper, Hannah; Rane, Deepali; Kelly, Jane; Del Rio, Carlos; Waller, Lance A

2016-05-01

Engagement in care is central to reducing mortality for HIV-infected persons and achieving the White House National AIDS Strategy of 80% viral suppression in the US by 2020. Where an HIV-infected person lives impacts his or her ability to achieve viral suppression. Reliable transportation access for healthcare may be a key determinant of this place-suppression relationship. ZIP code tabulation areas (ZCTAs) were the units of analysis. We used geospatial and ecologic analyses to examine spatial distributions of neighborhood-level variables (eg, transportation accessibility) and associations with: (1) community linkage to care, and (2) community viral suppression. Among Atlanta ZCTAs with data for newly diagnosed HIV cases (2006-2010), we used Moran I to evaluate spatial clustering and linear regression models to evaluate associations between neighborhood variables and outcomes. In 100 ZCTAs with 8413 newly diagnosed HIV-positive residents, a median of 60 HIV cases were diagnosed per ZCTA during the 5-year period. We found significant clustering of ZCTAs with low linkage to care and viral suppression (Moran I = 0.218, P < 0.05). In high-poverty ZCTAs, a 10% point increase in ZCTA-level household vehicle ownership was associated with a 4% point increase in linkage to care (P = 0.02, R = 0.16). In low-poverty ZCTAs, a 10% point increase in ZCTA-level household vehicle ownership was associated with a 30% point increase in ZCTA-level viral suppression (P = 0.01, R = 0.08). Correlations between transportation variables and community-level care linkage and viral suppression vary by area poverty level and provide opportunities for interventions beyond individual-level factors.

Revisiting the 'disaster and development' debate - Toward a broader understanding of macroeconomic risk and resilience.

PubMed

Mochizuki, Junko; Mechler, Reinhard; Hochrainer-Stigler, Stefan; Keating, Adriana; Williges, Keith

2014-01-01

Debate regarding the relationship between socioeconomic development and natural disasters remains at the fore of global discussions, as the potential risk from climate extremes and uncertainty pose an increasing threat to developmental prospects. This study reviews statistical investigations of disaster and development linkages, across topics of macroeconomic growth, public governance and others to identify key challenges to the current approach to macro-level statistical investigation. Both theoretically and qualitatively, disaster is known to affect development through a number of channels: haphazard development, weak institutions, lack of social safety nets and short-termism of our decision-making practices are some of the factors that drive natural disaster risk. Developmental potentials, including the prospects for sustainable and equitable growth, are in turn threatened by such accumulation of disaster risks. However, quantitative evidence regarding these complex causality chains remains contested due to several reasons. A number of theoretical and methodological limitations have been identified, including the use of GDP as a proxy measurement of welfare, issues with natural disaster damage reporting and the adoption of ad hoc model specifications and variables, which render interpretation and cross-comparison of statistical analysis difficult. Additionally, while greater attention is paid to economic and institutional parameters such as GDP, remittance, corruption and public expenditure as opposed to hard-to-quantify yet critical factors such as environmental conditions and social vulnerabilities. These are gaps in our approach that hamper our comprehensive understanding of the disaster-development nexus. Important areas for further research are identified, including recognizing and addressing the data constraints, incorporating sustainability and equity concerns through alternatives to GDP, and finding novel approaches to examining the complex and dynamic relationships between risk, vulnerability, resilience, adaptive capacity and development.

A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts

PubMed Central

2013-01-01

Background The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemented for such analyses are vulnerable to several key demographic factors and deliver a poor statistical power for detecting genuine associations and also a high false positive rate. Here, we present a likelihood-based statistical approach that accounts properly for non-random nature of case–control samples in regard of genotypic distribution at the loci in populations under study and confers flexibility to test for genetic association in presence of different confounding factors such as population structure, non-randomness of samples etc. Results We implemented this novel method together with several popular methods in the literature of GWAS, to re-analyze recently published Parkinson’s disease (PD) case–control samples. The real data analysis and computer simulation show that the new method confers not only significantly improved statistical power for detecting the associations but also robustness to the difficulties stemmed from non-randomly sampling and genetic structures when compared to its rivals. In particular, the new method detected 44 significant SNPs within 25 chromosomal regions of size < 1 Mb but only 6 SNPs in two of these regions were previously detected by the trend test based methods. It discovered two SNPs located 1.18 Mb and 0.18 Mb from the PD candidates, FGF20 and PARK8, without invoking false positive risk. Conclusions We developed a novel likelihood-based method which provides adequate estimation of LD and other population model parameters by using case and control samples, the ease in integration of these samples from multiple genetically divergent populations and thus confers statistically robust and powerful analyses of GWAS. On basis of simulation studies and analysis of real datasets, we demonstrated significant improvement of the new method over the non-parametric trend test, which is the most popularly implemented in the literature of GWAS. PMID:23394771

A statistical design for testing apomictic diversification through linkage analysis.

PubMed

Zeng, Yanru; Hou, Wei; Song, Shuang; Feng, Sisi; Shen, Lin; Xia, Guohua; Wu, Rongling

2014-03-01

The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory (Carya cathayensis) and pecan (C. illinoensis) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

Childhood Conduct Problems Are Associated with Increased Partnership and Parenting Difficulties in Adulthood

ERIC Educational Resources Information Center

Raudino, Alessandra; Woodward, Lianne J.; Fergusson, David M.; Horwood, L. John

2012-01-01

This paper uses data from a sample of 337 parents studied at age 30 to examine the linkages between childhood conduct problems assessed at ages 7-9 and later partnership and parenting outcomes. The key findings of this study were: 1) increasing levels of childhood conduct problems were associated with increased risk of partnership difficulties,…

An Exploration of Communities of Practice: From Lave and Wenger's Seminal Work to a U.S. Government Agency's Knowledge Sharing Program

ERIC Educational Resources Information Center

Chindgren, Tina M.

2005-01-01

The communities of practice model for knowledge sharing is examined in this conceptual paper. Key themes reflected in the literature--the linkage between knowledge and activity and the importance of relationships--are explored within the context of programs and practices within the National Aeronautics and Aerospace Agency (NASA) learning…

Roadmap for K-12 and Postsecondary Linkages: Key Focus Areas to Ensure Quality Implementation. Data for Action

ERIC Educational Resources Information Center

Data Quality Campaign, 2014

2014-01-01

States rely on data from both the K-12 and postsecondary sectors to inform policy discussions; chart the progress of students, schools, districts, colleges, and the state; pinpoint best practices and areas of need; allocate scarce resources; and make other important education decisions every day. However, states need to securely link limited, but…

Long–term functional group recovery of lotic macroinvertebrates from logging disturbance.Canadian Journal of Fisheries and Aquatic Sciences

Treesearch

Damon T. Ely; J. Bruce Wallace

2010-01-01

Clear-cut logging rapidly affects stream macroinvertebrates through substantial alteration of terrestrial–aquatic resource linkages; however, lesser known are the long-term influences of forest succession on benthic macroinvertebrate assemblages, which play key roles in stream ecosystem function. We compared secondary production and standing crops of detritus in two...

Implications of QRIS Design for the Distribution of Program Ratings and Linkages between Ratings and Observed Quality. OPRE Research Brief 2014-33

ERIC Educational Resources Information Center

Tout, Kathryn; Chien, Nina; Rothenberg, Laura; Li, Weilin

2014-01-01

This Brief compares three hypothetical Quality Rating and Improvement Systems (QRIS) that use different rating structures: block, points, and hybrid. Because the quality standards in the hypothetical QRIS are held relatively constant across structures, analyses can be conducted to determine how structure relates to key QRIS outcomes. Three…

Late Jurassic – early Cretaceous inversion of rift structures, and linkage of petroleum system elements across post-rift unconformity, U.S. Chukchi Shelf, arctic Alaska

USGS Publications Warehouse

Houseknecht, David W.; Connors, Christopher D.

2015-01-01

Oil-prone source rocks, reservoir-quality sandstone, migration pathways, and structural closure are linked intimately across the Jurassic unconformity, which reflects inversion. Thus, all these key petroleum systems elements were in place when Triassic source rocks entered the oil generation window during Cretaceous–Cenozoic stratigraphic burial.

Phytoplankton and Climate

NASA Technical Reports Server (NTRS)

Moisan, John R.

2009-01-01

Ocean phytoplankton supply about half of the oxygen that humans utilize to sustain life. In this lecture, we will explore how phytoplankton plays a critical role in modulating the Earth's climate. These tiny organisms are the base of the Ocean's food web. They can modulate the rate at which solar heat is absorbed by the ocean, either through direct absorption or through production of highly scattering cellular coverings. They take up and help sequester carbon dioxide, a key greenhouse gas that modulated the Earth's climate. They are the source of cloud nucleation gases that are key to cloud formation/processes. They are also able to modify the nutrient budgets of the ocean through active uptake of inert atmospheric nitrogen. Climate variations have a pronounced impact on phytoplankton dynamics. Long term variations in the climate have been studied through geological interpretations on its influence on phytoplankton populations. The presentation will focus on presenting the numerous linkages that have been observed between climate and phytoplankton and further discuss how present climate change scenarios are likely to impact phytoplankton populations as well as present findings from several studies that have tried to understand how the climate might react to the feedbacks from these numerous climate-phytop|ankton linkages.

Spatial and seasonal patterns in climate change, temperatures, and precipitation across the United States.

PubMed

Portmann, Robert W; Solomon, Susan; Hegerl, Gabriele C

2009-05-05

Changes in climate during the 20th century differ from region to region across the United States. We provide strong evidence that spatial variations in US temperature trends are linked to the hydrologic cycle, and we also present unique information on the seasonal and latitudinal structure of the linkage. We show that there is a statistically significant inverse relationship between trends in daily temperature and average daily precipitation across regions. This linkage is most pronounced in the southern United States (30-40 degrees N) during the May-June time period and, to a lesser extent, in the northern United States (40-50 degrees N) during the July-August time period. It is strongest in trends in maximum temperatures (T(max)) and 90th percentile exceedance trends (90PET), and less pronounced in the T(max) 10PET and the corresponding T(min) statistics, and it is robust to changes in analysis period. Although previous studies suggest that areas of increased precipitation may have reduced trends in temperature compared with drier regions, a change in sign from positive to negative trends suggests some additional cause. We show that trends in precipitation may account for some, but not likely all, of the cause point to evidence that shows that dynamical patterns (El Niño/Southern Oscillation, North Atlantic Oscillation, etc.) cannot account for the observed effects during May-June. We speculate that changing aerosols, perhaps related to vegetation changes, and increased strength of the aerosol direct and indirect effect may play a role in the observed linkages between these indices of temperature change and the hydrologic cycle.

An adaptive community-based participatory approach to formative assessment with high schools for obesity intervention*.

PubMed

Kong, Alberta S; Farnsworth, Seth; Canaca, Jose A; Harris, Amanda; Palley, Gabriel; Sussman, Andrew L

2012-03-01

In the emerging debate around obesity intervention in schools, recent calls have been made for researchers to include local community opinions in the design of interventions. Community-based participatory research (CBPR) is an effective approach for forming community partnerships and integrating local opinions. We used CBPR principles to conduct formative research in identifying acceptable and potentially sustainable obesity intervention strategies in 8 New Mexico school communities. We collected formative data from 8 high schools on areas of community interest for school health improvement through collaboration with local School Health Advisory Councils (SHACs) and interviews with students and parents. A survey based on formative results was created to assess acceptability of specific intervention strategies and was provided to SHACs. Quantitative data were analyzed using descriptive statistics while qualitative data were evaluated using an iterative analytic process for thematic identification. Key themes identified through the formative process included lack of healthy food options, infrequent curricular/extracurricular physical activity opportunities, and inadequate exposure to health/nutritional information. Key strategies identified as most acceptable by SHAC members included healthier food options and preparation, a healthy foods marketing campaign, yearly taste tests, an after-school noncompetitive physical activity program, and community linkages to physical activity opportunities. An adaptive CBPR approach for formative assessment can be used to identify obesity intervention strategies that address community school health concerns. Eight high school SHACs identified 6 school-based strategies to address parental and student concerns related to obesity. © 2012, American School Health Association.

An Adaptive Community-Based Participatory Approach to Formative Assessment With High Schools for Obesity Intervention*

PubMed Central

Kong, Alberta S.; Farnsworth, Seth; Canaca, Jose A.; Harris, Amanda; Palley, Gabriel; Sussman, Andrew L.

2013-01-01

BACKGROUND In the emerging debate around obesity intervention in schools, recent calls have been made for researchers to include local community opinions in the design of interventions. Community-based participatory research (CBPR) is an effective approach for forming community partnerships and integrating local opinions. We used CBPR principles to conduct formative research in identifying acceptable and potentially sustainable obesity intervention strategies in 8 New Mexico school communities. METHODS We collected formative data from 8 high schools on areas of community interest for school health improvement through collaboration with local School Health Advisory Councils (SHACs) and interviews with students and parents. A survey based on formative results was created to assess acceptability of specific intervention strategies and was provided to SHACs. Quantitative data were analyzed using descriptive statistics while qualitative data were evaluated using an iterative analytic process for thematic identification. RESULTS Key themes identified through the formative process included lack of healthy food options, infrequent curricular/extracurricular physical activity opportunities, and inadequate exposure to health/nutritional information. Key strategies identified as most acceptable by SHAC members included healthier food options and preparation, a healthy foods marketing campaign, yearly taste tests, an after-school noncompetitive physical activity program, and community linkages to physical activity opportunities. CONCLUSION An adaptive CBPR approach for formative assessment can be used to identify obesity intervention strategies that address community school health concerns. Eight high school SHACs identified 6 school-based strategies to address parental and student concerns related to obesity. PMID:22320339

Integrating Water, Actors, and Structure to Study Socio-Hydro-Ecological Systems

NASA Astrophysics Data System (ADS)

Hale, R. L.; Armstrong, A.; Baker, M. A.; Bedingfield, S.; Betts, D.; Buahin, C. A.; Buchert, M.; Crowl, T.; Dupont, R.; Endter-Wada, J.; Flint, C.; Grant, J.; Hinners, S.; Horns, D.; Horsburgh, J. S.; Jackson-Smith, D.; Jones, A. S.; Licon, C.; Null, S. E.; Odame, A.; Pataki, D. E.; Rosenberg, D. E.; Runburg, M.; Stoker, P.; Strong, C.

2014-12-01

Urbanization, climate uncertainty, and ecosystem change represent major challenges for managing water resources. Water systems and the forces acting upon them are complex, and there is a need to understand and generically represent the most important system components and linkages. We developed a framework to facilitate understanding of water systems including potential vulnerabilities and opportunities for sustainability. Our goal was to produce an interdisciplinary framework for water resources research to address water issues across scales (e.g., city to region) and domains (e.g., water supply and quality, urban and transitioning landscapes). An interdisciplinary project (iUTAH - innovative Urban Transitions and Aridregion Hydro-sustainability) with a large (N=~100), diverse team having expertise spanning the hydrologic, biological, ecological, engineering, social, planning, and policy sciences motivated the development of this framework. The framework was developed through review of the literature, meetings with individual researchers, and workshops with participants. The Structure-Water-Actor Framework (SWAF) includes three main components: water (quality and quantity), structure (natural, built, and social), and actors (individual and organizational). Key linkages include: 1) ecological and hydrological processes, 2) ecosystem and geomorphic change, 3) planning, design, and policy, 4) perceptions, information, and experience, 5) resource access, and 6) operational water use and management. Our expansive view of structure includes natural, built, and social components, allowing us to examine a broad set of tools and levers for water managers and decision-makers to affect system sustainability and understand system outcomes. We validate the SWAF and illustrate its flexibility to generate insights for three research and management problems: green stormwater infrastructure in an arid environment, regional water supply and demand, and urban river restoration. These applications show that the framework can help identify key components and linkages across diverse water systems.

Linking Data for Mothers and Babies in De-Identified Electronic Health Data

PubMed Central

Gilbert, Ruth; Cromwell, David; van der Meulen, Jan

2016-01-01

Objective Linkage of longitudinal administrative data for mothers and babies supports research and service evaluation in several populations around the world. We established a linked mother-baby cohort using pseudonymised, population-level data for England. Design and Setting Retrospective linkage study using electronic hospital records of mothers and babies admitted to NHS hospitals in England, captured in Hospital Episode Statistics between April 2001 and March 2013. Results Of 672,955 baby records in 2012/13, 280,470 (42%) linked deterministically to a maternal record using hospital, GP practice, maternal age, birthweight, gestation, birth order and sex. A further 380,164 (56%) records linked using probabilistic methods incorporating additional variables that could differ between mother/baby records (admission dates, ethnicity, 3/4-character postcode district) or that include missing values (delivery variables). The false-match rate was estimated at 0.15% using synthetic data. Data quality improved over time: for 2001/02, 91% of baby records were linked (holding the estimated false-match rate at 0.15%). The linked cohort was representative of national distributions of gender, gestation, birth weight and maternal age, and captured approximately 97% of births in England. Conclusion Probabilistic linkage of maternal and baby healthcare characteristics offers an efficient way to enrich maternity data, improve data quality, and create longitudinal cohorts for research and service evaluation. This approach could be extended to linkage of other datasets that have non-disclosive characteristics in common. PMID:27764135

Social Media Interventions to Promote HIV Testing, Linkage, Adherence, and Retention: Systematic Review and Meta-Analysis

PubMed Central

Gupta, Somya; Wang, Jiangtao; Hightow-Weidman, Lisa B; Muessig, Kathryn E; Tang, Weiming; Pan, Stephen; Pendse, Razia; Tucker, Joseph D

2017-01-01

Background Social media is increasingly used to deliver HIV interventions for key populations worldwide. However, little is known about the specific uses and effects of social media on human immunodeficiency virus (HIV) interventions. Objective This systematic review examines the effectiveness of social media interventions to promote HIV testing, linkage, adherence, and retention among key populations. Methods We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist and Cochrane guidelines for this review and registered it on the International Prospective Register of Systematic Reviews, PROSPERO. We systematically searched six databases and three conference websites using search terms related to HIV, social media, and key populations. We included studies where (1) the intervention was created or implemented on social media platforms, (2) study population included men who have sex with men (MSM), transgender individuals, people who inject drugs (PWID), and/or sex workers, and (3) outcomes included promoting HIV testing, linkage, adherence, and/or retention. Meta-analyses were conducted by Review Manager, version 5.3. Pooled relative risk (RR) and 95% confidence intervals were calculated by random-effects models. Results Among 981 manuscripts identified, 26 studies met the inclusion criteria. We found 18 studies from high-income countries, 8 in middle-income countries, and 0 in low-income countries. Eight were randomized controlled trials, and 18 were observational studies. All studies (n=26) included MSM; five studies also included transgender individuals. The focus of 21 studies was HIV testing, four on HIV testing and linkage to care, and one on antiretroviral therapy adherence. Social media interventions were used to do the following: build online interactive communities to encourage HIV testing/adherence (10 studies), provide HIV testing services (9 studies), disseminate HIV information (9 studies), and develop intervention materials (1 study). Of the studies providing HIV self-testing, 16% of participants requested HIV testing kits from social media platforms. Existing social media platforms such as Facebook (n=15) and the gay dating app Grindr (n=10) were used most frequently. Data from four studies show that HIV testing uptake increased after social media interventions (n=1283, RR 1.50, 95% CI 1.28-1.76). In the studies where social media interventions were participatory, HIV testing uptake was higher in the intervention arm than the comparison arm (n=1023, RR 1.64, 95% CI 1.19-2.26). Conclusions Social media interventions are effective in promoting HIV testing among MSM in many settings. Social media interventions to improve HIV services beyond HIV testing in low- and middle-income countries and among other key populations need to be considered. Trial Registration International Prospective Register of Systematic Reviews (PROSPERO): CRD42016048073; http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42016048073 (Archived by WebCite at http://www. webcitation.org/6usLCJK3v) PMID:29175811

Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily

DOE PAGES

McCulloch, Kathryn M.; McCranie, Emilianne K.; Smith, Jarrod A.; ...

2015-08-03

Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. In this paper, we have identified a conserved group of nonheme iron, α-ketoglutarate–dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases ofmore » everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Finally, our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.« less

Fine Mapping of 6q23.1 Identifies TULP4 as Contributing to Clefts.

PubMed

Vieira, Alexandre R; de Carvalho, Flavia M; Johnson, Lindsay; DeVos, Lauren; Swailes, Alexa L; Weber, Megan L; Deeley, Kathleen

2015-03-01

Objective : The aim of this work was to fine-map the region 6q23.1, which obtained suggestive linkage signal (logarithm of the odds [LOD] score = 2.22 under a recessive model) to cleft lip with or without cleft palate (CL±P) in our previous genome-wide linkage scan to identify possible genetic variants that may contribute to CL±P. Design : We used densely spaced markers spanning the entire 6q23.1 region to test for association with CL±P in a family cohort sample. Setting : Clinical information and DNA samples were obtained from families in the Philippines at their homes or primary health care clinics. Participants : The study sample consisted of 477 subjects (224 females and 253 males), segregating isolated CL±P, from 72 living in the same area in the Philippines. Main Outcome Measure : Overtransmission of alleles to persons born with CL±P. Results : We found statistical evidence of association between a marker of TULP4 (rs651333) with CL±P (P = .00007). Conclusions : Our results further support the linkage results for the chromosome 6q region and reveal a novel candidate gene for CL±P.

The linkage between household water consumption and rainfall in the semi-arid region of East Nusa Tenggara, Indonesia

NASA Astrophysics Data System (ADS)

Messakh, J. J.; Moy, D. L.; Mojo, D.; Maliti, Y.

2018-01-01

Several studies have shown that the amount of water consumption by communities will depend on the factors of water consumption patterns that are influenced by social, cultural, economic and local climate conditions. Research on the linkage between rainfall and household water consumption in semi-arid areas of Indonesia has never been done. This study has been conducted on 17 regions in NTT, and case study has taken samples in one town and one village. The research used survey and documentation method. The results show that the average amount of household water consumption in semi-arid region of East Nusa Tenggara is 107 liters / person / day. Statistical test results using Pearson correlation found r = -0.194 and sig = 0.448. This means that there is a negative correlation between rainfall and household water consumption. The greater the rainfall the smaller the consumption of water, or the smaller the rainfall the greater the consumption of water, but the linkage is not significant. Research shows that the amount of household water consumption will be influenced by many interrelated factors and none of the most dominant factors, including the size of the rainfall that occurs in a region.

Genome-wide QTL analysis for anxiety trait in bipolar disorder type I.

PubMed

Contreras, J; Hare, E; Chavarría-Soley, G; Raventós, H

2018-07-01

Genetic studies have been consistent that bipolar disorder type I (BPI) runs in families and that this familial aggregation is strongly influenced by genes. In a preliminary study, we proved that anxiety trait meets endophenotype criteria for BPI. We assessed 619 individuals from the Central Valley of Costa Rica (CVCR) who have received evaluation for anxiety following the same methodological procedure used for the initial pilot study. Our goal was to conduct a multipoint quantitative trait linkage analysis to identify quantitative trait loci (QTLs) related to anxiety trait in subjects with BPI. We conducted the statistical analyses using Quantitative Trait Loci method (Variance-components models), implemented in Sequential Oligogenic Linkage Analysis Routines (SOLAR), using 5606 single nucleotide polymorphism (SNPs). We identified a suggestive linkage signal with a LOD score of 2.01 at chromosome 2 (2q13-q14). Since confounding factors such as substance abuse, medical illness and medication history were not assessed in our study, these conclusions should be taken as preliminary. We conclude that region 2q13-q14 may harbor a candidate gene(s) with an important role in the pathophysiology of BPI and anxiety. Published by Elsevier B.V.

Globalization and health: a framework for analysis and action.

PubMed Central

Woodward, D.; Drager, N.; Beaglehole, R.; Lipson, D.

2001-01-01

Globalization is a key challenge to public health, especially in developing countries, but the linkages between globalization and health are complex. Although a growing amount of literature has appeared on the subject, it is piecemeal, and suffers from a lack of an agreed framework for assessing the direct and indirect health effects of different aspects of globalization. This paper presents a conceptual framework for the linkages between economic globalization and health, with the intention that it will serve as a basis for synthesizing existing relevant literature, identifying gaps in knowledge, and ultimately developing national and international policies more favourable to health. The framework encompasses both the indirect effects on health, operating through the national economy, household economies and health-related sectors such as water, sanitation and education, as well as more direct effects on population-level and individual risk factors for health and on the health care system. Proposed also is a set of broad objectives for a programme of action to optimize the health effects of economic globalization. The paper concludes by identifying priorities for research corresponding with the five linkages identified as critical to the effects of globalization on health. PMID:11584737

HIV self-testing in Peru: questionable availability, high acceptability but potential low linkage to care among men who have sex with men and transgender women.

PubMed

Bustamante, Maria Jose; Konda, Kelika A; Joseph Davey, Dvora; León, Segundo R; Calvo, Gino M; Salvatierra, Javier; Brown, Brandon; Caceres, Carlos F; Klausner, Jeffrey D

2017-02-01

HIV status awareness is key to prevention, linkage-to-care and treatment. Our study evaluated the accessibility and potential willingness of HIV self-testing among men who have sex with men (MSM) and transgender women in Peru. We surveyed four pharmacy chains in Peru to ascertain the commercial availability of the oral HIV self-test. The pharmacies surveyed confirmed that HIV self-test kits were available; however, those available were not intended for individual use, but for clinician use. We interviewed 147 MSM and 45 transgender women; nearly all (82%) reported willingness to perform the oral HIV self-test. However, only 55% of participants would definitely seek a confirmatory test in a clinic after an HIV-positive test result. Further, price may be a barrier, as HIV self-test kits were available for 18 USD, and MSM and transgender women were only willing to pay an average of 5 USD. HIV self-testing may facilitate increased access to HIV testing among some MSM/transgender women in Peru. However, price may prevent use, and poor uptake of confirmatory testing may limit linkage to HIV treatment and care.

Reflections on the evidence for a vulnerability locus for Schizophrenia on chromosome 6p24-22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kendler, K.S.; Straub, R.E.; MacLean, C.J.

A recent series of studies have attempted to replicate evidence for a vulnerability locus for schizophrenia on chromosome 6p initially detected in the Irish Study of High-Density Schizophrenia Families (ISHDSF). Here, we want to comment briefly on these findings and respond to some of the issues raised in the preceding article by Baron. We disclaim, however, any pretensions to a definitive interpretation of the available evidence. Our level of ignorance in the interpretation of linkage evidence for complex psychiatric syndromes is too profound. Rather, we seek to make educated guesses on the basis of our understanding of the principles ofmore » linkage analysis, on our knowledge of the problems of statistical inference and on our intuition of how genes might influence vulnerability to complex human behavioral traits. 27 refs.« less

DENBRAN: A basic program for a significance test for multivariate normality of clusters from branching patterns in dendrograms

NASA Astrophysics Data System (ADS)

Sneath, P. H. A.

A BASIC program is presented for significance tests to determine whether a dendrogram is derived from clustering of points that belong to a single multivariate normal distribution. The significance tests are based on statistics of the Kolmogorov—Smirnov type, obtained by comparing the observed cumulative graph of branch levels with a graph for the hypothesis of multivariate normality. The program also permits testing whether the dendrogram could be from a cluster of lower dimensionality due to character correlations. The program makes provision for three similarity coefficients, (1) Euclidean distances, (2) squared Euclidean distances, and (3) Simple Matching Coefficients, and for five cluster methods (1) WPGMA, (2) UPGMA, (3) Single Linkage (or Minimum Spanning Trees), (4) Complete Linkage, and (5) Ward's Increase in Sums of Squares. The program is entitled DENBRAN.

Enhanced reporting of deaths among Aboriginal and Torres Strait Islander peoples using linked administrative health datasets.

PubMed

Taylor, Lee K; Bentley, Jason; Hunt, Jennifer; Madden, Richard; McKeown, Sybille; Brandt, Peter; Baker, Deborah

2012-07-02

Aboriginal and Torres Strait Islander peoples are under-reported in administrative health datasets in NSW, Australia. Correct reporting of Aboriginal and Torres Strait Islander peoples is essential to measure the effectiveness of policies and programmes aimed at reducing the health disadvantage experienced by Aboriginal and Torres Strait Islander peoples. This study investigates the potential of record linkage to enhance reporting of deaths among Aboriginal and Torres Strait Islander peoples in NSW, Australia. Australian Bureau of Statistics death registration data for 2007 were linked with four population health datasets relating to hospitalisations, emergency department attendances and births. Reporting of deaths was enhanced from linked records using two methods, and effects on patterns of demographic characteristics and mortality indicators were examined. Reporting of deaths increased by 34.5% using an algorithm based on a weight of evidence of a person being Aboriginal or Torres Strait Islander, and by 56.6% using an approach based on 'at least one report' of a person being Aboriginal or Torres Strait Islander. The increase was relatively greater in older persons and those living in less geographically remote areas. Enhancement resulted in a reduction in the urban-remote differential in median age at death and increases in standardised mortality ratios particularly for chronic conditions. Record linkage creates a statistical construct that helps to correct under-reporting of deaths and potential bias in mortality statistics for Aboriginal and Torres Strait Islander peoples.

Design and efficient synthesis of novel GM2 analogues with respect to the elucidation of the function of GM2 activator.

PubMed

Komori, Tatsuya; Ando, Takayuki; Imamura, Akihiro; Li, Yu-Teh; Ishida, Hideharu; Kiso, Makoto

2008-10-01

To elucidate the mechanism underlying the hydrolysis of the GalNAcbeta1-->4Gal linkage in ganglioside GM2 [GalNAcbeta1-->4(NeuAcalpha2-->3)Galbeta1-->4Glcbeta1-->1' Cer] by beta-hexosaminidase A (Hex A) with GM2 activator protein, we designed and synthesized two kinds of GM2 linkage analogues-6'-NeuAc-GM2 and alpha-GalNAc-GM2. In this paper, the efficient and systematic synthesis of these GM2 analogues was described. The highlight of our synthesis process is that the key intermediates, newly developed sialyllactose derivatives, were efficiently prepared in sufficient quantities; these derivatives directly served as highly reactive glycosyl acceptors and coupled with GalNTroc donors to furnish the assembly of GM2 tetrasaccharides in large quantities.

Critical linkages between land-use transition and human health in the Himalayan region.

PubMed

Xu, Jianchu; Sharma, Rita; Fang, Jing; Xu, Yufen

2008-02-01

This article reviews critical linkages between land-use transition and human health in the Himalayan region by applying ecosystem approaches to human health (or EcoHealth). Land-use transition in the Himalayan and similar regions includes sedentarization, agricultural intensification, habitat modification, migration, change of livelihoods and lifestyles, biodiversity loss, and increasing flash floods. These transitions, which can have impacts on human health, are driven by state policies, a market economy, and climate change. Human health is dependent on access to ecosystem services for food, nutrition, medicine, fiber and shelter, fresh water, and clear air. Ecosystem management has been a key means of controlling disease vectors and creating suitable habitats for human well-being. The paper identifies the web of environmental factors that influence human health. Institutional and policy issues for land-use and health transitions are also discussed.

A social work contribution to suicide prevention through assertive brief psychotherapy and community linkage: use of the Manchester Short Assessment of Quality of Life (MANSA).

PubMed

Petrakis, Melissa; Joubert, Lynette

2013-01-01

There is a striking absence of literature articulating and evaluating clinical social work contributions to suicide prevention, despite considerable practice in this important field. This article reports on a model of assertive brief psychotherapeutic intervention and facilitated linkage to community services utilized in a prospective cohort study of emergency department suicide attempt aftercare. A key outcome measure, the Manchester Short Assessment of Quality of Life (MANSA), was used with 65 patients to assess psychosocial domains at initial presentation, 4-weeks, 3-months, and 6-months. There were significant improvements in the domains of work, finance, leisure, social life, living situation, personal safety and health by 3 months. There were highly significant correlations between psychosocial improvements and improved depression scores.

Inferring Demographic History Using Two-Locus Statistics.

PubMed

Ragsdale, Aaron P; Gutenkunst, Ryan N

2017-06-01

Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are more sensitive to demographic history than single-locus statistics such as the AFS. In particular, two-locus statistics escape the notorious confounding of depth and duration of a bottleneck, and they provide a means to estimate effective population size based on the recombination rather than mutation rate. We applied our approach to a Zambian population of Drosophila melanogaster Notably, using both single- and two-locus statistics, we inferred a substantially lower ancestral effective population size than previous works and did not infer a bottleneck history. Together, our results demonstrate the broad potential for two-locus statistics to enable powerful population genetic inference. Copyright © 2017 by the Genetics Society of America.

The Impact of Armor on the Design, Utilization and Survivability of Ground Vehicles: The History of Armor Development and Use

DTIC Science & Technology

2012-09-01

control functions. Components that are included in this category include the steering column / linkages as well as brakes . D. FIREPOWER COMPONENTS...COMPONENTS: STEERING AND BRAKES ......................48 D. FIREPOWER COMPONENTS: TURRET AND ARMAMENT .............49 E. PROTECTION COMPONENTS: HULL AND...Key Functional Area Propulsion Powertrain (Engine / Transmission) Tracks / Wheels Control Steering Brakes / Suspension Firepower Turret Armament

Developing models to predict the number of fire hotspots from an accumulated fuel dryness index by vegetation type and region in Mexico

Treesearch

D. Vega-Nieva; J. Briseño-Reyes; M. Nava-Miranda; E. Calleros-Flores; P. López-Serrano; J. Corral-Rivas; E. Montiel-Antuna; M. Cruz-López; M. Cuahutle; R. Ressl; E. Alvarado-Celestino; A. González-Cabán; E. Jiménez; J. Álvarez-González; A. Ruiz-González; R. Burgan; H. Preisler

2018-01-01

Understanding the linkage between accumulated fuel dryness and temporal fire occurrence risk is key for improving decision-making in forest fire management, especially under growing conditions of vegetation stress associated with climate change. This study addresses the development of models to predict the number of 10-day observed Moderate-Resolution Imaging...

APMP.T-K3.4: key comparison of realizations of the ITS-90 over the range -38.8344 °C to 419.527 °C

NASA Astrophysics Data System (ADS)

Joung, W.; Gam, K. S.; Achmadi, A.; Trisna, B. A.

2016-01-01

The APMP bilateral key comparison APMP.T-K3.4 was initiated on the request from RCM-LIPI (Indonesia) to link their national standards to the average reference values (ARVs) of the CCT-K3. Korea Research Institute of Standards and Science (KRISS, Republic of Korea) provided the linkage to the CCT-K3 for temperatures ranging from -38.8344 °C to 419.527 °C. In the APMP.T-K3.4, two standard platinum resistance thermometers (SPRTs) were chosen as the transfer instruments and were calibrated at the ITS-90 fixed-points in the comparison range. The fixed-points in this comparison included Zn freezing point (419.527 °C), Sn freezing point (231.928 °C), In freezing point (156.5985 °C), Ga melting point (29.7646 °C), and Hg triple point (-38.8344 °C). The comparison was carried out in a participant-pilot-participant sequence where KRISS served as the pilot. The linkage was based on the fixed-point resistance ratios of RCM-LIPI relative to the ARVs of the CCT-K3 via the difference between the fixed-point resistance ratios of KRISS and the ARVs of the CCT-K3. The temperature differences between the national standards of RCM-LIPI and the ARVs of the CCT-K3 were within the evaluated comparison uncertainties of the ATPM.T-K3.4. This report provides detailed information on the comparison results, linkage mechanism, and the Degree of Equivalence of the RCM-LIPI relative to the institutes having participated in the CCT-K3. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Inferring Species Richness and Turnover by Statistical Multiresolution Texture Analysis of Satellite Imagery

PubMed Central

Convertino, Matteo; Mangoubi, Rami S.; Linkov, Igor; Lowry, Nathan C.; Desai, Mukund

2012-01-01

Background The quantification of species-richness and species-turnover is essential to effective monitoring of ecosystems. Wetland ecosystems are particularly in need of such monitoring due to their sensitivity to rainfall, water management and other external factors that affect hydrology, soil, and species patterns. A key challenge for environmental scientists is determining the linkage between natural and human stressors, and the effect of that linkage at the species level in space and time. We propose pixel intensity based Shannon entropy for estimating species-richness, and introduce a method based on statistical wavelet multiresolution texture analysis to quantitatively assess interseasonal and interannual species turnover. Methodology/Principal Findings We model satellite images of regions of interest as textures. We define a texture in an image as a spatial domain where the variations in pixel intensity across the image are both stochastic and multiscale. To compare two textures quantitatively, we first obtain a multiresolution wavelet decomposition of each. Either an appropriate probability density function (pdf) model for the coefficients at each subband is selected, and its parameters estimated, or, a non-parametric approach using histograms is adopted. We choose the former, where the wavelet coefficients of the multiresolution decomposition at each subband are modeled as samples from the generalized Gaussian pdf. We then obtain the joint pdf for the coefficients for all subbands, assuming independence across subbands; an approximation that simplifies the computational burden significantly without sacrificing the ability to statistically distinguish textures. We measure the difference between two textures' representative pdf's via the Kullback-Leibler divergence (KL). Species turnover, or diversity, is estimated using both this KL divergence and the difference in Shannon entropy. Additionally, we predict species richness, or diversity, based on the Shannon entropy of pixel intensity.To test our approach, we specifically use the green band of Landsat images for a water conservation area in the Florida Everglades. We validate our predictions against data of species occurrences for a twenty-eight years long period for both wet and dry seasons. Our method correctly predicts 73% of species richness. For species turnover, the newly proposed KL divergence prediction performance is near 100% accurate. This represents a significant improvement over the more conventional Shannon entropy difference, which provides 85% accuracy. Furthermore, we find that changes in soil and water patterns, as measured by fluctuations of the Shannon entropy for the red and blue bands respectively, are positively correlated with changes in vegetation. The fluctuations are smaller in the wet season when compared to the dry season. Conclusions/Significance Texture-based statistical multiresolution image analysis is a promising method for quantifying interseasonal differences and, consequently, the degree to which vegetation, soil, and water patterns vary. The proposed automated method for quantifying species richness and turnover can also provide analysis at higher spatial and temporal resolution than is currently obtainable from expensive monitoring campaigns, thus enabling more prompt, more cost effective inference and decision making support regarding anomalous variations in biodiversity. Additionally, a matrix-based visualization of the statistical multiresolution analysis is presented to facilitate both insight and quick recognition of anomalous data. PMID:23115629

Low dose morphine adjuvant therapy for enhanced efficacy of antipsychotic drug action: potential involvement of endogenous morphine in the pathophysiology of schizophrenia.

PubMed

Stefano, George B; Králíčková, Milena; Ptacek, Radek; Kuzelova, Hana; Esch, Tobias; Kream, Richard M

2012-07-01

Major thematic threads linking extensive preclinical and clinical efforts have established a working mechanistic scheme whereby atypical antipsychotic drugs ameliorate negative DSM IV diagnostic criteria by effecting relatively potent blockade of serotonin (5-HT)(2A) receptors coupled with weaker antagonism of dopamine D(2) receptors in frontal cortical areas. These contentions are more or less supported by in vitro binding experiments employing cloned receptors on cultured cells, although significant functional involvement of 5-HT(2C) receptors has also been proposed. It is interesting that a key statistical analysis indicates a major shift in usage back to typical antipsychotic agents for management of schizophrenia from 1995-2008, whereas off-label usage of atypical antipsychotic agents was markedly increased or expanded for bipolar affective disorder. Importantly, meta-analyses generally did not support efficacy differences between the other atypical antipsychotics compared with the older typical agents. A critical examination of putative functional linkages of morphine and its type-selective mu opioid receptor to higher order cortical regulation of cognitive processes may provide novel insights into human behavioral processes that are severely impaired in schizophrenia spectrum disorders.

Identifying linkages between land use, geomorphology, and aquatic habitat in a mixed-use watershed.

PubMed

McIlroy, Susan K; Montagne, Cliff; Jones, Clain A; McGlynn, Brian L

2008-11-01

The potential impacts of land use on large woody debris (LWD) were examined in Sourdough Creek Watershed, a rapidly growing area encompassing Bozeman, Montana, USA. We identified six land classes within a 250 m buffer extending on either side of Sourdough Creek and assessed aquatic habitat and geomorphologic variables within each class. All LWD pieces were counted, and we examined 14 other variables, including undercut bank, sinuosity, and substrate composition. LWD numbers were generally low and ranged from 0 to 8.2 pieces per 50 m of stream. Linear regression showed that LWD increased with distance from headwaters, riparian forest width, and sinuosity in four of the six land classes. Statistically significant differences between land classes for many aquatic habitat and geomorphologic variables indicated the impacts of different land uses on stream structure. We also found that practices such as active wood removal played a key role in LWD abundance. This finding suggests that managers should prioritize public education and outreach concerning the importance of in-stream wood, especially in mixed-use watersheds where wood is removed for either aesthetic reasons or to prevent stream flooding.

Ecological changes and local knowledge in a giant honey bee (Apis dorsata F.) hunting community in Palawan, Philippines.

PubMed

Matias, Denise Margaret S; Borgemeister, Christian; von Wehrden, Henrik

2018-02-24

One of the traditional livelihood practices of indigenous Tagbanuas in Palawan, Philippines is wild honey hunting and gathering from the giant honey bee (Apis dorsata F.). In order to analyze the linkages of the social and ecological systems involved in this indigenous practice, we conducted spatial, quantitative, and qualitative analyses on field data gathered through mapping of global positioning system coordinates, community surveys, and key informant interviews. We found that only 24% of the 251 local community members surveyed could correctly identify the giant honey bee. Inferential statistics showed that a lower level of formal education strongly correlates with correct identification of the giant honey bee. Spatial analysis revealed that mean NDVI of sampled nesting tree areas has dropped from 0.61 in the year 1988 to 0.41 in 2015. However, those who correctly identified the giant honey bee lived in areas with high vegetation cover. Decreasing vegetation cover limits the presence of wild honey bees and this may also be limiting direct experience of the community with wild honey bees. However, with causality yet to be established, we recommend conducting further studies to concretely model feedbacks between ecological changes and local knowledge.

Measuring cancer in indigenous populations.

PubMed

Sarfati, Diana; Garvey, Gail; Robson, Bridget; Moore, Suzanne; Cunningham, Ruth; Withrow, Diana; Griffiths, Kalinda; Caron, Nadine R; Bray, Freddie

2018-05-01

It is estimated that there are 370 million indigenous peoples in 90 countries globally. Indigenous peoples generally face substantial disadvantage and poorer health status compared with nonindigenous peoples. Population-level cancer surveillance provides data to set priorities, inform policies, and monitor progress over time. Measuring the cancer burden of vulnerable subpopulations, particularly indigenous peoples, is problematic. There are a number of practical and methodological issues potentially resulting in substantial underestimation of cancer incidence and mortality rates, and biased survival rates, among indigenous peoples. This, in turn, may result in a deprioritization of cancer-related programs and policies among these populations. This commentary describes key issues relating to cancer surveillance among indigenous populations including 1) suboptimal identification of indigenous populations, 2) numerator-denominator bias, 3) problems with data linkage in survival analysis, and 4) statistical analytic considerations. We suggest solutions that can be implemented to strengthen the visibility of indigenous peoples around the world. These include acknowledgment of the central importance of full engagement of indigenous peoples with all data-related processes, encouraging the use of indigenous identifiers in national and regional data sets and mitigation and/or careful assessment of biases inherent in cancer surveillance methods for indigenous peoples. Copyright © 2018 Elsevier Inc. All rights reserved.

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.).

PubMed

Kumawat, Giriraj; Raje, Ranjeet S; Bhutani, Shefali; Pal, Jitendra K; Mithra, Amitha S V C R; Gaikwad, Kishor; Sharma, Tilak R; Singh, Nagendra K

2012-10-08

Pigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea. A population of 186 F2:3 lines derived from an intra-specific cross between inbred lines 'Pusa Dwarf' and 'HDM04-1' was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant. A large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant type and maturity traits in pigeonpea. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for utilization in the pigeonpea improvement.

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

USGS Publications Warehouse

Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

2009-01-01

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

Human-modified temperatures induce species changes: Joint attribution.

PubMed

Root, Terry L; MacMynowski, Dena P; Mastrandrea, Michael D; Schneider, Stephen H

2005-05-24

Average global surface-air temperature is increasing. Contention exists over relative contributions by natural and anthropogenic forcings. Ecological studies attribute plant and animal changes to observed warming. Until now, temperature-species connections have not been statistically attributed directly to anthropogenic climatic change. Using modeled climatic variables and observed species data, which are independent of thermometer records and paleoclimatic proxies, we demonstrate statistically significant "joint attribution," a two-step linkage: human activities contribute significantly to temperature changes and human-changed temperatures are associated with discernible changes in plant and animal traits. Additionally, our analyses provide independent testing of grid-box-scale temperature projections from a general circulation model (HadCM3).

Expected Monotonicity – A Desirable Property for Evidence Measures?

PubMed Central

Hodge, Susan E.; Vieland, Veronica J.

2010-01-01

We consider here the principle of ‘evidential consistency’ – that as one gathers more data, any well-behaved evidence measure should, in some sense, approach the true answer. Evidential consistency is essential for the genome-scan design (GWAS or linkage), where one selects the most promising locus(i) for follow-up, expecting that new data will increase evidence for the correct hypothesis. Earlier work [Vieland, Hum Hered 2006;61:144–156] showed that many popular statistics do not satisfy this principle; Vieland concluded that the problem stems from fundamental difficulties in how we measure evidence and argued for determining criteria to evaluate evidence measures. Here, we investigate in detail one proposed consistency criterion – expected monotonicity (ExpM) – for a simple statistical model (binomial) and four likelihood ratio (LR)-based evidence measures. We show that, with one limited exception, none of these measures displays ExpM; what they do display is sometimes counterintuitive. We conclude that ExpM is not a reasonable requirement for evidence measures; moreover, no requirement based on expected values seems feasible. We demonstrate certain desirable properties of the simple LR and demonstrate a connection between the simple and integrated LRs. We also consider an alternative version of consistency, which is satisfied by certain forms of the integrated LR and posterior probability of linkage. PMID:20664208

Magnetic Storms

NASA Technical Reports Server (NTRS)

Tsurutani, Bruce T.; Gonzalez, Walter D.

1998-01-01

One of the oldest mysteries in geomagnetism is the linkage between solar and geomagnetic activity. The 11-year cycles of both the numbers of sunspots and Earth geomagnetic storms were first noted by Sabine. A few years later, speculation on a causal relationship between flares and storms arose when Carrington reported that a large magnetic storm followed the great September 1859 solar flare. However, it was not until this century that a well-accepted statistical survey on large solar flares and geomagnetic storms was performed, and a significant correlation between flares and geomagnetic storms was noted. Although the two phenomena, one on the Sun and the other on the Earth, were statistically correlated, the exact physical linkage was still an unknown at this time. Various hypotheses were proposed, but it was not until interplanetary spacecraft measurements were available that a high-speed plasma stream rich in helium was associated with an intense solar flare. The velocity of the solar wind increased just prior to and during the helium passage, identifying the solar ejecta for the first time. Space plasma measurements and Skylab's coronagraph images of coronal mass elections (CMES) from the Sun firmly established the plasma link between the Sun and the Earth. One phenomenon associated with magnetic storms is brilliant "blood" red auroras, as shown.

The Hunt for Pristine Cretaceous Astronomical Rhythms at Demerara Rise (Cenomanian-Coniacian)

NASA Astrophysics Data System (ADS)

Ma, C.; Meyers, S. R.

2014-12-01

Rhythmic Upper Cretaceous strata from Demerara Rise (ODP leg 207) preserve a strong astronomical signature, and this attribute has facilitated the development of continuous astrochronologies to refine the geologic time scale and calibrate Late Cretaceous biogeochemical events. While the mere identification of astronomical rhythms is a crucial first step in many deep-time paleoceanographic investigations, accurate evaluation of often subtle amplitude and frequency modulations are required to: (1) robustly constrain the linkage between climate and sedimentation, and (2) evaluate the plausibility of different theoretical astrodynamical models. The availability of a wide range of geophysical, lithologic and geochemical data from multiple sites drilled at Demerara Rise - when coupled with recent innovations in the statistical analysis of cyclostratigraphic data - provides an opportunity to hunt for the most pristine record of Cretaceous astronomical rhythms at a tropical Atlantic location. To do so, a statistical metric is developed to evaluate the "internal" consistency of hypothesized astronomical rhythms observed in each data set, particularly with regard to the expected astronomical amplitude modulations. In this presentation, we focus on how the new analysis yields refinements to the existing astrochronologies, provides constraints on the linkages between climate and sedimentation (including the deposition of organic carbon-rich sediments at Demerara Rise), and allows a quantitative evaluation of the continuity of deposition across sites at multiple temporal scales.

Land Change Trends in the Great Plains: Linkages to Climate Variability and Socioeconomic Drivers

NASA Astrophysics Data System (ADS)

Drummond, M. A.

2009-12-01

Land use and land cover change have complex linkages to climate variability and change, socioeconomic driving forces, and land management challenges. To assess these land change dynamics and their driving forces in the Great Plains, we compare and contrast contemporary land conversion across seventeen ecoregions using Landsat remote sensing data and statistical analysis. Large area change analysis in agricultural regions is often hampered by the potential for substantial change detection error and the tendency for land conversions to occur in relatively small patches at the local level. To facilitate a regional scale analysis, a statistical sampling design of randomly selected 10-km by 10-km blocks is used in order to efficiently identify the types and rates of land conversions for four time periods between 1972 and 2000, stratified by relatively homogenous ecoregions. Results show a range of rates and processes of land change that vary by ecoregion contingent on the prevailing interactions between socioeconomic and environmental factors such as climate variability, water availability, and land quality. Ecoregions have differential climate and biophysical advantages for agricultural production and other land use change. Human actions further strengthen or dampen the characteristics of change through farm policy, technological advances, economic opportunities, population and demographic shifts, and surface and groundwater irrigation.

Theoretical electron scattering amplitudes and spin polarizations. Electron energies 100 to 1500 eV Part II. Be, N, O, Al, Cl, V, Co, Cu, As, Nb, Ag, Sn, Sb, I, and Ta targets

NASA Astrophysics Data System (ADS)

Wildhaber, M. L.; Wikle, C. K.; Anderson, C. J.; Franz, K. J.; Moran, E. H.; Dey, R.

2012-12-01

Recent decades have brought substantive changes in land use and climate across the earth, prompting a need to think of population and community ecology not as a static entity, but as a dynamic process. Increasingly there is evidence of ecological changes due to climate change. Although much of this evidence comes from ground-truth observations of biogeographic data, there is increasing reliance on models that relate climate variables to biological systems. Such models can then be used to explore potential changes to population and community level ecological systems in response to climate scenarios as obtained from global climate models (GCMs). A key issue associated with modeling ecosystem response to climate is GCM downscaling to regional and local ecological/biological response models that can be used in vulnerability and risk assessments of the potential effects of climate change. The need is for an explicit means for scaling results up or down multiple hierarchical levels and an effective assessment of the level of uncertainty surrounding current knowledge, data, and data collection methods with these goals identified as in need of acceleration in the U.S. Climate Change Science Program FY2009 Implementation Priorities. In the end, such work should provide the information needed to develop adaptation and mitigation methodologies to minimize the effects of directional and nonlinear climate change on the Nation's land, water, ecosystems, and biological populations. We are working to develop an approach that includes multi-scale and hierarchical Bayesian modeling of Missouri River sturgeon population dynamics. Statistical linkages are defined to quantify implications of climate on fish populations of the Missouri River ecosystem. This approach is a hybrid between physical (deterministic) downscaling and statistical downscaling, recognizing that there is uncertainty in both. The model must include linkages between climate and habitat, and between habitat and population. A key advantage of the hierarchical approach used in this study is that it incorporates various sources of observations and includes established scientific knowledge, and associated uncertainties. The goal is to evaluate the potential distributional changes in an ecological system, given distributional changes implied by a series of linked climate and system models under various emissions/use scenarios. The predictive modeling system being developed will be a powerful tool for evaluating management options for coping with global change consequences and assessing uncertainty of those evaluations. Specifically for the endangered pallid sturgeon (Scaphirhynchus albus), we are already able to assess potential effects of any climate scenario on growth and population size distribution. Future models will incorporate survival and reproduction. Ultimately, these models provide guidance for successful recovery and conservation of the pallid sturgeon. Here we present a basic outline of the approach we are developing and a simple pallid sturgeon example to demonstrate how multiple scales and parameter uncertainty are incorporated.

Reginald Crundall Punnett: First Arthur Balfour Professor of Genetics, Cambridge, 1912

PubMed Central

Edwards, A. W. F.

2012-01-01

R. C. Punnett, the codiscoverer of linkage with W. Bateson in 1904, had the good fortune to be invited to be the first Arthur Balfour Professor of Genetics at Cambridge University, United Kingdom, in 1912 when Bateson, for whom it had been intended, declined to leave his new appointment as first Director of the John Innes Horticultural Institute. We here celebrate the centenary of the first professorship dedicated to genetics, outlining Punnett’s career and his scientific contributions, with special reference to the discovery of “partial coupling” in the sweet pea (later “linkage”) and to the diagram known as Punnett’s square. His seeming reluctance as coauthor with Bateson to promote the reduplication hypothesis to explain the statistical evidence for linkage is stressed, as is his relationship with his successor as Arthur Balfour Professor, R. A. Fisher. The background to the establishment of the Professorship is also described. PMID:22964834

Meeting the Challenges of Regional Security

DTIC Science & Technology

1994-02-01

targets over time, assessing strike damage, and, of course, developing up-to- date maps of crucial urban and industrial areas. Coupled with modem digital ...of huge diverse data bases is key to dissecting criminal infrastructures, and identifying relevant regional and global linkages. New digital processing...cities). They can aid in reaction force planning and training. One 10-inch optical disc can easily store 25 (and display at any scale with 4- digit

Compelling Evidence for a Prostate Cancer Gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics

PubMed Central

Camp, Nicola J.; Cannon-Albright, Lisa A.; Farnham, James M.; Baffoe-Bonnie, Agnes B.; George, Asha; Powell, Isaac; Bailey-Wilson, Joan E.; Carpten, John D.; Giles, Graham G.; Hopper, John L.; Severi, Gianluca; English, Dallas R.; Foulkes, William D.; Maehle, Lovise; Moller, Pal; Eeles, Ros; Easton, Douglas; Badzioch, Michael D.; Whittemore, Alice S.; Oakley-Girvan, Ingrid; Hsieh, Chih-Lin; Dimitrov, Latchezar; Xu, Jianfeng; Stanford, Janet L.; Johanneson, Bo; Deutsch, Kerry; McIntosh, Laura; Ostrander, Elaine A.; Wiley, Kathleen E.; Isaacs, Sarah D.; Walsh, Patrick C.; Thibodeau, Stephen N.; McDonnell, Shannon K.; Hebbring, Scott; Schaid, Daniel J.; Lange, Ethan M.; Cooney, Kathleen A.; Tammela, Teuvo L.J.; Schleutker, Johanna; Paiss, Thomas; Maier, Christiane; Grönberg, Henrik; Wiklund, Fredrik; Emanuelsson, Monica; Isaacs, William B.

2009-01-01

Previously, an analysis of 14 extended, high-risk Utah pedigrees localized the chromosome 22q linkage region to 3.2 Mb at 22q12.3-13.1 (flanked on each side by three recombinants), which contained 31 annotated genes. In this large, multi-centered, collaborative study, we performed statistical recombinant mapping in fifty-four pedigrees selected to be informative for recombinant mapping from nine member groups of the International Consortium for Prostate Cancer Genetics (ICPCG). These 54 pedigrees included the 14 extended pedigrees from Utah and 40 pedigrees from eight other ICPCG member groups. The additional 40 pedigrees were selected from a total pool of 1,213 such that each pedigree was required to both contain at least four prostate cancer (PRCA) cases and exhibit evidence for linkage to the chromosome 22q region. The recombinant events in these 40 independent pedigrees confirmed the previously proposed region. Further, when all 54 pedigrees were considered, the three-recombinant consensus region was narrowed by more than a megabase to 2.2 Mb at chromosome 22q12.3 flanked by D22S281 and D22S683. This narrower region eliminated 20 annotated genes from that previously proposed, leaving only eleven genes. This region at 22q12.3 is the most consistently identified and smallest linkage region for PRCA. This collaborative study by the ICPCG illustrates the value of consortium efforts and the continued utility of linkage analysis using informative pedigrees to localize genes for complex diseases. PMID:17478474

Evidence of linkage and association on chromosome 20 for late-onset Alzheimer disease.

PubMed

Goddard, Katrina A B; Olson, Jane M; Payami, Haydeh; van der Voet, Monique; Kuivaniemi, Helena; Tromp, Gerard

2004-06-01

Recently, we reported evidence of linkage on chromosome 20 for Alzheimer disease (AD) using a novel statistical approach to incorporate covariates (e.g., age, ApoE genotype) into the analysis. These results suggest that very elderly subjects (>85 years), and individuals who carry an epsilon2 allele at the ApoE locus are more likely to be linked to this candidate region. The region on chromosome 20 includes a strong candidate gene, cystatin C (CST3), which has previously been associated with AD in case-control studies. We investigated these findings further by genotyping additional markers to narrow the candidate region, and to identify evidence of linkage disequilibrium as additional support for a susceptibility locus on chromosome 20. We selected 43 elderly sibships (89 subjects) from the NIMH AD Genetics Initiative based on current age older than 84 years, and identified 129 unrelated control subjects who were older than 84 years from the Oregon Brain Aging Study to conduct linkage and association studies in this region. Fourteen additional markers were evaluated, including 4 markers located within or near CST3. We narrowed the candidate region on chromosome 20 to an 11.8-cM region between markers D20S174 and D20S471, which includes the CST3 candidate gene. In addition, we observed evidence of association for markers located near the CST3 candidate gene, with P values between 0.002 and 0.08 for two-locus haplotypes. These results support the presence of a susceptibility locus for AD in the vicinity of CST3 for very elderly subjects with AD.

Matrilineal inheritance of a key mediator of prenatal maternal effects

PubMed Central

Ziegler, Ann-Kathrin; Pick, Joel L.; Okuliarová, Monika; Zeman, Michal

2016-01-01

Sex-linkage is predicted to evolve in response to sex-specific or sexually antagonistic selection. In line with this prediction, most sex-linked genes are associated with reproduction in the respective sex. In addition to traits directly involved in fertility and fecundity, mediators of maternal effects may be predisposed to evolve sex-linkage, because they indirectly affect female fitness through their effect on offspring phenotype. Here, we test for sex-linked inheritance of a key mediator of prenatal maternal effects in oviparous species, the transfer of maternally derived testosterone to the eggs. Consistent with maternal inheritance, we found that in Japanese quail (Coturnix japonica) granddaughters resemble their maternal (but not their paternal) grandmother in yolk testosterone deposition. This pattern of resemblance was not due to non-genetic priming effects of testosterone exposure during prenatal development, as an experimental manipulation of yolk testosterone levels did not affect the females' testosterone transfer to their own eggs later in life. Instead, W chromosome and/or mitochondrial variation may underlie the observed matrilineal inheritance pattern. Ultimately, the inheritance of mediators of maternal effects along the maternal line will allow for a fast and direct response to female-specific selection, thereby affecting the dynamics of evolutionary processes mediated by maternal effects. PMID:27629040

Quantifying Ubiquitin Signaling

PubMed Central

Ordureau, Alban; Münch, Christian; Harper, J. Wade

2015-01-01

Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), most notably phosphorylation. Flux through such pathways is typically dictated by the fractional stoichiometry of distinct regulatory modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events. A key regulatory feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems. PMID:26000850

Icefield-to-ocean linkages across the northern Pacific coastal temperate rainforest ecosystem

USGS Publications Warehouse

O'Neel, Shad; Hood, Eran; Bidlack, Allison L.; Fleming, Sean W.; Arimitsu, Mayumi L.; Arendt, Anthony; Burgess, Evan W.; Sergeant, Christopher J.; Beaudreau, Anne E.; Timm, Kristin; Hayward, Gregory D.; Reynolds, Joel H.; Pyare, Sanjay

2015-01-01

Rates of glacier mass loss in the northern Pacific coastal temperate rainforest (PCTR) are among the highest on Earth, and changes in glacier volume and extent will affect the flow regime and chemistry of coastal rivers, as well as the nearshore marine ecosystem of the Gulf of Alaska. Here we synthesize physical, chemical and biological linkages that characterize the northern PCTR ecosystem, with particular emphasis on the potential impacts of glacier change in the coastal mountain ranges on the surface–water hydrology, biogeochemistry, coastal oceanography and aquatic ecology. We also evaluate the relative importance and interplay between interannual variability and long-term trends in key physical drivers and ecological responses. To advance our knowledge of the northern PCTR, we advocate for cross-disciplinary research bridging the icefield-to-ocean ecosystem that can be paired with long-term scientific records and designed to inform decisionmakers.

Multiple convergent supergene evolution events in mating-type chromosomes.

PubMed

Branco, Sara; Carpentier, Fantin; Rodríguez de la Vega, Ricardo C; Badouin, Hélène; Snirc, Alodie; Le Prieur, Stéphanie; Coelho, Marco A; de Vienne, Damien M; Hartmann, Fanny E; Begerow, Dominik; Hood, Michael E; Giraud, Tatiana

2018-05-21

Convergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their prevalence or evolution. A recent study on anther-smut fungi documented supergene formation by rearrangements linking two key mating-type loci, controlling pre- and post-mating compatibility. Here further high-quality genome assemblies reveal four additional independent cases of chromosomal rearrangements leading to regions of suppressed recombination linking these mating-type loci in closely related species. Such convergent transitions in genomic architecture of mating-type determination indicate strong selection favoring linkage of mating-type loci into cosegregating supergenes. We find independent evolutionary strata (stepwise recombination suppression) in several species, with extensive rearrangements, gene losses, and transposable element accumulation. We thus show remarkable convergence in mating-type chromosome evolution, recurrent supergene formation, and repeated evolution of similar phenotypes through different genomic changes.

Quality improvement and emerging global health priorities

PubMed Central

Mensah Abrampah, Nana; Syed, Shamsuzzoha Babar; Hirschhorn, Lisa R; Nambiar, Bejoy; Iqbal, Usman; Garcia-Elorrio, Ezequiel; Chattu, Vijay Kumar; Devnani, Mahesh; Kelley, Edward

2018-01-01

Abstract Quality improvement approaches can strengthen action on a range of global health priorities. Quality improvement efforts are uniquely placed to reorient care delivery systems towards integrated people-centred health services and strengthen health systems to achieve Universal Health Coverage (UHC). This article makes the case for addressing shortfalls of previous agendas by articulating the critical role of quality improvement in the Sustainable Development Goal era. Quality improvement can stimulate convergence between health security and health systems; address global health security priorities through participatory quality improvement approaches; and improve health outcomes at all levels of the health system. Entry points for action include the linkage with antimicrobial resistance and the contentious issue of the health of migrants. The work required includes focussed attention on the continuum of national quality policy formulation, implementation and learning; alongside strengthening the measurement-improvement linkage. Quality improvement plays a key role in strengthening health systems to achieve UHC. PMID:29873793

Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology.

PubMed

Clutton-Brock, Tim; Sheldon, Ben C

2010-10-01

Many important questions in ecology and evolutionary biology can only be answered with data that extend over several decades and answering a substantial proportion of questions requires records of the life histories of recognisable individuals. We identify six advantages that long-term, individual based studies afford in ecology and evolution: (i) analysis of age structure; (ii) linkage between life history stages; (iii) quantification of social structure; (iv) derivation of lifetime fitness measures; (v) replication of estimates of selection; (vi) linkage between generations, and we review their impact on studies in six key areas of evolution and ecology. Our review emphasises the unusual opportunities and productivity of long-term, individual-based studies and documents the important role that they play in research on ecology and evolutionary biology as well as the difficulties they face. Copyright © 2010 Elsevier Ltd. All rights reserved.

2011 Rita Schaffer lecture: nanoparticles for intracellular nucleic acid delivery.

PubMed

Green, Jordan J

2012-07-01

Nanoparticles are a promising technology for delivery of new types of therapeutics. A polymer library approach has allowed engineering of polymeric particles that are particularly effective for the delivery of DNA and siRNA to human cells. Certain chemical structural motifs, degradable linkages, hydrophobicity, and biophysical properties are key for successful intracellular delivery. Small differences to biomaterial structure, and especially the type of degradable linkage in the polymers, can be critical for successful delivery of siRNA vs. DNA. Furthermore, subtle changes to biomaterial structure can facilitate cell-type gene delivery specificity between human brain cancer cells and healthy cells as well as between human retinal endothelial cells and epithelial cells. These polymeric nanoparticles are effective for nucleic acid delivery in a broad range of human cell types and have applications to regenerative medicine, ophthalmology, and cancer among many other biomedical research areas.

Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination.

PubMed

Shirak, Andrey; Seroussi, Eyal; Cnaani, Avner; Howe, Aimee E; Domokhovsky, Raisa; Zilberman, Noam; Kocher, Thomas D; Hulata, Gideon; Ron, Micha

2006-11-01

Recent studies have revealed that the major genes of the mammalian sex determination pathway are also involved in sex determination of fish. Several studies have reported QTL in various species and strains of tilapia, regions contributing to sex determination have been identified on linkage groups 1, 3, and 23. Genes contributing to sex-specific mortality have been detected on linkage groups 2, 6, and 23. To test whether the same genes might control sex determination in mammals and fishes, we mapped 11 genes that are considered putative master key regulators of sex determination: Amh, Cyp19, Dax1, Dmrt2, Dmrta2, Fhl3l, Foxl2, Ixl, Lhx9, Sf1, and Sox8. We identified polymorphisms in noncoding regions of these genes and genotyped these sites for 90 individuals of an F2 mapping family. Mapping of Dax1 joined LG16 and LG21 into a single linkage group. The Amh and Dmrta2 genes were mapped to two distinct regions of LG23. The Amh gene was mapped 5 cM from UNH879 within a QTL region for sex determination and 2 cM from UNH216 within a QTL region for sex-specific mortality. Dmrta2 was mapped 4 cM from UNH848 within another QTL region for sex determination. Cyp19 was mapped to LG1 far from a previously reported QTL region for sex determination on this chromosome. Seven other candidate genes mapped to LG4, -11, -12, -14, and -17.

Postdeployment Behavioral Health Screens and Linkage to the Veterans Health Administration for Army Reserve Component Members.

PubMed

Vanneman, Megan E; Harris, Alex H S; Chen, Cheng; Adams, Rachel Sayko; Williams, Thomas V; Larson, Mary Jo

2017-08-01

Approximately three to six months after returning from deployment, military service members complete the Post-Deployment Health Reassessment (PDHRA), which includes screens for alcohol misuse, depression, and posttraumatic stress disorder (PTSD). To determine whether Army Reserve Component (RC) members (Army National Guard and Army Reserve) with positive screening scores on the PDHRA receive needed care, the investigators examined the association between positive scores and enrollment and utilization of care ("linkage") in the Veterans Health Administration (VHA), as well as rescreening scores, diagnosis, and behavioral treatment in VHA. Mixed-effects regression models were used to predict linkage to VHA within six months after RC members (N=73,164) completed the PDHRA, with alcohol misuse, depression, and PTSD screen scores as key independent variables. Regression models were stratified by gender and National Guard versus Reserve status. Among those who linked to VHA (N=25,168), screening scores and subsequent diagnosis and treatment in VHA were also examined. Army RC members with positive PTSD and depression screening scores were more likely than those with negative screens to link to VHA, and most (54%-84%) received VHA treatment once diagnosed. Positive screens for alcohol misuse were associated with linkage to VHA for men but not for women, and treatment rates for alcohol use disorders were relatively low (0%-25%) for both men and women diagnosed as having an alcohol use disorder. The finding that Army RC members with greater indications of behavioral health problems linked to VHA is encouraging. However, more outreach and treatment engagement strategies could be directed to those with alcohol use disorder, particularly women.

Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex diseases.

PubMed

Abreu, P C; Greenberg, D A; Hodge, S E

1999-09-01

Several methods have been proposed for linkage analysis of complex traits with unknown mode of inheritance. These methods include the LOD score maximized over disease models (MMLS) and the "nonparametric" linkage (NPL) statistic. In previous work, we evaluated the increase of type I error when maximizing over two or more genetic models, and we compared the power of MMLS to detect linkage, in a number of complex modes of inheritance, with analysis assuming the true model. In the present study, we compare MMLS and NPL directly. We simulated 100 data sets with 20 families each, using 26 generating models: (1) 4 intermediate models (penetrance of heterozygote between that of the two homozygotes); (2) 6 two-locus additive models; and (3) 16 two-locus heterogeneity models (admixture alpha = 1.0,.7,.5, and.3; alpha = 1.0 replicates simple Mendelian models). For LOD scores, we assumed dominant and recessive inheritance with 50% penetrance. We took the higher of the two maximum LOD scores and subtracted 0.3 to correct for multiple tests (MMLS-C). We compared expected maximum LOD scores and power, using MMLS-C and NPL as well as the true model. Since NPL uses only the affected family members, we also performed an affecteds-only analysis using MMLS-C. The MMLS-C was both uniformly more powerful than NPL for most cases we examined, except when linkage information was low, and close to the results for the true model under locus heterogeneity. We still found better power for the MMLS-C compared with NPL in affecteds-only analysis. The results show that use of two simple modes of inheritance at a fixed penetrance can have more power than NPL when the trait mode of inheritance is complex and when there is heterogeneity in the data set.

Creative Activities in Music--A Genome-Wide Linkage Analysis.

PubMed

Oikkonen, Jaana; Kuusi, Tuire; Peltonen, Petri; Raijas, Pirre; Ukkola-Vuoti, Liisa; Karma, Kai; Onkamo, Päivi; Järvelä, Irma

2016-01-01

Creative activities in music represent a complex cognitive function of the human brain, whose biological basis is largely unknown. In order to elucidate the biological background of creative activities in music we performed genome-wide linkage and linkage disequilibrium (LD) scans in musically experienced individuals characterised for self-reported composing, arranging and non-music related creativity. The participants consisted of 474 individuals from 79 families, and 103 sporadic individuals. We found promising evidence for linkage at 16p12.1-q12.1 for arranging (LOD 2.75, 120 cases), 4q22.1 for composing (LOD 2.15, 103 cases) and Xp11.23 for non-music related creativity (LOD 2.50, 259 cases). Surprisingly, statistically significant evidence for linkage was found for the opposite phenotype of creative activity in music (neither composing nor arranging; NCNA) at 18q21 (LOD 3.09, 149 cases), which contains cadherin genes like CDH7 and CDH19. The locus at 4q22.1 overlaps the previously identified region of musical aptitude, music perception and performance giving further support for this region as a candidate region for broad range of music-related traits. The other regions at 18q21 and 16p12.1-q12.1 are also adjacent to the previously identified loci with musical aptitude. Pathway analysis of the genes suggestively associated with composing suggested an overrepresentation of the cerebellar long-term depression pathway (LTD), which is a cellular model for synaptic plasticity. The LTD also includes cadherins and AMPA receptors, whose component GSG1L was linked to arranging. These results suggest that molecular pathways linked to memory and learning via LTD affect music-related creative behaviour. Musical creativity is a complex phenotype where a common background with musicality and intelligence has been proposed. Here, we implicate genetic regions affecting music-related creative behaviour, which also include genes with neuropsychiatric associations. We also propose a common genetic background for music-related creative behaviour and musical abilities at chromosome 4.

Linking product-elicited emotional associations and sensory perceptions through a circumplex model based on valence and arousal: Five consumer studies.

PubMed

Jaeger, Sara R; Spinelli, Sara; Ares, Gastón; Monteleone, Erminio

2018-07-01

Sensory product characterisation by consumers is increasingly supplemented by measurement of emotional associations. However, studies that link products' sensory perception and emotional associations are still scarce. Five consumer studies were conducted using cashew nuts, peanuts, chocolate, fruit and processed tomatoes as the product categories. Consumers (n = 685) completed check-all-that-apply (CATA) questions to obtain sensory product perceptions and associations with emotion words. The latter were conceptualised and interpreted through a circumplex emotion model spanned by the dimensions of valence (pleasure to displeasure) and arousal (activation to deactivation). Through regression analysis, sensory terms were mapped to the circumplex model to represent statistical linkages with emotion words. Within a were interpretable. The most notable finding was the highly study-specific nature of the linkages, which was mainly attributed to the influence of product category. Methodological choices may also have been partly responsible for the differences. Three studies used a general emotion vocabulary (EsSense Profile®) and an identical number of sensory terms (n = 39). The less complete coverage of the emotional circumplex and the presence of synonymous sensory terms could have diminished the ability to interpret the results. Conversely, two studies used fewer emotion words and sensory terms and these, furthermore, were purposefully selected for the focal sets of samples. The linkages in these latter studies were more interpretable and this could suggest that customised vocabularies of modest length may be desirable when seeking to establish linkages between emotional associations and sensory characteristics of food/beverage stimuli. Purposeful inclusion of emotion words that fully span the circumplex emotion model may also be desirable. Overall, the research represents a new method for establishing linkages between the sensory properties and emotional association to food and beverage products. Copyright © 2018 Elsevier Ltd. All rights reserved.

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa–B. oleracea monosomic alien addition lines

PubMed Central

Heneen, Waheeb K.; Geleta, Mulatu; Brismar, Kerstin; Xiong, Zhiyong; Pires, J. Chris; Hasterok, Robert; Stoute, Andrew I.; Scott, Roderick J.; King, Graham J.; Kurup, Smita

2012-01-01

Background and Aims Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes. Methods A new batch of B. rapa–B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow's carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used. Key Results The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups. Conclusions A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker-assisted selection and breeding for yellow seeds. PMID:22628364

Relative Linkages of Stream Dissolved Oxygen with the Climatic, Hydrological, and Biogeochemical Drivers across the East Coast of U.S.A.

NASA Astrophysics Data System (ADS)

Abdul-Aziz, O. I.; Ahmed, S.

2017-12-01

Dissolved oxygen (DO) is a key indicator of stream water quality and ecosystem health. However, the temporal dynamics of stream DO is controlled by a multitude of interacting environmental drivers. The relative linkages of stream DO with the relevant environmental drivers were determined in this study across the U.S. East Coast by employing a systematic data analytics approach. The study analyzed temporal data for 51 water quality monitoring stations from USGS NWIS and EPA STORET databases. Principal component analysis and factor analysis, along with Pearson's correlation analysis, were applied to identify the interrelationships and unravel latent patterns among DO and the environmental drivers. Power law based partial least squares regression models with a bootstarp Monte-Carlo procedure (1000 iterations) were developed to reliably estimate the environmental linkages of DO by resolving multicollinearity. Based on the similarity of dominant drivers, the streams were categorized into three distinct environmental regimes. Stream DO in the northern part of temperate zone (e.g., northeast coast) had the strongest linkage with water temperature; suggesting an environmental regime with dominant climatic control. However, stream DO in the tropical zones (e.g., southeast Florida) was mostly driven by pH; indicating an environmental regime likely controlled by redox chemistry. Further, a transitional regime was found between the temperate and tropical zones, where stream DO was controlled by both water temperature and pH. The results suggested a strong effect of the climatic gradient (temperate to tropical) on stream DO along the East Coast. The identified environmental regimes and the regime-specific relative linkages provided new information on the dominant controls of coastal stream water quality dynamics. The findings would guide the planning and management of coastal stream water quality and ecosystem health across the U.S. East Coast and around the world.

Using patients’ experiences of adverse events to improve health service delivery and practice: protocol of a data linkage study of Australian adults age 45 and above

PubMed Central

Walton, Merrilyn; Smith-Merry, Jennifer; Harrison, Reema; Manias, Elizabeth; Iedema, Rick; Kelly, Patrick

2014-01-01

Introduction Evidence of patients’ experiences is fundamental to creating effective health policy and service responses, yet is missing from our knowledge of adverse events. This protocol describes explorative research redressing this significant deficit; investigating the experiences of a large cohort of recently hospitalised patients aged 45 years and above in hospitals in New South Wales (NSW), Australia. Methods and analysis The 45 and Up Study is a cohort of 265 000 adults aged 45 years and above in NSW. Patients who were hospitalised between 1 January and 30 June 2014 will be identified from this cohort using data linkage and a random sample of 20 000 invited to participate. A cross-sectional survey (including qualitative and quantitative components) will capture patients’ experiences in hospital and specifically of adverse events. Approximately 25% of respondents are likely to report experiencing an adverse event. Quantitative components will capture the nature and type of events as well as common features of patients’ experiences. Qualitative data provide contextual knowledge of their condition and care and the impact of the event on individuals. Respondents who do not report an adverse event will report their experience in hospital and be the control group. Statistical and thematic analysis will be used to present a patient perspective of their experiences in hospital; the characteristics of patients experiencing an adverse event; experiences of information sharing after an event (open disclosure) and the other avenues of redress pursued. Interviews with key policymakers and a document analysis will be used to create a map of the current practice. Ethics and dissemination Dissemination via a one-day workshop, peer-reviewed publications and conference presentations will enable effective clinical responses and service provision and policy responses to adverse events to be developed. PMID:25311039

Using patients' experiences of adverse events to improve health service delivery and practice: protocol of a data linkage study of Australian adults age 45 and above.

PubMed

Walton, Merrilyn; Jorm, Christine; Smith-Merry, Jennifer; Harrison, Reema; Manias, Elizabeth; Iedema, Rick; Kelly, Patrick

2014-10-13

Evidence of patients' experiences is fundamental to creating effective health policy and service responses, yet is missing from our knowledge of adverse events. This protocol describes explorative research redressing this significant deficit; investigating the experiences of a large cohort of recently hospitalised patients aged 45 years and above in hospitals in New South Wales (NSW), Australia. The 45 and Up Study is a cohort of 265,000 adults aged 45 years and above in NSW. Patients who were hospitalised between 1 January and 30 June 2014 will be identified from this cohort using data linkage and a random sample of 20,000 invited to participate. A cross-sectional survey (including qualitative and quantitative components) will capture patients' experiences in hospital and specifically of adverse events. Approximately 25% of respondents are likely to report experiencing an adverse event. Quantitative components will capture the nature and type of events as well as common features of patients' experiences. Qualitative data provide contextual knowledge of their condition and care and the impact of the event on individuals. Respondents who do not report an adverse event will report their experience in hospital and be the control group. Statistical and thematic analysis will be used to present a patient perspective of their experiences in hospital; the characteristics of patients experiencing an adverse event; experiences of information sharing after an event (open disclosure) and the other avenues of redress pursued. Interviews with key policymakers and a document analysis will be used to create a map of the current practice. Dissemination via a one-day workshop, peer-reviewed publications and conference presentations will enable effective clinical responses and service provision and policy responses to adverse events to be developed. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Linkage disequilibrium interval mapping of quantitative trait loci.

PubMed

Boitard, Simon; Abdallah, Jihad; de Rochambeau, Hubert; Cierco-Ayrolles, Christine; Mangin, Brigitte

2006-03-16

For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods. Under a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations. Our method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates.

Social Media Interventions to Promote HIV Testing, Linkage, Adherence, and Retention: Systematic Review and Meta-Analysis.

PubMed

Cao, Bolin; Gupta, Somya; Wang, Jiangtao; Hightow-Weidman, Lisa B; Muessig, Kathryn E; Tang, Weiming; Pan, Stephen; Pendse, Razia; Tucker, Joseph D

2017-11-24

Social media is increasingly used to deliver HIV interventions for key populations worldwide. However, little is known about the specific uses and effects of social media on human immunodeficiency virus (HIV) interventions. This systematic review examines the effectiveness of social media interventions to promote HIV testing, linkage, adherence, and retention among key populations. We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist and Cochrane guidelines for this review and registered it on the International Prospective Register of Systematic Reviews, PROSPERO. We systematically searched six databases and three conference websites using search terms related to HIV, social media, and key populations. We included studies where (1) the intervention was created or implemented on social media platforms, (2) study population included men who have sex with men (MSM), transgender individuals, people who inject drugs (PWID), and/or sex workers, and (3) outcomes included promoting HIV testing, linkage, adherence, and/or retention. Meta-analyses were conducted by Review Manager, version 5.3. Pooled relative risk (RR) and 95% confidence intervals were calculated by random-effects models. Among 981 manuscripts identified, 26 studies met the inclusion criteria. We found 18 studies from high-income countries, 8 in middle-income countries, and 0 in low-income countries. Eight were randomized controlled trials, and 18 were observational studies. All studies (n=26) included MSM; five studies also included transgender individuals. The focus of 21 studies was HIV testing, four on HIV testing and linkage to care, and one on antiretroviral therapy adherence. Social media interventions were used to do the following: build online interactive communities to encourage HIV testing/adherence (10 studies), provide HIV testing services (9 studies), disseminate HIV information (9 studies), and develop intervention materials (1 study). Of the studies providing HIV self-testing, 16% of participants requested HIV testing kits from social media platforms. Existing social media platforms such as Facebook (n=15) and the gay dating app Grindr (n=10) were used most frequently. Data from four studies show that HIV testing uptake increased after social media interventions (n=1283, RR 1.50, 95% CI 1.28-1.76). In the studies where social media interventions were participatory, HIV testing uptake was higher in the intervention arm than the comparison arm (n=1023, RR 1.64, 95% CI 1.19-2.26). Social media interventions are effective in promoting HIV testing among MSM in many settings. Social media interventions to improve HIV services beyond HIV testing in low- and middle-income countries and among other key populations need to be considered. International Prospective Register of Systematic Reviews (PROSPERO): CRD42016048073; http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42016048073 (Archived by WebCite at http://www. webcitation.org/6usLCJK3v). ©Bolin Cao, Somya Gupta, Jiangtao Wang, Lisa B Hightow-Weidman, Kathryn E Muessig, Weiming Tang, Stephen Pan, Razia Pendse, Joseph D. Tucker. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 24.11.2017.

Key Statistics from the National Survey of Family Growth: Vasectomy

MedlinePlus

... Birth Data NCHS Key Statistics from the National Survey of Family Growth - V Listing Recommend on Facebook ... What's this? Submit Button Related Sites NCHS Listservs Surveys and Data Collection Systems Vital Statistics: Birth Data ...

Online-to-offline models in HIV service delivery.

PubMed

Anand, Tarandeep; Nitpolprasert, Chattiya; Phanuphak, Nittaya

2017-09-01

Half the world's population has access to Internet and technologies, and utilization is near-ubiquitous among providers and key populations. Despite being so well connected; identifying, reaching and linking vulnerable populations to HIV clinical services remains a global challenge. This review highlights the emerging online-to-offline (O2O) models, their potential in scaling up services, and evaluating impact, and implications for future research. Globally, four major types of O2O models have been implemented, primarily in the West and Asia, especially among MSM and transgender women. These models have varying levels of impact in terms of reach, engagement, participation, linkage, and ability to track and monitor participants, and assess outcomes. Those integrated with offline sites enable seamless transition, dramatically reduce the O2O linkage time and demonstrate high linkage success (>73%). O2O models are ideal for at-risk, stigmatized, criminalized populations and for scaling-up biomedical prevention interventions such as preexposure and postexposure prophylaxis. O2O models represent novel and powerful solutions to reverse the pandemic and could help fill significant programmatic gaps in tracking individuals through HIV cascades. Providers, especially in resource-limited settings, could choose between a variety of current approaches highlighted in this review and employ no-cost or cost-effective technologies to transform their traditional models and leverage O2O models.

THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps

PubMed Central

Cheema, Jitender; Ellis, T. H. Noel; Dicks, Jo

2010-01-01

The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets. PMID:20494977

HTLV-1 Tax Functions as a Ubiquitin E3 Ligase for Direct IKK Activation via Synthesis of Mixed-Linkage Polyubiquitin Chains.

PubMed

Wang, Chong; Long, Wenying; Peng, Chao; Hu, Lin; Zhang, Qiong; Wu, Ailing; Zhang, Xiaoqing; Duan, Xiaotao; Wong, Catherine C L; Tanaka, Yuetsu; Xia, Zongping

2016-04-01

The HTLV-1 oncoprotein Tax plays a key role in CD4+ T cell transformation by promoting cell proliferation and survival, mainly through permanent activation of the NK-κB pathway and induction of many NF-κB target genes. Elucidating the underlying molecular mechanism is therefore critical in understanding HTLV-1-mediated transformation. Current studies have suggested multiple but controversial mechanisms regarding Tax-induced IKK activation mainly due to blending of primary Tax-induced IKK activation events and secondary IKK activation events induced by cytokines secreted by the primary Tax-induced IKK-NF-κB activation events. We reconstituted Tax-stimulated IKK activation in a cell-free system to dissect the essential cellular components for primary IKK activation by Tax and studied the underlying biochemical mechanism. We found that Tax is a putative E3 ubiquitin ligase, which, together with UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of free mixed-linkage polyubiquitin chains. These free mixed-linkage polyubiquitin chains are then responsible for direct IKK activation by binding to the NEMO subunit of IKK. Our studies revealed the biochemical function of Tax in the process of IKK activation, which utilizes the minimal cellular ubiquitination components for NF-κB activation.

HTLV-1 Tax Functions as a Ubiquitin E3 Ligase for Direct IKK Activation via Synthesis of Mixed-Linkage Polyubiquitin Chains

PubMed Central

Wang, Chong; Long, Wenying; Peng, Chao; Hu, Lin; Zhang, Qiong; Wu, Ailing; Zhang, Xiaoqing; Duan, Xiaotao; Wong, Catherine C. L.; Tanaka, Yuetsu; Xia, Zongping

2016-01-01

The HTLV-1 oncoprotein Tax plays a key role in CD4+ T cell transformation by promoting cell proliferation and survival, mainly through permanent activation of the NK-κB pathway and induction of many NF-κB target genes. Elucidating the underlying molecular mechanism is therefore critical in understanding HTLV-1-mediated transformation. Current studies have suggested multiple but controversial mechanisms regarding Tax-induced IKK activation mainly due to blending of primary Tax-induced IKK activation events and secondary IKK activation events induced by cytokines secreted by the primary Tax-induced IKK-NF-κB activation events. We reconstituted Tax-stimulated IKK activation in a cell-free system to dissect the essential cellular components for primary IKK activation by Tax and studied the underlying biochemical mechanism. We found that Tax is a putative E3 ubiquitin ligase, which, together with UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of free mixed-linkage polyubiquitin chains. These free mixed-linkage polyubiquitin chains are then responsible for direct IKK activation by binding to the NEMO subunit of IKK. Our studies revealed the biochemical function of Tax in the process of IKK activation, which utilizes the minimal cellular ubiquitination components for NF-κB activation. PMID:27082114

Ordered-subsets linkage analysis detects novel Alzheimer disease loci on chromosomes 2q34 and 15q22.

PubMed

Scott, William K; Hauser, Elizabeth R; Schmechel, Donald E; Welsh-Bohmer, Kathleen A; Small, Gary W; Roses, Allen D; Saunders, Ann M; Gilbert, John R; Vance, Jeffery M; Haines, Jonathan L; Pericak-Vance, Margaret A

2003-11-01

Alzheimer disease (AD) is a complex disorder characterized by a wide range, within and between families, of ages at onset of symptoms. Consideration of age at onset as a covariate in genetic-linkage studies may reduce genetic heterogeneity and increase statistical power. Ordered-subsets analysis includes continuous covariates in linkage analysis by rank ordering families by a covariate and summing LOD scores to find a subset giving a significantly increased LOD score relative to the overall sample. We have analyzed data from 336 markers in 437 multiplex (>/=2 sampled individuals with AD) families included in a recent genomic screen for AD loci. To identify genetic heterogeneity by age at onset, families were ordered by increasing and decreasing mean and minimum ages at onset. Chromosomewide significance of increases in the LOD score in subsets relative to the overall sample was assessed by permutation. A statistically significant increase in the nonparametric multipoint LOD score was observed on chromosome 2q34, with a peak LOD score of 3.2 at D2S2944 (P=.008) in 31 families with a minimum age at onset between 50 and 60 years. The LOD score in the chromosome 9p region previously linked to AD increased to 4.6 at D9S741 (P=.01) in 334 families with minimum age at onset between 60 and 75 years. LOD scores were also significantly increased on chromosome 15q22: a peak LOD score of 2.8 (P=.0004) was detected at D15S1507 (60 cM) in 38 families with minimum age at onset >/=79 years, and a peak LOD score of 3.1 (P=.0006) was obtained at D15S153 (62 cM) in 43 families with mean age at onset >80 years. Thirty-one families were contained in both 15q22 subsets, indicating that these results are likely detecting the same locus. There is little overlap in these subsets, underscoring the utility of age at onset as a marker of genetic heterogeneity. These results indicate that linkage to chromosome 9p is strongest in late-onset AD and that regions on chromosome 2q34 and 15q22 are linked to early-onset AD and very-late-onset AD, respectively.

Correlating regional natural hazards for global reinsurance risk assessment

NASA Astrophysics Data System (ADS)

Steptoe, Hamish; Maynard, Trevor; Economou, Theo; Fox, Helen; Wallace, Emily; Maisey, Paul

2016-04-01

Concurrent natural hazards represent an uncertainty in assessing exposure for the insurance industry. The recently implemented Solvency II Directive requires EU insurance companies to fully understand and justify their capital reserving and portfolio decisions. Lloyd's, the London insurance and reinsurance market, commissioned the Met Office to investigate the dependencies between different global extreme weather events (known to the industry as perils), and the mechanisms for these dependencies, with the aim of helping them assess their compound risk to the exposure of multiple simultaneous hazards. In this work, we base the analysis of hazard-to-hazard dependency on the interaction of different modes of global and regional climate variability. Lloyd's defined 16 key hazard regions, including Australian wildfires, flooding in China and EU windstorms, and we investigate the impact of 10 key climate modes on these areas. We develop a statistical model that facilitates rapid risk assessment whilst allowing for both temporal auto-correlation and, crucially, interdependencies between drivers. The simulator itself is built conditionally using autoregressive regression models for each driver conditional on the others. Whilst the baseline assumption within the (re)insurance industry is that different natural hazards are independent of each other, the assumption of independence of meteorological risks requires greater justification. Although our results suggest that most of the 120 hazard-hazard connections considered are likely to be independent of each other, 13 have significant dependence arising from one or more global modes of climate variability. This allows us to create a matrix of linkages describing the hazard dependency structure that Lloyd's can use to inform their understanding of risk.

Tourette's syndrome is not associated with interleukin-10 receptor 1 variants on chromosome 11q23.3.

PubMed

Kindler, Jochen; Schosser, Alexandra; Stamenkovic, Mara; Schloegelhofer, Monika; Leisch, Friedrich; Hornik, Kurt; Aschauer, Harald; Gasche, Christoph

2008-01-15

Interleukin-10 receptor 1 (IL-10R1) single nucleotide polymorphisms, located on chromosome 11q23 - a strong candidate for linkage with Tourette's syndrome (TS) - have been investigated for association with TS. DNA of 77 patients with a DSM-IV (Diagnostic and Statistical Manual IV) diagnosis of TS and 250 healthy controls was genotyped. IL-10R1 was not associated with TS.

Misclassification of childhood homicide on death certificates.

PubMed Central

Lapidus, G D; Gregorio, D I; Hansen, H

1990-01-01

Suspect classification of homicide deaths of Connecticut residents under 20 years of age was noted for 29 percent of cases examined. Misclassification was attributed to incomplete or erroneous information recorded on the death certificates, rather than errors in the designation of ICD-9 homicide codes. The results have important implications in the interpretation of vital statistics when homicide is listed as the cause of death and underscore the value of record linkage systems. PMID:2297072

Stochastically generating tree diameter lists to populate forest stands based on the linkage variables forest type and stand age

Treesearch

Bernard R. Parresol; F. Thomas Lloyd

2003-01-01

Forest inventory data were used to develop a standage-driven, stochastic predictor of unit-area, frequency weighted lists of breast high tree diameters (DBH). The average of mean statistics from 40 simulation prediction sets of an independent 78-plot validation dataset differed from the observed validation means by 0.5 cm for DBH, and by 12 trees/h for density. The 40...

Matrix Density-induced Mechanoregulation of Breast Cell Phenotype, Signaling, and Gene Expression through a FAK ERK Linkage

DTIC Science & Technology

2009-12-10

sites of integrin-clustering that link the actin cytoskeleton to the extracellular matrix (ECM; (Burridge et al., 1988)). The primary functions of...Hall, 1992). Furthermore, in fibroblasts, focal adhesion kinase (FAK), a key FA signaling molecule, is necessary for mechanosensing (Geiger et al...promotes FAK activation through phosphorylation on Y397 and Y925, followed by FAK- dependent extracellular signal-regulated kinase (ERK) phosphorylation

Enantioselective syntheses of lignin models: an efficient synthesis of B-O-4 dimers and trimers by using the Evans chiral auxiliary

Treesearch

Costyl N. Njiojob; Joseph J. Bozell; Brian K. Long; Thomas Elder; Rebecca E. Key; William T. Hartwig

2016-01-01

We describe an efficient five-step, enantioselective synthesis of (R,R)- and (S,S)-lignin dimer models possessing a B-O-4 linkage, by using the Evans chiral aldol reaction as a key step. Mitsunobu inversion of the (R,R)- or (S,S)-isomers generates the corresponding (R,S)- and (S,R)-diastereomers. We further extend this approach to the...

Manager-Organization Linkages: The Impact of Changing Work Environments.

DTIC Science & Technology

1979-11-01

later organizational identification.. .The reference to the company as a family , for example, has become a management cliche" (Katz & Kahn, 1978, p...34personal significance reinforcement" to be a key ingredient in the organizational commitment of managers in both business and government settings...of women into management seems, inevitably, to be an increase in the number of dual-caieer families (Hall & Hall, 1978" Schein, 1978). This, in turn

Statistical Inference and Simulation with StatKey

ERIC Educational Resources Information Center

Quinn, Anne

2016-01-01

While looking for an inexpensive technology package to help students in statistics classes, the author found StatKey, a free Web-based app. Not only is StatKey useful for students' year-end projects, but it is also valuable for helping students learn fundamental content such as the central limit theorem. Using StatKey, students can engage in…

Identification of linkages between potential Environmental and Social Impacts of Surface Mining and Ecosystem Services in Thar Coal field, Pakistan

NASA Astrophysics Data System (ADS)

Hina, A.

2017-12-01

Although Thar coal is recognized to be one of the most abundant fossil fuel that could meet the need to combat energy crisis of Pakistan, but there still remains a challenge to tackle the associated environmental and socio-ecological changes and its linkage to the provision of ecosystem services of the region. The study highlights the importance of considering Ecosystem service assessment to be undertaken in all strategic Environmental and Social Assessments of Thar coal field projects. The three-step approach has been formulated to link the project impacts to the provision of important ecosystem services; 1) Identification of impact indicators and parameters by analyzing the environmental and social impacts of surface mining in Thar Coal field through field investigation, literature review and stakeholder consultations; 2) Ranking of parameters and criteria alternatives using Multi-criteria Decision Analysis(MCDA) tool: (AHP method); 3) Using ranked parameters as a proxy to prioritize important ecosystem services of the region; The ecosystem services that were prioritized because of both high significance of project impact and high project dependence are highlighted as: Water is a key ecosystem service to be addressed and valued due to its high dependency in the area for livestock, human wellbeing, agriculture and other purposes. Crop production related to agricultural services, in association with supply services such as soil quality, fertility, and nutrient recycling and water retention need to be valued. Cultural services affected in terms of land use change and resettlement and rehabilitation factors are recommended to be addressed. The results of the analysis outline a framework of identifying these linkages as key constraints to foster the emergence of green growth and development in Pakistan. The practicality of implementing these assessments requires policy instruments and strategies to support human well-being and social inclusion while minimizing environmental degradation and loss of ecosystem services. Keywords Ecosystem service assessment; Environmental and Social Impact Assessment; coal mining; Thar Coal Field; Sustainable development

Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium

PubMed Central

Shete, Sanjay; Lau, Ching C; Houlston, Richard S; Claus, Elizabeth B; Barnholtz-Sloan, Jill; Lai, Rose; Il’yasova, Dora; Schildkraut, Joellen; Sadetzki, Siegal; Johansen, Christoffer; Bernstein, Jonine L; Olson, Sara H; Jenkins, Robert B; Yang, Ping; Vick, Nicholas A; Wrensch, Margaret; Davis, Faith G; McCarthy, Bridget J; Leung, Eastwood Hon-chiu; Davis, Caleb; Cheng, Rita; Hosking, Fay J; Armstrong, Georgina N; Liu, Yanhong; Yu, Robert K; Henriksson, Roger; Consortium, The Gliogene; Melin, Beatrice S; Bondy, Melissa L

2011-01-01

Gliomas, which generally have a poor prognosis, are the most common primary malignant brain tumors in adults. Recent genome-wide association studies have demonstrated that inherited susceptibility plays a role in the development of glioma. Although first-degree relatives of patients exhibit a two-fold increased risk of glioma, the search for susceptibility loci in familial forms of the disease has been challenging because the disease is relatively rare, fatal, and heterogeneous, making it difficult to collect sufficient biosamples from families for statistical power. To address this challenge, the Genetic Epidemiology of Glioma International Consortium (Gliogene) was formed to collect DNA samples from families with two or more cases of histologically confirmed glioma. In this study, we present results obtained from 46 U.S. families in which multipoint linkage analyses were undertaken using nonparametric (model-free) methods. After removal of high linkage disequilibrium SNPs, we obtained a maximum nonparametric linkage score (NPL) of 3.39 (P=0.0005) at 17q12–21.32 and the Z-score of 4.20 (P=0.000007). To replicate our findings, we genotyped 29 independent U.S. families and obtained a maximum NPL score of 1.26 (P=0.008) and the Z-score of 1.47 (P=0.035). Accounting for the genetic heterogeneity using the ordered subset analysis approach, the combined analyses of 75 families resulted in a maximum NPL score of 3.81 (P=0.00001). The genomic regions we have implicated in this study may offer novel insights into glioma susceptibility, focusing future work to identify genes that cause familial glioma. PMID:22037877

Comprehensive multi-stage linkage analyses identify a locus for adult height on chromosome 3p in a healthy Caucasian population.

PubMed

Ellis, Justine A; Scurrah, Katrina J; Duncan, Anna E; Lamantia, Angela; Byrnes, Graham B; Harrap, Stephen B

2007-04-01

There have been a number of genome-wide linkage studies for adult height in recent years. These studies have yielded few well-replicated loci, and none have been further confirmed by the identification of associated gene variants. The inconsistent results may be attributable to the fact that few studies have combined accurate phenotype measures with informative statistical modelling in healthy populations. We have performed a multi-stage genome-wide linkage analysis for height in 275 adult sibling pairs drawn randomly from the Victorian Family Heart Study (VFHS), a healthy population-based Caucasian cohort. Height was carefully measured in a standardised fashion on regularly calibrated equipment. Following genome-wide identification of a peak Z-score of 3.14 on chromosome 3 at 69 cM, we performed a fine-mapping analysis of this region in an extended sample of 392 two-generation families. We used a number of variance components models that incorporated assortative mating and shared environment effects, and we observed a peak LOD score of approximately 3.5 at 78 cM in four of the five models tested. We also demonstrated that the most prevalent model in the literature gave the worst fit, and the lowest LOD score (2.9) demonstrating the importance of appropriate modelling. The region identified in this study replicates the results of other genome-wide scans of height and bone-related phenotypes, strongly suggesting the presence of a gene important in bone growth on chromosome 3p. Association analyses of relevant candidate genes should identify the genetic variants responsible for the chromosome 3p linkage signal in our population.

Affected sib pair tests in inbred populations.

PubMed

Liu, W; Weir, B S

2004-11-01

The affected-sib-pair (ASP) method for detecting linkage between a disease locus and marker loci was first established 50 years ago, and since then numerous modifications have been made. We modify two identity-by-state (IBS) test statistics of Lange (Lange, 1986a, 1986b) to allow for inbreeding in the population. We evaluate the power and false positive rates of the modified tests under three disease models, using simulated data. Before estimating false positive rates, we demonstrate that IBS tests are tests of both linkage and linkage disequilibrium between marker and disease loci. Therefore, the null hypothesis of IBS tests should be no linkage and no LD. When the population inbreeding coefficient is large, the false positive rates of Lange's tests become much larger than the nominal value, while those of our modified tests remain close to the nominal value. To estimate power with a controlled false positive rate, we choose the cutoff values based on simulated datasets under the null hypothesis, so that both Lange's tests and the modified tests generate same false positive rate. The powers of Lange's z-test and our modified z-test are very close and do not change much with increasing inbreeding. The power of the modified chi-square test also stays stable when the inbreeding coefficient increases. However, the power of Lange's chi-square test increases with increasing inbreeding, and is larger than that of our modified chi-square test for large inbreeding coefficients. The power is high under a recessive disease model for both Lange's tests and the modified tests, though the power is low for additive and dominant disease models. Allowing for inbreeding is therefore appropriate, at least for diseases known to be recessive.

Development of a database of health insurance claims: standardization of disease classifications and anonymous record linkage.

PubMed

Kimura, Shinya; Sato, Toshihiko; Ikeda, Shunya; Noda, Mitsuhiko; Nakayama, Takeo

2010-01-01

Health insurance claims (ie, receipts) record patient health care treatments and expenses and, although created for the health care payment system, are potentially useful for research. Combining different types of receipts generated for the same patient would dramatically increase the utility of these receipts. However, technical problems, including standardization of disease names and classifications, and anonymous linkage of individual receipts, must be addressed. In collaboration with health insurance societies, all information from receipts (inpatient, outpatient, and pharmacy) was collected. To standardize disease names and classifications, we developed a computer-aided post-entry standardization method using a disease name dictionary based on International Classification of Diseases (ICD)-10 classifications. We also developed an anonymous linkage system by using an encryption code generated from a combination of hash values and stream ciphers. Using different sets of the original data (data set 1: insurance certificate number, name, and sex; data set 2: insurance certificate number, date of birth, and relationship status), we compared the percentage of successful record matches obtained by using data set 1 to generate key codes with the percentage obtained when both data sets were used. The dictionary's automatic conversion of disease names successfully standardized 98.1% of approximately 2 million new receipts entered into the database. The percentage of anonymous matches was higher for the combined data sets (98.0%) than for data set 1 (88.5%). The use of standardized disease classifications and anonymous record linkage substantially contributed to the construction of a large, chronologically organized database of receipts. This database is expected to aid in epidemiologic and health services research using receipt information.

Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.)

PubMed Central

2012-01-01

Background Pigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea. Results A population of 186 F2:3 lines derived from an intra-specific cross between inbred lines ‘Pusa Dwarf’ and ‘HDM04-1’ was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant. Conclusions A large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant type and maturity traits in pigeonpea. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for utilization in the pigeonpea improvement. PMID:23043321

Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks.

PubMed

Zhao, Huiying; Nyholt, Dale R; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

2017-06-14

Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path .

Continuous cost movement models

NASA Technical Reports Server (NTRS)

Limp, W. Fredrick

1991-01-01

Use of current space imaging systems and airborne platforms has direct use in survey design and site location when used in concert with a comprehensive GIS environment. Local conditions and site physical and chemical properties are key factors in successful applications. Conjoining of environmental constraints and site properties are present for the later prehistoric occupations in the Arkansas and Mississippi River areas. Direct linkages between comprehensive site databases and satellite images can be used to evaluate site distributions for research and management.

Network analysis to detect common strategies in Italian foreign direct investment

NASA Astrophysics Data System (ADS)

De Masi, G.; Giovannetti, G.; Ricchiuti, G.

2013-03-01

In this paper we reconstruct and discuss the network of Italian firms investing abroad, exploiting information from complex network analysis. This method, detecting the key nodes of the system (both in terms of firms and countries of destination), allows us to single out the linkages among firms without ex-ante priors. Moreover, through the examination of affiliates’ economic activity, it allows us to highlight different internationalization strategies of “leaders” in different manufacturing sectors.

Satellite freeze forecast system

NASA Technical Reports Server (NTRS)

Martsolf, J. D. (Principal Investigator)

1983-01-01

Provisions for back-up operations for the satellite freeze forecast system are discussed including software and hardware maintenance and DS/1000-1V linkage; troubleshooting; and digitized radar usage. The documentation developed; dissemination of data products via television and the IFAS computer network; data base management; predictive models; the installation of and progress towards the operational status of key stations; and digital data acquisition are also considered. The d addition of dew point temperature into the P-model is outlined.

INVESTIGATING ALTERNATIVES TO THE FISH EARLY-LIFE STAGE TEST: A STRATEGY FOR DISCOVERING AND ANNOTATING ADVERSE OUTCOME PATHWAYS FOR EARLY FISH DEVELOPMENT

PubMed Central

Villeneuve, Daniel; Volz, David C; Embry, Michelle R; Ankley, Gerald T; Belanger, Scott E; Léonard, Marc; Schirmer, Kristin; Tanguay, Robert; Truong, Lisa; Wehmas, Leah

2014-01-01

The fish early-life stage (FELS) test (Organisation for Economic Co-operation and Development [OECD] test guideline 210) is the primary test used internationally to estimate chronic fish toxicity in support of ecological risk assessments and chemical management programs. As part of an ongoing effort to develop efficient and cost-effective alternatives to the FELS test, there is a need to identify and describe potential adverse outcome pathways (AOPs) relevant to FELS toxicity. To support this endeavor, the authors outline and illustrate an overall strategy for the discovery and annotation of FELS AOPs. Key events represented by major developmental landmarks were organized into a preliminary conceptual model of fish development. Using swim bladder inflation as an example, a weight-of-evidence–based approach was used to support linkage of key molecular initiating events to adverse phenotypic outcomes and reduced young-of-year survival. Based on an iterative approach, the feasibility of using key events as the foundation for expanding a network of plausible linkages and AOP knowledge was explored and, in the process, important knowledge gaps were identified. Given the scope and scale of the task, prioritization of AOP development was recommended and key research objectives were defined relative to factors such as current animal-use restrictions in the European Union and increased demands for fish toxicity data in chemical management programs globally. The example and strategy described are intended to guide collective efforts to define FELS-related AOPs and develop resource-efficient predictive assays that address the toxicological domain of the OECD 210 test. Environ Toxicol Chem 2014;33:158–169. © 2013 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. PMID:24115264

Supplement to CCM.D-K4 'Hydrometer' report: linkage of EURAMET.M.D-K4 comparison, SIM.M.D-K4 comparison and the supplementary SIM.M.D-S2 to CCM.D-K4 'Hydrometer'

NASA Astrophysics Data System (ADS)

Lorefice, S.; Becerra, L. O.

2017-01-01

Evaluation of different types of comparisons to a common set of reference values of a CIPM key comparison is essential to satisfy the concept of the CIPM Mutual Recognition Arrangement (CIPM MRA), where the DoEs of any participant who took part in comparisons should be within the Calibration and Measurement Capability (CMC) section of the CIPM MRA Key Comparison Data Base. The subject of this supplementary report is therefore to present the equivalence of each National Metrological Institute (NMI) participant in the CCM.D-K4 'Hydrometer' key comparison, which was performed in the density range 600 kg/m3 to 2000 kg/m3 at the temperature of 20 °C, and the linkage of the European and Inter-American NMI results performed in the RMO.M.D-K4 comparisons as well as those of the supplementary SIM.M.D-S2 to the common set of KCRVs of the CCM.D-K4 'Hydrometer'. The linking procedure has been obtained by numerical simulation, based on the Monte Carlo method, in which the differences in the results of the different comparison between the intended laboratory and one or more linking laboratory/ies, which took part in both comparisons, are correlated with a continuous function describing the DoEs of the linking laboratory/ies with respect to the common set of KCRVs of the CCM.D-K4. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

[Encryption technique for linkable anonymizing].

PubMed

Okamoto, Etsuji

2004-06-01

Linkage of different records such as health insurance claims or medical records for the purpose of cohort studies or cancer registration usually requires matching with personal names and other personally identifiable data. The present study was conducted to examine the possibility of performing such privacy-sensitive procedures in a "linkable anonymizing" manner using encryption. While bidirectional communication entails encryption and deciphering, necessitating both senders and receivers sharing a common secret "key", record linkage entails only encryption and not deciphering because researchers do not need to know the identity of the linked person. This unidirectional nature relieves researchers from the historical problem of "key sharing" and enables data holders such as municipal governments and insurers to encrypt personal names in a relatively easy manner. The author demonstrates an encryption technique using readily available spread-sheet software, Microsoft Excel in a step-by-step fashion. Encoding Chinese characters into the numeric JIS codes and replacing the codes with a randomly assigned case-sensitive alphabet, all names of Japanese nationals will be encrypted into gibberish strings of alphabet, which can not be deciphered without the secret key. Data holders are able to release personal data without sacrificing privacy, even when accidental leakage occurs and researchers are still able to link records of the same name because encrypted texts, although gibberish, are unique to each name. Such a technical assurance of privacy protection is expected to satisfy the Privacy Protection Act or the Ethical Guidelines for Epidemiological Research and enhance public health research. Traditional encryption techniques, however, cannot be applied to cancer or stroke registration, because the registrar receives reports from numerous unspecified senders. The new public key encryption technique will enable disease registry in a linkable anonymizing manner. However various technical problems such as complexity, difficulties in registrar inquiries and risk of code-breaking make the encryption technique unsuitable for disease registry in the foreseeable future.

Health-industry linkages for local health: reframing policies for African health system strengthening

PubMed Central

Mackintosh, Maureen; Mugwagwa, Julius; Banda, Geoffrey; Tibandebage, Paula; Tunguhole, Jires; Wangwe, Samuel; Karimi Njeru, Mercy

2018-01-01

Abstract The benefits of local production of pharmaceuticals in Africa for local access to medicines and to effective treatment remain contested. There is scepticism among health systems experts internationally that production of pharmaceuticals in sub-Saharan Africa (SSA) can provide competitive prices, quality and reliability of supply. Meanwhile low-income African populations continue to suffer poor access to a broad range of medicines, despite major international funding efforts. A current wave of pharmaceutical industry investment in SSA is associated with active African government promotion of pharmaceuticals as a key sector in industrialization strategies. We present evidence from interviews in 2013–15 and 2017 in East Africa that health system actors perceive these investments in local production as an opportunity to improve access to medicines and supplies. We then identify key policies that can ensure that local health systems benefit from the investments. We argue for a ‘local health’ policy perspective, framed by concepts of proximity and positionality, which works with local priorities and distinct policy time scales and identifies scope for incentive alignment to generate mutually beneficial health–industry linkages and strengthening of both sectors. We argue that this local health perspective represents a distinctive shift in policy framing: it is not necessarily in conflict with ‘global health’ frameworks but poses a challenge to some of its underlying assumptions. PMID:29562286

Prediction for potential landslide zones using seismic amplitude in Liwan gas field, northern South China Sea

NASA Astrophysics Data System (ADS)

Li, Xishuang; Liu, Baohua; Liu, Lejun; Zheng, Jiewen; Zhou, Songwang; Zhou, Qingjie

2017-12-01

The Liwan (Lw) gas field located in the northern slope of the South China Sea (SCS) is extremely complex for its sea-floor topograghy, which is a huge challenge for the safety of subsea facilities. It is economically impractical to obtain parameters for risk assessment of slope stability through a large amount of sampling over the whole field. The linkage between soil shear strength and seabed peak amplitude derived from 2D/3D seismic data is helpful for understanding the regional slope-instability risk. In this paper, the relationships among seabed peak, acoustic impedance and shear strength of shallow soil in the study area were discussed based on statistical analysis results. We obtained a similar relationship to that obtained in other deep-water areas. There is a positive correlation between seabed peak amplitude and acoustic impedance and an exponential relationship between acoustic impedance and shear strength of sediment. The acoustic impedance is the key factor linking the seismic amplitude and shear strength. Infinite slope stability analysis results indicate the areas have a high potential of shallow landslide on slopes exceeding 15° when the thickness of loose sediments exceeds 8 m in the Lw gas field. Our prediction shows that they are mainly located in the heads and walls of submarine canyons.

[Linkage analysis of susceptibility loci in 2 target chromosomes in pedigrees with paranoid schizophrenia and undifferentiated schizophrenia].

PubMed

Zeng, Li-ping; Hu, Zheng-mao; Mu, Li-li; Mei, Gui-sen; Lu, Xiu-ling; Zheng, Yong-jun; Li, Pei-jian; Zhang, Ying-xue; Pan, Qian; Long, Zhi-gao; Dai, He-ping; Zhang, Zhuo-hua; Xia, Jia-hui; Zhao, Jing-ping; Xia, Kun

2011-06-01

To investigate the relationship of susceptibility loci in chromosomes 1q21-25 and 6p21-25 and schizophrenia subtypes in Chinese population. A genomic scan and parametric and non-parametric analyses were performed on 242 individuals from 36 schizophrenia pedigrees, including 19 paranoid schizophrenia and 17 undifferentiated schizophrenia pedigrees, from Henan province of China using 5 microsatellite markers in the chromosome region 1q21-25 and 8 microsatellite markers in the chromosome region 6p21-25, which were the candidates of previous studies. All affected subjects were diagnosed and typed according to the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revised (DSM-IV-TR; American Psychiatric Association, 2000). All subjects signed informed consent. In chromosome 1, parametric analysis under the dominant inheritance mode of all 36 pedigrees showed that the maximum multi-point heterogeneity Log of odds score method (HLOD) score was 1.33 (α = 0.38). The non-parametric analysis and the single point and multi-point nonparametric linkage (NPL) scores suggested linkage at D1S484, D1S2878, and D1S196. In the 19 paranoid schizophrenias pedigrees, linkage was not observed for any of the 5 markers. In the 17 undifferentiated schizophrenia pedigrees, the multi-point NPL score was 1.60 (P= 0.0367) at D1S484. The single point NPL score was 1.95(P= 0.0145) and the multi-point NPL score was 2.39 (P= 0.0041) at D1S2878. Additionally, the multi-point NPL score was 1.74 (P= 0.0255) at D1S196. These same three loci showed suggestive linkage during the integrative analysis of all 36 pedigrees. In chromosome 6, parametric linkage analysis under the dominant and recessive inheritance and the non-parametric linkage analysis of all 36 pedigrees and the 17 undifferentiated schizophrenia pedigrees, linkage was not observed for any of the 8 markers. In the 19 paranoid schizophrenias pedigrees, parametric analysis showed that under recessive inheritance mode the maximum single-point HLOD score was 1.26 (α = 0.40) and the multi-point HLOD was 1.12 (α = 0.38) at D6S289 in the chromosome 6p23. In nonparametric analysis, the single-point NPL score was 1.52 (P= 0.0402) and the multi-point NPL score was 1.92 (P= 0.0206) at D6S289. Susceptibility genes correlated with undifferentiated schizophrenia pedigrees from D1S484, D1S2878, D1S196 loci, and those correlated with paranoid schizophrenia pedigrees from D6S289 locus are likely present in chromosome regions 1q23.3 and 1q24.2, and chromosome region 6p23, respectively.

Representing Micro-Macro Linkages by Actor-Based Dynamic Network Models

PubMed Central

Snijders, Tom A.B.; Steglich, Christian E.G.

2014-01-01

Stochastic actor-based models for network dynamics have the primary aim of statistical inference about processes of network change, but may be regarded as a kind of agent-based models. Similar to many other agent-based models, they are based on local rules for actor behavior. Different from many other agent-based models, by including elements of generalized linear statistical models they aim to be realistic detailed representations of network dynamics in empirical data sets. Statistical parallels to micro-macro considerations can be found in the estimation of parameters determining local actor behavior from empirical data, and the assessment of goodness of fit from the correspondence with network-level descriptives. This article studies several network-level consequences of dynamic actor-based models applied to represent cross-sectional network data. Two examples illustrate how network-level characteristics can be obtained as emergent features implied by micro-specifications of actor-based models. PMID:25960578

Reframing Serial Murder Within Empirical Research.

PubMed

Gurian, Elizabeth A

2017-04-01

Empirical research on serial murder is limited due to the lack of consensus on a definition, the continued use of primarily descriptive statistics, and linkage to popular culture depictions. These limitations also inhibit our understanding of these offenders and affect credibility in the field of research. Therefore, this comprehensive overview of a sample of 508 cases (738 total offenders, including partnered groups of two or more offenders) provides analyses of solo male, solo female, and partnered serial killers to elucidate statistical differences and similarities in offending and adjudication patterns among the three groups. This analysis of serial homicide offenders not only supports previous research on offending patterns present in the serial homicide literature but also reveals that empirically based analyses can enhance our understanding beyond traditional case studies and descriptive statistics. Further research based on these empirical analyses can aid in the development of more accurate classifications and definitions of serial murderers.

Linking Stream Dissolved Oxygen with the Dynamic Environmental Drivers across the Pacific Coast of U.S.A.

NASA Astrophysics Data System (ADS)

Araya, F. Z.; Abdul-Aziz, O. I.

2017-12-01

This study utilized a systematic data analytics approach to determine the relative linkages of stream dissolved oxygen (DO) with the hydro-climatic and biogeochemical drivers across the U.S. Pacific Coast. Multivariate statistical techniques of Pearson correlation matrix, principal component analysis, and factor analysis were applied to a complex water quality dataset (1998-2015) at 35 water quality monitoring stations of USGS NWIS and EPA STORET. Power-law based partial least squares regression (PLSR) models with a bootstrap Monte Carlo procedure (1000 iterations) were developed to reliably estimate the relative linkages by resolving multicollinearity (Nash-Sutcliffe Efficiency, NSE = 0.50-0.94). Based on the dominant drivers, four environmental regimes have been identified and adequately described the system-data variances. In Pacific North West and Southern California, water temperature was the most dominant driver of DO in majority of the streams. However, in Central and Northern California, stream DO was controlled by multiple drivers (i.e., water temperature, pH, stream flow, and total phosphorus), exhibiting a transitional environmental regime. Further, total phosphorus (TP) appeared to be the limiting nutrient for most streams. The estimated linkages and insights would be useful to identify management priorities to achieve healthy coastal stream ecosystems across the Pacific Coast of U.S.A. and similar regions around the world. Keywords: Data analytics, water quality, coastal streams, dissolved oxygen, environmental regimes, Pacific Coast, United States.

Pseudoautosomal region in schizophrenia: linkage analysis of seven loci by sib-pair and lod-score methods.

PubMed

d'Amato, T; Waksman, G; Martinez, M; Laurent, C; Gorwood, P; Campion, D; Jay, M; Petit, C; Savoye, C; Bastard, C

1994-05-01

In a previous study, we reported a nonrandom segregation between schizophrenia and the pseudoautosomal locus DXYS14 in a sample of 33 sibships. That study has been extended by the addition of 16 new sibships from 16 different families. Data from six other loci of the pseudoautosomal region and of the immediately adjacent part of the X specific region have also been analyzed. Two methods of linkage analysis were used: the affected sibling pair (ASP) method and the lod-score method. Lod-score analyses were performed on the basis of three different models--A, B, and C--all shown to be consistent with the epidemiological data on schizophrenia. No clear evidence for linkage was obtained with any of these models. However, whatever the genetic model and the disease classification, maximum lod scores were positive with most of the markers, with the highest scores generally being obtained for the DXYS14 locus. When the ASP method was used, the earlier finding of nonrandom segregation between schizophrenia and the DXYS14 locus was still supported in this larger data set, at an increased level of statistical significance. Findings of ASP analyses were not significant for the other loci. Thus, findings obtained from analyses using the ASP method, but not the lod-score method, were consistent with the pseudoautosomal hypothesis for schizophrenia.

Linkage of osteoporosis to chromosome 20p12 and association to BMP2.

PubMed

Styrkarsdottir, Unnur; Cazier, Jean-Baptiste; Kong, Augustine; Rolfsson, Ottar; Larsen, Helene; Bjarnadottir, Emma; Johannsdottir, Vala D; Sigurdardottir, Margret S; Bagger, Yu; Christiansen, Claus; Reynisdottir, Inga; Grant, Struan F A; Jonasson, Kristjan; Frigge, Michael L; Gulcher, Jeffrey R; Sigurdsson, Gunnar; Stefansson, Kari

2003-12-01

Osteoporotic fractures are a major cause of morbidity and mortality in ageing populations. Osteoporosis, defined as low bone mineral density (BMD) and associated fractures, have significant genetic components that are largely unknown. Linkage analysis in a large number of extended osteoporosis families in Iceland, using a phenotype that combines osteoporotic fractures and BMD measurements, showed linkage to Chromosome 20p12.3 (multipoint allele-sharing LOD, 5.10; p value, 6.3 x 10(-7)), results that are statistically significant after adjusting for the number of phenotypes tested and the genome-wide search. A follow-up association analysis using closely spaced polymorphic markers was performed. Three variants in the bone morphogenetic protein 2 (BMP2) gene, a missense polymorphism and two anonymous single nucleotide polymorphism haplotypes, were determined to be associated with osteoporosis in the Icelandic patients. The association is seen with many definitions of an osteoporotic phenotype, including osteoporotic fractures as well as low BMD, both before and after menopause. A replication study with a Danish cohort of postmenopausal women was conducted to confirm the contribution of the three identified variants. In conclusion, we find that a region on the short arm of Chromosome 20 contains a gene or genes that appear to be a major risk factor for osteoporosis and osteoporotic fractures, and our evidence supports the view that BMP2 is at least one of these genes.

Sex versus asex: An analysis of the role of variance conversion.

PubMed

Lewis-Pye, Andrew E M; Montalbán, Antonio

2017-04-01

The question as to why most complex organisms reproduce sexually remains a very active research area in evolutionary biology. Theories dating back to Weismann have suggested that the key may lie in the creation of increased variability in offspring, causing enhanced response to selection. Under appropriate conditions, selection is known to result in the generation of negative linkage disequilibrium, with the effect of recombination then being to increase genetic variance by reducing these negative associations between alleles. It has therefore been a matter of significant interest to understand precisely those conditions resulting in negative linkage disequilibrium, and to recognise also the conditions in which the corresponding increase in genetic variation will be advantageous. Here, we prove rigorous results for the multi-locus case, detailing the build up of negative linkage disequilibrium, and describing the long term effect on population fitness for models with and without bounds on fitness contributions from individual alleles. Under the assumption of large but finite bounds on fitness contributions from alleles, the non-linear nature of the effect of recombination on a population presents serious obstacles in finding the genetic composition of populations at equilibrium, and in establishing convergence to those equilibria. We describe techniques for analysing the long term behaviour of sexual and asexual populations for such models, and use these techniques to establish conditions resulting in higher fitnesses for sexually reproducing populations. Copyright © 2017 Elsevier Inc. All rights reserved.

Endemism hotspots are linked to stable climatic refugia

PubMed Central

Noss, Reed

2017-01-01

Background Centres of endemism have received much attention from evolutionists, biogeographers, ecologists and conservationists. Climatic stability is often cited as a major reason for the occurrences of these geographic concentrations of species which are not found anywhere else. The proposed linkage between endemism and climatic stability raises unanswered questions about the persistence of biodiversity during the present era of rapidly changing climate. Key Questions The current status of evidence linking geographic centres of endemism to climatic stability over evolutionary time was examined. The following questions were asked. Do macroecological analyses support such an endemism–stability linkage? Do comparative studies find that endemic species display traits reflecting evolution in stable climates? Will centres of endemism in microrefugia or macrorefugia remain relatively stable and capable of supporting high biological diversity into the future? What are the implications of the endemism–stability linkage for conservation? Conclusions Recent work using the concept of climate change velocity supports the classic idea that centres of endemism occur where past climatic fluctuations have been mild and where mountainous topography or favourable ocean currents contribute to creating refugia. Our knowledge of trait differences between narrow endemics and more widely distributed species remains highly incomplete. Current knowledge suggests that centres of endemism will remain relatively climatically buffered in the future, with the important caveat that absolute levels of climatic change and species losses in these regions may still be large. PMID:28064195

The Building Game: From Enumerative Combinatorics to Conformational Diffusion

NASA Astrophysics Data System (ADS)

Johnson-Chyzhykov, Daniel; Menon, Govind

2016-08-01

We study a discrete attachment model for the self-assembly of polyhedra called the building game. We investigate two distinct aspects of the model: (i) enumerative combinatorics of the intermediate states and (ii) a notion of Brownian motion for the polyhedral linkage defined by each intermediate that we term conformational diffusion. The combinatorial configuration space of the model is computed for the Platonic, Archimedean, and Catalan solids of up to 30 faces, and several novel enumerative results are generated. These represent the most exhaustive computations of this nature to date. We further extend the building game to include geometric information. The combinatorial structure of each intermediate yields a systems of constraints specifying a polyhedral linkage and its moduli space. We use a random walk to simulate a reflected Brownian motion in each moduli space. Empirical statistics of the random walk may be used to define the rates of transition for a Markov process modeling the process of self-assembly.

Opportunities and challenges for real-world studies on chronic inflammatory joint diseases through data enrichment and collaboration between national registers: the Nordic example

PubMed Central

Chatzidionysiou, Katerina; Hetland, Merete Lund; Frisell, Thomas; Di Giuseppe, Daniela; Hellgren, Karin; Glintborg, Bente; Nordström, Dan; Aaltonen, Kalle; Törmänen, Minna RK; Klami Kristianslund, Eirik; Kvien, Tore K; Provan, Sella A; Guðbjörnsson, Bjorn; Dreyer, Lene; Kristensen, Lars Erik; Jørgensen, Tanja Schjødt; Jacobsson, Lennart; Askling, Johan

2018-01-01

There are increasing needs for detailed real-world data on rheumatic diseases and their treatments. Clinical register data are essential sources of information that can be enriched through linkage to additional data sources such as national health data registers. Detailed analyses call for international collaborative observational research to increase the number of patients and the statistical power. Such linkages and collaborations come with legal, logistic and methodological challenges. In collaboration between registers of inflammatory arthritides in Sweden, Denmark, Norway, Finland and Iceland, we plan to enrich, harmonise and standardise individual data repositories to investigate analytical approaches to multisource data, to assess the viability of different logistical approaches to data protection and sharing and to perform collaborative studies on treatment effectiveness, safety and health-economic outcomes. This narrative review summarises the needs and potentials and the challenges that remain to be overcome in order to enable large-scale international collaborative research based on clinical and other types of data. PMID:29682328

Mapping of a gene responsible for dermatitis in NOA (Naruto Research Institute Otsuka Atrichia) mice, an animal model of allergic dermatitis.

PubMed

Natori, K; Tamari, M; Watanabe, O; Onouchi, Y; Shiomoto, Y; Kubo, S; Nakamura, Y

1999-01-01

The NOA (Naruto Research Institute Otsuka Atrichia) mouse is an animal model of allergic or atopic dermatitis, a condition characterized by ulcerative skin lesions with accumulation of mast cells and increased serum IgE. These features of the murine disease closely resemble human atopy and atopic disorders. We performed linkage analysis in NOA back-cross progeny, as a step toward identifying and isolating a gene responsible for the NOA phenotype. We crossed NOA mice with five other murine strains (C57BL/6J, IQI, C3H/HeJ, DBA/2J, and BALB/cByJ) and then bred back-cross animals. Using microsatellite markers, we scanned the entire genomes of 559 N2 offspring from the five parental strains. Linkage analysis revealed a significant association between ulcerative skin lesions and markers on murine chromosome 14. Statistical analysis indicated that the critical region was assigned to the vicinity of D14Mit236 and D14Mit160.

Results for five sets of forensic genetic markers studied in a Greek population sample.

PubMed

Tomas, C; Skitsa, I; Steinmeier, E; Poulsen, L; Ampati, A; Børsting, C; Morling, N

2015-05-01

A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex®, Argus X-12 and PowerPlex® Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm-Šidák correction. Statistically significant (P<0.05) levels of linkage disequilibrium were observed between markers within two of the studied X-chromosome linkage groups. AMOVA analyses of the five sets of markers did not show population structure when the individuals were grouped according to their geographic origin. The Greek population grouped closely to the other European populations measured by F(ST)(*) distances. The match probability ranged from a value of 1 in 2×10(7) males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73×10(21) individuals for 16 autosomal STRs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Pleiotropic QTL on chromosome 19q13 for triglycerides and adiposity: the HERITAGE Family Study.

PubMed

Feitosa, Mary F; Rice, Treva; North, Kari E; Kraja, Aldi; Rankinen, Tuomo; Leon, Arthur S; Skinner, James S; Blangero, John; Bouchard, Claude; Rao, D C

2006-04-01

Motivated by strong correlations between plasma levels of triglycerides (TG) and adiposity traits, we conducted a series of bivariate genome-wide linkage analyses of TG with body mass index (BMI), total fat mass (FAT), percentage of body fat (FATPC), and abdominal subcutaneous fat (ASF). Maximum lod scores of 3.3, 3.0, 2.2 and 2.4, respectively, were found on chromosome 19q13. This linkage region includes the APOE gene, a predictor of variation in lipid-lipoprotein levels, and the hormone-sensitive lipase (LIPE) gene, a key enzyme in the mobilization of fatty acids from triglyceride stores. In addition, the adiposity measures together with the APOE marker showed significant association with TG levels (p = 0.02 to p = 0.03). In summary, these results suggest that one or more QTLs in the 19q13 region jointly influence TG levels and adiposity. Polymorphisms in the APOE gene, and possibly LIPE gene, appear to be strong candidates for the source of this pleiotropic QTL.

Quantifying ubiquitin signaling.

PubMed

Ordureau, Alban; Münch, Christian; Harper, J Wade

2015-05-21

Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), including phosphorylation. Flux through such pathways is dictated by the fractional stoichiometry of distinct modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events, illustrated with the PINK1/PARKIN pathway. A key feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems. Copyright © 2015 Elsevier Inc. All rights reserved.

Combining Different Privacy-Preserving Record Linkage Methods for Hospital Admission Data.

PubMed

Stausberg, Jürgen; Waldenburger, Andreas; Borgs, Christian; Schnell, Rainer

2017-01-01

Record linkage (RL) is the process of identifying pairs of records that correspond to the same entity, for example the same patient. The basic approach assigns to each pair of records a similarity weight, and then determines a certain threshold, above which the two records are considered to be a match. Three different RL methods were applied under privacy-preserving conditions on hospital admission data: deterministic RL (DRL), probabilistic RL (PRL), and Bloom filters. The patient characteristics like names were one-way encrypted (DRL, PRL) or transformed to a cryptographic longterm key (Bloom filters). Based on one year of hospital admissions, the data set was split randomly in 30 thousand new and 1,5 million known patients. With the combination of the three RL-methods, a positive predictive value of 83 % (95 %-confidence interval 65 %-94 %) was attained. Thus, the application of the presented combination of RL-methods seem to be suited for other applications of population-based research.

Coupling socioeconomic and lake systems for sustainability: a conceptual analysis using Lake St. Clair region as a case study.

PubMed

Mavrommati, Georgia; Baustian, Melissa M; Dreelin, Erin A

2014-04-01

Applying sustainability at an operational level requires understanding the linkages between socioeconomic and natural systems. We identified linkages in a case study of the Lake St. Clair (LSC) region, part of the Laurentian Great Lakes system. Our research phases included: (1) investigating and revising existing coupled human and natural systems frameworks to develop a framework for this case study; (2) testing and refining the framework by hosting a 1-day stakeholder workshop and (3) creating a causal loop diagram (CLD) to illustrate the relationships among the systems' key components. With stakeholder assistance, we identified four interrelated pathways that include water use and discharge, land use, tourism and shipping that impact the ecological condition of LSC. The interrelationships between the pathways of water use and tourism are further illustrated by a CLD with several feedback loops. We suggest that this holistic approach can be applied to other case studies and inspire the development of dynamic models capable of informing decision making for sustainability.

An Introduction to Social Network Data Analytics

NASA Astrophysics Data System (ADS)

Aggarwal, Charu C.

The advent of online social networks has been one of the most exciting events in this decade. Many popular online social networks such as Twitter, LinkedIn, and Facebook have become increasingly popular. In addition, a number of multimedia networks such as Flickr have also seen an increasing level of popularity in recent years. Many such social networks are extremely rich in content, and they typically contain a tremendous amount of content and linkage data which can be leveraged for analysis. The linkage data is essentially the graph structure of the social network and the communications between entities; whereas the content data contains the text, images and other multimedia data in the network. The richness of this network provides unprecedented opportunities for data analytics in the context of social networks. This book provides a data-centric view of online social networks; a topic which has been missing from much of the literature. This chapter provides an overview of the key topics in this field, and their coverage in this book.

Underestimated AMOC Variability and Implications for AMV and Predictability in CMIP Models

NASA Astrophysics Data System (ADS)

Yan, Xiaoqin; Zhang, Rong; Knutson, Thomas R.

2018-05-01

The Atlantic Meridional Overturning Circulation (AMOC) has profound impacts on various climate phenomena. Using both observations and simulations from the Coupled Model Intercomparison Project Phase 3 and 5, here we show that most models underestimate the amplitude of low-frequency AMOC variability. We further show that stronger low-frequency AMOC variability leads to stronger linkages between the AMOC and key variables associated with the Atlantic multidecadal variability (AMV), and between the subpolar AMV signal and northern hemisphere surface air temperature. Low-frequency extratropical northern hemisphere surface air temperature variability might increase with the amplitude of low-frequency AMOC variability. Atlantic decadal predictability is much higher in models with stronger low-frequency AMOC variability and much lower in models with weaker or without AMOC variability. Our results suggest that simulating realistic low-frequency AMOC variability is very important, both for simulating realistic linkages between AMOC and AMV-related variables and for achieving substantially higher Atlantic decadal predictability.

ZnCl 2 induced catalytic conversion of softwood lignin to aromatics and hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hongliang; Zhang, Libing; Deng, Tiansheng

2016-01-01

Selective cleavage of C-O-C bonds in lignin without disrupting C-C linkages can result in releasing aromatic monomers and dimers that can be subsequently converted into chemicals and fuels. Results showed that both biomass-derived lignin and lignin model compounds were depolymerized in a highly concentrated ZnCl2 solution. Zn2+ ions in highly concentrated ZnCl2 solutions appeared to selectively coordinate with C-O-C bonds to cause key linkages of lignin much easier to cleave. In 63 wt.% ZnCl2 solution at 200 °C for 6 h, nearly half of the softwood technical lignin was converted to liquid products, of which the majority was alkylphenols. Resultsmore » indicated that most β-O-4 and Cmethyl-OAr bonds of model compounds were cleaved undersame conditions, providing a foundation towards understanding lignin depolymerization in a concentrated ZnCl2 solution. The phenolic products were further converted into cyclic hydrocarbons via hydrodeoxygenation and coupling reactions by co-catalyst Ru/C.« less

Regulation of E2s: A Role for Additional Ubiquitin Binding Sites?

PubMed

Middleton, Adam J; Wright, Joshua D; Day, Catherine L

2017-11-10

Attachment of ubiquitin to proteins relies on a sophisticated enzyme cascade that is tightly regulated. The machinery of ubiquitylation responds to a range of signals, which remarkably includes ubiquitin itself. Thus, ubiquitin is not only the central player in the ubiquitylation cascade but also a key regulator. The ubiquitin E3 ligases provide specificity to the cascade and often bind the substrate, while the ubiquitin-conjugating enzymes (E2s) have a pivotal role in determining chain linkage and length. Interaction of ubiquitin with the E2 is important for activity, but the weak nature of these contacts has made them hard to identify and study. By reviewing available crystal structures, we identify putative ubiquitin binding sites on E2s, which may enhance E2 processivity and the assembly of chains of a defined linkage. The implications of these new sites are discussed in the context of known E2-ubiquitin interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis.

PubMed

Schindelman, G; Morikami, A; Jung, J; Baskin, T I; Carpita, N C; Derbyshire, P; McCann, M C; Benfey, P N

2001-05-01

To control organ shape, plant cells expand differentially. The organization of the cellulose microfibrils in the cell wall is a key determinant of differential expansion. Mutations in the COBRA (COB) gene of Arabidopsis, known to affect the orientation of cell expansion in the root, are reported here to reduce the amount of crystalline cellulose in cell walls in the root growth zone. The COB gene, identified by map-based cloning, contains a sequence motif found in proteins that are anchored to the extracellular surface of the plasma membrane through a glycosylphosphatidylinositol (GPI) linkage. In animal cells, this lipid linkage is known to confer polar localization to proteins. The COB protein was detected predominately on the longitudinal sides of root cells in the zone of rapid elongation. Moreover, COB RNA levels are dramatically upregulated in cells entering the zone of rapid elongation. Based on these results, models are proposed for the role of COB as a regulator of oriented cell expansion.

COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis

PubMed Central

Schindelman, Gary; Morikami, Atsushi; Jung, Jee; Baskin, Tobias I.; Carpita, Nicholas C.; Derbyshire, Paul; McCann, Maureen C.; Benfey, Philip N.

2001-01-01

To control organ shape, plant cells expand differentially. The organization of the cellulose microfibrils in the cell wall is a key determinant of differential expansion. Mutations in the COBRA (COB) gene of Arabidopsis, known to affect the orientation of cell expansion in the root, are reported here to reduce the amount of crystalline cellulose in cell walls in the root growth zone. The COB gene, identified by map-based cloning, contains a sequence motif found in proteins that are anchored to the extracellular surface of the plasma membrane through a glycosylphosphatidylinositol (GPI) linkage. In animal cells, this lipid linkage is known to confer polar localization to proteins. The COB protein was detected predominately on the longitudinal sides of root cells in the zone of rapid elongation. Moreover, COB RNA levels are dramatically upregulated in cells entering the zone of rapid elongation. Based on these results, models are proposed for the role of COB as a regulator of oriented cell expansion. PMID:11331607

The voluntary community health movement in India: a strengths, weaknesses, opportunities, and threats (SWOT) analysis.

PubMed

Sharma, M; Bhatia, G

1996-12-01

There has been a prolific growth of voluntary organizations in India since independence in 1947. One of the major areas of this growth has been in the field of community health. The purpose of this article is to historically trace the voluntary movement in community health in India, analyze the current status, and predict future trends of voluntary efforts. A review of the literature in the form of a Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis was the method of this study. Some of the key trends which emerged as the priority areas for progress and for strengthening voluntary organizations in the future were enhancing linkages between health and development; building upon collective force; greater utilization of participatory training; establishing egalitarian and effectual linkages for decision making at the international level; developing self-reliant community-based models; and the need for attaining holistic empowerment at individual, organizational, and community levels through "duty consciousness" as opposed to merely asking for rights.

Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

PubMed

Greenberg, David A; Zhang, Junying; Shmulewitz, Dvora; Strug, Lisa J; Zimmerman, Regina; Singh, Veena; Marathe, Sudhir

2005-12-30

The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. 2) To observe the effect on genetic analysis and gene discovery of a complex set of gene x gene interactions. 3) To allow comparison of microsatellite vs. large-scale single-nucleotide polymorphism (SNP) data. 4) To allow testing of association to identify the disease gene and the effect of moderate marker x marker linkage disequilibrium. 5) To observe the effect of different ascertainment/disease definition schemes on the analysis. Data was distributed in two forms. Data distributed to participants contained about 1,000 SNPs and 400 microsatellite markers. Internet-obtainable data consisted of a finer 10,000 SNP map, which also contained data on controls. While disease characteristics and parameters were constant, four "studies" used varying ascertainment schemes based on differing beliefs about disease characteristics. One of the studies contained multiplex two- and three-generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different phenotypes, which were themselves heterogeneous. The population parameters were calibrated so that the major genes could be discovered by linkage analysis in most datasets. The association evidence was more difficult to calibrate but was designed to find statistically significant association in 50% of datasets. We also simulated some marker x marker linkage disequilibrium around some of the genes and also in areas without disease genes. We tried two different methods to simulate the linkage disequilibrium.

Creative Activities in Music – A Genome-Wide Linkage Analysis

PubMed Central

Oikkonen, Jaana; Kuusi, Tuire; Peltonen, Petri; Raijas, Pirre; Ukkola-Vuoti, Liisa; Karma, Kai; Onkamo, Päivi; Järvelä, Irma

2016-01-01

Creative activities in music represent a complex cognitive function of the human brain, whose biological basis is largely unknown. In order to elucidate the biological background of creative activities in music we performed genome-wide linkage and linkage disequilibrium (LD) scans in musically experienced individuals characterised for self-reported composing, arranging and non-music related creativity. The participants consisted of 474 individuals from 79 families, and 103 sporadic individuals. We found promising evidence for linkage at 16p12.1-q12.1 for arranging (LOD 2.75, 120 cases), 4q22.1 for composing (LOD 2.15, 103 cases) and Xp11.23 for non-music related creativity (LOD 2.50, 259 cases). Surprisingly, statistically significant evidence for linkage was found for the opposite phenotype of creative activity in music (neither composing nor arranging; NCNA) at 18q21 (LOD 3.09, 149 cases), which contains cadherin genes like CDH7 and CDH19. The locus at 4q22.1 overlaps the previously identified region of musical aptitude, music perception and performance giving further support for this region as a candidate region for broad range of music-related traits. The other regions at 18q21 and 16p12.1-q12.1 are also adjacent to the previously identified loci with musical aptitude. Pathway analysis of the genes suggestively associated with composing suggested an overrepresentation of the cerebellar long-term depression pathway (LTD), which is a cellular model for synaptic plasticity. The LTD also includes cadherins and AMPA receptors, whose component GSG1L was linked to arranging. These results suggest that molecular pathways linked to memory and learning via LTD affect music-related creative behaviour. Musical creativity is a complex phenotype where a common background with musicality and intelligence has been proposed. Here, we implicate genetic regions affecting music-related creative behaviour, which also include genes with neuropsychiatric associations. We also propose a common genetic background for music-related creative behaviour and musical abilities at chromosome 4. PMID:26909693

Simulation Study of Evacuation Control Center Operations Analysis

DTIC Science & Technology

2011-06-01

28 4.3 Baseline Manning (Runs 1, 2, & 3) . . . . . . . . . . . . 30 4.3.1 Baseline Statistics Interpretation...46 Appendix B. Key Statistic Matrix: Runs 1-12 . . . . . . . . . . . . . 48 Appendix C. Blue Dart...Completion Time . . . 33 11. Paired T result - Run 5 v. Run 6: ECC Completion Time . . . 35 12. Key Statistics : Run 3 vs. Run 9

Research needs to better understand Lake Ontario ecosystem function: A workshop summary

USGS Publications Warehouse

Stewart, Thomas J.; Rudstam, Lars G.; Watkins, James M.; Johnson, Timothy B.; Weidel, Brian C.; Koops, Marten A.

2016-01-01

Lake Ontario investigators discussed and interpreted published and unpublished information during two workshops to assess our current understanding of Lake Ontario ecosystem function and to identify research needs to guide future research and monitoring activities. The purpose of this commentary is to summarize key investigative themes and hypotheses that emerged from the workshops. The outcomes of the workshop discussions are organized under four themes: spatial linkages and interactions, drivers of primary production, trophic transfer, and human interactions.

12. VIEW OF TYPICAL CELL LOCKING MECHANISM, BUILDING 220 CELL ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. VIEW OF TYPICAL CELL LOCKING MECHANISM, BUILDING 220 CELL BLOCK 'A'. THE FACE PLATE OF THE CELL LOCK IS SHOWN REMOVED, EXPOSING THE ELECTROMAGNETIC LOCKING MECHANISM COMPRISING OF 2 MICROSWITCHES FOR LOCK POSITION INDICATION (FRONT LEFT CENTER AND REAR RIGHT CENTER OF PANEL); KEY SLOT MECHANICAL LOCK; LOCK SPRING (UPPER RIGHT OF PANEL); ELECTRIC SOLENOID (BOTTOM RIGHT CORNER OF PANEL); AND MISCELLANEOUS MECHANICAL LINKAGES. - U.S. Naval Base, Pearl Harbor, Brig, Neville Way near Ninth Street at Marine Barracks, Pearl City, Honolulu County, HI

On the Equidecomposability of a Regular Triangle and A Square of Equal Areas.

DTIC Science & Technology

1984-01-01

Hogo Steinhaus OMathematical Snapshots , is not correct. ANS (MOS) Subject Classifications: 51-01, 51N20 Key Words: Equidecomposability of plane...It is shown that the solution of the problem of the title, as given in the first snapshot of H. Steinhaus ’ "Mathematical Snapshots" is not correct...490985 This accuracy should be sufficient for the realization of the ingenious linkage of four polygons (1) as described by Steinhaus (See (2, Figure 1.3

Thermal management and design for optical refrigeration

NASA Astrophysics Data System (ADS)

Symonds, G.; Farfan, B. G.; Ghasemkhani, M. R.; Albrecht, A. R.; Sheik-Bahae, M.; Epstein, R. I.

2016-03-01

We present our recent work in developing a robust and versatile optical refrigerator. This work focuses on minimizing parasitic energy losses through efficient design and material optimization. The cooler's thermal linkage system and housing are studied using thermal analysis software to minimize thermal gradients through the device. Due to the extreme temperature differences within the device, material selection and characterization are key to constructing an efficient device. We describe the design constraints and material selections necessary for thermally efficient and durable optical refrigeration.

The importance of endophenotypes in schizophrenia research.

PubMed

Braff, David L

2015-04-01

Endophenotypes provide a powerful neurobiological platform from which we can understand the genomic and neural substrates of schizophrenia and other common complex neuropsychiatric disorders. The Consortium on the Genetics of Schizophrenia (COGS) has conducted multisite studies on carefully selected key neurocognitive and neurophysiological endophenotypes in 300 families (COGS-1) and then in a follow up multisite case-control study of 2471 subjects (COGS-2). Endophenotypes are neurobiologically informed quantitative measures that show deficits in probands and their first degree relatives. They are more amenable to statistical analysis than are "fuzzy" qualitative clinical traits or confoundingly heterogeneous diagnostic categories. Endophenotypes are also viewed as uniquely informative in traditional diagnosis-based as well as emerging NIMH Research Domain (RDoC) contexts, offering a bridge between the two approaches to psychopathology classification and research. Endo- or intermediate phenotypes are heritable, and in the COGS-1 cohort their level of heritability is in the same range as is the heritability of schizophrenia itself, using the same statistical methods and subjects to assess both. Because we can demonstrate endophenotypes link to both gene networks and neural circuits on the one hand and also to real-life function, endophenotypes provide a critically important bridge for "connecting the dots" between genes, cells, circuits, information processing, neurocognition and functional impairment and personalized treatment selection in schizophrenia patients. By connecting schizophrenia risk genes with neurobiologically informed endophenotypes, and via the use of association, linkage, sequencing, stem cell and other strategies, we can provide our field with new neurobiologically informed information in our efforts to understand and treat schizophrenia. Evolving views, data and new analytic strategies about schizophrenia risk, pathology and treatment are described in this Viewpoint and in the accompanying Special Issue reports. Published by Elsevier B.V.

Accuracy of probabilistic and deterministic record linkage: the case of tuberculosis.

PubMed

Oliveira, Gisele Pinto de; Bierrenbach, Ana Luiza de Souza; Camargo, Kenneth Rochel de; Coeli, Cláudia Medina; Pinheiro, Rejane Sobrino

2016-08-22

To analyze the accuracy of deterministic and probabilistic record linkage to identify TB duplicate records, as well as the characteristics of discordant pairs. The study analyzed all TB records from 2009 to 2011 in the state of Rio de Janeiro. A deterministic record linkage algorithm was developed using a set of 70 rules, based on the combination of fragments of the key variables with or without modification (Soundex or substring). Each rule was formed by three or more fragments. The probabilistic approach required a cutoff point for the score, above which the links would be automatically classified as belonging to the same individual. The cutoff point was obtained by linkage of the Notifiable Diseases Information System - Tuberculosis database with itself, subsequent manual review and ROC curves and precision-recall. Sensitivity and specificity for accurate analysis were calculated. Accuracy ranged from 87.2% to 95.2% for sensitivity and 99.8% to 99.9% for specificity for probabilistic and deterministic record linkage, respectively. The occurrence of missing values for the key variables and the low percentage of similarity measure for name and date of birth were mainly responsible for the failure to identify records of the same individual with the techniques used. The two techniques showed a high level of correlation for pair classification. Although deterministic linkage identified more duplicate records than probabilistic linkage, the latter retrieved records not identified by the former. User need and experience should be considered when choosing the best technique to be used. Analisar a acurácia das técnicas determinística e probabilística para identificação de registros duplicados de tuberculose, assim como as características dos pares discordantes. Foram analisados todos os registros de tuberculose no período de 2009 a 2011 do estado do Rio de Janeiro. Foi desenvolvido algoritmo para relacionamento determinístico, usando conjunto de 70 regras, a partir da combinação de fragmentos das variáveis-chave com ou sem modificações (Soundex ou substring). Cada regra era formada por três ou mais fragmentos. Para a abordagem probabilística, foi necessário estabelecer ponto de corte para o escore, acima do qual os links seriam classificados automaticamente como pertencentes ao mesmo indivíduo. O ponto de corte foi obtido por meio do relacionamento da base de dados Sistema de Informação de Agravos de Notificação - Tuberculose com ela mesma, posterior revisão manual e curvas ROC e precision-recall. Foram calculadas a sensibilidade e especificidade para análise de acurácia. A acurácia variou de 87,2% a 95,2% para sensibilidade e 99,8% a 99,9% para especificidade para as técnicas probabilística e determinística, respectivamente. A presença de valores faltantes para as variáveis-chave e o baixo percentual da medida de similaridade para o nome e data de nascimento foram os principais responsáveis pela não identificação dos registros do mesmo indivíduo pelas técnicas utilizadas. As duas técnicas apresentam alta concordância para a classificação como par. Apesar de a técnica determinística ter identificado mais registros duplicados que a probabilística, a segunda recuperou registros não identificados pela primeira. A necessidade e a experiência do usuário devem ser consideradas para a escolha da técnica a ser utilizada.

Are genes associated with energy metabolism important in asthma and BMI?

PubMed

Szczepankiewicz, Aleksandra; Breborowicz, Anna; Sobkowiak, Paulina; Popiel, Anna

2009-02-01

Increased serum leptin levels have been observed in asthmatic patients. Leptin, via proliferation and activation of Th2 cells, may induce inflammation in asthma. It has also been demonstrated that leptin mRNA expression and protein levels increase in response to inflammatory stimuli. We hypothesized that polymorphisms in the leptin receptor, leptin and ghrelin genes, may affect their expression and, therefore, be responsible for altered response to increased leptin levels observed in asthma. To our knowledge, there were no studies on a potential role of LEPR, LEP, and GHRL polymorphisms in asthma. We analyzed 129 pediatric patients with asthma and 114 healthy children from the control group ranging from 6 to 18 years of age. The diagnosis of allergic asthma was based on clinical symptoms, the lung function test, and the positive skin prick test and/or increased immunoglobulin E (IgE) levels. Polymorphisms were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Statistical analyses were performed with Statistica v.7.1 software (Statistica, StatSoft, Poland; available free at http://www.broad.mit.edu/mpg/haploview/index.php). Linkage disequilibrium analysis was performed with Haploview v.4.0. We observed a statistically significant association of the 3'UTR A/G and the -2549A/G polymorphisms of the leptin gene with asthma. No association with asthma was observed for the K109R and the Q223R polymorphisms of the LEPR gene and the Met72Leu polymorphism of the ghrelin gene. In the analysis of body mass index (BMI) stratified by genotype, we found an association of the -2549A/G LEP, but not of LEPR and GHRL polymorphisms, with higher BMI values in asthmatic patients. We found suggestive evidence for linkage between the two polymorphisms of the LEPR gene (D' = 0.84 CI: 0.71-0.92; r(2) = 0.29) in linkage disequilibrium analysis: The GG haplotype was more frequent in the control healthy group (p = 0.057). No linkage disequilibrium was detected between LEP polymorphisms. Polymorphisms of the leptin gene may be associated with asthma and higher BMI in asthmatic patients. Polymorphisms of the LEPR and GHRL seem unlikely to be associated with asthma or BMI in our sample. The results of haplotype analysis for the LEPR gene may suggest a protective role of the GG haplotype against asthma; however, studies on larger groups are necessary to confirm the observed trend towards association.

Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME (UltraH3) Linkage is a key for Occurrence of Last Universal Common Ancestral (LUCA) Community: Where is it, Lost City or Kairei (Rainbow)?

NASA Astrophysics Data System (ADS)

Takai, K.; Inagaki, F.; Nakamura, K.; Suzuki, K.; Kumagai, H.

2005-12-01

Deep-sea hydrothermal system has been recognized one of the most plausible places for origin of life in this planet. This hypothesis has been supported by evidences from multidisciplinary scientific fields. In geology, it has been demonstrated that the potentially most ancient microbial fossils are retrieved from the paleoenvironment, that might be related with deep-sea hydrothermal systems in the Archean. Chemical reactions suggesting prebiotic chemical evolution (synthesis of amino acids, nucleic acids and hydrocarbon, and polymerization of these molecules) are observed under the simulated physical and chemical conditions of the deep-sea hydrothermal vents in the laboratory. In addition, phylogenetic analyses of all the lives in this planet have clearly revealed that hyperthermophiles inhabiting deep-sea hydrothermal systems represent the deepest lineage of the life. Supposed that the Archean deep-sea hydrothermal system hosted the origin of life, what was the first life? We are pursuing the energy metabolism of our last universal common ancestor (LUCA) and the environmental settings hosting the LUCA. It is definitely expected that the genesis of LUCA occurred at high temperatures of locally organics-rich microenvironment around deep-sea hydrothermal field and the first energy metabolism depended on fermentation of simple amino acids, organic acids and sugars. However, these organics were immediately consumed by the hyperthermophilic LUCA activity. Inheritance of the LUCA needed to evolve the energy and carbon acquisitions to more stable and efficient mode. Chemolithoautotrophy might be the best because a plenty of reductive gas components were always provided by the hydrothermal activity. Hyperthermophilic chemolithoautotrophs could serve as the primary producers and could foster the heterotrophic fellows. This was the genesis of the last universal common ancestral (LUCA) community of life. We hypothesize that the LUCA community was metabolically approximated to hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) currently discovered beneath the Central Indian Ridge hydrothermal field. The environmental settings for the occurrence of HyperSLiME are now being characterized and an important linkage among the occurrence of HyperSLiME, extraordinary amount of hydrogen in the hydrothermal fluids and ultramfics-hosted hydrothermal systems is proposed. This ultramafics-hydrothermalism-hydrogen-HyperSLiME (UltraH3) linkage is very likely a key for the genesis of the LUCA community. We would like to discuss the possible UltraH3 linkage in the Archean earth. In addition, we would like to discuss which of modern deep-sea hydrothermal systems is the most plausible proxy for the Archean LUCA habitats.

Summary of Key Operating Statistics: Data Collected from the 2009 Annual Institutional Report

ERIC Educational Resources Information Center

Accrediting Council for Independent Colleges and Schools, 2010

2010-01-01

The Accrediting Council for Independent Colleges and Schools (ACICS) provides the Summary of Key Operating Statistics (KOS) as an annual review of the performance and key measurements of the more than 800 private post-secondary institutions we accredit. This edition of the KOS contains information based on the 2009 Annual Institutional Reports…

Improving record linkage performance in the presence of missing linkage data.

PubMed

Ong, Toan C; Mannino, Michael V; Schilling, Lisa M; Kahn, Michael G

2014-12-01

Existing record linkage methods do not handle missing linking field values in an efficient and effective manner. The objective of this study is to investigate three novel methods for improving the accuracy and efficiency of record linkage when record linkage fields have missing values. By extending the Fellegi-Sunter scoring implementations available in the open-source Fine-grained Record Linkage (FRIL) software system we developed three novel methods to solve the missing data problem in record linkage, which we refer to as: Weight Redistribution, Distance Imputation, and Linkage Expansion. Weight Redistribution removes fields with missing data from the set of quasi-identifiers and redistributes the weight from the missing attribute based on relative proportions across the remaining available linkage fields. Distance Imputation imputes the distance between the missing data fields rather than imputing the missing data value. Linkage Expansion adds previously considered non-linkage fields to the linkage field set to compensate for the missing information in a linkage field. We tested the linkage methods using simulated data sets with varying field value corruption rates. The methods developed had sensitivity ranging from .895 to .992 and positive predictive values (PPV) ranging from .865 to 1 in data sets with low corruption rates. Increased corruption rates lead to decreased sensitivity for all methods. These new record linkage algorithms show promise in terms of accuracy and efficiency and may be valuable for combining large data sets at the patient level to support biomedical and clinical research. Copyright © 2014 Elsevier Inc. All rights reserved.

Privacy preserving interactive record linkage (PPIRL).

PubMed

Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

2014-01-01

Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.

Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.

PubMed

Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh

2016-07-01

Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

Probabilistic record linkage

PubMed Central

Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

2016-01-01

Abstract Studies involving the use of probabilistic record linkage are becoming increasingly common. However, the methods underpinning probabilistic record linkage are not widely taught or understood, and therefore these studies can appear to be a ‘black box’ research tool. In this article, we aim to describe the process of probabilistic record linkage through a simple exemplar. We first introduce the concept of deterministic linkage and contrast this with probabilistic linkage. We illustrate each step of the process using a simple exemplar and describe the data structure required to perform a probabilistic linkage. We describe the process of calculating and interpreting matched weights and how to convert matched weights into posterior probabilities of a match using Bayes theorem. We conclude this article with a brief discussion of some of the computational demands of record linkage, how you might assess the quality of your linkage algorithm, and how epidemiologists can maximize the value of their record-linked research using robust record linkage methods. PMID:26686842

Privacy preserving interactive record linkage (PPIRL)

PubMed Central

Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

2014-01-01

Objective Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human–machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. Methods In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. Results We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Conclusions Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human–machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility. PMID:24201028

Measuring primary care practice performance within an integrated delivery system: a case study.

PubMed

Stewart, Louis J; Greisler, David

2002-01-01

This article examines the use of an integrated performance measurement system to plan and control primary care service delivery within an integrated delivery system. We review a growing body of literature that focuses on the development and implementation of management reporting systems among healthcare providers. Our study extends the existing literature by examining the use of performance information generated by an integrated performance measurement system within a healthcare organization. We conduct our examination through a case study of the WMG Primary Care Medicine Group, the primary care medical group practice of WellSpan Health System. WellSpan Health System is an integrated delivery system that serves south central Pennsylvania and northern Maryland. Our study examines the linkage between WellSpan Health's strategic objectives and its primary care medicine group's integrated performance measurement system. The conceptual design of this integrated performance measurement system combines financial metrics with practice management and clinical operating metrics to provide a more complete picture of medical group performance. Our findings demonstrate that WellSpan Health was able to achieve superior financial results despite a weak linkage between its integrated performance measurement system and its strategic objectives. WellSpan Health achieved this objective for its primary care medicine group by linking clinical performance information to physician compensation and reporting practice management performance through the use of statistical process charts. They found that the combined mechanisms of integrated performance measurement and statistical process control charts improved organizational learning and communications between organizational stakeholders.

Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

PubMed

Olsen, Aaron M; Westneat, Mark W

2016-12-01

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570-1583, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Ischemic cardiovascular disease in workers occupationally exposed to urban air pollution - A systematic review.

PubMed

De Marchis, Paola; Verso, Maria Gabriella; Tramuto, Fabio; Amodio, Emanuele; Picciotto, Diego

2018-03-14

Cardiovascular disease is the first cause of morbidity and mortality worldwide. Among several known risk factors, researchers also focus their attention on the chronic exposure to air pollution. There is much evidence that exposure to air pollution, especially to ultrafine particles, can damage the endothelium and can favour cardiovascular diseases in the general population. Occupational exposition could be an additive risk factor for the cardiovascular system. This article presents a scientific review of the linkage between occupational exposure to air pollution and ischemic heart disease. A scientific review was undertaken, followed by PRISMA Statements. Observational studies were selected from several scientific databases, likesuch as Pubmed, Google Scholar, Nioshtic-2 and Reserchgate, searching for selected key words: police workers, professional drivers, mail carriers, filling station attendants, road cleaners, garage workers, motor vehicles and engine maintenance. All the key words were combined with "Boolean Operators" with the following words: cardiovascular (or cardiac) disease, cardiovascular function, cardiovascular system, ischemic heart disease, coronary disease, myocardial infarction. During the systematic research, the focus was on retrospective and prospective studies from January 1990 - December 2014. Both the retrospective and prospective studies showed an increased risk of ischemic heart disease in occupationally occupied people exposed to air pollution. Only one study presented a ly minor risk. The findings of this systematic review suggest a possible linkage between occupational exposure to urban air pollution, especially to motor exhaust and particulate, and ischemic heart disease.

Mapping Quantitative Traits in Unselected Families: Algorithms and Examples

PubMed Central

Dupuis, Josée; Shi, Jianxin; Manning, Alisa K.; Benjamin, Emelia J.; Meigs, James B.; Cupples, L. Adrienne; Siegmund, David

2009-01-01

Linkage analysis has been widely used to identify from family data genetic variants influencing quantitative traits. Common approaches have both strengths and limitations. Likelihood ratio tests typically computed in variance component analysis can accommodate large families but are highly sensitive to departure from normality assumptions. Regression-based approaches are more robust but their use has primarily been restricted to nuclear families. In this paper, we develop methods for mapping quantitative traits in moderately large pedigrees. Our methods are based on the score statistic which in contrast to the likelihood ratio statistic, can use nonparametric estimators of variability to achieve robustness of the false positive rate against departures from the hypothesized phenotypic model. Because the score statistic is easier to calculate than the likelihood ratio statistic, our basic mapping methods utilize relatively simple computer code that performs statistical analysis on output from any program that computes estimates of identity-by-descent. This simplicity also permits development and evaluation of methods to deal with multivariate and ordinal phenotypes, and with gene-gene and gene-environment interaction. We demonstrate our methods on simulated data and on fasting insulin, a quantitative trait measured in the Framingham Heart Study. PMID:19278016

Novel linkage disequilibrium clustering algorithm identifies new lupus genes on meta-analysis of GWAS datasets.

PubMed

Saeed, Mohammad

2017-05-01

Systemic lupus erythematosus (SLE) is a complex disorder. Genetic association studies of complex disorders suffer from the following three major issues: phenotypic heterogeneity, false positive (type I error), and false negative (type II error) results. Hence, genes with low to moderate effects are missed in standard analyses, especially after statistical corrections. OASIS is a novel linkage disequilibrium clustering algorithm that can potentially address false positives and negatives in genome-wide association studies (GWAS) of complex disorders such as SLE. OASIS was applied to two SLE dbGAP GWAS datasets (6077 subjects; ∼0.75 million single-nucleotide polymorphisms). OASIS identified three known SLE genes viz. IFIH1, TNIP1, and CD44, not previously reported using these GWAS datasets. In addition, 22 novel loci for SLE were identified and the 5 SLE genes previously reported using these datasets were verified. OASIS methodology was validated using single-variant replication and gene-based analysis with GATES. This led to the verification of 60% of OASIS loci. New SLE genes that OASIS identified and were further verified include TNFAIP6, DNAJB3, TTF1, GRIN2B, MON2, LATS2, SNX6, RBFOX1, NCOA3, and CHAF1B. This study presents the OASIS algorithm, software, and the meta-analyses of two publicly available SLE GWAS datasets along with the novel SLE genes. Hence, OASIS is a novel linkage disequilibrium clustering method that can be universally applied to existing GWAS datasets for the identification of new genes.

Analysis of the linkage between rain and flood regime and its application to regional flood frequency estimation

NASA Astrophysics Data System (ADS)

Cunderlik, Juraj M.; Burn, Donald H.

2002-04-01

Improving techniques of flood frequency estimation at ungauged sites is one of the foremost goals of contemporary hydrology. River flood regime is a resultant reflection of a composite catchment hydrologic response to flood producing processes. In this sense the process of identifying homogeneous pooling groups can be plausibly based on catchment similarity in flood regime. Unfortunately the application of any pooling approach that is based on flood regime is restricted to gauged sites. Because flood regime can be markedly determined by rainfall regime, catchment similarity in rainfall regime can be an alternative option for identifying flood frequency pooling groups. An advantage of such a pooling approach is that rainfall data are usually spatially and temporary more abundant than flood data and the approach can also be applied at ungauged sites. Therefore in this study we have quantified the linkage between rainfall and flood regime and explored the appropriateness of substituting rainfall regime for flood regime in regional pooling schemes. Two different approaches to describing rainfall regime similarity using tools of directional statistics have been tested and used for evaluation of the potential of rainfall regime for identification of hydrologically homogeneous pooling groups. The outputs were compared to an existing pooling framework adopted in the Flood Estimation Handbook. The results demonstrate that regional pooling based on rainfall regime information leads to a high number of initially homogeneous groups and seems to be a sound pooling alternative for catchments with a close linkage between rain and flood regimes.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

PubMed

Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

2015-01-01

Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

On the linkage between Arctic sea ice and Mid-latitude weather pattern: the situation in East Asia

NASA Astrophysics Data System (ADS)

Gu, S.; Zhang, Y.; Wu, Q.

2017-12-01

The influence of Arctic changes on the weather patterns in the highly populated mid-latitude is a complex and controversial topic with considerable uncertainties such as the low signal-to-noise, ill-suited metrics of circulation changes and the missing of dynamical understanding. In this study, the possible linkage between the Arctic sea ice concentration (SIC) and the wintertime weather patterns in East Asia is investigated by comparing groups of statistical and diagnostic analyses. Our study shows a robust relationship between the early autumn SIC in Barents, Kara, Laptev and East Siberia Sea and the energies of wintertime transient activities corresponding to the weather patterns over East Asia on inter-annual time scales. With the reduction of SIC in autumn, the wintertime synoptic (2-10 day) kinetic energy in the north of Eurasia decreases while the low-frequency (10-30 days) kinetic energy, which corresponds to persistent weather patterns, exhibits an evident and dominant increase over the north of Caspian Sea, Lake Baikal and the Ural Mountain. With the reduction of SIC, the intra-seasonal temperature fluctuations present coherent changes over a broader region as well, with significant increase of the low-frequency variability in the vast north of Tibet Plateau and East Asia. The changes of the low-frequency transient activities may be attributed to the slowly southward propagating wave energies from polar regions. However, no consistent stratosphere signals are found associated with such linkage on inter-annual time scales.

The waviness of the extratropical jet and daily weather extremes

NASA Astrophysics Data System (ADS)

Röthlisberger, Matthias; Martius, Olivia; Pfahl, Stephan

2016-04-01

In recent years the Northern Hemisphere mid-latitudes have experienced a large number of weather extremes with substantial socio-economic impact, such as the European and Russian heat waves in 2003 and 2010, severe winter floods in the United Kingdom in 2013/2014 and devastating winter storms such as Lothar (1999) and Xynthia (2010) in Central Europe. These have triggered an engaged debate within the scientific community on the role of human induced climate change in the occurrence of such extremes. A key element of this debate is the hypothesis that the waviness of the extratropical jet is linked to the occurrence of weather extremes, with a wavier jet stream favouring more extremes. Previous work on this topic is expanded in this study by analyzing the linkage between a regional measure of jet waviness and daily temperature, precipitation and wind gust extremes. We show that indeed such a linkage exists in many regions of the world, however this waviness-extremes linkage varies spatially in strength and sign. Locally, it is strong only where the relevant weather systems, in which the extremes occur, are affected by the jet waviness. Its sign depends on how the frequency of occurrence of the relevant weather systems is correlated with the occurrence of high and low jet waviness. These results go beyond previous studies by noting that also a decrease in waviness could be associated with an enhanced number of some weather extremes, especially wind gust and precipitation extremes over western Europe.

Sources of global climate data and visualization portals

USGS Publications Warehouse

Douglas, David C.

2014-01-01

Climate is integral to the geophysical foundation upon which ecosystems are structured. Knowledge about mechanistic linkages between the geophysical and biological environments is essential for understanding how global warming may reshape contemporary ecosystems and ecosystem services. Numerous global data sources spanning several decades are available that document key geophysical metrics such as temperature and precipitation, and metrics of primary biological production such as vegetation phenology and ocean phytoplankton. This paper provides an internet directory to portals for visualizing or servers for downloading many of the more commonly used global datasets, as well as a description of how to write simple computer code to efficiently retrieve these data. The data are broadly useful for quantifying relationships between climate, habitat availability, and lower-trophic-level habitat quality - especially in Arctic regions where strong seasonality is accompanied by intrinsically high year-to-year variability. If defensible linkages between the geophysical (climate) and the biological environment can be established, general circulation model (GCM) projections of future climate conditions can be used to infer future biological responses. Robustness of this approach is, however, complicated by the number of direct, indirect, or interacting linkages involved. For example, response of a predator species to climate change will be influenced by the responses of its prey and competitors, and so forth throughout a trophic web. The complexities of ecological systems warrant sensible and parsimonious approaches for assessing and establishing the role of natural climate variability in order to substantiate inferences about the potential effects of global warming.

Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex.

PubMed

Portis, Ezio; Scaglione, Davide; Acquadro, Alberto; Mauromicale, Giovanni; Mauro, Rosario; Knapp, Steven J; Lanteri, Sergio

2012-05-23

The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species' haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.

Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations.

PubMed

Verta, Jukka-Pekka; Landry, Christian R; MacKay, John

2016-07-01

Regulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long-lived such as in the case of conifer trees. We developed an RNA sequencing (RNA-seq)-based approach for both expression-quantitative trait locus (eQTL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) eQTLs. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self-fertilized white spruce (Picea glauca) individual to dissect eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs linked to the expressed genes was particularly complex, consisting of cis-acting, trans-acting and, surprisingly, compensatory cis-trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTLs were under compensation, indicating that close linkage between compensatory cis-trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid-diploid eQTL analysis in spruce revealed that compensatory cis-trans eQTLs segregate within populations and evolve in close genetic linkage. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Efficient sequential and parallel algorithms for record linkage.

PubMed

Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

2014-01-01

Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Our sequential and parallel algorithms have been tested on a real dataset of 1,083,878 records and synthetic datasets ranging in size from 50,000 to 9,000,000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm.

Interventions to improve or facilitate linkage to or retention in pre-ART (HIV) care and initiation of ART in low- and middle-income settings – a systematic review

PubMed Central

Govindasamy, Darshini; Meghij, Jamilah; Negussi, Eyerusalem Kebede; Baggaley, Rachel Clare; Ford, Nathan; Kranzer, Katharina

2014-01-01

Introduction Several approaches have been taken to reduce pre-antiretroviral therapy (ART) losses between HIV testing and ART initiation in low- and middle-income countries, but a systematic assessment of the evidence has not yet been undertaken. The aim of this systematic review is to assess the potential for interventions to improve or facilitate linkage to or retention in pre-ART care and initiation of ART in low- and middle-income settings. Methods An electronic search was conducted on Medline, Embase, Global Health, Web of Science and conference databases to identify studies describing interventions aimed at improving linkage to or retention in pre-ART care or initiation of ART. Additional searches were conducted to identify on-going trials on this topic, and experts in the field were contacted. An assessment of the risk of bias was conducted. Interventions were categorized according to key domains in the existing literature. Results A total of 11,129 potentially relevant citations were identified, of which 24 were eligible for inclusion, with the majority (n=21) from sub-Saharan Africa. In addition, 15 on-going trials were identified. The most common interventions described under key domains included: health system interventions (i.e. integration in the setting of antenatal care); patient convenience and accessibility (i.e. point-of-care CD4 count (POC) testing with immediate results, home-based ART initiation); behaviour interventions and peer support (i.e. improved communication, patient referral and education) and incentives (i.e. food support). Several interventions showed favourable outcomes: integration of care and peer supporters increased enrolment into HIV care, medical incentives increased pre-ART retention, POC CD4 testing and food incentives increased completion of ART eligibility screening and ART initiation. Most studies focused on the general adult patient population or pregnant women. The majority of published studies were observational cohort studies, subject to an unclear risk of bias. Conclusions Findings suggest that streamlining services to minimize patient visits, providing adequate medical and peer support, and providing incentives may decrease attrition, but the quality of the current evidence base is low. Few studies have investigated combined interventions, or assessed the impact of interventions across the HIV cascade. Results from on-going trials investigating POC CD4 count testing, patient navigation, rapid ART initiation and mobile phone technology may fill the quality of evidence gap. Further high-quality studies on key population groups are required, with interventions informed by previously reported barriers to care. PMID:25095831

A guide to evaluating linkage quality for the analysis of linked data.

PubMed

Harron, Katie L; Doidge, James C; Knight, Hannah E; Gilbert, Ruth E; Goldstein, Harvey; Cromwell, David A; van der Meulen, Jan H

2017-10-01

Linked datasets are an important resource for epidemiological and clinical studies, but linkage error can lead to biased results. For data security reasons, linkage of personal identifiers is often performed by a third party, making it difficult for researchers to assess the quality of the linked dataset in the context of specific research questions. This is compounded by a lack of guidance on how to determine the potential impact of linkage error. We describe how linkage quality can be evaluated and provide widely applicable guidance for both data providers and researchers. Using an illustrative example of a linked dataset of maternal and baby hospital records, we demonstrate three approaches for evaluating linkage quality: applying the linkage algorithm to a subset of gold standard data to quantify linkage error; comparing characteristics of linked and unlinked data to identify potential sources of bias; and evaluating the sensitivity of results to changes in the linkage procedure. These approaches can inform our understanding of the potential impact of linkage error and provide an opportunity to select the most appropriate linkage procedure for a specific analysis. Evaluating linkage quality in this way will improve the quality and transparency of epidemiological and clinical research using linked data. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

Drought propagation in the Paraná Basin, Brazil: from rainfall deficits to impacts on reservoir storage

NASA Astrophysics Data System (ADS)

Melo, D. D.; Wendland, E.

2017-12-01

The sensibility and resilience of hydrologic systems to climate changes are crucial for estimating potential impacts of droughts, responsible for major economic and human losses globally. Understanding how droughts propagate is a key element to develop a predictive understanding for future management and mitigation strategies. In this context, this study investigated the drought propagation in the Paraná Basin (PB), Southeast Brazil, a major hydroelectricity producing region with 32 % (60 million people) of the country's population. Reservoir storage (RESS), river discharge (Q) and rainfall (P) data were used to assess the linkages between meteorological and hydrological droughts, characterized by the Standard Precipitation Index (SPI) and Streamflow Drought Index (SDI), respectively. The data are from 37 sub-basins within the PB, consisting of contributing areas of 37 reservoirs (250 km3 of stored water) within the PB for the period between 1995 and 2015. The response time (RT) of the hydrologic system to droughts, given as the time lag between P, Q and RESS, was quantified using a non-parametric statistical method that combines cumulative sums and Bootstrap resampling technique. Based on our results, the RTs of the hydrologic system of the PB varies from 0 to 6 months, depending on a number of aspects: lithology, topography, dam operation, etc. Linkages between SPI and SDI indicated that the anthropogenic control (dam operation) plays an important role in buffering drought impacts to downstream sub-basins: SDI decreased from upstream to downstream despite similar SPI values over the whole area. Comparisons between sub-basins, with variable drainage sizes (5,000 - 50,000 km2), confirmed the benefice of upstream reservoirs in reducing hydrological droughts. For example, the RT for a 4,800 km2 basin was 6 months between P and Q and 9 months between Q and RESS, under anthropogenic control. Conversely, the RT to precipitation for a reservoir subjected to natural controls only (no major human influence on storage and routing) was less than 1 month for both Q and RESS. This study underscores the importance of the reservoirs in the Paraná basin in reducing drought impacts on water supply and energy generation.

[Problems with Using Hospital Quality Reports as a Secondary Data Source for Health Services Research in Germany].

PubMed

Kraska, R A; de Cruppe, W; Geraedts, M

2017-07-01

Background Since 2005, German hospitals are required by law to publish structured quality reports (QRs). Because of the detailed data basis, the QRs are being increasingly used for secondary data analyses in health services research. Up until now, methodological difficulties that can cause distorted results of the analyses have essentially been overlooked. The aim of this study is to systematically list the methodological problems associated with using QR and to suggest solution strategies. Methods The QRs from 2006-2012 form the basis of the analyses and were aggregated in a database using an individualized data linkage procedure. Thereafter, a correlation analysis between a quality indicator and the staffing of hospitals was conducted, serving as an example for both cross-sectional as well as longitudinal studies. The resulting methodological problems are described qualitatively and quantitatively, and potential solutions are derived from the statistical literature. Results In each reporting year, 2-15% of the hospitals delivered no QR. In 2-16% of the QRs, it is not recognizable whether a report belongs to a hospital network or a single location. In addition, 6-66% of the location reports falsely contain data from the hospital network. 10% of the hospitals changed their institution code (IC), in 5% of the cases, the same "IC-location-number-combination" was used for different hospitals over the years. Therefore, 10-20% of the QRs cannot be linked with the IC as key variable. As a remedy for the linking of QR, the combination of the IC, the address and the number of beds represents a suitable solution. Using this solution, hospital network reports, location reports and missing reports can be identified and considered in an analysis. Conclusions Secondary data analyses with quality reports provide a high potential for error due to the inconsistent data base and the problems of the data linkage procedure. These can distort calculated parameters and limit the validity of results. Only the unequivocal identification of the reporting hospitals guarantees meaningful results. © Georg Thieme Verlag KG Stuttgart · New York.

82 Key Statistics on Work and Family Issues. The National Report on Work & Family. Special Report #9.

ERIC Educational Resources Information Center

Bureau of National Affairs, Inc., Washington, DC.

This report was prepared because of the growing national interest in the questions of work and family dynamics. It puts together 82 key statistics on work and family issues in four major areas: child care, parental leave, alternative work schedules, and elder care. In addition, a chapter of miscellaneous statistics covers areas such as the…

Bottom-up linkages between primary production, zooplankton, and fish in a shallow, hypereutrophic lake.

PubMed

Matsuzaki, Shin-Ichiro S; Suzuki, Kenta; Kadoya, Taku; Nakagawa, Megumi; Takamura, Noriko

2018-06-09

Nutrient supply is a key bottom-up control of phytoplankton primary production in lake ecosystems. Top-down control via grazing pressure by zooplankton also constrains primary production, and primary production may simultaneously affect zooplankton. Few studies have addressed these bidirectional interactions. We used convergent cross-mapping (CCM), a numerical test of causal associations, to quantify the presence and direction of the causal relationships among environmental variables (light availability, surface water temperature, NO 3 -N, and PO 4 -P), phytoplankton community composition, primary production, and the abundances of five functional zooplankton groups (large-cladocerans, small-cladocerans, rotifers, calanoids, and cyclopoids) in Lake Kasumigaura, a shallow, hypereutrophic lake in Japan. CCM suggested that primary production was causally influenced by NO 3 -N and phytoplankton community composition; there was no detectable evidence of a causal effect of zooplankton on primary production. Our results also suggest that rotifers and cyclopoids were forced by primary production, and cyclopoids were further influenced by rotifers. However, our CCM suggested that primary production was weakly influenced by rotifers (i.e., bidirectional interaction). These findings may suggest complex linkages between nutrients, primary production, and rotifers and cyclopoids, a pattern that has not been previously detected or has been neglected. We used linear regression analysis to examine the relationships between the zooplankton community and pond smelt (Hypomesus nipponensis), the most abundant planktivore and the most important commercial fish species in Lake Kasumigaura. The relative abundance of pond smelt was significantly and positively correlated with the abundances of rotifers and cyclopoids, which were causally influenced by primary production. This finding suggests that bottom-up linkages between nutrient, primary production, and zooplankton abundance might be a key mechanism supporting high planktivore abundance in eutrophic lakes. Because increases in primary production and cyanobacteria blooms are likely to occur simultaneously in hypereutrophic lakes, our study highlights the need for ecosystem management to resolve the conflict between good water quality and high fishery production. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Linkage Disequilibrium Under Recurrent Bottlenecks

PubMed Central

Schaper, E.; Eriksson, A.; Rafajlovic, M.; Sagitov, S.; Mehlig, B.

2012-01-01

To model deviations from selectively neutral genetic variation caused by different forms of selection, it is necessary to first understand patterns of neutral variation. Best understood is neutral genetic variation at a single locus. But, as is well known, additional insights can be gained by investigating multiple loci. The resulting patterns reflect the degree of association (linkage) between loci and provide information about the underlying multilocus gene genealogies. The statistical properties of two-locus gene genealogies have been intensively studied for populations of constant size, as well as for simple demographic histories such as exponential population growth and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright–Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci in samples of two chromosomes. This covariance reflects the degree of association and thus linkage disequilibrium between these loci. We find, first, that an effective population-size approximation describes the numerically observed association between two loci provided that recombination occurs either much faster or much more slowly than the population-size fluctuations. Second, when recombination occurs frequently between but rarely within bottlenecks, we observe that the association of gene histories becomes independent of physical distance over a certain range of distances. Third, we show that in this case, a commonly used measure of linkage disequilibrium, σd2 (closely related to r^2), fails to capture the long-range association between two loci. The reason is that constituent terms, each reflecting the long-range association, cancel. Fourth, we analyze a limiting case in which the long-range association can be described in terms of a Xi coalescent allowing for simultaneous multiple mergers of ancestral lines. PMID:22048021

Genetic analysis of abdominal aortic aneurysms (AAA)

DOE Office of Scientific and Technical Information (OSTI.GOV)

St. Jean, P.L.; Hart, B.K.; Zhang, X.C.

1994-09-01

The association between AAA and gender, smoking (SM), hypertension (HTN) and inguinal herniation (IH) was examined in 141 AAA probands and 139 of their 1st degree relatives with aortic exam (36 affected, 103 unaffected). There was no significant difference between age at diagnosis of affecteds and age at exam of unaffecteds. Of 181 males, 142 had AAA; of 99 females, 35 had AAA. Using log-linear modeling AAA was significantly associated at the 5% level with gender, SM and HTN but not IH. The association of AAA with SM and HTN held when males and females were analyzed separately. HTN wasmore » -1.5 times more common in both affected males and females, while SM was 1.5 and 2 times more common in affected males and females, respectively. Tests of association and linkage analyses were performed with relevant candidate genes: 3 COL3A1 polymorphisms (C/T, ALA/THR, AvaII), 2 ELN polymorphisms (SER/GLY, (CA)n), FBN1(TAAA)n, 2 APOB polymorphisms (Xbal,Ins/Del), CLB4B (CA)n, PI and markers D1S243 (CA)n, HPR (CA)n and MFD23(CA)n. The loci were genotyped in > 100 AAA probands and > 95 normal controls. No statistically significant evidence of association at the 5% level was obtained for any of the loci using chi-square test of association. 28 families with 2 or more affecteds were analyzed using the affected pedigree member method (APM) and lod-score analyses. There was no evidence for linkage with any loci using APM. Lod-score analysis under an autosomal recessive model resulted in excluding linkage (lod score < -2) of all loci to AAA at {theta}=0.0. Under an autosomal dominant model, linkage was excluded at {theta}=0.0 to ELN, APOB, CLG4B, D1S243, HPR and MFD23. The various genes previously proposed in AAA pathogenesis are neither associated nor casually related in our study population.« less

MICA diversity and linkage disequilibrium with HLA-B alleles in renal-transplant candidates in southern Brazil.

PubMed

Yamakawa, Roger Haruki; Saito, Patrícia Keiko; Gelmini, Geórgia Fernanda; da Silva, José Samuel; Bicalho, Maria da Graça; Borelli, Sueli Donizete

2017-01-01

The major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located centromerically to the human leukocyte antigen (HLA)-B. The short distance between these loci in the MHC indicates the presence of linkage disequilibrium (LD). Similarly to the HLA, the MICA is highly polymorphic, and this polymorphism has not been well documented in different populations. In this study, we estimated the allelic frequencies of MICA and the linkage disequilibrium with HLA-B alleles in 346 renal-transplant candidates in southern Brazil. MICA and HLA were typed using the polymerase chain reaction-sequence-specific primer method (PCR-SSO), combined with the Luminex technology. A total of 19 MICA allele groups were identified. The most frequent allele groups were MICA*008 (21.6%), MICA*002 (17.0%) and MICA*004 (14.8%). The most common haplotypes were MICA*009-B*51 (7.8%), MICA*004-B*44 (6.06%) and MICA*002-B*35 (5.63%). As expected from the proximity of the MICA and HLA-B loci, most haplotypes showed strong LD. Renal patients and healthy subjects in the same region of Brazil showed statistically significant differences in their MICA polymorphisms. The MICA*027 allele group was more frequent in renal patients (Pc = 0.018, OR: 3.421, 95% CI: 1.516-7.722), while the MICA*019 allele group was more frequent in healthy subjects (Pc = 0.001, OR: 0.027, 95% CI: 0.002-0.469). This study provided information on the distribution of MICA polymorphisms and linkage disequilibrium with HLA-B alleles in Brazilian renal-transplant candidates. This information should help to determine the mechanisms of susceptibility to different diseases in patients with chronic kidney disease, and to elucidate the mechanisms involved in allograft rejection associated with MICA polymorphisms in a Brazilian population.

Quantitative trait loci (QTLs) for water use and crop production traits co-locate with major QTL for tolerance to water deficit in a fine-mapping population of pearl millet (Pennisetum glaucum L. R.Br.).

PubMed

Tharanya, Murugesan; Kholova, Jana; Sivasakthi, Kaliamoorthy; Seghal, Deepmala; Hash, Charles Tom; Raj, Basker; Srivastava, Rakesh Kumar; Baddam, Rekha; Thirunalasundari, Thiyagarajan; Yadav, Rattan; Vadez, Vincent

2018-04-21

Four genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes. Water saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress. This research aimed at demonstrating the close relationship between traits measured at different levels of plant organization, some putatively involved in water stress adaptation, and those responsible for agronomic performance. A fine-mapping population of pearl millet, segregating for a previously identified quantitative trait locus (QTL) for adaptation to terminal drought stress on LG02, was phenotyped for traits at different levels of plant organization in different experimental environments (pot culture, high-throughput phenotyping platform, lysimeters, and field). The linkages among traits across the experimental systems were analysed using principal component analysis and QTL co-localization approach. Four regions within the LG02-QTL were found and revealed substantial co-mapping of water use and agronomic traits. These regions, identified across experimental systems, provided genetic evidence of the tight linkages between traits phenotyped at a lower level of plant organization and agronomic traits assessed in the field, therefore deepening our understanding of complex traits and then benefiting both geneticists and breeders. In short: (1) under no/mild stress conditions, increasing biomass and tiller production increased water use and eventually yield; (2) under severe stress conditions, water savings at vegetative stage, from lower plant vigour and fewer tillers in that population, led to more water available during grain filling, expression of stay-green phenotypes, and higher yield.

The genetics of domestication of yardlong bean, Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis

PubMed Central

Kongjaimun, Alisa; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Vaughan, Duncan A.; Srinives, Peerasak

2012-01-01

Background and Aims The genetics of domestication of yardlong bean [Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis] is of particular interest because the genome of this legume has experienced divergent domestication. Initially, cowpea was domesticated from wild cowpea in Africa; in Asia a vegetable form of cowpea, yardlong bean, subsequently evolved from cowpea. Information on the genetics of domestication-related traits would be useful for yardlong bean and cowpea breeding programmes, as well as comparative genome study among members of the genus Vigna. The objectives of this study were to identify quantitative trait loci (QTLs) for domestication-related traits in yardlong bean and compare them with previously reported QTLs in closely related Vigna. Methods Two linkage maps were developed from BC1F1 and F2 populations from the cross between yardlong bean (V. unguiculata ssp. unguiculata cv.-gr. sesquipedalis) accession JP81610 and wild cowpea (V. unguiculata ssp. unguiculata var. spontanea) accession TVnu457. Using these linkage maps, QTLs for 24 domestication-related traits were analysed and mapped. QTLs were detected for traits related to seed, pod, stem and leaf. Key Results Most traits were controlled by between one and 11 QTLs. QTLs for domestication-related traits show co-location on several narrow genomic regions on almost all linkage groups (LGs), but especially on LGs 3, 7, 8 and 11. Major QTLs for sizes of seed, pod, stem and leaf were principally located on LG7. Pleiotropy or close linkage of genes for the traits is suggested in these chromosome regions. Conclusions This is the first report of QTLs for domestication-related traits in yardlong bean. The results provide a foundation for marker-assisted selection of domestication-related QTLs in yardlong bean and enhance understanding of domestication in the genus Vigna. PMID:22419763

Microseismic Event Grouping Based on PageRank Linkage at the Newberry Volcano Geothermal Site

NASA Astrophysics Data System (ADS)

Aguiar, A. C.; Myers, S. C.

2016-12-01

The Newberry Volcano DOE FORGE site in Central Oregon has been stimulated two times using high-pressure fluid injection to study the Enhanced Geothermal Systems (EGS) technology. Several hundred microseismic events were generated during the first stimulation in the fall of 2012. Initial locations of this microseismicity do not show well defined subsurface structure in part because event location uncertainties are large (Foulger and Julian, 2013). We focus on this stimulation to explore the spatial and temporal development of microseismicity, which is key to understanding how subsurface stimulation modifies stress, fractures rock, and increases permeability. We use PageRank, Google's initial search algorithm, to determine connectivity within the events (Aguiar and Beroza, 2014) and assess signal-correlation topology for the micro-earthquakes. We then use this information to create signal families and compare these to the spatial and temporal proximity of associated earthquakes. We relocate events within families (identified by PageRank linkage) using the Bayesloc approach (Myers et al., 2007). Preliminary relocations show tight spatial clustering of event families as well as evidence of events relocating to a different cluster than originally reported. We also find that signal similarity (linkage) at several stations, not just one or two, is needed in order to determine that events are in close proximity to one another. We show that indirect linkage of signals using PageRank is a reliable way to increase the number of events that are confidently determined to be similar to one another, which may lead to efficient and effective grouping of earthquakes with similar physical characteristics, such as focal mechanisms and stress drop. Our ultimate goal is to determine whether changes in the state of stress and/or changes in the generation of subsurface fracture networks can be detected using PageRank topology as well as aid in the event relocation to obtain more accurate subsurface structure. Prepared by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-699142.

Capsular Sialyltransferase Specificity Mediates Different Phenotypes in Streptococcus suis and Group B Streptococcus

PubMed Central

Roy, David; Takamatsu, Daisuke; Okura, Masatoshi; Goyette-Desjardins, Guillaume; Van Calsteren, Marie-Rose; Dumesnil, Audrey; Gottschalk, Marcelo; Segura, Mariela

2018-01-01

The capsular polysaccharide (CPS) represents a key virulence factor for most encapsulated streptococci. Streptococcus suis and Group B Streptococcus (GBS) are both well-encapsulated pathogens of clinical importance in veterinary and/or human medicine and responsible for invasive systemic diseases. S. suis and GBS are the only Gram-positive bacteria which express a sialylated CPS at their surface. An important difference between these two sialylated CPSs is the linkage between the side-chain terminal galactose and sialic acid, being α-2,6 for S. suis but α-2,3 for GBS. It is still unclear how sialic acid may affect CPS production and, consequently, the pathogenesis of the disease caused by these two bacterial pathogens. Here, we investigated the role of sialic acid and the putative effect of sialic acid linkage modification in CPS synthesis using inter-species allelic exchange mutagenesis. To this aim, a new molecular biogenetic approach to express CPS with modified sialic acid linkage was developed. We showed that sialic acid (and its α-2,6 linkage) is crucial for S. suis CPS synthesis, whereas for GBS, CPS synthesis may occur in presence of an α-2,6 sialyltransferase or in absence of sialic acid moiety. To evaluate the effect of the CPS composition/structure on sialyltransferase activity, two distinct capsular serotypes within each bacterial species were compared (S. suis serotypes 2 and 14 and GBS serotypes III and V). It was demonstrated that the observed differences in sialyltransferase activity and specificity between S. suis and GBS were serotype unrestricted. This is the first time that a study investigates the interspecies exchange of capsular sialyltransferase genes in Gram-positive bacteria. The obtained mutants represent novel tools that could be used to further investigate the immunomodulatory properties of sialylated CPSs. Finally, in spite of common CPS structural characteristics and similarities in the cps loci, sialic acid exerts differential control of CPS expression by S. suis and GBS. PMID:29666608

A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

PubMed Central

Jairin, Jirapong; Kobayashi, Tetsuya; Yamagata, Yoshiyuki; Sanada-Morimura, Sachiyo; Mori, Kazuki; Tashiro, Kosuke; Kuhara, Satoru; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Yamamoto, Kimiko; Matsumura, Masaya; Yasui, Hideshi

2013-01-01

In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH. PMID:23204257

A Statistical Analysis of IrisCode and Its Security Implications.

PubMed

Kong, Adams Wai-Kin

2015-03-01

IrisCode has been used to gather iris data for 430 million people. Because of the huge impact of IrisCode, it is vital that it is completely understood. This paper first studies the relationship between bit probabilities and a mean of iris images (The mean of iris images is defined as the average of independent iris images.) and then uses the Chi-square statistic, the correlation coefficient and a resampling algorithm to detect statistical dependence between bits. The results show that the statistical dependence forms a graph with a sparse and structural adjacency matrix. A comparison of this graph with a graph whose edges are defined by the inner product of the Gabor filters that produce IrisCodes shows that partial statistical dependence is induced by the filters and propagates through the graph. Using this statistical information, the security risk associated with two patented template protection schemes that have been deployed in commercial systems for producing application-specific IrisCodes is analyzed. To retain high identification speed, they use the same key to lock all IrisCodes in a database. The belief has been that if the key is not compromised, the IrisCodes are secure. This study shows that even without the key, application-specific IrisCodes can be unlocked and that the key can be obtained through the statistical dependence detected.

A statistical analysis of the elastic distortion and dislocation density fields in deformed crystals

DOE PAGES

Mohamed, Mamdouh S.; Larson, Bennett C.; Tischler, Jonathan Z.; ...

2015-05-18

The statistical properties of the elastic distortion fields of dislocations in deforming crystals are investigated using the method of discrete dislocation dynamics to simulate dislocation structures and dislocation density evolution under tensile loading. Probability distribution functions (PDF) and pair correlation functions (PCF) of the simulated internal elastic strains and lattice rotations are generated for tensile strain levels up to 0.85%. The PDFs of simulated lattice rotation are compared with sub-micrometer resolution three-dimensional X-ray microscopy measurements of rotation magnitudes and deformation length scales in 1.0% and 2.3% compression strained Cu single crystals to explore the linkage between experiment and the theoreticalmore » analysis. The statistical properties of the deformation simulations are analyzed through determinations of the Nye and Kr ner dislocation density tensors. The significance of the magnitudes and the length scales of the elastic strain and the rotation parts of dislocation density tensors are demonstrated, and their relevance to understanding the fundamental aspects of deformation is discussed.« less

A statistical inference for concentrations of benzo[a]pyrene partially measured in the ambient air of an industrial city in Korea

NASA Astrophysics Data System (ADS)

Kim, Yongku; Seo, Young-Kyo; Baek, Sung-Ok

2013-12-01

Although large quantities of air pollutants are released into the atmosphere, they are partially monitored and routinely assessed for their health implications. This paper proposes a statistical model describing the temporal behavior of hazardous air pollutants (HAPs), which can have negative effects on human health. Benzo[a]pyrene (BaP) is selected for statistical modeling. The proposed model incorporates the linkage between BaP and meteorology and is specifically formulated to identify meteorological effects and allow for seasonal trends. The model is used to estimate and forecast temporal fields of BaP conditional on observed (or forecasted) meteorological conditions, including temperature, precipitation, wind speed, and air quality. The effects of BaP on human health are examined by characterizing health indicators, namely the cancer risk and the hazard quotient. The model provides useful information for the optimal monitoring period and projection of future BaP concentrations for both industrial and residential areas in Korea.

Genetics and epidemiology, congenital anomalies and cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedman, J.M.

1997-03-01

Many of the basic statistical methods used in epidemiology - regression, analysis of variance, and estimation of relative risk, for example - originally were developed for the genetic analysis of biometric data. The familiarity that many geneticists have with this methodology has helped geneticists to understand and accept genetic epidemiology as a scientific discipline. It worth noting, however, that most of the work in genetic epidemiology during the past decade has been devoted to linkage and other family studies, rather than to population-based investigations of the type that characterize much of mainstream epidemiology. 30 refs., 2 tabs.

The Use of a Bayesian Hierarchy to Develop and Validate a Co-Morbidity Score to Predict Mortality for Linked Primary and Secondary Care Data from the NHS in England

PubMed Central

Card, Tim R.; West, Joe

2016-01-01

Background We have assessed whether the linkage between routine primary and secondary care records provided an opportunity to develop an improved population based co-morbidity score with the combined information on co-morbidities from both health care settings. Methods We extracted all people older than 20 years at the start of 2005 within the linkage between the Hospital Episodes Statistics, Clinical Practice Research Datalink, and Office for National Statistics death register in England. A random 50% sample was used to identify relevant diagnostic codes using a Bayesian hierarchy to share information between similar Read and ICD 10 code groupings. Internal validation of the score was performed in the remaining 50% and discrimination was assessed using Harrell’s C statistic. Comparisons were made over time, age, and consultation rate with the Charlson and Elixhauser indexes. Results 657,264 people were followed up from the 1st January 2005. 98 groupings of codes were derived from the Bayesian hierarchy, and 37 had an adjusted weighting of greater than zero in the Cox proportional hazards model. 11 of these groupings had a different weighting dependent on whether they were coded from hospital or primary care. The C statistic reduced from 0.88 (95% confidence interval 0.88–0.88) in the first year of follow up, to 0.85 (0.85–0.85) including all 5 years. When we stratified the linked score by consultation rate the association with mortality remained consistent, but there was a significant interaction with age, with improved discrimination and fit in those under 50 years old (C = 0.85, 0.83–0.87) compared to the Charlson (C = 0.79, 0.77–0.82) or Elixhauser index (C = 0.81, 0.79–0.83). Conclusions The use of linked population based primary and secondary care data developed a co-morbidity score that had improved discrimination, particularly in younger age groups, and had a greater effect when adjusting for co-morbidity than existing scores. PMID:27788230

Public relations effectiveness in public health institutions.

PubMed

Springston, Jeffrey K; Weaver Lariscy, Ruth Ann

2005-01-01

This article explores public relations effectiveness in public health institutions. First, the two major elements that comprise public relations effectiveness are discussed: reputation management and stakeholder relations. The factors that define effective reputation management are examined, as are the roles of issues and crisis management in building and maintaining reputation. The article also examines the major facets of stakeholder relations, including an inventory of stakeholder linkages and key audiences, such as the media. Finally, methods of evaluating public relations effectiveness at both the program level and the institutional level are explored.

Main-chain supramolecular block copolymers.

PubMed

Yang, Si Kyung; Ambade, Ashootosh V; Weck, Marcus

2011-01-01

Block copolymers are key building blocks for a variety of applications ranging from electronic devices to drug delivery. The material properties of block copolymers can be tuned and potentially improved by introducing noncovalent interactions in place of covalent linkages between polymeric blocks resulting in the formation of supramolecular block copolymers. Such materials combine the microphase separation behavior inherent to block copolymers with the responsiveness of supramolecular materials thereby affording dynamic and reversible materials. This tutorial review covers recent advances in main-chain supramolecular block copolymers and describes the design principles, synthetic approaches, advantages, and potential applications.

Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm.

PubMed

Teh, Chee-Keng; Ong, Ai-Ling; Kwong, Qi-Bin; Apparow, Sukganah; Chew, Fook-Tim; Mayes, Sean; Mohamed, Mohaimi; Appleton, David; Kulaveerasingam, Harikrishna

2016-01-08

GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10(-4)) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.

HLA-linked rheumatoid arthritis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasstedt, S.J.; Clegg, D.O.; Ingles, L.

Twenty-eight pedigrees were ascertained through pairs of first-degree relatives diagnosed with rheumatoid arthritis (RA). RA was confirmed in 77 pedigree members including probands; the absence of disease was verified in an additional 261 pedigree members. Pedigree members were serologically typed for HLA. We used likelihood analysis to statistically characterize the HLA-linked RA susceptibility locus. The genetic model assumed tight linkage to HLA. The analysis supported the existence of an HLA-linked RA susceptibility locus, estimated the lifetime penetrance as 41% in male homozygotes and as 48% in female homozygotes. Inheritance was recessive in males and was nearly recessive in females. Inmore » addition, the analysis attributed 78% of the variance within genotypes to genetic or environmental effects shared by siblings. The genetic model inferred in this analysis is consistent with previous association, linkage, and familial aggregation studies of RA. The inferred HLA-linked RA susceptibility locus accounts for approximately one-fifth of the RA in the population. Although other genes may account for the remaining familial RA, a large portion of RA cases may occur sporadically. 79 refs., 9 tabs.« less

QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed.

PubMed

Ates, Duygu; Aldemir, Secil; Yagmur, Bulent; Kahraman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Muhammed Bahattin

2018-05-04

This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross "CDC Redberry" × "ILL7502". Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn) concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTL for Mn concentration were identified using composite interval mapping (CIM). All QTL were statistically significant and explained 15.3-24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts. Copyright © 2018 Ates et al.

Environmental Roots of the Late Bronze Age Crisis

PubMed Central

Kaniewski, David; Van Campo, Elise; Guiot, Joël; Le Burel, Sabine; Otto, Thierry; Baeteman, Cecile

2013-01-01

The Late Bronze Age world of the Eastern Mediterranean, a rich linkage of Aegean, Egyptian, Syro-Palestinian, and Hittite civilizations, collapsed famously 3200 years ago and has remained one of the mysteries of the ancient world since the event’s retrieval began in the late 19th century AD/CE. Iconic Egyptian bas-reliefs and graphic hieroglyphic and cuneiform texts portray the proximate cause of the collapse as the invasions of the “Peoples-of-the-Sea” at the Nile Delta, the Turkish coast, and down into the heartlands of Syria and Palestine where armies clashed, famine-ravaged cities abandoned, and countrysides depopulated. Here we report palaeoclimate data from Cyprus for the Late Bronze Age crisis, alongside a radiocarbon-based chronology integrating both archaeological and palaeoclimate proxies, which reveal the effects of abrupt climate change-driven famine and causal linkage with the Sea People invasions in Cyprus and Syria. The statistical analysis of proximate and ultimate features of the sequential collapse reveals the relationships of climate-driven famine, sea-borne-invasion, region-wide warfare, and politico-economic collapse, in whose wake new societies and new ideologies were created. PMID:23967146

[Registry of the Italian Institute for Occupational Prevention and Safety of local productive units: methodology and structure].

PubMed

Scarselli, A; Leva, A; Campo, G; Marconi, M; Nesti, M; Erba, P

2005-01-01

The Italian Institute for Occupational Prevention and Safety (ISPESL) carried out a register of enterprises operating in industry, services and agriculture sector to provide information on their location, economical activity and occupational data. This database has been built merging administrative files from the National Institute of Social Security (INPS) and the Computer Science Society of Italian Chambers of Commerce (InfoCamere). Enterprises have been classified by economic sector - in accordance with ISTAT (National Statistics Institute) "Ateco91" classification--and by accuracy level of the record linkage. In details, three different subsystems have been set up: (A) enterprises satisfying linkage; (B) enterprises in InfoCamere file not linked with INPS file; (C) enterprises in INPS file not linked with InfoCamere file. In the whole, 6.026.676 factories have been collected, of which 1.188.784 in group A, 4.543.091 in group B and 294.801 in group C. Establishing a database of information on industries may be useful to improve preventive programs and to plan health care surveillance systems.

The impact of meteorology on ozone in Houston

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eder, B.K.; Davis, J.M.; Nychka, D.

1997-12-31

This paper compares the results from both a one-stage hierarchical clustering technique (average linkage) and a two-stage technique (average linkage then k-means) as part of an objective meteorological Classification scheme designed to better elucidate ozone`s dependence on meteorology in the Houston, Texas, area. When applied to twelve years of meteorological data (1981-1992), each technique identified seven statistically distinct meteorological regimes, the majority of which exhibited significantly different daily 1-hour maximum ozone (O{sub 3}) concentrations. While both clustering approaches proved successful, the two-stage approach did appear superior in terms of better segregation of the mean O{sub 3}, concentrations. Both approaches indicatedmore » that the largest mean daily one-hour maximum concentrations are associated with migrating anticyclones and not with the quasi-permanent Bermuda High that often dominates the southeastern United States during the summer. As a result, maximum ozone concentrations are just as likely during the months of April, May, September and October as they are during the summer months. These findings support and help explain the unique O{sub 3}, climatology experienced by the Houston area.« less

Sudden unexpected death in infants in the Oxford Record Linkage Area: The mother

PubMed Central

Fedrick, Jean

1974-01-01

Of the 206 cases of sudden unexpected death in infancy (SUD) 170 were linked with the maternity information and birth certificates on the Oxford Record Linkage files. Statistically highly significant correlations were demonstrated with low maternal age, high parity, and low social class, the last two associations being more marked among the mothers of infants who died after the 12th week. Each case of SUD was then matched with three control livebirths for maternal age, parity, civil state of mother, social class, year and hospital of delivery, and as closely as possible for area of residence. A comparison of mothers of cases with those of the controls revealed a highly significant preponderance of women who were born outside the area, and no significant effect with maternal religion, previous pregnancy loss, or ABO blood group. Other pregnancies occurring to the case and control mothers between 1965 and 1971 were also traced. It was shown that the infant dying an SUD was more likely to have been conceived within six months of the birth of his preceding sib. PMID:4854522

101 Key Statistics on Work and Family for the 1990s. The BNA Special Report Series on Work and Family: Special Report No. 21.

ERIC Educational Resources Information Center

Bureau of National Affairs, Inc., Washington, DC.

This special report updates a September, 1988 Bureau of National Affairs (BNA) special report, "82 Key Statistics on Work and Family Issues," by presenting 101 new statistics on work and family concerns. Data concern: (1) child care; (2) parental leave; (3) elder care; (4) flexible work schedules; and (5) miscellaneous issues, such as…

Factors influencing environmental attitude: The relationship between environmental attitude defensibility and cognitive reasoning level

NASA Astrophysics Data System (ADS)

Yount, James R.; Horton, Phillip B.

The purpose of this study was to investigate the relationship between factors believed to contribute to the formation of environmental attitudes by college nonscience majors. Key relationships addressed were the effects of a university environmental studies course on (a) environmental attitudes, (b) the amount of factual information that is brought to bear on an environmental attitude decision (defensibility), and (c) the linkages between the affective and the cognitive domains of freshman and sophomore students. When compared to the control group, the students who attended an environmental studies class did not significantly change their attitudes, but they did exhibit increases in their total [F(3, 132) = 5.91, p < 0.01] and count [F(3, 132) = 4.86, p < 0.01] levels of defensibility. These findings corroborate work performed by Kinsey (1978) and Kinsey and Wheatley (1980, 1984). In addition, students in the environmental studies course who had higher cognitive reasoning scores were more prone to increase defensibility [F(6, 129) = 3.78, p < 0.01]. These data imply a linkage between cognitive and affective domains in the environmental attitude decision-making process.

Selective digestion of Ba2+/Ca2+ alginate gel microdroplets for single-cell handling

NASA Astrophysics Data System (ADS)

Odaka, Masao; Hattori, Akihiro; Matsuura, Kenji; Yasuda, Kenji

2018-06-01

Cells encapsuled by polymer microdroplets are an effective platform for the identification and separation of individual cells for single-cell-based analysis. However, a key challenge is to maintain and release the captured cells in the microdroplets selectively, nondestructively, and noninvasively. We developed a simple method of encapsulating cells in alginate microdroplets having different digestion characteristics. Cells were diluted with an alginate polymer of sol state and encapsulated into microdroplets with Ba2+ and Ca2+ by a spray method. When a chelating buffer was applied, alginate gel microdroplets were digested according to the difference in chelating efficiency of linkage-divalent cations; hence, two types of alginate microdroplets were formed. Moreover, we examined the capability of the alginate gel to exchange linkage-divalent cations and found that both Ca2+ exchange in Ba-alginate microdroplets and Ba2+ exchange in Ca-alginate microdroplets occurred. These results indicate that the potential applications of a mixture of alginate microdroplets with different divalent cations control the selective digestion of microdroplets to improve the high-throughput, high-content microdroplet-based separation, analysis, or storage of single cells.

The contribution of veterinary medicine to public health and poverty reduction in developing countries.

PubMed

Muma, John B; Mwacalimba, Kennedy K; Munang'andu, Hetron M; Matope, Gift; Jenkins, Akinbowale; Siamudaala, Victor; Mweene, Aaron S; Marcotty, Tanguy

2014-01-01

Few studies have explicitly examined the linkages between human health, animal disease control and poverty alleviation. This paper reviews the contribution that veterinary medicine can make to poverty alleviation in sub-Saharan Africa. Our analysis attempts to explore aspects of this contribution under five themes: food production; food safety; impact and control of zoonotic infections; promotion of ecotourism; and environmental protection. While these areas of human activity have, more or less, fallen under the influence of the veterinary profession to varying degrees, we attempt to unify this mandate using a 'One Health' narrative, for the purpose of providing clarity on the linkages between the veterinary and other professions, livestock production and poverty alleviation. Future opportunities for improving health and reducing poverty in the context of developing African countries are also discussed. We conclude that veterinary science is uniquely positioned to play a key role in both poverty reduction and the promotion of health, a role that can be enhanced through the reorientation of the profession's goals and the creation of synergies with allied and related professions.

Human health and the water environment: using the DPSEEA framework to identify the driving forces of disease.

PubMed

Gentry-Shields, Jennifer; Bartram, Jamie

2014-01-15

There is a growing awareness of global forces that threaten human health via the water environment. A better understanding of the dynamic between human health and the water environment would enable prediction of the significant driving forces and effective strategies for coping with or preventing them. This report details the use of the Driving Force-Pressure-State-Exposure-Effect-Action (DPSEEA) framework to explore the linkage between water-related diseases and their significant driving forces. The DPSEEA frameworks indicate that a select group of driving forces, including population growth, agriculture, infrastructure (dams and irrigation), and climate change, is at the root cause of key global disease burdens. Construction of the DPSEEA frameworks also allows for the evaluation of public health interventions. Sanitation was found to be a widely applicable and effective intervention, targeting the driver/pressure linkage of most of the water-related diseases examined. Ultimately, the DPSEEA frameworks offer a platform for constituents in both the health and environmental fields to collaborate and commit to a common goal targeting the same driving forces. © 2013.

Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides.

PubMed

Tamura, Kazune; Hemsworth, Glyn R; Déjean, Guillaume; Rogers, Theresa E; Pudlo, Nicholas A; Urs, Karthik; Jain, Namrata; Davies, Gideon J; Martens, Eric C; Brumer, Harry

2017-10-10

Microbial utilization of complex polysaccharides is a major driving force in shaping the composition of the human gut microbiota. There is a growing appreciation that finely tuned polysaccharide utilization loci enable ubiquitous gut Bacteroidetes to thrive on the plethora of complex polysaccharides that constitute "dietary fiber." Mixed-linkage β(1,3)/β(1,4)-glucans (MLGs) are a key family of plant cell wall polysaccharides with recognized health benefits but whose mechanism of utilization has remained unclear. Here, we provide molecular insight into the function of an archetypal MLG utilization locus (MLGUL) through a combination of biochemistry, enzymology, structural biology, and microbiology. Comparative genomics coupled with growth studies demonstrated further that syntenic MLGULs serve as genetic markers for MLG catabolism across commensal gut bacteria. In turn, we surveyed human gut metagenomes to reveal that MLGULs are ubiquitous in human populations globally, which underscores the importance of gut microbial metabolism of MLG as a common cereal polysaccharide. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Irreversible covalent modification of type I dehydroquinase with a stable Schiff base.

PubMed

Tizón, Lorena; Maneiro, María; Peón, Antonio; Otero, José M; Lence, Emilio; Poza, Sergio; van Raaij, Mark J; Thompson, Paul; Hawkins, Alastair R; González-Bello, Concepción

2015-01-21

The irreversible inhibition of type I dehydroquinase (DHQ1), the third enzyme of the shikimic acid pathway, is investigated by structural, biochemical and computational studies. Two epoxides, which are mimetics of the natural substrate, were designed as irreversible inhibitors of the DHQ1 enzyme and to study the binding requirements of the linkage to the enzyme. The epoxide with the S configuration caused the covalent modification of the protein whereas no reaction was obtained with its epimer. The first crystal structure of DHQ1 from Salmonella typhi covalently modified by the S epoxide, which is reported at 1.4 Å, revealed that the modified ligand is surprisingly covalently attached to the essential Lys170 by the formation of a stable Schiff base. The experimental and molecular dynamics simulation studies reported here highlight the huge importance of the conformation of the C3 carbon of the ligand for covalent linkage to this type of aldolase I enzyme, revealed the key role played by the essential His143 as a Lewis acid in this process and show the need for a neatly closed active site for catalysis.

Developing the next generation of dissemination and implementation researchers: insights from initial trainees.

PubMed

Stamatakis, Katherine A; Norton, Wynne E; Stirman, Shannon W; Melvin, Cathy; Brownson, Ross C

2013-03-12

Dissemination and implementation (D&I) research is a relatively young discipline, underscoring the importance of training and career development in building and sustaining the field. As such, D&I research faces several challenges in designing formal training programs and guidance for career development. A cohort of early-stage investigators (ESI) recently involved in an implementation research training program provided a resource for formative data in identifying needs and solutions around career development. Responses outlined fellows' perspectives on the perceived usefulness and importance of, as well as barriers to, developing practice linkages, acquiring additional methods training, academic advancement, and identifying institutional supports. Mentorship was a cross-cutting issue and was further discussed in terms of ways it could foster career advancement in the context of D&I research. Advancing an emerging field while simultaneously developing an academic career offers a unique challenge to ESIs in D&I research. This article summarizes findings from the formative data that outlines some directions for ESIs and provides linkages to the literature and other resources on key points.

Extension of the lod score: the mod score.

PubMed

Clerget-Darpoux, F

2001-01-01

In 1955 Morton proposed the lod score method both for testing linkage between loci and for estimating the recombination fraction between them. If a disease is controlled by a gene at one of these loci, the lod score computation requires the prior specification of an underlying model that assigns the probabilities of genotypes from the observed phenotypes. To address the case of linkage studies for diseases with unknown mode of inheritance, we suggested (Clerget-Darpoux et al., 1986) extending the lod score function to a so-called mod score function. In this function, the variables are both the recombination fraction and the disease model parameters. Maximizing the mod score function over all these parameters amounts to maximizing the probability of marker data conditional on the disease status. Under the absence of linkage, the mod score conforms to a chi-square distribution, with extra degrees of freedom in comparison to the lod score function (MacLean et al., 1993). The mod score is asymptotically maximum for the true disease model (Clerget-Darpoux and Bonaïti-Pellié, 1992; Hodge and Elston, 1994). Consequently, the power to detect linkage through mod score will be highest when the space of models where the maximization is performed includes the true model. On the other hand, one must avoid overparametrization of the model space. For example, when the approach is applied to affected sibpairs, only two constrained disease model parameters should be used (Knapp et al., 1994) for the mod score maximization. It is also important to emphasize the existence of a strong correlation between the disease gene location and the disease model. Consequently, there is poor resolution of the location of the susceptibility locus when the disease model at this locus is unknown. Of course, this is true regardless of the statistics used. The mod score may also be applied in a candidate gene strategy to model the potential effect of this gene in the disease. Since, however, it ignores the information provided both by disease segregation and by linkage disequilibrium between the marker alleles and the functional disease alleles, its power of discrimination between genetic models is weak. The MASC method (Clerget-Darpoux et al., 1988) has been designed to address more efficiently the objectives of a candidate gene approach.

Cost analysis of two community-based HIV testing service modalities led by a Non-Governmental Organization in Cape Town, South Africa.

PubMed

Meehan, Sue-Ann; Beyers, Nulda; Burger, Ronelle

2017-12-02

In South Africa, the financing and sustainability of HIV services is a priority. Community-based HIV testing services (CB-HTS) play a vital role in diagnosis and linkage to HIV care for those least likely to utilise government health services. With insufficient estimates of the costs associated with CB-HTS provided by NGOs in South Africa, this cost analysis explored the cost to implement and provide services at two NGO-led CB-HTS modalities and calculated the costs associated with realizing key HIV outputs for each CB-HTS modality. The study took place in a peri-urban area where CB-HTS were provided from a stand-alone centre and mobile service. Using a service provider (NGO) perspective, all inputs were allocated by HTS modality with shared costs apportioned according to client volume or personnel time. We calculated the total cost of each HTS modality and the cost categories (personnel, capital and recurring goods/services) across each HTS modality. Costs were divided into seven pre-determined project components, used to examine cost drivers. HIV outputs were analysed for each HTS modality and the mean cost for each HIV output was calculated per HTS modality. The annual cost of the stand-alone and mobile modalities was $96,616 and $77,764 respectively, with personnel costs accounting for 54% of the total costs at the stand-alone. For project components, overheads and service provision made up the majority of the costs. The mean cost per person tested at stand-alone ($51) was higher than at the mobile ($25). Linkage to care cost at the stand-alone ($1039) was lower than the mobile ($2102). This study provides insight into the cost of an NGO led CB-HTS project providing HIV testing and linkage to care through two CB-HIV testing modalities. The study highlights; (1) the importance of including all applicable costs (including overheads) to ensure an accurate cost estimate that is representative of the full service implementation cost, (2) the direct link between test uptake and mean cost per person tested, and (3) the need for effective linkage to care strategies to increase linkage and thereby reduce the mean cost per person linked to HIV care.

Mortality experience of the 1986-2000 National Health Interview Survey Linked Mortality Files participants.

PubMed

Ingram, Deborah D; Lochner, Kimberly A; Cox, Christine S

2008-10-01

The National Center for Health Statistics (NCHS) has produced the 1986-2000 National Health Interview Survey (NHIS) Linked Mortality Files by linking eligible adults in the 1986-2000 NHIS cohorts through probabilistic record linkage to the National Death Index to obtain mortality follow-up through December 31, 2002. The resulting files contain more than 120,000 deaths and an average of 9 years of survival time. To assess how well mortality was ascertained in the linked mortality files, NCHS has conducted a comparison of the mortality experience of the 1986-2000 NHIS cohorts with that of the U.S. population. This report presents the results of this comparative mortality assessment. Methods The survival of each annual NHIS cohort was compared with that of the U.S. population during the same period. Cumulative survival probabilities for each annual NHIS cohort were derived using the Kaplan-Meier product limit method, and corresponding cumulative survival probabilities were computed for the U.S. population using information from annual U.S. life tables. The survival probabilities were calculated at various lengths of follow-up for each age-race-sex group of each NHIS cohort and for the U.S. population. Results As expected, mortality tended to be underestimated in the NHIS cohorts because the sample includes only civilian, noninstitutionalized persons, but this underestimation generally was not statistically significant. Statistically significant differences increased with length of follow-up, occurred more often for white females than for the other race-sex groups, and occurred more often in the oldest age groups. In general, the survival experience of the age-race-sex groups of each NHIS cohort corresponds quite closely to that of the U.S. population, providing support that the ascertainment of mortality through the probabilistic record linkage accurately reflects the mortality experience of the NHIS cohorts.

Measurement-device-independent quantum key distribution with source state errors and statistical fluctuation

NASA Astrophysics Data System (ADS)

Jiang, Cong; Yu, Zong-Wen; Wang, Xiang-Bin

2017-03-01

We show how to calculate the secure final key rate in the four-intensity decoy-state measurement-device-independent quantum key distribution protocol with both source errors and statistical fluctuations with a certain failure probability. Our results rely only on the range of only a few parameters in the source state. All imperfections in this protocol have been taken into consideration without assuming any specific error patterns of the source.

Social networks, social support, and mortality among older people in Japan.

PubMed

Sugisawa, H; Liang, J; Liu, X

1994-01-01

This study examined the effects of social networks and social support on the mortality of a national probability sample of 2,200 elderly Japanese persons during a three-year period. The direct and indirect effects of social relationships were assessed by using hazard rate models in conjunction with ordinary least squares regressions. Among the five measures of social relationships, social participation is shown to have a strong impact on mortality, and this effect remains statistically significant when other factors are considered. Social participation, social support, and feelings of loneliness are found to have indirect effects on the mortality of the Japanese elders through their linkages with chronic diseases, functional status, and self-rated health. On the other hand, marital status and social contacts are not shown to have statistically significant effects on the risk of dying, either directly or indirectly.

Gender identity disorders and multiple sclerosis risk: A national record-linkage study.

PubMed

Pakpoor, Julia; Wotton, Clare J; Schmierer, Klaus; Giovannoni, Gavin; Goldacre, Michael J

2016-11-01

An altered balance of gonadal hormones in males with gender identity disorders (GIDs) may increase multiple sclerosis (MS) risk both inherently and secondary to treatment in undergoing male-to-female conversion. We investigated any association between GIDs and MS through analysis of record-linked hospital statistics. Analysis of English Hospital Episode Statistics, 1999-2012. The adjusted rate ratio (RR) of MS following GIDs in males was 6.63 (95% confidence interval (95% CI) = 1.81-17.01, p = 0.0002). The RR of MS following GIDs in females was 1.44 (95% CI = 0.47-3.37, p = 0.58). We report a strong association between GIDs and MS in male-to-females, supporting a potential role for low testosterone and/or feminising hormones on MS risk in males. © The Author(s), 2016.

Testing association and linkage using affected-sib-parent study designs.

PubMed

Millstein, Joshua; Siegmund, Kimberly D; Conti, David V; Gauderman, W James

2005-11-01

We have developed a method for jointly testing linkage and association using data from affected sib pairs and their parents. We specify a conditional logistic regression model with two covariates, one that quantifies association (either direct association or indirect association via linkage disequilibrium), and a second that quantifies linkage. The latter covariate is computed based on expected identity-by-descend (ibd) sharing of marker alleles between siblings. In addition to a joint test of linkage and association, our general framework can be used to obtain a linkage test comparable to the mean test (Blackwelder and Elston [1985] Genet. Epidemiol. 2:85-97), and an association test comparable to the Family-Based Association Test (FBAT; Rabinowitz and Laird [2000] Hum. Hered. 50:211-223). We present simulation results demonstrating that our joint test can be more powerful than some standard tests of linkage or association. For example, with a relative risk of 2.7 per variant allele at a disease locus, the estimated power to detect a nearby marker with a modest level of LD was 58.1% by the mean test (linkage only), 69.8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping. Copyright 2005 Wiley-Liss, Inc.

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.

PubMed Central

McKeigue, P M

1997-01-01

Where recent admixture has occurred between two populations that have different disease rates for genetic reasons, family-based association studies can be used to map the genes underlying these differences, if the ancestry of the alleles at each locus examined can be assigned to one of the two founding populations. This article explores the statistical power and design requirements of this approach. Markers suitable for assigning the ancestry of genomic regions could be defined by grouping alleles at closely spaced microsatellite loci into haplotypes, or generated by representational difference analysis. For a given relative risk between populations, the sample size required to detect a disease locus that accounts for this relative risk by linkage-disequilibrium mapping in an admixed population is not critically dependent on assumptions about genotype penetrances or allele frequencies. Using the transmission-disequilibrium test to search the genome for a locus that accounts for a relative risk of between 2 and 3 in a high-risk population, compared with a low-risk population, generally requires between 150 and 800 case-parent pairs of mixed descent. The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture. This approach has greater statistical power than allele-sharing designs and has obvious applications to the genetics of hypertension, non-insulin-dependent diabetes, and obesity. PMID:8981962

Covariance Between Genotypic Effects and its Use for Genomic Inference in Half-Sib Families

PubMed Central

Wittenburg, Dörte; Teuscher, Friedrich; Klosa, Jan; Reinsch, Norbert

2016-01-01

In livestock, current statistical approaches utilize extensive molecular data, e.g., single nucleotide polymorphisms (SNPs), to improve the genetic evaluation of individuals. The number of model parameters increases with the number of SNPs, so the multicollinearity between covariates can affect the results obtained using whole genome regression methods. In this study, dependencies between SNPs due to linkage and linkage disequilibrium among the chromosome segments were explicitly considered in methods used to estimate the effects of SNPs. The population structure affects the extent of such dependencies, so the covariance among SNP genotypes was derived for half-sib families, which are typical in livestock populations. Conditional on the SNP haplotypes of the common parent (sire), the theoretical covariance was determined using the haplotype frequencies of the population from which the individual parent (dam) was derived. The resulting covariance matrix was included in a statistical model for a trait of interest, and this covariance matrix was then used to specify prior assumptions for SNP effects in a Bayesian framework. The approach was applied to one family in simulated scenarios (few and many quantitative trait loci) and using semireal data obtained from dairy cattle to identify genome segments that affect performance traits, as well as to investigate the impact on predictive ability. Compared with a method that does not explicitly consider any of the relationship among predictor variables, the accuracy of genetic value prediction was improved by 10–22%. The results show that the inclusion of dependence is particularly important for genomic inference based on small sample sizes. PMID:27402363

A study of chromosome 4p markers and dopamine D5 receptor gene in schizophrenia and bipolar disorder.

PubMed

Asherson, P; Mant, R; Williams, N; Cardno, A; Jones, L; Murphy, K; Collier, D A; Nanko, S; Craddock, N; Morris, S; Muir, W; Blackwood, B; McGuffin, P; Owen, M J

1998-07-01

There are several lines of evidence which suggest that chromosome 4p may contain a major susceptibility locus for the functional psychoses. We previously reported a family (family 50) with cases of schizophrenia and schizoaffective disorder which gave maximum lod scores of 1.96 and 1.84 respectively with the markers D4S403 and a microsatellite near to DRD5 (DRD5-M). More recently Blackwood and co-workers described a family segregating bipolar and unipolar affective disorders which gives a maximum lod score of 4.1 with the marker D4S394, which lies 10 cM from D4S403. They obtained a combined maximum lod of 3.3 in their total sample of 12 bipolar families and found significant evidence of heterogeneity (chi 2 = 18.8, df = 2, P = 0.00008). Here we report the results of a linkage study of chromosome 4p markers in a sample of 24 multiply affected families with schizophrenia and related disorders. We obtained an overall maximum lod of 1.12 with D4S403 under both dominant and recessive modes of transmission, with no statistical support for heterogeneity within our sample. Examination of family by family data shows that only family 50 appears to show linkage at this locus. However, a discrepancy exists since our study examined families fulfilling criteria for a linkage study of schizophrenia while Blackwood et al examined families included in a genetic linkage study of bipolar disorder. This may be explained by the clinical features displayed by members of family 50, which show that all the affected members have some affective symptoms. It is therefore possible that a broad phenotype including unipolar depression, bipolar disorder, schizoaffective disorder and schizophrenia when accompanied by significant affective symptoms can result from mutations within a gene in this region. The dopamine D5 receptor gene lies within the region identified by the linkage studies and is therefore a major candidate for the putative disease gene. In family 50 we have looked for mutations of DRD5 by sequence analysis of the coding region and single stranded conformational polymorphism (SSCP) analysis of the promoter. SSCP analysis of the coding and promoter regions have also been carried out in unrelated cases of DSM-IIIR schizophrenia. Finally association studies of the (TC)n repeat in the promoter and schizophrenia, and DRD5-M and bipolar disorder were performed. These studies provided no further evidence supporting the possibility that mutations in DRD5 give rise to the linkage findings or are acting as susceptibility loci in schizophrenia or bipolar disorder.

Growth chronology of Greenland Cockles (Serripes groenlandicus) from Bear Island, Svalbard, Norway

NASA Astrophysics Data System (ADS)

Carroll, Michael; Ambrose, William; Locke, William; Wanamaker, Alan

2017-04-01

Climate change is occurring rapidly in the Arctic, and observing the links between environmental drivers and biological effects can provide key information on the ecosystem consequences of climate change. Analysis of shell-based records of mollusks (sclerochronology) provides an effective and expanding approach to reconstructing environmental-ecological linkages. In particular, annually resolved archives can be key indicators of how climate change manifests in the marine ecosystem. We developed a master growth chronology of the Greenland Cockle (Serripes groenlandicus) from Bear Island (Bjørnøya), Svalbard, Norway (74°41'N, 18°56'E) from analysis of annual shell increments. The chronology was developed from 20 individuals ranging in age from 24 to 45 years old (the oldest known individuals of this species to date). The chronology, expressed as a standardized growth index (SGI), extended from 1968 to 2012 and exhibited a cyclical pattern, with decadal periods of high growth, alternating with slower growth intervals. We also identified significant relationships between large-scale climate regimes (e.g. NAO, AMO), local environmental conditions (e.g. sea temperature, sea ice), and shell growth. Additionally, growth chronologies, and environmental linkages were compared from this, near the southern extent of the Barents Sea polar front, with other Arctic locations influenced by different water masses to examine the nature of the environmental regulation on shell growth of this species in the Barents Sea and Arctic Ocean. We conclude that the Greenland Cockle is quite sensitive to environmental changes over annual to decadal scales and therefore can serve as a proxy of climate change effects on ecosystem processes in the Arctic.

Data linkage capabilities in Australia: practical issues identified by a Population Health Research Network 'Proof of Concept project'.

PubMed

Mitchell, Rebecca J; Cameron, Cate M; McClure, Rod J; Williamson, Ann M

2015-08-01

To describe the practical issues that need to be overcome to conduct national data linkage projects in Australia and propose recommendations to improve efficiency. Review of the processes, documentation and applications required to conduct national data linkage in Australia. The establishment of state and national data linkage centres in Australia has placed Australia at the forefront of research linking health-related administrative data collections. However, improvements are needed to reduce the clerical burden on researchers, simplify the process of obtaining ethics approval, improve data accessibility, and thus improve the efficiency of data linkage research. While a sound state and national data linkage infrastructure is in place, the current complexity, duplication and lack of cohesion undermines any attempts to conduct research involving national record linkage in a timely manner. Data linkage applications and Human Research Ethics Committee approval processes need to be streamlined and duplication removed, in order to reduce the administrative and financial burden on researchers if national data linkage research is to be viable. © 2015 Public Health Association of Australia.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption

PubMed Central

2015-01-01

Objective Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. Methods To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Results Our solution supports evaluation of the D′ measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. Conclusions With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical. PMID:26732892

Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia.

PubMed

Cannon, Tyrone D; Thompson, Paul M; van Erp, Theo G M; Huttunen, Matti; Lonnqvist, Jouko; Kaprio, Jaakko; Toga, Arthur W

2006-01-01

There is an urgent need to decipher the complex nature of genotype-phenotype relationships within the multiple dimensions of brain structure and function that are compromised in neuropsychiatric syndromes such as schizophrenia. Doing so requires sophisticated methodologies to represent population variability in neural traits and to probe their heritable and molecular genetic bases. We have recently developed and applied computational algorithms to map the heritability of, as well as genetic linkage and association to, neural features encoded using brain imaging in the context of three-dimensional (3D), populationbased, statistical brain atlases. One set of algorithms builds on our prior work using classical twin study methods to estimate heritability by fitting biometrical models for additive genetic, unique, and common environmental influences. Another set of algorithms performs regression-based (Haseman-Elston) identical-bydescent linkage analysis and genetic association analysis of DNA polymorphisms in relation to neural traits of interest in the same 3D population-based brain atlas format. We demonstrate these approaches using samples of healthy monozygotic (MZ) and dizygotic (DZ) twin pairs, as well as MZ and DZ twin pairs discordant for schizophrenia, but the methods can be generalized to other classes of relatives and to other diseases. The results confirm prior evidence of genetic influences on gray matter density in frontal brain regions. They also provide converging evidence that the chromosome 1q42 region is relevant to schizophrenia by demonstrating linkage and association of markers of the Transelin-Associated-Factor-X and Disrupted-In- Schizophrenia-1 genes with prefrontal cortical gray matter deficits in twins discordant for schizophrenia.

The Topographic Design of River Channels for Form-Process Linkages.

PubMed

Brown, Rocko A; Pasternack, Gregory B; Lin, Tin

2016-04-01

Scientists and engineers design river topography for a wide variety of uses, such as experimentation, site remediation, dam mitigation, flood management, and river restoration. A recent advancement has been the notion of topographical design to yield specific fluvial mechanisms in conjunction with natural or environmental flow releases. For example, the flow convergence routing mechanism, whereby shear stress and spatially convergent flow migrate or jump from the topographic high (riffle) to the low point (pool) from low to high discharge, is thought to be a key process able to maintain undular relief in gravel bedded rivers. This paper develops an approach to creating riffle-pool topography with a form-process linkage to the flow convergence routing mechanism using an adjustable, quasi equilibrium synthetic channel model. The link from form to process is made through conceptualizing form-process relationships for riffle-pool couplets into geomorphic covariance structures (GCSs) that are then quantitatively embedded in a synthetic channel model. Herein, GCSs were used to parameterize a geometric model to create five straight, synthetic river channels with varying combinations of bed and width undulations. Shear stress and flow direction predictions from 2D hydrodynamic modeling were used to determine if scenarios recreated aspects of the flow convergence routing mechanism. Results show that the creation of riffle-pool couplets that experience flow convergence in straight channels requires GCSs with covarying bed and width undulations in their topography as supported in the literature. This shows that GCSs are a useful way to translate conceptualizations of form-process linkages into quantitative models of channel form.

Linkages between the South and East Asian summer monsoons: a review and revisit

NASA Astrophysics Data System (ADS)

Ha, Kyung-Ja; Seo, Ye-Won; Lee, June-Yi; Kripalani, R. H.; Yun, Kyung-Sook

2017-07-01

The relationship between the South Asia monsoon (SAM) and the East Asia monsoon (EAM) possibly modulated by both external forcings and internal dynamics has been a long-standing and controversial issue in climate sciences. This study reviews their linkages as revealed in modern records and model simulations during the past, present and future, and provides a comprehensive explanation of the key mechanisms controlling the diversity of the SAM-EAM relationship. Particular attention is paid to several external forcings that modulate the relationship, including El Niño and Southern Oscillation, Indian Ocean Dipole mode (IODM), boreal summer teleconnections, and Eurasian snow extent on intraseasonal to interdecadal timescales. The major focus is placed on two integral views of the inter-connection between the two monsoon systems: one is the positive inter-correlation, which is associated with decaying El Niño and developing Indian Ocean sea surface temperature (SST) warming anomalies; the other is the negative inter-correlation, resulting from developing El Niño and western Pacific SST cooling. The IODM mode also has a delayed impact on the negative connection by modulating Eurasian snow cover. The observed evidence reveals that the recent intensification of the negative relationship is attributable to the strengthening of the zonal SST gradient along the Indian Ocean, western Pacific, and eastern Pacific. Analysis of experiments in the fifth phase of the Coupled Model Intercomparison Project further indicates a possibility for the negative linkage to be further enhanced under anthropogenic global warming with considerable interdecadal modulation in mid and late twenty-first century.

Efficient sequential and parallel algorithms for record linkage

PubMed Central

Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

2014-01-01

Background and objective Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Methods Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Results Our sequential and parallel algorithms have been tested on a real dataset of 1 083 878 records and synthetic datasets ranging in size from 50 000 to 9 000 000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). Conclusions We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm. PMID:24154837

Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

PubMed Central

2012-01-01

Background The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection. PMID:22621324

iSAW: Integrating Structure, Actors, and Water to study socio-hydro-ecological systems

NASA Astrophysics Data System (ADS)

Hale, Rebecca L.; Armstrong, Andrea; Baker, Michelle A.; Bedingfield, Sean; Betts, David; Buahin, Caleb; Buchert, Martin; Crowl, Todd; Dupont, R. Ryan; Ehleringer, James R.; Endter-Wada, Joanna; Flint, Courtney; Grant, Jacqualine; Hinners, Sarah; Horsburgh, Jeffery S.; Jackson-Smith, Douglas; Jones, Amber S.; Licon, Carlos; Null, Sarah E.; Odame, Augustina; Pataki, Diane E.; Rosenberg, David; Runburg, Madlyn; Stoker, Philip; Strong, Courtenay

2015-03-01

Urbanization, climate, and ecosystem change represent major challenges for managing water resources. Although water systems are complex, a need exists for a generalized representation of these systems to identify important components and linkages to guide scientific inquiry and aid water management. We developed an integrated Structure-Actor-Water framework (iSAW) to facilitate the understanding of and transitions to sustainable water systems. Our goal was to produce an interdisciplinary framework for water resources research that could address management challenges across scales (e.g., plot to region) and domains (e.g., water supply and quality, transitioning, and urban landscapes). The framework was designed to be generalizable across all human-environment systems, yet with sufficient detail and flexibility to be customized to specific cases. iSAW includes three major components: structure (natural, built, and social), actors (individual and organizational), and water (quality and quantity). Key linkages among these components include: (1) ecological/hydrologic processes, (2) ecosystem/geomorphic feedbacks, (3) planning, design, and policy, (4) perceptions, information, and experience, (5) resource access and risk, and (6) operational water use and management. We illustrate the flexibility and utility of the iSAW framework by applying it to two research and management problems: understanding urban water supply and demand in a changing climate and expanding use of green storm water infrastructure in a semi-arid environment. The applications demonstrate that a generalized conceptual model can identify important components and linkages in complex and diverse water systems and facilitate communication about those systems among researchers from diverse disciplines.

Acceptance of the Use of HIV Surveillance Data for Care Engagement: National and Local Community Perspectives

PubMed Central

Evans, David; Van Gorder, Dana; Morin, Stephen F.; Steward, Wayne T.; Gaffney, Stuart; Charlebois, Edwin D.

2015-01-01

Background Use of surveillance data including laboratory results (e.g. CD4 and HIV RNA) by public health departments to facilitate linkage, retention, and re-engagement of HIV-infected individuals in health care is on the rise. This is part of the goal of increasing the proportion of infected persons achieving virologic suppression. However, this use of surveillance data is not without controversy, particularly among some providers and people living with HIV. Methods We conducted informal discussions with key stakeholders and a literature search, and held a national think tank in November 2012, bringing together 31 representatives of the federal government, county and state officials, health care providers, and community-based organizations. A follow-up community consultation specific to San Francisco was held January 24, 2014, with 10 participants. Notes from these activities were used as data for this analysis. Results The think tank identified three strategies utilizing HIV surveillance data to aid in care engagement: 1) provider-mediated – where health department staff work with the provider of record on re-engagement, 2) electronic linkages between surveillance databases and medical records databases, and 3) direct outreach – where trained health department staff reach out to persons out of care. Participants also developed recommendations for minimizing harm, guidance on meaningful stakeholder involvement, and a consensus statement in support of the use of HIV surveillance data in care engagement. Conclusions Acceptance of the use of surveillance data for HIV care linkage, retention, and re-engagement is achievable, particularly if stakeholders have been engaged in the design, conduct, and evaluation of programs. PMID:25867776

The Heuristics of Statistical Argumentation: Scaffolding at the Postsecondary Level

ERIC Educational Resources Information Center

Pardue, Teneal Messer

2017-01-01

Language plays a key role in statistics and, by extension, in statistics education. Enculturating students into the practice of statistics requires preparing them to communicate results of data analysis. Statistical argumentation is one way of providing structure to facilitate discourse in the statistics classroom. In this study, a teaching…

Structural synthesis of linkages for quadruped bio-robot legs

NASA Astrophysics Data System (ADS)

Antonescu, O.; Robu, C.; Antonescu, P.

2016-08-01

The paper presents a few kinematic schemes of planar mechanisms with bars (linkages) used as part of the quadruped robot legs. The Dunshee linkage having only four elements as crank-rocker mechanism is analyzed. Further, the Klann linkage, which is accomplished by amplifying the crank-rocker mechanism with a dyadic kinematic chain, is also presented. More than that, the Jansen linkage, which is obtained by extending and amplifying the crank-rocker mechanism with two dyadic kinematic chains, is also analyzed. At the end of the paper, the authors present a novel linkage application consisting of a quadric kinematic chain.

Selection of Marine Corps Drill Instructors

DTIC Science & Technology

1980-03-01

8 4. ., ey- Construction and Cross-Validation Statistics for Drill Instructor School Performance Success Keys...Race, and School Attrition ........... ............................. ... 15 13. Key- Construction and Cross-Validation Statistics for Drill... constructed form, the Alternation Ranking of Series Drill Instruc- tors. In this form, DIs in a Series are ranked from highest to lowest in terms of their

Validation of an instrument to measure inter-organisational linkages in general practice.

PubMed

Amoroso, Cheryl; Proudfoot, Judith; Bubner, Tanya; Jayasinghe, Upali W; Holton, Christine; Winstanley, Julie; Beilby, Justin; Harris, Mark F

2007-12-03

Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice's linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. An interview to measure surgery-level (rather than individual clinician-level) clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations). Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. The resulting General Practice Clinical Linkages Interview (GP-CLI) is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however, comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples exploring the impact, outcomes, and facilitators of high quality clinical linkages in general practice.

Particle swarm optimization with recombination and dynamic linkage discovery.

PubMed

Chen, Ying-Ping; Peng, Wen-Chih; Jian, Ming-Chung

2007-12-01

In this paper, we try to improve the performance of the particle swarm optimizer by incorporating the linkage concept, which is an essential mechanism in genetic algorithms, and design a new linkage identification technique called dynamic linkage discovery to address the linkage problem in real-parameter optimization problems. Dynamic linkage discovery is a costless and effective linkage recognition technique that adapts the linkage configuration by employing only the selection operator without extra judging criteria irrelevant to the objective function. Moreover, a recombination operator that utilizes the discovered linkage configuration to promote the cooperation of particle swarm optimizer and dynamic linkage discovery is accordingly developed. By integrating the particle swarm optimizer, dynamic linkage discovery, and recombination operator, we propose a new hybridization of optimization methodologies called particle swarm optimization with recombination and dynamic linkage discovery (PSO-RDL). In order to study the capability of PSO-RDL, numerical experiments were conducted on a set of benchmark functions as well as on an important real-world application. The benchmark functions used in this paper were proposed in the 2005 Institute of Electrical and Electronics Engineers Congress on Evolutionary Computation. The experimental results on the benchmark functions indicate that PSO-RDL can provide a level of performance comparable to that given by other advanced optimization techniques. In addition to the benchmark, PSO-RDL was also used to solve the economic dispatch (ED) problem for power systems, which is a real-world problem and highly constrained. The results indicate that PSO-RDL can successfully solve the ED problem for the three-unit power system and obtain the currently known best solution for the 40-unit system.

Evaluation of record linkage of two large administrative databases in a middle income country: stillbirths and notifications of dengue during pregnancy in Brazil.

PubMed

Paixão, Enny S; Harron, Katie; Andrade, Kleydson; Teixeira, Maria Glória; Fiaccone, Rosemeire L; Costa, Maria da Conceição N; Rodrigues, Laura C

2017-07-17

Due to the increasing availability of individual-level information across different electronic datasets, record linkage has become an efficient and important research tool. High quality linkage is essential for producing robust results. The objective of this study was to describe the process of preparing and linking national Brazilian datasets, and to compare the accuracy of different linkage methods for assessing the risk of stillbirth due to dengue in pregnancy. We linked mothers and stillbirths in two routinely collected datasets from Brazil for 2009-2010: for dengue in pregnancy, notifications of infectious diseases (SINAN); for stillbirths, mortality (SIM). Since there was no unique identifier, we used probabilistic linkage based on maternal name, age and municipality. We compared two probabilistic approaches, each with two thresholds: 1) a bespoke linkage algorithm; 2) a standard linkage software widely used in Brazil (ReclinkIII), and used manual review to identify further links. Sensitivity and positive predictive value (PPV) were estimated using a subset of gold-standard data created through manual review. We examined the characteristics of false-matches and missed-matches to identify any sources of bias. From records of 678,999 dengue cases and 62,373 stillbirths, the gold-standard linkage identified 191 cases. The bespoke linkage algorithm with a conservative threshold produced 131 links, with sensitivity = 64.4% (68 missed-matches) and PPV = 92.5% (8 false-matches). Manual review of uncertain links identified an additional 37 links, increasing sensitivity to 83.7%. The bespoke algorithm with a relaxed threshold identified 132 true matches (sensitivity = 69.1%), but introduced 61 false-matches (PPV = 68.4%). ReclinkIII produced lower sensitivity and PPV than the bespoke linkage algorithm. Linkage error was not associated with any recorded study variables. Despite a lack of unique identifiers for linking mothers and stillbirths, we demonstrate a high standard of linkage of large routine databases from a middle income country. Probabilistic linkage and manual review were essential for accurately identifying cases for a case-control study, but this approach may not be feasible for larger databases or for linkage of more common outcomes.

Linkages between public and non-government sectors in healthcare: A case study from Uttar Pradesh, India.

PubMed

Srivastava, Aradhana; Bhattacharyya, Sanghita; Gautham, Meenakshi; Schellenberg, Joanna; Avan, Bilal I

2016-12-01

Effective utilisation of collaborative non-governmental organisation (NGO)-public health system linkages in pluralistic health systems of developing countries can substantially improve equity and quality of services. This study explores level and types of linkages between public health sector and NGOs in Uttar Pradesh (UP), an underprivileged state of India, using a social science model for the first time. It also identifies gaps and challenges for effective linkage. Two NGOs were selected as case studies. Data collection included semi-structured in-depth interviews with senior staff and review of records and reporting formats. Formal linkages of NGOs with the public health system related to registration, participation in district level meetings, workforce linkages and sharing information on government-supported programmes. Challenges included limited data sharing, participation in planning and limited monitoring of regulatory compliances. Linkage between public health system and NGOs in UP was moderate, marked by frequent interaction and some reciprocity in information and resource flows, but weak participation in policy and planning. The type of linkage could be described as 'complementarity', entailing information and resource sharing but not joint action. Stronger linkage is required for sustained and systematic collaboration, with joint planning, implementation and evaluation.

RNF8- and Ube2S-Dependent Ubiquitin Lysine 11-Linkage Modification in Response to DNA Damage.

PubMed

Paul, Atanu; Wang, Bin

2017-05-18

Ubiquitin modification of proteins plays pivotal roles in the cellular response to DNA damage. Given the complexity of ubiquitin conjugation due to the formation of poly-conjugates of different linkages, functional roles of linkage-specific ubiquitin modification at DNA damage sites are largely unclear. We identify that Lys11-linkage ubiquitin modification occurs at DNA damage sites in an ATM-dependent manner, and ubiquitin-modifying enzymes, including Ube2S E2-conjugating enzyme and RNF8 E3 ligase, are responsible for the assembly of Lys11-linkage conjugates on damaged chromatin, including histone H2A/H2AX. We show that RNF8- and Ube2S-dependent Lys11-linkage ubiquitin conjugation plays an important role in regulating DNA damage-induced transcriptional silencing, distinct from the role of Lys63-linkage ubiquitin in the recruitment of DNA damage repair proteins 53BP1 and BRCA1. Thus, our study highlights the importance of linkage-specific ubiquitination at DNA damage sites, and it reveals that Lys11-linkage ubiquitin modification plays a crucial role in the DNA damage response. Copyright © 2017 Elsevier Inc. All rights reserved.

Terminal sialic acid linkages determine different cell infectivities of human parainfluenza virus type 1 and type 3.

PubMed

Fukushima, Keijo; Takahashi, Tadanobu; Ito, Seigo; Takaguchi, Masahiro; Takano, Maiko; Kurebayashi, Yuuki; Oishi, Kenta; Minami, Akira; Kato, Tatsuya; Park, Enoch Y; Nishimura, Hidekazu; Takimoto, Toru; Suzuki, Takashi

2014-09-01

Human parainfluenza virus type 1 (hPIV1) and type 3 (hPIV3) initiate infection by sialic acid binding. Here, we investigated sialic acid linkage specificities for binding and infection of hPIV1 and hPIV3 by using sialic acid linkage-modified cells treated with sialidases or sialyltransferases. The hPIV1 is bound to only α2,3-linked sialic acid residues, whereas hPIV3 is bound to α2,6-linked sialic acid residues in addition to α2,3-linked sialic acid residues in human red blood cells. α2,3 linkage-specific sialidase treatment of LLC-MK2 cells and A549 cells decreased the infectivity of hPIV1 but not that of hPIV3. Treatment of A549 cells with α2,3 linkage-specific sialyltransferase increased infectivities of both hPIV1 and hPIV3, whereas α2,6 linkage-specific sialyltransferase treatment increased only hPIV3 infectivity. Clinical isolates also showed similar sialic acid linkage specificities. We concluded that hPIV1 utilizes only α2,3 sialic acid linkages and that hPIV3 makes use of α2,6 sialic acid linkages in addition to α2,3 sialic acid linkages as viral receptors. Copyright © 2014. Published by Elsevier Inc.

Distribution of Model-based Multipoint Heterogeneity Lod Scores

PubMed Central

Xing, Chao; Morris, Nathan; Xing, Guan

2011-01-01

The distribution of two-point heterogeneity lod scores (HLOD) has been intensively investigated because the conventional χ2 approximation to the likelihood ratio test is not directly applicable. However, there was no study investigating the distribution of the multipoint HLOD despite its wide application. Here we want to point out that, compared with the two-point HLOD, the multipoint HLOD essentially tests for homogeneity given linkage and follows a relatively simple limiting distribution 12χ02+12χ12, which can be obtained by established statistical theory. We further examine the theoretical result by simulation studies. PMID:21104892

ENSO related variability in the Southern Hemisphere, 1948-2000

NASA Astrophysics Data System (ADS)

Ribera, Pedro; Mann, Michael E.

2003-01-01

The spatiotemporal evolution of Southern Hemisphere climate variability is diagnosed based on the use of the NCEP reanalysis (1948-2000) dataset. Using the MTM-SVD analysis method, significant narrowband variability is isolated from the multi-variate dataset. It is found that the ENSO signal exhibits statistically significant behavior at quasiquadrennial (3-6 yr) timescales for the full time-period. A significant quasibiennial (2-3 yr) timescales emerges only for the latter half of period. Analyses of the spatial evolution of the two reconstructed signals shed additional light on linkages between low and high-latitude Southern Hemisphere climate anomalies.

Pilot personality and crew coordination - Implications for training and selection

NASA Technical Reports Server (NTRS)

Chidester, Thomas R.; Helmreich, Robert L.; Gregorich, Steven E.; Geis, Craig E.

1991-01-01

It is contended that past failures to find linkages between performance and personality were due to a combination of premature performance evaluation, inadequate statistical modeling, and/or the reliance on data gathered in contrived as opposed to realistic situations. The goal of the research presented is to isolate subgroups of pilots along performance-related personality dimensions and to document limits on the impact of crew coordination training between the groups. Three different profiles were identified through cluster analysis of personality scales that replicated across samples and predicted attitude change following training in crew coordination.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

PubMed

de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

2012-10-04

Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

PubMed Central

2012-01-01

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

Physiological Linkage in Couples and its Implications for Individual and Interpersonal Functioning: A Literature Review

PubMed Central

Timmons, Adela C.; Margolin, Gayla; Saxbe, Darby E.

2015-01-01

Do partners’ levels of physiological arousal become linked in close relationships? The term “physiological linkage” describes covariation between people in their moment-to-moment physiological states. The current review presents a conceptual framework to guide research on linkage in romantic relationships and discusses the potential implications of being “linked.” Evidence of linkage was found across a broad range of physiological indices and in a variety of contexts, including during laboratory-based conflict and in daily life. Four hypotheses regarding how linkage relates to individual and interpersonal functioning are evaluated: (1) co-activation of the sympathetic nervous system or hypothalamic-pituitary adrenal axis is “bad,” (2) moderate physiological linkage is “just right,” (3) physiological linkage is problematic if the individual or couple is overloaded, and (4) the implications of physiological linkage depend on the emotional context. We found partial support for the first hypothesis and determined that more research is needed to evaluate the remaining hypotheses. Linkage in cortisol was negatively associated with relationship satisfaction; but at the same time, linkage in multiple systems was positively associated with indices of relationship connectedness, such as the amount of time spent together and the ability to identify the emotions of one’s partner. These results suggest that linkage may confer benefits but also may put couples at risk if they become entrenched in patterns of conflict or stress. With research in this area burgeoning in recent years, this review indicates that linkage is a promising construct with applications for interventions targeting individual health and couple functioning. PMID:26147932

Work–Family Conflict and Health Among Working Parents: Potential Linkages for Family Studies and Social Neuroscience

PubMed Central

Grzywacz, Joseph G.; Smith, Amy M.

2016-01-01

In this paired article the authors review research on paid work, parenting, and health in order to isolate fundamental questions and issues that remain unaddressed. Next, consistent with the theme of this special issue, the authors introduce social neuroscience and highlight how this emerging multidisciplinary science offers substantial promise for advancing key unresolved issues in the paid work, parenting, and health literature. The article concludes with suggestions for promising areas of research wherein family scientists and social neuroscientists could build collaborative research to address gaps in the work–family literature. PMID:27840467

Identification of two novel proanthocyanidins in green Tea.

PubMed

Lakenbrink, C; Engelhardt, U H; Wray, V

1999-11-01

The isolation and structural elucidation of epiafzelechingallate-(4beta-->8)-epicatechingallate (EAG-4beta-->8-ECG) and epiafzelechingallate-(4beta-->6)-epicatechingallate (EAG-4beta-->6-ECG) in green tea samples are described. The combination of various 2D NMR techniques allowed a full structural determination of the underivatized proanthocyanidins even though broadening of the signals did not allow observation of some key correlations that characterize the location of the interflavonoid linkage. The differences in the NMR spectra of the new compounds allowed formulation of criteria for the discrimination between the 4-->6 and 4-->8 isomers in this type of compound.

Reasoning about Informal Statistical Inference: One Statistician's View

ERIC Educational Resources Information Center

Rossman, Allan J.

2008-01-01

This paper identifies key concepts and issues associated with the reasoning of informal statistical inference. I focus on key ideas of inference that I think all students should learn, including at secondary level as well as tertiary. I argue that a fundamental component of inference is to go beyond the data at hand, and I propose that statistical…

Children in Africa: Key Statistics on Child Survival, Protection and Development

ERIC Educational Resources Information Center

UNICEF, 2014

2014-01-01

This report presents key statistics relating to: (1) child malnutrition in Africa; (2) HIV/AIDS and Malaria in Africa; (3) child marriage, birth registration and Female Genital Mutilation/Cutting (FGM/C); (4) education in Africa; (5) child mortality in Africa; (6) Drinking water and sanitation in Africa; and (7) maternal health in Africa.…

The policy-dependent statistics and induced heterogeneity of the supported agents on the inter and intra company levels

NASA Astrophysics Data System (ADS)

Horváth, Denis; Maliková, Zuzana; Lučkaničová, Martina

2015-09-01

We present a simulation model of the technological innovations based on the former Guardiola's concept which relies on the notion of technological barriers. The central, novel feature of our proposal is the assumption that barriers can be reduced allowing public support to R&D. However, this can be applied under the different policies. The statistical treatment of the simulation results demonstrated that support of the elitist (super-threshold) innovating units yields higher innovation rate, but more profound variation of the technological levels. On the other hand, the favoring of innovators with sub-threshold technological levels may lead to the more integrated technological world. Simultaneously, we use the same model to study the effects of supporting knowledge sharing (that is to say, lowering sharing barriers) on average organizational knowledge. An interesting aspect of the model represents self-organized adjustment of the probabilistic parameters related to the social linkages.

Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics.

PubMed Central

Sobel, E.; Lange, K.

1996-01-01

The introduction of stochastic methods in pedigree analysis has enabled geneticists to tackle computations intractable by standard deterministic methods. Until now these stochastic techniques have worked by running a Markov chain on the set of genetic descent states of a pedigree. Each descent state specifies the paths of gene flow in the pedigree and the founder alleles dropped down each path. The current paper follows up on a suggestion by Elizabeth Thompson that genetic descent graphs offer a more appropriate space for executing a Markov chain. A descent graph specifies the paths of gene flow but not the particular founder alleles traveling down the paths. This paper explores algorithms for implementing Thompson's suggestion for codominant markers in the context of automatic haplotyping, estimating location scores, and computing gene-clustering statistics for robust linkage analysis. Realistic numerical examples demonstrate the feasibility of the algorithms. PMID:8651310

Focusing ecological research for conservation.

PubMed

Cristescu, Bogdan; Boyce, Mark S

2013-11-01

Ecologists are increasingly actively involved in conservation. We identify five key topics from a broad sweep of ecology that merit research attention to meet conservation needs. We examine questions from landscape ecology, behavioral ecology, ecosystem dynamics, community ecology, and nutrient cycling related to key topics. Based on literature review and publication trend assessment, consultation with colleagues, and roundtable discussions at the 24th International Congress for Conservation Biology, focused research on the following topics could benefit conservation while advancing ecological understanding: 1. Carbon sequestration, requiring increased linkages to biodiversity conservation; 2. Ecological invasiveness, challenging our ability to find solutions to ecological aliens; 3. Individual variation, having applications in the conservation of rare species; 4. Movement of organisms, integrating ecological processes across landscapes and scales and addressing habitat fragmentation; and 5. Trophic-level interactions, driving ecological dynamics at the ecosystem-level. Addressing these will require cross-disciplinary research under the overarching framework of conservation ecology.

Treating Substance Use Disorders in the Criminal Justice System

PubMed Central

Hiller, Matthew; Hamilton, Leah

2013-01-01

The large number of individuals with substance use disorders involved in the nation’s criminal justice system (CJS) represents a unique opportunity, as well as challenges, in addressing the dual concerns of public safety and public health. Unfortunately, a low proportion of those who could benefit from treatment actually receive it while involved in the CJS. This article presents a review of recent research on the effectiveness of major substance abuse treatment interventions used at different possible linkage points during criminal justice case processing, including diversion, jail, prison, and community supervision. This is followed by a discussion of key research and practice issues, including low rates of treatment access and under-utilization of medication-assisted treatment. Concluding comments discuss principles of effective treatment for offenders and identify key gaps in research and practice that need to be addressed to improve and expand provision of effective treatment for offenders. PMID:24132733

Linkage mapping in sheep and deer identifies a conserved pecora ruminant linkage group orthologous to two regions of HSA16 and a portion of HSA7Q

DOE Office of Scientific and Technical Information (OSTI.GOV)

Broom, J.E.; Tate, M.L.; Dodds, K.G.

1996-05-01

Two orthologous linkage groups have been mapped in sheep and deer. Seven loci have been mapped in deer, and 12 in sheep. The sheep linkage group is assigned of ovine chromosome 24. The linkage groups consist of loci from the short arm of human chromosome 16, spanning the region containing the human Batten disease locus, and from human chromosome 7. One locus from the long arm of human chromosome 16 is also present, demonstrating a previously unknown rearrangement between human and ruminant chromosomes. There is no significant difference in marker order and distances between the two linkage groups, implying thatmore » this linkage pattern was present in the genome of the common ancestor of the pecora ruminants. 35 refs., 1 fig., 2 tabs.« less

Validity of deterministic record linkage using multiple indirect personal identifiers: linking a large registry to claims data.

PubMed

Setoguchi, Soko; Zhu, Ying; Jalbert, Jessica J; Williams, Lauren A; Chen, Chih-Ying

2014-05-01

Linking patient registries with administrative databases can enhance the utility of the databases for epidemiological and comparative effectiveness research. However, registries often lack direct personal identifiers, and the validity of record linkage using multiple indirect personal identifiers is not well understood. Using a large contemporary national cardiovascular device registry and 100% Medicare inpatient data, we linked hospitalization-level records. The main outcomes were the validity measures of several deterministic linkage rules using multiple indirect personal identifiers compared with rules using both direct and indirect personal identifiers. Linkage rules using 2 or 3 indirect, patient-level identifiers (ie, date of birth, sex, admission date) and hospital ID produced linkages with sensitivity of 95% and specificity of 98% compared with a gold standard linkage rule using a combination of both direct and indirect identifiers. Ours is the first large-scale study to validate the performance of deterministic linkage rules without direct personal identifiers. When linking hospitalization-level records in the absence of direct personal identifiers, provider information is necessary for successful linkage. © 2014 American Heart Association, Inc.

Phase-Division-Based Dynamic Optimization of Linkages for Drawing Servo Presses

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Gang; Wang, Li-Ping; Cao, Yan-Ke

2017-11-01

Existing linkage-optimization methods are designed for mechanical presses; few can be directly used for servo presses, so development of the servo press is limited. Based on the complementarity of linkage optimization and motion planning, a phase-division-based linkage-optimization model for a drawing servo press is established. Considering the motion-planning principles of a drawing servo press, and taking account of work rating and efficiency, the constraints of the optimization model are constructed. Linkage is optimized in two modes: use of either constant eccentric speed or constant slide speed in the work segments. The performances of optimized linkages are compared with those of a mature linkage SL4-2000A, which is optimized by a traditional method. The results show that the work rating of a drawing servo press equipped with linkages optimized by this new method improved and the root-mean-square torque of the servo motors is reduced by more than 10%. This research provides a promising method for designing energy-saving drawing servo presses with high work ratings.

Defining window-boundaries for genomic analyses using smoothing spline techniques

DOE PAGES

Beissinger, Timothy M.; Rosa, Guilherme J.M.; Kaeppler, Shawn M.; ...

2015-04-17

High-density genomic data is often analyzed by combining information over windows of adjacent markers. Interpretation of data grouped in windows versus at individual locations may increase statistical power, simplify computation, reduce sampling noise, and reduce the total number of tests performed. However, use of adjacent marker information can result in over- or under-smoothing, undesirable window boundary specifications, or highly correlated test statistics. We introduce a method for defining windows based on statistically guided breakpoints in the data, as a foundation for the analysis of multiple adjacent data points. This method involves first fitting a cubic smoothing spline to the datamore » and then identifying the inflection points of the fitted spline, which serve as the boundaries of adjacent windows. This technique does not require prior knowledge of linkage disequilibrium, and therefore can be applied to data collected from individual or pooled sequencing experiments. Moreover, in contrast to existing methods, an arbitrary choice of window size is not necessary, since these are determined empirically and allowed to vary along the genome.« less

Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

EPA Pesticide Factsheets

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.This dataset is associated with the following publication:Waits , E., J. Martinson , B. Rinner, S. Morris, D. Proestou, D. Champlin , and D. Nacci. Genetic linkage map and comparative genome analysis for the estuarine Atlanti

[Linkage to care among new human immunodeficiency virus diagnoses in Spain].

PubMed

Oliva, Jesús; Malo, Carmen; Fernández, Ana; Izquierdo, Ana; Marcos, Henar; Cevallos, Carlos; Castilla, Jesús; García, Rocio; Díez, Mercedes

2014-03-01

To describe linkage to care among new HIV diagnoses in Spain; and to estimate factors associated to linkage to care within three months after diagnosis. The distribution of the time elapsing between the date of HIV diagnosis and the date of first determination of CD4 (considered to be the date of linkage to care) was calculated among new HIV diagnoses in 2010 in the seven Autonomous Regions participating, where data on date of CD4 count was available. Linkage to care was considered «correct» if done within three months after diagnosis. Factors associated to correct linkage to care were estimated using logistic regression. A total of 1769 new HIV diagnoses were included. Of them, 83.1% had evidence of linkage to care within a year, and 75.7% were linked within three months after diagnosis. Being an injectable drug user (IDU) was the only factor inversely associated with linkage to care within 3 months (OR = 0.3; 95% CI: 0.2-0.6). In Spain linkage to care after HIV diagnosis is good, but there is still room for improvement, especially among IDUs. Copyright © 2013 Elsevier España, S.L. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Privacy-preserving record linkage on large real world datasets.

PubMed

Randall, Sean M; Ferrante, Anna M; Boyd, James H; Bauer, Jacqueline K; Semmens, James B

2014-08-01

Record linkage typically involves the use of dedicated linkage units who are supplied with personally identifying information to determine individuals from within and across datasets. The personally identifying information supplied to linkage units is separated from clinical information prior to release by data custodians. While this substantially reduces the risk of disclosure of sensitive information, some residual risks still exist and remain a concern for some custodians. In this paper we trial a method of record linkage which reduces privacy risk still further on large real world administrative data. The method uses encrypted personal identifying information (bloom filters) in a probability-based linkage framework. The privacy preserving linkage method was tested on ten years of New South Wales (NSW) and Western Australian (WA) hospital admissions data, comprising in total over 26 million records. No difference in linkage quality was found when the results were compared to traditional probabilistic methods using full unencrypted personal identifiers. This presents as a possible means of reducing privacy risks related to record linkage in population level research studies. It is hoped that through adaptations of this method or similar privacy preserving methods, risks related to information disclosure can be reduced so that the benefits of linked research taking place can be fully realised. Copyright © 2013 Elsevier Inc. All rights reserved.

Impact of Bridging Income Generation with Group Integrated Care (BIGPIC) on Hypertension and Diabetes in Rural Western Kenya.

PubMed

Pastakia, Sonak D; Manyara, Simon M; Vedanthan, Rajesh; Kamano, Jemima H; Menya, Diana; Andama, Benjamin; Chesoli, Cleophas; Laktabai, Jeremiah

2017-05-01

Rural settings in Sub-Saharan Africa (SSA) consistently report low participation in non-communicable disease (NCD) treatment programs and poor outcomes. The objective of this study is to assess the impact of the implementation of a patient-centered rural NCD care delivery model called Bridging Income Generation through grouP Integrated Care (BIGPIC). The study prospectively tracked participation and health outcomes for participants in a screening event and compared linkage frequencies to a historical comparison group. Rural Kenyan participants attending a voluntary NCD screening event were included within the BIGPIC model of care. The BIGPIC model utilizes a contextualized care delivery model designed to address the unique barriers faced in rural settings. This model emphasizes the following steps: (1) find patients in the community, (2) link to peer/microfinance groups, (3) integrate education, (4) treat in the community, (5) enhance economic sustainability and (6) generate demand for care through incentives. The primary outcome is the linkage frequency, which measures the percentage of patients who return for care after screening positive for either hypertension and/or diabetes. Secondary measures include retention frequencies defined as the percentage of patients remaining engaged in care throughout the 9-month follow-up period and changes in systolic (SBP) and diastolic blood pressure (DBP) and blood sugar over 12 months. Of the 879 individuals who were screened, 14.2 % were confirmed to have hypertension, while only 1.4 % were confirmed to have diabetes. The implementation of a comprehensive microfinance-linked, community-based, group care model resulted in 72.4 % of screen-positive participants returning for subsequent care, of which 70.3 % remained in care through the 12 months of the evaluation period. Patients remaining in care demonstrated a statistically significant mean decline of 21 mmHg in SBP [95 % CI (13.9 to 28.4), P < 0.01] and 5 mmHg drop in DBP [95 % CI (1.4 to 7.6), P < 0.01]. The implementation of a contextualized care delivery model built around the unique needs of rural SSA participants led to statistically significant improvements in linkage to care and blood pressure reduction.

Linked Records of Children with Traumatic Brain Injury. Probabilistic Linkage without Use of Protected Health Information.

PubMed

Bennett, T D; Dean, J M; Keenan, H T; McGlincy, M H; Thomas, A M; Cook, L J

2015-01-01

Record linkage may create powerful datasets with which investigators can conduct comparative effectiveness studies evaluating the impact of tests or interventions on health. All linkages of health care data files to date have used protected health information (PHI) in their linkage variables. A technique to link datasets without using PHI would be advantageous both to preserve privacy and to increase the number of potential linkages. We applied probabilistic linkage to records of injured children in the National Trauma Data Bank (NTDB, N = 156,357) and the Pediatric Health Information Systems (PHIS, N = 104,049) databases from 2007 to 2010. 49 match variables without PHI were used, many of them administrative variables and indicators for procedures recorded as International Classification of Diseases, 9th revision, Clinical Modification codes. We validated the accuracy of the linkage using identified data from a single center that submits to both databases. We accurately linked the PHIS and NTDB records for 69% of children with any injury, and 88% of those with severe traumatic brain injury eligible for a study of intervention effectiveness (positive predictive value of 98%, specificity of 99.99%). Accurate linkage was associated with longer lengths of stay, more severe injuries, and multiple injuries. In populations with substantial illness or injury severity, accurate record linkage may be possible in the absence of PHI. This methodology may enable linkages and, in turn, comparative effectiveness studies that would be unlikely or impossible otherwise.

[MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

PubMed

Liu, Ren-Hu; Meng, Jin-Ling

2003-05-01

MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

PubMed

Shi, Yuan Yuan; Sun, Liang Xian; Huang, Zachary Y; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

2013-01-01

The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

Adjusting for founder relatedness in a linkage analysis using prior information.

PubMed

Sheehan, N A; Egeland, T

2008-01-01

In genetic linkage studies, while the pedigrees are generally known, background relatedness between the founding individuals, assumed by definition to be unrelated, can seriously affect the results of the analysis. Likelihood approaches to relationship estimation from genetic marker data can all be expressed in terms of finding the most likely pedigree connecting the individuals of interest. When the true relationship is the main focus, the set of all possible alternative pedigrees can be too large to consider. However, prior information is often available which, when incorporated in a formal and structured way, can restrict this set to a manageable size thus enabling the calculation of a posterior distribution from which inferences can be drawn. Here, the unknown relationships are more of a nuisance factor than of interest in their own right, so the focus is on adjusting the results of the analysis rather than on direct estimation. In this paper, we show how prior information on founder relationships can be exploited in some applications to generate a set of candidate extended pedigrees. We then weight the relevant pedigree-specific likelihoods by their posterior probabilities to adjust the lod score statistics. (c) 2007 S. Karger AG, Basel

Major histocompatibility complex class I chain related gene-A microsatellite polymorphism shows secondary association with type 1 diabetes and celiac disease in North Indians.

PubMed

Kumar, N; Sharma, G; Kaur, G; Tandon, N; Bhatnagar, S; Mehra, N

2012-10-01

Microsatellite polymorphism in exon 5 of major histocompatibility complex class I chain related gene-A (MIC-A) has been implicated in the etiology of autoimmune diseases including type 1 diabetes (T1D) and celiac disease (CD). In this study on North Indian population, the MIC-A5.1 allele, carrying a premature termination codon in transmembrane region, was observed with increased frequency in T1D (29.6%, odds ratio OR = 2.1, P = 0.00017) and CD patients (40.3%, OR = 3.37, P = 1.67E-05) than in controls (16.7%). When the MIC-A5.1 association was adjusted for linkage with human leukocyte antigen (HLA)-DR3, the statistical significance of the association was abolished. This implies that the observed association of MIC-A5.1 is due to its linkage disequilibrium (D' = 0.94) with HLA-B8-DR3-DQ2 haplotype and is secondary to the overall association with DR3 positive MHC haplotypes. © 2012 John Wiley & Sons A/S.

Robustness of linkage strategy that leads to large-scale cooperation.

PubMed

Inaba, Misato; Takahashi, Nobuyuki; Ohtsuki, Hisashi

2016-11-21

One of the most well-known models to characterize cooperation among unrelated individuals is Social dilemma (SD). However there is no consensus about how to solve the SD by itself. Since SDs are often embedded in other social interactions, including indirect reciprocity games (IR), human can coordinate their behaviors across multiple games. Such coordination is called 'linkage'. Recently linkage has been considered as a promising solution to resolve SDs, since excluding SD defectors (i.e. those who defected in SD) from indirectly reciprocal relationships functions as a costless sanction. A previous study performed mathematical modeling and revealed that a linkage strategy, which cooperates in SD and engages in the Standing strategy in IR based on the recipients' behaviors in both SD and IR, was an ESS against a non-linkage strategy which defects in SD and engages in the Standing strategy in IR based on recipients' behaviors only in IR (Panchanathan and Boyd, 2004). In order to investigate the robustness of the linkage strategy, we devised a non-linkage strategy, which cooperates in SD but does not link two games. First, we conducted a mathematical analysis and demonstrated that the linkage strategy was not an ESS against cooperating non-linkage strategy. Second, we conducted a series of agent-based computer simulations to examine how the strategies perform in situations in which various types of errors can occur. Our results showed that the linkage strategy was an ESS only when there are implementation errors in SD. However, the equilibrium of the linkage strategy was unstable when there are perception errors. Since we know that humans are not free from perception errors in their social life, future studies will need to show how perception errors can be overcome in order to provide support for the conclusion that linkage is a plausible solution to SDs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mapping Quantitative Trait Loci in Crosses between Outbred Lines Using Least Squares

PubMed Central

Haley, C. S.; Knott, S. A.; Elsen, J. M.

1994-01-01

The use of genetic maps based upon molecular markers has allowed the dissection of some of the factors underlying quantitative variation in crosses between inbred lines. For many species crossing inbred lines is not a practical proposition, although crosses between genetically very different outbred lines are possible. Here we develop a least squares method for the analysis of crosses between outbred lines which simultaneously uses information from multiple linked markers. The method is suitable for crosses where the lines may be segregating at marker loci but can be assumed to be fixed for alternative alleles at the major quantitative trait loci (QTLs) affecting the traits under analysis (e.g., crosses between divergent selection lines or breeds with different selection histories). The simultaneous use of multiple markers from a linkage group increases the sensitivity of the test statistic, and thus the power for the detection of QTLs, compared to the use of single markers or markers flanking an interval. The gain is greater for more closely spaced markers and for markers of lower information content. Use of multiple markers can also remove the bias in the estimated position and effect of a QTL which may result when different markers in a linkage group vary in their heterozygosity in the F(1) (and thus in their information content) and are considered only singly or a pair at a time. The method is relatively simple to apply so that more complex models can be fitted than is currently possible by maximum likelihood. Thus fixed effects and effects of background genotype can be fitted simultaneously with the exploration of a single linkage group which will increase the power to detect QTLs by reducing the residual variance. More complex models with several QTLs in the same linkage group and two-locus interactions between QTLs can similarly be examined. Thus least squares provides a powerful tool to extend the range of crosses from which QTLs can be dissected whilst at the same time allowing flexible and realistic models to be explored. PMID:8005424

Hydrolytic stability of pneumococcal group 6 (type 6A and 6B) capsular polysaccharides.

PubMed Central

Zon, G; Szu, S C; Egan, W; Robbins, J D; Robbins, J B

1982-01-01

The hydrolyses of the immunologically cross-reactive and constitutionally isomeric group 6 pneumococcal polysaccharides, types 6A and 6B, were investigated by 31P nuclear magnetic resonance spectroscopy, gel filtration through Sepharose 4B, reducing-sugar analysis, and rocket immunoelectrophoresis. Phosphorus nuclear magnetic resonance spectroscopy showed that cleavage of the repeating-unit phosphodiester linkages at pH 10, 60 degrees C was considerably faster (greater than 10(3) ) for the type 6A than the type 6B polysaccharide. Under these reaction conditions, 31P nuclear magnetic resonance kinetic measurements showed that the Na+ form of the type 6A polysaccharide underwent phosphodiester-linkage hydrolysis two times slower than the corresponding Ca+2 form; a stoichiometrically excess amount of Ca+2 caused a 30-fold enhancement of the latter hydrolysis rate. The spectroscopic characterization of phosphorus-containing end groups resulting from hydrolysis of the type 6A polymer provided additional mechanistic information. Heating the type 6A and 6B polysaccharides at 56 degrees C for various times led to gel filtration coefficients of distribution (Kd values) which indicated that the type 6A material underwent size reductions considerably faster than did the type 6B antigen; these increased Kd values qualitatively correlated with the loss of immunochemical reactivity measured by rocket immunoelectrophoresis. The application of a statistical theory to the depolymerization of the type 6A and 6B polysaccharides was consistent with random bond cleavage, as evidenced by the calculated versus measured gel filtration patterns. Although the molecular changes causing the size reductions were not fully elaborated, it was established that the acetal linkages of the type 6A and 6B polysaccharides were comparatively resistant to hydrolysis and that depolymerization by hydrolysis of the phosphodiester linkage was a major factor only in the type 6A structure. It was concluded that the hydrolytic stability of the type 6B antigen would favor its use in the polyvalent pneumococcal vaccine rather than the cross-reactive, but comparatively unstable, type 6A polysaccharide, if all other factors are equal. Images PMID:7107011

Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm

PubMed Central

Teh, Chee-Keng; Ong, Ai-Ling; Kwong, Qi-Bin; Apparow, Sukganah; Chew, Fook-Tim; Mayes, Sean; Mohamed, Mohaimi; Appleton, David; Kulaveerasingam, Harikrishna

2016-01-01

GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10−4) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential. PMID:26743827

Quantifying sources of bias in longitudinal data linkage studies of child abuse and neglect: measuring impact of outcome specification, linkage error, and partial cohort follow-up.

PubMed

Parrish, Jared W; Shanahan, Meghan E; Schnitzer, Patricia G; Lanier, Paul; Daniels, Julie L; Marshall, Stephen W

2017-12-01

Health informatics projects combining statewide birth populations with child welfare records have emerged as a valuable approach to conducting longitudinal research of child maltreatment. The potential bias resulting from linkage misspecification, partial cohort follow-up, and outcome misclassification in these studies has been largely unexplored. This study integrated epidemiological survey and novel administrative data sources to establish the Alaska Longitudinal Child Abuse and Neglect Linkage (ALCANLink) project. Using these data we evaluated and quantified the impact of non-linkage misspecification and single source maltreatment ascertainment use on reported maltreatment risk and effect estimates. The ALCANLink project integrates the 2009-2011 Alaska Pregnancy Risk Assessment Monitoring System (PRAMS) sample with multiple administrative databases through 2014, including one novel administrative source to track out-of-state emigration. For this project we limited our analysis to the 2009 PRAMS sample. We report on the impact of linkage quality, cohort follow-up, and multisource outcome ascertainment on the incidence proportion of reported maltreatment before age 6 and hazard ratios of selected characteristics that are often available in birth cohort linkage studies of maltreatment. Failure to account for out-of-state emigration biased the incidence proportion by 12% (from 28.3% w to 25.2% w ), and the hazard ratio (HR) by as much as 33% for some risk factors. Overly restrictive linkage parameters biased the incidence proportion downwards by 43% and the HR by as much as 27% for some factors. Multi-source linkages, on the other hand, were of little benefit for improving reported maltreatment ascertainment. Using the ALCANLink data which included a novel administrative data source, we were able to observe and quantify bias to both the incidence proportion and HR in a birth cohort linkage study of reported child maltreatment. Failure to account for out-of-state emigration and low-quality linkage methods may induce bias in longitudinal data linkage studies of child maltreatment which other researchers should be aware of. In this study multi-agency linkage did not lead to substantial increased detection of reported maltreatment. The ALCANLink methodology may be a practical approach for other states interested in developing longitudinal birth cohort linkage studies of maltreatment that requires limited resources to implement, provides comprehensive data elements, and can facilitate comparability between studies.

Perspectives of Post-Acute Transition of Care for Cardiac Surgery Patients

PubMed Central

Stoicea, Nicoleta; You, Tian; Eiterman, Andrew; Hartwell, Clifton; Davila, Victor; Marjoribanks, Stephen; Florescu, Cristina; Bergese, Sergio Daniel; Rogers, Barbara

2017-01-01

Post-acute care (PAC) facilities improve patient recovery, as measured by activities of daily living, rehabilitation, hospital readmission, and survival rates. Seamless transitions between discharge and PAC settings continue to be challenges that hamper patient outcomes, specifically problems with effective communication and coordination between hospitals and PAC facilities at patient discharge, patient adherence and access to cardiac rehabilitation (CR) services, caregiver burden, and the financial impact of care. The objective of this review is to examine existing models of cardiac transitional care, identify major challenges and social factors that affect PAC, and analyze the impact of current transitional care efforts and strategies implemented to improve health outcomes in this patient population. We intend to discuss successful methods to address the following aspects: hospital-PAC linkages, improved discharge planning, caregiver burden, and CR access and utilization through patient-centered programs. Regular home visits by healthcare providers result in decreased hospital readmission rates for patients utilizing home healthcare while improved hospital-PAC linkages reduced hospital readmissions by 25%. We conclude that widespread adoption of improvements in transitional care will play a key role in patient recovery and decrease hospital readmission, morbidity, and mortality. PMID:29230400

Phylogenetic and Kinetic Characterization of a Suite of Dehydrogenases from a Newly Isolated Bacterium, Strain SG61-1L, That Catalyze the Turnover of Guaiacylglycerol-β-Guaiacyl Ether Stereoisomers

PubMed Central

Palamuru, Shannu; Dellas, Nikki; Pearce, Stephen L.; Warden, Andrew C.; Oakeshott, John G.

2015-01-01

Lignin is a complex aromatic polymer found in plant cell walls that makes up 15 to 40% of plant biomass. The degradation of lignin substructures by bacteria is of emerging interest because it could provide renewable alternative feedstocks and intermediates for chemical manufacturing industries. We have isolated a bacterium, strain SG61-1L, that rapidly degrades all of the stereoisomers of one lignin substructure, guaiacylglycerol-β-guaiacyl ether (GGE), which contains a key β-O-4 linkage found in most intermonomer linkages in lignin. In an effort to understand the rapid degradation of GGE by this bacterium, we heterologously expressed and kinetically characterized a suite of dehydrogenase candidates for the first known step of GGE degradation. We identified a clade of active GGE dehydrogenases and also several other dehydrogenases outside this clade that were all able to oxidize GGE. Several candidates exhibited stereoselectivity toward the GGE stereoisomers, while others had higher levels of catalytic performance than previously described GGE dehydrogenases for all four stereoisomers, indicating a variety of potential applications for these enzymes in the manufacture of lignin-derived commodities. PMID:26386069

Perspectives of Post-Acute Transition of Care for Cardiac Surgery Patients.

PubMed

Stoicea, Nicoleta; You, Tian; Eiterman, Andrew; Hartwell, Clifton; Davila, Victor; Marjoribanks, Stephen; Florescu, Cristina; Bergese, Sergio Daniel; Rogers, Barbara

2017-01-01

Post-acute care (PAC) facilities improve patient recovery, as measured by activities of daily living, rehabilitation, hospital readmission, and survival rates. Seamless transitions between discharge and PAC settings continue to be challenges that hamper patient outcomes, specifically problems with effective communication and coordination between hospitals and PAC facilities at patient discharge, patient adherence and access to cardiac rehabilitation (CR) services, caregiver burden, and the financial impact of care. The objective of this review is to examine existing models of cardiac transitional care, identify major challenges and social factors that affect PAC, and analyze the impact of current transitional care efforts and strategies implemented to improve health outcomes in this patient population. We intend to discuss successful methods to address the following aspects: hospital-PAC linkages, improved discharge planning, caregiver burden, and CR access and utilization through patient-centered programs. Regular home visits by healthcare providers result in decreased hospital readmission rates for patients utilizing home healthcare while improved hospital-PAC linkages reduced hospital readmissions by 25%. We conclude that widespread adoption of improvements in transitional care will play a key role in patient recovery and decrease hospital readmission, morbidity, and mortality.

The tropolone-isobutylamine complex: a hydrogen-bonded troponoid without dominant π-π interactions.

PubMed

Vealey, Zachary N; Mercado, Brandon Q; Vaccaro, Patrick H

2016-10-01

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...π, or ion-π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C 4 H 12 N + ·C 7 H 5 O 2 - , has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz. π-π, C-H...π, and ion-π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor-acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

Use of record linkage to examine alcohol use in pregnancy.

PubMed

Burns, Lucy; Mattick, Richard P; Cooke, Margaret

2006-04-01

To date, no population-level data have been published examining the obstetric and neonatal outcomes for women with an alcohol-related hospital admission during pregnancy compared with the general obstetric population. This information is critical to planning and implementing appropriate services. Antenatal and delivery admissions to New South Wales (NSW) hospitals from the NSW Inpatient Statistics Collection were linked to birth information from the NSW Midwives Data Collection over a 5-year period (1998-2002). Birth admissions were flagged as positive for maternal alcohol use where a birth admission or any pregnancy admission for that birth involved an alcohol-related International Statistical Classification of Diseases and Related Health Problems, 10th Revision, Australian Modification (ICD-10-AM) code. Key demographic, obstetric, and neonatal variables were compared for births to mothers in the alcohol group with births where no alcohol-related ICD10-AM was recorded. A total of 416,834 birth records were analyzed over a 5-year period (1998-2002). In this time, 342 of these were coded as positive for at least 1 alcohol-related ICD-10-AM diagnosis. Mothers in the alcohol group had a higher number of previous pregnancies, smoked more heavily, were not privately insured, and were more often indigenous. They also presented later on in their pregnancy to antenatal services and were more likely to arrive at hospital unbooked for delivery. Deliveries involved less epidural and local and more general anesthesia. Cesarean sections were more common to women in the alcohol group and were performed more often for intrauterine growth retardation. Neonates born to women in the alcohol group were smaller for gestational age, had lower Apgar scores at 5 minutes, and were admitted to special care nursery more often. This study shows that linked population-level administrative data provide a powerful new source of information for examining the maternal and neonatal outcomes associated with alcohol use in pregnancy.

Linking Development Benefits to Neighborhoods: A Manual of Community-Based Strategies. Technical Bulletin.

ERIC Educational Resources Information Center

Casale, Ellen

This manual collects experiences of successful linkage programs to demonstrate the promise of linkage and to show its limits and risks. It is intended to help communities assess the capacity of linkage to meet their needs and evaluate the considerable commitment this strategy requires. (In linkage programs, developers who receive community…

Apparatus to position a microelectromechanical platform

DOEpatents

Miller, Samuel Lee; Rodgers, Murray Steven

2003-09-23

The present invention comprises a microelectromechanical positioner to achieve substantially translational positioning of a platform without rotational motion, thereby maintaining a constant angular orientation of the platform during movement. A linkage mechanism of the positioner can comprise parallelogram linkages to constrain the rotational motion of the platform. Such linkages further can comprise flexural hinges or other turning joints at the linkage pivots to eliminate the need for rubbing surfaces. A plurality of the linkage mechanisms can be used to enable translational motion of the platform with two degrees of freedom. A variety of means can be used to actuate the positioner. Independent actuation of the anchor links of the linkage mechanisms with rotary electrostatic actuators can be used to provide controlled translational movement of the platform.

Evaluating Common Hypotheses for Violence in Central America

DTIC Science & Technology

2016-12-01

53  Table 6.  Key Police Statistics , 2013 ........................................................................58  Table 7.  Length of...unemployment and the lack of social mobility as a key driver to delinquency , especially for young adult males.5 Some attribute increasing violence in...as well as statistics and other metrics that might reveal correlations between policies and violence rates. 13 II. EVALUATING THE STRUCTURAL

Health-risk correlates of video-game playing among adults.

PubMed

Weaver, James B; Mays, Darren; Sargent Weaver, Stephanie; Kannenberg, Wendi; Hopkins, Gary L; Eroğlu, Doğan; Bernhardt, Jay M

2009-10-01

Although considerable research suggests that health-risk factors vary as a function of video-game playing among young people, direct evidence of such linkages among adults is lacking. The goal of this study was to distinguish adult video-game players from nonplayers on the basis of personal and environmental factors. It was hypothesized that adults who play video games, compared to nonplayers, would evidence poorer perceptions of their health, greater reliance on Internet-facilitated social support, more extensive media use, and higher BMI. It was further hypothesized that different patterns of linkages between video-game playing and health-risk factors would emerge by gender. A cross-sectional, Internet-based survey was conducted in 2006 with a sample of adults from the Seattle-Tacoma area (n=562), examining health risks; media use behaviors and perceptions, including those related to video-game playing; and demographics. Statistical analyses conducted in 2008 to compare video-game players and nonplayers included bivariate descriptive statistics, stepwise discriminant analysis, and ANOVA. A total of 45.1% of respondents reported playing video games. Female video-game players reported greater depression (M=1.57) and poorer health status (M=3.90) than female nonplayers (depression, M=1.13; health status, M=3.57). Male video-game players reported higher BMI (M=5.31) and more Internet use time (M=2.55) than male nonplayers (BMI, M=5.19; Internet use, M=2.36). The only determinant common to female and male video-game players was greater reliance on the Internet for social support. A number of determinants distinguished video-game players from nonplayers, and these factors differed substantially between men and women. The data illustrate the need for further research among adults to clarify how to use digital opportunities more effectively to promote health and prevent disease.

French Registry on Acute ST-elevation and non ST-elevation Myocardial Infarction 2010. FAST-MI 2010

PubMed Central

Hanssen, Michel; Cottin, Yves; Khalife, Khalife; Hammer, Laure; Goldstein, Patrick; Puymirat, Etienne; Mulak, Geneviève; Drouet, Elodie; Pace, Benoit; Schultz, Eric; Bataille, Vincent; Ferrières, Jean; Simon, Tabassome

2012-01-01

Aim of FAST-MI 2010 To gather data on characteristics, management and outcomes of patients hospitalised for acute myocardial infarction (AMI) at the end of 2010 in France. Interventions To provide cardiologists and health authorities national and regional data on AMI management every 5 years. Setting Metropolitan France. 213 academic (n=38), community (n=110), army hospitals (n=2), private clinics (n=63), representing 76% of centres treating AMI patients. Inclusion from 1 October 2010. Population Consecutive patients included during 1 month, with a possible extension of recruitment up to one additional month (132 centres); 4169 patients included over the entire recruitment period, 3079 during the first 31 days; 249 additional patients declining participation (5.6%). Startpoints Consecutive adults with ST-elevation and non-ST-elevation AMI with symptom onset ≤48 h. Patients with AMI following cardiovascular procedures excluded. Data capture Web-based collection of 385 items (demographic, medical, biologic, management data) recorded online from source files by external research technicians; case-record forms with automatic quality checks. Centralised biology in voluntary centres to collect DNA samples and serum. Long-term follow-up organised centrally with interrogation of municipal registry offices, patients' physicians, and direct contact with the patients. Data quality Data management in Toulouse University. Statistical analyses: Université Paris Descartes, Université de Toulouse, Université Pierre et Marie Curie-Paris 06, Paris. Endpoints and linkages to other data In-hospital events; cardiovascular events, hospital admissions and mortality during follow-up. Linkage with Institute for National Statistics. Access to data Available for research to any participating clinician upon request to executive committee (fastmi2010@yahoo.fr). PMID:22523054

Map refinement of locus RP13 to human chromosome 17p13.3 in a second family with autosomal dominant retinitis pigmentosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kojis, T.L.; Heinzmann, C.; Ngo, J.T.

1996-02-01

In order to elucidate the genetic basis of autosomal dominant retinitis pigmentosa (adRP) in a large eight-generation family (UCLA-RP09) of British descent, we assessed linkage between the UCLA-RP09 adRP gene and numerous genetic loci, including eight adRP candidate genes, five anonymous adRP-linked DNA loci, and 20 phenotypic markers. Linkage to the UCLA-RP09 disease gene was excluded for all eight candidate genes analyzed, including rhodopsin (RP4) and peripherin/RDS (RP7), for the four adRP loci RP1, RP9, RP10 and RP11, as well as for 17 phenotypic markers. The anonymous DNA marker locus D17S938, linked to adRP locus RP13 on chromosome 17p13.1, yieldedmore » a suggestive but not statistically significant positive lod score. Linkage was confirmed between the UCLA-RP09 adRP gene and markers distal to D17S938 in the chromosomal region 17p13.3. A reanalysis of the original RP13 data from a South African adRP family of British descent, in conjunction with our UCLA-RP09 data, suggests that only one adRP locus exists on 17p but that it maps to a more telomeric position, at band 17p13.3, than previously reported. Confirmation of the involvement of RP13 in two presumably unrelated adRP families, both of British descent, suggests that this locus is a distinct adRP gene in a proportion of British, and possibly other, adRP families. 39 refs., 4 figs., 3 tabs.« less

Role of T cell receptor delta gene in susceptibility to celiac disease.

PubMed

Roschmann, E; Wienker, T F; Volk, B A

1996-02-01

There is a strong genetic influence on the susceptibility to celiac disease. Although in the vast majority of patients with celiac disease, the HLA-DQ(alpha1*0501, beta1*0201) heterodimer encoded by the alleles HLA-DQA1*0501 and HLA-DQB1*0201 seems to confer the primary disease susceptibility, it cannot be excluded that other genes contribute to disease susceptibility, as indicated by the difference in concordance rates between monozygotic twins and HLA identical siblings (70% vs. 30%). Obviously other genes involved in the genetic control of T cell mediated immune response could potentially influence susceptibility to celiac disease. The density of T cells using the gammadelta T cell receptor (TCR) is considerably increased in the jejunal epithelium of patients with celiac disease, an abnormality considered to be specific for celiac disease. This suggests an involvement of gammadelta T cells in the pathogenesis of the disease. To ascertain whether the TCR delta (TCRD) gene contributes to celiac disease susceptibility we carried out an association study and genetic linkage analysis using a highly polymorphic microsatellite marker at the TCRD locus on chromosome 14q11.2. The association study demonstrated no significant difference in allele frequencies of the TCRD gene marker between celiac disease patients and controls; accordingly, the relative risk estimates did not reach the level of statistical significance. In the linkage analysis, performed in 23 families, the logarithm of the odds (LOD) scores calculated for celiac disease versus the TCRD gene marker excluded linkage, suggesting that there is no determinant contributing to celiac disease status at or 5 cM distant to the analyzed TCRD gene marker. In conclusion, the results of the present study provide no evidence that the analyzed TCRD gene contributes substantially to celiac disease susceptibility.

Understanding the linkages between social safety nets and childhood violence: a review of the evidence from low- and middle-income countries

PubMed Central

Peterman, Amber; Neijhoft, Anastasia (Naomi); Cook, Sarah; Palermo, Tia M

2017-01-01

Abstract As many as one billion children experience violence every year, and household- and community-level poverty are among the risk factors for child protection violations. Social safety nets (SSNs) are a main policy tool to address poverty and vulnerability, and there is substantial evidence demonstrating positive effects on children’s health and human capital. This paper reviews evidence and develops a framework to understand linkages between non-contributory SSNs and the experience of childhood emotional, physical and sexual violence in low- and middle-income countries. We catalogue 14 rigorous impact evaluations, 11 of which are completed, analysing 57 unique impacts on diverse violence indicators. Among these impacts, approximately one in five represent statistically significant protective effects on childhood violence. Promising evidence relates to sexual violence among female adolescents in Africa, while there is less clear evidence of significant impacts in other parts of the developing world, and on young child measures, including violent discipline. Further, few studies are set up to meaningfully unpack mechanisms between SSNs and childhood violence; however, those most commonly hypothesized operate at the household level (through increases in economic security and reductions in poverty-related stress), the interpersonal level (improved parental behaviours, caregiving practices, improved psychosocial well-being) and at the child-level (protective education and decreases in problem or risky behaviours). It is important to emphasize that traditional SSNs are never designed with violence prevention as primary objectives, and thus should not be considered as standalone interventions to reduce risks for childhood violence. However, SSNs, particularly within integrated protection systems, appear to have potential to reduce violence risk. Linkages between SSNs and childhood violence are understudied, and investments should be made to close this evidence gap. PMID:28444197

Children with life-limiting conditions in paediatric intensive care units: a national cohort, data linkage study.

PubMed

Fraser, Lorna K; Parslow, Roger

2017-07-13

To determine how many children are admitted to paediatric intensive care unit (PICU) with life-limiting conditions (LLCs) and their outcomes. National cohort, data-linkage study. PICUs in England. Children admitted to a UK PICU (1 January 2004 and 31 March 2015) were identified in the Paediatric Intensive Care Audit Network dataset. Linkage to hospital episodes statistics enabled identification of children with a LLC using an International Classification of Diseases (ICD10) code list. Random-effects logistic regression was undertaken to assess risk of death in PICU. Flexible parametric survival modelling was used to assess survival in the year after discharge. Overall, 57.6% (n=89 127) of PICU admissions and 72.90% (n=4821) of deaths in PICU were for an individual with a LLC.The crude mortality rate in PICU was 5.4% for those with a LLC and 2.7% of those without a LLC. In the fully adjusted model, children with a LLC were 75% more likely than those without a LLC to die in PICU (OR 1.75 (95% CI 1.64 to 1.87)).Although overall survival to 1 year postdischarge was 96%, children with a LLC were 2.5 times more likely to die in that year than children without a LLC (OR 2.59 (95% CI 2.47 to 2.71)). Children with a LLC accounted for a large proportion of the PICU population. There is an opportunity to integrate specialist paediatric palliative care services with paediatric critical care to enable choice around place of care for these children and families. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Contributions of PTCH Gene Variants to Isolated Cleft Lip and Palate

PubMed Central

Mansilla, M.A.; Cooper, M.E.; Goldstein, T.; Castilla, E.E.; Camelo, J.S. Lopez; Marazita, M.L.; Murray, J.C.

2007-01-01

Objective Mutations in patched (PTCH) cause the nevoid basal cell carcinoma syndrome (NBCCS), or Gorlin syndrome. Nevoid basal cell carcinoma syndrome may present with developmental anomalies, including rib and craniofacial abnormalities, and predisposes to several tumor types, including basal cell carcinoma and medulloblastoma. Cleft palate is found in 4% of individuals with nevoid basal cell carcinoma syndrome. Because there might be specific sequence alterations in PTCH that limit expression to orofacial clefting, a genetic study of PTCH was undertaken in cases with cleft lip and/or palate (CL/P) known not to have nevoid basal cell carcinoma syndrome. Results Seven new normal variants spread along the entire gene and three missense mutations were found among cases with cleft lip and/or palate. One of these variants (P295S) was not found in any of 1188 control samples. A second variant was found in a case and also in 1 of 1119 controls. The third missense (S827G) was found in 5 of 1369 cases and in 5 of 1104 controls and is likely a rare normal variant. Linkage and linkage desequilibrium also was assessed using normal variants in and adjacent to the PTCH gene in 220 families (1776 individuals), each with two or more individuals with isolated clefting. Although no statistically significant evidence of linkage (multipoint HLOD peak = 2.36) was uncovered, there was borderline evidence of significant transmission distortion for one haplotype of two single nucleotide polymorphisms located within the PTCH gene (p = .08). Conclusion Missense mutations in PTCH may be rare causes of isolated cleft lip and/or palate. An as yet unidentified variant near PTCH may act as a modifier of cleft lip and/or palate. PMID:16405370

Poor medication adherence to bisphosphonates and high self-perception of aging in elderly female patients with osteoporosis.

PubMed

Wu, X; Wei, D; Sun, B; Wu, X N

2016-10-01

Non-adherence to bisphosphonates exposes the elderly female osteoporosis patients to an increased risk of fracture. This was one of the first studies to explore the relationship between medication adherence and self-perception of aging. Feelings of lacking control and expectations for negative events, beliefs of illness's chronic duration nature, and its linkage with aging were associated with of poor medication adherence. To examine the relationship between medication adherence to bisphosphonates and self-perception of aging in elderly female patients with osteoporosis. This was a cross-sectional survey. A convenience sample of 245 elderly female patients with osteoporosis prescribed regular oral bisphosphonate therapy was recruited from three tertiary hospitals in China. Sociodemographic and osteoporosis-related data, Morisky Medication Adherence Scale-8 (MMAS-8) and Aging Perceptions Questionnaire (APQ) data were collected. Mean adherence score measured by MMAS-8 was 4.46(SD = 1.91; range, 0.25-7.00). Percentages of good and poor adherence were 28.6 and 71.4 %, which showed a poor medication adherence. Six domains of APQ statistically significantly associated with medication adherence. Interestingly, with control of age, educational status, marital status, and symptoms accompanying osteoporosis as covariates in the multivariate linear regression model, the effects of three domains disappeared. Significantly, worse adherence was observed in those patients who had higher feelings of lack of control, more expectations for negative events, more beliefs of osteoporosis's chronic duration nature and its linkage with aging. We conclude that feelings of lacking control, expectations for negative events, beliefs of illness's chronic duration nature, and its linkage with aging were associated with poor medication adherence in elderly female patients with osteoporosis. Concerns about self-perception of aging need to be addressed in order to improve medication adherence.

Differences in Selected HIV Care Continuum Outcomes Among People Residing in Rural, Urban, and Metropolitan Areas-28 US Jurisdictions.

PubMed

Nelson, John A; Kinder, Anna; Johnson, Anna Satcher; Hall, H Irene; Hu, Xiaohong; Sweet, Donna; Guido, Alyssa; Katner, Harold; Janelle, Jennifer; Gonzalez, Maribel; Paz, Natalia Martínez; Ledonne, Charlotte; Henry, Jason; Bramel, Theresa; Harris, Jeanne

2018-12-01

The HIV care continuum is used to monitor success in HIV diagnosis and treatment among persons living with HIV in the United States. Significant differences exist along the HIV care continuum between subpopulations of people living with HIV; however, differences that may exist between residents of rural and nonrural areas have not been reported. We analyzed the Centers for Disease Control and Prevention's National HIV Surveillance System data on adults and adolescents (≥13 years) with HIV diagnosed in 28 jurisdictions with complete reporting of HIV-related lab results. Lab data were used to assess linkage to care (≥1 CD4 or viral load test ≤3 months of diagnosis), retention in care (≥2 CD4 and/or viral load tests ≥3 months apart), and viral suppression (viral load <200 copies/mL) among persons living with HIV. Residence at diagnosis was grouped into rural (<50,000 population), urban (50,000-499,999 population), and metropolitan (≥500,000 population) categories for statistical comparison. Prevalence ratios and 95% CI were calculated to assess significant differences in linkage, retention, and viral suppression. Although greater linkage to care was found for rural residents (84.3%) compared to urban residents (83.3%) and metropolitan residents (81.9%), significantly lower levels of retention in care and viral suppression were found for residents of rural (46.2% and 50.0%, respectively) and urban (50.2% and 47.2%) areas compared to residents of metropolitan areas (54.5% and 50.8%). Interventions are needed to increase retention in care and viral suppression among people with HIV in nonmetropolitan areas of the United States. © 2016 National Rural Health Association.

Data linkage of inpatient hospitalization and workers' claims data sets to characterize occupational falls.

PubMed

Bunn, Terry L; Slavova, Svetla; Bathke, Arne

2007-07-01

The identification of industry, occupation, and associated injury costs for worker falls in Kentucky have not been fully examined. The purpose of this study was to determine the associations between industry and occupation and 1) hospitalization length of stay; 2) hospitalization charges; and 3) workers' claims costs in workers suffering falls, using linked inpatient hospitalization discharge and workers' claims data sets. Hospitalization cases were selected with ICD-9-CM external cause of injury codes for falls and payer code of workers' claims for years 2000-2004. Selection criteria for workers'claims cases were International Association of Industrial Accident Boards and Commissions Electronic Data Interchange Nature (IAIABCEDIN) injuries coded as falls and/or slips. Common data variables between the two data sets such as date of birth, gender, date of injury, and hospital admission date were used to perform probabilistic data linkage using LinkSolv software. Statistical analysis was performed with non-parametric tests. Construction falls were the most prevalent for male workers and incurred the highest hospitalization and workers' compensation costs, whereas most female worker falls occurred in the services industry. The largest percentage of male worker falls was from one level to another, while the largest percentage of females experienced a fall, slip, or trip (not otherwise classified). When male construction worker falls were further analyzed, laborers and helpers had longer hospital stays as well as higher total charges when the worker fell from one level to another. Data linkage of hospitalization and workers' claims falls data provides additional information on industry, occupation, and costs that are not available when examining either data set alone.

Defining a staged-based process for economic and financial evaluations of mHealth programs.

PubMed

LeFevre, Amnesty E; Shillcutt, Samuel D; Broomhead, Sean; Labrique, Alain B; Jones, Tom

2017-01-01

Mobile and wireless technology for health (mHealth) has the potential to improve health outcomes by addressing critical health systems constraints that impede coverage, utilization, and effectiveness of health services. To date, few mHealth programs have been implemented at scale and there remains a paucity of evidence on their effectiveness and value for money. This paper aims to improve understanding among mHealth program managers and key stakeholders of how to select methods for economic evaluation (comparative analysis for determining value for money) and financial evaluation (determination of the cost of implementing an intervention, estimation of costs for sustaining or expanding an intervention, and assessment of its affordability). We outline a 6 stage-based process for selecting and integrating economic and financial evaluation methods into the monitoring and evaluation of mHealth solutions including (1) defining the program strategy and linkages with key outcomes, (2) assessment of effectiveness, (3) full economic evaluation or partial evaluation, (4) sub-group analyses, (5) estimating resource requirements for expansion, (6) affordability assessment and identification of models for financial sustainability. While application of these stages optimally occurs linearly, finite resources, limited technical expertise, and the timing of evaluation initiation may impede this. We recommend that analysts prioritize economic and financial evaluation methods based on programmatic linkages with health outcomes; alignment with an mHealth solution's broader stage of maturity and stage of evaluation; overarching monitoring and evaluation activities; stakeholder evidence needs; time point of initiation; and available resources for evaluations.

The Evolution of Integrated Assessment and Emerging Challenges in the Assessment of Human and Natural System Interactions

NASA Astrophysics Data System (ADS)

Clarke, L.

2017-12-01

Integrated assessment (IA) modeling and research has a long history, spanning over 30 years since its inception and addressing a wide range of contemporary issues along the way. Over the last decade, IA modeling and research has emerged as one of the primary analytical methods for understanding the complex interactions between human and natural systems, from the interactions between energy, water, and land/food systems to the interplay between health, climate, and air pollution. IA modeling and research is particularly well-suited for the analysis of these interactions because it is a discipline that strives to integrate representations of multiple systems into consistent computational platforms or frameworks. In doing so, it explicitly confronts the many tradeoffs that are frequently necessary to manage complexity and computational cost while still representing the most important interactions and overall, coupled system behavior. This talk explores the history of IA modeling and research as a means to better understand its role in the assessment of contemporary issues at the confluence of human and natural systems. It traces the evolution of IA modeling and research from initial exploration of long-term emissions pathways, to the role of technology in the global evolution of the energy system, to the key linkages between land and energy systems and, more recently, the linkages with water, air pollution, and other key systems and issues. It discusses the advances in modeling that have emerged over this evolution and the biggest challenges that still present themselves as we strive to better understand the most important interactions between human and natural systems and the implications of these interactions for human welfare and decision making.

Productivity in the barents sea--response to recent climate variability.

PubMed

Dalpadado, Padmini; Arrigo, Kevin R; Hjøllo, Solfrid S; Rey, Francisco; Ingvaldsen, Randi B; Sperfeld, Erik; van Dijken, Gert L; Stige, Leif C; Olsen, Are; Ottersen, Geir

2014-01-01

The temporal and spatial dynamics of primary and secondary biomass/production in the Barents Sea since the late 1990s are examined using remote sensing data, observations and a coupled physical-biological model. Field observations of mesozooplankton biomass, and chlorophyll a data from transects (different seasons) and large-scale surveys (autumn) were used for validation of the remote sensing products and modeling results. The validation showed that satellite data are well suited to study temporal and spatial dynamics of chlorophyll a in the Barents Sea and that the model is an essential tool for secondary production estimates. Temperature, open water area, chlorophyll a, and zooplankton biomass show large interannual variations in the Barents Sea. The climatic variability is strongest in the northern and eastern parts. The moderate increase in net primary production evident in this study is likely an ecosystem response to changes in climate during the same period. Increased open water area and duration of open water season, which are related to elevated temperatures, appear to be the key drivers of the changes in annual net primary production that has occurred in the northern and eastern areas of this ecosystem. The temporal and spatial variability in zooplankton biomass appears to be controlled largely by predation pressure. In the southeastern Barents Sea, statistically significant linkages were observed between chlorophyll a and zooplankton biomass, as well as between net primary production and fish biomass, indicating bottom-up trophic interactions in this region.

A Socio-spatial Dimension of Local Creative Industry Development in Semarang and Kudus Batik Clusters

NASA Astrophysics Data System (ADS)

Nugroho, P.

2018-02-01

Creative industries existence is inseparable from the underlying social construct which provides sources for creativity and innovation. The working of social capital in a society facilitates information exchange, knowledge transfer and technology acquisition within the industry through social networks. As a result, a socio-spatial divide exists in directing the growth of the creative industries. This paper aims to examine how such a socio-spatial divide contributes to the local creative industry development in Semarang and Kudus batik clusters. Explanatory sequential mixed methods approach covering a quantitative approach followed by a qualitative approach is chosen to understand better the interplay between tangible and intangible variables in the local batik clusters. Surveys on secondary data taken from the government statistics and reports, previous studies, and media exposures are completed in the former approach to identify clustering pattern of the local batik industry and the local embeddedness factors which have shaped the existing business environment. In-depth interviews, content analysis, and field observations are engaged in the latter approach to explore reciprocal relationships between the elements of social capital and the local batik cluster development. The result demonstrates that particular social ties have determined the forms of spatial proximity manifested in forward and backward business linkages. Trust, shared norms, and inherited traditions are the key social capital attributes that lead to such a socio-spatial divide. Therefore, the intermediating roles of the bridging actors are necessary to encouraging cooperation among the participating stakeholders for a better cluster development.

Productivity in the Barents Sea - Response to Recent Climate Variability

PubMed Central

Dalpadado, Padmini; Arrigo, Kevin R.; Hjøllo, Solfrid S.; Rey, Francisco; Ingvaldsen, Randi B.; Sperfeld, Erik; van Dijken, Gert L.; Stige, Leif C.; Olsen, Are; Ottersen, Geir

2014-01-01

The temporal and spatial dynamics of primary and secondary biomass/production in the Barents Sea since the late 1990s are examined using remote sensing data, observations and a coupled physical-biological model. Field observations of mesozooplankton biomass, and chlorophyll a data from transects (different seasons) and large-scale surveys (autumn) were used for validation of the remote sensing products and modeling results. The validation showed that satellite data are well suited to study temporal and spatial dynamics of chlorophyll a in the Barents Sea and that the model is an essential tool for secondary production estimates. Temperature, open water area, chlorophyll a, and zooplankton biomass show large interannual variations in the Barents Sea. The climatic variability is strongest in the northern and eastern parts. The moderate increase in net primary production evident in this study is likely an ecosystem response to changes in climate during the same period. Increased open water area and duration of open water season, which are related to elevated temperatures, appear to be the key drivers of the changes in annual net primary production that has occurred in the northern and eastern areas of this ecosystem. The temporal and spatial variability in zooplankton biomass appears to be controlled largely by predation pressure. In the southeastern Barents Sea, statistically significant linkages were observed between chlorophyll a and zooplankton biomass, as well as between net primary production and fish biomass, indicating bottom-up trophic interactions in this region. PMID:24788513

Assessing the Potential and Limitations of Leveraging Food Sovereignty to Improve Human Health.

PubMed

Jones, Andrew D; Fink Shapiro, Lilly; Wilson, Mark L

2015-01-01

Food sovereignty has been defined as "the right of peoples to healthy and culturally appropriate food produced through ecologically sound and sustainable methods, and their right to define their own food and agriculture systems." Human health is an implied component of this definition through the principle of healthy food. In fact, improved human health is commonly cited as a benefit of transforming food production away from the dominant practices of industrial agriculture. Yet, does the use of "ecologically sound and sustainable methods" of food production necessarily translate into better human health outcomes? Does greater choice in defining an agricultural or food system create gains in health and well-being? We elucidate the conceptual linkages between food sovereignty and human health, critically examine the empirical evidence supporting or refuting these linkages, and identify research gaps and key priorities for the food sovereignty-human health research agenda. Five domains of food sovereignty are discussed including: (1) use of agroecological management practices for food production, (2) the localization of food production and consumption, (3) promotion of social justice and equity, (4) valuation of traditional knowledge, and (5) the transformation of economic and political institutions and structures to support self-determination. We find that although there are many plausible linkages between food sovereignty and human health, the empirical evidence in support of the hypothesis that increasing food sovereignty yields improvements to human health is weak. We propose that a concerted effort to generate new empirical evidence on the health implications of these domains of food sovereignty is urgently needed, and suggest areas of research that may be crucial for addressing the gaps in the evidence base.

Assessing the Potential and Limitations of Leveraging Food Sovereignty to Improve Human Health

PubMed Central

Jones, Andrew D.; Fink Shapiro, Lilly; Wilson, Mark L.

2015-01-01

Food sovereignty has been defined as “the right of peoples to healthy and culturally appropriate food produced through ecologically sound and sustainable methods, and their right to define their own food and agriculture systems.” Human health is an implied component of this definition through the principle of healthy food. In fact, improved human health is commonly cited as a benefit of transforming food production away from the dominant practices of industrial agriculture. Yet, does the use of “ecologically sound and sustainable methods” of food production necessarily translate into better human health outcomes? Does greater choice in defining an agricultural or food system create gains in health and well-being? We elucidate the conceptual linkages between food sovereignty and human health, critically examine the empirical evidence supporting or refuting these linkages, and identify research gaps and key priorities for the food sovereignty-human health research agenda. Five domains of food sovereignty are discussed including: (1) use of agroecological management practices for food production, (2) the localization of food production and consumption, (3) promotion of social justice and equity, (4) valuation of traditional knowledge, and (5) the transformation of economic and political institutions and structures to support self-determination. We find that although there are many plausible linkages between food sovereignty and human health, the empirical evidence in support of the hypothesis that increasing food sovereignty yields improvements to human health is weak. We propose that a concerted effort to generate new empirical evidence on the health implications of these domains of food sovereignty is urgently needed, and suggest areas of research that may be crucial for addressing the gaps in the evidence base. PMID:26636062

Concepts associated with a unified life cycle analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whelan, Gene; Peffers, Melissa S.; Tolle, Duane A.

There is a risk associated with most things in the world, and all things have a life cycle unto themselves, even brownfields. Many components can be described by a''cycle of life.'' For example, five such components are life-form, chemical, process, activity, and idea, although many more may exist. Brownfields may touch upon several of these life cycles. Each life cycle can be represented as independent software; therefore, a software technology structure is being formulated to allow for the seamless linkage of software products, representing various life-cycle aspects. Because classes of these life cycles tend to be independent of each other,more » the current research programs and efforts do not have to be revamped; therefore, this unified life-cycle paradigm builds upon current technology and is backward compatible while embracing future technology. Only when two of these life cycles coincide and one impacts the other is there connectivity and a transfer of information at the interface. The current framework approaches (e.g., FRAMES, 3MRA, etc.) have a design that is amenable to capturing (1) many of these underlying philosophical concepts to assure backward compatibility of diverse independent assessment frameworks and (2) linkage communication to help transfer the needed information at the points of intersection. The key effort will be to identify (1) linkage points (i.e., portals) between life cycles, (2) the type and form of data passing between life cycles, and (3) conditions when life cycles interact and communicate. This paper discusses design aspects associated with a unified life-cycle analysis, which can support not only brownfields but also other types of assessments.« less