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Sample records for oxford record linkage

  1. Probabilistic record linkage.

    PubMed

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-06-01

    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

  2. Probabilistic record linkage

    PubMed Central

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-01-01

    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

  3. 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

  4. Efficient Record Linkage Algorithms Using Complete Linkage Clustering

    PubMed Central

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times. PMID:27124604

  5. Private Medical Record Linkage with Approximate Matching

    PubMed Central

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

    2010-01-01

    Federal regulations require patient data to be shared for reuse in a de-identified manner. However, disparate providers often share data on overlapping populations, such that a patient’s record may be duplicated or fragmented in the de-identified repository. To perform unbiased statistical analysis in a de-identified setting, it is crucial to integrate records that correspond to the same patient. Private record linkage techniques have been developed, but most methods are based on encryption and preclude the ability to determine similarity, decreasing the accuracy of record linkage. The goal of this research is to integrate a private string comparison method that uses Bloom filters to provide an approximate match, with a medical record linkage algorithm. We evaluate the approach with 100,000 patients’ identifiers and demographics from the Vanderbilt University Medical Center. We demonstrate that the private approximation method achieves sensitivity that is, on average, 3% higher than previous methods. PMID:21346965

  6. 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

  7. 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

  8. Client and Birth Record Linkage: A Method, Biases, and Lessons.

    ERIC Educational Resources Information Center

    Holian, John

    1996-01-01

    Describes record linkage as a data-generating technique, and presents a method for linking client records to live and stillbirth records, using 32,974 births in the Cleveland (Ohio) area. Biases that can enter the linkage process and general research issues related to record linkage are discussed. (SLD)

  9. A simple heuristic for blindfolded record linkage

    PubMed Central

    Lowe, Henry; Das, Amar; Ferris, Todd

    2012-01-01

    Objectives To address the challenge of balancing privacy with the need to create cross-site research registry records on individual patients, while matching the data for a given patient as he or she moves between participating sites. To evaluate the strategy of generating anonymous identifiers based on real identifiers in such a way that the chances of a shared patient being accurately identified were maximized, and the chances of incorrectly joining two records belonging to different people were minimized. Methods Our hypothesis was that most variation in names occurs after the first two letters, and that date of birth is highly reliable, so a single match variable consisting of a hashed string built from the first two letters of the patient's first and last names plus their date of birth would have the desired characteristics. We compared and contrasted the match algorithm characteristics (rate of false positive v. rate of false negative) for our chosen variable against both Social Security Numbers and full names. Results In a data set of 19 000 records, a derived match variable consisting of a 2-character prefix from both first and last names combined with date of birth has a 97% sensitivity; by contrast, an anonymized identifier based on the patient's full names and date of birth has a sensitivity of only 87% and SSN has sensitivity 86%. Conclusion The approach we describe is most useful in situations where privacy policies preclude the full exchange of the identifiers required by more sophisticated and sensitive linkage algorithms. For data sets of sufficiently high quality this effective approach, while producing a lower rate of matching than more complex algorithms, has the merit of being easy to explain to institutional review boards, adheres to the minimum necessary rule of the HIPAA privacy rule, and is faster and less cumbersome to implement than a full probabilistic linkage. PMID:22298567

  10. Construction of a virtual EPR and automated contextual linkage to multiple sources of support information on the Oxford Clinical Intranet.

    PubMed

    Kay, J D; Nurse, D

    1999-01-01

    We have used internet-standard tools to provide access for clinicians to the components of the electronic patient record held on multiple remote disparate systems. Through the same interface we have provided access to multiple knowledgebases, some written locally and others published elsewhere. We have developed linkage between these two types of information which removes the need for the user to drill down into each knowledgebase to search for relevant information. This approach may help in the implementation of evidence-based practice. The major problems appear to be semantic rather than technological. The intranet was developed at low cost and is now in routine use. This approach appears to be transferable across systems and organisations.

  11. 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.

  12. Which are the best identifiers for record linkage?

    PubMed

    Quantin, Catherine; Binquet, Christine; Bourquard, Karima; Pattisina, Ronny; Gouyon-Cornet, Béatrice; Ferdynus, Cyril; Gouyon, Jean-Bernard; François-André, Allaert

    2004-01-01

    As a linkage using less informative identifiers could lead to linkage errors, it is essential to quantify the information associated to each identifier. The aim of this study was to estimate the discriminating power of different identifiers susceptible to be used in a record linkage process. This work showed the interest of three identifiers when linking data concerning a same patient using an automatic procedure based on the method proposed by Jaro; the date of birth, the first and the last names seemed to be the more appropriate identifiers. Including a poorly discriminating identifier like gender did not improve the results. Moreover, adding a second christian name, often missing, increased linkage errors. On the contrary, it seemed that using a phonetic treatment adapted to the French language could improve the results of linkage in comparison to the Soundex. However, whatever, the method used it seems necessary to improve the quality of identifier collection as it could greatly influence linkage results.

  13. RLT-S: A Web System for Record Linkage

    PubMed Central

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2015-01-01

    Background Record linkage integrates records across multiple related data sources identifying duplicates and accounting for possible errors. Real life applications require efficient algorithms to merge these voluminous data sources to find out all records belonging to same individuals. Our recently devised highly efficient record linkage algorithms provide best-known solutions to this challenging problem. Method We have developed RLT-S, a freely available web tool, which implements our single linkage clustering algorithm for record linkage. This tool requires input data sets and a small set of configuration settings about these files to work efficiently. RLT-S employs exact match clustering, blocking on a specified attribute and single linkage based hierarchical clustering among these blocks. Results RLT-S is an implementation package of our sequential record linkage algorithm. It outperforms previous best-known implementations by a large margin. The tool is at least two times faster for any dataset than the previous best-known tools. Conclusions RLT-S tool implements our record linkage algorithm that outperforms previous best-known algorithms in this area. This website also contains necessary information such as instructions, submission history, feedback, publications and some other sections to facilitate the usage of the tool. Availability RLT-S is integrated into http://www.rlatools.com, which is currently serving this tool only. The tool is freely available and can be used without login. All data files used in this paper have been stored in https://github.com/abdullah009/DataRLATools. For copies of the relevant programs please see https://github.com/abdullah009/RLATools. PMID:25942687

  14. 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.

  15. Postmarketing drug surveillance by record linkage in Tayside.

    PubMed

    Crombie, I K; Brown, S V; Hamley, J G

    1984-09-01

    The feasibility of conducting postmarketing drug surveillance by record linkage in Tayside was assessed. The key feature of the method is that all hospital discharge data are already computerised by the area health board and may be accessed through the unique community health number (CHNo) which has been allocated to all Tayside residents. The 12 861 prescriptions for cimetidine dispensed in Tayside over a nine month period were collected and the CHNo identified for 76%. These corresponded to 3802 individuals and their discharge data, together with those for an equal number of controls matched by age, sex, and general practitioner were retrieved from the computer. The expected excess of those diseases for which cimetidine is prescribed (peptic ulcer and oesophagitis) was observed. Other drug-disease associations were observed but may have been due to confounding and emphasise the inadequacy of community based controls. The major advantages of record linkage are, firstly, the low cost of the method, the present study costing just over pounds 12 000, and, secondly, the duration of patient follow up which may may be extended for as many years as required simply by rerunning the computer programs. To assemble large patient cohorts the study would have to be extended to other area health boards that are currently developing similar computer systems. Record linkage may provide a cost effective method for the follow up of patients to identify serious adverse drug reactions, particularly those that take several years to develop.

  16. 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

  17. Effects of record linkage errors on registry-based follow-up studies.

    PubMed

    Brenner, H; Schmidtmann, I; Stegmaier, C

    1997-12-15

    The importance of reliable record linkage for high quality-population-based disease registration is widely recognized. Systematic methodologic work is lacking, however, on the effects of record linkage errors on the use of disease registries for epidemiologic purposes. The present paper provides algebraic models describing the effects of record linkage errors on monitoring survival of registered patients, which is commonly performed by matching registry records against a database of death certificates, and on registry-based incidence follow-up of external cohorts. Homonym errors, that is, erroneous linkage of records that pertain to distinct individuals, lead to underestimation of survival of registered patients and to overestimation of disease incidence among external cohorts linked to the registry, while synonym errors, that is, failure to link notifications on the same individual, have opposite effects. The magnitude of effects of record linkage errors are illustrated with numerical examples.

  18. Iowa record-linkage study: death rates in psychiatric patients.

    PubMed

    Black, D W

    1998-09-01

    The Iowa record-linkage study was developed to investigate death rates in psychiatric patients, and involved computer matching of death certificates with a roster of patients. A list of all patients admitted to our hospital from 1972 through 1981 was obtained and after removing duplicate entries the list was pared to 5412 names. The record included multiple identifiers (e.g., name, gender, date-of-birth, hospital number). This information was then linked by computer with all Iowa death certificates for the same period; a total of 331 deaths were identified. Patients were assigned to a single psychiatric diagnostic category based on a computer program that reviewed each patient's clinical diagnoses and picked the one with the highest priority in a hierarchy we had created. Age and sex adjusted mortality tables were constructed, allowing us to compute expected numbers of deaths. Relative risk for premature death was greatest among women, and those under 20 years. Risk was associated with all psychiatric diagnoses and was significantly higher among patients of either gender with an organic mental disorder or schizophrenia; women with acute schizophrenia, depressive neuroses, alcoholism, drug abuse, and psychophysiological disorders; and men with neuroses. Death from natural causes, especially from heart disease, was significantly excessive among women, while death from accidents and suicides was excessive for both men and women. The overall SMR was 1.65 (P < 0.001). Most importantly, we found that the greatest excess of mortality occurred within the first 2 years following hospital discharge. Thus, we were able to demonstrate that risk of mortality in general, and of suicide specifically, differed according to age, gender, diagnosis, and portion of the follow-up. We have subsequently used this method to investigate specific risk factors associated with mortality in mood disorders, schizophrenia, and antisocial personality disorder. Findings from these studies are

  19. Use of graph theory measures to identify errors in record linkage.

    PubMed

    Randall, Sean M; Boyd, James H; Ferrante, Anna M; Bauer, Jacqueline K; Semmens, James B

    2014-07-01

    Ensuring high linkage quality is important in many record linkage applications. Current methods for ensuring quality are manual and resource intensive. This paper seeks to determine the effectiveness of graph theory techniques in identifying record linkage errors. A range of graph theory techniques was applied to two linked datasets, with known truth sets. The ability of graph theory techniques to identify groups containing errors was compared to a widely used threshold setting technique. This methodology shows promise; however, further investigations into graph theory techniques are required. The development of more efficient and effective methods of improving linkage quality will result in higher quality datasets that can be delivered to researchers in shorter timeframes.

  20. Empirical aspects of record linkage across multiple data sets using statistical linkage keys: the experience of the PIAC cohort study

    PubMed Central

    2010-01-01

    Background In Australia, many community service program data collections developed over the last decade, including several for aged care programs, contain a statistical linkage key (SLK) to enable derivation of client-level data. In addition, a common SLK is now used in many collections to facilitate the statistical examination of cross-program use. In 2005, the Pathways in Aged Care (PIAC) cohort study was funded to create a linked aged care database using the common SLK to enable analysis of pathways through aged care services. Linkage using an SLK is commonly deterministic. The purpose of this paper is to describe an extended deterministic record linkage strategy for situations where there is a general person identifier (e.g. an SLK) and several additional variables suitable for data linkage. This approach can allow for variation in client information recorded on different databases. Methods A stepwise deterministic record linkage algorithm was developed to link datasets using an SLK and several other variables. Three measures of likely match accuracy were used: the discriminating power of match key values, an estimated false match rate, and an estimated step-specific trade-off between true and false matches. The method was validated through examining link properties and clerical review of three samples of links. Results The deterministic algorithm resulted in up to an 11% increase in links compared with simple deterministic matching using an SLK. The links identified are of high quality: validation samples showed that less than 0.5% of links were false positives, and very few matches were made using non-unique match information (0.01%). There was a high degree of consistency in the characteristics of linked events. Conclusions The linkage strategy described in this paper has allowed the linking of multiple large aged care service datasets using a statistical linkage key while allowing for variation in its reporting. More widely, our deterministic algorithm

  1. Associations between selected immune-mediated diseases and tuberculosis: record-linkage studies

    PubMed Central

    2013-01-01

    Background Previous studies have suggested that there may be an association between some immune-mediated diseases and risk of tuberculosis (TB). Methods We analyzed a database of linked statistical records of hospital admissions and death certificates for the whole of England (1999 to 2011), and a similar database (the Oxford Record Linkage Study (ORLS)) for a region of southern England in an earlier period. Rate ratios for TB were determined, comparing immune-mediated disease cohorts with comparison cohorts. Results In the all-England dataset, there were significantly elevated risks of TB after hospital admission for the following individual immune-mediated diseases: Addison's disease, ankylosing spondylitis, autoimmune hemolytic anemia, chronic active hepatitis, coeliac disease, Crohn's disease, dermatomyositis, Goodpasture's syndrome, Hashimoto's thyroiditis, idiopathic thrombocytopenia purpura (ITP), myasthenia gravis, myxedema, pemphigoid, pernicious anemia, polyarteritis nodosa, polymyositis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic lupus erythematosus (SLE), thyrotoxicosis and ulcerative colitis. Particularly high levels of risk were found for Addison’s disease (rate ratio (RR) = 11.9 (95% CI 9.5 to 14.7)), Goodpasture’s syndrome (RR = 10.8 (95% CI 4.0 to 23.5)), SLE (RR = 9.4 (95% CI 7.9 to 11.1)), polymyositis (RR = 8.0 (95% CI 4.9 to 12.2)), polyarteritis nodosa (RR = 6.7 (95% CI 3.2 to 12.4)), dermatomyositis (RR = 6.6 (95% CI 3.0 to 12.5)), scleroderma (RR = 6.1 (95% CI 4.4 to 8.2)) and autoimmune hemolytic anemia (RR = 5.1 (95% CI 3.4 to 7.4)). Conclusions These two databases show that patients with some immune-mediated diseases have an increased risk of TB, although we cannot explicitly state the direction of risk or exclude confounding. Further study of these associations is warranted, and these findings may aid TB screening, control and treatment policies. PMID:23557090

  2. Record linkage to correct under-ascertainment of cancers in HIV cohorts: The Sinikithemba HIV clinic linkage project.

    PubMed

    Sengayi, Mazvita; Spoerri, Adrian; Egger, Matthias; Kielkowski, Danuta; Crankshaw, Tamaryn; Cloete, Christie; Giddy, Janet; Bohlius, Julia

    2016-09-15

    The surveillance of HIV-related cancers in South Africa is hampered by the lack of systematic collection of cancer diagnoses in HIV cohorts and the absence of HIV status in cancer registries. To improve cancer ascertainment and estimate cancer incidence, we linked records of adults (aged ≥ 16 years) on antiretroviral treatment (ART) enrolled at Sinikithemba HIV clinic, McCord Hospital in KwaZulu-Natal (KZN) with the cancer records of public laboratories in KZN province using probabilistic record linkage (PRL) methods. We calculated incidence rates for all cancers, Kaposi sarcoma (KS), cervix, non-Hodgkin's lymphoma and non-AIDS defining cancers (NADCs) before and after inclusion of linkage-identified cancers with 95% confidence intervals (CIs). A total of 8,721 records of HIV-positive patients were linked with 35,536 cancer records. Between 2004 and 2010, we identified 448 cancers, 82% (n = 367) were recorded in the cancer registry only, 10% (n = 43) in the HIV cohort only and 8% (n = 38) both in the HIV cohort and the cancer registry. The overall cancer incidence rate in patients starting ART increased from 134 (95% CI 91-212) to 877 (95% CI 744-1,041) per 100,000 person-years after inclusion of linkage-identified cancers. Incidence rates were highest for KS (432, 95% CI 341-555), followed by cervix (259, 95% CI 179-390) and NADCs (294, 95% CI 223-395) per 100,000 person-years. Ascertainment of cancer in HIV cohorts is incomplete, PRL is both feasible and essential for cancer ascertainment. PMID:27098265

  3. 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…

  4. Accuracy of probabilistic and deterministic record linkage: the case of tuberculosis

    PubMed Central

    de Oliveira, Gisele Pinto; Bierrenbach, Ana Luiza de Souza; de Camargo, Kenneth Rochel; Coeli, Cláudia Medina; Pinheiro, Rejane Sobrino

    2016-01-01

    ABSTRACT OBJECTIVE To analyze the accuracy of deterministic and probabilistic record linkage to identify TB duplicate records, as well as the characteristics of discordant pairs. METHODS 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. RESULTS 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. CONCLUSIONS 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. PMID:27556963

  5. Contribution of record linkage to vital status determination in cancer patients.

    PubMed

    Fournel, Isabelle; Schwarzinger, Michaël; Binquet, Christine; Benzenine, Eric; Hill, Catherine; Quantin, Catherine

    2009-01-01

    To assess the performance of vital status determination by record linkage between a hospital database and the French national mortality database with anonymised data in order to adhere to French legislation. Hospital database of the Institut Gustave Roussy (IGR), the largest cancer centre in France, and the French mortality databases from 1998-2004 were used for this record linkage. A phonetic code adapted to French language was first applied to identifiers. The last name, maiden name, all first names and the date of birth were then each rendered anonymous using irreversible hash coding. Record linkage, using the probabilistic method developed by Jaro, was based on four fields: the last name, first given name, date of birth and code of birth place. Other variables were used for further automatic and manual validation. Linkage results were very satisfactory for the 10,089 patients included: sensitivity was 94.8% and specificity 99.5%. The positive and negative likelihood ratios were respectively 190 and 0.05. The main causes of discordances were erroneous or incomplete information such as unrecorded maiden name in the hospital database. Results were improved by adding manual validation to electronic matching: sensitivity rose to 97.2% and specificity to 99.4%. Record linkage using anonymised data applied to large scale hospital data is possible and has good validity. This method offers new prospects for large prognostic studies based on hospital data provided that the diagnosis date is systematically recorded in the hospital database.

  6. A peculiar aspect of patients' safety: the discriminating power of identifiers for record linkage.

    PubMed

    Quantin, Catherine; Binquet, Christine; Bourquard, Karima; Pattisina, Ronny; Gouyon-Cornet, Béatrice; Ferdynus, Cyril; Gouyon, Jean-Bernard; Allaert, François-André

    2004-01-01

    Today, one of the main stake of the interfaced health information systems or networks is to be able to gather the different parts of the medical record of a patient without any risk to mix them with those of one other patient. This objective could appear easy to reach but only in theory because in practice many name are misspelled or erroneous and a great attention has to be paid to define what is the best identifier to link medical record. As a linkage using less informative identifiers could lead to linkage errors, it is essential to quantify the information associated to each identifier. The aim of this study was to estimate the discriminating power of different identifiers susceptible to be used in a record linkage process. This work showed the interest of three identifiers when linking data concerning a same patient using an automatic procedure based on the method proposed by Jaro; the date of birth, the first and the last names seemed to be the more appropriate identifiers. Including a poorly discriminating identifier like gender did not improve the results. Moreover, adding a second christian name, often missing, increased linkage errors. On the contrary, it seemed that using a phonetic treatment adapted to the French language could improve the results of linkage in comparison to the Soundex. However, whatever, the method used it seems necessary to improve the quality of identifier collection as it could greatly influence linkage results.

  7. Creating a Powerful Platform to Explore Health in a Correctional Population: A Record Linkage Study.

    PubMed

    McIsaac, Kathryn E; Farrell MacDonald, Shanna; Chong, Nelson; Moser, Andrea; Moineddin, Rahim; Colantonio, Angela; Nathens, Avery; Matheson, Flora I

    2016-01-01

    We used record linkage to create a data repository of health information of persons who were federally incarcerated in Ontario and Canada. We obtained records from 56,867 adults who were federally incarcerated between January 1, 1998 and December 31, 2011 from the Correctional Service of Canada; 15,248 records belonged to individuals residing in Ontario, Canada. We linked these records to the Registered Persons Database (RPDB) which contained records from 18,116,996 individuals eligible for health care in Ontario. Out of 56,867 OMS records, 22,844 (40.2%) were linked to the RPDB. Looking only at those incarcerated in Ontario, 98%, (14 953 of 15248) records were linked to RPDB. Most records of persons in Ontario-based facilities were linked deterministically. Linkage rates were lower for women, minority groups, and substance users. In conclusion, record linkage enabled the creation of a valuable data repository: there are no electronic medical records for correctional populations in Canada, making it more difficult to profile their health. PMID:27532612

  8. Creating a Powerful Platform to Explore Health in a Correctional Population: A Record Linkage Study

    PubMed Central

    McIsaac, Kathryn E.; Farrell MacDonald, Shanna; Chong, Nelson; Moser, Andrea; Moineddin, Rahim; Colantonio, Angela; Nathens, Avery; Matheson, Flora I.

    2016-01-01

    We used record linkage to create a data repository of health information of persons who were federally incarcerated in Ontario and Canada. We obtained records from 56,867 adults who were federally incarcerated between January 1, 1998 and December 31, 2011 from the Correctional Service of Canada; 15,248 records belonged to individuals residing in Ontario, Canada. We linked these records to the Registered Persons Database (RPDB) which contained records from 18,116,996 individuals eligible for health care in Ontario. Out of 56,867 OMS records, 22,844 (40.2%) were linked to the RPDB. Looking only at those incarcerated in Ontario, 98%, (14 953 of 15248) records were linked to RPDB. Most records of persons in Ontario-based facilities were linked deterministically. Linkage rates were lower for women, minority groups, and substance users. In conclusion, record linkage enabled the creation of a valuable data repository: there are no electronic medical records for correctional populations in Canada, making it more difficult to profile their health. PMID:27532612

  9. Issues in identification and linkage of patient records across an integrated delivery system.

    PubMed

    Arellano, M G; Weber, G I

    1998-01-01

    Historically, the health information systems community has viewed linking personal records as a mundane task. The oversimplified view that routine database manipulation can accurately identify multiple records for a single individual is erroneous, an assumption based on a misperception of the quality of the underlying data. Such data have been adversely affected by the evolution of individual facility patient indexes from multiple systems and the results of backload procedures, and the lack of focus on the need for data integrity by users of the automated systems. Much of the random, invalid data we identify on a daily basis is directly associated with the need for system users to place data in the patient record while they face the situation of having no obvious data field in which to place them. Combined with an underlying lack of standards for the collection of personal identification information, this results in pure chaos when reviewing an MPI file containing a million records at the start of a linkage evaluation project. We have documented the considerable effort that must therefore be made in standardizing the MPI files using stringent analytical procedures and applying common edit routines before commencing record linkage. This preprocessing effort must then be supplemented with sophisticated matching procedures that can handle the dual challenge of minimizing false negatives (the failure to identify true linkages) and false positives (the incorrect linking of records that do not represent the same person). The identification of pairs of linked records does not, however, complete an EPI loading. Because it is fairly common for a multiple facility linkage evaluation to identify more than two medical record numbers for the same patient, and the primary goal of an EPI is to assign a unique identifier for the patient which will link that patient's multiple files, it becomes necessary to develop a means of readily associating three or more records for the same

  10. Birth Outcomes and Academic Achievement in Childhood: A Population Record Linkage Study

    ERIC Educational Resources Information Center

    Moore, Elizabeth A.; Harris, Felicity; Laurens, Kristin R.; Green, Melissa J.; Brinkman, Sally; Lenroot, Rhoshel K.; Carr, Vaughan J.

    2014-01-01

    Poor academic performance during childhood predicts later adverse outcomes, and could be targeted for improvement if detected early. This study used population-based record linkage to examine the association between early life risk factors and academic achievement at two different stages of development using two different cohorts: a kindergarten…

  11. Chronic disease in the workplace and the environment. Record linkage: methodologic and legal issues.

    PubMed

    Beebe, G W

    1984-01-01

    Research on chronic disease arising from occupational exposure typically requires that events widely separated in time be linked through records created and maintained by more than one institution or agency. Too little attention is paid, in creating record forms, to the mechanics of record linkage and to the nature of the information needed for studies of the effect of the workplace on health. Record linkage also suffers from a highly decentralized federal statistical system and from changes in privacy legislation and in public attitudes toward personal privacy, changes motivated by invasions of privacy that have arisen from activities entirely unrelated to medical research. If medical research capabilities are to match the information needs of society a more adequate balance will have to be struck between those needs and personal privacy.

  12. Multiple sclerosis after infectious mononucleosis: record linkage study

    PubMed Central

    Goldacre, M.; Wotton, C.; Seagroatt, V.; Yeates, D.

    2004-01-01

    Objective: To ascertain if infectious mononucleosis is a risk factor for the development of multiple sclerosis (MS); and, if it is, whether its effect is close to or remote in time from the onset of MS. Design: Analysis of database of linked abstracts of records of hospital admission and death. Setting: Health region in central southern England. Main outcome measure: Ratio of rate of MS in a cohort of people admitted to hospital with infectious mononucleosis to the rate in a comparison cohort. Results: Considering all time intervals from admission with infection to admission with MS, there was a non-significant increase of risk of MS in the infectious mononucleosis cohort (rate ratio 2.17, 95% confidence intervals 0.79 to 4.77). At the interval of 10 years or more, there was a significant increase in risk of MS (rate ratio 4.01, 1.48 to 8.93). The mean time from infectious mononucleosis to first admission with MS was 14 years. Conclusion: This study adds support to the evidence that Epstein-Barr virus, the cause of infectious mononucleosis, is associated with MS. Its role is probably as an initiator of the disease process of MS, or as a contributor to its early development, rather than as an activator of latent, existing disease. PMID:15547068

  13. Record linkage in Australian epidemiological research: health benefits, privacy safeguards and future potential.

    PubMed

    Sibthorpe, B; Kliewer, E; Smith, L

    1995-06-01

    Epidemiologists are increasingly concerned with the health effects of interventions and of exposure to noninfectious agents, but there may be long periods between exposure and outcome. Collecting information from respondents is a costly and often inefficient way of obtaining the longitudinal data necessary to study these effects. Linking existing data can be an effective and efficient alternative. However, it is often not practicable to obtain informed consent from the individuals whose records are to be linked. This raises important issues relating to protection of privacy. This paper examines the health benefits and privacy issues of epidemiological and health services research involving record linkage in Australia. The future potential for studies based on record linkage is discussed in the context of recent national and international developments in data protection. In the interests of public health and the rational use of health resources a balance must be struck between protecting individual privacy and conducting such health research for the common good.

  14. Designing an Algorithm to Preserve Privacy for Medical Record Linkage With Error-Prone Data

    PubMed Central

    Pal, Doyel; Chen, Tingting; Khethavath, Praveen

    2014-01-01

    Background Linking medical records across different medical service providers is important to the enhancement of health care quality and public health surveillance. In records linkage, protecting the patients’ privacy is a primary requirement. In real-world health care databases, records may well contain errors due to various reasons such as typos. Linking the error-prone data and preserving data privacy at the same time are very difficult. Existing privacy preserving solutions for this problem are only restricted to textual data. Objective To enable different medical service providers to link their error-prone data in a private way, our aim was to provide a holistic solution by designing and developing a medical record linkage system for medical service providers. Methods To initiate a record linkage, one provider selects one of its collaborators in the Connection Management Module, chooses some attributes of the database to be matched, and establishes the connection with the collaborator after the negotiation. In the Data Matching Module, for error-free data, our solution offered two different choices for cryptographic schemes. For error-prone numerical data, we proposed a newly designed privacy preserving linking algorithm named the Error-Tolerant Linking Algorithm, that allows the error-prone data to be correctly matched if the distance between the two records is below a threshold. Results We designed and developed a comprehensive and user-friendly software system that provides privacy preserving record linkage functions for medical service providers, which meets the regulation of Health Insurance Portability and Accountability Act. It does not require a third party and it is secure in that neither entity can learn the records in the other’s database. Moreover, our novel Error-Tolerant Linking Algorithm implemented in this software can work well with error-prone numerical data. We theoretically proved the correctness and security of our Error

  15. A machine learning approach to create blocking criteria for record linkage.

    PubMed

    Giang, Phan H

    2015-03-01

    Record linkage, a part of data cleaning, is recognized as one of most expensive steps in data warehousing. Most record linkage (RL) systems employ a strategy of using blocking filters to reduce the number of pairs to be matched. A blocking filter consists of a number of blocking criteria. Until recently, blocking criteria are selected manually by domain experts. This paper proposes a new method to automatically learn efficient blocking criteria for record linkage. Our method addresses the lack of sufficient labeled data for training. Unlike previous works, we do not consider a blocking filter in isolation but in the context of an accompanying matcher which is employed after the blocking filter. We show that given such a matcher, the labels (assigned to record pairs) that are relevant for learning are the labels assigned by the matcher (link/nonlink), not the labels assigned objectively (match/unmatch). This conclusion allows us to generate an unlimited amount of labeled data for training. We formulate the problem of learning a blocking filter as a Disjunctive Normal Form (DNF) learning problem and use the Probably Approximately Correct (PAC) learning theory to guide the development of algorithm to search for blocking filters. We test the algorithm on a real patient master file of 2.18 million records. The experimental results show that compared with filters obtained by educated guess, the optimal learned filters have comparable recall but reduce throughput (runtime) by an order-of-magnitude factor.

  16. SOEMPI: A Secure Open Enterprise Master Patient Index Software Toolkit for Private Record Linkage

    PubMed Central

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

    2014-01-01

    To mitigate bias in multi-institutional research studies, healthcare organizations need to integrate patient records. However, this process must be accomplished without disclosing the identities of the corresponding patients. Various private record linkage (PRL) techniques have been proposed, but there is a lack of translation into practice because no software suite supports the entire PRL lifecycle. This paper addresses this issue with the introduction of the Secure Open Enterprise Master Patient Index (SOEMPI). We show how SOEMPI covers the PRL lifecycle, illustrate the implementation of several PRL protocols, and provide a runtime analysis for the integration of two datasets consisting of 10,000 records. While the PRL process is slower than a non-secure setting, our analysis shows the majority of processes in a PRL protocol require several seconds or less and that SOEMPI completes the process in approximately two minutes, which is a practical amount of time for integration. PMID:25954421

  17. [Performance of record linkage for cancer registry data linked with mammography screening data].

    PubMed

    Giersiepen, K; Bachteler, T; Gramlich, T; Reiher, J; Schubert, B; Novopashenny, I; Schnell, R

    2010-07-01

    The evaluation of the German Mammography Screening Program requires record linkage with data from cancer registries in order to measure the number of false-negative mammograms and interval cancers. This study aims at evaluating the performance of the established linkage method based on identifiers encrypted by the standard procedure of the German cancer registries. In addition, the results are compared with an alternative method based on plain text identifiers. A total of 16,572 records from the Bremen Mammography Screening Pilot Study were linked with data from the Bremen Cancer Registry. Based on a gold standard set of matching record pairs, homonym and synonym errors were determined. Given the customary threshold value in cancer registries, the plain text method showed a lower rate of synonym errors (2.1-5.1%) and a lower rate of homonym errors (0.01-0.15%). As 10.4 million women are invited to take part biennially in screening, the corresponding figures would be 3,237 homonym errors for the standard procedure and 294 using the plain text method provided equivalent conditions. The 11-fold increase in the homonym error rate documents the trade-off for better data protection using encrypted data. PMID:20652484

  18. Design and implementation of a privacy preserving electronic health record linkage tool in Chicago

    PubMed Central

    Cashy, John P; Jackson, Kathryn L; Pah, Adam R; Goel, Satyender; Boehnke, Jörn; Humphries, John Eric; Kominers, Scott Duke; Hota, Bala N; Sims, Shannon A; Malin, Bradley A; French, Dustin D; Walunas, Theresa L; Meltzer, David O; Kaleba, Erin O; Jones, Roderick C; Galanter, William L

    2015-01-01

    Objective To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research. Methods The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches. Results The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually reconciled set of 11 292 patients as a gold standard, the software achieved a sensitivity of 96% and a specificity of 100%, with a majority of the missed matches accounted for by patients with both a missing social security number and last name change. Using 3 disease examples, it is demonstrated that the software can reduce duplication of patient records across sites by as much as 28%. Conclusions Software that standardizes the assignment of a unique seeded hash identifier merged through an agreed upon third-party honest broker can enable large-scale secure linkage of EHR data for epidemiologic and public health research. The software algorithm can improve future epidemiologic research by providing more comprehensive data given that patients may make use of multiple healthcare systems. PMID:26104741

  19. Medical record linkage in health information systems by approximate string matching and clustering

    PubMed Central

    Sauleau, Erik A; Paumier, Jean-Philippe; Buemi, Antoine

    2005-01-01

    Background Multiplication of data sources within heterogeneous healthcare information systems always results in redundant information, split among multiple databases. Our objective is to detect exact and approximate duplicates within identity records, in order to attain a better quality of information and to permit cross-linkage among stand-alone and clustered databases. Furthermore, we need to assist human decision making, by computing a value reflecting identity proximity. Methods The proposed method is in three steps. The first step is to standardise and to index elementary identity fields, using blocking variables, in order to speed up information analysis. The second is to match similar pair records, relying on a global similarity value taken from the Porter-Jaro-Winkler algorithm. And the third is to create clusters of coherent related records, using graph drawing, agglomerative clustering methods and partitioning methods. Results The batch analysis of 300,000 "supposedly" distinct identities isolates 240,000 true unique records, 24,000 duplicates (clusters composed of 2 records) and 3,000 clusters whose size is greater than or equal to 3 records. Conclusion Duplicate-free databases, used in conjunction with relevant indexes and similarity values, allow immediate (i.e.: real-time) proximity detection when inserting a new identity. PMID:16219102

  20. World Health and the Oxford International Biomedical Centre.

    PubMed

    Pasternak, Charles A

    2004-04-01

    Some of the problems associated with World Health are considered. The Oxford International Biomedical Centre (OIBC) was launched in 1992 to respond to those challenges. Its mission and goals, track record, and new programmes are described.

  1. Record linkage and the identification of long-term environmental hazards.

    PubMed

    Acheson, E D

    1979-07-18

    The long-term effects of toxic substances in man that have been discovered so far have involved gross relative risks or bizarre effects, or have stumbled upon by chance or because of special circumstances. These facts and some recent epidemiological evidence together suggest that a systematic approach with better methods would reveal the effects of many more toxic substances, particularly in manufacturing industry. Record linkage is a powerful tool because it makes possible the correlation of indicators of exposure with indicators of the biological effect of such exposure in the same persons or in their progeny even after considerable periods of time have elapsed. A system of linked records exists in England and Wales which is at present used by research workers to follow up samples of persons defined in various ways, e.g. in respect of exposure to a suspected toxic factor. In this way hypotheses about substances causing cancer or other lethal effects can be tested. It is suggested that there are two additional ways in which record linkage techniques could be used to identify substances with long-term toxic effects: the first would be by setting up a register of women employed in industry during pregnancy and linking this register to records of the occurrence of congenital malformations and of stillbirth or death in their children; the second would be to follow samples of workers in manufacturing industry, notably those engaged in the manufacture of products from raw materials including the chemical industry, to death and to the development of cancer. Regular analyses of material from these two systems of linked records would provide the basis for a monitoring system for certain gross effects of long-term toxic substances in man. There are two principal obstacles to further progress in this field. The first is the lack of a clear statement of public policy concerning the issues of confidentiality and informed consent in the use of identifiable personal records for

  2. Comparison of individual follow-up and computerized record linkage using the Canadian Mortality Data Base.

    PubMed

    Shannon, H S; Jamieson, E; Walsh, C; Julian, J A; Fair, M E; Buffet, A

    1989-01-01

    We compared two methods of ascertaining mortality in a historical prospective mortality study. Computerized Record Linkage (CRL) with the centralized historical Canadian Mortality Data Base (CMDB) was carried out on 2469 men and an attempt was also made to trace the subjects by individual follow-up (IFU). All but 88 were traced and 60 were reported to be dead. CRL was able to locate the deaths of three men who had been untraced by IFU. Contradictory information on vital status was obtained on 5 subjects--in 4 of them, the discrepancy was resolved in favour of CRL. Overall, CRL using the CMDB performed very well. We also consider factors that affect the relative costs of the two methods, which should be balanced against the accuracy of information obtained.

  3. Oxford dictionary of Physics

    NASA Astrophysics Data System (ADS)

    Isaacs, Alan

    The dictionary is derived from the Concise Science Dictionary, first published by Oxford University Press in 1984 (third edition, 1996). It consists of all the entries relating to physics in that dictionary, together with some of those entries relating to astronomy that are required for an understanding of astrophysics and many entries that relate to physical chemistry. It also contains a selection of the words used in mathematics that are relevant to physics, as well as the key words in metal science, computing, and electronics. For this third edition a number of words from quantum field physics and statistical mechanics have been added. Cosmology and particle physics have been updated and a number of general entries have been expanded.

  4. Reform and Resistance at Oxford

    ERIC Educational Resources Information Center

    Labi, Aisha

    2006-01-01

    In recent years, both Harvard and Oxford Universities have been rattled by reform-minded--some say brash--leaders determined to question the status quo. At Harvard, President Lawrence H. Summers proved too controversial for his own good and is scheduled to step down this month after five contentious years in office. But at Oxford, John Hood, who…

  5. New South Wales Child Development Study (NSW-CDS): an Australian multiagency, multigenerational, longitudinal record linkage study

    PubMed Central

    Carr, Vaughan J; Harris, Felicity; Raudino, Alessandra; Luo, Luming; Kariuki, Maina; Liu, Enwu; Tzoumakis, Stacy; Smith, Maxwell; Holbrook, Allyson; Bore, Miles; Brinkman, Sally; Lenroot, Rhoshel; Dix, Katherine; Dean, Kimberlie; Laurens, Kristin R; Green, Melissa J

    2016-01-01

    Purpose The initial aim of this multiagency, multigenerational record linkage study is to identify childhood profiles of developmental vulnerability and resilience, and to identify the determinants of these profiles. The eventual aim is to identify risk and protective factors for later childhood-onset and adolescent-onset mental health problems, and other adverse social outcomes, using subsequent waves of record linkage. The research will assist in informing the development of public policy and intervention guidelines to help prevent or mitigate adverse long-term health and social outcomes. Participants The study comprises a population cohort of 87 026 children in the Australian State of New South Wales (NSW). The cohort was defined by entry into the first year of full-time schooling in NSW in 2009, at which time class teachers completed the Australian Early Development Census (AEDC) on each child (with 99.7% coverage in NSW). The AEDC data have been linked to the children's birth, health, school and child protection records for the period from birth to school entry, and to the health and criminal records of their parents, as well as mortality databases. Findings to date Descriptive data summarising sex, geographic and socioeconomic distributions, and linkage rates for the various administrative databases are presented. Child data are summarised, and the mental health and criminal records data of the children's parents are provided. Future plans In 2015, at age 11 years, a self-report mental health survey was administered to the cohort in collaboration with government, independent and Catholic primary school sectors. A second record linkage, spanning birth to age 11 years, will be undertaken to link this survey data with the aforementioned administrative databases. This will enable a further identification of putative risk and protective factors for adverse mental health and other outcomes in adolescence, which can then be tested in subsequent record linkages

  6. Oxford exploding spires.

    PubMed

    Guest, I

    1974-05-01

    Barbara Ward in her keynote address to the Conference on Exploding Cities, held in Oxford England, made the point that the current problems of the cities can only worsen as the world's population doubles by the year 2000 and the worst hit will be the cities of the developing nations. Between 1950 and 2000 urban populations will rise from 500 million to 1000 million, but the equivalent rise in the 3rd world will be from 500 million to 2200 million. The Conference was more successful in identifying the problems and their causes than in proposing solutions. The inadequacy of urban transport was emphasized repeatedly. Crime emerges as another urban headache. Pollution was another popular theme, and shanties were thoroughly examined. Positive proposals too often took the form of self-evident truths. In all cases the message is clear: the 1st prerequisite to urban planning is central control and, if necessary, public ownership of land. A succession of speakers advocated more self-help for the communities which have emerged on the periphery of so many urban centers. Elizabeth Jelin, from Buenos Aires, argued that these communities -- and shanty towns are the most obvious manifestation -- should no longer be viewed as marginal. They perform essential services, especially in terms of employment, and cannot be moved without severe disruption. Self-help was the beacon held up to delegates, despite the warnings that it would lead to complacency on the part of authorities.

  7. 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.

  8. Women Leaders in Oxford House.

    PubMed

    Timpo, Phyllis; Price, Temple; Salina, Doreen; Witek, Caroline; Pommer, Nicole; Jason, Leonard A

    2014-01-01

    This qualitative study examined women assuming leadership roles in Oxford Houses, which are communal, democratically run recovery settings for substance use disorder. Semi-structured interviews were conducted with 10 women Oxford House leaders who shared their thoughts and experiences on leadership. Several themes emerged from qualitative data analysis, most notably that stepping up and accepting a leadership role in Oxford House had a positive effect on self-esteem, which is vital to women with a history of substance abuse. Barriers to leadership were also identified such as negative interpersonal relationships with other women. A number of methods mentioned to increase the number of women leaders included: developing workshops, providing positive encouragement, and accessing existing female role models. The implications of this study are discussed. PMID:25419529

  9. Women Leaders in Oxford House

    PubMed Central

    Timpo, Phyllis; Price, Temple; Salina, Doreen; Witek, Caroline; Pommer, Nicole; Jason, Leonard A.

    2014-01-01

    This qualitative study examined women assuming leadership roles in Oxford Houses, which are communal, democratically run recovery settings for substance use disorder. Semi-structured interviews were conducted with 10 women Oxford House leaders who shared their thoughts and experiences on leadership. Several themes emerged from qualitative data analysis, most notably that stepping up and accepting a leadership role in Oxford House had a positive effect on self-esteem, which is vital to women with a history of substance abuse. Barriers to leadership were also identified such as negative interpersonal relationships with other women. A number of methods mentioned to increase the number of women leaders included: developing workshops, providing positive encouragement, and accessing existing female role models. The implications of this study are discussed. PMID:25419529

  10. Women Leaders in Oxford House.

    PubMed

    Timpo, Phyllis; Price, Temple; Salina, Doreen; Witek, Caroline; Pommer, Nicole; Jason, Leonard A

    2014-01-01

    This qualitative study examined women assuming leadership roles in Oxford Houses, which are communal, democratically run recovery settings for substance use disorder. Semi-structured interviews were conducted with 10 women Oxford House leaders who shared their thoughts and experiences on leadership. Several themes emerged from qualitative data analysis, most notably that stepping up and accepting a leadership role in Oxford House had a positive effect on self-esteem, which is vital to women with a history of substance abuse. Barriers to leadership were also identified such as negative interpersonal relationships with other women. A number of methods mentioned to increase the number of women leaders included: developing workshops, providing positive encouragement, and accessing existing female role models. The implications of this study are discussed.

  11. Following Up Crack Users after Hospital Discharge Using Record Linkage Methodology: An Alternative to Find Hidden Populations.

    PubMed

    Gonçalves, Veralice Maria; Pedroso, Rosemeri; dos Santos, Antônio Marcos; Diemen, Lisia Von; Pechansky, Flavio

    2015-01-01

    This paper presents the probabilistic record linkage (PRL) methodology as an alternative way to find or follow up hard-to-reach population as crack users. PRL was based on secondary data from public health information systems and the strategy used from standardization; phonetic encoding and the rounds of matching data were described. A total of 293 patient records from medical database and two administrative datasets obtained from Ministry of Health Information Systems were used. Patient information from the medical database was the identifiers to the administrative datasets containing data on outpatient treatment and hospital admissions. 40% of patient records were found in the hospital database and 12% were found in the outpatient database; 95% of the patients were hospitalized up to 5 times, and only 10 out of them had outpatient information. The record linkage methodology by linking government databases may help to address research questions about the path of patients in the care network without spending time and financial resources with primary data collection. PMID:26425565

  12. Embracing the Sparse, Noisy, and Interrelated Aspects of Patient Demographics for use in Clinical Medical Record Linkage.

    PubMed

    Ash, Stephen M; Ip-Lin, King

    2015-01-01

    Duplicate patient records in health information systems have received increased attention in recent time due to regulatory incentives to integrate the healthcare enterprise. Historically, most patient record matching systems have been limited to simple applications of the Fellegi-Sunter theory of record linkage with edit distance based string similarity measurements. String similarity approaches ignore the rich semantic information present by reducing it to a simple syntactic comparison of characters. This work describes an updated approach to building clinical medical record linkage systems, which embraces the unavoidable problems present in real-world patient matching. Using a ground truth dataset of a real patient population, we demonstrate that systems built in this fashion improve recall by 76% with little reduction in precision. This result empirically demonstrates the size of the gap between sophisticated systems and naïve approaches. Additionally, it accentuates the difficulty in estimating the false negative error in this setting as previous research has reported much higher levels of recall, due, in part, to measuring from biased samples. PMID:26306279

  13. Following Up Crack Users after Hospital Discharge Using Record Linkage Methodology: An Alternative to Find Hidden Populations

    PubMed Central

    Gonçalves, Veralice Maria; Pedroso, Rosemeri; dos Santos, Antônio Marcos; Diemen, Lisia Von; Pechansky, Flavio

    2015-01-01

    This paper presents the probabilistic record linkage (PRL) methodology as an alternative way to find or follow up hard-to-reach population as crack users. PRL was based on secondary data from public health information systems and the strategy used from standardization; phonetic encoding and the rounds of matching data were described. A total of 293 patient records from medical database and two administrative datasets obtained from Ministry of Health Information Systems were used. Patient information from the medical database was the identifiers to the administrative datasets containing data on outpatient treatment and hospital admissions. 40% of patient records were found in the hospital database and 12% were found in the outpatient database; 95% of the patients were hospitalized up to 5 times, and only 10 out of them had outpatient information. The record linkage methodology by linking government databases may help to address research questions about the path of patients in the care network without spending time and financial resources with primary data collection. PMID:26425565

  14. Embracing the Sparse, Noisy, and Interrelated Aspects of Patient Demographics for use in Clinical Medical Record Linkage

    PubMed Central

    Ash, Stephen M.; Ip-Lin, King

    2015-01-01

    Duplicate patient records in health information systems have received increased attention in recent time due to regulatory incentives to integrate the healthcare enterprise. Historically, most patient record matching systems have been limited to simple applications of the Fellegi-Sunter theory of record linkage with edit distance based string similarity measurements. String similarity approaches ignore the rich semantic information present by reducing it to a simple syntactic comparison of characters. This work describes an updated approach to building clinical medical record linkage systems, which embraces the unavoidable problems present in real-world patient matching. Using a ground truth dataset of a real patient population, we demonstrate that systems built in this fashion improve recall by 76% with little reduction in precision. This result empirically demonstrates the size of the gap between sophisticated systems and naïve approaches. Additionally, it accentuates the difficulty in estimating the false negative error in this setting as previous research has reported much higher levels of recall, due, in part, to measuring from biased samples. PMID:26306279

  15. Inaccurate Ascertainment of Morbidity and Mortality due to Influenza in Administrative Databases: A Population-Based Record Linkage Study

    PubMed Central

    Muscatello, David J.; Amin, Janaki; MacIntyre, C. Raina; Newall, Anthony T.; Rawlinson, William D.; Sintchenko, Vitali; Gilmour, Robin; Thackway, Sarah

    2014-01-01

    Background Historically, counting influenza recorded in administrative health outcome databases has been considered insufficient to estimate influenza attributable morbidity and mortality in populations. We used database record linkage to evaluate whether modern databases have similar limitations. Methods Person-level records were linked across databases of laboratory notified influenza, emergency department (ED) presentations, hospital admissions and death registrations, from the population (∼6.9 million) of New South Wales (NSW), Australia, 2005 to 2008. Results There were 2568 virologically diagnosed influenza infections notified. Among those, 25% of 40 who died, 49% of 1451 with a hospital admission and 7% of 1742 with an ED presentation had influenza recorded on the respective database record. Compared with persons aged ≥65 years and residents of regional and remote areas, respectively, children and residents of major cities were more likely to have influenza coded on their admission record. Compared with older persons and admitted patients, respectively, working age persons and non-admitted persons were more likely to have influenza coded on their ED record. On both ED and admission records, persons with influenza type A infection were more likely than those with type B infection to have influenza coded. Among death registrations, hospital admissions and ED presentations with influenza recorded as a cause of illness, 15%, 28% and 1.4%, respectively, also had laboratory notified influenza. Time trends in counts of influenza recorded on the ED, admission and death databases reflected the trend in counts of virologically diagnosed influenza. Conclusions A minority of the death, hospital admission and ED records for persons with a virologically diagnosed influenza infection identified influenza as a cause of illness. Few database records with influenza recorded as a cause had laboratory confirmation. The databases have limited value for estimating incidence

  16. Storytelling through animation: Oxford Sparks

    NASA Astrophysics Data System (ADS)

    Pyle, D. M.; Cook, A.

    2013-12-01

    Oxford Sparks is a portal that launched in 2012, with the aim of bringing together resources that have been created across the University of Oxford and elsewhere for the purpose of wider engagement with science. To bring attention to this site, Oxford Sparks developed a set of high-quality short animations, each designed to tell a story relating to a current area of science. These animations have been launched on YouTube, and will shortly be available on iTunesU, and have covered broad areas of science from subduction zones (';Underwater Volcano Disaster'), through the early history of the solar system (';Rogue Planet') to the workings of the Large Hadron Collider (';A quick look around the LHC'). The animations have each been developed in close collaboration with researchers, created by a team with experience of education, engagement and outreach. The two minute scripts are intended to be both widely accessible and viewable as ';stand alone' stories. To this end, the scripts are humorous; while the animations are delightfully quirky, and created by professional animator with a degree-level science background. The animations are also intended to be used as ';lesson starters' in school, and educational activities graded for different age groups are being developed in parallel with the animations. They have been used, successfully, on pre-university summer schools, and in university classes. We are gathering both quantitative (analytics) and qualitative (school teacher and student focus group) feedback to monitor the success of the project, and to understand the strengths and weaknesses of the approach. In the first year since launch, Oxford Sparks animations were viewed over 80,000 times on YouTube, in part due to the surge of interest in the Large Hadron Collider animation after the discovery of the Higgs Boson.

  17. Speleothem records of western Mediterranean. Hydrological variability along the Last Interglacial Period and marine linkages

    NASA Astrophysics Data System (ADS)

    Torner, Judit; Cacho, Isabel; Moreno, Ana; Stoll, Heather; Belmonte, Anchel; Sierro, Francisco J.; Frigola, Jaime; Martrat, Belen; Fornós, Joan; Arnau Fernández, Pedro; Hellstrom, John; Cheng, Hai; Edwards, R. Lawrence

    2016-04-01

    This study aims to identify and characterize regional hydrological variability in the western Mediterranean region in base to different geochemical parameters (δ18O, δ13C, and Mg/Ca ratios). Speleothems have been recovered from several caves located in southern central Pyrenees one and the others form the Balearic Islands. Their chronologies have been constructed in base on U/Th absolute dating and indicate that the speleothem sequences cover the end of the last interglacial and the glacial inception. One of the most remarkable features of the records is the intense and abrupt shift toward more arid conditions that marks the end of the last interglacial (MIS 5e). Furthermore, our speleothem records also show relatively humid but highly variable hydrological conditions during the interstadial periods from MIS 5c to 5a. These speleothem records have been compared with new generated western Mediterranean marine records from the Balearic Sea (MD99-2343) and Alboran Sea (OPD-977). Marine records include (1) proxies of sea surface temperature and changes in evaporation-precipitation rates based on pair analysis of δ18O and the Mg/Ca ratios in planktonic foraminifera Globigerina bulloides; (2) proxies of deep-water currents associated with the Western Mediterranean Deep Water (WMDW) based on grain size analyses. The results reveal that arid conditions on land were coeval with cold sea surface sub-stages (MIS 5b and 5d), and also with increases in the intensity of the WMDW-related currents. By contrast, humid and hydrological unstable atmosphere conditions were synchronous with sea surface warm sub-stages, and lower WMDW-related currents intensities (MIS 5a, c and e). Consequently, our results highly evidence a strong atmospheric-oceanic coupling, involving parallel changes in both surface but also deep western Mediterranean Sea conditions during the last interglacial period and the glacial inception.

  18. Marine and Lacustrine Turbidite Records: Testing Linkages and Estimating Ground Motions, Central Cascadia Margin, USA

    NASA Astrophysics Data System (ADS)

    Hausmann, R. B.; Goldfinger, C.; Black, B.; Collins, T.; Romsos, C. G.; Medeiros, L.; Mutschler, M.; Galer, S.; Raymond, R.; Morey, A. E.

    2015-12-01

    We are investigating a potential paleoseismic record at Bull Run Lake, 165 km inland and 280 km landward of the tip of the plate boundary thrust, at the latitude of Portland, Oregon, central Cascadia margin. Bull Run is a landslide dammed lake in a cirque basin on the western flanks of Mt. Hood. Bull Run is potentially a good paleoseismic site, with no major stream inputs and a small catchment basin. The watershed and lake are faulted, and may contain ashes and evidence of crustal faulting. The lake was investigated by Raymond (1983), who cored the lake and found an orderly stratigraphic sequence with a number of minerogenic disturbance events (turbidites) and the Mazama Ash. The bulk ages of several of the disturbance events dated in Raymond's cores overlap well-known Cascadia earthquakes, including the AD 1700 event and several prior earthquakes, suggesting potential for this site. We collected full coverage high-resolution multibeam and backscatter data, along with a high resolution grid of CHIRP sub-bottom profiles, and seven new sediment gravity cores. We find that the turbidite record in the lake is well imaged in the high-resolution chirp data, and is found throughout the lake, including at least one basin isolated from the main basin. The continuity of the turbidite record shows little or no relationship to the minor stream inlets, suggesting the disturbance beds are not likely to be storm related. Many faint laminae may contain a storm record. Subtle channels from north and south sides of the lake feed an axial channel that terminates at the eastern shore. Lake sidewall failures are evident on the north and south walls, and occur with and without imageable tabular blocky slide debris where sedimented slopes exceed ~ 22-25 deg. Smaller failures visible in backscatter data are found on slopes as low as 12 degrees. We conducted diver investigations of several of the landslide areas, collecting hand push core samples and in-situ vane shear torquemeter

  19. Linkage methods for connecting children with parents in electronic health record and state public health insurance data.

    PubMed

    Angier, Heather; Gold, Rachel; Crawford, Courtney; P O'Malley, Jean; J Tillotson, Carrie; Marino, Miguel; DeVoe, Jennifer E

    2014-11-01

    The objective of this study was to develop methodologies for creating child-parent 'links' in two healthcare-related data sources. We linked children and parents who were patients in a network of Oregon clinics with a shared electronic health record (EHR), using data that reported the child's emergency contact information or the 'guarantor' for the child's visits. We also linked children and parents enrolled in the Oregon Health Plan (OHP; Oregon's public health insurance programs), using administrative data; here, we defined a 'child' as aged <19 years and identified potential 'parents' from among adults sharing the same OHP household identification (ID) number. In both data sources, parents had to be 12-55 years older than the child. We used OHP individual client ID and EHR patient ID numbers to assess the quality of our linkages through cross-validation. Of the 249,079 children in the EHR dataset, we identified 62,967 who had a 'linkable' parent with patient information in the EHR. In the OHP data, 889,452 household IDs were assigned to at least one child; 525,578 with a household ID had a 'linkable' parent (272,578 households). Cross-validation of linkages revealed 99.8 % of EHR links validated in OHP data and 97.7 % of OHP links validated in EHR data. The ability to link children and their parents in healthcare-related datasets will be useful to inform efforts to improve children's health. Thus, we developed strategies for linking children with their parents in an EHR and a public health insurance administrative dataset.

  20. Automatic spike sorting for extracellular electrophysiological recording using unsupervised single linkage clustering based on grey relational analysis

    NASA Astrophysics Data System (ADS)

    Lai, Hsin-Yi; Chen, You-Yin; Lin, Sheng-Huang; Lo, Yu-Chun; Tsang, Siny; Chen, Shin-Yuan; Zhao, Wan-Ting; Chao, Wen-Hung; Chang, Yao-Chuan; Wu, Robby; Shih, Yen-Yu I.; Tsai, Sheng-Tsung; Jaw, Fu-Shan

    2011-06-01

    Automatic spike sorting is a prerequisite for neuroscience research on multichannel extracellular recordings of neuronal activity. A novel spike sorting framework, combining efficient feature extraction and an unsupervised clustering method, is described here. Wavelet transform (WT) is adopted to extract features from each detected spike, and the Kolmogorov-Smirnov test (KS test) is utilized to select discriminative wavelet coefficients from the extracted features. Next, an unsupervised single linkage clustering method based on grey relational analysis (GSLC) is applied for spike clustering. The GSLC uses the grey relational grade as the similarity measure, instead of the Euclidean distance for distance calculation; the number of clusters is automatically determined by the elbow criterion in the threshold-cumulative distribution. Four simulated data sets with four noise levels and electrophysiological data recorded from the subthalamic nucleus of eight patients with Parkinson's disease during deep brain stimulation surgery are used to evaluate the performance of GSLC. Feature extraction results from the use of WT with the KS test indicate a reduced number of feature coefficients, as well as good noise rejection, despite similar spike waveforms. Accordingly, the use of GSLC for spike sorting achieves high classification accuracy in all simulated data sets. Moreover, J-measure results in the electrophysiological data indicating that the quality of spike sorting is adequate with the use of GSLC.

  1. Risk of individual malignant neoplasms in patients with sickle cell disease: English national record linkage study

    PubMed Central

    Seminog, Olena O; Ogunlaja, Oyindamola I; Yeates, David

    2016-01-01

    Objective Case reports suggest that there may be an increased risk of some cancers associated with sickle cell disease. However, population-based studies are scarce and there is no comprehensive enumeration of the risks across the whole range of site-specific cancers. Our aim was to provide this. Design We used an English national dataset of linked statistical records of hospital admissions and deaths from 1999 to 2011 to undertake a retrospective cohort study. Setting England. Participants Records of all hospital admissions in England with SCD or with conditions included in the control cohort. Main outcome measures Rate ratios were calculated comparing rates of cancer in a sickle cell disease cohort and a control cohort, confining the analyses to people whose ethnicity was recorded as Black. Results Comparing the sickle cell disease cohort with the cohort without sickle cell disease, the rate ratio for all cancers combined was 2.1 (95% confidence interval 1.7–2.5). There were significantly high rate ratios for haematological malignancies, including Hodgkin’s lymphoma (rate ratio 3.7, 1.5–8.4), non-Hodgkin’s lymphoma (2.6, 1.3–4.8), multiple myeloma (5.5, 2.8–10.1), lymphoid leukaemia (3.3, 1.3–8.0) and myeloid leukaemia (10.0, 4.6–21.5). Four solid tumours showed elevated rate ratios: colon cancer (2.8, 1.2–5.5), non-melanoma skin cancer (4.4, 1.3–12.2), kidney cancer (5.4, 2.3–11.5) and thyroid cancer (5.1, 1.3–15.4). Conclusions The risk of some malignancies may be raised in patients with sickle cell disease. However, this study was based on administrative data without the scope to validate these against patients’ full clinical records. Our findings need confirmation or refutation. If confirmed, work to elucidate, at the genetic and molecular level, why people with sickle cell disease have elevated risks of individual cancers might make contributions to the fundamental understanding of carcinogenesis. PMID:27325377

  2. Planned Repeat Cesarean Section at Term and Adverse Childhood Health Outcomes: A Record-Linkage Study

    PubMed Central

    Black, Mairead; Bhattacharya, Siladitya; Philip, Sam; Norman, Jane E.; McLernon, David J.

    2016-01-01

    Background Global cesarean section (CS) rates range from 1% to 52%, with a previous CS being the commonest indication. Labour following a previous CS carries risk of scar rupture, with potential for offspring hypoxic brain injury, leading to high rates of repeat elective CS. However, the effect of delivery by CS on long-term outcomes in children is unclear. Increasing evidence suggests that in avoiding exposure to maternal bowel flora during labour or vaginal birth, offspring delivered by CS may be adversely affected in terms of energy uptake from the gut and immune development, increasing obesity and asthma risks, respectively. This study aimed to address the evidence gap on long-term childhood outcomes following repeat CS by comparing adverse childhood health outcomes after (1) planned repeat CS and (2) unscheduled repeat CS with those that follow vaginal birth after CS (VBAC). Methods and Findings A data-linkage cohort study was performed. All second-born, term, singleton offspring delivered between 1 January 1993 and 31 December 2007 in Scotland, UK, to women with a history of CS (n = 40,145) were followed up until 31 January 2015. Outcomes assessed included obesity at age 5 y, hospitalisation with asthma, learning disability, cerebral palsy, and death. Cox regression and binary logistic regression were used as appropriate to compare outcomes following planned repeat CS (n = 17,919) and unscheduled repeat CS (n = 8,847) with those following VBAC (n = 13,379). Risk of hospitalisation with asthma was greater following both unscheduled repeat CS (3.7% versus 3.3%, adjusted hazard ratio [HR] 1.18, 95% CI 1.05–1.33) and planned repeat CS (3.6% versus 3.3%, adjusted HR 1.24, 95% CI 1.09–1.42) compared with VBAC. Learning disability and death were more common following unscheduled repeat CS compared with VBAC (3.7% versus 2.3%, adjusted odds ratio 1.64, 95% CI 1.17–2.29, and 0.5% versus 0.4%, adjusted HR 1.50, 95% CI 1.00–2.25, respectively). Risk of obesity

  3. Residential segregation, dividing walls and mental health: a population-based record linkage study

    PubMed Central

    Maguire, Aideen; French, Declan; O'Reilly, Dermot

    2016-01-01

    Background Neighbourhood segregation has been described as a fundamental determinant of physical health, but literature on its effect on mental health is less clear. While most previous research has relied on conceptualised measures of segregation, Northern Ireland is unique as it contains physical manifestations of segregation in the form of segregation barriers (or ‘peacelines’) which can be used to accurately identify residential segregation. Methods We used population-wide health record data on over 1.3 million individuals, to analyse the effect of residential segregation, measured by both the formal Dissimilarity Index and by proximity to a segregation barrier, on the likelihood of poor mental health. Results Using multilevel logistic regression models, we found residential segregation measured by the Dissimilarity Index poses no additional risk to the likelihood of poor mental health after adjustment for area-level deprivation. However, residence in an area segregated by a ‘peaceline’ increases the likelihood of antidepressant medication by 19% (OR=1.19, 95% CI 1.14 to 1.23) and anxiolytic medication by 39% (OR=1.39, 95% CI 1.32 to 1.48), even after adjustment for gender, age, conurbation, deprivation and crime. Conclusions Living in an area segregated by a ‘peaceline’ is detrimental to mental health suggesting segregated areas characterised by a heightened sense of ‘other’ pose a greater risk to mental health. The difference in results based on segregation measure highlights the importance of choice of measure when studying segregation. PMID:26858342

  4. Leadership Styles of Oxford House Officers

    PubMed Central

    Komer, Anne C; Jason, Leonard A; Harvey, Ronald; Olson, Brad

    2015-01-01

    Oxford House recovery homes are unusual compared to most recovery homes in that they function entirely without the use of staff; instead members are elected to officer positions. The aim of this study was to perform preliminary analysis of the types of leadership styles utilized by members of oxford house. Twentynine house residents of five Oxford Houses were asked to rate their own leadership styles using the leader behavior description questionnaire and the multifactor leader questionnaire. Results showed that participants were more likely to use person-oriented behaviors above task-oriented actions. Transformational leadership was associated with higher outcomes than Transactional leadership. Implications for future research are discussed. PMID:26380329

  5. The linkage between marine sediment records and changes in Holocene Saharan landscape: simulating the dust cycle

    NASA Astrophysics Data System (ADS)

    Egerer, Sabine; Claussen, Martin; Reick, Christian; Stanelle, Tanja

    2016-04-01

    Marine sediment records reveal an abrupt and strong increase in dust deposition in the North Atlantic at the end of the African Humid Period about 4.9 ka to 5.5 ka ago (deMenocal et al., 2000; McGee et al., 2013). The change in dust flux has been attributed to varying Saharan land surface cover. Alternatively, the enhanced dust accumulation is linked to enhanced surface winds and a consequent intensification of coastal upwelling. We present simulation results from a recent sensitivity study, where we demonstrate for the first time the direct link between dust accumulation in marine cores and changes in Saharan land surface during the Holocene. We have simulated timeslices of he mid-Holocene (6 ka BP) and pre-industrial (1850 AD) dust cycle as a function of Saharan land surface cover and atmosphere-ocean conditions using the coupled atmosphere-aerosol model ECHAM6.1-HAM2.1. We prescribe mid-Holocene vegetation cover based on a vegetation reconstruction from pollen data (Hoelzmann et al., 1998) and mid-Holocene lake surface area is determined using a water routing and storage model (Tegen et al., 2002). In agreement with data from marine sediment cores, our simulations show that mid-Holocene dust deposition fluxes in the North Atlantic were two to three times lower compared with pre-industrial fluxes. We identify Saharan land surface characteristics to be the main control on dust transport from North Africa to the North Atlantic. We conclude that the variation in dust accumulation in marine cores is likely related to a transition of the Saharan landscape during the Holocene and not due to changes in atmospheric or ocean conditions alone. Reference: deMenocal, P., Ortiz, J., Guilderson, T., Adkins, J., Sarnthein, M., Baker, L., and Yarusinsky, M.: Abrupt onset and termination of the African Humid Period:: rapid climate responses to gradual insolation forcing, Quaternary Science Reviews, 19, 347-361, 2000. Hoelzmann, P., Jolly, D., Harrison, S. P., Laarif, F

  6. The Making of the "Oxford English Dictionary."

    ERIC Educational Resources Information Center

    Winchester, Simon

    2003-01-01

    Summarizes remarks made to open the Gallaudet University conference on Dictionaries and the Standardization of languages. It concerns the making of what is arguably the world's greatest dictionary, "The Oxford English Dictionary." (VWL)

  7. High Hospitalization Rates in Survivors of Childhood Cancer: A Longitudinal Follow-Up Study Using Medical Record Linkage.

    PubMed

    Sieswerda, Elske; Font-Gonzalez, Anna; Reitsma, Johannes B; Dijkgraaf, Marcel G W; Heinen, Richard C; Jaspers, Monique W; van der Pal, Helena J; van Leeuwen, Flora E; Caron, Huib N; Geskus, Ronald B; Kremer, Leontien C

    2016-01-01

    Hospitalization rates over time of childhood cancer survivors (CCS) provide insight into the burden of unfavorable health conditions on CCS and health care resources. The objective of our study was to examine trends in hospitalizations of CCS and risk factors in comparison with the general population. We performed a medical record linkage study of a cohort of 1564 ≥five-year CCS with national registers. We obtained a random sample of the general population matched on year of birth, gender and calendar year per CCS retrieved. We quantified and compared hospitalization rates of CCS and reference persons from 1995 until 2005, and we analyzed risk factors for hospitalization within the CCS cohort with multivariable Poisson models. We retrieved hospitalization information from 1382 CCS and 25583 reference persons. The overall relative hospitalization rate (RHR) was 2.2 (95%CI:1.9-2.5) for CCS compared to reference persons. CCS with central nervous system and solid tumors had highest RHRs. Hospitalization rates in CCS were increased compared to reference persons up to at least 30 years after primary diagnosis, with highest rates 5-10 and 20-30 years after primary cancer. RHRs were highest for hospitalizations due to neoplasms (10.7; 95%CI:7.1-16.3) and endocrine/nutritional/metabolic disorders (7.3; 95%CI:4.6-11.7). Female gender (P<0.001), radiotherapy to head and/or neck (P<0.001) or thorax and/or abdomen (P = 0.03) and surgery (P = 0.01) were associated with higher hospitalization rates in CCS. In conclusion, CCS have increased hospitalization rates compared to the general population, up to at least 30 years after primary cancer treatment. These findings imply a high and long-term burden of unfavorable health conditions after childhood cancer on survivors and health care resources. PMID:27433937

  8. High Hospitalization Rates in Survivors of Childhood Cancer: A Longitudinal Follow-Up Study Using Medical Record Linkage

    PubMed Central

    Sieswerda, Elske; Font-Gonzalez, Anna; Reitsma, Johannes B.; Dijkgraaf, Marcel G. W.; Heinen, Richard C.; Jaspers, Monique W.; van der Pal, Helena J.; van Leeuwen, Flora E.; Caron, Huib N.

    2016-01-01

    Hospitalization rates over time of childhood cancer survivors (CCS) provide insight into the burden of unfavorable health conditions on CCS and health care resources. The objective of our study was to examine trends in hospitalizations of CCS and risk factors in comparison with the general population. We performed a medical record linkage study of a cohort of 1564 ≥five-year CCS with national registers. We obtained a random sample of the general population matched on year of birth, gender and calendar year per CCS retrieved. We quantified and compared hospitalization rates of CCS and reference persons from 1995 until 2005, and we analyzed risk factors for hospitalization within the CCS cohort with multivariable Poisson models. We retrieved hospitalization information from 1382 CCS and 25583 reference persons. The overall relative hospitalization rate (RHR) was 2.2 (95%CI:1.9–2.5) for CCS compared to reference persons. CCS with central nervous system and solid tumors had highest RHRs. Hospitalization rates in CCS were increased compared to reference persons up to at least 30 years after primary diagnosis, with highest rates 5–10 and 20–30 years after primary cancer. RHRs were highest for hospitalizations due to neoplasms (10.7; 95%CI:7.1–16.3) and endocrine/nutritional/metabolic disorders (7.3; 95%CI:4.6–11.7). Female gender (P<0.001), radiotherapy to head and/or neck (P<0.001) or thorax and/or abdomen (P = 0.03) and surgery (P = 0.01) were associated with higher hospitalization rates in CCS. In conclusion, CCS have increased hospitalization rates compared to the general population, up to at least 30 years after primary cancer treatment. These findings imply a high and long-term burden of unfavorable health conditions after childhood cancer on survivors and health care resources. PMID:27433937

  9. High Hospitalization Rates in Survivors of Childhood Cancer: A Longitudinal Follow-Up Study Using Medical Record Linkage.

    PubMed

    Sieswerda, Elske; Font-Gonzalez, Anna; Reitsma, Johannes B; Dijkgraaf, Marcel G W; Heinen, Richard C; Jaspers, Monique W; van der Pal, Helena J; van Leeuwen, Flora E; Caron, Huib N; Geskus, Ronald B; Kremer, Leontien C

    2016-01-01

    Hospitalization rates over time of childhood cancer survivors (CCS) provide insight into the burden of unfavorable health conditions on CCS and health care resources. The objective of our study was to examine trends in hospitalizations of CCS and risk factors in comparison with the general population. We performed a medical record linkage study of a cohort of 1564 ≥five-year CCS with national registers. We obtained a random sample of the general population matched on year of birth, gender and calendar year per CCS retrieved. We quantified and compared hospitalization rates of CCS and reference persons from 1995 until 2005, and we analyzed risk factors for hospitalization within the CCS cohort with multivariable Poisson models. We retrieved hospitalization information from 1382 CCS and 25583 reference persons. The overall relative hospitalization rate (RHR) was 2.2 (95%CI:1.9-2.5) for CCS compared to reference persons. CCS with central nervous system and solid tumors had highest RHRs. Hospitalization rates in CCS were increased compared to reference persons up to at least 30 years after primary diagnosis, with highest rates 5-10 and 20-30 years after primary cancer. RHRs were highest for hospitalizations due to neoplasms (10.7; 95%CI:7.1-16.3) and endocrine/nutritional/metabolic disorders (7.3; 95%CI:4.6-11.7). Female gender (P<0.001), radiotherapy to head and/or neck (P<0.001) or thorax and/or abdomen (P = 0.03) and surgery (P = 0.01) were associated with higher hospitalization rates in CCS. In conclusion, CCS have increased hospitalization rates compared to the general population, up to at least 30 years after primary cancer treatment. These findings imply a high and long-term burden of unfavorable health conditions after childhood cancer on survivors and health care resources.

  10. Detecting referral and selection bias by the anonymous linkage of practice, hospital and clinic data using Secure and Private Record Linkage (SAPREL): case study from the evaluation of the Improved Access to Psychological Therapy (IAPT) service

    PubMed Central

    2011-01-01

    Background The evaluation of demonstration sites set up to provide improved access to psychological therapies (IAPT) comprised the study of all people identified as having common mental health problems (CMHP), those referred to the IAPT service, and a sample of attenders studied in-depth. Information technology makes it feasible to link practice, hospital and IAPT clinic data to evaluate the representativeness of these samples. However, researchers do not have permission to browse and link these data without the patients' consent. Objective To demonstrate the use of a mixed deterministic-probabilistic method of secure and private record linkage (SAPREL) - to describe selection bias in subjects chosen for in-depth evaluation. Method We extracted, pseudonymised and used fuzzy logic to link multiple health records without the researcher knowing the patient's identity. The method can be characterised as a three party protocol mainly using deterministic algorithms with dynamic linking strategies; though incorporating some elements of probabilistic linkage. Within the data providers' safe haven we extracted: Demographic data, hospital utilisation and IAPT clinic data; converted post code to index of multiple deprivation (IMD); and identified people with CMHP. We contrasted the age, gender, ethnicity and IMD for the in-depth evaluation sample with people referred to IAPT, use hospital services, and the population as a whole. Results The in IAPT-in-depth group had a mean age of 43.1 years; CI: 41.0 - 45.2 (n = 166); the IAPT-referred 40.2 years; CI: 39.4 - 40.9 (n = 1118); and those with CMHP 43.6 years SEM 0.15. (n = 12210). Whilst around 67% of those with a CMHP were women, compared to 70% of those referred to IAPT, and 75% of those subject to in-depth evaluation (Chi square p < 0.001). The mean IMD score for the in-depth evaluation group was 36.6; CI: 34.2 - 38.9; (n = 166); of those referred to IAPT 38.7; CI: 37.9 - 39.6; (n = 1117); and of people with CMHP 37.6; CI 37

  11. Harry Judge and Oxford: College and University

    ERIC Educational Resources Information Center

    Halsey, A. H.

    2008-01-01

    Has Harry Judge's career reproduced in a lifetime the centuries-old history of Brasenose College and the University of Oxford? His biography and the history of his college in relation to Christian belief and modern university reform are briefly recapitulated. All tell a story of adaptation and modernisation, the man short, the college long, the…

  12. The Oxford English Dictionary: A Brief History.

    ERIC Educational Resources Information Center

    Fritze, Ronald H.

    1989-01-01

    Reviews the development of English dictionaries in general and the Oxford English Dictionary (OED) in particular. The discussion covers the decision by the Philological Society to create the dictionary, the principles that guided its development, the involvement of James Augustus Henry Murray, the magnitude and progress of the project, and the…

  13. The Oxford Picture Dictionary. Beginning Workbook.

    ERIC Educational Resources Information Center

    Fuchs, Marjorie

    The beginning workbook of the Oxford Picture Dictionary is in full color and offers vocabulary reinforcement activities that correspond page for page with the dictionary. Clear and simple instructions with examples make it suitable for independent use in the classroom or at home. The workbook has up-to-date art and graphics, explaining over 3700…

  14. The "New Oxford English Dictionary" Project.

    ERIC Educational Resources Information Center

    Fawcett, Heather

    1993-01-01

    Describes the conversion of the 22,000-page Oxford English Dictionary to an electronic version incorporating a modified Standard Generalized Markup Language (SGML) syntax. Explains that the database designers chose structured markup because it supports users' data searching needs, allows textual components to be extracted or modified, and allows…

  15. Improving the evidence base for promoting quality and equity of surgical care using population-based linkage of administrative health records.

    PubMed

    Hall, Sonĵa E; Holman, C D'Arcy J; Finn, Judith; Semmens, James B

    2005-10-01

    This paper highlights the uses of population-based linkage of administrative health records to improve the quality, safety, and equity of surgical care. The primary focus of the paper is on the transfer of this type of research into policy and practice. In the modern era of evidence-based medicine, it is essential that not only is new evidence incorporated into clinical practice, but that the implementation and associated costs are monitored; this requires the setting of appropriate benchmarking criteria. Furthermore, it is imperative that all members of the population receive optimal health care and people are not discriminated against because of socio-economic, locational, or racial factors. The use of data linkage can assist with examining these aspects of health care and this paper provides real-life examples such as costs and adverse events from laparoscopic cholecystectomy, event monitoring for post-operative venous thrombosis, and inequalities in cancer care. The influence of these studies on clinical practice and policy is also discussed. Furthermore, this paper discusses the strengths and weaknesses of data linkage research and how to avoid pitfalls. Health researchers, clinicians, and policy-makers will find the discussion of these issues useful in their everyday practice.

  16. Oxford House Recovery Homes: Characteristics and Effectiveness

    PubMed Central

    Jason, Leonard A.; Ferrari, Joseph R.

    2010-01-01

    One of the largest examples of a community-based, mutual-help residential community for high risk substance abuse individuals is Oxford House. In the U.S., over 9,800 people live in these self-run dwellings where they obtain jobs, pay utility bills, and learn to be responsible citizens. Beginning with one single rented residence in the mid 1970s, Oxford Houses now number over 1,300. These rented homes are helping to deal with drug addiction and community re-entry by providing stable housing without any limits on length of stay, a network of job opportunities, and support for abstinence. An exploration of the research on these unique settings highlights the strengths of such a community-based approach to addressing addiction. New roles for psychologists in working with these types of support systems are identified. PMID:20577571

  17. The Oxford Knee Score; problems and pitfalls.

    PubMed

    Whitehouse, Sarah L; Blom, Ashley W; Taylor, Adrian H; Pattison, Giles T R; Bannister, Gordon C

    2005-08-01

    The Oxford Knee Score is a self-completed patient based outcome score. We audited the outcome of total knee arthroplasty at our unit using the Oxford Knee Score. The hypothesis of this study is that the OKS can be easily and accurately completed by unassisted patients. Of 856 patients who had undergone total knee arthroplasty and were given questionnaires, 769 (90%) responded. 624 (81%) of the respondents managed to complete the questionnaire. A number of the 12 items composing the questionnaire posed problems for the patients and a number of items were left blank. Item 4 (concerning walking time) was omitted in 82 (13%) of the 624 completed questionnaires. Calculation of Cronbach's alpha for internal consistency suggests that there are redundancies within the Score. Limitations in some of the items of the scale suggest the need for reconsideration and reformulation of questions and response categories. This study suggests that where detailed assessment of outcome is required, such as for outcome studies or controlled trials, the Oxford Knee Score, in its present form, is not ideal for use as a postal questionnaire.

  18. Oxford House: deaf-affirmative support for substance abuse recovery.

    PubMed

    Alvarez, Josefina; Adebanjo, Aderonke M; Davidson, Michelle K; Jason, Leonard A; Davis, Margaret I

    2006-01-01

    Deaf individuals seeking substance abuse recovery are less likely to have access to treatment and aftercare services because of a lack of culturally and linguistically specific programs and insufficient information about existing services. Previous research indicates that Oxford House, a network of resident-run recovery homes, serves a diverse group of individuals in recovery. However, research has not addressed the experiences of Deaf Oxford House residents. The present study found no significant differences between Deaf and hearing men living in Oxford House in terms of sense of community and abstinence self-efficacy. However, while most of the hearing participants were employed, none of the Deaf Oxford House members were. The study's findings indicate that Oxford House may be a promising Deaf-affirmative alternative for individuals seeking recovery from substance abuse. However, since Oxford Houses are self-supporting, Oxford Houses designed for the Deaf community may face unique economic challenges. PMID:17225636

  19. Rheumatic Heart Disease-Attributable Mortality at Ages 5–69 Years in Fiji: A Five-Year, National, Population-Based Record-Linkage Cohort Study

    PubMed Central

    Parks, Tom; Kado, Joseph; Miller, Anne E.; Ward, Brenton; Heenan, Rachel; Colquhoun, Samantha M.; Bärnighausen, Till W.; Mirabel, Mariana; Bloom, David E.; Bailey, Robin L.; Tukana, Isimeli N.; Steer, Andrew C.

    2015-01-01

    Background Rheumatic heart disease (RHD) is considered a major public health problem in developing countries, although scarce data are available to substantiate this. Here we quantify mortality from RHD in Fiji during 2008–2012 in people aged 5–69 years. Methods and Findings Using 1,773,999 records derived from multiple sources of routine clinical and administrative data, we used probabilistic record-linkage to define a cohort of 2,619 persons diagnosed with RHD, observed for all-cause mortality over 11,538 person-years. Using relative survival methods, we estimated there were 378 RHD-attributable deaths, almost half of which occurred before age 40 years. Using census data as the denominator, we calculated there were 9.9 deaths (95% CI 9.8–10.0) and 331 years of life-lost (YLL, 95% CI 330.4–331.5) due to RHD per 100,000 person-years, standardised to the portion of the WHO World Standard Population aged 0–69 years. Valuing life using Fiji’s per-capita gross domestic product, we estimated these deaths cost United States Dollar $6,077,431 annually. Compared to vital registration data for 2011–2012, we calculated there were 1.6-times more RHD-attributable deaths than the number reported, and found our estimate of RHD mortality exceeded all but the five leading reported causes of premature death, based on collapsed underlying cause-of-death diagnoses. Conclusions Rheumatic heart disease is a leading cause of premature death as well as an important economic burden in this setting. Age-standardised death rates are more than twice those reported in current global estimates. Linkage of routine data provides an efficient tool to better define the epidemiology of neglected diseases. PMID:26371755

  20. The Oxford Handbook of the Development of Play. First Edition. Oxford Library of Psychology

    ERIC Educational Resources Information Center

    Pellegrini, Anthony D., Ed.

    2010-01-01

    The role of play in human development has long been the subject of controversy. Despite being championed by many of the foremost scholars of the twentieth century, play has been dogged by underrepresentation and marginalization in literature across the scientific disciplines. "The Oxford Handbook of the Development of Play" marks the first attempt…

  1. The accuracy of ascertaining vital status in a historical cohort study of synthetic textiles workers using computerized record linkage to the Canadian Mortality Data Base.

    PubMed

    Goldberg, M S; Carpenter, M; Thériault, G; Fair, M

    1993-01-01

    Vital status of a cohort of 10,211 Quebec, synthetic textiles workers was ascertained through a probabilistic record linkage to the Canadian Mortality Data Base (CMDB); 5,033 of these workers were also traced using other sources. There was agreement in the vital status of all but 60 of the subjects traced jointly through the CMDB and the alternate sources. 41 subjects were declared 'deceased' from the CMDB but 'alive' from the alternate sources; it is likely that these subjects were indeed deceased. 19 subjects, declared 'deceased' with a fair degree of certainty from the alternate sources, were not identified from the computer search of the CMDB; 17 were found manually on the microfiche death records and two died outside of Canada. The probability of identifying deceased and living subjects from the CMDB was therefore estimated to be 98.2% (95% confidence interval: 97.5-98.7%) and about 100%, respectively. Estimates of cost are also presented, and it is concluded that use of the CMDB is the method of choice for tracing moderate to large cohorts.

  2. Cervical Abnormalities Are More Common among Indigenous than Other Australian Women: A Retrospective Record-Linkage Study, 2000-2011.

    PubMed

    Whop, Lisa J; Baade, Peter; Garvey, Gail; Cunningham, Joan; Brotherton, Julia M L; Lokuge, Kamalini; Valery, Patricia C; O'Connell, Dianne L; Canfell, Karen; Diaz, Abbey; Roder, David; Gertig, Dorota M; Moore, Suzanne P; Condon, John R

    2016-01-01

    Indigenous Australian women have much higher incidence of cervical cancer compared to non-Indigenous women. Despite an organised cervical screening program introduced 25 years ago, a paucity of Indigenous-identified data in Pap Smear Registers remains. Prevalence of cervical abnormalities detected among the screened Indigenous population has not previously been reported. We conducted a retrospective cohort study of population-based linked health records for 1,334,795 female Queensland residents aged 20-69 years who had one or more Pap smears during 2000-2011; from linked hospital records 23,483 were identified as Indigenous. Prevalence was calculated separately for Indigenous and non-Indigenous women, for cytology-detected low-grade (cLGA) and high-grade abnormalities (cHGA), and histologically confirmed high-grade abnormalities (hHGA). Odds ratios (OR) were estimated from logistic regression analysis. In 2010-2011 the prevalence of hHGA among Indigenous women (16.6 per 1000 women screened, 95% confidence interval [CI] 14.6-18.9) was twice that of non-Indigenous women (7.5 per 1000 women screened, CI 7.3-7.7). Adjusted for age, area-level disadvantage and place of residence, Indigenous women had higher prevalence of cLGA (OR 1.4, CI 1.3-1.4), cHGA (OR 2.2, CI 2.1-2.3) and hHGA (OR 2.0, CI 1.9-2.1). Our findings show that Indigenous women recorded on the Pap Smear Register have much higher prevalence for cLGA, cHGA and hHGA compared to non-Indigenous women. The renewed cervical screening program, to be implemented in 2017, offers opportunities to reduce the burden of abnormalities and invasive cancer among Indigenous women and address long-standing data deficiencies. PMID:27064273

  3. Cervical Abnormalities Are More Common among Indigenous than Other Australian Women: A Retrospective Record-Linkage Study, 2000–2011

    PubMed Central

    Whop, Lisa J.; Baade, Peter; Garvey, Gail; Cunningham, Joan; Brotherton, Julia M. L.; Lokuge, Kamalini; Valery, Patricia C.; O’Connell, Dianne L.; Canfell, Karen; Diaz, Abbey; Roder, David; Gertig, Dorota M.; Moore, Suzanne P.; Condon, John R.

    2016-01-01

    Indigenous Australian women have much higher incidence of cervical cancer compared to non-Indigenous women. Despite an organised cervical screening program introduced 25 years ago, a paucity of Indigenous-identified data in Pap Smear Registers remains. Prevalence of cervical abnormalities detected among the screened Indigenous population has not previously been reported. We conducted a retrospective cohort study of population-based linked health records for 1,334,795 female Queensland residents aged 20–69 years who had one or more Pap smears during 2000–2011; from linked hospital records 23,483 were identified as Indigenous. Prevalence was calculated separately for Indigenous and non-Indigenous women, for cytology-detected low-grade (cLGA) and high-grade abnormalities (cHGA), and histologically confirmed high-grade abnormalities (hHGA). Odds ratios (OR) were estimated from logistic regression analysis. In 2010–2011 the prevalence of hHGA among Indigenous women (16.6 per 1000 women screened, 95% confidence interval [CI] 14.6–18.9) was twice that of non-Indigenous women (7.5 per 1000 women screened, CI 7.3–7.7). Adjusted for age, area-level disadvantage and place of residence, Indigenous women had higher prevalence of cLGA (OR 1.4, CI 1.3–1.4), cHGA (OR 2.2, CI 2.1–2.3) and hHGA (OR 2.0, CI 1.9–2.1). Our findings show that Indigenous women recorded on the Pap Smear Register have much higher prevalence for cLGA, cHGA and hHGA compared to non-Indigenous women. The renewed cervical screening program, to be implemented in 2017, offers opportunities to reduce the burden of abnormalities and invasive cancer among Indigenous women and address long-standing data deficiencies. PMID:27064273

  4. Cervical Abnormalities Are More Common among Indigenous than Other Australian Women: A Retrospective Record-Linkage Study, 2000-2011.

    PubMed

    Whop, Lisa J; Baade, Peter; Garvey, Gail; Cunningham, Joan; Brotherton, Julia M L; Lokuge, Kamalini; Valery, Patricia C; O'Connell, Dianne L; Canfell, Karen; Diaz, Abbey; Roder, David; Gertig, Dorota M; Moore, Suzanne P; Condon, John R

    2016-01-01

    Indigenous Australian women have much higher incidence of cervical cancer compared to non-Indigenous women. Despite an organised cervical screening program introduced 25 years ago, a paucity of Indigenous-identified data in Pap Smear Registers remains. Prevalence of cervical abnormalities detected among the screened Indigenous population has not previously been reported. We conducted a retrospective cohort study of population-based linked health records for 1,334,795 female Queensland residents aged 20-69 years who had one or more Pap smears during 2000-2011; from linked hospital records 23,483 were identified as Indigenous. Prevalence was calculated separately for Indigenous and non-Indigenous women, for cytology-detected low-grade (cLGA) and high-grade abnormalities (cHGA), and histologically confirmed high-grade abnormalities (hHGA). Odds ratios (OR) were estimated from logistic regression analysis. In 2010-2011 the prevalence of hHGA among Indigenous women (16.6 per 1000 women screened, 95% confidence interval [CI] 14.6-18.9) was twice that of non-Indigenous women (7.5 per 1000 women screened, CI 7.3-7.7). Adjusted for age, area-level disadvantage and place of residence, Indigenous women had higher prevalence of cLGA (OR 1.4, CI 1.3-1.4), cHGA (OR 2.2, CI 2.1-2.3) and hHGA (OR 2.0, CI 1.9-2.1). Our findings show that Indigenous women recorded on the Pap Smear Register have much higher prevalence for cLGA, cHGA and hHGA compared to non-Indigenous women. The renewed cervical screening program, to be implemented in 2017, offers opportunities to reduce the burden of abnormalities and invasive cancer among Indigenous women and address long-standing data deficiencies.

  5. Stennis hosts NASA Night in Oxford

    NASA Technical Reports Server (NTRS)

    2010-01-01

    A young visitor to the Powerhouse Community Arts and Cultural Center in Oxford, Miss., enjoys a balloon rocket transportation activity during a NASA Night in the Neighborhood on March 29. NASA's John C. Stennis Space Center near Bay St. Louis visited the center with a variety of space-related displays and educational activities. Events targeted for children included moon phasers and build-your-own rocket transportation exercises, as well as an astronaut ice cream tasting station. Visitors also were able to take photos in the astronaut suit display. Displays focused on the 40th anniversaries of the Apollo 11 and Apollo 13 lunar missions, the International Space Station, and various aspects of Stennis work. The event was sponsored by the NASA Office of External Affairs and Education at Stennis.

  6. Oxford CyberSEM: remote microscopy

    NASA Astrophysics Data System (ADS)

    Rahman, M.; Kirkland, A.; Cockayne, D.; Meyer, R.

    2008-08-01

    The Internet has enabled researchers to communicate over vast geographical distances, sharing ideas and documents. e-Science, underpinned by Grid [1] and Web Services, has enabled electronic communications to the next level where, in addition to document sharing, researchers can increasingly control high precision scientific instruments over the network. The Oxford CyberSEM project developed a simple Java applet via which samples placed in a JEOL 5510LV Scanning Electron Microscope (SEM) can be manipulated and examined collaboratively over the Internet. Designed with schoolchildren in mind, CyberSEM does not require any additional hardware or software other than a generic Java-enabled web browser. This paper reflects on both the technical and social challenges in designing real-time systems for controlling scientific equipments in collaborative environments. Furthermore, it proposes potential deployment beyond the classroom setting.

  7. Reflections on a Week in Oxford

    NASA Astrophysics Data System (ADS)

    Murphy, Tara

    2012-04-01

    When Bob asked me a couple of days ago to give this talk, he said it should be ``pithy and wise.'' When I spoke to Aris the next day he said it should be ``informal and funny.'' Then Elizabeth spoke to me and said it would be great if it was ``controversial and challenging.'' I mentioned to Aris just before dinner that I had put a talk together, and he said ``Oh, you've written a talk-I thought it would be something more spontaneous!'' Faced with an obviously impossible spec, I did what any reasonable programmer would do and rewrote the spec myself. So what I'm going to talk about this evening is a reflection on my week in Oxford.

  8. Oxford and the Mandarin Culture: The Past that Is Gone

    ERIC Educational Resources Information Center

    Bogdanor, Vernon

    2006-01-01

    Why was Oxford the home of the mandarin and why has the era of the mandarin come to an end? The era of the mandarin was inaugurated by T. H. Green, who sought, through the gospel of citizenship, to provide a philosophy for an age of religious doubt. Green's moralism served in Oxford as a substitute for the social sciences, which came to be…

  9. The Oxford Companion to the Earth

    NASA Astrophysics Data System (ADS)

    Hancock, Paul L.

    2001-06-01

    Here is a wealth of information on planet Earth, ranging from the heights of the ionsphere down to the red-hot molten core. Written by some 200 expert contributors, and illustrated with over 600 pictures, including 16 pages of color plates, The Oxford Companion to the Earth offers 900 alphabetically arranged entries that cover everything from deserts and wetlands to mountains, caves, glaciers, and coral reefs. There are articles on natural phenomena such as tornadoes and tsunamis, volcanoes and earthquakes, jet streams and weather fronts; on the history of Earth, including the origin of life, Burgess Shale fauna, dinosaurs, and the Ice Ages; on key figures, such as Agassiz, Cuvier, Darwin, and Lamarck; and on such important ecological concerns as acid rain, the ozone layer, industrial waste disposal, and the greenhouse effect. The Companion also examines the great sources of wealth to be found in the Earth, from coal and oil to gold, silver, and diamonds, and many curious land formations, from sinkholes and fiords to yardangs and quicksand. There are brief entries on rock types, from amber to travertine, and extensive essays on cutting-edge aspects of the earth sciences, such as seismology and marine geology. The Companion includes extensive cross-references, suggested further reading, an index, and many useful appendices, with a geological timescale, facts and figures about the Earth, and a table of chemical elements. The Oxford Companion to the Earth is a unique reference work, offering unrivaled coverage of our home planet. Generously illustrated and vividly written, it is a treasure house of information for all lovers of natural history, geology, and ecology, whether professional or amateur.

  10. Wait times to rheumatology care for patients with rheumatic diseases: a data linkage study of primary care electronic medical records and administrative data

    PubMed Central

    Widdifield, Jessica; Bernatsky, Sasha; Thorne, J. Carter; Bombardier, Claire; Jaakkimainen, R. Liisa; Wing, Laura; Paterson, J. Michael; Ivers, Noah; Butt, Debra; Lyddiatt, Anne; Hofstetter, Catherine; Ahluwalia, Vandana; Tu, Karen

    2016-01-01

    Background: The Wait Time Alliance recently established wait time benchmarks for rheumatology consultations in Canada. Our aim was to quantify wait times to primary and rheumatology care for patients with rheumatic diseases. Methods: We identified patients from primary care practices in the Electronic Medical Record Administrative data Linked Database who had referrals to Ontario rheumatologists over the period 2000-2013. To assess the full care pathway, we identified dates of symptom onset, presentation in primary care and referral from electronic medical records. Dates of rheumatologist consultations were obtained by linking with physician service claims. We determined the duration of each phase of the care pathway (symptom onset to primary care encounter, primary care encounter to referral, and referral to rheumatologist consultation) and compared them with established benchmarks. Results: Among 2430 referrals from 168 family physicians, 2015 patients (82.9%) were seen by 146 rheumatologists within 1 year of referral. Of the 2430 referrals, 2417 (99.5%) occurred between 2005 and 2013. The main reasons for referral were osteoarthritis (32.4%) and systemic inflammatory rheumatic diseases (30.6%). Wait times varied by diagnosis and geographic region. Overall, the median wait time from referral to rheumatologist consultation was 74 (interquartile range 27-101) days; it was 66 (interquartile range 18-84) days for systemic inflammatory rheumatic diseases. Wait time benchmarks were not achieved, even for the most urgent types of referral. For systemic inflammatory rheumatic diseases, most of the delays occurred before referral. Interpretation: Rheumatology wait times exceeded established benchmarks. Targeted efforts are needed to promote more timely access to both primary and rheumatology care. Routine linkage of electronic medical records with administrative data may help fill important gaps in knowledge about waits to primary and specialty care. PMID:27398365

  11. Hospital admissions for vitamin D related conditions and subsequent immune-mediated disease: record-linkage studies

    PubMed Central

    2013-01-01

    Background Previous studies have suggested that there may be an association between vitamin D deficiency and the risk of developing immune-mediated diseases. Methods We analyzed a database of linked statistical records of hospital admissions and death registrations for the whole of England (from 1999 to 2011). Rate ratios for immune-mediated disease were determined, comparing vitamin D deficient cohorts (individuals admitted for vitamin D deficiency or markers of vitamin D deficiency) with comparison cohorts. Results After hospital admission for either vitamin D deficiency, osteomalacia or rickets, there were significantly elevated rates of Addison’s disease, ankylosing spondylitis, autoimmune hemolytic anemia, chronic active hepatitis, celiac disease, Crohn’s disease, diabetes mellitus, pemphigoid, pernicious anemia, primary biliary cirrhosis, rheumatoid arthritis, Sjogren’s syndrome, systemic lupus erythematosus, thyrotoxicosis, and significantly reduced risks for asthma and myxoedema. Conclusions This study shows that patients with vitamin D deficiency may have an increased risk of developing some immune-mediated diseases, although we cannot rule out reverse causality or confounding. Further study of these associations is warranted and these data may aid further public health studies. PMID:23885887

  12. Land-ocean linkages over orbital and millennial timescales recorded in Late Quaternary sediments of the Japan Sea

    NASA Astrophysics Data System (ADS)

    Tada, Ryuji; Irino, Tomohisa; Koizumi, Itaru

    1999-04-01

    Late Quaternary sediments of the Japan Sea are characterized by centimeter- to meter-scale alternations of dark and light layers which are synchronous basinwide. High-resolution analyses of the sediments from Ocean Drilling Program site 797 reveal that deposition of the meter-scale alternations reflect variations in paleoceanographic conditions which were closely associated with glacio-eustatic sea level changes through the modulation of the volume and character of the influx to the sea through the Tsushima Strait. The centimeter- to decimeter-scale alternations reflect millennial-scale variations which are possibly associated with Dansgaard-Oeschger (D-O) cycles, with each dark layer appearing to correspond to an interstadial. This variability is attributed to the development of a humid climate in central to eastern Asia and the consequent increase in discharge from the Huanghe and Changjiang Rivers during interstadials. This caused expansion of the East China Sea coastal water (ECSCW), which penetrated more strongly into the Japan Sea. The increased influence of the lower-salinity, nutrient-enriched ECSCW reduced deep water ventilation and enhanced the surface productivity, leading to the development of anoxic bottom waters and deposition of the dark layers. Thus the centimeter- to decimeter-scale alternations of the dark and light layers record wet and dry cycles in central to eastern Asia possibly associated with D-O cycles.

  13. Correlations of siblings' and mothers' utilisation of primary and hospital health care: a record linkage study in Western Australia.

    PubMed

    Ward, Alison M; de Klerk, Nick; Pritchard, Douglas; Firth, Martin; Holman, C D'Arcy J

    2006-03-01

    A relationship between maternal and child use of general practitioners (GPs) has been shown to exist for some time, however, the reasons for this relationship are not clear and the extent to which this relationship extends to tertiary care is unknown. The aim of this study was to examine the relationships between the utilisation of health care by siblings and mothers over a 14 year period. A retrospective cohort study of 756 mothers and their 1494 children up to age 14 years was conducted in three general practices in Western Australia. Medicare claims and hospital morbidity records for 1984-1997 were linked using deterministic and probabilistic matching. Generalised Estimating Equations and correlations were used to examine the relationships between the utilisation of primary and hospital health care by family members. Significant correlations were found between hospital admissions of all participants and their GP visits, specialist visits, pathology and diagnostic imaging combined and hospital length of stay. There was a strong association between siblings' use of GPs. A child's rate of GP attendance increased with that of its mother. There was a weak but significant relationship between siblings' use of hospitals, and a child's hospital admission rate increased with that of its mother. It is concluded that there is a strong relationship between siblings' use of GPs and a weaker but still significant association between the hospital admissions of siblings. As expected, there were strong associations between mother and child visits to GPs. There was also an association between a mother's use of hospital and that of her children. This finding reduces the plausibility that the relationships found between utilisation of health care by siblings and mothers can be explained entirely by behavioural factors, and suggests the presence of intergenerational correlation of morbidity.

  14. Validation of a Hierarchical Deterministic Record-Linkage Algorithm Using Data From 2 Different Cohorts of Human Immunodeficiency Virus-Infected Persons and Mortality Databases in Brazil

    PubMed Central

    Saraceni, Valeria; Tuboi, Suely H.; Moulton, Lawrence H.; Chaisson, Richard E.; Cavalcante, Solange C.; Durovni, Betina; Faulhaber, José C.; Golub, Jonathan E.; King, Bonnie; Schechter, Mauro; Harrison, Lee H.

    2008-01-01

    Loss to follow-up is a major source of bias in cohorts of patients with human immunodeficiency virus (HIV) and could lead to underestimation of mortality. The authors developed a hierarchical deterministic linkage algorithm to be used primarily with cohorts of HIV-infected persons to recover vital status information for patients lost to follow-up. Data from patients known to be deceased in 2 cohorts in Rio de Janeiro, Brazil, and data from the Rio de Janeiro State mortality database for 1999–2006 were used to validate the algorithm. A fully automated procedure yielded a sensitivity of 92.9% and specificity of 100% when no information was missing. When the automated procedure was combined with clerical review, in a scenario of 5% death prevalence and 20% missing mothers’ names, sensitivity reached 96.5% and specificity 100%. In a practical application, the algorithm significantly increased death rates and decreased the rate of loss to follow-up in the cohorts. The finding that 23.9% of matched records did not give HIV or acquired immunodeficiency syndrome as the cause of death reinforces the need to search all-cause mortality databases and alerts for possible underestimation of death rates. These results indicate that the algorithm is accurate enough to recover vital status information on patients lost to follow-up in cohort studies. PMID:18849301

  15. The Colville River Delta as a Natural Recorder of Historical Changes in Organic Carbon Sources: Linkages with Climate Change

    NASA Astrophysics Data System (ADS)

    Schreiner, K. M.; Bianchi, T. S.; Allison, M. A.; Miller, A. J.; Marcantonio, F.

    2011-12-01

    The Colville River in Alaska is the largest river in North America that drains only continuously permafrosted tundra, and as such provides a unique signal of historical changes in one of the world's most vulnerable areas to climate changes. Additionally, the Colville flows into Simpson's Lagoon, an area of the Alaskan Beaufort coast protected by a barrier island chain, lessening the impacts of Arctic storms and ice grounding on sediment mixing. Cores collected from the Colville river delta in August of 2010 were found to be composed of muddy, organic-rich, well-laminated sediments. The 2.5 to 3 meter length of each core spans about one to two thousand years of Holocene history, including the entire Anthropocene and much of the late Holocene. Two cores were sampled for this data set - one from close to the river mouth, and one from farther east in Simpson's Lagoon. Samples were taken every 2 cm for the entire length of both cores. Bulk analyses including percent organic carbon, percent nitrogen, and stable carbon isotopic analysis were performed, and compound specific analyses including lignin-phenol and algal pigment analyses were performed. These analyses show significant changes in carbon storage over the time period represented by the cores, and appear to indicate changes in terrestrial carbon delivery to the cores over time. Specifically, the delivery of more isotopically depleted carbon from -27% at depth to values oscillating to -33% at the surface likely indicates two things, summarized below, which are also supported by variations in chemical biomarkers. These results show, one, an increase in the delivery to the lagoon of woody shrub inputs coupled with, two, an increase in the delivery of fresh-water phytoplankton detritus over the past few hundred years. These recorded changes in deltaic sediments may, in part, be consistent with previous observations of enhanced woody shrub encroachment and an increase in the areal extent of permafrost lakes on the

  16. Rheumatoid Arthritis and Incidence of Twelve Initial Presentations of Cardiovascular Disease: A Population Record-Linkage Cohort Study in England

    PubMed Central

    Pujades-Rodriguez, Mar; Duyx, Bram; Thomas, Sara L.; Stogiannis, Dimitris; Rahman, Anisur; Smeeth, Liam; Hemingway, Harry

    2016-01-01

    Introduction While rheumatoid arthritis is an established risk factor for cardiovascular disease (CVD), our knowledge of how the pattern of risk varies for different cardiovascular phenotypes is incomplete. The association between rheumatoid arthritis and the initial presentation of 12 types of CVDs were examined in a contemporary population of men and women of a wide age range. Methods CALIBER data, which links primary care, hospital and mortality data in England, was analysed. A cohort of people aged ≥18 years and without history of CVD was assembled and included all patients with prospectively recorded rheumatoid arthritis from January 1997, until March 2010, matched with up to ten people without rheumatoid arthritis by age, sex and general practice. The associations between rheumatoid arthritis and the initial presentation of 12 types of CVDs were estimated using multivariable random effects Poisson regression models. Results The analysis included 12,120 individuals with rheumatoid arthritis and 121,191 comparators. Of these, 2,525 patients with and 18,146 without rheumatoid arthritis developed CVDs during a median of 4.2 years of follow-up. Patients with rheumatoid arthritis had higher rates of myocardial infarction (adjusted incidence ratio [IRR] = 1.43, 95%CI 1.21–1.70), unheralded coronary death (IRR = 1.60, 95%CI 1.18–2.18), heart failure (IRR = 1.61, 95%CI 1.43–1.83), cardiac arrest (HR = 2.26, 95%CI 1.69–3.02) and peripheral arterial disease (HR = 1.36, 95%CI 1.14–1.62); and lower rates of stable angina (HR = 0.83, 95%CI 0.73–0.95). There was no evidence of association with cerebrovascular diseases, abdominal aortic aneurysm or unstable angina, or of interactions with sex or age. Conclusions The observed associations with some but not all types of CVDs inform both clinical practice and the selection of cardiovascular endpoints for trials and for the development of prognostic models for patients with rheumatoid arthritis. PMID:26978266

  17. Identifying risk factors for progression to critical care admission and death among individuals with acute pancreatitis: a record linkage analysis of Scottish healthcare databases

    PubMed Central

    Mole, Damian J; Gungabissoon, Usha; Johnston, Philip; Cochrane, Lynda; Hopkins, Leanne; Wyper, Grant M A; Skouras, Christos; Dibben, Chris; Sullivan, Frank; Morris, Andrew; Ward, Hester J T; Lawton, Andrew M; Donnan, Peter T

    2016-01-01

    Objectives Acute pancreatitis (AP) can initiate systemic complications that require support in critical care (CC). Our objective was to use the unified national health record to define the epidemiology of AP in Scotland, with a specific focus on deterministic and prognostic factors for CC admission in AP. Setting Health boards in Scotland (n=4). Participants We included all individuals in a retrospective observational cohort with at least one episode of AP (ICD10 code K85) occurring in Scotland from 1 April 2009 to 31 March 2012. 3340 individuals were coded as AP. Methods Data from 16 sources, spanning general practice, community prescribing, Accident and Emergency attendances, hospital in-patient, CC and mortality registries, were linked by a unique patient identifier in a national safe haven. Logistic regression and gamma models were used to define independent predictive factors for severe AP (sAP) requiring CC admission or leading to death. Results 2053 individuals (61.5% (95% CI 59.8% to 63.2%)) met the definition for true AP (tAP). 368 patients (17.9% of tAP (95% CI 16.2% to 19.6%)) were admitted to CC. Predictors of sAP were pre-existing angina or hypertension, hypocalcaemia and age 30–39 years, if type 2 diabetes mellitus was present. The risk of sAP was lower in patients with multiple previous episodes of AP. In-hospital mortality in tAP was 5.0% (95% CI 4.1% to 5.9%) overall and 21.7% (95% CI 19.9% to 23.5%) in those with tAP necessitating CC admission. Conclusions National record-linkage analysis of routinely collected data constitutes a powerful resource to model CC admission and prognosticate death during AP. Mortality in patients with AP who require CC admission remains high. PMID:27311912

  18. Same organization, same electronic health records (EHRs) system, different use: exploring the linkage between practice member communication patterns and EHR use patterns in an ambulatory care setting

    PubMed Central

    Leykum, Luci K; McDaniel, Reuben R

    2011-01-01

    Objective Despite efforts made by ambulatory care organizations to standardize the use of electronic health records (EHRs), practices often incorporate these systems into their work differently from each other. One potential factor contributing to these differences is within-practice communication patterns. The authors explore the linkage between within-practice communication patterns and practice-level EHR use patterns. Design Qualitative study of six practices operating within the same multi-specialty ambulatory care organization using the same EHR system. Semistructured interviews and direct observation were conducted with all physicians, nurses, medical assistants, practice managers, and non-clinical staff from each practice. Measurements An existing model of practice relationships was used to analyze communication patterns within the practices. Practice-level EHR use was defined and analyzed as the ways in which a practice uses an EHR as a collective or a group—including the degree of feature use, level of EHR-enabled communication, and frequency that EHR use changes in a practice. Interview and observation data were analyzed for themes. Based on these themes, within-practice communication patterns were categorized as fragmented or cohesive, and practice-level EHR use patterns were categorized as heterogeneous or homogeneous. Practices where EHR use was uniformly high across all users were further categorized as having standardized EHR use. Communication patterns and EHR use patterns were compared across the six practices. Results Within-practice communication patterns were associated with practice-level EHR use patterns. In practices where communication patterns were fragmented, EHR use was heterogeneous. In practices where communication patterns were cohesive, EHR use was homogeneous. Additional analysis revealed that practices that had achieved standardized EHR use (uniformly high EHR use across all users) exhibited high levels of mindfulness and

  19. Is medical perspective on clinical governance practices associated with clinical units’ performance and mortality? A cross-sectional study through a record-linkage procedure

    PubMed Central

    Sarchielli, Guido; De Plato, Giovanni; Cavalli, Mario; Albertini, Stefano; Nonni, Ilaria; Bencivenni, Lucia; Montali, Arianna; Ventura, Antonio; Montali, Francesca

    2016-01-01

    Objective: Assessment of the knowledge and application as well as perceived utility by doctors of clinical governance tools in order to explore their impact on clinical units’ performance measured through mortality rates and efficiency indicators. Methods: This research is a cross-sectional study with a deterministic record-linkage procedure. The sample includes n = 1250 doctors (n = 249 chiefs of clinical units; n = 1001 physicians) working in six public hospitals located in the Emilia-Romagna Region in Italy. Survey instruments include a checklist and a research-made questionnaire which were used for data collection about doctors’ knowledge and application as well as perceived utility of clinical governance tools. The analysis was based on clinical units’ performance indicators which include patients’ mortality, extra-region active mobility rate, average hospital stay, bed occupancy, rotation and turnover rates, and the comparative performance index as efficiency indicators. Results: The clinical governance tools are known and applied differently in all the considered clinical units. Significant differences emerged between roles and organizational levels at which the medical leadership is carried out. The levels of knowledge and application of clinical governance practices are correlated with the clinical units’ efficiency indicators (bed occupancy rate, bed turnover interval, and extra-region mobility). These multiple linear regression analyses highlighted that the clinical governance knowledge and application is correlated with clinical units’ mortality rates (odds ratio, −8.677; 95% confidence interval, −16.654, −0.700). Conclusion: The knowledge and application, as well as perceived utility by medical professionals of clinical governance tools, are associated with the mortality rates of their units and with some efficiency indicators. However, the medical frontline staff seems to not consider homogeneously useful the clinical

  20. Oxford phase III meniscal bearing fracture: case report.

    PubMed

    Lim, Hong-Chul; Shon, Won-Yong; Kim, Seung-Ju; Bae, Ji-Hoon

    2014-01-01

    Meniscal bearing fracture is a rare complication of phase III Oxford unicompartmental knee replacement (UKR). We report a case of a meniscal bearing fracture that occurred 7 years after phase III Oxford medial UKR. The meniscal bearing showed uneven delamination of the polyethylene in the thinnest articular surface and an impingement lesion. This lesion initiated a fatigue crack that propagated to cause failure of the meniscal bearing. This is the first report of a meniscal bearing fracture without a posterior marker wire.

  1. BOOK REVIEW: The Oxford Companion to Cosmology

    NASA Astrophysics Data System (ADS)

    Coles, Peter

    2008-10-01

    Cosmology has a special status as a science, as it strives to combine the quantitative statistical rigour of observational astronomy with a theoretical framework emerging from rather speculative ideas about fundamental physics. It also has wider repercussions too, as the quest for an understanding of the origin of the Universe sometimes strays into territory traditionally associated with religious modes of enquiry. The Oxford Companion to Cosmology aims to provide a 'comprehensive but accessible overview' of this 'enduringly popular subject' suitable for students, teachers and others with a serious interest in cosmology. It consists of an introductory overview about the big bang cosmological model, followed by an encyclopedia-like section containing over 300 entries of varying length and technical level. One of the authors (Liddle) is a theorist and the other (Loveday) an observer, so between them they have sufficient authority to cover all aspects of the vigorous interplay between these two facets of the discipline. This is not the sort of volume that can easily be read from cover to cover. The best way to test its effectiveness is to dip into it randomly. In my sampling of the entries I found most to be well-written and informative. The first entry I looked at ('correlation function') had an incorrect formula in it, but I didn't find any further significant errors, which says something about the limitations of statistical inference! The only criticisms I have are very minor. Some of the figures are so small as to be virtually invisible to an oldie like me. I also think the book would have benefitted from more references, and am not sure the web links given in their place will prove very useful as these tend to be rather ephemeral. Overall, though, I would say that the book succeeds admirably in its aims. About ten years ago, I was involved in compiling a similar volume, which ended up as The Routledge Companion to the New Cosmology. I will refrain from trying to

  2. Neurosurgery at the Radcliffe Infirmary, Oxford: a history.

    PubMed

    Aziz, T Z; Adams, C B

    1995-09-01

    Neurosurgery started in Oxford in 1938. In this article, we commence the story of Oxford neurosurgery with Thomas Willis and trace the historical thread through William Osler, Charles Sherrington, John Fulton, and Harvey Cushing to Hugh Cairns. The department in Oxford is renowned for the training of neurosurgeons. The initial stimulus for this was the abundance of neurosurgical and neurological expertise in Oxford during World War II with Cairns, and this tradition continued with Joe Pennybacker and his successors. The large and ever increasing work load ensures trainees a wide exposure to challenging neurosurgical problems. An increasing emphasis placed on research has resulted in the creation of two posts; each consists of half-time clinical neurosurgery and half-time research. Hugh Cairns organized the department along "Cushing lines." This organization still exists, allowing us to treat a large number of patients with relatively few beds and an average length of patient stay less than 6 days. We look to the future with confidence.

  3. Early recovery after fast-track Oxford unicompartmental knee arthroplasty

    PubMed Central

    2012-01-01

    Background and purpose After total knee arthroplasty with conventional surgical approach, more than half of the quadriceps extension strength is lost in the first postoperative month. Unicompartmental knee arthroplasty (UKA) operated with minimally invasive surgery (MIS) results in less operative trauma. We investigated changes in leg-extension power (LEP) in the first month after MIS Oxford UKA and its relation to pain, knee motion, functional performance, and knee function. Patients and methods In 35 consecutive Oxford UKA patients, LEP was measured 1 week before and 1 month after surgery together with knee motion, knee swelling, the 30-second chair-stand test, and Oxford knee score. Assessment of knee pain at rest and walking was done using a visual analog scale. Results 30 patients were discharged on the day after surgery, and 5 on the second day after surgery. LEP and functional performance reached the preoperative level after 1 month. Only slight postoperative knee swelling was observed with rapid restoration of knee flexion and function. A high level of pain during the first postoperative night and day fell considerably thereafter. None of the patients needed physiotherapy supervision in the first month after discharge. Interpretation Fast-track MIS Oxford UKA with discharge on the day after surgery is safe and leads to early recovery of knee motion and strength even when no physiotherapy is used. PMID:22313368

  4. Classic Classroom Activities: The Oxford Picture Dictionary Program.

    ERIC Educational Resources Information Center

    Weiss, Renee; Adelson-Goldstein, Jayme; Shapiro, Norma

    This teacher resource book offers over 100 reproducible communicative practice activities and 768 picture cards based on the vocabulary of the Oxford Picture Dictionary. Teacher's notes and instructions, including adaptations for multilevel classes, are provided. The activities book has up-to-date art and graphics, explaining over 3700 words. The…

  5. Oxford House: Deaf-Affirmative Support for Substance Abuse Recovery

    ERIC Educational Resources Information Center

    Alvarez, Josefina; Adebanjo, Aderonke M.; Davidson, Michelle K.; Jason, Leonard A.; Davis, Margaret I.

    2006-01-01

    Deaf individuals seeking substance abuse recovery are less likely to have access to treatment and aftercare services because of a lack of culturally and linguistically specific programs and insufficient information about existing services. Previous research indicates that Oxford House, a network of resident-run recovery homes, serves a diverse…

  6. The Oxford Ethnography Conference: A Place in History?

    ERIC Educational Resources Information Center

    Walford, Geoffrey

    2011-01-01

    This paper gives a history of the Oxford Ethnography Conference. Over more than three decades, a regular conference of sociologists of education and ethnographers has met and produced a series of academic writings. The paper describes some of the interrelationships between developments that occurred within the conference and external changes to…

  7. Continuity and Change: The Integration of Oxford University's Libraries

    ERIC Educational Resources Information Center

    Moran, Barbara B.

    2005-01-01

    Prior to 1997, the University of Oxford in Great Britain had approximately one hundred autonomous libraries with little coordination of services, collection development, or management among them. In that year a new director was hired with the mandate to integrate many of these libraries into one centralized system. Over the past seven years…

  8. Reconciling late Quaternary transgressions in the Bohai Sea, China to the global sea level changes, and new linkage of sedimentary records to three astronomical rhythms

    NASA Astrophysics Data System (ADS)

    Yi, Liang

    2013-04-01

    Terminations. Science 326, 248-252. Ding, Z.L., Yu, Z.W., Rutter, N.W., Liu, T.S., 1994. Towards an orbital time scale for chinese loess deposits. Quaternary Science Reviews 13, 39-70. IOCAS (Institute of Oceanology, Chinese Academy of Sciences), 1985. Bohai Sea Geology. Science Press, Beijing, China. Liu, T., 2009. Loess and Arid Environment. Anhui Science & Techonology Press, Hefei, China. Wang, Y., Cheng, H., Edwards, R.L., An, Z., Wu, J., Chen, C.-C., Dorale, J.A., 2001. A High-Resolution Absolute-Dated Late Pleistocene Monsoon Record from Hulu Cave, China. Science 294, 2345-2348. Wang, Y., Cheng, H., Edwards, R.L., Kong, X., Shao, X., Chen, S., Wu, J., Jiang, X., Wang, X., An, Z., 2008. Millennial- and orbital-scale changes in the East Asian monsoon over the past 224,000 years. Nature 451, 1090-1093. Yi, L., Yu, H., Ortiz, J.D., Xu, X., Chen, S., Ge, J., Hao, Q., Yao, J., Shi, X., Peng, S., 2012a. Late Quaternary linkage of sedimentary records to three astronomical rhythms and the Asian monsoon, inferred from a coastal borehole in the south Bohai Sea, China. Palaeogeography, Palaeoclimatology, Palaeoecology 329-310, 101-117. Yi, L., Lai, Z.P., Yu, H.J., Xu, X.Y., Su, Q., Yao, J., Wang, X.L., Shi, X., 2012b. Chronologies of sedimentary changes in the south Bohai Sea, China: Constraints from luminescence and radiocarbon dating. Boreas, doi: 10.1111/j.1502-3885.2012.00271.x. Yi, L., Yu, H.J., Ortiz, J.D., Xu, X.Y., Qiang, X.K., Huang, H.J., Shi, X., Deng, C.L., 2012c. A reconstruction of late Pleistocene relative sea level in the south Bohai Sea, China, based on sediment grain-size analysis. Sedimentary Geology 281, 88-100. Zhao, S., Yang, G., Cang, S., Zhang, H., Huang, Q., Xia, D., Wang, Y., Liu, F., Liu, C., 1978. Transgression's stratas and shoreline changes in the south coast of Bohai Bay, China. Oceanologia et Limnologia Sinica 9, 15-25.

  9. Ten- to 15-year results of the Oxford Phase III mobile unicompartmental knee arthroplasty

    PubMed Central

    Lisowski, L. A.; Meijer, L. I.; van den Bekerom, M. P. J.; Pilot, P.; Lisowski, A. E.

    2016-01-01

    Aims The interest in unicompartmental knee arthroplasty (UKA) for medial osteoarthritis has increased rapidly but the long-term follow-up of the Oxford UKAs has yet to be analysed in non-designer centres. We have examined our ten- to 15-year clinical and radiological follow-up data for the Oxford Phase III UKAs. Patients and Methods Between January 1999 and January 2005 a total of 138 consecutive Oxford Phase III arthroplasties were performed by a single surgeon in 129 patients for medial compartment osteoarthritis (71 right and 67 left knees, mean age 72.0 years (47 to 91), mean body mass index 28.2 (20.7 to 52.2)). Both clinical data and radiographs were prospectively recorded and obtained at intervals. Of the 129 patients, 32 patients (32 knees) died, ten patients (12 knees) were not able to take part in the final clinical and radiological assessment due to physical and mental conditions, but via telephone interview it was confirmed that none of these ten patients (12 knees) had a revision of the knee arthroplasty. One patient (two knees) was lost to follow-up. Results The mean follow-up was 11.7 years (10 to 15). A total of 11 knees (8%) were revised. The survival at 15 years with revision for any reason as the endpoint was 90.6% (95% confidence interval (CI) 85.2 to 96.0) and revision related to the prosthesis was 99.3% (95% CI 97.9 to 100). The mean total Knee Society Score was 47 (0 to 80) pre-operatively and 81 (30 to 100) at latest follow-up. The mean Oxford Knee Score was 19 (12 to 40) pre-operatively and 42 (28 to 55) at final follow-up. Radiolucency beneath the tibial component occurred in 22 of 81 prostheses (27.2%) without evidence of loosening. Conclusion This study supports the use of UKA in medial compartment osteoarthritis with excellent long-term functional and radiological outcomes with an excellent 15-year survival rate. Cite this article: Bone Joint J 2016;98-B(10 Suppl B):41–7. PMID:27694515

  10. Promising short-term clinical results of the cementless Oxford phase III medial unicondylar knee prosthesis

    PubMed Central

    van Dorp, Karin B; Breugem, Stefan JM; Bruijn, Daniël J; Driessen, Marcel JM

    2016-01-01

    AIM: To investigate the short-term clinical results of the Oxford phase III cementless medial unicondylar knee prosthesis (UKP) compared to the cemented medial UKP. METHODS: We conducted a cross-sectional study in a tertairy orthopedic centre between the period of May 2010 and September 2012. We included 99 medial UKP in 97 patients and of these UKP, 53 were cemented and 46 were cementless. Clinical outcome was measured using a questionnaire, containing a visual analogue scale (VAS) for pain, Oxford Knee score, Kujala score and SF-12 score. Knee function was tested using the American Knee Society score. Complications, reoperations and revisions were recorded. Statistical significance was defined as a P value < 0.05. RESULTS: In a mean follow-up time of 19.5 mo, three cemented medial UKP were revised to a total knee prosthesis. Reasons for revision were malrotation of the tibial component, aseptic loosening of the tibial component and progression of osteoarthritis in the lateral- and patellofemoral compartment. In five patients a successful reoperation was performed, because of impingement or (sub)luxation of the polyethylene bearing. Patients with a reoperation were significant younger than patients in the primary group (56.7 vs 64.0, P = 0.01) and were more likely to be male (85.7% vs 38.8%, P = 0.015). Overall the cementless medial UKP seems to perform better, but the differences in clinical outcome are not significant; a VAS pain score of 7.4 vs 11.7 (P = 0.22), an Oxford Knee score of 43.3 vs 41.7 (P = 0.27) and a Kujala score of 79.6 vs 78.0 (P = 0.63). The American Knee Society scores were slightly better in the cementless group with 94.5 vs 90.2 (P = 0.055) for the objective score and 91.2 vs 87.8 (P = 0.25) for the subjective score. CONCLUSION: The cementless Oxford phase III medial UKP shows good short-term clinical results, when used in a specialist clinic by an experienced surgeon. PMID:27114932

  11. Submicron elemental mapping with the oxford scanning proton microprobe

    NASA Astrophysics Data System (ADS)

    Grime, G. W.; Watt, F.; Chapman, J. R.

    1987-03-01

    Following recent modifications to the Oxford scanning proton microprobe (SPM) a beam spot diameter of 0.5 μm has been achieved at a beam current of 20-30 pA of 4 MeV protons. This has been confirmed by scanning both a copper test grid and microcrystals of barium sulphate. The potential of using high spatial resolutions in microbiology has been explored by scanning a single mouse cell.

  12. A High-Resolution Late Holocene Record of Rainfall From Lake Edward, Equatorial Africa: Linkages Between the African and Indian Monsoons

    NASA Astrophysics Data System (ADS)

    Russell, J. M.; Johnson, T. C.

    2005-12-01

    High-resolution analyses of the chemical composition of calcite and the biogenic silica content of sediments from piston cores spanning the past 3,500 years from Lake Edward, Uganda-Congo, document multidecadal to millennial-scale climate variability in the heart of equatorial Africa. Major drought events in the Lake Edward record occur at about 500, 850, 1500, ~2000, and 2700 cal yr BP, in addition to numerous other events of lesser magnitude/duration. Comparison of our record to other Holocene records of African lake levels suggests that most of these intervals of drought affected most of equatorial East Africa. However, wet conditions at about 500 cal yrs BP at sites to the east of Lake Edward could indicate spatial heterogeneity within the African continent during the "Little Ice Age", which could have resulted from complex interactions between the African (Atlantic) and Indian Ocean monsoons. Spectral analysis of our drought record, sampled at a 3-year step, shows evidence for numerous multidecadal to century-scale drought periods in the region. The periodicities observed do not appear linked to solar forcing; rather, periods of ~125, ~70, ~28, and ~18 years apparent in our record as well as other records from the Indian Ocean basin may arise from climate variability internal to the tropical oceans, in particular the Indo-Pacific. Lastly, the Lake Edward record suggests that the climate of equatorial Africa has been unusually stable and generally wet for the past ca. 100 years. This stability appears unusual in light of the considerable climate variability suggested by our record for the past several millennia, a finding with clear implications for East African societies.

  13. Record-linkage comparison of verbal autopsy and routine civil registration death certification in rural north-east South Africa: 2006–09

    PubMed Central

    Joubert, Jané; Bradshaw, Debbie; Kabudula, Chodziwadziwa; Rao, Chalapati; Kahn, Kathleen; Mee, Paul; Tollman, Stephen; Lopez, Alan D; Vos, Theo

    2014-01-01

    Background: South African civil registration (CR) provides a key data source for local health decision making, and informs the levels and causes of mortality in data-lacking sub-Saharan African countries. We linked mortality data from CR and the Agincourt Health and Socio-demographic Surveillance System (Agincourt HDSS) to examine the quality of rural CR data. Methods: Deterministic and probabilistic techniques were used to link death data from 2006 to 2009. Causes of death were aggregated into the WHO Mortality Tabulation List 1 and a locally relevant short list of 15 causes. The matching rate was compared with informant-reported death registration. Using the VA diagnoses as reference, misclassification patterns, sensitivity, positive predictive values and cause-specific mortality fractions (CSMFs) were calculated for the short list. Results: A matching rate of 61% [95% confidence interval (CI): 59.2 to 62.3] was attained, lower than the informant-reported registration rate of 85% (CI: 83.4 to 85.8). For the 2264 matched cases, cause agreement was 15% (kappa 0.1083, CI: 0.0995 to 0.1171) for the WHO list, and 23% (kappa 0.1631, CI: 0.1511 to 0.1751) for the short list. CSMFs were significantly different for all but four (tuberculosis, cerebrovascular disease, other heart disease, and ill-defined natural) of the 15 causes evaluated. Conclusion: Despite data limitations, it is feasible to link official CR and HDSS verbal autopsy data. Data linkage proved a promising method to provide empirical evidence about the quality and utility of rural CR mortality data. Agreement of individual causes of death was low but, at the population level, careful interpretation of the CR data can assist health prioritization and planning. PMID:25146564

  14. The Oxford Guide to the History of Physics and Astronomy

    NASA Astrophysics Data System (ADS)

    Heilbron, John L.

    2005-06-01

    With over 150 alphabetically arranged entries about key scientists, concepts, discoveries, technological innovations, and learned institutions, the Oxford Guide to Physics and Astronomy traces the history of physics and astronomy from the Renaissance to the present. For students, teachers, historians, scientists, and readers of popular science books such as Galileo's Daughter , this guide deciphers the methods and philosophies of physics and astronomy as well as the historical periods from which they emerged. Meant to serve the lay reader and the professional alike, this book can be turned to for the answer to how scientists learned to measure the speed of light, or consulted for neat, careful summaries of topics as complicated as quantum field theory and as vast as the universe. The entries, each written by a noted scholar and edited by J. L. Heilbron, Professor of History and Vice Chancellor, Emeritus, University of California, Berkeley, reflect the most up-to-date research and discuss the applications of the scientific disciplines to the wider world of religion, law, war, art and literature. No other source on these two branches of science is as informative or as inviting. Thoroughly cross-referenced and accented by dozens of black and white illustrations, the Oxford Guide to Physics and Astronomy is the source to turn to for anyone looking for a quick explanation of alchemy, x-rays and any type of matter or energy in between.

  15. Some aspects of management and outcome of acute coronary heart disease in Oxford region.

    PubMed Central

    Acheson, R M; Sanderson, C

    1977-01-01

    (1) Over 15 months, 532 consecutive admissions to the CCU at the Radcliffe Oxford were studied; of these 333 were cases of myocardial infarction, and 319 were first admissions for this condition. Information about survival and return to work was collected for 300. A further 30 had artificial pacemakers inserted; there were 141 (26%) of the 532 cases which did not require the special care offered by the CCU. (2) Of 300 patients for whom data were available, 27 were recorded as having received DC shock. In hospital, case fatality was significantly higher among those requiring DC shock than among the remainder. Overall the 3-year survival rates were 47 per cent among those receiving shock, and 62 per cent among the remainder, compared with an expected 91 per cent for a population of the same age and sex. (3) Among men aged under 65 years, 6 of 11 who received shock, compared with 117 (77%) who did not receive shock, returned to work after leaving hospital. (4) Rates of admission to the CCU of cases of myocardial infarction per 1000 standardised population among people living in the areas around Oxford City were estimated as being 58 per cent of admission rates of cases among residents of the city. (5) The case incidence of ventricular fibrillation and the case fatality rate were both higher among those living in the environs than among those living in the city, but these differences were not statistically significant. (6) It is also concluded that insufficient is known about the factors underlying the general practitioner's decision to commit a case of myocardial infarction to other than short ambulance journeys or about the effects of such journeys on prognosis. PMID:831741

  16. From Oxford to Hawaii ecophysiological barriers limit human progression in ten sport monuments.

    PubMed

    Desgorces, François-Denis; Berthelot, Geoffroy; El Helou, Nour; Thibault, Valérie; Guillaume, Marion; Tafflet, Muriel; Hermine, Olivier; Toussaint, Jean-François

    2008-01-01

    In order to understand the determinants and trends of human performance evolution, we analyzed ten outdoor events among the oldest and most popular in sports history. Best performances of the Oxford-Cambridge boat race (since 1836), the channel crossing in swimming (1875), the hour cycling record (1893), the Elfstedentocht speed skating race (1909), the cross country ski Vasaloppet (1922), the speed ski record (1930), the Streif down-hill in Kitzbühel (1947), the eastward and westward sailing transatlantic records (1960) and the triathlon Hawaii ironman (1978) all follow a similar evolutive pattern, best described through a piecewise exponential decaying model (r(2) = 0.95+/-0.07). The oldest events present highest progression curvature during their early phase. Performance asymptotic limits predicted from the model may be achieved in fourty years (2049+/-32 y). Prolonged progression may be anticipated in disciplines which further rely on technology such as sailing and cycling. Human progression in outdoor sports tends to asymptotic limits depending on physiological and environmental parameters and may temporarily benefit from further technological progresses.

  17. From Oxford to Hawaii Ecophysiological Barriers Limit Human Progression in Ten Sport Monuments

    PubMed Central

    Desgorces, François-Denis; Berthelot, Geoffroy; El Helou, Nour; Thibault, Valérie; Guillaume, Marion; Tafflet, Muriel; Hermine, Olivier; Toussaint, Jean-François

    2008-01-01

    In order to understand the determinants and trends of human performance evolution, we analyzed ten outdoor events among the oldest and most popular in sports history. Best performances of the Oxford-Cambridge boat race (since 1836), the channel crossing in swimming (1875), the hour cycling record (1893), the Elfstedentocht speed skating race (1909), the cross country ski Vasaloppet (1922), the speed ski record (1930), the Streif down-hill in Kitzbühel (1947), the eastward and westward sailing transatlantic records (1960) and the triathlon Hawaii ironman (1978) all follow a similar evolutive pattern, best described through a piecewise exponential decaying model (r2 = 0.95±0.07). The oldest events present highest progression curvature during their early phase. Performance asymptotic limits predicted from the model may be achieved in fourty years (2049±32 y). Prolonged progression may be anticipated in disciplines which further rely on technology such as sailing and cycling. Human progression in outdoor sports tends to asymptotic limits depending on physiological and environmental parameters and may temporarily benefit from further technological progresses. PMID:18985149

  18. The Oxford scanning proton microprobe: A medical diagnostic application

    NASA Astrophysics Data System (ADS)

    Watt, F.; Grime, G. W.; Takacs, J.; Vaux, D. J. T.

    1984-04-01

    Primary biliary cirrhosis (PBC) is a disease characterised by progressive destruction of small intrahepatic bile ducts, cholestasis, and high levels of copper within the liver. The Oxford 1 μm scanning proton microprobe (SPM) has been used to construct elemental maps of a 7 μm section of diseased liver at several different magnifications. The results of these investigations have shown that the copper is distributed in small deposits ( < 5 μm) at specific locations in the liver. Further there appears to be a 1:1 atomic correlation between copper and sulphur, indicating the presence of an inorganic salt or a protein with approximately equal numbers of copper and sulphur atoms.

  19. Two Oxford science professors, F. Soddy and J. S. E. Townsend.

    PubMed

    Bleaney, B

    2002-01-01

    Recounts some anecdotes about Frederick Soddy (1877-1956), a professor of chemistry at Oxford University between 1919 and 1936, and Sir John Townsend (1868-1957), Wykeham Professor of Physics at Oxford between 1900 and 1941. The anecdotes flesh out the human portraits of the two scientists, indicating, among other things, Soddy's capacity for intellectual quarrels and Townsend's sometimes forgetful nature.

  20. Holocene climate change evidence from high-resolution loess/paleosol records and the linkage to fire-climate change-human activities in the Horqin dunefield in northern China

    NASA Astrophysics Data System (ADS)

    Mu, Yan; Qin, Xiaoguang; Zhang, Lei; Xu, Bing

    2016-05-01

    The combination of high-resolution sedimentary paleoclimate proxies of total organic carbon and magnetic susceptibility of a loess/paleosol section with black carbon (BC) records provides us with information about climate change and the linkage of fire-climate change-vegetation-human activities in the Horqin dunefield over the past 11,600 cal yr BP. We found that during 11,600-8000 cal yr BP (the early Holocene), the area was dominated by a dry climate. The vegetation coverage was low, which limited the extent of fire. The Holocene optimum can be placed between 8000 and 3200 cal yr BP, and during this period, anthropogenic fire was a key component of total fire occurrence as the intensity of human activity increased. The development of agricultural activities and the growing population during this period increased the use of fire for cooking food and burning for cultivation and land fertilization purposes. During 2800-2600 cal yr BP, a warm/moister climate prevailed and was associated with a high degree of pedogenesis and vegetation cover density, evident at 2700 cal yr BP. Fires may have contributed to human survival by enabling the cooking of food in the warm and wet climate. In the period since 2000 cal yr BP, fires linked to agriculture may have led to increased biomass burning associated with agricultural activity.

  1. Linkage results in Schizophrenia

    SciTech Connect

    Baron, M.

    1996-04-09

    In setting a model for replication studies, the collective effort by the various investigators is praiseworthy. The linkage reported is intriguing, but given the aforementioned caveats it would be premature to dub it {open_quotes}significant -- and, probably, confirmed.{close_quotes} The extent to which a real genetic effect exists on chromosome 6p24-22 remains to be seen. Compelling confirmation, which further study might proffer, would be a welcome boost to a fledgling enterprise, where other findings of promise have faltered or failed to gain unequivocal support. The caution advised in this commentary may guide the design and interpretation of other linkage studies in psychiatric disorders.

  2. The 'gender gap' in final examination results at Oxford University.

    PubMed

    Mellanby, J; Martin, M; O'Doherty, J

    2000-08-01

    A lower proportion of women than men obtain first class degrees at British universities (the so-called gender gap). At Oxford University, this difference is not seen in all degree subjects but is found both in some Arts and in some Science subjects. We have used a questionnaire administered under supervision to undergraduates 2 to 3 months before their final examination to assess factors which might be expected to affect examination performance. These included measures of verbal and non-verbal reasoning (Alice Heim AH6 test), self-esteem, motivation, responses to stresses of examinations and of personal relationships, happiness, risk-taking and working patterns. We have also obtained a detailed breakdown of the marks the students were given in the examination. Women scored higher on negative emotions while men scored higher on self-esteem, their perception of their own academic efficacy and on risk-taking strategies, but none of these factors predicted outcome. Verbal reasoning ability did predict outcome but there was no gender difference. Hence, it is concluded that the gender gap is not due to any of these individual differences and is more likely to be related to the nature of the academic assessment system.

  3. A gift from Oxford: the Osler-Thomas connection.

    PubMed

    Golden, Richard L

    2012-10-01

    In June 1926, Dr. Henry M. Thomas Jr. ("Hal") received as a gift from Grace Osler in Oxford an Einhorn Duodenal Bucket Set that had belonged to Sir William Osler. The Thomases were a distinguished multigenerational physician family of Baltimore with high educational standards and major accomplishments in medicine and medical education. An extraordinary number of the Thomas women earned doctorates and made significant contributions in an era when this was a pioneering achievement. This is exemplified by Martha Carey Thomas, who earned a PhD in 1882 and served as dean and president of Bryn Mawr College for women. As a leading feminist and member of the Women's Fund Committee, she was a major force in providing the endowment that permitted the opening of the Johns Hopkins School of Medicine under the strict stipulations that admission requirements include an undergraduate degree and that women be admitted on the basis of total equality with men. Osler established relationships that extended over three generations of the Thomas family during his Baltimore tenure, an influence that proved mutually beneficial. PMID:23077379

  4. A gift from Oxford: the Osler-Thomas connection

    PubMed Central

    2012-01-01

    In June 1926, Dr. Henry M. Thomas Jr. (“Hal”) received as a gift from Grace Osler in Oxford an Einhorn Duodenal Bucket Set that had belonged to Sir William Osler. The Thomases were a distinguished multigenerational physician family of Baltimore with high educational standards and major accomplishments in medicine and medical education. An extraordinary number of the Thomas women earned doctorates and made significant contributions in an era when this was a pioneering achievement. This is exemplified by Martha Carey Thomas, who earned a PhD in 1882 and served as dean and president of Bryn Mawr College for women. As a leading feminist and member of the Women's Fund Committee, she was a major force in providing the endowment that permitted the opening of the Johns Hopkins School of Medicine under the strict stipulations that admission requirements include an undergraduate degree and that women be admitted on the basis of total equality with men. Osler established relationships that extended over three generations of the Thomas family during his Baltimore tenure, an influence that proved mutually beneficial. PMID:23077379

  5. Transitions and Linkages.

    ERIC Educational Resources Information Center

    Ilfeld, Ellen M., Ed.; Hanssen, Elizabeth, Ed.

    1997-01-01

    If children are to benefit from a healthy, supportive early childhood experience, it is important to strengthen transitions between early childhood experiences in educational and care settings and the more formal educational system. This issue of Coordinator's Notebook focuses on strengthening linkages and transitions between home, preschool, and…

  6. Validation of the Oxford Participation and Activities Questionnaire

    PubMed Central

    Morley, David; Dummett, Sarah; Kelly, Laura; Dawson, Jill; Fitzpatrick, Ray; Jenkinson, Crispin

    2016-01-01

    Purpose There is growing interest in the management of long-term conditions and in keeping people active and participating in the community. Testing the effectiveness of interventions that aim to affect activities and participation can be challenging without a well-developed, valid, and reliable instrument. This study therefore aims to develop a patient-reported outcome measure, the Oxford Participation and Activities Questionnaire (Ox-PAQ), which is theoretically grounded in the World Health Organization’s International Classification of Functioning, Disability, and Health (ICF) and fully compliant with current best practice guidelines. Methods Questionnaire items generated from patient interviews and based on the nine chapters of the ICF were administered by postal survey to 386 people with three neurological conditions: motor neuron disease, multiple sclerosis, and Parkinson’s disease. Participants also completed the Medical Outcomes Study (MOS) 36-Item Short Form Health Survey (SF-36) and EQ-5D-5L. Results Thus, 334 participants completed the survey, a response rate of 86.5%. Factor analysis techniques identified three Ox-PAQ domains, consisting of 23 items, accounting for 72.8% of variance. Internal reliability for the three domains was high (Cronbach’s α: 0.81–0.96), as was test–retest reliability (intraclass correlation: 0.83–0.92). Concurrent validity was demonstrated through highly significant relationships with relevant domains of the MOS SF-36 and the EQ- 5D-5L. Assessment of known-groups validity identified significant differences in Ox-PAQ scores among the three conditions included in the survey. Conclusion Results suggest that the Ox-PAQ is a valid and reliable measure of participation and activity. The measure will now be validated in a range of further conditions, and additional properties, such as responsiveness, will also be assessed in the next phase of the instrument’s development. PMID:27366108

  7. Linkage map integration

    SciTech Connect

    Collins, A.; Teague, J.; Morton, N.E.; Keats, B.J.

    1996-08-15

    The algorithms that drive the map+ program for locus-oriented linkage mapping are presented. They depend on the enhanced location database program ldb+ to specify an initial comprehensive map that includes all loci in the summary lod file. Subsequently the map may be edited or order constrained and is automatically improved by estimating the location of each locus conditional on the remainder, beginning with the most discrepant loci. Operating characteristics permit rapid and accurate construction of linkage maps with several hundred loci. The map+ program also performs nondisjunction mapping with tests of nonstandard recombination. We have released map+ on Internet as a source program in the C language together with the location database that now includes the LODSOURCE database. 28 refs., 5 tabs.

  8. Physics in Oxford, 1839-1939 - Laboratories, Learning, and College Life

    NASA Astrophysics Data System (ADS)

    Fox, Robert; Gooday, Graeme

    2005-08-01

    Physics in Oxford 1839-1939 offers a challenging new interpretation of pre-war physics at the University of Oxford, which was far more dynamic than most historians and physicists have been prepared to believe. It explains, on the one hand, how attempts to develop the University's Clarendon Laboratory by Robert Clifton, Professor of Experimental Philosophy from 1865 to 1915, were thwarted by academic politics and funding problems, and latterly by Clifton's idiosyncratic concern with precision instrumentation. Conversely, by examining in detail the work of college fellows and their laboratories, the book reconstructs the decentralized environment that allowed physics to enter on a period of conspicuous vigor in the late nineteenth and early twentieth centuries, especially at the characteristically Oxonian intersections between physics, physical chemistry, mechanics, and mathematics. Whereas histories of Cambridge physics have tended to focus on the self-sustaining culture of the Cavendish Laboratory, it was Oxford's college-trained physicists who enabled the discipline to flourish in due course in university as well as college facilities, notably under the newly appointed professors, J. S. E. Townsend from 1900 and F. A. Lindemann from 1919. This broader perspective allows us to understand better the vitality with which physicists in Oxford responded to the demands of wartime research on radar and techniques relevant to atomic weapons and laid the foundations for the dramatic post-war expansion in teaching and research that has endowed Oxford with one of the largest and most dynamic schools of physics in the world.

  9. A YANKEE AT OXFORD: JOHN WILLIAM DRAPER AT THE BRITISH ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE AT OXFORD, 30 JUNE 1860.

    PubMed

    Ungureanu, James C

    2016-06-20

    This paper contributes to the revisionist historiography on the legendary encounter between Samuel Wilberforce and Thomas Henry Huxley at the 1860 meeting in Oxford of the British Association for the Advancement of Science. It discusses the contents of a series of letters written by John William Draper and his family reflecting on his experience at that meeting. The letters have recently been rediscovered and have been neither published nor examined at full length. After a preliminary discussion on the historiography of the Oxford debate, the paper discloses the contents of the letters and then assesses them in the light of other contemporary accounts. The letters offer a nuanced reinterpretation of the event that supports the growing move towards a revisionist account. PMID:27386714

  10. LINKAGE programs: linkage analysis for monogenic cardiovascular diseases.

    PubMed

    Li, Lin; Wang, Qing K; Rao, Shaoqi

    2006-01-01

    Identification of the genes for a human disease provides significant insights into the molecular mechanism underlying the pathogenesis of the disease. A human disease gene can be identified by its chromosomal location (positional cloning). Linkage analysis is a key step in positional cloning. For monogenic disorders with a known inheritance pattern, model-based linkage analysis is effective in mapping the disease location. Therefore, model-based linkage analysis can provide a powerful tool to positional cloning of some specific molecular determinants that co-segregate with disease phenotypes in the isolated samples (e.g., large and multiplex impaired pedigrees). This chapter describes model-based human genetic linkage analysis as implemented in the LINKAGE computer package. First, we introduce the basic concepts and principles for genetic analysis of monogenic disorders. Then, we demonstrate the usages of the programs by analyzing several examples of hypothetical pedigrees with the inheritance modes of autosomal-dominant, autosomal-recessive, and genetic heterogeneity. PMID:17071989

  11. Apprenticeship - School Linkage Implementation Manual.

    ERIC Educational Resources Information Center

    Martin, Sharon T.; And Others

    Developed to assist interested sponsors in implementing apprenticeship-school linkage projects, this guide is intended to organize the collective experiences of those who have implemented the demonstration projects to highlight the day-to-day mechanics involved. Section 1 overviews apprenticeship-school linkage. In section 2 factors are described…

  12. Developing a Structured Teaching Plan for Psychiatry Tutors at Oxford University

    ERIC Educational Resources Information Center

    Al-Taiar, Hasanen

    2014-01-01

    Purpose: The purpose of this thesis was to examine the teaching ways I undertook in teaching medical students and to examine the use of a structured teaching plan for the academic and clinical tutors in psychiatry. The teaching plan was developed for use, initially by Oxford University Academic tutors at the Department of Psychiatry. In addition,…

  13. If You Build It, They Will Scan: Oxford University's Exploration of Community Collections

    ERIC Educational Resources Information Center

    Lee, Stuart D.; Lindsay, Kate

    2009-01-01

    Traditional large digitization projects demand massive resources from the central unit (library, museum, or university) that has acquired funding for them. Another model, enabled by easy access to cameras, scanners, and web tools, calls for public contributions to community collections of artifacts. In 2009, the University of Oxford ran a…

  14. Making Academic OER Easy: Reflections on Technology and Openness at Oxford University

    ERIC Educational Resources Information Center

    Highton, Melissa; Fresen, Jill; Wild, Joanna

    2011-01-01

    Due to its stringent entry requirements, academic reputation and world ranking, Oxford University in the United Kingdom is perceived by some as being a closed, exclusive, and elitist institution. As learning technologists working in the institution, we have experienced an enthusiasm amongst academic colleagues for openness in publication and…

  15. Teacher Education at Oxford University: James Is Alive but Living in Karachi

    ERIC Educational Resources Information Center

    Pring, Richard

    2008-01-01

    The arguments at Oxford about the start of teacher education within the University have been repeated many times and in many ways, not least in the 1972 James Committee. The strong advocacy there for much greater attention to, and investment in, continuing professional development may not have won the day in England, but, through the influence of…

  16. Software for relativistic atomic structure theory: The grasp project at oxford

    SciTech Connect

    Parpia, F.A.; Grant, I.P. )

    1991-08-05

    GRASP is an acronym for General-purpose Relativistic Atomic Structure Program. The objective of the GRASP project at Oxford is to produce user-friendly state-of-the-art multiconfiguration Dirac-Fock (MCDF) software packages for rleativistic atomic structure theory.

  17. Critical Thinking in the Oxford Tutorial: A Call for an Explicit and Systematic Approach

    ERIC Educational Resources Information Center

    Cosgrove, Rush

    2011-01-01

    This paper summarises a study focusing on the extent to which the Oxford tutorial fosters critical thinking in students. In doing so, it aims to contribute to a largely ignored area of research regarding teaching pedagogy and classroom practice. The results of this study successfully reveal that participating tutors were primarily concerned with…

  18. Mathematics Education. Anglo-Soviet Seminar (1st, Oxford, England, September 8-16, 1981).

    ERIC Educational Resources Information Center

    Wilson, Bryan, Ed.

    This report presents 23 papers prepared for the first Anglo-Soviet Seminar on Mathematics Education, held in Oxford in September 1981. Ten leading British mathematics educators met with six Soviet participants for an intensive program of information sharing and discussion which covered the teaching and learning of mathematics at all school levels.…

  19. The Why, What, and Impact of GPA at Oxford Brookes University

    ERIC Educational Resources Information Center

    Andrews, Matthew

    2016-01-01

    This paper examines the introduction at Oxford Brookes University of a Grade Point Average (GPA) scheme alongside the traditional honours degree classification. It considers the reasons for the introduction of GPA, the way in which the scheme was implemented, and offers an insight into the impact of GPA at Brookes. Finally, the paper considers…

  20. Evaluating "Blair's Educational Legacy?": Some Comments on the Special Issue of "Oxford Review of Education"

    ERIC Educational Resources Information Center

    Whitty, Geoff

    2009-01-01

    The December 2008 special issue of the "Oxford Review of Education" provided a review of education policy during Tony Blair's tenure as Prime Minister. This paper forms a response to the ten contributions to that special issue and discusses some of the issues raised in them. While a few positive aspects of education under New Labour were…

  1. 75 FR 52484 - Proposed Removal and Amendment of Class E Airspace, Oxford, CT

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-26

    ...; (2) is not a ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February...: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389... amend Class E airspace extending upward from 700 feet at Oxford, CT. Decommissioning of the...

  2. Lessons from the Round Table: Literacy Professionals Find Common Ground in Oxford

    ERIC Educational Resources Information Center

    Paterson, Wendy A.

    2007-01-01

    In July, 2006, Literacy Professionals from across the United States met at Lady Margaret College in Oxford University to discuss research and practice in the teaching of reading and the expansion of literacy. In a tense national climate, reading researchers refer to contrasting theories of teaching reading as "the reading wars," but at…

  3. Grammar Coding in the "Oxford Advanced Learner's Dictionary of Current English."

    ERIC Educational Resources Information Center

    Wekker, Herman

    1992-01-01

    Focuses on the revised system of grammar coding for verbs in the fourth edition of the "Oxford Advanced Learner's Dictionary of Current English" (OALD4), comparing it with two other similar dictionaries. It is shown that the OALD4 is found to be more favorable on many criteria than the other comparable dictionaries. (16 references) (VWL)

  4. When Tradition Meets Modern Law: Changing the Role of the Oxford University Proctors

    ERIC Educational Resources Information Center

    Walford, Geoffrey

    2004-01-01

    This article discusses the changes in statutes that were necessary to ensure that the duties and responsibilities of the ancient post of proctor at Oxford University were brought into line with the Human Rights Act 1998. As there is no other university with a similarly powerful proctorial system, the changes in legislation may seem to be of only…

  5. Fairness and Undergraduate Admission: A Qualitative Exploration of Admissions Choices at the University of Oxford

    ERIC Educational Resources Information Center

    Zimdars, Anna

    2010-01-01

    The article investigates unequal admissions patterns at the University of Oxford. Statistical work shows differences in admission rates by social class, ethnicity, gender, qualification status and secondary schooling. In-depth interviews with admissions tutors, college and university officials and observations of eight admissions meetings provide…

  6. Deliberate Self-Harm in Adolescents in Oxford, 1985-1995.

    ERIC Educational Resources Information Center

    Hawton, Keith; Fagg, Joan; Simkin, Sue; Bale, Elizabeth; Bond, Alison

    2000-01-01

    Reviews data collected by the Oxford Monitoring System for Attempted Suicide in teenagers between 1985-1995 to determine trends in acts of deliberate self-harm. Notes substantial increase in number of episodes of deliberate self-harm for both males and females. Discusses implications for hospital and counseling professionals and well as…

  7. Personal miniature electrophysiological tape recorder

    NASA Astrophysics Data System (ADS)

    Green, H.

    1981-11-01

    The use of a personal miniature electrophysiological tape recorder to measure the physiological reactions of space flight personnel to space flight stress and weightlessness is described. The Oxford Instruments Medilog recorder, a battery-powered, four-channel cassette tape recorder with 24 hour endurance is carried on the person and will record EKG, EOG, EEG, and timing and event markers. The data will give information about heart rate and morphology changes, and document adaptation to zero gravity on the part of subjects who, unlike highly trained astronauts, are more representative of the normal population than were the subjects of previous space flight studies.

  8. Personal miniature electrophysiological tape recorder

    NASA Technical Reports Server (NTRS)

    Green, H.

    1981-01-01

    The use of a personal miniature electrophysiological tape recorder to measure the physiological reactions of space flight personnel to space flight stress and weightlessness is described. The Oxford Instruments Medilog recorder, a battery-powered, four-channel cassette tape recorder with 24 hour endurance is carried on the person and will record EKG, EOG, EEG, and timing and event markers. The data will give information about heart rate and morphology changes, and document adaptation to zero gravity on the part of subjects who, unlike highly trained astronauts, are more representative of the normal population than were the subjects of previous space flight studies.

  9. Exploring linkage disequilibrium.

    PubMed

    Baird, Stuart J E

    2015-09-01

    Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton ). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles ). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al. ). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD. PMID:26261040

  10. Higher Education: Labor Market Linkage.

    ERIC Educational Resources Information Center

    Asayeghn, Desta

    1982-01-01

    Examines the methodology of three case studies investigating the linkage between higher education and the world of work in the Sudan, Zambia, and Tanzania. Summarizes 12 main findings. Suggests the studies remain traditional human resources planning efforts. (NEC)

  11. Linkages in thermal copolymers of lysine

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Suzuki, F.

    1975-01-01

    The thermal copolymerization of lysine with other alpha-amino acids was studied. The identity of the second amino acid influences various properties of the polymer obtained, including the proportion of alpha and epsilon linkages of lysine. A review of linkages in proteinoids indicates alpha and beta linkages for aspartic acid, alpha and gamma linkages for glutamic acid, alpha and epsilon linkages for lysine, and alpha linkages for other amino acids. Thermal proteinoids are thus more complex in types of linkage than are proteins.

  12. The results of Oxford unicompartmental knee arthroplasty in the United States

    PubMed Central

    Emerson, R. H.; Alnachoukati, O.; Barrington, J.; Ennin, K.

    2016-01-01

    Aims Approved by the Food and Drug Administration in 2004, the Phase III Oxford Medial Partial Knee is used to treat anteromedial osteoarthritis (AMOA) in patients with an intact anterior cruciate ligament. This unicompartmental knee arthroplasty (UKA) is relatively new in the United States, and therefore long-term American results are lacking. Patients and Methods This is a single surgeon, retrospective study based on prospectively collected data, analysing a consecutive series of primary UKAs using the Phase III mobile-bearing Oxford Knee and Phase III instrumentation. Between July 2004 and December 2006, the senior author (RHE) carried out a medial UKA in 173 patients (213 knees) for anteromedial osteoarthritis or avascular necrosis (AVN). A total of 95 patients were men and 78 were women. Their mean age at surgery was 67 years (38 to 89) and mean body mass index 29.87 kg/m2 (17 to 62). The mean follow-up was ten years (4 to 11). Results Survivorship of the Oxford UKA at ten years was 88%, using life table analysis. Implant survivorship at ten years was 95%. The most common cause for revision was the progression of osteoarthritis in the lateral compartment. The mean knee score element of the American Knee Society Score (AKSS) was 50 pre-operatively and increased to 93 post-operatively. The mean AKSS function score was 56 pre-operatively rising to 78 post-operatively Conclusion This ten-year follow-up study of the Oxford UKA undertaken in the United States shows good survivorship and excellent function in a wide selection of patients with AMOA and AVN. Cite this article: Bone Joint J 2016;98-B(10 Suppl B):34–40. PMID:27694514

  13. Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.

    PubMed

    Deschamps, Stéphane; Mudge, Joann; Cameron, Connor; Ramaraj, Thiruvarangan; Anand, Ajith; Fengler, Kevin; Hayes, Kevin; Llaca, Victor; Jones, Todd J; May, Gregory

    2016-01-01

    The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) "2D" sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy. PMID:27350167

  14. The epidemiology of attempted suicide in the Oxford area, England (1989-1992).

    PubMed

    Hawton, K; Fagg, J; Simkin, S; Mills, J

    1994-01-01

    The epidemiological and clinical characteristics of attempted suicide in Oxford, United Kingdom, between 1989 and 1992 are reported on the basis of data collected as part of the WHO/EURO Multicentre Study of Parasuicide in Europe. Some further findings for the period 1976-1992 are also described. Rates of attempted suicide were particularly high among females aged 15-19 years. There was a very marked association in males and females between attempted suicide and both lower socioeconomic status and unemployment. The percentage of first-time attempters entering the attempted suicide population remained steady between 1976 and 1992, with approximately two-thirds of attempters each year making their first attempts. There was a great increase in the use of paracetamol (acetominophen) for self-poisoning between 1976 and 1992, this being involved in 14.3% of overdoses in 1976 and 43.2% in 1992. On the basis of the Oxford rates, there are approximately 100,000 general hospital admissions for attempted suicide each year in England and Wales, approximately 19,000 involving teenagers (mostly girls). Oxford has a similar pattern of attempted suicide to that in the rest of the UK. The findings indicate that the UK has one of the highest rates of attempted suicide in Europe. PMID:7859480

  15. Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

    PubMed Central

    Deschamps, Stéphane; Mudge, Joann; Cameron, Connor; Ramaraj, Thiruvarangan; Anand, Ajith; Fengler, Kevin; Hayes, Kevin; Llaca, Victor; Jones, Todd J.; May, Gregory

    2016-01-01

    The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) “2D” sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy. PMID:27350167

  16. Data linkage infrastructure for cross-jurisdictional health-related research in Australia

    PubMed Central

    2012-01-01

    Background The Centre for Data Linkage (CDL) has been established to enable national and cross-jurisdictional health-related research in Australia. It has been funded through the Population Health Research Network (PHRN), a national initiative established under the National Collaborative Research Infrastructure Strategy (NCRIS). This paper describes the development of the processes and methodology required to create cross-jurisdictional research infrastructure and enable aggregation of State and Territory linkages into a single linkage “map”. Methods The CDL has implemented a linkage model which incorporates best practice in data linkage and adheres to data integration principles set down by the Australian Government. Working closely with data custodians and State-based data linkage facilities, the CDL has designed and implemented a linkage system to enable research at national or cross-jurisdictional level. A secure operational environment has also been established with strong governance arrangements to maximise privacy and the confidentiality of data. Results The development and implementation of a cross-jurisdictional linkage model overcomes a number of challenges associated with the federated nature of health data collections in Australia. The infrastructure expands Australia’s data linkage capability and provides opportunities for population-level research. The CDL linkage model, infrastructure architecture and governance arrangements are presented. The quality and capability of the new infrastructure is demonstrated through the conduct of data linkage for the first PHRN Proof of Concept Collaboration project, where more than 25 million records were successfully linked to a very high quality. Conclusions This infrastructure provides researchers and policy-makers with the ability to undertake linkage-based research that extends across jurisdictional boundaries. It represents an advance in Australia’s national data linkage capabilities and sets the scene

  17. Education: Linkages with Economic Development.

    ERIC Educational Resources Information Center

    Clouser, Rodney L.

    A review of the literature of research in education and economics revealed very limited linkages between education (human capital) and economic development. Much of the economic development research has been carried out in developing nations and is case-study based. Many case studies concentrate on identifying factors that influence location or…

  18. Increasing use of private practice by patients in Oxford requiring common elective surgical operations.

    PubMed Central

    McPherson, K; Coulter, A; Stratton, I

    1985-01-01

    A random sample of 6000 people from eight general practices in and around Oxford was studied to ascertain their surgical histories and method of care received. The proportion of operations that were performed privately had increased with time and had a steep gradient according to social class. Different procedures had different likelihoods of being performed privately, but the age and sex of the patient had a non-significant association with private surgery. Adjustment for possible confounding variables using logistic analysis indicated that in the 1980s elective surgery is five times more likely to be performed privately than it was at the institution of the National Health Service. PMID:3929946

  19. Legal impediments to data linkage.

    PubMed

    Xafis, V; Thomson, C; Braunack-Mayer, A J; Duszynski, K M; Gold, M S

    2011-12-01

    Large numbers of electronic health data collections have been accumulated by both government and non-government agencies and organisations. Such collections primarily assist with the management of health services and the provision of health care programs, with only a minority of these data collections also intended for research purposes. A number of constraints are placed on access to such data for the purposes of research, including data linkage. This article examines those factors arising from the intricacies of Australia's privacy legislation landscape which impede access to such collections. The relevant issues discussed include issues relating to the existence of multiple privacy and health privacy Acts, the recommendations made by the Australian Law Reform Commission in relation to the Privacy Act 1988 (Cth) and the constraints placed on the conduct of data-linkage research which arise from legislation that relates specifically to certain data collections.

  20. Emissivity Measurements and Laboratory Intercalibration at PSF of Oxford University and PEL of DLR

    NASA Astrophysics Data System (ADS)

    Maturilli, A.; Bowles, N. E.; Thomas, I. R.; Helbert, J.

    2013-09-01

    Emissivity spectra of analogue materials are needed for the analysis of remote sensing emission spectra of airless surfaces. The increasing number of planetary missions to the Moon, Mercury, asteroids, and other minor bodies require appropriate laboratory set-ups to fulfill those requirements. Two independent groups, one at Oxford University and the other at the German Aerospace Center (DLR) in Berlin provide suitable chambers for emissivity measurements in vacuum. The Planetary Spectroscopy Facility (PSF) of the Oxford University favored a high vacuum, low to average sample temperatures, and a limited spectral range for measurements, mostly inspired from lunar and asteroids environment. At the Planetary Emissivity Laboratory (PEL) of DLR, the set-up allows measuring in low-moderate vacuum, for sample temperatures from low to very high (> 1000 K) and in an extended spectral range (1 to over 100μm), with Mercury being the principal driver of chamber design. To understand the influence of environment parameters on emissivity spectra, we measured a fine (0-25 μm) sample of volcanic dust from Iceland (PEL ID 00000240) under several environmental conditions at PSF, and for comparison under standard conditions at PEL.

  1. Proteinases, their receptors and inflammatory signalling: the Oxford South Parks Road connection*

    PubMed Central

    Hollenberg, M D

    2015-01-01

    In keeping with the aim of the Paton Memorial Lecture to ‘facilitate the historical study of pharmacology’, this overview, which is my distinct honour to write, represents a ‘Janus-like’ personal perspective looking both backwards and forwards at the birth and growth of ‘receptor molecular pharmacology’ with special relevance to inflammatory diseases. The overview begins in the Oxford Department of Pharmacology in the mid-1960s and then goes on to provide a current perspective of signalling by proteinases. Looking backwards, the synopsis describes the fruitful Oxford Pharmacology Department infrastructure that Bill Paton generated in keeping with the blueprint begun by his predecessor, J H Burn. Looking forwards, the overview illustrates the legacy of that environment in generating some of the first receptor ligand-binding data and providing the inspiration and vision for those like me who were training in the department at the same time. With apologies, I mention only in passing a number of individuals who benefitted from the ‘South Parks Road connection’ using myself as one of the ‘outcome study’ examples. It is also by looking forward that I can meet the complementary aim of summarizing the lecture presented at a ‘BPS 2014 Focused Meeting on Cell Signalling’ to provide an overview of the role of proteinases and their signalling mechanisms in the setting of inflammation. PMID:25521749

  2. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

    PubMed Central

    Goodwin, Sara; Gurtowski, James; Ethe-Sayers, Scott; Deshpande, Panchajanya; Schatz, Michael C.; McCombie, W. Richard

    2015-01-01

    Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5–50 kbp) at such high error rates (between ∼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly. PMID:26447147

  3. Personal exposures and microenvironment concentrations of PM 2.5, VOC, NO 2 and CO in Oxford, UK

    NASA Astrophysics Data System (ADS)

    Lai, H. K.; Kendall, M.; Ferrier, H.; Lindup, I.; Alm, S.; Hänninen, O.; Jantunen, M.; Mathys, P.; Colvile, R.; Ashmore, M. R.; Cullinan, P.; Nieuwenhuijsen, M. J.

    Between 1998 and 2000 in Oxford, UK, simultaneous personal exposures and microenvironmental measurements (home indoor, home outdoor and work indoor) to fine particulate matters PM 2.5, volatile organic compounds (VOC), nitrogen dioxide (NO 2) and carbon monoxide (CO) were carried out once per person among 50 adults over a 48-h period. Thirty-seven elements in PM 2.5 and 30 different VOCs were analysed. Questionnaires were distributed to record their time-activity patterns and exposure-related information. Results showed that participants spent more time (89.5%) in all indoors than in other microenvironments. Geometric mean (GM) of personal and home indoor levels of PM 2.5, 14 elements (aluminium, arsenic, bromine, calcium, copper, iron, gallium, potassium, sodium, phosphorus, lead, selenium, silicon, titanium), total VOC (TVOC) and 8 individual compounds (nonane, decane, undecane, trimethylbenzene, toluene, benzaldehyde, alpha-pinene and d-limonene) were over 20% higher than their GM outdoor levels. Those of NO 2, 5 aromatic VOCs (benzene, o-xylene, ethylbenzene, propylbenzene, m, p-xylene) and 5 other elements (chlorine, magnesium, manganese, sulphur, zinc) were close to their GM outdoor levels. For PM 2.5 and TVOC, personal exposures and residential indoor levels (in GM) were about 2 times higher among the tobacco-smoke exposed group compared to the non-smoke exposed group, suggesting that smoking is an important determinant of these exposures. Determinants for CO were visualised by real-time monitoring, and we showed that the peak levels of personal exposure to CO were associated with smoking, cooking and transportation activities. Moderate to good correlations were only found between the personal exposures and residential indoor levels for both PM 2.5 ( r=0.60, p<0.001) and NO 2 ( r=0.47, p=0.003).

  4. 100,000-year-long terrestrial record of millennial-scale linkage between eastern North American mid-latitude paleovegetation shifts and Greenland ice-core oxygen isotope trends

    NASA Astrophysics Data System (ADS)

    Litwin, Ronald J.; Smoot, Joseph P.; Pavich, Milan J.; Markewich, Helaine W.; Brook, George; Durika, Nancy J.

    2013-09-01

    We document frequent, rapid, strong, millennial-scale paleovegetation shifts throughout the late Pleistocene, within a 100,000+ yr interval (~ 115-15 ka) of terrestrial sediments from the mid-Atlantic Region (MAR) of North America. High-resolution analyses of fossil pollen from one core locality revealed a continuously shifting sequence of thermally dependent forest assemblages, ranging between two endmembers: subtropical oak-tupelo-bald cypress-gum forest and high boreal spruce-pine forest. Sedimentary textural evidence indicates fluvial, paludal, and loess deposition, and paleosol formation, representing sequential freshwater to subaerial environments in which this record was deposited. Its total age-depth model, based on radiocarbon and optically stimulated luminescence ages, ranges from terrestrial oxygen isotope stages (OIS) 6 to 1. The particular core sub-interval presented here is correlative in trend and timing to that portion of the oxygen isotope sequence common among several Greenland ice cores: interstades GI2 to GI24 (≈ OIS2-5 d). This site thus provides the first evidence for an essentially complete series of 'Dansgaard-Oeschger' climate events in the MAR. These data reveal that the ~ 100,000 yr preceding the Late Glacial and Holocene in the MAR of North America were characterized by frequently and dynamically changing climate states, and by vegetation shifts that closely tracked the Greenland paleoclimate sequence.

  5. Does location of patellofemoral chondral lesion influence outcome after Oxford medial compartmental knee arthroplasty?

    PubMed Central

    Konan, S.; Haddad, F. S.

    2016-01-01

    Aims Medial unicompartmental knee arthroplasty (UKA) is associated with successful outcomes in carefully selected patient cohorts. We hypothesised that severity and location of patellofemoral cartilage lesions significantly influences functional outcome after Oxford medial compartmental knee arthroplasty. Patients and Methods We reviewed 100 consecutive UKAs at minimum eight-year follow-up (96 to 132). A single surgeon performed all procedures. Patients were selected based on clinical and plain radiographic assessment. All patients had end-stage medial compartment osteoarthritis (OA) with sparing of the lateral compartment and intact anterior cruciate ligaments. None of the patients had end-stage patellofemoral OA, but patients with anterior knee pain or partial thickness chondral loss were not excluded. There were 57 male and 43 female patients. The mean age at surgery was 69 years (41 to 82). At surgery the joint was carefully inspected for patellofemoral chondral loss and this was documented based on severity of cartilage loss (0 to 4 Outerbridge grading) and topographic location (medial, lateral, central, and superior or inferior). Functional scores collected included Oxford Knee Score (OKS), patient satisfaction scale and University College Hospital (UCH) knee score. Intraclass correlation was used to compare chondral damage to outcomes. Results All patients documented significant improvement in pain and improved functional scores at mid-term follow-up. There were four revisions (mean 2.9 years, 2 to 4; standard deviation (sd) 0.9) in this cohort, three for tibial loosening and one for femoral loosening. There was one infection that was treated with debridement and insert exchange. The mean OKS improved from 23.2 (sd 7.1) to 39.1 (sd 6.9); p < 0.001. The cohort with central and lateral grade 3 patellofemoral OA documented lower mean satisfaction with pain (90, sd 11.8) and function (87.5, sd 10.3) on the patient satisfaction scale. On the UCH scale, patients

  6. Valgus subsidence of the tibial component in cementless Oxford unicompartmental knee replacement

    PubMed Central

    Liddle, A. D.; Pandit, H. G.; Jenkins, C.; Lobenhoffer, P.; Jackson, W. F. M.; Dodd, C. A. F.; Murray, D. W.

    2014-01-01

    The cementless Oxford unicompartmental knee replacement has been demonstrated to have superior fixation on radiographs and a similar early complication rate compared with the cemented version. However, a small number of cases have come to our attention where, after an apparently successful procedure, the tibial component subsides into a valgus position with an increased posterior slope, before becoming well-fixed. We present the clinical and radiological findings of these six patients and describe their natural history and the likely causes. Two underwent revision in the early post-operative period, and in four the implant stabilised and became well-fixed radiologically with a good functional outcome. This situation appears to be avoidable by minor modifications to the operative technique, and it appears that it can be treated conservatively in most patients. Cite this article: Bone Joint J 2014;96-B:345–9. PMID:24589789

  7. Valgus subsidence of the tibial component in cementless Oxford unicompartmental knee replacement.

    PubMed

    Liddle, A D; Pandit, H G; Jenkins, C; Lobenhoffer, P; Jackson, W F M; Dodd, C A F; Murray, D W

    2014-03-01

    The cementless Oxford unicompartmental knee replacement has been demonstrated to have superior fixation on radiographs and a similar early complication rate compared with the cemented version. However, a small number of cases have come to our attention where, after an apparently successful procedure, the tibial component subsides into a valgus position with an increased posterior slope, before becoming well-fixed. We present the clinical and radiological findings of these six patients and describe their natural history and the likely causes. Two underwent revision in the early post-operative period, and in four the implant stabilised and became well-fixed radiologically with a good functional outcome. This situation appears to be avoidable by minor modifications to the operative technique, and it appears that it can be treated conservatively in most patients.

  8. Derivation of uranium residual radioactive material guidelines for the former Alba Craft Laboratory site, Oxford, Ohio

    SciTech Connect

    Nimmagadda, M.; Faillace, E.; Yu, C.

    1994-01-01

    Residual radioactive material guidelines for uranium were derived for the former Alba Craft Laboratory site in Oxford, Ohio. This site has been identified for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy (DOE). Single nuclide and total uranium guidelines were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the former Alba Craft Laboratory site should not exceed a dose of 30 mrem/yr following remedial action for the current use and likely future use scenarios or a dose of 100 mrem/yr for less likely future use scenarios (Yu et al. 1993). The DOE residual radioactive material guideline computer code, RESRAD, which implements the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation.

  9. Validation of an Italian version of the Oxford happiness inventory in adolescence.

    PubMed

    Meleddu, Mauro; Guicciardi, Marco; Scalas, L Francesca; Fadda, Daniela

    2012-01-01

    An Italian adaptation of the Oxford Happiness Inventory was administered to 782 adolescents. Exploratory structural equation modeling (ESEM) was used to examine the first- and second-order factorial structure of the scale and its invariance across gender; internal consistency and construct validity were also investigated. ESEM underlined a 5-factor structure (mastery and self-fulfillment, satisfaction with life, vigor, social interest, and social cheerfulness) that measures positive psychological functioning. These dimensions form a single latent construct of general psychological well-being. The scale showed adequate internal consistency values and strong measurement invariance across gender. Finally, regarding convergent validity, both total scale and subscales were positively correlated with extraversion and self-esteem, were negatively correlated with neuroticism, and displayed no correlation with psychoticism.

  10. BirdFlu2009: Avian Influenza and Human Health. 9-10 September 2009, Oxford, UK.

    PubMed

    Temperton, Nigel

    2009-11-01

    The BirdFlu2009 meeting entitled Avian Influenza and Human Health, held in Oxford, included topics covering new developments in the control of seasonal, avian and swine influenza virus infection, with a focus on the human-animal interface. This conference report highlights selected presentations on sialidase therapy for influenza infection, the use of IVIgs to study antibody diversity and reactivity, detecting oseltamivir carboxylate in waste water, H5N1 infection in Egyptian children, preparedness for an influenza pandemic and an indirect sandwich ELISA to detect H5 avian influenza virus. Investigational drugs discussed include NEX-DAS-181 (NexBio Inc) and MVA-NP-M1 (The Edward Jenner Institute for Vaccine Research). PMID:19844852

  11. Italian normative data for a stroke specific cognitive screening tool: the Oxford Cognitive Screen (OCS).

    PubMed

    Mancuso, M; Varalta, V; Sardella, L; Capitani, D; Zoccolotti, P; Antonucci, G

    2016-10-01

    Cognitive deficits occur in most stroke patients and cognitive impairment is an important predictor of adverse long term outcome. However, current screening measures, such as the Mini Mental State Examination or the Montreal Cognitive Assessment, do not provide information tuned for evaluating the impact of cognitive impairment in the early phase after stroke. The Oxford Cognitive Screen (OCS) represents an important new development in this regard. The OCS is now available for assessment of Italian individuals and the aim of this study is to standardize the OCS on a large sample of healthy Italian participants stratified for age, gender and education level. Results confirmed the influence of these factors in several of the OCS tasks. Age-, education- and gender-adjusted norms are provided for the ten sub-tests of the test. The availability of normative data represents an important prerequite for the reliable use of OCS with stroke patients. PMID:27395388

  12. Italian normative data for a stroke specific cognitive screening tool: the Oxford Cognitive Screen (OCS).

    PubMed

    Mancuso, M; Varalta, V; Sardella, L; Capitani, D; Zoccolotti, P; Antonucci, G

    2016-10-01

    Cognitive deficits occur in most stroke patients and cognitive impairment is an important predictor of adverse long term outcome. However, current screening measures, such as the Mini Mental State Examination or the Montreal Cognitive Assessment, do not provide information tuned for evaluating the impact of cognitive impairment in the early phase after stroke. The Oxford Cognitive Screen (OCS) represents an important new development in this regard. The OCS is now available for assessment of Italian individuals and the aim of this study is to standardize the OCS on a large sample of healthy Italian participants stratified for age, gender and education level. Results confirmed the influence of these factors in several of the OCS tasks. Age-, education- and gender-adjusted norms are provided for the ten sub-tests of the test. The availability of normative data represents an important prerequite for the reliable use of OCS with stroke patients.

  13. A survival analysis of 1084 knees of the Oxford unicompartmental knee arthroplasty

    PubMed Central

    Bottomley, N.; Jones, L. D.; Rout, R.; Alvand, A.; Rombach, I.; Evans, T.; Jackson, W. F. M.; Beard, D. J.; Price, A. J.

    2016-01-01

    Aims The aim of this to study was to compare the previously unreported long-term survival outcome of the Oxford medial unicompartmental knee arthroplasty (UKA) performed by trainee surgeons and consultants. Patients and Methods We therefore identified a previously unreported cohort of 1084 knees in 947 patients who had a UKA inserted for anteromedial knee arthritis by consultants and surgeons in training, at a tertiary arthroplasty centre and performed survival analysis on the group with revision as the endpoint. Results The ten-year cumulative survival rate for revision or exchange of any part of the prosthetic components was 93.2% (95% confidence interval (CI) 86.1 to 100, number at risk 45). Consultant surgeons had a nine-year cumulative survival rate of 93.9% (95% CI 90.2 to 97.6, number at risk 16). Trainee surgeons had a cumulative nine-year survival rate of 93.0% (95% CI 90.3 to 95.7, number at risk 35). Although there was no differences in implant survival between consultants and trainees (p = 0.30), there was a difference in failure pattern whereby all re-operations performed for bearing dislocation (n = 7), occurred in the trainee group. This accounted for 0.6% of the entire cohort and 15% of the re-operations. Conclusion This is the largest single series of the Oxford UKA ever reported and demonstrates that good results can be achieved by a heterogeneous group of surgeons, including trainees, if performed within a high-volume centre with considerable experience with the procedure. Cite this article: Bone Joint J 2016;(10 Suppl B):22–7. PMID:27694512

  14. Photographic monitoring of soiling and decay of roadside walls in central Oxford, England

    NASA Astrophysics Data System (ADS)

    Thornbush, Mary J.; Viles, Heather A.

    2008-12-01

    As part of the Environmental Monitoring of Integrated Transport Strategies (EMITS) project, which examined the impact of the Oxford Transport Strategy (OTS) on the soiling and decay of buildings and structures in central Oxford, England, a simple photographic survey of a sample of roadside walls was carried out in 1997, with re-surveys in 1999 and 2003. Thirty photographs were taken each time, covering an area of stonework approximately 30 × 30 cm in dimensions at 1-1.3 m above pavement level. The resulting images have been used to investigate, both qualitatively as well as quantitatively, the progression of soiling and decay. Comparison of images by eye reveals a number of minor changes in soiling and decay patterns, but generally indicates stability except at one site where dramatic, superficial damage occurred over 2 years. Quantitative analysis of decay features (concavities resulting from surface blistering, flaking, and scaling), using simple techniques in Adobe Photoshop, shows variable pixel-based size proportions of concavities across 6 years of survey. Colour images (in Lab Color) generally have a reduced proportion of pixels, representing decay features in comparison to black and white (Grayscale) images. The study conveys that colour images provide more information both for general observations of soiling and decay patterns and for segmentation of decay-produced concavities. The study indicates that simple repeat photography can reveal useful information about changing patterns of both soiling and decay, although unavoidable variation in external lighting conditions between re-surveys is a factor limiting the accuracy of change detection.

  15. Linkage map construction involving a reciprocal translocation.

    PubMed

    Farré, A; Benito, I Lacasa; Cistué, L; de Jong, J H; Romagosa, I; Jansen, J

    2011-03-01

    This paper is concerned with a novel statistical-genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to 'pseudo-linkage': the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the "pseudo-linkage" using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation.

  16. Gripper deploying and inverting linkage

    DOEpatents

    Minichan, Richard L.; Killian, Mark A.

    1993-01-01

    An end effector deploying and inverting linkage. The linkage comprises an air cylinder mounted in a frame or tube, a sliding bracket next to the air cylinder, a stopping bracket depending from the frame and three, pivotally-attached links that are attached to the end effector and to each other in such a way as to be capable of inverting the end effector and translating it laterally. The first of the three links is a straight element that is moved up and down by the shaft of the air cylinder. The second link is attached at one end to the stopping bracket and to the side of the end effector at the other end. The first link is attached near the middle of the second, sharply angled link so that, as the shaft of the air cylinder moves up and down, the second link rotates about an axis perpendicular to the frame and inverts and translates the end effector. The rotation of the second link is stopped at both ends when the link engages stops on the stopping bracket. The third link, slightly angled, is attached to the sliding bracket at one end and to the end of the end effector at the other. The third helps to control the end effector in its motion.

  17. Gripper deploying and inverting linkage

    DOEpatents

    Minichan, R.L.; Killian, M.A.

    1993-03-02

    An end effector deploying and inverting linkage. The linkage comprises an air cylinder mounted in a frame or tube, a sliding bracket next to the air cylinder, a stopping bracket depending from the frame and three, pivotally-attached links that are attached to the end effector and to each other in such a way as to be capable of inverting the end effector and translating it laterally. The first of the three links is a straight element that is moved up and down by the shaft of the air cylinder. The second link is attached at one end to the stopping bracket and to the side of the end effector at the other end. The first link is attached near the middle of the second, sharply angled link so that, as the shaft of the air cylinder moves up and down, the second link rotates about an axis perpendicular to the frame and inverts and translates the end effector. The rotation of the second link is stopped at both ends when the link engages stops on the stopping bracket. The third link, slightly angled, is attached to the sliding bracket at one end and to the end of the end effector at the other. The third helps to control the end effector in its motion.

  18. International Perspectives on Quality in Higher Education (Oxford, England, July 30-August 5, 2000). EPI Monograph Series on Higher Education.

    ERIC Educational Resources Information Center

    Janosik, Steven M., Ed.; Creamer, Don G., Ed.; Alexander, M. David, Ed.

    This monograph contains the invited papers of the major speakers at the Educational Policy Institute's Invitational Conference on Quality in Higher Education held at Oxford University, summer 2000. The purpose of the conference was to discuss how quality is being defined and measured in the context of higher education. The papers are: (1) "Quality…

  19. The Psychometric Analysis of the Persian Version of the Strategy Inventory for Language Learning of Rebecca L. Oxford

    ERIC Educational Resources Information Center

    Fazeli, Seyed Hossein

    2012-01-01

    The current study aims to analyze the psychometric qualities of the Persian adapted version of Strategy Inventory for Language Learning (SILL) developed by Rebecca L. Oxford (1990). Three instruments were used: Persian adapted version of SILL, a Background Questionnaire, and Test of English as a Foreign Language. Two hundred and thirteen Iranian…

  20. Degrees of Influence: The Politics of Honorary Degrees in the Universities of Oxford and Cambridge, 1900-2000

    ERIC Educational Resources Information Center

    Heffernan, Michael; Jons, Heike

    2007-01-01

    The universities of Oxford and Cambridge had developed different attitudes towards the award of honorary degrees through the early and middle decades of the twentieth century. Recently, both have adopted a similar cautious and apolitical stance. This essay describes the role of honorary degrees in the production and reproduction of their cultural…

  1. INNOVATIVE TECHNOLOGY VERIFICATION REPORT XRF TECHNOLOGIES FOR MEASURING TRACE ELEMENTS IN SOIL AND SEDIMENT OXFORD ED2000 XRF ANALYZER

    EPA Science Inventory

    The Oxford ED2000 x-ray fluorescence (XRF) analyzer was demonstrated under the U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation (SITE) Program. The field portion of the demonstration was conducted in January 2005 at the Kennedy Athletic, Recr...

  2. Perceptions of College Life, Emotional Well-being and Patterns of Drug and Alcohol Use among Oxford Undergraduates.

    ERIC Educational Resources Information Center

    Sell, Louise; Robson, Philip

    1998-01-01

    Investigates the levels of psychological health, stress, social attitudes, and the pattern of alcohol and drug consumption among the undergraduates in a single college within Oxford University (England). Reveals a high level of contentment with college life, a small minority of unhappy students, and no correlation between drug/alcohol use and…

  3. Identification of linkage phase by parental genotypes

    SciTech Connect

    Aksenovich, T.I.

    1995-08-01

    The possibility of using the phenotypic characteristics of parents for identifying the linkage phase in offspring is analyzed. It is demonstrated that parents with similar phenotypes (or marker genotypes) carry no information about the gene linkage phase in diheterozygous offspring. The probability of a certain linkage phase remains the same in all informative crossings. It depends on the model of inheritance of the analyzed alternative trait and is similar for di- and polyallelic markers. The frequencies of informative crossings and the probability of the linkage phase for different models of inheritance of the analyzed and marker traits are estimated. 17 refs., 2 tabs.

  4. An introduction to recombination and linkage analysis

    SciTech Connect

    Mcpeek, M.S.

    1996-12-31

    With a garden as his laboratory, Mendel was able to discern basic probabilistic laws of heredity. Although it first appeared as a baffling exception to one of Mendel`s principles, the phenomenon of variable linkage between characters was soon recognized to be a powerful tool in the process of chromosome mapping and location of genes of interest. In this introduction, we first describe Mendel`s work and the subsequent discovery of linkage. Next we describe the apparent cause of variable linkage, namely recombination, and we introduce linkage analysis. 33 refs., 1 fig., 2 tabs.

  5. Linkage disequilibrium in human populations

    PubMed Central

    Lonjou, Christine; Zhang, Weihua; Collins, Andrew; Tapper, William J.; Elahi, Eiram; Maniatis, Nikolas; Morton, Newton E.

    2003-01-01

    Whereas the human linkage map appears on limited evidence to be constant over populations, maps of linkage disequilibrium (LD) vary among populations that differ in gene history. The greatest difference is between populations of sub-Saharan origin and populations remotely derived from Africa after a major bottleneck that reduced their heterozygosity and altered their Malecot parameters, increasing the intercept M that reflects association in founders and decreasing the exponential decline ɛ. Variation among populations within this ethnic dichotomy is much smaller. These observations validate use of a cosmopolitan LD map based on a sizeable sample representing a large population reliably typed for markers at high density. Then an LD map for a region or isolate within an ethnic group may be created by fitting the sample LD to the cosmopolitan map, estimating Malecot parameters simultaneously. The cosmopolitan map scaled by ɛ recovers 95% of the information that a local map at the same density gives and therefore more than the information in a low-resolution local map. Relative to a Eurasian cosmopolitan map the scaling factors are estimated to be 0.82 for isolates of European descent, 1.53 for Yorubans, and 1.74 for African Americans. These observations are consistent with a common bottleneck (perhaps but not necessarily speciation) ≈173,500 years ago, if the bottleneck associated with migration out of Africa was 100,000 years ago. Eurasian populations (especially isolates with numerous cases) are efficient for genome scans, and populations of recent African origin (such as African Americans) are efficient for identification of causal polymorphisms within a candidate sequence. PMID:12721363

  6. Examining the Linkage Between FRAMES and GMS

    SciTech Connect

    Whelan, Gene; Castleton, Karl J.

    2006-02-13

    Because GMS provides so many features, of which some are also addressed by FRAMES, it could represent a platform to link to FRAMES, or FRAMES could represent a platform to link to GMS. The focus of this summary is to examine the strengths and weaknesses of the potential linkage direction and provide recommendations for the linkage between FRAMES and GMS.

  7. Linkage Disequilibrium Mapping of Meat Quality QTL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies based on linkage analysis have identified broad areas in the bovine genome associated with meat quality. Linkage disequilibrium (LD) analyses have the potential to identify narrower regions and point towards candidate genes. Tenderness and marbling were chosen to be evaluated in a ...

  8. Guidelines for College and University Linkages Abroad.

    ERIC Educational Resources Information Center

    American Council on Education, Washington, DC.

    This publication contains guidelines for U.S. institutions seeking linkages with institutions in other countries. It is the second revision of a document originally published in 1984. The guidelines are designed to help start the process, outline procedures to follow, and identify difficulties that might be avoided. Three types of linkages are…

  9. Linkage Manual V, Social Studies II.

    ERIC Educational Resources Information Center

    Piltch, Benjamin

    The linkage manual presents social studies material in story outline form. Linkage refers to the bonding of study skills (particularly logical thinking and reading) with subject area content. The document is intended as an aid to intermediate and junior high school classroom teachers as they develop and/or adapt social studies materials to meet…

  10. Genetic Linkage Heterogeneity in Myotubular Myopathy

    PubMed Central

    Samson, F.; Mesnard, L.; Heimburger, M.; Hanauer, A.; Chevallay, M.; Mercadier, J. J.; Pelissier, J. F.; Feingold, N.; Junien, C.; Mandel, J.-L.; Fardeau, M.

    1995-01-01

    Myotubular myopathy is a severe congenital disease inherited as an X-linked trait (MTM1; McKusick 31040). It has been mapped to the long arm of chromosome X, to the Xq27-28 region. Significant linkage has subsequently been established for the linkage group comprised of DXS304, DXS15, DXS52, and F8C in several studies. To date, published linkage studies have provided no evidence of genetic heterogeneity in severe neonatal myotubular myopathy (XLMTM). We have investigated a family with typical XLMTM in which no linkage to these markers was found. Our findings strongly suggest genetic heterogeneity in myotubular myopathy and indicate that great care should be taken when using Xq28 markers in linkage studies for prenatal diagnosis and genetic counseling. ImagesFigure 1Figure 2Figure 3Figure 5 PMID:7611280

  11. A model for linkage analysis with apomixis.

    PubMed

    Hou, Wei; Lin, Shen; Li, Yao; Pang, Xiaoming; Zeng, Yanru; Wu, Rongling

    2011-09-01

    Apomixis, or asexual reproduction through seeds, occurs in over 400 species of angiosperms. Although apomixis can favorably perpetuate desired genotypes through successive seed generation, it may also bring about some difficulty for linkage analysis and quantitative trait locus mapping. In this article, we explore the issue of how apomixis affects the precision and power of linkage analysis with molecular markers. We derive a statistical model for estimating the linkage between different markers when some progeny are derived from apomixis. The model was constructed within the maximum likelihood framework and implemented with the EM algorithm. A series of procedures are formulated to test the linkage of markers, the rate of apomixis, and the degree of genetic interference during meiosis. The model was examined and validated through simulation studies. The model will provide a tool for linkage mapping and evolutionary studies for plant species that undergo apomixis.

  12. Tribal Linkage and Race Data Quality for American Indians in a State Cancer Registry

    PubMed Central

    Johnson, Jennifer C.; Soliman, Amr S.; Tadgerson, Dan; Copeland, Glenn E.; Seefeld, David A.; Pingatore, Noel L.; Haverkate, Rick; Banerjee, Mousumi; Roubidoux, Marilyn A.

    2014-01-01

    Background Racial misclassification of American Indian and Alaska Native (AI/AN) individuals as non-AI/AN in cancer registries presents problems for cancer surveillance, research, and public health practice. The aim of this study was to investigate the efficiency of tribal linkages in enhancing the quality of racial information in state cancer registries. Methods Registry Plus™ Link Plus 2.0 probabilistic record linkage software was used to link the Michigan state cancer registry data (1985–2004; 1,031,168 cancer cases) to the tribal membership roster (40,340 individuals) in July of 2007. A data set was created containing AI/AN cancer cases identified by the state registry, Indian Health Service (IHS) linkages, and tribal linkage. The differences between these three groups of individuals were compared by distribution of demographic, diagnostic, and county-level characteristics using multilevel analysis (conducted in 2007–2008). Results From 1995 to 2004, the tribal enrollment file showed linkages to 670 cancer cases (583 individuals) and the tribal linkage led to the identification of 190 AI/AN cancer cases (168 individuals) that were classified as non-AI/AN in the registry. More than 80% of tribal members were reported as non-AI/AN to the registry. Individuals identified by IHS or tribal linkages were different from those reported to be AI/AN in terms of stage at diagnosis, tumor confirmation, and characteristics of the county of diagnosis, including contract health services availability, tribal health services availability, and proportion of AI/AN residents. Conclusions The data linkage between tribal and state cancer registry data sets improved racial classification validity of AI/AN Michigan cancer cases. Assessing tribal linkages is a simple, noninvasive way to improve the accuracy of state cancer data for AI/AN populations and to generate tribe-specific cancer information. PMID:19356888

  13. Resource linkages and sustainable development

    NASA Astrophysics Data System (ADS)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  14. Validating tumor linkage using the NAACCR site pairs table.

    PubMed

    Bringman, Deborah; Phillips, Jerri Linn; Williams, Judy; Young, John L

    2009-01-01

    The objective of this study is to illustrate use of the Site Pairs Table developed by the North American Association of Central Cancer Registries (NAACCR) Record Linkage Work Group to validate tumor linkage in a central registry database and to identify potential cases with inaccurate tumor linkage. Central registries often receive reports for patients with multiple tumors, and they receive multiple reports from different sources for the same tumor. Tumor site pairs (pairs of unique tumors for patients with multiple tumors) ought not refer to the same tumor as represented in the Site Pairs Table. Likewise, abstract pairs (pairs of abstracts relating to the same tumor) ought to be identified during the tumor linkage process as belonging to the same tumor. Three central cancer registries represented on the work group contributed data to the study. The data included cases diagnosed 1992-2003 and represented 143,288 patients with multiple tumors and 280,227 tumors with multiple abstracts. Totals of 181,118 tumor site pairs and 391,670 abstract site pairs were generated from the data and compared to the Site Pairs Table. Of the abstract site pairs 381,389 (97.4%) were found in the Site Pairs Table. One registry reviewed its portion of the 2.6% not found in the table and determined 12% of the cases were incorrectly linked and should change from one tumor to two tumors. Of the tumor site pairs, 144,793 (80%) were not found in the Site Pairs Table. Further evaluation of the remaining 20% by paired site and laterality, histology and timing showed 19.3% were considered unique tumors and 0.7% were identified as potential cases with inaccurate tumor linkage. Two registries reviewed their portion of these cases. One registry changed two tumors to one tumor on 44% of the cases they reviewed. The other registry changed two tumors to one tumor on 53% of the cases they reviewed. Analyzing site pairs within the registry database using the Site Pairs Table assists in identifying

  15. Inside Solomon's house: an archaeological study of the Old Ashmolean chymical laboratory in Oxford.

    PubMed

    Martinón-Torres, Marcos

    2012-03-01

    This paper is based on the archaeological and analytical study of the laboratory remains from the Officina Chimica of the Old Ashmolean Museum in Oxford. Following a contextualisation of this laboratory, founded in the wake of Bacon's utopian idea of Solomon's Temple, it is argued that the assemblage is likely to date from the late seventeenth century and thus be connected to the work of Robert Plot, Christopher White, and, indirectly, Robert Boyle. The analytical study of the equipment reveals that the chymists at the Old Ashmolean obtained crucibles from the best manufacturers in Europe, and that they used these and other utensils for experiments involving mercury, sulphur, zinc, lead glass, manganese, and antimony. The importance of these elements for early modern chymistry is discussed in the light of relevant historical sources, including some of Boyle's chymical texts. Altogether, these finds illustrate some of the rich diversity of experiments that took place in one of the most prominent laboratories of the period, showing strong connections with longstanding alchemical concerns as well as with cutting-edge research and development ventures.

  16. Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.

    PubMed Central

    Davies, Neil; Field, Dawn; Amaral-Zettler, Linda; Barker, Katharine; Bicak, Mesude; Bourlat, Sarah; Coddington, Jonathan; Deck, John; Drummond, Alexei; Gilbert, Jack A.; Glöckner, Frank Oliver; Kottmann, Renzo; Meyer, Chris; Morrison, Norman; Obst, Matthias; Robbins, Robert; Schriml, Lynn; Sterk, Peter; Stones-Havas, Steven

    2014-01-01

    This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.

  17. Radiological characterization survey results for Gaskill Hall, Miami University, Oxford, Ohio (OXO015)

    SciTech Connect

    Kleinhans, K.R.; Murray, M.E.; Carrier, R.F.

    1996-04-01

    Between October 1952 and February 1957, National Lead of Ohio (NLO), a primary contractor for the Atomic Energy Commission (AEC), subcontracted certain uranium machining operations to Alba Craft Laboratory, Incorporated, located at 10-14 West Rose Avenue, Oxford, Ohio. In 1992, personnel from Oak Ridge National Laboratory (ORNL) confirmed the presence of residual radioactive materials from the AEC-related operations in and around the facility in amounts exceeding the applicable Department of Energy (DOE) guidelines. Although the amount of uranium found on the property posed little health hazard if left undisturbed, the levels were sufficient to require remediation to bring radiological conditions into compliance with current guidelines, thus ensuring that the public and the environment are protected. Because it was suspected that uranium may have been used in the past in the immediate vicinity of Alba Craft in a Miami University building a team from ORNL, performed a radiological characterization survey of that structure in January 1994. The survey was conducted at the request of DOE as a precautionary measure to ensure that no radioactive residuals were present at levels exceeding guidelines. The survey included the determination of directly measured radiation levels and the collection of smear samples to detect possible removable alpha and beta-gamma activity levels, and comparison of these data to the guidelines. Results of the survey showed that all measurements were below the applicable guideline limits set by DOE.

  18. Study of general practice consultations and menopausal problems. Oxford General Practitioners Menopause Study Group.

    PubMed Central

    Barlow, D H; Brockie, J A; Rees, C M

    1991-01-01

    OBJECTIVE--To investigate the nature of work related to the menopause in general practice. DESIGN--Questionnaire study over six months among general practitioners after each consultation with a woman aged 40-69 at which issues related to the climacteric had been discussed. SETTING--9 General practices in the Oxford area. SUBJECTS--416 Women who had 572 consultations. MAIN OUTCOME MEASURES--Age, menopausal state, and first or subsequent consultation. Symptoms were classified together with the treatment and the outcome of the consultation. RESULTS--The consultation rate varied greatly between practices, the overall rate being 4.4%. There were many premenopausal women and women in their 60s presenting; women with hysterectomies presented more often--36% (37/103) of women with hysterectomies had more than one consultation compared with 26% (38/144) for premenopausal women and 24% (38/155) for postmenopausal women. 409 women had symptoms and 218 were prescribed oestrogen treatment. 156 of the consultations involved discussion and advice only. Only four women were referred to a local specialist clinic. CONCLUSION--There is a low overall use of hormone replacement therapy in the general postmenopausal population despite the recent media coverage of its benefits in the prevention of osteoporosis and subsequent fractures. PMID:1998795

  19. Backscattering spectroscopy developments for the University of Oxford Scanning External Proton Milliprobe (SEPM)

    NASA Astrophysics Data System (ADS)

    Jarjis, R. A.

    1996-09-01

    An external beam facility has recently been developed at the University of Oxford with the aim of carrying out non-sampling material characterisations on objects which are kept at atmospheric pressure using magnetically focused scanning beam of protons. This publication deals with one part of the developments, which is the application of backscattering spectroscopy in both operational diagnosis and the analysis of solids and gases. Results are reported for tests using an experimental external beam nozzle incorporating a window for extracting the proton beam from the vacuum to a helium gas flushed external chamber housing a Si(Li) detector and a semi-conductor charged-particle detector. The latter is used in the backscattering analysis of objects whilst a second charged-particle detector is also incorporated under vacuum in order to monitor backscattering signals originating from the window and the gas present in the vicinity of the analysis volume. The aim of the development is to create controlled conditions for comprehensive analysis using both PIXE and RBS. Two new backscattering techniques are reported in this publication: (a) External Beam Multi-Dimensional Analysis (EBMA) and (b) Resonant Scattering Multi-Dimensional Analysis (RSMA). In addition, we report on the findings of an initial study of using EBMA to assess gold layer application in Japanese porcelain and Islamic manuscripts, and using RSMA in investigating gas dynamics.

  20. Prevalence and severity of feeding and nutritional problems in children with neurological impairment: Oxford Feeding Study.

    PubMed

    Sullivan, P B; Lambert, B; Rose, M; Ford-Adams, M; Johnson, A; Griffiths, P

    2000-10-01

    The aim of this study was to estimate the prevalence and severity of feeding and nutritional problems in children with neurological impairment within a defined geographical area. In a cross-sectional study, a validated questionnaire was sent to 377 parents of children (aged 4 to 13 years) on the Oxford Register of Early Childhood Impairments with oromotor dysfunction. The return rate was 72%. Of these, 93% had cerebral palsy; 47% were unable to walk; 78% had speech difficulty; and 28% continuous drooling of saliva. Gastrointestinal problems were commonly encountered: 59% were constipated; 22% had significant problems with vomiting, and 31% had suffered at least one chest infection in the previous 6 months. Feeding problems were prevalent: 89% needed help with feeding and 56% choked with food; 20% of parents described feeding as stressful and unenjoyable. Prolonged feeding times (3h/day) were reported by 28%. Only 8% of participants received caloric supplements and 8% were fed via gastrostomy tube. Even though 38% of respondents considered their child to be underweight, 64% of children had never had their feeding and nutrition assessed. The results highlight that feeding problems in children with neurological impairment are common and severe, causing parental concern. Many of these children would benefit from nutritional assessment and management as part of their overall care.

  1. Inside Solomon's house: an archaeological study of the Old Ashmolean chymical laboratory in Oxford.

    PubMed

    Martinón-Torres, Marcos

    2012-03-01

    This paper is based on the archaeological and analytical study of the laboratory remains from the Officina Chimica of the Old Ashmolean Museum in Oxford. Following a contextualisation of this laboratory, founded in the wake of Bacon's utopian idea of Solomon's Temple, it is argued that the assemblage is likely to date from the late seventeenth century and thus be connected to the work of Robert Plot, Christopher White, and, indirectly, Robert Boyle. The analytical study of the equipment reveals that the chymists at the Old Ashmolean obtained crucibles from the best manufacturers in Europe, and that they used these and other utensils for experiments involving mercury, sulphur, zinc, lead glass, manganese, and antimony. The importance of these elements for early modern chymistry is discussed in the light of relevant historical sources, including some of Boyle's chymical texts. Altogether, these finds illustrate some of the rich diversity of experiments that took place in one of the most prominent laboratories of the period, showing strong connections with longstanding alchemical concerns as well as with cutting-edge research and development ventures. PMID:22701934

  2. Validity and Cross-Cultural Adaptation of the Persian Version of the Oxford Elbow Score

    PubMed Central

    Ebrahimzadeh, Mohammad H.; Kachooei, Amir Reza; Vahedi, Ehsan; Moradi, Ali; Mashayekhi, Zeinab; Hallaj-Moghaddam, Mohammad; Azami, Mehran; Birjandinejad, Ali

    2014-01-01

    Oxford Elbow Score (OES) is a patient-reported questionnaire used to assess outcomes after elbow surgery. The aim of this study was to validate and adapt the OES into Persian language. After forward-backward translation of the OES into Persian, a total number of 92 patients after elbow surgeries completed the Persian OES along with the Persian DASH and SF-36. To assess test-retest reliability, 31 randomly selected patients (34%) completed the Persian OES again after three days while abstaining from all forms of therapeutic regimens. Reliability of the Persian OES was assessed by measuring intraclass correlation coefficient (ICC) for test-retest reliability and Cronbach's alpha for internal consistency. Spearman's correlation coefficient was used to test the construct validity. Cronbach's alpha coefficient was 0.92 showing excellent reliability. Cronbach's alpha for function, pain, and social-psychological subscales was 0.95, 0.86, and 0.85, respectively. Intraclass correlation coefficient (ICC) was 0.85 for the overall questionnaire and 0.90, 0.76, and 0.75 for function, pain, and social-psychological subscales, respectively. Construct validity was confirmed as the Spearman correlation between OES and DASH was 0.80. Persian OES is a valid and reliable patient-reported outcome measure to assess postsurgical elbow status in Persian speaking population. PMID:25214845

  3. Tackling Shell Shock in Great War Oxford: Thomas Saxty Good, William McDougall, and James Arthur Hadfield.

    PubMed

    Stewart, John

    2016-01-01

    Shell shock was an important object of diagnostic and therapeutic concern in Oxford during the Great War. The efforts of three Oxford physicians--Thomas Saxty Good, William McDougall, and James Arthur Hadfield--are of particular significance to our story. All worked on the problem at various sites throughout the city. They often collaborated. All were committed to employing innovative techniques such as psychotherapy and hypnosis. Each rose, to differing extents, to prominence in the field of psychological medicine during the succeeding decades. Yet all have been neglected in the current historiography. I argue that a close examination of their practices reveals a curious combination of therapeutic pragmatism and psychoanalytically informed techniques that later helped inform clinical psychology's challenge to psychiatry's dominance over the concept and care of mental disorder.

  4. Tackling Shell Shock in Great War Oxford: Thomas Saxty Good, William McDougall, and James Arthur Hadfield.

    PubMed

    Stewart, John

    2016-01-01

    Shell shock was an important object of diagnostic and therapeutic concern in Oxford during the Great War. The efforts of three Oxford physicians--Thomas Saxty Good, William McDougall, and James Arthur Hadfield--are of particular significance to our story. All worked on the problem at various sites throughout the city. They often collaborated. All were committed to employing innovative techniques such as psychotherapy and hypnosis. Each rose, to differing extents, to prominence in the field of psychological medicine during the succeeding decades. Yet all have been neglected in the current historiography. I argue that a close examination of their practices reveals a curious combination of therapeutic pragmatism and psychoanalytically informed techniques that later helped inform clinical psychology's challenge to psychiatry's dominance over the concept and care of mental disorder. PMID:27344909

  5. Leading a double life in 17th-century Oxford: Ralph Bathurst (1620-1704), physician-physiologist and cleric.

    PubMed

    Guy, Jean M

    2006-02-01

    Ralph Bathurst spent most of his working life in Trinity College, Oxford. Strongly influenced by William Harvey, he was a friend and colleague of Thomas Willis, Robert Boyle and many other eminent experimentalists. His intended career as an Anglican priest and theologian was frustrated during the Commonwealth. Instead, he trained as a physician and practised in Abingdon in Berkshire and in the Navy. His examination papers for the degrees of Bachelor and Doctor of Medicine survived and were printed many years after his death. This paper, summarizing the three Latin lectures on respiration given for his doctoral degree in 1654, throws light on the physiological research carried out in Oxford at that time. The lectures included clinical observations, the results of experiments performed by himself and others, and speculations on the chemistry of air in the era before Joseph Priestley. PMID:16435028

  6. The REBUS-MCNP linkage.

    SciTech Connect

    Stevens, J. G.; Nuclear Engineering Division

    2009-04-24

    The Reduced Enrichment Research and Test Reactor (RERTR) Program uses the REBUS-PC computer code to provide reactor physics and core design information such as neutron flux distributions in space, energy, and time, and to track isotopic changes in fuel and neutron absorbers with burnup. REBUS-PC models the complete fuel cycle including shuffling capability. REBUS-PC evolved using the neutronic capabilities of multi-group diffusion theory code DIF3D 9.0, but was extended to apply the continuous energy Monte Carlo code MCNP for one-group fluxes and cross-sections. The linkage between REBUS-PC and MCNP has recently been modernized and extended, as described in this manual. REBUS-PC now calls MCNP via a system call so that the user can apply any valid MCNP executable. The interface between REBUS-PC and MCNP requires minimal changes to an existing MCNP model, and little additional input. The REBUS-MCNP interface can also be used in conjunction with DIF3D neutronics to update an MCNP model with fuel compositions predicted using a DIF3D based depletion.

  7. Linkage Disequilibrium in Wild Mice

    PubMed Central

    Laurie, Cathy C; Nickerson, Deborah A; Anderson, Amy D; Weir, Bruce S; Livingston, Robert J; Dean, Matthew D; Smith, Kimberly L; Schadt, Eric E; Nachman, Michael W

    2007-01-01

    Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD) in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1) Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2) they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3) LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits. PMID:17722986

  8. Model averaging in linkage analysis.

    PubMed

    Matthysse, Steven

    2006-06-01

    Methods for genetic linkage analysis are traditionally divided into "model-dependent" and "model-independent," but there may be a useful place for an intermediate class, in which a broad range of possible models is considered as a parametric family. It is possible to average over model space with an empirical Bayes prior that weights models according to their goodness of fit to epidemiologic data, such as the frequency of the disease in the population and in first-degree relatives (and correlations with other traits in the pleiotropic case). For averaging over high-dimensional spaces, Markov chain Monte Carlo (MCMC) has great appeal, but it has a near-fatal flaw: it is not possible, in most cases, to provide rigorous sufficient conditions to permit the user safely to conclude that the chain has converged. A way of overcoming the convergence problem, if not of solving it, rests on a simple application of the principle of detailed balance. If the starting point of the chain has the equilibrium distribution, so will every subsequent point. The first point is chosen according to the target distribution by rejection sampling, and subsequent points by an MCMC process that has the target distribution as its equilibrium distribution. Model averaging with an empirical Bayes prior requires rapid estimation of likelihoods at many points in parameter space. Symbolic polynomials are constructed before the random walk over parameter space begins, to make the actual likelihood computations at each step of the random walk very fast. Power analysis in an illustrative case is described. (c) 2006 Wiley-Liss, Inc. PMID:16652369

  9. Linkage: from particulate to interactive genetics.

    PubMed

    Falk, Raphael

    2003-01-01

    Genetics was established on a strict particulate conception of heredity. Genetic linkage, the deviation from independent segregation of Mendelian factors, was conceived as a function of the material allocation of the factors to the chromosomes, rather than to the multiple effects (pleiotropy) of discrete factors. Although linkage maps were abstractions they provided strong support for the chromosomal theory of inheritance. Direct Cytogenetic evidence was scarce until X-ray induced major chromosomal rearrangements allowed direct correlation of genetic and cytological rearrangements. Only with the discovery of the polytenic giant chromosomes in Drosophila larvae in the 1930s were the virtual maps backed up by physical maps of the genetic loci. Genetic linkage became a pivotal experimental tool for the examination of the integration of genetic functions in development and in evolution. Genetic mapping has remained a hallmark of genetic analysis. The location of genes in DNA is a modern extension of the notion of genetic linkage.

  10. Linkage studies in primary open angle glaucoma

    SciTech Connect

    Avramopoulos, D.; Grigoriadu, M.; Kitsos, G.

    1994-09-01

    Glaucoma is a leading cause of blindness worldwide. The majority of glaucoma is associated with an open, normal appearing anterior chamber angle and is termed primary open angle glaucoma (POAG, MIM 137760). It is characterized by elevated intraocular pressure and onset in middle age or later. A subset of POAG with juvenile onset has recently been linked to chromosome 1q in two families with autosomal dominant inheritance. Eleven pedigrees with autosomal dominant POG (non-juvenile-onset) have been identified in Epirus, Greece. In the present study DNA samples have been collected from 50 individuals from one large pedigree, including 12 affected individuals. Preliminary results of linkage analysis with chromosome 1 microsatellites using the computer program package LINKAGE Version 5.1 showed no linkage with the markers previously linked to juvenile-onset POAG. Further linkage analysis is being pursued, and the results will be presented.

  11. Investigations of Three-Point Linkage

    ERIC Educational Resources Information Center

    Mertens, Thomas R.

    1972-01-01

    Describes sequence of activities for teaching three-point linkage concept and gene-mapping to high school biology students. Includes laboratory experiments and hypothetical examples for classroom discussion. (PS)

  12. Resource linkages and sustainable development

    NASA Astrophysics Data System (ADS)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  13. The Role of Pedigree Information in Combined Linkage Disequilibrium and Linkage Mapping of Quantitative Trait Loci in a General Complex Pedigree

    PubMed Central

    Lee, S. H.; Van der Werf, J. H. J.

    2005-01-01

    Combined linkage disequilibrium and linkage (LDL) mapping can exploit historical as well as recent and observed recombinations in a recorded pedigree. We investigated the role of pedigree information in LDL mapping and the performance of LDL mapping in general complex pedigrees. We compared using complete and incomplete genotypic data, spanning 5 or 10 generations of known pedigree, and we used bi- or multiallelic markers that were positioned at 1- or 5-cM intervals. Analyses carried out with or without pedigree information were compared. Results were compared with linkage mapping in some of the data sets. Linkage mapping or LDL mapping with sparse marker spacing (∼5 cM) gave a poorer mapping resolution without considering pedigree information compared to that with considering pedigree information. The difference was bigger in a pedigree of more generations. However, LDL mapping with closely linked markers (∼1 cM) gave a much higher mapping resolution regardless of using pedigree information. This study shows that when marker spacing is dense and there is considerable linkage disequilibrium generated from historical recombinations between flanking markers and QTL, the loss of power due to ignoring pedigree information is negligible and mapping resolution is very high. PMID:15677753

  14. Hydrology of the Little Androscoggin River Valley aquifer, Oxford County, Maine

    USGS Publications Warehouse

    Morrissey, D.J.

    1983-01-01

    The Little Androscoggin River valley aquifer, a 15-square-mile sand and gravel valley-fill aquifer in southwestern Maine, is the source of water for the towns of Norway, Oxford, and South Paris. Estimated inflows to the aquifer during the 1981 water year were 16.4 cubic feet per second from precipitation directly on the aquifer, 11.2 cubic feet per second from till covered uplands adjacent to the aquifer, and 1.4 cubic feet per second from surface-water leakage. Outflows from the aquifer were 26.7 cubic feet per second to surface water and 2.3 cubic feet per second to wells. A finite-difference ground-water flow model was used to simulate conditions observed in the aquifer during 1981. Model conditions observed in the aquifer during 1981. Model simulations indicate that a 50 percent reduction of average 1981 recharge to the aquifer would cause water level declines of up to 20 feet in some areas. Model simulations of increased pumping at a high yield well in the northern part of the aquifer indicate that resulting changes in the water table will not be sufficient to intercept groundwater contaminated by a sludge disposal site. Water in the aquifer is low in dissolved solids (average for 38 samples was 67 mg/L), slightly acidic and soft. Ground-water contamination has occurred near a sludge-disposal site and in the vicinity of a sanitary landfill. Dissolved solids in ground water near the sludge disposal site were as much as ten times greater than average background values for the aquifer. (USGS)

  15. Neurodevelopmental Outcome of Extremely Low Birth Weight Infants from the Vermont Oxford Network: 1998–2003

    PubMed Central

    Mercier, Charles E.; Dunn, Michael S.; Ferrelli, Karla R.; Howard, Diantha B.; Soll, Roger F.

    2010-01-01

    Background Physicians and parents face significant uncertainties when making care decisions for extremely low birth weight (ELBW) infants. Many published estimates of death and developmental outcome are from well-funded university programs and may not reflect outcomes of infants from a variety of settings. The best estimates of the probabilities of death and severe disability combine local experience and published data. Objective: To describe the neurodevelopmental outcome of ELBW infants from centers of the ELBW Infant Follow-Up Group of the Vermont Oxford Network (VON) and to identify characteristics associated with severe disability. Methods Predefined measures of living situation, health and developmental outcome were collected at 18–24 months’ corrected age for infants born from July 1, 1998 to December 31, 2003 with birth weights of 401–1,000 g at 33 North American VON centers. Logistic regression was used to identify characteristics associated with severe disability. Results 6,198 ELBW infants were born and survived until hospital discharge; by the time of follow-up, 88 infants (1.4%) had died. Of the remaining 6,110 infants, 3,567 (58.4%) were evaluated. Severe disability occurred in 34% of the assessed infants. Multivariate logistic regression suggested cystic periventricular leukomalacia, congenital malformation and severe intraventricular hemorrhage were the characteristics most highly associated with severe disability. There were marked variations among the follow-up clinics in the attrition rate. Conclusion ELBW infants completing evaluation were at a high risk for severe disability. There are considerable differences among participating centers in attrition at follow-up. Further resources will be needed to study the effect of follow-up care for this group of infants. PMID:19940516

  16. Postremediation dose assessment for the former Alba Craft Laboratory site, Oxford, Ohio

    SciTech Connect

    Kamboj, S.; Nimmagadda, M.; Yu, C.

    1996-04-01

    Potential maximum radiation dose rates were calculated for the former Alba Craft Laboratory site in Oxford, Ohio, which was involved in machining of uranium metal in the 1950s for the U.S. atomic energy program. The site is not currently being used. The residual radioactive material guidelines (RESRAD) computer code, which implements the methodology described in the US Department of Energy`s (DOE`s) manual for establishing residual radioactive material guidelines, was sued in this evaluation. Three potential land use scenarios were considered for the former Alba Craft site; the scenarios vary with regard to the type of site use, time spent at the site by the exposed individual, and sources of food consumed. Scenario A (a possible land use scenario) assumed industrial use of the site; Scenario B (a likely future land use scenario) assumed residential use of the site; and Scenario C (a possible but unlikely land use scenario) assumed the presence of a resident farmer. For scenario A, it was assumed that any water used for domestic or industrial activities would be from uncontaminated off-site municipal sources. The water used for drinking, household purposes, and irrigation was assumed to be from uncontaminated municipal sources in Scenario B; groundwater drawn from a well located at the downgradient edge of the contaminated zone would be the only source of water for drinking, irrigation, and raising livestock in Scenario C. The results of the evaluation indicated that the DOE dose limit of 100 mrem/yr would not be exceeded for any of the scenarios analyzed. The potential maximum dose rates for Scenarios A, B, and C are 0.64, 2.0, and 11 mrem/yr, respectively.

  17. Assessing the performance of the Oxford Nanopore Technologies MinION

    PubMed Central

    Laver, T.; Harrison, J.; O’Neill, P.A.; Moore, K.; Farbos, A.; Paszkiewicz, K.; Studholme, D.J.

    2015-01-01

    The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data. PMID:26753127

  18. Development of the Oxford Participation and Activities Questionnaire: constructing an item pool

    PubMed Central

    Kelly, Laura; Jenkinson, Crispin; Dummett, Sarah; Dawson, Jill; Fitzpatrick, Ray; Morley, David

    2015-01-01

    Purpose The Oxford Participation and Activities Questionnaire is a patient-reported outcome measure in development that is grounded on the World Health Organization International Classification of Functioning, Disability, and Health (ICF). The study reported here aimed to inform and generate an item pool for the new measure, which is specifically designed for the assessment of participation and activity in patients experiencing a range of health conditions. Methods Items were informed through in-depth interviews conducted with 37 participants spanning a range of conditions. Interviews aimed to identify how their condition impacted their ability to participate in meaningful activities. Conditions included arthritis, cancer, chronic back pain, diabetes, motor neuron disease, multiple sclerosis, Parkinson’s disease, and spinal cord injury. Transcripts were analyzed using the framework method. Statements relating to ICF themes were recast as questionnaire items and shown for review to an expert panel. Cognitive debrief interviews (n=13) were used to assess items for face and content validity. Results ICF themes relevant to activities and participation in everyday life were explored, and a total of 222 items formed the initial item pool. This item pool was refined by the research team and 28 generic items were mapped onto all nine chapters of the ICF construct, detailing activity and participation. Cognitive interviewing confirmed the questionnaire instructions, items, and response options were acceptable to participants. Conclusion Using a clear conceptual basis to inform item generation, 28 items have been identified as suitable to undergo further psychometric testing. A large-scale postal survey will follow in order to refine the instrument further and to assess its psychometric properties. The final instrument is intended for use in clinical trials and interventions targeted at maintaining or improving activity and participation. PMID:26056503

  19. Positional Cloning by Linkage Disequilibrium

    PubMed Central

    Maniatis, Nikolas; Collins, Andrew; Gibson, Jane; Zhang, Weihua; Tapper, William; Morton, Newton E.

    2004-01-01

    Recently, metric linkage disequilibrium (LD) maps that assign an LD unit (LDU) location for each marker have been developed (Maniatis et al. 2002). Here we present a multiple pairwise method for positional cloning by LD within a composite likelihood framework and investigate the operating characteristics of maps in physical units (kb) and LDU for two bodies of data (Daly et al. 2001; Jeffreys et al. 2001) on which current ideas of blocks are based. False-negative indications of a disease locus (type II error) were examined by selecting one single-nucleotide polymorphism (SNP) at a time as causal and taking its allelic count (0, 1, or 2, for the three genotypes) as a pseudophenotype, Y. By use of regression and correlation, association between every pseudophenotype and the allelic count of each SNP locus (X) was based on an adaptation of the Malecot model, which includes a parameter for location of the putative gene. By expressing locations in kb or LDU, greater power for localization was observed when the LDU map was fitted. The efficiency of the kb map, relative to the LDU map, to describe LD varied from a maximum of 0.87 to a minimum of 0.36, with a mean of 0.62. False-positive indications of a disease locus (type I error) were examined by simulating an unlinked causal SNP and the allele count was used as a pseudophenotype. The type I error was in good agreement with Wald’s likelihood theorem for both metrics and all models that were tested. Unlike tests that select only the most significant marker, haplotype, or haploset, these methods are robust to large numbers of markers in a candidate region. Contrary to predictions from tagging SNPs that retain haplotype diversity, the sample with smaller size but greater SNP density gave less error. The locations of causal SNPs were estimated with the same precision in blocks and steps, suggesting that block definition may be less useful than anticipated for mapping a causal SNP. These results provide a guide to

  20. Comparing Linkage Designs Based on Land Facets to Linkage Designs Based on Focal Species

    PubMed Central

    Brost, Brian M.; Beier, Paul

    2012-01-01

    Least-cost modeling for focal species is the most widely used method for designing conservation corridors and linkages. However, these designs depend on today's land covers, which will be altered by climate change. We recently proposed an alternative approach based on land facets (recurring landscape units of relatively uniform topography and soils). The rationale is that corridors with high continuity of individual land facets will facilitate movement of species associated with each facet today and in the future. Conservation practitioners might like to know whether a linkage design based on land facets is likely to provide continuity of modeled breeding habitat for species needing connectivity today, and whether a linkage for focal species provides continuity and interspersion of land facets. To address these questions, we compared linkages designed for focal species and land facets in three landscapes in Arizona, USA. We used two variables to measure linkage utility, namely distances between patches of modeled breeding habitat for 5–16 focal species in each linkage, and resistance profiles for focal species and land facets between patches connected by the linkage. Compared to focal species designs, linkage designs based on land facets provided as much or more modeled habitat connectivity for 25 of 28 species-landscape combinations, failing only for the three species with the most narrowly distributed habitat. Compared to land facets designs, focal species linkages provided lower connectivity for about half the land facets in two landscapes. In areas where a focal species approach to linkage design is not possible, our results suggest that conservation practitioners may be able to implement a land facets approach with some confidence that the linkage design would serve most potential focal species. In areas where focal species designs are possible, we recommend using the land facet approach to complement, rather than replace, focal species approaches. PMID

  1. Likelihood ratio tests for linkage and linkage disequilibrium: Asymptotic distribution and power

    SciTech Connect

    1996-05-01

    Terwilliger proposes an interesting likelihood ratio test for linkage disequilibrium that appears conservative under the null hypothesis and powerful when one of several alleles is positively associated with the disease. We discuss in detail the aspects of linkage disequilibrium with a simpler asymptotic distribution. 3 refs.

  2. Oxford graduates' perceptions of a global health master's degree: a case study

    PubMed Central

    2011-01-01

    Introduction Low and middle-income countries suffer an ongoing deficit of trained public health workers, yet optimizing postgraduate education to best address these training needs remains a challenge. Much international public health education literature has focused on global capacity building and/or the description of innovative programmes, but less on quality and appropriateness. Case description The MSc in Global Health Science at the University of Oxford is a relatively new, full-time one year master's degree in international public health. The programme is intended for individuals with significant evidence of commitment to health in low and middle income countries. The intake is small, with only about 25 students each year, but they are from diverse professional and geographical backgrounds. Given the diversity of their backgrounds, we wanted to determine the extent to which student background influenced their perceptions of the quality of their learning experience and their learning outcomes. We conducted virtual or face-to-face semi-structured individual interviews with students who had graduated from the course at least one year previously. Of the 2005 to 2007 intake years, 52 of 63 graduates (83%) were interviewed. We used thematic analysis to analyze the data, then linked results to student characteristics. Discussion The findings from the evaluation suggested that all MSc GHS graduates who spoke with us, irrespective of background, appreciated the curriculum structure drawing on the strengths of a small, diverse student group, and the contribution the programme had made to their breadth of understanding and their careers. This evaluation also demonstrated the feasibility of an educational evaluation conducted several years after programme completion and when graduates were 'in the field'. This is important in ensuring international public health programmes are relevant to the day-to-day work of public health practitioners and researchers in low and

  3. Automating occupational protection records systems

    SciTech Connect

    Lyon, M.; Martin, J.B.

    1991-10-01

    Occupational protection records have traditionally been generated by field and laboratory personnel, assembled into files in the safety office, and eventually stored in a warehouse or other facility. Until recently, these records have been primarily paper copies, often handwritten. Sometimes, the paper is microfilmed for storage. However, electronic records are beginning to replace these traditional methods. The purpose of this paper is to provide guidance for making the transition to automated record keeping and retrieval using modern computer equipment. This paper describes the types of records most readily converted to electronic record keeping and a methodology for implementing an automated record system. The process of conversion is based on a requirements analysis to assess program needs and a high level of user involvement during the development. The importance of indexing the hard copy records for easy retrieval is also discussed. The concept of linkage between related records and its importance relative to reporting, research, and litigation will be addressed. 2 figs.

  4. Intragroup Emotions: Physiological Linkage and Social Presence.

    PubMed

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion-communicative expression and physiological state-to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  5. Linkage and association to genetic markers.

    PubMed

    Elston, R C

    1995-01-01

    Genetic markers that are sufficiently polymorphic (as measured by their heterozygosities) can be used in linkage and association analyses to detect Mendelian segregation underlying disease phenotypes. Each type of analysis can either be based on a specific genetic model or not make any assumptions about the mode of inheritance of the disease. Principles underlying these methods are reviewed, and the assumptions underlying them stressed. Association analyses are more powerful, provided there is linkage disequilibrium between the marker and disease loci; however, only linkage analyses have power in the absence of such disequilibrium. For this reason, models that allow for both kinds of tests are preferred, and such models must adequately approximate the complexity of the disease being studied.

  6. A Genetic Linkage Map for Cattle

    PubMed Central

    Bishop, M. D.; Kappes, S. M.; Keele, J. W.; Stone, R. T.; Sunden, SLF.; Hawkins, G. A.; Toldo, S. S.; Fries, R.; Grosz, M. D.; Yoo, J.; Beattie, C. W.

    1994-01-01

    We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL). PMID:7908653

  7. A microsatellite linkage map of Drosophila mojavensis

    PubMed Central

    Staten, Regina; Schully, Sheri Dixon; Noor, Mohamed AF

    2004-01-01

    Background Drosophila mojavensis has been a model system for genetic studies of ecological adaptation and speciation. However, despite its use for over half a century, no linkage map has been produced for this species or its close relatives. Results We have developed and mapped 90 microsatellites in D. mojavensis, and we present a detailed recombinational linkage map of 34 of these microsatellites. A slight excess of repetitive sequence was observed on the X-chromosome relative to the autosomes, and the linkage groups have a greater recombinational length than the homologous D. melanogaster chromosome arms. We also confirmed the conservation of Muller's elements in 23 sequences between D. melanogaster and D. mojavensis. Conclusions The microsatellite primer sequences and localizations are presented here and made available to the public. This map will facilitate future quantitative trait locus mapping studies of phenotypes involved in adaptation or reproductive isolation using this species. PMID:15163351

  8. Intragroup Emotions: Physiological Linkage and Social Presence

    PubMed Central

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion—communicative expression and physiological state—to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  9. Delivering proportionate governance in the era of eHealth: Making linkage and privacy work together.

    PubMed

    Sethi, Nayha; Laurie, Graeme T

    2013-06-01

    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.

  10. IRT test equating in complex linkage plans.

    PubMed

    Battauz, Michela

    2013-07-01

    Linkage plans can be rather complex, including many forms, several links, and the connection of forms through different paths. This article studies item response theory equating methods for complex linkage plans when the common-item nonequivalent group design is used. An efficient way to average equating coefficients that link the same two forms through different paths will be presented and the asymptotic standard errors of indirect and average equating coefficients are derived. The methodology is illustrated using simulations studies and a real data example. PMID:25106395

  11. A linkage study of malignant hyperthermia (MH).

    PubMed

    Bender, K; Senff, H; Wienker, T F; Spiess-Kiefer, C; Lehmann-Horn, F

    1990-03-01

    Five German families segregating for malignant hyperthermia (MH) were tested for linkage relationships using 35 serological and biochemical markers. Slightly positive lod scores were obtained with MNS, EsD, C3 and P. The relation with the C3 locus on chromosome 19p13.3-13.2 (z = 0.72, theta = 0.11) is of some interest, since genetic linkage of MH with several polymorphic DNA markers from the 19q12-13.2 region has been reported (McCarthy et al. 1989).

  12. Linkage Rate Between Data From Health Checks and Health Insurance Claims in the Japan National Database

    PubMed Central

    Okamoto, Etsuji

    2014-01-01

    Background Japan’s National Database (NDB) includes data on health checks and health insurance claims, is linkable using hash functions, and is available for research use. However, the linkage rate between health check and health insurance claims data has not been investigated. Methods Linkage rate was evaluated by comparing observed medical and pharmaceutical charges among health check recipients in fiscal year (FY) 2009 (N = 21 588 883) with expected charges from the same population when record linkage was complete. Using the NDB, observed charges were estimated from the first published result of linking health check recipients in FY2009 and their health insurance claims in FY2010. Expected charges were estimated by combining 3 publicly available datasets, including data from the Medical Care Benefit Survey and an ad-hoc report by the Japan Health Insurance Association. Results Only 14.9% of expected charges were linked by the NDB. The linkage rate was higher for women than for men (18.2% vs 12.4%) and for elderly adults as compared with younger adults (>25% vs <10%). Conclusions The linkage rate in the NDB was so low that any research linking health check and health insurance claims will not be reliable. Causes for the low linkage rate include differences between health check and health insurance claims data in name format (eg, insertion of a space between family and given names) and date of birth (Japanese vs Gregorian calendar). Investigation of the causes for the low linkage rate and measures for improvement are urgently needed. PMID:24317344

  13. Irish study of high-density Schizophrenia families: Field methods and power to detect linkage

    SciTech Connect

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

    1996-04-09

    Large samples of multiplex pedigrees will probably be needed to detect susceptibility loci for schizophrenia by linkage analysis. Standardized ascertainment of such pedigrees from culturally and ethnically homogeneous populations may improve the probability of detection and replication of linkage. The Irish Study of High-Density Schizophrenia Families (ISHDSF) was formed from standardized ascertainment of multiplex schizophrenia families in 39 psychiatric facilities covering over 90% of the population in Ireland and Northern Ireland. We here describe a phenotypic sample and a subset thereof, the linkage sample. Individuals were included in the phenotypic sample if adequate diagnostic information, based on personal interview and/or hospital record, was available. Only individuals with available DNA were included in the linkage sample. Inclusion of a pedigree into the phenotypic sample required at least two first, second, or third degree relatives with non-affective psychosis (NAP), one of whom had schizophrenia (S) or poor-outcome schizoaffective disorder (PO-SAD). Entry into the linkage sample required DNA samples on at least two individuals with NAP, of whom at least one had S or PO-SAD. Affection was defined by narrow, intermediate, and broad criteria. 75 refs., 6 tabs.

  14. 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. PMID:21868128

  15. The stability of the femoral component in the Oxford unicompartmental knee replacement: a comparison of single and twin peg designs.

    PubMed

    Reiner, T; Jaeger, S; Schwarze, M; Klotz, M C; Beckmann, N A; Bitsch, R G

    2014-07-01

    Aseptic loosening of the femoral component is an important indication for revision surgery in unicompartmental knee replacement (UKR). A new design of femoral component with an additional peg was introduced for the cemented Oxford UKR to increase its stability. The purpose of this study was to compare the primary stability of the two designs of component. Medial Oxford UKR was performed in 12 pairs of human cadaver knees. In each pair, one knee received the single peg and one received the twin peg design. Three dimensional micromotion and subsidence of the component in relation to the bone was measured under cyclical loading at flexion of 40° and 70° using an optical measuring system. Wilcoxon matched pairs signed-rank test was performed to detect differences between the two groups. There was no significant difference in the relative micromotion (p = 0.791 and 0.380, respectively) and subsidence (p = 0.301 and 0.176, respectively) of the component between the two groups at both angles of flexion. Both designs of component offered good strength of fixation in this cadaver study.

  16. Changing patterns of soiling and microbial growth on building stone in Oxford, England after implementation of a major traffic scheme.

    PubMed

    Thornbush, M; Viles, H

    2006-08-15

    Surfaces of freshly cut Bath limestone exposed along various roadsides before and after the reduction of traffic in the historical city centre of Oxford, England (following the Oxford Transport Strategy or OTS), presented an opportunity to investigate changes in soiling and fungal growth in relation to changing traffic pollution. Spectrophotometric data using an X-Rite SP68 sphere spectrophotometer provided quantitative information on soiling before and after the OTS. Scanning electron microscopy (SEM) provided a means to view and quantify the microbial inhabitants in detail, using a technique which registered and counted branching beaded structures. Results indicated that at Longwall Street soiling became more pronounced and microbial cover lower, with the reverse occurring at High Street where the greatest improvements in surface lightness were found. Other sites showed less clearcut responses in soiling and microbial growth. Overall, microbial growth was pronounced within hollows on stone surfaces before the OTS, with some signs of spreading of growths away from hollows after the OTS. A complex relationship between air pollution, soiling, and microfloral growths is revealed by the study which needs to be taken into account in soiling management strategies.

  17. Oxford Shoulder Score: A Cross-Cultural Adaptation and Validation Study of the Persian Version in Iran

    PubMed Central

    Ebrahimzadeh, Mohammad H.; Birjandinejad, Ali; Razi, Shiva; Mardani-Kivi, Mohsen; Reza Kachooei, Amir

    2015-01-01

    Background: Oxford shoulder score is a specific 12-item patient-reported tool for evaluation of patients with inflammatory and degenerative disorders of the shoulder. Since its introduction, it has been translated and culturally adapted in some Western and Eastern countries. The aim of this study was to translate the Oxford Shoulder Score (OSS) in Persian and to test its validity and reliability in Persian speaking population in Iran. Methods: One hundred patients with degenerative or inflammatory shoulder problem participated in the survey in 2012. All patients completed the Persian version of OSS, Persian DASH and the SF-36 for testing validity. Randomly, 37 patients filled out the Persian OSS again three days after the initial visit to assess the reliability of the questionnaire. Results: Cronbach’s alpha coefficient was 0.93. The intraclass correlation coefficient was 0.93. In terms of validity, there was a significant correlation between the Persian OSS and DASH and SF-36 scores (P<0.001). Conclusion: The Persian version of the OSS proved to be a valid, reliable, and reproducible tool as demonstrated by high Cronbach’s alpha and Pearson’s correlation coefficients. The Persian transcript of OSS is administrable to Persian speaking patients with shoulder condition and it is understandable by them. PMID:26379346

  18. Ohio At-Risk Linkage Team Project. A Report on Three State Team Projects. Linkage Survey. Linkage Workshop for Local Teams. Identification of Exemplary Local Linkages.

    ERIC Educational Resources Information Center

    Imel, Susan; Sandoval, Gloria T.

    To implement an action plan developed during an institute on building linkages for at-risk youth and adults through vocational technical education, a team of representatives from the Ohio Departments of Education and Human Services undertook three activities. First, a survey was sent to 832 Ohio educators and human services personnel to identify…

  19. ARE COASTAL WETLAND-LAKE LINKAGES IMPORTANT?

    EPA Science Inventory

    Because coastal werlands typically comprise only a small percentage of the overall surface area in large lakes, an assumption has often been made that functional links between wetlands and the lake proper are of little significance. Recent investigations of functional linkages be...

  20. Automated linkage analysis in psychiatric disorders

    SciTech Connect

    He, L.; Mansfield, D.C.; Brown, A.F.; Green, D.K.

    1995-06-19

    A genome-wide search for linkage of microsatellite markers to chromosomal loci containing genes responsible for the major psychoses is a laborious task which can be carried out with greater speed and economy by introducing automation to several steps in the procedure. We describe the use of the Automated Linkage Preprocessor (ALP) program for the computer analysis of the waveform generated by fluorescein-labelled markers after electrophoretic separation. (To obtain a copy send a request to A.F. Brown at the below MRC address or use Anonymous FTP to ftp.hgu.mrc.ac.uk. Software is in directory pub/ALP.) The program runs on a PC in the Microsoft Windows environment, and is used in conjunction with an automated laser fluorescence (ALF) sequencer (Pharmacia) and its Fragment Manager{trademark} software to detect and size the PCR products, filter out peaks of fluorescence due to nonallele fragments, and generate genotypes in a format suitable for direct input to standard linkage analysis programs. The method should offer the advantages of speed, accuracy, and reduced cost. Its use in linkage studies in a large family with manic-depressive illness is discussed. 14 refs., 3 figs., 1 tab.

  1. Probabilistic Linkage of Prehospital and Outcomes Data in Out-of-hospital Cardiac Arrest

    PubMed Central

    Mumma, Bryn E.; Diercks, Deborah B.; Danielsen, Beate; Holmes, James F.

    2014-01-01

    Objective Lack of longitudinal patient outcome data is an important barrier in emergency medical services (EMS) research. We aimed to demonstrate the feasibility of linking prehospital data from the California EMS Information Systems (CEMSIS) database to outcomes data from the California Office of Statewide Health Planning and Development (OSHPD) database for patients with out-of-hospital cardiac arrest (OHCA). Methods We included patients age 18 years or older who sustained non-traumatic OHCA and were included in the 2010–2011 CEMSIS databases. The CEMSIS database is a unified EMS data collection system for California. The OSHPD database is a comprehensive data collection system for patient-level inpatient and emergency department encounters in California. OHCA patients were identified in the CEMSIS database using cardiac rhythm, procedures, medications, and provider impression. Probabilistic linkage blocks were created using in hospital death or one of the following primary or secondary diagnoses (I CD-9-CM) in the OSHPD databases: cardiac arrest (427.5), sudden death (798), ventricular tachycardia (427.1), ventricular fibrillation (427.4), and acute myocardial infarction (410.xx). Blocking variables included incident date, gender, date of birth, age, and/or destination facility. Due to the volume of cases, match thresholds were established based on clerical record review for each block individually. Match variables included incident date, destination facility, date of birth, sex, race, and ethnicity. Results Of the 14,603 cases of OHCA we identified in the prehospital databases, 91 (0.6%) duplicate records were excluded. Overall, 46% of the data used in the linkage algorithm were missing in CEMSIS. We linked 4,961/14,512 (34.2%) records. Linkage rates varied significantly by local EMS agency, ranging from 1.4% to 61.1% (OR for linkage 0.009–0.76; p<0.0001). After excluding the local EMS agency with the outlying low linkage rate, we linked 4,934/12,596 (39

  2. Three Degree of Freedom Parallel Mechanical Linkage

    NASA Technical Reports Server (NTRS)

    Adelstein, Bernard D. (Inventor)

    1998-01-01

    A three degree of freedom parallel mechanism or linkage that couples three degree of freedom translational displacements at an endpoint, such as a handle, a hand grip, or a robot tool, to link rotations about three axes that are fixed with respect to a common base or ground link. The mechanism includes a three degree of freedom spherical linkage formed of two closed loops, and a planar linkage connected to the endpoint. The closed loops are rotatably interconnected, and made of eight rigid links connected by a plurality of single degree of freedom revolute joints. Three of these revolute joints are base joints and are connected to a common ground. such that the axis lines passing through the revolute joints intersect at a common fixed center point K forming the center of a spherical work volume in which the endpoint is capable of moving. 'Me three degrees of freedom correspond to the spatial displacement of the endpoint, for instance. The mechanism provides a new overall spatial kinematic linkage composed of a minimal number of rigid links and rotary joints. The mechanism has improved mechanical stiffness, and conveys mechanical power bidirectionally between the human operator and the electromechanical actuators. It does not require gears, belts. cable, screw or other types of transmission elements, and is useful in applications requiring full backdrivability. Thus, this invention can serve as the mechanical linkage for actively powered devices such as compliant robotic manipulators and force-reflecting hand controllers, and passive devices such as manual input devices for computers and other systems.

  3. Weak linkage between the heaviest rainfall and tallest storms

    PubMed Central

    Hamada, Atsushi; Takayabu, Yukari N.; Liu, Chuntao; Zipser, Edward J.

    2015-01-01

    Conventionally, the heaviest rainfall has been linked to the tallest, most intense convective storms. However, the global picture of the linkage between extreme rainfall and convection remains unclear. Here we analyse an 11-year record of spaceborne precipitation radar observations and establish that a relatively small fraction of extreme convective events produces extreme rainfall rates in any region of the tropics and subtropics. Robust differences between extreme rainfall and convective events are found in the rainfall characteristics and environmental conditions, irrespective of region; most extreme rainfall events are characterized by less intense convection with intense radar echoes not extending to extremely high altitudes. Rainfall characteristics and environmental conditions both indicate the importance of warm-rain processes in producing extreme rainfall rates. Our results demonstrate that, even in regions where severe convective storms are representative extreme weather events, the heaviest rainfall events are mostly associated with less intense convection. PMID:25708295

  4. External linkage tie permits reduction in ducting system flange thickness

    NASA Technical Reports Server (NTRS)

    Pfleger, R. O.

    1966-01-01

    External linkage tie reduces flange thickness and increases seal efficiency in high pressure ducting and piping systems. The linkage transmits the pressure separating load to the tube wall behind the flange allowing the flange to support only the seal.

  5. Syphilis in pregnancy and congenital syphilis in Amazonas State, Brazil: an evaluation using database linkage.

    PubMed

    Soeiro, Claudia Marques de Oliveira; Miranda, Angélica Espinosa; Saraceni, Valeria; Santos, Marcelo Cordeiro dos; Talhari, Sinesio; Ferreira, Luiz Carlos de Lima

    2014-04-01

    This study analyzes notification of syphilis in pregnancy and congenital syphilis in Amazo- nas State, Brazil, from 2007 to 2009 and verifies underreporting in databases in the National Information System on Diseases of Notification (SINAN) and the occurrence of perinatal deaths associated with congenital syphilis and not reported in the Mortality Information System (SIM). This was a cross-sectional study with probabilistic record linkage between the SINAN and SIM. There were 666 reports of syphilis in pregnant women, including 224 in 2007 (3.8/1,000), 244(4.5/1,000) in 2008, and 198(4.0/1,000) in 2009. The study found 486 cases of congenital syphilis, of which 153 in 2007 (2.1/1,000), 193 in 2008 (2.6/1,000), and 140 in 2009 (2.0/1,000). After linkage of the SINAN databases, 237 pregnant women (35.6%) had cases of congenital syphilis reported. The SIM recorded 4,905 perinatal deaths, of which 57.8% were stillbirths. Probabilistic record linkage between SIM and SINAN-Congenital Syphilis yielded 13 matched records. The use of SINAN and SIM may not reflect the total magnitude of syphilis, but provide the basis for monitoring and analyzing this health problem, with a view towards planning and management. PMID:24896047

  6. Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes.

    PubMed

    Wu, Weiwei; Hao, Honglei; Liu, Qiuling; Han, Xian; Wu, Yeda; Cheng, Jianding; Lu, Dejian

    2014-09-01

    The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.

  7. The Linking Agent and FLS: Research Supported Assumptions about Linkage.

    ERIC Educational Resources Information Center

    Springfield, Charlotte; Anderson, E. Chris

    This paper describes the Florida Linkage System (FLS), which was designed to help schools throughout the state improve their problem-solving processes and knowledge utilization. While the system's goals are listed and a model for its linkage strategy is outlined, the major portion of the report discusses three findings about the linkage strategy…

  8. Kids Talk: Strategic Language Use in Later Childhood. Oxford Studies in Sociolinguistics.

    ERIC Educational Resources Information Center

    Hoyle, Susan M., Ed.; Adger, Carolyn Temple, Ed.

    Attention to the language practices of school-age children and teenagers is essential for a complete understanding of how language use can vary in the social construction of everyday activity across the life span. This book examines a wide variety of language practices using data from naturally occurring recorded talk and careful observation of…

  9. Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males.

    PubMed

    Hayes, B J; Gjuvsland, A; Omholt, S

    2006-07-01

    Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependent on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA. PMID:16685283

  10. Adjustable throttle linkage for outboard motors

    SciTech Connect

    Dunham, W.D.; Miller, G.L.

    1986-02-17

    An adjustable throttle linkage is described for use in controlling operation of an internal combustion engine having a carburetor including a pivotable throttle valve, a throttle valve position control member operably connected to the throttle valve and movable so as to control the position of the throttle valve, and a throttle lever for controlling the position of the throttle valve. The adjustable throttle linkage comprises a connecting link having one end connected to one of the throttle lever and the control member, and having a threaded portion, means for adjustably connecting the threaded portion to the other of the throttle lever and the control member. The adjustable connecting means includes a slot in the other of the throttle lever and the control member, and a rotatable member threaded onto the threaded portion and receive in the slot such that rotation of the rotatable member causes relative movement between the link and the other of the throttle lever and the control member.

  11. Linkage of typical pseudoachondroplasia to chromosome 19

    SciTech Connect

    Hecht, J.T.; Deere, M.; Conner, B.; Horton, W.A. ); Francomano, C.A. ); Briggs, M.D.; Cohn, D.H. ); Warman, M. ); Blanton, S.H. )

    1993-12-01

    Pseudoachondroplasia (PSACH) is an autosomal dominant dwarfing condition associated with disproportionate short stature, marked joint deformities, and early onset osteoarthritis. Previous linkage studies have excluded linkage to cartilage and noncartilagenous extracellular matrix candidate genes. Here, the authors report mapping the pseudoachondroplasia gene to chromosome 19. Maximum lod scores of 4.70, 4.15, and 4.86 at [theta] = 0.00 were found for D19S212, D19S215, and D19S49, respectively. Multipoint analysis suggests the following order: D19S253-D19S199-(D19S212/PSACH/D19S215)-D19S222-D19S49. 24 refs., 4 figs., 1 tab.

  12. Linkages among global and regional air issues

    SciTech Connect

    Maarouf, A.R.

    1997-11-01

    Six air issues are currently on science and policy agendas in Canada and elsewhere. These are climate change, stratospheric ozone depletion, acidic deposition, SMOG, suspended particulate matter, and hazardous air pollutants. It is now recognized that these issues are interrelated, and they may interact to cause negative as well as some beneficial effects. The linkages among these issues must therefore be better understood in order to develop effective policies to deal with this ensemble of related issues. This paper illustrates through several examples the linkages among the air issues. It also points to potentially conflicting policies arising from the single-issue approach, and it emphasizes the need for better integration of air issues. 14 refs., 1 tab.

  13. Permethylation Linkage Analysis Techniques for Residual Carbohydrates

    NASA Astrophysics Data System (ADS)

    Price, Neil P. J.

    Permethylation analysis is the classic approach to establishing the position of glycosidic linkages between sugar residues. Typically, the carbohydrate is derivatized to form acid-stable methyl ethers, hydrolyzed, peracetylated, and analyzed by gas chromatography-mass spectrometry. The position of glycosidic linkages in the starting carbohydrate are apparent from the mass spectra as determined by the location of acetyl residues. The completeness of permethylation is dependent upon the choice of base catalyst and is readily confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry mass spectrometry. For the permethylation of β-cyclodextrin, Hakomori dimsyl base is shown to be superior to the NaOH-dimethyl sulfoxide system, and the use of the latter resulted in selective under-methylation of the 3-hydroxy groups. These techniques are highly applicable to residual carbohydrates from biofuel processes.

  14. Kosnarite, KZr2(PO4)3, a new mineral from Mount Mica and Black Mountain, Oxford County, Maine

    USGS Publications Warehouse

    Brownfield, M.E.; Foord, E.E.; Sutley, S.J.; Botinelly, T.

    1993-01-01

    Kosnarite, ideally KZr2(PO4)3, has been identified as part of a late-stage, secondary phosphate mineral assemblage from the Mount Mica pegmatite at Paris, and from the Black Mountain pegmatite, Rumford, Oxford County, Maine. Kosnarite from Mount Mica occurs as pseudocubic rhombohedral crystals, as much as 0.9 mm in maximum dimension, that display the dominant {102} form. Color ranges from pale blue to blue-green to nearly colorless. The mineral has a white streak, is transparent, has a vitreous luster, and is nonfluorescent in ultraviolet light. It has a hardness of 4.5, is brittle with a conchoidal fracture, and has perfect {102} cleavage. Kosnarite from Black Mountain is almost pure KZr2(PO4)3 with only trace amounts of Hf, Mn, Na, and Rb. The mineral is one of three known alkali zirconium phosphates; the others are gainesite and the Cs analogue of gainesite. -from Author

  15. Structure and apoprotein linkages of phycourobilin.

    PubMed

    Killilea, S D; O'Carra, P

    1985-03-15

    R-Phycoerythrin contains two covalently bound bilin prosthetic groups, phycoerythrobilin and phycourobilin. The two chromophore types were separated as their peptide-bound derivatives by subjecting tryptic digests of R-phycoerythrin to adsorption chromatography on Sephadex G-25. The structure and apoprotein linkages of the bound phycoerythrobilin were found to be identical with those previously reported for this phycobilin [Killilea, O'Carra & Murphy (1980) Biochem. J. 187, 311-320]. Phycourobilin is a tetrapyrrole, containing no oxo bridges and has the same order of side chains as IX alpha bilins. The chromophore is linked to the peptide through two and possibly three of its pyrrole rings. One linkage possibly consists of an ester bond between the hydroxy group of a serine residue and the propionic acid side chain of one of the inner rings. The second linkage is a labile thioether bond between a cysteine residue and the C2 side chain of pyrrole ring A. The third linkage is a stable thioether bond between a cysteine residue and the alpha-carbon atom of the C2 side chain of pyrrole ring D. Ring D is unsaturated and is attached to ring C through a saturated carbon bridge. Rings B and C have a conjugated system of five bonds, as found in other urobilinoid pigments. Ring A is attached to ring B via a saturated carbon bridge. Both of the alpha-positions of ring A are in the reduced state, but the ring does contain an unsaturated centre (probably a double bond between the beta-carbon and the ring nitrogen atom). The presence of this double bond and its isomerization into the bridge position between rings A and B would explain the extension of the conjugated system of phycourobilin to that of a phycoerythrobilinoid/rhodenoid pigment in acid or alkali. PMID:3838665

  16. Structure and apoprotein linkages of phycourobilin.

    PubMed Central

    Killilea, S D; O'Carra, P

    1985-01-01

    R-Phycoerythrin contains two covalently bound bilin prosthetic groups, phycoerythrobilin and phycourobilin. The two chromophore types were separated as their peptide-bound derivatives by subjecting tryptic digests of R-phycoerythrin to adsorption chromatography on Sephadex G-25. The structure and apoprotein linkages of the bound phycoerythrobilin were found to be identical with those previously reported for this phycobilin [Killilea, O'Carra & Murphy (1980) Biochem. J. 187, 311-320]. Phycourobilin is a tetrapyrrole, containing no oxo bridges and has the same order of side chains as IX alpha bilins. The chromophore is linked to the peptide through two and possibly three of its pyrrole rings. One linkage possibly consists of an ester bond between the hydroxy group of a serine residue and the propionic acid side chain of one of the inner rings. The second linkage is a labile thioether bond between a cysteine residue and the C2 side chain of pyrrole ring A. The third linkage is a stable thioether bond between a cysteine residue and the alpha-carbon atom of the C2 side chain of pyrrole ring D. Ring D is unsaturated and is attached to ring C through a saturated carbon bridge. Rings B and C have a conjugated system of five bonds, as found in other urobilinoid pigments. Ring A is attached to ring B via a saturated carbon bridge. Both of the alpha-positions of ring A are in the reduced state, but the ring does contain an unsaturated centre (probably a double bond between the beta-carbon and the ring nitrogen atom). The presence of this double bond and its isomerization into the bridge position between rings A and B would explain the extension of the conjugated system of phycourobilin to that of a phycoerythrobilinoid/rhodenoid pigment in acid or alkali. PMID:3838665

  17. Hidden linkages between urbanization and food systems.

    PubMed

    Seto, Karen C; Ramankutty, Navin

    2016-05-20

    Global societies are becoming increasingly urban. This shift toward urban living is changing our relationship with food, including how we shop and what we buy, as well as ideas about sanitation and freshness. Achieving food security in an era of rapid urbanization will require considerably more understanding about how urban and food systems are intertwined. Here we discuss some potential understudied linkages that are ripe for further examination.

  18. Hidden linkages between urbanization and food systems.

    PubMed

    Seto, Karen C; Ramankutty, Navin

    2016-05-20

    Global societies are becoming increasingly urban. This shift toward urban living is changing our relationship with food, including how we shop and what we buy, as well as ideas about sanitation and freshness. Achieving food security in an era of rapid urbanization will require considerably more understanding about how urban and food systems are intertwined. Here we discuss some potential understudied linkages that are ripe for further examination. PMID:27199419

  19. A genomic survey of linkage disequilibrium

    SciTech Connect

    Peterson, A.; Freimer, N.; Slakin, M.

    1994-09-01

    Linkage disequilibrium (LD), the association of alleles between two or more loci, is a powerful tool for genetic mapping. LD is governed by recombination, mutation, selection, and population admixture; little is known about their relative importance or the distribution of LD across the genome. We used microsatellite markers to conduct a survey of the genomic distribution of LD on chromosome 4, which was chosen because an available radiation hybrid map enabled assessment of LD distribution based on genetic as well as physical distance. To minimize the effect of admixture, we studied a population from Finland, which has a long history of relative isolation. We compared the informativeness of haplotyped and genotyped samples. 33 markers were typed; 29 significant pairwise associations were observed (p<0.05). Although LD was detected between several loci apparently separated by > 2 cM on linkage maps, it was rarely detected between loci separated by more than 40 centiRays on the radiation hybrid map (about 2 megabases). In several instances, LD was not detected between adjacent markers apparently seperated by < 1 cM. In most of these cases, one locus had low heterozygosity or multiple recombination events were directly observed. Contrary to expectation, there was no evident correlation between the ratio of genetic/physical distance and detection of LD; this is likely partially due to the imprecision of linkage maps over small distances. Detection of LD was roughly equivalent in the haplotyped and genotyped samples, probably reflecting the inadequacy of current methods for detection of LD across multiple loci in a single analysis. Conclusion: LD is widely distributed across large genome regions. Marker heterozygosity and physical distance are correlated with detection of LD, and directly observed recombination events may be more useful than linkage maps in evaluating genetic distance in relation to detection of LD.

  20. A Novel Method for Estimating Linkage Maps

    PubMed Central

    Tan, Yuan-De; Fu, Yun-Xin

    2006-01-01

    The goal of linkage mapping is to find the true order of loci from a chromosome. Since the number of possible orders is large even for a modest number of loci, the problem of finding the optimal solution is known as a NP-hard problem or traveling salesman problem (TSP). Although a number of algorithms are available, many either are low in the accuracy of recovering the true order of loci or require tremendous amounts of computational resources, thus making them difficult to use for reconstructing a large-scale map. We developed in this article a novel method called unidirectional growth (UG) to help solve this problem. The UG algorithm sequentially constructs the linkage map on the basis of novel results about additive distance. It not only is fast but also has a very high accuracy in recovering the true order of loci according to our simulation studies. Since the UG method requires n − 1 cycles to estimate the ordering of n loci, it is particularly useful for estimating linkage maps consisting of hundreds or even thousands of linked codominant loci on a chromosome. PMID:16783016

  1. Genetic linkage for Darier disease (keratosis follicularis)

    SciTech Connect

    Kennedy, J.L.; King, N.; Perkins, M.

    1995-01-30

    Darier disease is an autosomal dominant skin disorder characterized by abnormal keratinocyte adhesion. Recent data have provided evidence for linkage of the Darier disease locus to 12q23-24.1 in British families. We have carried out linkage analysis using the 12q markers D12S58, D12S84, D12S79, D12S86, PLA2, and D12S63 in 6 Canadian families. Pairwise linkage analysis generated positive lod scores at all 6 markers at various recombination fractions, and each family showed positive lod scores with more than one marker. The peak lod score in the multipoint analysis (Z{sub max}) was 5.5 in the interval between markers D12S58 and D12S84. These positive lod scores in North American families of varied European ancestry confirm the location of the Darier disease gene, and suggest genetic homogeneity. The future identification and sequencing of the gene responsible for Darier disease should lead to improved understanding of the disease and of keratinocyte adhesion in general. 22 refs., 2 figs., 2 tabs.

  2. Methods for genetic linkage analysis using trisomies

    SciTech Connect

    Feingold, E.; Lamb, N.E.; Sherman, S.L.

    1995-02-01

    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of {open_quotes}susceptibility{close_quotes} alleles inherited from the nondisjoining parent give increased likelihood of having the trait. Our mapping method is similar to identity-by-descent-based mapping methods using affected relative pairs and also to methods for mapping recessive traits using inbred individuals by looking for markers with greater than expected homozygosity by descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected homozygosity in the chromosomes inherited from the nondisjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the trait gene, a confidence interval for that distance, and methods for computing power and sample sizes. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers and how to test candidate genes. 20 refs., 5 figs., 1 tab.

  3. 'Linkage' pharmaceutical evergreening in Canada and Australia

    PubMed Central

    Faunce, Thomas A; Lexchin, Joel

    2007-01-01

    'Evergreening' is not a formal concept of patent law. It is best understood as a social idea used to refer to the myriad ways in which pharmaceutical patent owners utilise the law and related regulatory processes to extend their high rent-earning intellectual monopoly privileges, particularly over highly profitable (either in total sales volume or price per unit) 'blockbuster' drugs. Thus, while the courts are an instrument frequently used by pharmaceutical brand name manufacturers to prolong their patent royalties, 'evergreening' is rarely mentioned explicitly by judges in patent protection cases. The term usually refers to threats made to competitors about a brand-name manufacturer's tactical use of pharmaceutical patents (including over uses, delivery systems and even packaging), not to extension of any particular patent over an active product ingredient. This article focuses in particular on the 'evergreening' potential of so-called 'linkage' provisions, imposed on the regulatory (safety, quality and efficacy) approval systems for generic pharmaceuticals of Canada and Australia, by specific articles in trade agreements with the US. These 'linkage' provisions have also recently appeared in the Korea-US Free Trade Agreement (KORUSFTA). They require such drug regulators to facilitate notification of, or even prevent, any potential patent infringement by a generic pharmaceutical manufacturer. This article explores the regulatory lessons to be learnt from Canada's and Australia's shared experience in terms of minimizing potential adverse impacts of such 'linkage evergreening' provisions on drug costs and thereby potentially on citizen's access to affordable, essential medicines. PMID:17543113

  4. 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.

  5. Reform and Planning of Higher Education, Symposium at Oxford, 31st March-5th April 1974. Council of Europe Information Bulletin. Vol. 3, 1974.

    ERIC Educational Resources Information Center

    Council of Europe, Strasbourg (France). Documentation Center for Education in Europe.

    Presented in this document are the conference papers on Reform and Planning of Higher Education, held in Oxford, England, March 31-April 5, 1974. This symposium was centered on the British experience and the present state of thinking in the United Kingdom, and includes fifteen papers read by British lecturers and five by non-British lecturers that…

  6. Does the Oxford Reading Pen Enhance Reading Accuracy and Comprehension for Students with Reading Difficulties in a Classroom Environment? An Implementation Trial

    ERIC Educational Resources Information Center

    Johnson, Ian

    2008-01-01

    This article was undertaken to determine whether the Oxford Reading Pen (ORP) could enable students with reading difficulties to read and comprehend text at their chronological age. A small sample of students with reading difficulties was involved in a trial to ascertain the impact of using the ORP within their classroom reading activities. The…

  7. The acceptability of repeat Internet-based hybrid diet assessment of previous 24-h dietary intake: administration of the Oxford WebQ in UK Biobank.

    PubMed

    Galante, Julieta; Adamska, Ligia; Young, Alan; Young, Heather; Littlejohns, Thomas J; Gallacher, John; Allen, Naomi

    2016-02-28

    Although dietary intake over a single 24-h period may be atypical of an individual's habitual pattern, multiple 24-h dietary assessments can be representative of habitual intake and help in assessing seasonal variation. Web-based questionnaires are convenient for the participant and result in automatic data capture for study investigators. This study reports on the acceptability of repeated web-based administration of the Oxford WebQ--a 24-h recall of frequency from a set food list suitable for self-completion from which energy and nutrient values can be automatically generated. As part of the UK Biobank study, four invitations to complete the Oxford WebQ were sent by email over a 16-month period. Overall, 176 012 (53% of those invited) participants completed the online version of the Oxford WebQ at least once and 66% completed it more than once, although only 16% completed it on all four occasions. The response rate for any one round of invitations varied between 34 and 26%. On most occasions, the Oxford WebQ was completed on the same day that they received the invitation, although this was less likely if sent on a weekend. Participants who completed the Oxford WebQ tended to be white, female, slightly older, less deprived and more educated, which is typical of health-conscious volunteer-based studies. These findings provide preliminary evidence to suggest that repeated 24-h dietary assessment via the Internet is acceptable to the public and a feasible strategy for large population-based studies. PMID:26652593

  8. Bayesian model selection for multiple QTLs mapping combining linkage disequilibrium and linkage.

    PubMed

    Jiang, Dan; Ma, Guoda; Yang, Runqing; Li, Keshen; Fang, Ming

    2014-01-01

    Linkage disequilibrium (LD) mapping is able to localize quantitative trait loci (QTL) within a rather small region (e.g. 2 cM), which is much narrower than linkage analysis (LA, usually 20 cM). The multilocus LD method utilizes haplotype information around putative mutation and takes historical recombination events into account, and thus provides a powerful method for further fine mapping. However, sometimes there are more than one QTLs in the region being studied. In this study, the Bayesian model selection implemented via the Markov chain Monte Carlo (MCMC) method is developed for fine mapping of multiple QTLs using haplotype information in a small region. The method combines LD as well as linkage information. A series of simulation experiments were conducted to investigate the behavior of the method. The results showed that this new multiple QTLs method was more efficient in separating closely linked QTLs than single-marker association studies. PMID:25579473

  9. Bayesian model selection for multiple QTLs mapping combining linkage disequilibrium and linkage.

    PubMed

    Jiang, Dan; Ma, Guoda; Yang, Runqing; Li, Keshen; Fang, Ming

    2014-09-19

    Linkage disequilibrium (LD) mapping is able to localize quantitative trait loci (QTL) within a rather small region (e.g. 2 cM), which is much narrower than linkage analysis (LA, usually 20 cM). The multilocus LD method utilizes haplotype information around putative mutation and takes historical recombination events into account, and thus provides a powerful method for further fine mapping. However, sometimes there are more than one QTLs in the region being studied. In this study, the Bayesian model selection implemented via the Markov chain Monte Carlo (MCMC) method is developed for fine mapping of multiple QTLs using haplotype information in a small region. The method combines LD as well as linkage information. A series of simulation experiments were conducted to investigate the behavior of the method. The results showed that this new multiple QTLs method was more efficient in separating closely linked QTLs than single-marker association studies.

  10. A Microsatellite Genetic Linkage Map for Xiphophorus

    PubMed Central

    Walter, R. B.; Rains, J. D.; Russell, J. E.; Guerra, T. M.; Daniels, C.; Johnston, Dennis A.; Kumar, Jay; Wheeler, A.; Kelnar, K.; Khanolkar, V. A.; Williams, E. L.; Hornecker, J. L.; Hollek, L.; Mamerow, M. M.; Pedroza, A.; Kazianis, S.

    2004-01-01

    Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between “male” and “female” maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent

  11. Carburetion system including an adjustable throttle linkage

    SciTech Connect

    Du Bois, C.G.; Falig, J.D.

    1986-03-25

    A throttle linkage assembly is described comprising a throttle shaft rotatable about a throttle shaft axis between an idle position and a wide open throttle position, a throttle plate fixed on the throttle shaft, a driven lever pivotable about the throttle shaft axis between various angles relative to the throttle plate, and means for fixing the driven lever at a selected angle relative to the throttle plate an adjustment lever fixedly connected to the throttle adjacent the driven lever, and means for releasably securing the driven lever to the adjustment lever.

  12. Linkage mapping bovine EST-based SNP

    PubMed Central

    Snelling, Warren M; Casas, Eduardo; Stone, Roger T; Keele, John W; Harhay, Gregory P; Bennett, Gary L; Smith, Timothy PL

    2005-01-01

    Background Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. Results Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. Conclusion Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and

  13. A trial linkage of the road accident and vehicle registration files.

    PubMed

    Lindeijer, J E

    1987-04-01

    Vehicle characteristics are of importance in all phases of road accident. None, however, are recorded by the police on the road accident registration form in The Netherlands. By linking the Vehicle Registration file to the Road Accident file a number of important vehicle characteristics can be added to the accident record. Theoretically it had to be possible to link both files because there was a common key variable viz. the vehicle registration number, which in The Netherlands is unique and stays with the vehicle its whole life. The test linkage was aimed at determining whether it was also practically possible. It was furthermore aimed at determining the completeness and reliability of both files. The fatal accidents of 1981 were selected to serve for the test because only fatal accidents are completely recorded, and 1981 was the most recent available year at the time. These limitations made it possible for SWOV to carry out a manual control on vehicle make and model, as this is often recorded by the police. Based on the conformity found, the validity of the linking by vehicle registration number was found to be 94% and the reliability at least 95%. The conclusion is therefore that the linkage can be accomplished in practice and that it reliably adds useful vehicle characteristics to the police records on fatal road accidents. This complementary information is in the first place important for deeper analysis of the relationship between, on the one hand, accident and injury characteristics and, on the other hand, the vehicle characteristics.

  14. Constructing a linkage-linkage disequilibrium map using dominant-segregating markers.

    PubMed

    Zhu, Xuli; Dong, Leiming; Jiang, Libo; Li, Huan; Sun, Lidan; Zhang, Hui; Yu, Weiwu; Liu, Haokai; Dai, Wensheng; Zeng, Yanru; Wu, Rongling

    2016-02-01

    The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage-LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage-LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.

  15. Searching for epistasis and linkage heterogeneity by correlations of pedigree-specific linkage scores.

    PubMed

    Schaid, Daniel J; McDonnell, Shannon K; Carlson, Erin E; Thibodeau, Stephen N; Stanford, Janet L; Ostrander, Elaine A

    2008-07-01

    Recognizing that multiple genes are likely responsible for common complex traits, statistical methods are needed to rapidly screen for either interacting genes or locus heterogeneity in genetic linkage data. To achieve this, some investigators have proposed examining the correlation of pedigree linkage scores between pairs of chromosomal regions, because large positive correlations suggest interacting loci and large negative correlations suggest locus heterogeneity (Cox et al. [1999]; Maclean et al. [1993]). However, the statistical significance of these extreme correlations has been difficult to determine due to the autocorrelation of linkage scores along chromosomes. In this study, we provide novel solutions to this problem by using results from random field theory, combined with simulations to determine the null correlation for syntenic loci. Simulations illustrate that our new methods control the Type-I error rates, so that one can avoid the extremely conservative Bonferroni correction, as well as the extremely time-consuming permutational method to compute P-values for non-syntenic loci. Application of these methods to prostate cancer linkage studies illustrates interpretation of results and provides insights into the impact of marker information content on the resulting statistical correlations, and ultimately the asymptotic P-values.

  16. [Linkage analysis of serial sex crimes].

    PubMed

    Yokota, Kaeko; Watanabe, Kazumi; Wachi, Taeko; Otsuka, Yusuke; Kuraishi, Hiroki; Fujita, Goro

    2015-08-01

    The purpose of this study was twofold: first, to create an index for a behavioral linkage analysis of serial sex crimes, and second, to construct a predictive model for the analysis. Data on 720 sex crimes (rape, indecent assault) committed by 360 offenders arrested between 1993 and 2005 throughout Japan were collected. The following seven behaviors were examined during a series of analyses aimed at illustrating the effectiveness of crime linkage in serial sex crimes: victim age group, area type, publicness of offense site, weapon, time, contact method, and day of the week. The results indicated that six of the seven behaviors (excluding "day of the week") significantly distinguished between linked and unlinked crime pairs. Under a logistic regression of these six variables, which were dichotomously coded in terms of the concordance or discordance between each pair of incidents, the area under the receiver operating characteristic (ROC) curve was 0.85 (95% CI = 0.82-0.87), indicating a high level of discriminative accuracy in identifying disparate sex crimes committed by the same person. PMID:26402952

  17. Methods for genetic linkage analysis using trisomies

    SciTech Connect

    Feingold, E.; Lamb, N.E.; Sherman, S.L.

    1994-09-01

    Certain genetic disorders (e.g. congenital cataracts, duodenal atresia) are rare in the general population, but more common in people with Down`s syndrome. We present a method for using individuals with trisomy 21 to map genes for such traits. Our methods are analogous to methods for mapping autosomal dominant traits using affected relative pairs by looking for markers with greater than expected identity-by-descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected reduction to homozygosity in the chromosomes inherited form the non-disjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the gene, a confidence interval for that distance, and methods for computing power and sample sizes. The methods are described in the context of gene-dosage model for the etiology of the disorder, but can be extended to other models. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers, how to test candidate genes, and how to handle the effect of reduced recombination associated with maternal meiosis I non-disjunction.

  18. [Linkage analysis of serial sex crimes].

    PubMed

    Yokota, Kaeko; Watanabe, Kazumi; Wachi, Taeko; Otsuka, Yusuke; Kuraishi, Hiroki; Fujita, Goro

    2015-08-01

    The purpose of this study was twofold: first, to create an index for a behavioral linkage analysis of serial sex crimes, and second, to construct a predictive model for the analysis. Data on 720 sex crimes (rape, indecent assault) committed by 360 offenders arrested between 1993 and 2005 throughout Japan were collected. The following seven behaviors were examined during a series of analyses aimed at illustrating the effectiveness of crime linkage in serial sex crimes: victim age group, area type, publicness of offense site, weapon, time, contact method, and day of the week. The results indicated that six of the seven behaviors (excluding "day of the week") significantly distinguished between linked and unlinked crime pairs. Under a logistic regression of these six variables, which were dichotomously coded in terms of the concordance or discordance between each pair of incidents, the area under the receiver operating characteristic (ROC) curve was 0.85 (95% CI = 0.82-0.87), indicating a high level of discriminative accuracy in identifying disparate sex crimes committed by the same person.

  19. A linkage study of bipolar disorder

    SciTech Connect

    Kelsoe, J.R.; Sadovnick, A.D.; Remick, R.A.

    1994-09-01

    We are currently surveying the genome with polymorphic DNA markers in search of loci linked to bipolar disorder (manic-depressive illness) in three populations: 20 families (175 subjects) from the general North American population from San Diego (UCSD) and Vancouver (UBC); 3 Icelandic families (55 subjects); and an Old Order Amish pedigree 110 (118 subjects). Over 50 markers on chromosomes 1, 2, 5, 11, 17, 18, 20 and 21 have been examined. All markers have been tested in the Amish and Icelandic families, and a portion of them in the UCSD/UBC families, which we have only recently begun genotyping. The following candidate genes have been examined: {beta}-TSH, dopamine transporter (HDAT), {beta}2 adrenergic receptor (ADRB2), glucocorticoid type II receptor (GRL), D2 dopamine receptor, serotonin transporter (HSERT), and G{alpha}s G protein subunit (GNAS1). Linkage analysis was conducted using an autosomal dominant model with age-dependent reduced penetrance. Subjects with bipolar, schizoaffective, or recurrent major depressive disorders were considered affected. No significant evidence for linkage was obtained. Mildly positive lods ranging between 1.1 and 1.6 were obtained for three loci: D11S29, HDAT, and GRL.

  20. Model-free linkage analysis of a binary trait.

    PubMed

    Xu, Wei; Bull, Shelley B; Mirea, Lucia; Greenwood, Celia M T

    2012-01-01

    Genetic linkage analysis aims to detect chromosomal regions containing genes that influence risk of specific inherited diseases. The presence of linkage is indicated when a disease or trait cosegregates through the families with genetic markers at a particular region of the genome. Two main types of genetic linkage analysis are in common use, namely model-based linkage analysis and model-free linkage analysis. In this chapter, we focus solely on the latter type and specifically on binary traits or phenotypes, such as the presence or absence of a specific disease. Model-free linkage analysis is based on allele-sharing, where patterns of genetic similarity among affected relatives are compared to chance expectations. Because the model-free methods do not require the specification of the inheritance parameters of a genetic model, they are preferred by many researchers at early stages in the study of a complex disease. We introduce the history of model-free linkage analysis in Subheading 1. Table 1 describes a standard model-free linkage analysis workflow. We describe three popular model-free linkage analysis methods, the nonparametric linkage (NPL) statistic, the affected sib-pair (ASP) likelihood ratio test, and a likelihood approach for pedigrees. The theory behind each linkage test is described in this section, together with a simple example of the relevant calculations. Table 4 provides a summary of popular genetic analysis software packages that implement model-free linkage models. In Subheading 2, we work through the methods on a rich example providing sample software code and output. Subheading 3 contains notes with additional details on various topics that may need further consideration during analysis.

  1. Invasive pneumococcal disease in Oxford, 1985–2001: a retrospective case series

    PubMed Central

    Grant, C; Harnden, A; Jewell, G; Knox, K; Peto, T; Crook, D

    2003-01-01

    Aims: To describe a series of children with invasive pneumococcal disease (IPD). Methods: A review of patient records for children aged 0–18 years admitted to the John Radcliffe Hospital with IPD from 1985 to 2001. Social deprivation was measured by the Jarman index. The proportion of children with congenital abnormalities was compared with national data. Results: We identified 140 children with IPD; complete data were available for 136 children. The median age at diagnosis was 1.5 years. The social deprivation score of households of children with IPD was higher than that of the average Oxfordshire household (-2.5 v -7.3, p < 0.001). Forty four per cent of cases had at least one preceding health problem. The children with preceding health problems were significantly older than those with no preceding problems (median age 2.67 years, interquartile range 1.21 to 6.20 versus 1.11 years, interquartile range 0.51 to 2.21; p < 0.001). There was an increased risk of IPD for children with central nervous system malformations (OR = 99, 95% CI 31 to 236), congenital heart disease (OR = 62, 95% CI 24 to 131), and chromosomal abnormalities (OR = 32, 95% CI 6.6 to 96). Conclusions: There is an increased risk of IPD associated with increased social deprivation; and also with central nervous system malformations, congenital heart disease, and chromosomal abnormalities. PMID:12876171

  2. LINKAGE BETWEEN PRODUCTION AND RESPIRATION ON THE LOUISIANA CONTINENTAL SHELF.

    EPA Science Inventory

    Abstract for presentation. Original title, "PRIMARY PRODUCTION, BACTERIOPLANKTON PRODUCTION, AND COMMUNITY RESPIRATION IN STRATIFIED WATERS OF THE NORTHERN GULF OF MEXICO CONTINENTAL SHELF: LINKAGE TO HYPOXIA."

  3. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

    PubMed Central

    Oikonomopoulos, Spyros; Wang, Yu Chang; Djambazian, Haig; Badescu, Dunarel; Ragoussis, Jiannis

    2016-01-01

    To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules. PMID:27554526

  4. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations.

    PubMed

    Oikonomopoulos, Spyros; Wang, Yu Chang; Djambazian, Haig; Badescu, Dunarel; Ragoussis, Jiannis

    2016-01-01

    To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules. PMID:27554526

  5. Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing.

    PubMed

    Hargreaves, Adam D; Mulley, John F

    2015-01-01

    Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0-2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5' and 3' UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species. PMID:26623194

  6. Results of the radiological survey at the former Alba Craft Laboratory site properties, Oxford, Ohio (OXO001)

    SciTech Connect

    Murray, M.E.; Brown, K.S.; Mathis, R.A.

    1993-03-01

    At the request of the US Department of Energy (DOE), a team from Oak Ridge National Laboratory conducted a radiological survey at the former Alba Craft Laboratory Site Properties, Oxford, Ohio. The survey was performed in July and September of 1992. The purpose of the survey was to determine whether the property was contaminated with radioactive residues, primarily [sup 238]U, from uranium machining operations conducted for National Lead of Ohio, a prime Atomic Energy Commission contractor. The survey included scan measurement of direct radiation levels inside and outside the former laboratory, outdoors on eight properties adjoining the former laboratory, and the city right-of-way adjacent to the surveyed properties. Radionuclide concentrations were determined in outdoor surface and subsurface soil samples taken from each property and the exterior of the laboratory. Fixed surface residual radioactivity was measured inside the laboratory and outside the building. Air samples were collected, direct exposure was measured, and samples were collected to measure transferable radioactivity inside the building. Results of the survey indicate areas where surface and soil contamination level s are above the DOE guidelines for uncontrolled areas.

  7. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations.

    PubMed

    Oikonomopoulos, Spyros; Wang, Yu Chang; Djambazian, Haig; Badescu, Dunarel; Ragoussis, Jiannis

    2016-08-24

    To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.

  8. Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing

    PubMed Central

    Hargreaves, Adam D.

    2015-01-01

    Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species. PMID:26623194

  9. The Relevance Aura of Bibliographic Records.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.

    1997-01-01

    Analyzes relevance assessments of topical descriptors for bibliographic records for two dimensions: (1) a vertical conceptual hierarchy of broad to narrow descriptors, and (2) a horizontal linkage of related terms. The data were analyzed for a semantic distance and semantic direction effect as postulated by the Semantic Distance Model. (Author/LRW)

  10. CD Recorders.

    ERIC Educational Resources Information Center

    Falk, Howard

    1998-01-01

    Discussion of CD (compact disc) recorders describes recording applications, including storing large graphic files, creating audio CDs, and storing material downloaded from the Internet; backing up files; lifespan; CD recording formats; continuous recording; recording software; recorder media; vulnerability of CDs; basic computer requirements; and…

  11. A five year experience of the use of factor IX type DE(I) concentrate for the treatment of Christmas disease of Oxford.

    PubMed

    Lane, J L; Rizza, C R; Snape, T J

    1975-08-01

    A survey is presented of the use of the Oxford type DE(I) II-IX-X concentrate in the treatment of Christmas disease in Oxford from January 1970 to September 1974. 72 different patients were treated with a total of 2436 bottles of this concentrate from 143 different batches (each bottle containing 800-1000 units of factor IX). Although most doses were given for the treatment of minor haemorrhages into joints and muscles, 717 bottles of concentrate were used to treat 11 patients who underwent 14 major surgical operations. No episode of intravascular clotting or pulmonary embolism was seen in any patient receiving the concentrate. A detailed study of the plasma levels of factor V, VIII, total progressive antithrombin, platelets and fibrinogen degradation products was carried out before and after transfusion of type DE(I) concentrate in 14 patients. No significant alteration in those factors was found after the transfusion.

  12. 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. PMID:18179066

  13. Energy maps for glycosidic linkage conformations.

    PubMed

    French, Alfred D

    2015-01-01

    Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

  14. Linkage arms for minimizing piston wobble

    SciTech Connect

    Langstroth, S.W.

    1992-07-28

    This patent describes an internal combustion engine having a block within which at least one piston is attached to a crankshaft by a connecting rod between the crankpin of the crankshaft and the wrist pin of the piston. This patent describes improvement in a fixed gear concentric with the axis of the crankshaft and coupled to the block; a follower gear concentric with the crankpin; at least one intermediate gear coupling the fixed gear to the follower gear; wherein the ratio of the gears is such that the follower gear orbits the fixed gear and does not rotate; and linkage arms interconnecting the follower gear and the piston for preventing the rotation of the piston about the wrist pin.

  15. How population growth affects linkage disequilibrium.

    PubMed

    Rogers, Alan R

    2014-08-01

    The "LD curve" relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. This article derives new results about the last of these effects. When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population shrinks, the LD curve rises but remains relatively flat. As LD converges toward a new equilibrium, its time path may not be monotonic. Following an episode of growth, for example, it declines to a low value before rising toward the new equilibrium. These changes happen at different rates for different LD statistics. They are especially slow for estimates of [Formula: see text], which therefore allow inferences about ancient population history. For the human population of Europe, these results suggest a history of population growth.

  16. Linkage of PRA models. Phase 1, Results

    SciTech Connect

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ``Linkage of PRA Models`` project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ``linking`` analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ``generic`` classification scheme to groups plants based upon a particular plant attribute.

  17. The impact of a growing minority population on identification of duplicate records in an enterprise data warehouse.

    PubMed

    Duvall, Scott L; Fraser, Alison M; Kerber, Richard A; Mineau, Geraldine P; Thomas, Alun

    2010-01-01

    Patient medical records are often fragmented across disparate healthcare databases, potentially resulting in duplicate records that may be detrimental to health care services. These duplicate records can be found through a process called record linkage. This paper describes a set of duplicate records in a medical data warehouse found by linking to an external resource containing family history and vital records. Our objective was to investigate the impact database characteristics and linkage methods have on identifying duplicate records using an external resource. Frequency counts were made for demographic field values and compared between the set of duplicate records, the data warehouse, and the external resource. Considerations for understanding the relationship that records labeled as duplicates have with dataset characteristics and linkage methods were identified. Several noticeable patterns were identified where frequency counts between sets deviated from what was expected including how the growth of a minority population affected which records were identified as duplicates. Record linkage is a complex process where results can be affected by subtleties in data characteristics, changes in data trends, and reliance on external data sources. These changes should be taken into account to ensure any anomalies in results describe real effects and are not artifacts caused by datasets or linkage methods. This paper describes how frequency count analysis can be an effective way to detect and resolve anomalies in linkage results and how external resources that provide additional contextual information can prove useful in discovering duplicate records.

  18. The impact of a growing minority population on identification of duplicate records in an enterprise data warehouse.

    PubMed

    Duvall, Scott L; Fraser, Alison M; Kerber, Richard A; Mineau, Geraldine P; Thomas, Alun

    2010-01-01

    Patient medical records are often fragmented across disparate healthcare databases, potentially resulting in duplicate records that may be detrimental to health care services. These duplicate records can be found through a process called record linkage. This paper describes a set of duplicate records in a medical data warehouse found by linking to an external resource containing family history and vital records. Our objective was to investigate the impact database characteristics and linkage methods have on identifying duplicate records using an external resource. Frequency counts were made for demographic field values and compared between the set of duplicate records, the data warehouse, and the external resource. Considerations for understanding the relationship that records labeled as duplicates have with dataset characteristics and linkage methods were identified. Several noticeable patterns were identified where frequency counts between sets deviated from what was expected including how the growth of a minority population affected which records were identified as duplicates. Record linkage is a complex process where results can be affected by subtleties in data characteristics, changes in data trends, and reliance on external data sources. These changes should be taken into account to ensure any anomalies in results describe real effects and are not artifacts caused by datasets or linkage methods. This paper describes how frequency count analysis can be an effective way to detect and resolve anomalies in linkage results and how external resources that provide additional contextual information can prove useful in discovering duplicate records. PMID:20841858

  19. Student-Teacher Linkage Verification: Model Process and Recommendations

    ERIC Educational Resources Information Center

    Watson, Jeffery; Graham, Matthew; Thorn, Christopher A.

    2012-01-01

    As momentum grows for tracking the role of individual educators in student performance, school districts across the country are implementing projects that involve linking teachers to their students. Programs that link teachers to student outcomes require a verification process for student-teacher linkages. Linkage verification improves accuracy by…

  20. Linkages between ACE Vocational Provision and Mainstream VET.

    ERIC Educational Resources Information Center

    Saunders, John

    A study investigated linkages between adult community education (ACE) and mainstream vocational education and training (VET) in Australia, which enable people to move between the two sectors in their pursuit of vocational learning, and the ways in which linkages might be improved or new ones developed. The data from the study were derived from 69…

  1. Appliation of rad-sequencing to linkage mapping in citrus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

  2. The question of linkages in environment and development

    SciTech Connect

    Myers, N.

    1993-05-01

    To make the world more manageable, humans have split it up into disciplinary components such as nations, communities, economic sectors, ecological zones, and scientific disciplines. However, the preoccupation with a certain sector often means the larger perspective is lost. Dynamic interactions between the sectors are as important as the sectors themselves. This article examines the entire issue of linkages. It starts with a conceptual framework analyzing the character and prevalence of linkages, using the oceans as an illustration with its sectors of fisheries, biodiversity, pollution, technology, climate, and energy. Different types of linkages are discussed: linked linages (e.g., economic links serving to reflect or reinforce environmental linkages and vice versa); synergized linkages (e.g.: acid rain in the humid tropics); present/future linages. Examples of super-scope linkages are given: developing world debt; agricultural subsidies; marginal people in marginal environments. Finally the problem of institutional indifference to linkages and world responses to linkages - policy interventions and planning, programing and management - are discussed. 53 refs.

  3. A microsatellite genetic linkage map of black rockfish ( Sebastes schlegeli)

    NASA Astrophysics Data System (ADS)

    Chu, Guannan; Jiang, Liming; He, Yan; Yu, Haiyang; Wang, Zhigang; Jiang, Haibin; Zhang, Quanqi

    2014-12-01

    Ovoviviparous black rockfish ( Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 cM and average inter-marker space of 13.3 cM. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 cM and average inter-marker distance of 12.4 cM. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

  4. Taiwan Schizophrenia Linkage Study: lessons learned from endophenotype-based genome-wide linkage scans and perspective.

    PubMed

    Chen, Wei J

    2013-10-01

    Taiwan Schizophrenia Linkage Study (TSLS) was initiated with a linkage strategy for locating multiple genes, each of small to moderate effect, and aimed to recruit a large enough sample of pairs of affected siblings and their families ascertained from a multisite study. With a sample of 607 families successfully recruited, a total of 2,242 individuals (1,207 affected and 1,035 unaffected) from 557 families were genotyped using 386 microsatellite markers spaced at an average of 9-cM intervals. Here the author reviews the establishment of TSLS and initial signal derived from linkage scan using the diagnosis of schizophrenia. Based on the limited success of the initial linkage analysis, a sufficient-component causal model is proposed to incorporate endophenotypes and genes for schizophrenia. Four types of candidate endophenotype measured in TSLS, including schizotypal personality, Continuous Performance Test, Wisconsin Card Sorting Test, and niacin skin flush test, are briefly described. The author discusses different strategies of linkage analysis incorporating these endophenotypes, including quantitative trait loci (QTL) linkage analysis, clustering-derived subgroups, ordered subset analysis (OSA), and latent classes for linkage scan. Then the author summarizes the linkage signals generated from seven studies of endophenotype-based linkage analysis using TSLS, including QTL scan of neurocognitive performance, QTL scan of niacin skin flush, the family cluster of attention deficit and execution deficit, OSA by schizophrenia-schizotypy factors, nested OSA by age at onset and neurocognitive performance, and the latent class of deficit schizophrenia for linkage analysis. The perspective of combining next-generation sequencing with linkage analysis of families is also discussed.

  5. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

    NASA Astrophysics Data System (ADS)

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

    2016-09-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

  6. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

    PubMed Central

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H

    2016-01-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides. PMID:27580973

  7. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages.

    PubMed

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H

    2016-01-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides. PMID:27580973

  8. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    SciTech Connect

    Field, L.L.; Nagatomi, J.

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  9. A comparison of foot kinematics in people with normal- and flat-arched feet using the Oxford Foot Model.

    PubMed

    Levinger, Pazit; Murley, George S; Barton, Christian J; Cotchett, Matthew P; McSweeney, Simone R; Menz, Hylton B

    2010-10-01

    Foot posture is thought to influence predisposition to overuse injuries of the lower limb. Although the mechanisms underlying this proposed relationship are unclear, it is thought that altered foot kinematics may play a role. Therefore, this study was designed to investigate differences in foot motion between people with normal- and flat-arched feet using the Oxford Foot Model (OFM). Foot posture in 19 participants was documented as normal-arched (n=10) or flat-arched (n=9) using a foot screening protocol incorporating measurements from weightbearing antero-posterior and lateral foot radiographs. Differences between the groups in triplanar motion of the tibia, rearfoot and forefoot during walking were evaluated using a three-dimensional motion analysis system incorporating a multi-segment foot model (OFM). Participants with flat-arched feet demonstrated greater peak forefoot plantar-flexion (-13.7° ± 5.6° vs -6.5° ± 3.7°; p=0.004), forefoot abduction (-12.9° ± 6.9° vs -1.8° ± 6.3°; p=0.002), and rearfoot internal rotation (10.6° ± 7.5° vs -0.2°± 9.9°; p=0.018) compared to those with normal-arched feet. Additionally, participants with flat-arched feet demonstrated decreased peak forefoot adduction (-7.0° ± 9.2° vs 5.6° ± 7.3°; p=0.004) and a trend towards increased rearfoot eversion (-5.8° ± 4.4° vs -2.5° ± 2.6°; p=0.06). These findings support the notion that flat-arched feet have altered motion associated with greater pronation during gait; factors that may increase the risk of overuse injury.

  10. Translation, cultural adaptation and reproducibility of the Oxford Shoulder Score questionnaire for Brazil, among patients with rheumatoid arthritis.

    PubMed

    Lima, Eider da Silva; Natour, Jamil; Moreira, Emilia; Jones, Anamaria

    2016-01-01

    CONTEXT AND OBJECTIVE Although shoulder questionnaires validated for Brazil do exist, none of them are aimed at populations with rheumatic disease. We believe that the Oxford Shoulder Score (OSS) may be useful in this population. The objective of this study was to translate the OSS, adapt it to Brazilian culture and test its reproducibility. DESIGN AND SETTING Validation study conducted in university outpatient clinics. METHODS The OSS was translated into Portuguese by two English teachers and was then retranslated into English by two native English teachers. These translations were reviewed by a committee to establish the version of OSS-Brazil to be administered to 30 patients with rheumatoid arthritis (RA) and shoulder pain, in order to test the cultural adaptation. The validity and reproducibility was tested among another 30 patients with RA and shoulder pain, of both genders and aged 18 to 65 years. The internal consistency and reproducibility were analyzed. The following instruments were evaluated: OSS-Brazil; a numerical scale for shoulder pain; DASH; HAQ and SF-36. RESULTS The internal consistency was 0.957 and the intra and inter-rater reproducibility was 0.917 and 0.861, respectively. A high level of correlation was found between OSS-Brazil and the following: HAQ (-0.663), DASH (-0.731) and the SF-36 domains of functional capacity (0.589), physical aspects (0.507), pain (0.624), general state of health (0.444), vitality (0.634) and mental health (0.578). CONCLUSION OSS-Brazil was successfully translated and adapted, and this version exhibited good internal consistency, reliability and construct validity. PMID:26648280

  11. Pollen–pistil interactions and self-incompatibility in the Asteraceae: new insights from studies of Senecio squalidus (Oxford ragwort)

    PubMed Central

    Allen, Alexandra M.; Thorogood, Christopher J.; Hegarty, Matthew J.; Lexer, Christian; Hiscock, Simon J.

    2011-01-01

    Background Pollen–pistil interactions are an essential prelude to fertilization in angiosperms and determine compatibility/incompatibility. Pollen–pistil interactions have been studied at a molecular and cellular level in relatively few families. Self-incompatibility (SI) is the best understood pollen–pistil interaction at a molecular level where three different molecular mechanisms have been identified in just five families. Here we review studies of pollen–pistil interactions and SI in the Asteraceae, an important family that has been relatively understudied in these areas of reproductive biology. Scope We begin by describing the historical literature which first identified sporophytic SI (SSI) in species of Asteraceae, the SI system later identified and characterized at a molecular level in the Brassicaceae. Early structural and cytological studies in these two families suggested that pollen–pistil interactions and SSI were similar, if not the same. Recent cellular and molecular studies in Senecio squalidus (Oxford ragwort) have challenged this belief by revealing that despite sharing the same genetic system of SSI, the Brassicaceae and Asteraceae molecular mechanisms are different. Key cellular differences have also been highlighted in pollen–stigma interactions, which may arise as a consequence of the Asteraceae possessing a ‘semi-dry’ stigma, rather than the ‘dry’ stigma typical of the Brassicaceae. The review concludes with a summary of recent transcriptomic analyses aimed at identifying proteins regulating pollen–pistil interactions and SI in S. squalidus, and by implication the Asteraceae. The Senecio pistil transcriptome contains many novel pistil-specific genes, but also pistil-specific genes previously shown to play a role in pollen–pistil interactions in other species. Conclusions Studies in S. squalidus have shown that stigma structure and the molecular mechanism of SSI in the Asteraceae and Brassicaceae are different. The

  12. A microsatellite (SSR) based linkage map of Brassica rapa.

    PubMed

    Kapoor, Rahul; Banga, Surindar Singh; Banga, Shashi Kaur

    2009-11-30

    In the present study we describe the construction of a genetic linkage map for the Brassica rapa (AA) genome that will act as a key resource in undertaking future structural and functional genomic studies in B. rapa. A F(2) mapping population consisting of 48 F(2) individual plants developed following hybridization of 2 inbred lines Bathari mandi and IC 331817 was used to construct the map. The map comprises 53 SSR markers derived from 3 different public domain resources. Nine linkage groups along with a small subgroup were identified and designated as R(1)-R(9) through alignment and orientation using SSR markers in common with existing B. rapa reference linkage maps. The total length of the genetic linkage map was 354.6 cm with an average interval of 6.6 cm between adjacent loci. The length of linkage groups ranged from 28.0 cm to 44.2 cm for R(6) and R(1A), respectively. The number variability of markers in the 9 linkage groups ranged from 3 for R(6) to 10 for R(1). Of the 53 SSR markers assigned to the linkage groups, only 5 (9.4%) showed deviation from the expected segregation ratio. The development of this map is vital to the genome integration and genetic information and will enable the international research community to share resources and data for the improvement of B. rapa and other cultivated Brassica species.

  13. Changes in fault length distributions due to fault linkage

    NASA Astrophysics Data System (ADS)

    Xu, Shunshan; Nieto-Samaniego, A. F.; Alaniz-Álvarez, S. A.; Velasquillo-Martínez, L. G.; Grajales-Nishimura, J. M.; García-Hernández, J.; Murillo-Muñetón, G.

    2010-01-01

    Fault linkage plays an important role in the growth of faults. In this paper we analyze a published synthetic model to simulate fault linkage. The results of the simulation indicate that fault linkage is the cause of the shallower local slopes on the length-frequency plots. The shallower local slopes lead to two effects. First, the curves of log cumulative number against log length exhibit fluctuating shapes as reported in literature. Second, for a given fault population, the power-law exponents after linkage are negatively related to the linked length scales. Also, we present datasets of fault length measured from four structural maps at the Cantarell oilfield in the southern Gulf of Mexico (offshore Campeche). The results demonstrate that the fault length data, corrected by seismic resolution at the tip fault zone, also exhibit fluctuating curves of log cumulative frequency vs. log length. The steps (shallower slopes) on the curves imply the scale positions of fault linkage. We conclude that fault linkage is the main reason for the fluctuating shapes of log cumulative frequency vs. log length. On the other hand, our data show that the two-tip faults are better for linear analysis between maximum displacement ( D) and length ( L). Evidently, two-tip faults underwent fewer fault linkages and interactions.

  14. A transparent and transportable methodology for evaluating Data Linkage software.

    PubMed

    Ferrante, Anna; Boyd, James

    2012-02-01

    There has been substantial growth in Data Linkage (DL) activities in recent years. This reflects growth in both the demand for, and the supply of, linked or linkable data. Increased utilisation of DL "services" has brought with it increased need for impartial information about the suitability and performance capabilities of DL software programs and packages. Although evaluations of DL software exist; most have been restricted to the comparison of two or three packages. Evaluations of a large number of packages are rare because of the time and resource burden placed on the evaluators and the need for a suitable "gold standard" evaluation dataset. In this paper we present an evaluation methodology that overcomes a number of these difficulties. Our approach involves the generation and use of representative synthetic data; the execution of a series of linkages using a pre-defined linkage strategy; and the use of standard linkage quality metrics to assess performance. The methodology is both transparent and transportable, producing genuinely comparable results. The methodology was used by the Centre for Data Linkage (CDL) at Curtin University in an evaluation of ten DL software packages. It is also being used to evaluate larger linkage systems (not just packages). The methodology provides a unique opportunity to benchmark the quality of linkages in different operational environments.

  15. Mitonuclear linkage disequilibrium in human populations

    PubMed Central

    Sloan, Daniel B.; Fields, Peter D.; Havird, Justin C.

    2015-01-01

    There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy. PMID:26378221

  16. Mitonuclear linkage disequilibrium in human populations.

    PubMed

    Sloan, Daniel B; Fields, Peter D; Havird, Justin C

    2015-09-22

    There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.

  17. Linkage and the Limits to Natural Selection

    PubMed Central

    Barton, N. H.

    1995-01-01

    The probability of fixation of a favorable mutation is reduced if selection at other loci causes inherited variation in fitness. A general method for calculating the fixation probability of an allele that can find itself in a variety of genetic backgrounds is applied to find the effect of substitutions, fluctuating polymorphisms, and deleterious mutations in a large population. With loose linkage, r, the effects depend on the additive genetic variance in relative fitness, var (W), and act by reducing effective population size by (N/N(e)) = 1 + var (W)/2r(2). However, tightly linked loci can have a substantial effect not predictable from N(e). Linked deleterious mutations reduce the fixation probability of weakly favored alleles by exp(-2U/R), where U is the total mutation rate and R is the map length in Morgans. Substitutions can cause a greater reduction: an allele with advantage s < s(crit) = (π(2)/6) log(e) (S/s)[var(W)/R] is very unlikely to be fixed. (S is the advantage of the substitution impeding fixation.) Fluctuating polymorphisms at many (n) linked loci can also have a substantial effect, reducing fixation probability by exp [ &2Kn var(W)/R] [K = -1/E((u - u)(2)/uv) depending on the frequencies (u,v) at the selected polymorphisms]. Hitchhiking due to all three kinds of selection may substantially impede adaptation that depends on weakly favored alleles. PMID:7498757

  18. Linkage analysis in familial Angelman syndrome

    SciTech Connect

    Wagstaff, J. ); Shugart, Y.Y. ); Lalande, M. Howard Hughes Medical Institute, Boston, MA )

    1993-07-01

    Familial Angelman syndrome (AS) can result from mutations in chromosome 15q11q13 that, when transmitted from father to child, result in no phenotypic abnormality but, when transmitted from mother to child, cause AS. These mutations therefore behave neither as dominant nor as recessive mutations but, rather, show an imprinted mode of inheritance. The authors have analyzed two sibling pairs with AS and a larger family with four AS offspring of three sisters with several recently described microsatellite polymorphisms in the AS region. AS siblings inherited the same maternal alleles at the GABRB3 and GABRA5 loci, and the unaffected siblings of AS individuals inherited the other maternal alleles at these loci. In one of the AS sibling pairs, analysis of a recombination event indicates that the mutation responsible for AS is distal to locus D15S63. This result is consistent with a previously described imprinted submicroscopic deletion causing AS, a deletion that includes loci D15S10, D15S113, and GABRB3, all distal to D15S63. The analysis of the larger AS family provides the first clear demonstration of a new mutation in nondeletion AS. Analysis of linkage of AS to GABRB3 in these three families, on the assumption of imprinted inheritance (i.e., penetrance of an AS mutation is 1 if transmitted maternally and is 0 if transmitted paternally), indicates a maximum lod score of 3.52 at 6 = 0. 34 refs., 4 figs., 1 tab.

  19. Identifying marker typing incompatibilities in linkage analysis

    SciTech Connect

    Stringham, H.M.; Boehnke, M.

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  20. Multipoint linkage detection in the presence of heterogeneity.

    PubMed

    Chiu, Yen-Feng; Liang, Kung-Yee; Beaty, Terri H

    2002-06-01

    Linkage heterogeneity is common for complex diseases. It is well known that loss of statistical power for detecting linkage will result if one assumes complete homogeneity in the presence of linkage heterogeneity. To this end, Smith (1963, Annals of Human Genetics 27, 175-182) proposed an admixture model to account for linkage heterogeneity. It is well known that for this model, the conventional chi-squared approximation to the likelihood ratio test for no linkage does not apply even when the sample size is large. By dealing with nuclear families and one marker at a time for genetic diseases with simple modes of inheritance, score-based test statistics (Liang and Rathouz, 1999, Biometrics 55, 65-74) and likelihood-ratio-based test statistics (Lemdani and Pons, 1995, Biometrics 51, 1033-1041) have been proposed which have a simple large-sample distribution under the null hypothesis of linkage. In this paper, we extend their work to more practical situations that include information from multiple markers and multi-generational pedigrees while allowing for a class of general genetic models. Three different approaches are proposed to eliminate the nuisance parameters in these test statistics. We show that all three approaches lead to the same asymptotic distribution under the null hypothesis of no linkage. Simulation results show that the proposed test statistics have adequate power to detect linkage and that the performances of these two classes of test statistics are quite comparable. We have applied the proposed method to a family study of asthma (Barnes et al., 1996), in which the score-based test shows evidence of linkage with p-value <0.0001 in the region of interest on chromosome 12. Additionally, we have implemented this score-based test within the frequently used computer package GENEHUNTER.

  1. Spectroscopic manifestation of stretching vibrations of glycosidic linkage in polysaccharides

    NASA Astrophysics Data System (ADS)

    Nikonenko, N. A.; Buslov, D. K.; Sushko, N. I.; Zhbankov, R. G.

    2005-10-01

    Manifestation of stretching vibrations of glycosidic linkage in the infrared spectra of polysaccharides (native, microcrystalline, mercerized celluloses, amylose, starches) has been studied using the regularized method of deconvolution. It has been shown that the glycosidic linkage formation in the polysaccharides is characterized by the appearance of new absorption bands in the 1175-1140 cm -1 range as compared to their corresponding monomers. In the 1000-920 cm -1 region differences between the infrared spectra of polysaccharides due to the changes in the glycosidic linkage configuration have been found.

  2. Magnetic Recording.

    ERIC Educational Resources Information Center

    Lowman, Charles E.

    A guide to the technology of magnetic recorders used in such fields as audio recording, broadcast and closed-circuit television, instrumentation recording, and computer data systems is presented. Included are discussions of applications, advantages, and limitations of magnetic recording, its basic principles and theory of operation, and its…

  3. Middle cerebral O₂ delivery during the modified Oxford maneuver increases with sodium nitroprusside and decreases during phenylephrine.

    PubMed

    Stewart, Julian M; Medow, Marvin S; DelPozzi, Andrew; Messer, Zachary R; Terilli, Courtney; Schwartz, Christopher E

    2013-06-01

    The modified Oxford maneuver is the reference standard for assessing arterial baroreflex function. The maneuver comprises a systemic bolus injection of 100 μg sodium nitroprusside (SNP) followed by 150 μg phenylephrine (PE). On the one hand, this results in an increase in oxyhemoglobin and total hemoglobin followed by a decrease within the cerebral sample volume illuminated by near-infrared spectroscopy (NIRS). On the other hand, it produces a decrease in cerebral blood flow velocity (CBFv) within the middle cerebral artery (MCA) during SNP and an increase in CBFv during PE as measured by transcranial Doppler ultrasound. To resolve this apparent discrepancy, we hypothesized that SNP dilates, whereas PE constricts, the MCA. We combined transcranial Doppler ultrasound of the right MCA with NIRS illuminating the right frontal cortex in 12 supine healthy subjects 18-24 yr old. Assuming constant O₂ consumption and venous saturation, as estimated by partial venous occlusion plethysmography, we used conservation of mass (continuity) equations to estimate the changes in arterial inflow (ΔQa) and venous outflow (ΔQv) of the NIRS-illuminated area. Oxyhemoglobin and total hemoglobin, respectively, increased by 13.6 ± 1.6 and 15.2 ± 1.4 μmol/kg brain tissue with SNP despite hypotension and decreased by 6 ± 1 and 7 ± 1 μmol/kg with PE despite hypertension. SNP increased ΔQa by 0.36 ± .03 μmol·kg(-1)·s(-1) (21.6 μmol·kg(-1)·min(-1)), whereas CBFv decreased from 71 ± 2 to 62 ± 2 cm/s. PE decreased ΔQa by 0.27 ± .2 μmol·kg(-1)·s(-1) (16.2 μmol·kg(-1)·min(-1)), whereas CBFv increased to 75 ± 3 cm/s. These results are consistent with dilation of the MCA by SNP and constriction by PE. PMID:23564308

  4. Middle cerebral O2 delivery during the modified Oxford maneuver increases with sodium nitroprusside and decreases during phenylephrine

    PubMed Central

    Medow, Marvin S.; DelPozzi, Andrew; Messer, Zachary R.; Terilli, Courtney; Schwartz, Christopher E.

    2013-01-01

    The modified Oxford maneuver is the reference standard for assessing arterial baroreflex function. The maneuver comprises a systemic bolus injection of 100 μg sodium nitroprusside (SNP) followed by 150 μg phenylephrine (PE). On the one hand, this results in an increase in oxyhemoglobin and total hemoglobin followed by a decrease within the cerebral sample volume illuminated by near-infrared spectroscopy (NIRS). On the other hand, it produces a decrease in cerebral blood flow velocity (CBFv) within the middle cerebral artery (MCA) during SNP and an increase in CBFv during PE as measured by transcranial Doppler ultrasound. To resolve this apparent discrepancy, we hypothesized that SNP dilates, whereas PE constricts, the MCA. We combined transcranial Doppler ultrasound of the right MCA with NIRS illuminating the right frontal cortex in 12 supine healthy subjects 18–24 yr old. Assuming constant O2 consumption and venous saturation, as estimated by partial venous occlusion plethysmography, we used conservation of mass (continuity) equations to estimate the changes in arterial inflow (ΔQa) and venous outflow (ΔQv) of the NIRS-illuminated area. Oxyhemoglobin and total hemoglobin, respectively, increased by 13.6 ± 1.6 and 15.2 ± 1.4 μmol/kg brain tissue with SNP despite hypotension and decreased by 6 ± 1 and 7 ± 1 μmol/kg with PE despite hypertension. SNP increased ΔQa by 0.36 ± .03 μmol·kg−1·s−1 (21.6 μmol·kg−1·min−1), whereas CBFv decreased from 71 ± 2 to 62 ± 2 cm/s. PE decreased ΔQa by 0.27 ± .2 μmol·kg−1·s−1 (16.2 μmol·kg−1·min−1), whereas CBFv increased to 75 ± 3 cm/s. These results are consistent with dilation of the MCA by SNP and constriction by PE. PMID:23564308

  5. The Peace Movement: An Exercise in Micro-Macro Linkages.

    ERIC Educational Resources Information Center

    Galtung, Johan

    1988-01-01

    Contends that the basic assumption of the peace movement is the abuse of military power by the state. Argues that the peace movement is most effective through linkages with cultural, political, and economic forces in society. (BSR)

  6. An autosomal genetic linkage map of the sheep genome

    SciTech Connect

    Crawford, A.M.; Ede, A.J.; Pierson, C.A.

    1995-06-01

    We report the first extensive ovine genetic linkage map covering 2070 cM of the sheep genome. The map was generated from the linkage analysis of 246 polymorphic markers, in nine three-generation full-sib pedigrees, which make up the AgResearch International Mapping Flock. We have exploited many markers from cattle so that valuable comparisons between these two ruminant linkage maps can be made. The markers, used in the segregation analyses, comprised 86 anonymous microsatellite markers derived from the sheep genome, 126 anonymous microsatellites from cattle, one from deer, and 33 polymorphic markers of various types associated with known genes. The maximum number of informative meioses within the mapping flock was 22. The average number of informative meioses per marker was 140 (range 18-209). Linkage groups have been assigned to all 26 sheep autosomes. 102 refs., 8 figs., 5 tabs.

  7. 72. Detail of eyebar linkage between main anchorage beams at ...

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

    72. Detail of eyebar linkage between main anchorage beams at base of statue and anchorage beam between levels 4 and 5. February 1984. - Statue of Liberty, Liberty Island, Manhattan, New York County, NY

  8. Linkage studies of Myotonia congenita and Paramyotonia congenita.

    PubMed

    Bender, K; Senff, H; Steiert, A; Lagodny, H; Wienker, T F; Koch, M

    1989-08-01

    Six German families segregating for Myotonia congenita (MC) and eight families from Germany and Great Britain with Paramyotonia congenita (PC) were tested for linkage relationships using 35 serological and biochemical markers. No linkage of MC to any of the markers was evident, but a positive sum of lod scores for PC vs. the HP locus (z = 1.16, theta = 0.16) was found. The results encourage further investigations involving chromosome 16 markers.

  9. [Linkage disequilibrium analysis for microsatellite loci in six cattle breeds].

    PubMed

    Kiseleva, T Iu; Kantanen, J; Vorob'ev, N I; Podoba, B E; Terletskiĭ, V P

    2014-04-01

    Autosomal microsatellites are valuable tools for investigating genetic diversity and population structure and making conservation decisions to preserve valuable breeds of domestic animals. We carried out a linkage disequilibrium analysis using 29 microsatellite markers in six cattle populations: Suksun, Istoben, Yaroslavl, Kholmogory, Grey Ukrainian and Pechora type Kholmogory breeds. We discovered a significant linkage between microsatellites INRA037 and CSRM60 in Grey Ukrainian breed.

  10. The new philosophy of psychiatry: its (recent) past, present and future: a review of the Oxford University Press series International Perspectives in Philosophy and Psychiatry

    PubMed Central

    Banner, Natalie F; Thornton, Tim

    2007-01-01

    There has been a recent growth in philosophy of psychiatry that draws heavily (although not exclusively) on analytic philosophy with the aim of a better understanding of psychiatry through an analysis of some of its fundamental concepts. This 'new philosophy of psychiatry' is an addition to both analytic philosophy and to the broader interpretation of mental health care. Nevertheless, it is already a flourishing philosophical field. One indication of this is the new Oxford University Press series International Perspectives in Philosophy and Psychiatry seven volumes of which (by Bolton and Hill; Bracken and Thomas; Fulford, Morris, Sadler, and Stanghellini; Hughes, Louw, and Sabat; Pickering; Sadler; and Stanghellini) are examined in this critical review.

  11. Stochastic deletion-insertion algorithm to construct dense linkage maps

    PubMed Central

    Wu, Jixiang; Lou, Xiang-Yang; Gonda, Michael

    2011-01-01

    In this study, we proposed a stochastic deletion-insertion (SDI) algorithm for constructing large-scale linkage maps. This SDI algorithm was compared with three published approximation approaches, the seriation (SER), neighbor mapping (NM), and unidirectional growth (UG) approaches, on the basis of simulated F2 data with different population sizes, missing genotype rates, and numbers of markers. Simulation results showed that the SDI method had a similar or higher percentage of correct linkage orders than the other three methods. This SDI algorithm was also applied to a real dataset and compared with the other three methods. The total linkage map distance (cM) obtained by the SDI method (148.08 cM) was smaller than the distance obtained by SER (225.52 cM) and two published distances (150.11 cM and 150.38 cM). Since this SDI algorithm is stochastic, a more accurate linkage order can be quickly obtained by repeating this algorithm. Thus, this SDI method, which combines the advantages of accuracy and speed, is an important addition to the current linkage mapping toolkit for constructing improved linkage maps. PMID:21927641

  12. Recombination patterns reveal information about centromere location on linkage maps.

    PubMed

    Limborg, Morten T; McKinney, Garrett J; Seeb, Lisa W; Seeb, James E

    2016-05-01

    Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres - an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half-tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination - a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high-density maps in species with strong recombination interference and will enrich many existing and future mapping resources. PMID:26561199

  13. Optimized linkage and quenching strategies for quantum dot molecular beacons.

    PubMed

    Cady, Nathaniel C; Strickland, Aaron D; Batt, Carl A

    2007-04-01

    Quantum dot (QD) molecular beacons were explored for sequence-specific DNA detection. The effectiveness of multiple linkage strategies and fluorescence quenchers were compared in hybridization-based assays. To compare linkage strategies, covalent amide linkage and streptavidin-biotin binding were used to link semiconductor QDs to molecular beacon DNA. Amide-linked beacons showed a 57% greater fluorescence increase than streptavidin-linked beacons when hybridized to 200 pmol of target DNA. The specificity of the molecular beacons, however, was similar for both linkage methods. Hybridization of both QD molecular beacons with non-complementary target DNA resulted in approximately 50% lower fluorescence intensity than hybridization with complementary DNA. The effectiveness of different quencher moieties was also evaluated. Iowa Black and 1.4 nm Nanogold-quenched molecular beacons exhibited approximately 2-fold greater fluorescence increases than dabcyl-quenched beacons when hybridized to complementary target. Specificity for target DNA was also confirmed through hybridization assays with non-complementary DNA. To provide insight into differences between the QD molecular beacons and the linkage strategies used, the hydrodynamic radius of each was measured. These measurements indicated that the larger radius of the streptavidin QDs (13.5 nm) than the carboxyl QDs (7 nm) could have a negative effect on FRET-based quenching for QD molecular beacons. These data outline the importance of choosing proper linkage methods and quencher moieties for creating high-quality QD molecular beacons.

  14. Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches.

    PubMed

    Garcia-Gámez, E; Gutiérrez-Gil, B; Suarez-Vega, A; de la Fuente, L F; Arranz, J J

    2013-09-01

    In this study, 2 procedures were used to analyze a data set from a whole-genome scan, one based on linkage analysis information and the other combing linkage disequilibrium and linkage analysis (LDLA), to determine the quantitative trait loci (QTL) influencing milk production traits in sheep. A total of 1,696 animals from 16 half-sib families were genotyped using the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) and analysis was performed using a daughter design. Moreover, the same data set has been previously investigated through a genome-wide association (GWA) analysis and a comparison of results from the 3 methods has been possible. The linkage analysis and LDLA methodologies yielded different results, although some significantly associated regions were common to both procedures. The linkage analysis detected 3 overlapping genome-wise significant QTL on sheep chromosome (OAR) 2 influencing milk yield, protein yield, and fat yield, whereas 34 genome-wise significant QTL regions were detected using the LDLA approach. The most significant QTL for protein and fat percentages was detected on OAR3, which was reported in a previous GWA analysis. Both the linkage analysis and LDLA identified many other chromosome-wise significant associations across different sheep autosomes. Additional analyses were performed on OAR2 and OAR3 to determine the possible causality of the most significant polymorphisms identified for these genetic effects by the previously reported GWA analysis. For OAR3, the analyses demonstrated additional genetic proof of the causality previously suggested by our group for a single nucleotide polymorphism located in the α-lactalbumin gene (LALBA). In summary, although the results shown here suggest that in commercial dairy populations, the LDLA method exhibits a higher efficiency to map QTL than the simple linkage analysis or linkage disequilibrium methods, we believe that comparing the 3 analysis methods is the best approach to obtain a global

  15. Linkages between terrestrial ecosystems and the atmosphere

    NASA Technical Reports Server (NTRS)

    Bretherton, Francis; Dickinson, Robert E.; Fung, Inez; Moore, Berrien, III; Prather, Michael; Running, Steven W.; Tiessen, Holm

    1992-01-01

    The primary research issue in understanding the role of terrestrial ecosystems in global change is analyzing the coupling between processes with vastly differing rates of change, from photosynthesis to community change. Representing this coupling in models is the central challenge to modeling the terrestrial biosphere as part of the earth system. Terrestrial ecosystems participate in climate and in the biogeochemical cycles on several temporal scales. Some of the carbon fixed by photosynthesis is incorporated into plant tissue and is delayed from returning to the atmosphere until it is oxidized by decomposition or fire. This slower (i.e., days to months) carbon loop through the terrestrial component of the carbon cycle, which is matched by cycles of nutrients required by plants and decomposers, affects the increasing trend in atmospheric CO2 concentration and imposes a seasonal cycle on that trend. Moreover, this cycle includes key controls over biogenic trace gas production. The structure of terrestrial ecosystems, which responds on even longer time scales (annual to century), is the integrated response to the biogeochemical and environmental constraints that develop over the intermediate time scale. The loop is closed back to the climate system since it is the structure of ecosystems, including species composition, that sets the terrestrial boundary condition in the climate system through modification of surface roughness, albedo, and, to a great extent, latent heat exchange. These separate temporal scales contain explicit feedback loops which may modify ecosystem dynamics and linkages between ecosystems and the atmosphere. The long-term change in climate, resulting from increased atmospheric concentrations of greenhouse gases (e.g., CO2, CH4, and nitrous oxide (N2O)) will further modify the global environment and potentially induce further ecosystem change. Modeling these interactions requires coupling successional models to biogeochemical models to

  16. Localization of the Krabbe disease gene (GALC) on chromosome 14 by multipoint linkage analysis

    SciTech Connect

    Oehlmann, R.; Wenger, D.A.; Knowlton, R.G. ); Zlotogora, J. )

    1993-12-01

    The gene responsible for Krabbe disease, an autosomal recessive disorder caused by deficiency of galactocerebrosidase (GALC), was localized by multipoint linkage analysis on chromosome 14. Eight mapped dinucleotide repeat polymorphisms were tested for linkage to GALC. Two-point linkage analysis demonstrated close linkage of GALC and D14S48, with [cflx [Zeta

  17. Use of a novel medium, the Polymyxin Ceftazidime Oxford Medium, for isolation of Listeria monocytogenes from raw or non-pasteurized foods.

    PubMed

    Martínez-Gonzáles, N E; Martínez-Chávez, L; Cabrera-Díaz, E; Martínez-Cárdenas, C; Gutiérrez-González, P; Castillo, A

    2016-05-01

    Polymyxin Ceftazidime Oxford Medium (PCOM), a novel selective and differential plating medium for Listeria monocytogenes was compared with Modified Oxford Agar (MOX) for efficacy to isolate L. monocytogenes and other Listeria spp. naturally present in non-pasteurized Mexican-style cheese (n = 50), non-pasteurized fresh squeezed orange juice (n = 50), raw beef chunks (n = 36), and fresh cabbage (n = 125). Samples were collected from retail markets and farms in Mexico and tested following the US Department of Agriculture enrichment technique. Listeria spp. were isolated from 23.4% of analyzed samples, and from those, 75.0% corresponded to raw beef chunks, 38.0% to non-pasteurized Mexican-style cheese, and 30.0% to fresh squeezed orange juice. No Listeria spp. were isolated from fresh cabbage samples. L. monocytogenes was recovered from 15.3% of food samples analyzed. Non-pasteurized Mexican-style cheese showed the highest proportion of L. monocytogenes positive samples (36.0%), followed by orange juice (26.0%) and raw beef (25.0%). The frequency of isolation of Listeria spp. and L. monocytogenes was not different (P > 0.05) between PCOM and MOX. The advantages of using PCOM when comparing to MOX, include the easier way to identify Listeria species, the lower cost per plate and the availability of its ingredients for Latin-American countries.

  18. The Polymyxin Ceftazidime Oxford Medium as an alternative selective and differential medium for isolation of Listeria monocytogenes from raw or unpasteurized food.

    PubMed

    Martínez-Gonzáles, N E; Martínez-Chávez, L; Martínez-Cárdenas, C; Cabrera-Díaz, E; Castillo, A

    2014-04-01

    The Polymyxin Ceftazidime Oxford Medium (PCOM) was developed to recover Listeria monocytogenes from raw or unpasteurized foods. It contains esculin-ferric ammonium citrate as indicator system for Listeria growth, and ceftazidime and polymyxin B as selective agents, which are available in several Latin American countries. Comparison of PCOM, Modified Oxford Medium (MOX) and Tryptic Soy agar with 0.6% yeast extract (TSAYE) indicated that both selective media were equally effective at recovering four individual strains of L. monocytogenes (Scott A, V7, California and broccoli), and a mixture of these strains (LMM) (P > 0.05). The ability of PCOM, MOX, TSAYE and TSAYE supplemented with 4% NaCl to recover heat, acid and freeze-damaged LMM was similar for all media (P > 0.05). The PCOM proved to be effective at isolating colonies of LMM from inoculated raw beef chunks, unpasteurized orange juice, cabbage, and Mexican-style cheese by direct plating and by the US Department of Agriculture's Food Safety and Inspection Service enrichment method. Differentiation of L. monocytogenes colonies was easier on PCOM than on MOX for foods with high levels of background microbiota. Based on the evaluations performed on foods naturally contaminated with L. monocytogenes, PCOM was a more economical alternative than MOX for selective and differential isolation of Listeria from raw or unpasteurized foods.

  19. Use of a novel medium, the Polymyxin Ceftazidime Oxford Medium, for isolation of Listeria monocytogenes from raw or non-pasteurized foods.

    PubMed

    Martínez-Gonzáles, N E; Martínez-Chávez, L; Cabrera-Díaz, E; Martínez-Cárdenas, C; Gutiérrez-González, P; Castillo, A

    2016-05-01

    Polymyxin Ceftazidime Oxford Medium (PCOM), a novel selective and differential plating medium for Listeria monocytogenes was compared with Modified Oxford Agar (MOX) for efficacy to isolate L. monocytogenes and other Listeria spp. naturally present in non-pasteurized Mexican-style cheese (n = 50), non-pasteurized fresh squeezed orange juice (n = 50), raw beef chunks (n = 36), and fresh cabbage (n = 125). Samples were collected from retail markets and farms in Mexico and tested following the US Department of Agriculture enrichment technique. Listeria spp. were isolated from 23.4% of analyzed samples, and from those, 75.0% corresponded to raw beef chunks, 38.0% to non-pasteurized Mexican-style cheese, and 30.0% to fresh squeezed orange juice. No Listeria spp. were isolated from fresh cabbage samples. L. monocytogenes was recovered from 15.3% of food samples analyzed. Non-pasteurized Mexican-style cheese showed the highest proportion of L. monocytogenes positive samples (36.0%), followed by orange juice (26.0%) and raw beef (25.0%). The frequency of isolation of Listeria spp. and L. monocytogenes was not different (P > 0.05) between PCOM and MOX. The advantages of using PCOM when comparing to MOX, include the easier way to identify Listeria species, the lower cost per plate and the availability of its ingredients for Latin-American countries. PMID:26742621

  20. Landscape response to normal fault growth and linkage in the Southern Apennines, Italy.

    NASA Astrophysics Data System (ADS)

    Roda-Boluda, Duna; Whittaker, Alex

    2016-04-01

    It is now well-established that landscape can record spatial and temporal variations in tectonic rates. However, decoding this information to extract detailed histories of fault growth is often a complex problem that requires careful integration of tectonic and geomorphic data sets. Here, we present new data addressing both normal fault evolution and coupled landscape response for two normal faults in the Southern Apennines: the Vallo di Diano and East Agri faults. By integrating published constraints with new data, we show that these faults have total throws of up to 2100 m, and Holocene throw rates of up to 1 mm/yr at their maximum. We demonstrate that geomorphology is effectively recording tectonics, with relief, channel and catchment slopes varying along fault strike as normal fault activity does. Therefore, valuable information about fault growth and interaction can be extracted from their geomorphic expression. We use the spatial distribution of knickpoints on the footwall channels to infer two episodes of base level change, which can be associated with distinct fault interaction events. From our detailed fault throw profiles, we reconstruct the amount of throw accumulated after each of these events, and the segments involved in each, and we use slip rate enhancement factors derived from fault interaction theory to estimate the magnitude of the tectonic perturbation in each case. From this approach, we are able to reconstruct pre-linkage throw rates, and we estimate that fault linkage events likely took place 0.7 ± 0.2 Ma and 1.9 ± 0.6 Ma in the Vallo di Diano fault, and 1.1 ± 0.1 and 2.3 ± 0.9 Ma in the East Agri fault. Our study suggests that both faults started their activity at 3.6 ± 0.5 Ma. These fault linkage scenarios are consistent with the knickpoint heights, and may relate to soft-linkage interaction with the Southern Apennines normal fault array, the existence of which has been the subject of considerable debate. Our combined geomorphic and

  1. Two-locus linkage analysis in multiple sclerosis (MS)

    SciTech Connect

    Tienari, P.J. Univ. of Helsinki ); Terwilliger, J.D.; Ott, J. ); Palo, J. ); Peltonen, L. )

    1994-01-15

    One of the major challenges in genetic linkage analyses is the study of complex diseases. The authors demonstrate here the use of two-locus linkage analysis in multiple sclerosis (MS), a multifactorial disease with a complex mode of inheritance. In a set of Finnish multiplex families, they have previously found evidence for linkage between MS susceptibility and two independent loci, the myelin basic protein gene (MBP) on chromosome 18 and the HLA complex on chromosome 6. This set of families provides a unique opportunity to perform linkage analysis conditional on two loci contributing to the disease. In the two-trait-locus/two-marker-locus analysis, the presence of another disease locus is parametrized and the analysis more appropriately treats information from the unaffected family member than single-disease-locus analysis. As exemplified here in MS, the two-locus analysis can be a powerful method for investigating susceptibility loci in complex traits, best suited for analysis of specific candidate genes, or for situations in which preliminary evidence for linkage already exists or is suggested. 41 refs., 6 tabs.

  2. Autosomal dominant distal myopathy: Linkage to chromosome 14

    SciTech Connect

    Laing, N.G.; Laing, B.A.; Wilton, S.D.; Dorosz, S.; Mastaglia, F.L.; Kakulas, B.A.; Robbins, P.; Meredith, C.; Honeyman, K.; Kozman, H.

    1995-02-01

    We have studied a family segregating a form of autosomal dominant distal myopathy (MIM 160500) and containing nine living affected individuals. The myopathy in this family is closest in clinical phenotype to that first described by Gowers in 1902. A search for linkage was conducted using microsatellite, VNTR, and RFLP markers. In total, 92 markers on all 22 autosomes were run. Positive linkage was obtained with 14 of 15 markers tested on chromosome 14, with little indication of linkage elsewhere in the genome. Maximum two-point LOD scores of 2.60 at recombination fraction .00 were obtained for the markers MYH7 and D14S64 - the family structure precludes a two-point LOD score {ge} 3. Recombinations with D14S72 and D14S49 indicate that this distal myopathy locus, MPD1, should lie between these markers. A multipoint analysis assuming 100% penetrance and using the markers D14S72, D14S50, MYH7, D14S64, D14S54, and D14S49 gave a LOD score of exactly 3 at MYH7. Analysis at a penetrance of 80% gave a LOD score of 2.8 at this marker. This probable localization of a gene for distal myopathy, MPD1, on chromosome 14 should allow other investigators studying distal myopathy families to test this region for linkage in other types of the disease, to confirm linkage or to demonstrate the likely genetic heterogeneity. 24 refs., 3 figs., 1 tab.

  3. Estimating parental relationship in linkage analysis of recessive traits

    SciTech Connect

    Merette, C.; Ott, J.

    1996-05-17

    In linkage analysis of recessive traits, parental relationship is important. For the case that it is unknown, the question is investigated as to whether estimating parental relationship and using the estimated relationship in linkage analysis is beneficial. Results show that estimating parental relationship can reliably be carried out on the basis of 50-100 genetic marker loci (analysis based on theory by Thompson). Misspecification of parental relationship leads to a loss of linkage informativeness, but not to false-positive evidence for linkage. An asymptotic bias in the recombination fraction estimate occurs when parents are unrelated and falsely taken to be related, but no such bias is seen when related parents are taken to be unrelated. Results from this investigation suggest that an estimated parental relationship may be used in linkage analysis as if it were the correct relationship, when evidence for the estimated relationship is supported by a likelihood ratio of at least 10:1 against the parents being unrelated. 9 refs., 2 figs., 5 tabs.

  4. Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve

    NASA Astrophysics Data System (ADS)

    Shi, Yaohua; Guo, Ximing; Gu, Zhifeng; Wang, Aimin; Wang, Yan

    2010-05-01

    Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio ( P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.

  5. The first genetic linkage map of Eucommia ulmoides.

    PubMed

    Wang, Dawei; Li, Yu; Li, Long; Wei, Yongcheng; Li, Zhouqi

    2014-04-01

    In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F1 population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.

  6. The 13th International Workshop on H-mode Physics and Transport Barriers (Oxford, UK, 2011) The 13th International Workshop on H-mode Physics and Transport Barriers (Oxford, UK, 2011)

    NASA Astrophysics Data System (ADS)

    Saibene, G.

    2012-11-01

    The 13th International Workshop on H-mode Physics and Transport Barriers, held in Lady Margaret Hall College in Oxford in October 2011 continues the tradition of bi-annual international meetings dedicated to the study of transport barriers in fusion plasmas. The first meeting of this series took place in S Diego (CA, US) in 1987, and since then scientists in the fusion community studying the formation and effects of transport barriers in plasmas have been meeting at this small workshop to discuss progress, new experimental evidence and related theoretical studies. The first workshops were strongly focussed on the characterization and understanding of the H-mode plasma, discovered in ASDEX in 1982. Tokamaks throughout the entire world were able to reproduce the H-mode transition in the following few years and since then the H-mode has been recognised as a pervasive physics feature of toroidally confined plasmas. Increased physics understanding of the H-mode transition and of the properties of H-mode plasmas, together with extensive development of diagnostic capabilities for the plasma edge, led to the development of edge transport barrier studies and theory. The H-mode Workshop reflected this extension in interest, with more and more contributions discussing the phenomenology of edge transport barriers and instabilities (ELMs), L-H transition and edge transport barrier formation theory. In the last 15 years, in response to the development of fusion plasma studies, the scientific scope of the workshop has been broadened to include experimental and theoretical studies of both edge and internal transport barriers, including formation and sustainment of transport barriers for different transport channels (energy, particle and momentum). The 13th H-mode Workshop was organized around six leading topics, and, as customary for this workshop, a lead speaker was selected for each topic to present to the audience the state-of-the-art, new understanding and open issues, as well

  7. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    PubMed

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  8. Software for analysis and manipulation of genetic linkage data.

    PubMed

    Weaver, R; Helms, C; Mishra, S K; Donis-Keller, H

    1992-06-01

    We present eight computer programs written in the C programming language that are designed to analyze genotypic data and to support existing software used to construct genetic linkage maps. Although each program has a unique purpose, they all share the common goals of affording a greater understanding of genetic linkage data and of automating tasks to make computers more effective tools for map building. The PIC/HET and FAMINFO programs automate calculation of relevant quantities such as heterozygosity, PIC, allele frequencies, and informativeness of markers and pedigrees. PREINPUT simplifies data submissions to the Centre d'Etude du Polymorphisme Humain (CEPH) data base by creating a file with genotype assignments that CEPH's INPUT program would otherwise require to be input manually. INHERIT is a program written specifically for mapping the X chromosome: by assigning a dummy allele to males, in the nonpseudoautosomal region, it eliminates falsely perceived noninheritances in the data set. The remaining four programs complement the previously published genetic linkage mapping software CRI-MAP and LINKAGE. TWOTABLE produces a more readable format for the output of CRI-MAP two-point calculations; UNMERGE is the converse to CRI-MAP's merge option; and GENLINK and LINKGEN automatically convert between the genotypic data file formats required by these packages. All eight applications read input from the same types of data files that are used by CRI-MAP and LINKAGE. Their use has simplified the management of data, has increased knowledge of the content of information in pedigrees, and has reduced the amount of time needed to construct genetic linkage maps of chromosomes. PMID:1598906

  9. Software for analysis and manipulation of genetic linkage data.

    PubMed

    Weaver, R; Helms, C; Mishra, S K; Donis-Keller, H

    1992-06-01

    We present eight computer programs written in the C programming language that are designed to analyze genotypic data and to support existing software used to construct genetic linkage maps. Although each program has a unique purpose, they all share the common goals of affording a greater understanding of genetic linkage data and of automating tasks to make computers more effective tools for map building. The PIC/HET and FAMINFO programs automate calculation of relevant quantities such as heterozygosity, PIC, allele frequencies, and informativeness of markers and pedigrees. PREINPUT simplifies data submissions to the Centre d'Etude du Polymorphisme Humain (CEPH) data base by creating a file with genotype assignments that CEPH's INPUT program would otherwise require to be input manually. INHERIT is a program written specifically for mapping the X chromosome: by assigning a dummy allele to males, in the nonpseudoautosomal region, it eliminates falsely perceived noninheritances in the data set. The remaining four programs complement the previously published genetic linkage mapping software CRI-MAP and LINKAGE. TWOTABLE produces a more readable format for the output of CRI-MAP two-point calculations; UNMERGE is the converse to CRI-MAP's merge option; and GENLINK and LINKGEN automatically convert between the genotypic data file formats required by these packages. All eight applications read input from the same types of data files that are used by CRI-MAP and LINKAGE. Their use has simplified the management of data, has increased knowledge of the content of information in pedigrees, and has reduced the amount of time needed to construct genetic linkage maps of chromosomes.

  10. A Primary Male Autosomal Linkage Map of the Horse Genome

    PubMed Central

    Lindgren, Gabriella; Sandberg, Kaj; Persson, Helena; Marklund, Stefan; Breen, Matthew; Sandgren, Björn; Carlstén, Johan; Ellegren, Hans

    1998-01-01

    A primary male autosomal linkage map of the domestic horse (Equus caballus) has been developed by segregation analysis of 140 genetic markers within eight half-sib families. The family material comprised four Standardbred trotters and four Icelandic horses, with a total of 263 offspring. The marker set included 121 microsatellite markers, eight protein polymorphisms, five RFLPs, three blood group polymorphisms, two PCR–RFLPs, and one single strand conformation polymorphism (SSCP). One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different chromosomes (ECA1, ECA2, ECA3, ECA4, ECA5, ECA6, ECA7, ECA9, ECA10, ECA11, ECA13, ECA15, ECA16, ECA18, ECA19, ECA21, ECA22, and ECA30). The average distance between linked markers was 12.6 cM and the longest linkage group measured 103 cM. The total map distance contained within linkage groups was 679 cM. If the distances covered outside the ends of linkage groups and by unlinked markers were included, it was estimated that the marker set covered at least 1500 cM, that is, at least 50% of the genome. A comparison of the relationship between genetic and physical distances in anchored linkage groups gave ratios of 0.5–0.8 cM per Mb of DNA. This would suggest that the total male recombinational distance in the horse is 2000 cM; this value is lower than that suggested by chiasma counts. The present map should provide an important framework for future genome mapping in the horse. PMID:9750194

  11. Combined RAPD and RFLP molecular linkage map of asparagus.

    PubMed

    Jiang, C; Lewis, M E; Sink, K C

    1997-02-01

    Two linkage maps of asparagus (Asparagus officinalis L.) were constructed using a double pseudotestcross mapping strategy with restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and allozymes as markers in a population generated from crossing MW25 x A19, two heterozygous parents. All data were inverted and combined with the natural data to detect linkages in repulsion phase. Two sets of data, one for each parent, were formed according to the inheritance patterns of the markers. The maternal MW25 map has a total of 163 marker loci placed in 13 linkage groups covering 1281 cM, with an average and a maximum distance between adjacent loci of 7.9 and 29 cM, respectively. The paternal A19 map has 183 marker loci covering 1324 cM in 9 linkage groups, with an average and a maximum distance between two adjacent loci of 7.7 and 29 cM, respectively. Six multiallelic RFLPs segregating in the pattern a/c x b/c and eight heterozygous loci (four RAPDs, and four RFLPs segregating in the pattern a/b x a/b (HZ loci)) were common to both maps. These 14 loci were used as bridges to align homologous groups between the two maps. In this case, RFLPs were more frequent and informative than RAPDs. Nine linkage groups in the MW25 map were homologous to six groups in the A19 map. In two cases, two or more bridge loci were common to a group; thus, the orientation of homologous linkage groups was also determined. In four other cases, only one locus was common to the two homologous groups and the orientation was unknown. Mdh, four RFLPs, and 14 RAPDs were assigned to chromosome L5, which also has the sex locus M. PMID:18464808

  12. Robust vibration control of flexible linkage mechanisms using piezoelectric films

    NASA Astrophysics Data System (ADS)

    Liao, Wen-Hwei; Chou, Jyh-Horng; Horng, Ing-Rong

    1997-08-01

    Based on the state space model of the flexible linkage mechanism equipped with piezoelectric films, a robust control methodology for suppressing elastodynamic responses of the high-speed flexible linkage mechanism with linear time-varying parameter perturbations by employing an observer-based feedback controller is presented. The instability caused by the linear time-varying parameter perturbations and the instability caused by the combined effect of control and observation spillover are investigated and carefully prevented by two robust stability criteria proposed in this paper. Numerical simulation of a slider - crank mechanism example is performed to evaluate the improvement of the elastodynamic responses.

  13. Mapping autism risk loci using genetic linkage and chromosomal rearrangements

    PubMed Central

    Szatmari, Peter; Paterson, Andrew; Zwaigenbaum, Lonnie; Roberts, Wendy; Brian, Jessica; Liu, Xiao-Qing; Vincent, John; Skaug, Jennifer; Thompson, Ann; Senman, Lili; Feuk, Lars; Qian, Cheng; Bryson, Susan; Jones, Marshall; Marshall, Christian; Scherer, Stephen; Vieland, Veronica; Bartlett, Christopher; Mangin, La Vonne; Goedken, Rhinda; Segre, Alberto; Pericak-Vance, Margaret; Cuccaro, Michael; Gilbert, John; Wright, Harry; Abramson, Ruth; Betancur, Catalina; Bourgeron, Thomas; Gillberg, Christopher; Leboyer, Marion; Buxbaum, Joseph; Davis, Kenneth; Hollander, Eric; Silverman, Jeremy; Hallmayer, Joachim; Lotspeich, Linda; Sutcliffe, James; Haines, Jonathan; Folstein, Susan; Piven, Joseph; Wassink, Thomas; Sheffield, Val; Geschwind, Daniel; Bucan, Maja; Brown, Ted; Cantor, Rita; Constantino, John; Gilliam, Conrad; Herbert, Martha; Lajonchere, Clara; Ledbetter, David; Lese-Martin, Christa; Miller, Janet; Nelson, Stan; Samango-Sprouse, Carol; Spence, Sarah; State, Matthew; Tanzi, Rudolph; Coon, Hilary; Dawson, Geraldine; Devlin, Bernie; Estes, Annette; Flodman, Pamela; Klei, Lambertus; Mcmahon, William; Minshew, Nancy; Munson, Jeff; Korvatska, Elena; Rodier, Patricia; Schellenberg, Gerard; Smith, Moyra; Spence, Anne; Stodgell, Chris; Tepper, Ping Guo; Wijsman, Ellen; Yu, Chang-En; Rogé, Bernadette; Mantoulan, Carine; Wittemeyer, Kerstin; Poustka, Annemarie; Felder, Bärbel; Klauck, Sabine; Schuster, Claudia; Poustka, Fritz; Bölte, Sven; Feineis-Matthews, Sabine; Herbrecht, Evelyn; Schmötzer, Gabi; Tsiantis, John; Papanikolaou, Katerina; Maestrini, Elena; Bacchelli, Elena; Blasi, Francesca; Carone, Simona; Toma, Claudio; Van Engeland, Herman; De Jonge, Maretha; Kemner, Chantal; Koop, Frederieke; Langemeijer, Marjolein; Hijmans, Channa; Staal, Wouter; Baird, Gillian; Bolton, Patrick; Rutter, Michael; Weisblatt, Emma; Green, Jonathan; Aldred, Catherine; Wilkinson, Julie-Anne; Pickles, Andrew; Le Couteur, Ann; Berney, Tom; Mcconachie, Helen; Bailey, Anthony; Francis, Kostas; Honeyman, Gemma; Hutchinson, Aislinn; Parr, Jeremy; Wallace, Simon; Monaco, Anthony; Barnby, Gabrielle; Kobayashi, Kazuhiro; Lamb, Janine; Sousa, Ines; Sykes, Nuala; Cook, Edwin; Guter, Stephen; Leventhal, Bennett; Salt, Jeff; Lord, Catherine; Corsello, Christina; Hus, Vanessa; Weeks, Daniel; Volkmar, Fred; Tauber, Maïté; Fombonne, Eric; Shih, Andy; Meyer, Kacie

    2007-01-01

    Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with ≥ 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. PMID:17322880

  14. SOFTWARE REVIEW: Oxford Personal Revision Guides: A-level Physics 1999/2000 Syllabus GCSE Physics 1999/2000 Syllabus

    NASA Astrophysics Data System (ADS)

    Parker, Kerry

    2000-09-01

    Is it any better than a textbook and a pad of A4 paper? That's the question we have to ask if we consider investing in a `Revision' CD-ROM. Of course, nothing, in our lifetimes, will quite replace the students' own notes, some paper and a pencil. But, so far as private study is concerned, the computer offers a number of potential advantages: sound, animation, hyperlinks, interactivity, a calculator and a clock. For those with a modem, we can add Internet connections too. A few years ago the only revision materials available for computers were simply electronic versions of textbooks: a few animations and voice commentaries, with maybe a few multiple choice tests was the best you could expect. I was universally disappointed with all such CD-ROMs; they were a waste of money. At last things are changing and theseOxford Personal Revision Guides are definitely software of the new generation: there is commentary, there are animated diagrams (ripple tanks, Hertzsprung-Russell diagrams, falling stones...), there are plenty of hyperlinks to other sections of the CD, and to exam board websites on the Internet, so that students can check their own syllabus.... This CD is not a rip-off! The software uses Microscoft Internet Explorer to produce a screen that looks as if you are connected to the Internet. Few students will have any problems in navigating the system. It is a massive piece of programming requiring a fairly modern PC (Pentium 166, 32 MB RAM, quad-speed CD-ROM drive and a good monitor and sound card really are the minimum; I loaded the programme on an older machine and it struggled!). Installation took a good while because the software insists on installing/updating Internet Explorer to 5.0 and checking for, and loading if necessary, Real Player 7, Microsoft Java Virtual Machine and Macromedia Shockwave 7.0.2 Player. Once all this was loaded it worked extremely well, and at first I kept imagining that I was in fact connected to a fantastic educational site on the web

  15. Studies of linkage in populations. XIII. A unique cause of linkage disequilibrium in natural populations of Drosophila robusta.

    PubMed

    Levitan, M; Etges, W J

    1998-06-01

    Natural populations of Drosophila robusta are polymorphic for chromosomal gene arrangements in most of its range, the deciduous forests of North America east of the Rocky Mountains. Many of the gene arrangements are the result of paracentric inversions on both arms of the metacentric second chromosome. They are frequently in linkage disequilibrium, determined in many areas largely, or entirely, by differing frequencies of cis and trans forms of the double heterokaryotypes and their component linkage combinations. Presence and degree of linkage disequilibrium in these populations varies with locality and gender, with males from southern localities exhibiting the largest deviation from equilibrium. Analysis of the extensive karyotype data encompassing the entire species range collected over the past 50 years shows that natural selection is primarily responsible for maintaining these complex polymorphisms.

  16. Tropical-Subpolar Linkages in the North Atlantic during the last Glacial Period

    NASA Astrophysics Data System (ADS)

    Vautravers, M. J.; Hodell, D. A.

    2010-12-01

    We studied millennial-scale changes in planktonic foraminifera assemblages from the last glacial period in a high-resolution core (KN166-14-JPC13) recovered from the southern part of the Gardar Drift in the subpolar North Atlantic. Similar to recent findings reported by Jonkers et al. (2010), we also found that the sub-polar North Atlantic Ocean experienced some seasonal warming during each of the Heinrich Events (HEs). In addition, increasing abundances of tropical species are found just prior to the IRD event marking the end of each Bond cycle, suggesting that summer warming may have been involved in triggering Heinrich events. We suggest that tropical-subtropical water transported via the Gulf Stream and North Atlantic Drift may have triggered the collapse of large NH ice-shelves. Sharp decreases in polar species are tied to abrupt warming following Heinrich Events as documented in Greenland Ice cores and other marine records in the North Atlantic. The record bears a strong resemblance to the tropical record of Cariaco basin (Peterson et al., 2000), suggesting strong tropical-subpolar linkages in the glacial North Atlantic. Enhanced spring productivity, possibly related to eddy activity along the Subpolar Front, is recorded by increased shell size, high δ13C in G. bulloides and other biological indices early during the transition from HE stadials to the following interstadial.

  17. 75 FR 74089 - Records Schedules; Availability and Request for Comments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-30

    ... are scanned images of respondent census forms; the Individual Census Record File containing response data and linkage information to the scanned images; summary data files that provide population totals... program policy files. 13. Department of State, Bureau of Administration (N1-059-10-16, 13 items,...

  18. Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef.

    PubMed

    Smith, Shavannor M; Yuan, Yinan; Doust, Andrew N; Bennetzen, Jeffrey L

    2012-03-01

    Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the "Green Revolution." All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral divergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous/paralogous relationships. The genetic diversity in the 31 studied accessions was organized into a relatively small number of haplotypes (2-4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide diversity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2-4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin.

  19. International workshop on Chromosome 12 held at St. Catherine`s College, Oxford, England, September 18--20, 1992. Final report

    SciTech Connect

    Gemmill, R.

    1992-12-31

    The First International Mapping Workshop on Human Chromosome 12 was held on Sept. 18--20, 1992, at St Catherine`s College, Oxford, UK. The meeting was hosted by Ian Craig and organized by Drs. Craig, Gemmill and Kutcherlapati. It was attended by 50 participants primarily from Europe and the USA. The workshop was highly successful and achieved the major goal of fostering direct and personal interactions between investigators with strong research interests in this chromosome. Participants reviewed the status of several critical aspects of chromosome mapping and prepared consensus views of the current state of knowledge. In addition, lists of resources available for this chromosome including somatic cell hybrids, individual DNA clones and libraries and genetic markers were prepared.

  20. The clinical outcome of minimally invasive Phase 3 Oxford unicompartmental knee arthroplasty: a 15-year follow-up of 1000 UKAs.

    PubMed

    Pandit, H; Hamilton, T W; Jenkins, C; Mellon, S J; Dodd, C A F; Murray, D W

    2015-11-01

    There have been concerns about the long-term survival of unicompartmental knee arthroplasty (UKA). This prospective study reports the 15-year survival and ten-year functional outcome of a consecutive series of 1000 minimally invasive Phase 3 Oxford medial UKAs (818 patients, 393 men, 48%, 425 women, 52%, mean age 66 years; 32 to 88). These were implanted by two surgeons involved with the design of the prosthesis to treat anteromedial osteoarthritis and spontaneous osteonecrosis of the knee, which are recommended indications. Patients were prospectively identified and followed up independently for a mean of 10.3 years (5.3 to 16.6). At ten years, the mean Oxford Knee Score was 40 (standard deviation (sd) 9; 2 to 48): 79% of knees (349) had an excellent or good outcome. There were 52 implant-related re-operations at a mean of 5.5 years (0.2 to 14.7). The most common reasons for re-operation were arthritis in the lateral compartment (2.5%, 25 knees), bearing dislocation (0.7%, seven knees) and unexplained pain (0.7%, seven knees). When all implant-related re-operations were considered as failures, the ten-year rate of survival was 94% (95% confidence interval (CI) 92 to 96) and the 15-year survival rate 91% (CI 83 to 98). When failure of the implant was the endpoint the 15-year survival was 99% (CI 96 to 100). This is the only large series of minimally invasive UKAs with 15-year survival data. The results support the continued use of minimally invasive UKA for the recommended indications.

  1. Oxford-Style Debates in a Microbiology Course for Majors: A Method for Delivering Content and Engaging Critical Thinking Skills †

    PubMed Central

    Boucaud, Dwayne W.; Nabel, Michael; Eggers, Christian H.

    2013-01-01

    Developing scientific expertise in the classroom involves promoting higher-order cognitive skills as well as content mastery. Effective use of constructivism can facilitate these outcomes. However this is often difficult to accomplish when delivery of content is paramount. Utilizing many of the tenets of constructivist pedagogy, we have designed an Oxford-style debate assignment to be used in an introductory microbiology course. Two teams of students were assigned a debatable topic within microbiology. Over a five-week period students completed an informative web page consisting of three parts: background on the topic, data-based positions for each side of the argument, and a data-based persuasive argument to support their assigned position. This was followed by an in-class presentation and debate. Analysis of student performance on knowledge-based questions shows that students retain debate-derived content acquired primarily outside of lectures significantly better than content delivered during a normal lecture. Importantly, students who performed poorly on the lecture-derived questions did as well on debate-derived questions as other students. Students also performed well on questions requiring higher-order cognitive skills and in synthesizing data-driven arguments in support of a position during the debate. Student perceptions of their knowledge-base in areas covered by the debate and their skills in using scientific databases and analyzing primary literature showed a significant increase in pre- and postassignment comparisons. Our data demonstrate that an Oxford-style debate can be used effectively to deliver relevant content, increase higher-order cognitive skills, and increase self-efficacy in science-specific skills, all contributing to developing expertise in the field. PMID:23858349

  2. SOFTWARE REVIEW: Oxford Personal Revision Guides: A-level Physics 1999/2000 Syllabus GCSE Physics 1999/2000 Syllabus

    NASA Astrophysics Data System (ADS)

    Parker, Kerry

    2000-09-01

    Is it any better than a textbook and a pad of A4 paper? That's the question we have to ask if we consider investing in a `Revision' CD-ROM. Of course, nothing, in our lifetimes, will quite replace the students' own notes, some paper and a pencil. But, so far as private study is concerned, the computer offers a number of potential advantages: sound, animation, hyperlinks, interactivity, a calculator and a clock. For those with a modem, we can add Internet connections too. A few years ago the only revision materials available for computers were simply electronic versions of textbooks: a few animations and voice commentaries, with maybe a few multiple choice tests was the best you could expect. I was universally disappointed with all such CD-ROMs; they were a waste of money. At last things are changing and theseOxford Personal Revision Guides are definitely software of the new generation: there is commentary, there are animated diagrams (ripple tanks, Hertzsprung-Russell diagrams, falling stones...), there are plenty of hyperlinks to other sections of the CD, and to exam board websites on the Internet, so that students can check their own syllabus.... This CD is not a rip-off! The software uses Microscoft Internet Explorer to produce a screen that looks as if you are connected to the Internet. Few students will have any problems in navigating the system. It is a massive piece of programming requiring a fairly modern PC (Pentium 166, 32 MB RAM, quad-speed CD-ROM drive and a good monitor and sound card really are the minimum; I loaded the programme on an older machine and it struggled!). Installation took a good while because the software insists on installing/updating Internet Explorer to 5.0 and checking for, and loading if necessary, Real Player 7, Microsoft Java Virtual Machine and Macromedia Shockwave 7.0.2 Player. Once all this was loaded it worked extremely well, and at first I kept imagining that I was in fact connected to a fantastic educational site on the web

  3. Geographic Differences in Genetic Locus Linkages for Borrelia burgdorferi

    PubMed Central

    Travinsky, Bridgit; Bunikis, Jonas

    2010-01-01

    Borrelia burdorferi genotype in the northeastern United States is associated with Lyme borreliosis severity. Analysis of DNA sequences of the outer surface protein C gene and rrs-rrlA intergenic spacer from extracts of Ixodes spp. ticks in 3 US regions showed linkage disequilibrium between the 2 loci within a region but not consistently between regions. PMID:20587192

  4. 20 CFR 628.545 - Linkages and coordination.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... TITLE II OF THE JOB TRAINING PARTNERSHIP ACT Program Design Requirements for Programs Under Title II of the Job Training Partnership Act § 628.545 Linkages and coordination. (a) General requirements. (1) To..., and with appropriate education and training agencies, such as local JOBS programs, Employment...

  5. 20 CFR 628.545 - Linkages and coordination.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... TITLE II OF THE JOB TRAINING PARTNERSHIP ACT Program Design Requirements for Programs Under Title II of the Job Training Partnership Act § 628.545 Linkages and coordination. (a) General requirements. (1) To..., and with appropriate education and training agencies, such as local JOBS programs, Employment...

  6. Behavioural case linkage with solved and unsolved crimes.

    PubMed

    Tonkin, Matthew; Woodhams, Jessica; Bull, Ray; Bond, John W

    2012-10-10

    Offender behaviour is used to distinguish between crimes committed by the same person (linked crimes) and crimes committed by different people (unlinked crimes) through behavioural case linkage. There is growing evidence to support the use of behavioural case linkage by investigative organisations such as the police, but this research is typically limited to samples of solved crime that do not reflect how this procedure is used in real life. The current paper extends previous research by testing the potential for behavioural case linkage in a sample containing both solved and unsolved crimes. Discrimination accuracy is examined across crime categories (e.g. a crime pair containing a car theft and a residential burglary), across crime types (e.g. a crime pair containing a residential burglary and a commercial burglary), and within crime types (e.g. a crime pair containing two residential burglaries) using the number of kilometres (intercrime distance) and the number of days (temporal proximity) between offences to distinguish between linked and unlinked crimes. The intercrime distance and/or the temporal proximity were able to achieve statistically significant levels of discrimination accuracy across crime categories, across crime types, and within crime types as measured by Receiver Operating Characteristic (ROC) analysis. This suggests that behavioural case linkage can be used to assist the investigation, detection and prosecution of prolific and versatile serial offenders.

  7. Genetic linkage study of bipolar disorder and the serotonin transporter

    SciTech Connect

    Kelsoe, J.R.; Morison, M.; Mroczkowski-Parker, Z.; Bergesch, P.; Rapaport, M.H.; Mirow, A.L.

    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 Old 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.

  8. Broad scan linkage analysis in a large Tourette family pedigree

    SciTech Connect

    Peiffer, A.; Leppert, M.; Wetering, B.J.M. van der

    1994-09-01

    Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.

  9. Solid-Phase Synthesis of Oligodeoxynucleotide Analogs Containing Phosphorodithioate Linkages.

    PubMed

    Yang, Xianbin

    2016-01-01

    The oligodeoxynucleotide phosphorodithioate modification (PS2-ODN) uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphordiester backbone linkage. Like a natural phosphodiester ODN backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-ODNs are highly stable to nucleases and numerous in vitro assays have demonstrated their biological activity. For example, PS2-ODNs activated RNase H in vitro, strongly inhibited human immunodeficiency virus (HIV) reverse transcriptase, induced B-cell proliferation and differentiation, and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-ODNs has spawned a variety of strategies for synthesizing, isolating, and characterizing this compounds. ODN-thiophosphoramidite monomers are commercially available from either AM Biotechnologies or Glen Research and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of ODNs having PS2 internucleotide linkages. © 2016 by John Wiley & Sons, Inc. PMID:27584703

  10. Project INTERACT: An Interagency Linkage System between Education and Rehabilitation.

    ERIC Educational Resources Information Center

    Gutterman, June K.; Todd, Julie

    Project INTERACT was designed to develop a local model linkage system, an interagency effort between the Ohio Rehabilitation Services Commission (RSC) and the Ohio Department of Education (ODE), Division of Special Education (DSE) to improve the joint delivery of services to severely handicapped students. It was also intended to design and/or…

  11. Apprenticeship Linkages to Secondary Education and Other Training Programs.

    ERIC Educational Resources Information Center

    Cantor, Jeffrey A.

    This study was undertaken to identify facilitators barriers to effective linkages of secondary education and other training programs with registered apprenticeship programs. Analysis was conducted through case studies and surveys of programs that were identified nationally. U.S. apprenticeship programs had the following weaknesses: variable…

  12. Base-Catalyzed Linkage Isomerization: An Undergraduate Inorganic Kinetics Experiment.

    ERIC Educational Resources Information Center

    Jackson, W. G.; And Others

    1981-01-01

    Describes kinetics experiments completed in a single two-hour laboratory period at 25 degrees Centigrade of nitrito to nitro rearrangement, based on the recently discovered base-catalysis path. Includes information on synthesis and characterization of linkage isomers, spectrophotometric techniques, and experimental procedures. (SK)

  13. Teaching Linkage and Problem Translating Skills in Chemistry

    ERIC Educational Resources Information Center

    Lee, Kam Wah Lucille; Yap, Kueh Chin; Goh, Ngoh Khang; Chia, Lian-Sai; Tang, Woh Un

    2004-01-01

    This study examines the effects of teaching Linkage and Problem Translating Skills on students' problem-solving performance and their learning of the five cognitive variables namely, Concept Relatedness, Idea Association, Problem Translating Skill, Non-Specific but Relevant Knowledge and Specific Knowledge. Seventy three Grade 9 (Secondary 3)…

  14. Environmental Scientists' Perceptions of the Science-Policy Linkage.

    ERIC Educational Resources Information Center

    Alm, Leslie R.; Simon, Marc

    2001-01-01

    Describes the criticisms coming from scientists on the assessment report on acid rain released by the National Acid Preparation Assessment Program (NAPAP) with the purpose of providing relevant information to policy makers about acid rain. Investigates n=129 scientists' point of view on the linkage of science to policy. (YDS)

  15. Business and Education Linkage Activities. Lake County, Illinois.

    ERIC Educational Resources Information Center

    Flesher, Jeffrey W.

    A study was conducted to establish a baseline profile of business and education linkage activities in Lake County, Illinois. Data were collected through a survey questionnaire sent to 242 public and private K-12 schools in Lake County. Two rounds of mailings resulted in the return of 109 usable forms, or 45 percent of the population. Telephone…

  16. Typology of Empirical Attributes: Dissimilarity Linkage Analysis (DLA).

    ERIC Educational Resources Information Center

    Dubin, Robert; Champoux, Joseph E.

    Dissimilarity Linkage Analysis (DLA) is an extremely simple procedure for developing a typology from empirical attributes that permits the clustering of entities. First the procedure develops a taxonomy of types from empirical attributes possessed by entities in the sample. Second, the procedure assigns entities to one, and only one, type in the…

  17. Low Cost Computer Graphics Simulation of Basic Kinematic Linkages.

    ERIC Educational Resources Information Center

    Smith, Donald A.; Jacquot, Raymond G.

    1984-01-01

    Presents algorithms for the simulation and motion display of the three basic kinematic devices: (1) four bar linkages; (2) the slider crank; and (3) the inverted slider crank mechanisms. The algorithms were implemented on a Commodore-VIC 20 microcomputer system with 6500 bytes of available memory. (Author/JN)

  18. Linkages between Vocational Education and Training Providers and Industry.

    ERIC Educational Resources Information Center

    Choi, Jihee; Misko, Josie; Kang, Kyeong-Jong; Phan, Oanh

    A study described the general and vocational education and training (VET) systems in Korea and Australia, focusing on the role of training providers and industry in the delivery of entry-level vocational education and training in both countries. The study also analyzed the nature of the linkages established between VET institutions in the two…

  19. A Genetic Linkage Map of the Male Goat Genome

    PubMed Central

    Vaiman, D.; Schibler, L.; Bourgeois, F.; Oustry, A.; Amigues, Y.; Cribiu, E. P.

    1996-01-01

    This paper presents a first genetic linkage map of the goat genome. Primers derived from the flanking sequences of 612 bovine, ovine and goat microsatellite markers were gathered and tested for amplification with goat DNA under standardized PCR conditions. This screen made it possible to choose a set of 55 polymorphic markers that can be used in the three species and to define a panel of 223 microsatellites suitable for the goat. Twelve half-sib paternal goat families were then used to build a linkage map of the goat genome. The linkage analysis made it possible to construct a meiotic map covering 2300 cM, i.e., >80% of the total estimated length of the goat genome. Moreover, eight cosmids containing microsatellites were mapped by fluorescence in situ hybridization in goat and sheep. Together with 11 microsatellite-containing cosmids previously mapped in cattle (and supposing conservation of the banding pattern between this species and the goat) and data from the sheep map, these results made the orientation of 15 linkage groups possible. Furthermore, 12 coding sequences were mapped either genetically or physically, providing useful data for comparative mapping. PMID:8878693

  20. Automation of genetic linkage analysis using florescent microsatellite markers

    SciTech Connect

    Mansfield, D.C.; Brown, A.F.; Green, D.K.

    1994-11-15

    Automation of the typing of genetic markers offers advantages of speed, accuracy, and cost in the mapping of genetic traits and the construction of high-resolution linkage maps. The authors have developed an automated linkage analysis system by (i) using a robotic pipettor to set up polymerase chain reactions (PCR) to amplify microsatellites with incorporation of a single fluorescent label; (ii) using an automated sequencing apparatus for detection of the PCR products; (iii) sizing alleles automatically by the use of internal and external standards; (iv) iteratively filtering out nonallelic fragments and checking for Mendelian consistency; (v) calculating the probabilities of selected genotypes; and (vi) automatically formatting the results for input to linkage analysis programs. The method provides accurate sizing of alleles, minimizes the risk of error during manual reading and transcription of data, and increases the throughput of reliable data. It brings any consistencies or ambiguities in the data to the attention of the user and facilitates examination of the raw data. The ALF/ALP system, together with new, optimized microsatellite sets, particularly tetranucleotide repeats, is likely to be well-suited to fully automatic genetic linkage analysis. 32 refs., 2 figs., 2 tabs.

  1. Linkages over Time between Adolescents' Relationships with Parents and Friends

    ERIC Educational Resources Information Center

    De Goede, Irene H. A.; Branje, Susan J. T.; Delsing, Marc J. M. H.; Meeus, Wim H. J.

    2009-01-01

    This 5-wave longitudinal study examines linkages over time between adolescents' perceptions of relationships with parents and friends with respect to support, negative interaction, and power. A total of 575 early adolescents (54.1% boys) and 337 middle adolescents (43.3% boys) participated. Path analyses mainly showed bidirectional associations…

  2. Lessons from the Legacy of Canada-China University Linkages

    ERIC Educational Resources Information Center

    Hayhoe, Ruth; Pan, Julia; Zha, Qiang

    2013-01-01

    This article looks at a series of university linkages between Canadian and Chinese universities that were supported by the Canadian International Development Agency as a result of a development agreement signed in 1983 between the two governments. It first reviews relevant theoretical literature on higher education in a global context, and…

  3. Teaching Principles of Linkage and Gene Mapping with the Tomato.

    ERIC Educational Resources Information Center

    Hawk, James A.; And Others

    1980-01-01

    A three-point linkage system in tomatoes is used to explain concepts of gene mapping, linking and statistical analysis. The system is designed for teaching the effective use of statistics, and the power of genetic analysis from statistical analysis of phenotypic ratios. (Author/SA)

  4. Can University-Industry Linkages Stimulate Student Employability?

    ERIC Educational Resources Information Center

    Ishengoma, Esther; Vaaland, Terje I.

    2016-01-01

    Purpose: The purpose of this paper is to identify important university-industry linkage (UIL) activities that can stimulate the likelihood of employability among students. Design/methodology/approach: A total of 404 respondents located in Tanzania, comprising students, faculty members and employees from 20 companies operating within the oil and…

  5. 20 CFR 628.545 - Linkages and coordination.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... TITLE II OF THE JOB TRAINING PARTNERSHIP ACT Program Design Requirements for Programs Under Title II of the Job Training Partnership Act § 628.545 Linkages and coordination. (a) General requirements. (1) To..., and with appropriate education and training agencies, such as local JOBS programs, Employment...

  6. Cancer in the offspring of radiation workers: a record linkage study.

    PubMed Central

    Draper, G. J.; Little, M. P.; Sorahan, T.; Kinlen, L. J.; Bunch, K. J.; Conquest, A. J.; Kendall, G. M.; Kneale, G. W.; Lancashire, R. J.; Muirhead, C. R.; O'Connor, C. M.; Vincent, T. J.

    1997-01-01

    OBJECTIVES: To test the "Gardner hypothesis" that childhood leukaemia and non-Hodgkin lymphoma can be caused by fathers' exposure to ionising radiation before the conception of the child, and, more generally, to investigate whether such radiation exposure of either parent is a cause of childhood cancer. DESIGN: Case-control study. SETTING: Great Britain. SUBJECTS: 35,949 children diagnosed as having cancer, together with matched controls. MAIN OUTCOME MEASURES: Parental employment as radiation worker as defined by inclusion in the National Registry for Radiation Workers and being monitored for external radiation before conception of child; cumulative dose of external ionising radiation for various periods of employment before conception; dose during pregnancy. RESULTS: After cases studied by Gardner and colleagues were excluded, fathers of children with leukaemia or non-Hodgkin lymphoma were significantly more likely than fathers of controls to have been radiation workers (relative risk 1.77, 95% confidence interval 1.05 to 3.03) but there was no dose-response relation for any of the exposure periods studied; indeed, the association was greatest for those with doses below the level of detection. No increased risk was found for fathers with a lifetime preconception dose of 100 mSv or more, or with a dose in the 6 months before conception of 10 mSv or more. There was no increased risk for the group of other childhood cancers. Mothers' radiation work was associated with a significant increase of childhood cancer (relative risk 5.00, 1.42 to 26.94; based on 15 cases and 3 controls). Only four of the case mothers and no controls were radiation workers during pregnancy. CONCLUSIONS: These results do not support the hypothesis that paternal preconception irradiation is a cause of childhood leukaemia and non-Hodgkin lymphoma; the observed associations may be chance findings or results from exposure to infective or other agents. If there is any increased risk for the children of fathers who are radiation workers, it is small in absolute terms: in Britain the average risk by age 15 years is 6.5 per 10,000; our best estimate, using all available data, is that the increase is 5.4 per 10,000. For mothers, the numbers are too small for reliable estimates of the risk, if any, to be made. PMID:9393219

  7. The phenotypic difference discards sib-pair QTL linkage information

    SciTech Connect

    Wright, F.A. |

    1997-03-01

    Kruglyak and Lander provide an important synthesis of methods for (IBD) sib-pair linkage mapping, with an emphasis on the use of complete multipoint inheritance information for each sib pair. These procedures are implemented in the computer program MAPMAKER/SIBS, which performs interval mapping for dichotomous and quantitative traits. The authors present three methods for mapping quantitative trait loci (QTLs): a variant of the commonly used Haseman-Elston regression approach, a maximum-likelihood procedure involving variance components, and a rank-based nonparametric procedure. These approaches and related work use the magnitude of the difference in the sibling phenotype values for each sib pair as the observation for analysis. Linkage is detected if siblings sharing more alleles IBD have similar phenotypes (i.e., a small difference in the phenotype values), while siblings sharing fewer alleles IBD have less similar phenotypes. Such techniques have been used to detect linkage for a number of quantitative traits. However, the exclusive reliance on the phenotypic differences may be due in large part to historical inertia. A likelihood argument is presented here to show that, under certain classical assumptions, the phenotypic differences do not contain the full likelihood information for QTL mapping. Furthermore, considerable gains in power to detect linkage can be achieved with an expanded likelihood model. The development here is related to previous work, which incorporates the full set of phenotypic data using likelihood and robust quasi-likelihood methods. The purpose of this letter is not to endorse a particular approach but to spur research in alternative and perhaps more powerful linkage tests. 17 refs.

  8. Candidate genes for nicotine dependence via linkage, epistasis, and bioinformatics.

    PubMed

    Sullivan, Patrick F; Neale, Benjamin M; van den Oord, Edwin; Miles, Michael F; Neale, Michael C; Bulik, Cynthia M; Joyce, Peter R; Straub, Richard E; Kendler, Kenneth S

    2004-04-01

    Many smoking-related phenotypes are substantially heritable. One genome scan of nicotine dependence (ND) has been published and several others are in progress and should be completed in the next 5 years. The goal of this hypothesis-generating study was two-fold. First, we present further analyses of our genome scan data for ND published by Straub et al. [1999: Mol Psychiatry 4:129-144] (PMID: 10208445). Second, we used the method described by Cox et al. [1999: Nat Genet 21:213-215] (PMID: 9988276) to search for epistatic loci across the markers used in the genome scan. The overall results of the genome scan nearly reached the rigorous Lander and Kruglyak [1995: Nat Genet 11:241-247] criteria for "significant" linkage with the best findings on chromosomes 10 and 2. We then looked for correspondence between genes located in the 10 regions implicated in affected sibling pair (ASP) and epistatic linkage analyses with a list of genes suggested by microarray studies of experimental nicotine exposure and candidate genes from the literature. We found correspondence between linkage and microarray/candidate gene studies for genes involved with the mitogen-activated protein kinase (MAPK) signaling system, nuclear factor kappa B (NFKB) complex, neuropeptide Y (NPY) neurotransmission, a nicotinic receptor subunit (CHRNA2), the vesicular monoamine transporter (SLC18A2), genes in pathways implicated in human anxiety (HTR7, TDO2, and the endozepine-related protein precursor, DKFZP434A2417), and the micro 1-opioid receptor (OPRM1). Although the hypotheses resulting from these linkage and bioinformatic analyses are plausible and intriguing, their ultimate worth depends on replication in additional linkage samples and in future experimental studies. PMID:15048644

  9. Disentangling linkage disequilibrium and linkage from dense single-nucleotide polymorphism trio data.

    PubMed

    Clarke, Geraldine M; Cardon, Lon R

    2005-12-01

    Parent-offspring trios are widely collected for disease gene-mapping studies and are being extensively genotyped as part of the International HapMap Project. With dense maps of markers on trios, the effects of LD and linkage can be separated, allowing estimation of recombination rates in a model-free setting. Here we define a model-free multipoint method on the basis of dense sequence polymorphism data from parent-offspring trios to estimate intermarker recombination rates. We use simulations to show that this method has up to 92% power to detect recombination hotspots of intensity 25 times background over a region of size 10 kb typed at density 1 marker per 2.5 kb and almost 100% power to detect large hotspots of intensity >125 times background over regions of size 10 kb typed with just 1 marker per 5 kb (alpha = 0.05). We found strong agreement at megabase scales between estimates from our method applied to HapMap trio data and estimates from the genetic map. At finer scales, using Centre d'Etude du Polymorphisme Humain (CEPH) pedigree data across a 10-Mb region of chromosome 20, a comparison of population recombination rate estimates obtained from our method with estimates obtained using a coalescent-based approximate-likelihood method implemented in PHASE 2.0 shows detection of the same coldspots and most hotspots: The Spearman rank correlation between the estimates from our method and those from PHASE is 0.58 (p < 2.2(-16)).

  10. 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.

  11. Saturation of an intra-gene pool linkage map: toward unified consensus linkage map in common bean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Map-based cloning to find genes of interest and marker assisted selection (MAS) requires good genetic maps with high reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers in includin...

  12. Nickel-catalyzed proton-deuterium exchange (HDX) procedures for glycosidic linkage analysis of complex carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of non-carbohydrate substituents. The glycosidic linkage positions are often de...

  13. OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis

    PubMed Central

    Mevissen, Tycho E.T.; Hospenthal, Manuela K.; Geurink, Paul P.; Elliott, Paul R.; Akutsu, Masato; Arnaudo, Nadia; Ekkebus, Reggy; Kulathu, Yogesh; Wauer, Tobias; El Oualid, Farid; Freund, Stefan M.V.; Ovaa, Huib; Komander, David

    2013-01-01

    Summary Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates. PMID:23827681

  14. 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. PMID:26759145

  15. Research on University-Industry Linkages: The State of the Art. AIR 1984 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Melchiori, Gerlinda S.

    Issues concerning research partnerships between universities and industry are reviewed. Attention is directed to: the genesis of partnerships, a typology of linkages, salient incentives for academe and commerce, currently perceived barriers, qualitative assessment of linkages, and recommendations for the improvement of partnerships. Linkages fall…

  16. Communication for Change in Education: Educational Linkage Programs in the 1970's.

    ERIC Educational Resources Information Center

    Butler-Paisley, Matilda; Paisley, William

    Educational linkage is a system for sharing facts, ideas, values, and skills related to educational work. An extensive survey was made of educational linkage programs, and an evaluation procedure for these programs was designed. Over 40 linkage models were classified as to level of sponsorship and/or service, institutional setting, services…

  17. HIV and cancer registry linkage identifies a substantial burden of cancers in persons with HIV in India.

    PubMed

    Godbole, Sheela V; Nandy, Karabi; Gauniyal, Mansi; Nalawade, Pallavi; Sane, Suvarna; Koyande, Shravani; Toyama, Joy; Hegde, Asha; Virgo, Phil; Bhatia, Kishor; Paranjape, Ramesh S; Risbud, Arun R; Mbulaiteye, Sam M; Mitsuyasu, Ronald T

    2016-09-01

    We utilized computerized record-linkage methods to link HIV and cancer databases with limited unique identifiers in Pune, India, to determine feasibility of linkage and obtain preliminary estimates of cancer risk in persons living with HIV (PLHIV) as compared with the general population.Records of 32,575 PLHIV were linked to 31,754 Pune Cancer Registry records (1996-2008) using a probabilistic-matching algorithm. Cancer risk was estimated by calculating standardized incidence ratios (SIRs) in the early (4-27 months after HIV registration), late (28-60 months), and overall (4-60 months) incidence periods. Cancers diagnosed prior to or within 3 months of HIV registration were considered prevalent.Of 613 linked cancers to PLHIV, 188 were prevalent, 106 early incident, and 319 late incident. Incident cancers comprised 11.5% AIDS-defining cancers (ADCs), including cervical cancer and non-Hodgkin lymphoma (NHL), but not Kaposi sarcoma (KS), and 88.5% non-AIDS-defining cancers (NADCs). Risk for any incident cancer diagnosis in early, late, and combined periods was significantly elevated among PLHIV (SIRs: 5.6 [95% CI 4.6-6.8], 17.7 [95% CI 15.8-19.8], and 11.5 [95% CI 10-12.6], respectively). Cervical cancer risk was elevated in both incidence periods (SIRs: 9.6 [95% CI 4.8-17.2] and 22.6 [95% CI 14.3-33.9], respectively), while NHL risk was elevated only in the late incidence period (SIR: 18.0 [95% CI 9.8-30.20]). Risks for NADCs were dramatically elevated (SIR > 100) for eye-orbit, substantially (SIR > 20) for all-mouth, esophagus, breast, unspecified-leukemia, colon-rectum-anus, and other/unspecified cancers; moderately elevated (SIR > 10) for salivary gland, penis, nasopharynx, and brain-nervous system, and mildly elevated (SIR > 5) for stomach. Risks for 6 NADCs (small intestine, testis, lymphocytic leukemia, prostate, ovary, and melanoma) were not elevated and 5 cancers, including multiple myeloma not seen.Our study demonstrates the feasibility of

  18. High-density genetic linkage mapping in turbot (Scophthalmus maximus L.) based on SNP markers and major sex- and growth-related regions detection.

    PubMed

    Wang, Weiji; Hu, Yulong; Ma, Yu; Xu, Liyong; Guan, Jiantao; Kong, Jie

    2015-01-01

    This paper describes the development of a high density consensus genetic linkage map of a turbot (Scophthalmus maximus L.) family composed of 149 mapping individuals using Single Nucleotide Polymorphisms (SNP) developed using the restriction-site associated DNA (RAD) sequencing technique with the restriction enzyme, PstI. A total of 6,647 SNPs were assigned to 22 linkage groups, which is equal to the number of chromosome pairs in turbot. For the first time, the average marker interval reached 0.3958 cM, which is equal to approximately 0.1203 Mb of the turbot genome. The observed 99.34% genome coverage indicates that the linkage map was genome-wide. A total of 220 Quantitative Traits Locus (QTLs) associated with two body length traits, two body weight traits in different growth periods and sex determination were detected with an LOD > 5.0 in 12 linkage groups (LGs), which explained the corresponding phenotypic variance (R2), ranging from 14.4-100%. Among them, 175 overlapped with linked SNPs, and the remaining 45 were located in regions between contiguous SNPs. According to the QTLs related to growth trait distribution and the changing of LGs during different growth periods, the growth traits are likely controlled by multi-SNPs distributed on several LGs; the effect of these SNPs changed during different growth periods. Most sex-related QTLs were detected at LG 21 with a linkage span of 70.882 cM. Additionally, a small number of QTLs with high feasibility and a narrow R2 distribution were also observed on LG7 and LG14, suggesting that multi LGs or chromosomes might be involved in sex determination. High homology was recorded between LG21 in Cynoglossus semilaevis and turbot. This high-saturated turbot RAD-Seq linkage map is undoubtedly a promising platform for marker assisted selection (MAS) and flatfish genomics research.

  19. Familial Scheuermann disease: a genetic and linkage study.

    PubMed Central

    McKenzie, L; Sillence, D

    1992-01-01

    Scheuermann juvenile kyphosis or Scheuermann disease is the most frequent cause of kyphosis in adolescence. However, the natural history and genetic basis is still unknown. Reports of identical radiological changes in monozygotic twins, sib recurrence, and transmission over three generations suggest underlying heritability. In this study, 12 probands were referred to us. Upon radiological examination of the proband's parents and sibs, seven were shown to have familial Scheuermann disease with an autosomal dominant pattern of inheritance. Of the remaining five probands, four had chromosomal anomalies. The three largest pedigrees were subjected to linkage analysis with three candidate genes: Duffy, COL1A1, and COL1A2. Linkage of Scheuermann disease was excluded with Duffy (lod score = -2.195 at theta = 0.10) and COL1A2 (lod score = -2.750 at theta = 0.05) in these families. Images PMID:1552543

  20. Adaptable Hydrogel Networks with Reversible Linkages for Tissue Engineering

    PubMed Central

    Wang, Huiyuan

    2015-01-01

    Adaptable hydrogels have recently emerged as a promising platform for three-dimensional (3D) cell encapsulation and culture. In conventional, covalently crosslinked hydrogels, degradation is typically required to allow complex cellular functions to occur, leading to bulk material degradation. In contrast, adaptable hydrogels are formed by reversible crosslinks. Through breaking and re-forming of the reversible linkages, adaptable hydrogels can be locally modified to permit complex cellular functions while maintaining their long-term integrity. In addition, these adaptable materials can have biomimetic viscoelastic properties that make them well suited for several biotechnology and medical applications. In this review, adaptable hydrogel design considerations and linkage selections are overviewed, with a focus on various cell compatible crosslinking mechanisms that can be exploited to form adaptable hydrogels for tissue engineering. PMID:25989348

  1. Maximum-likelihood estimation of gene location by linkage disequilibrium

    SciTech Connect

    Hill, W.G. ); Weir, B.S. )

    1994-04-01

    Linkage disequilibrium, D, between a polymorphic disease and mapped markers can, in principle, be used to help find the map position of the disease gene. Likelihoods are therefore derived for the value of D conditional on the observed number of haplotypes in the sample and on the population parameter Nc, where N is the effective population size and c the recombination fraction between the disease and marker loci. The likelihood is computed explicitly for the case of two loci with heterozygote superiority and, more generally, by computer simulations assuming a steady state of constant population size and selective pressures or neutrality. It is found that the likelihood is, in general, not very dependent on the degree of selection at the loci and is very flat. This suggests that precise information on map position will not be obtained from estimates of linkage disequilibrium. 15 refs., 5 figs., 21 tabs.

  2. The Linkage Between Oxygenation and Subunit Dissociation in Human Hemoglobin

    PubMed Central

    Ackers, Gary K.; Halvorson, Herbert R.

    1974-01-01

    The use of subunit dissociation as a means of probing intersubunit contact energy changes which accompany cooperative ligand binding has been studied for the case of human hemoglobin. An analysis is presented delineating the information that can be obtained from the linkage relationships between ligand binding and subunit dissociation of hemoglobin tetramers into dimers. The analysis defines (a) the variation of the saturation function, Ȳ, with total protein concentration, (b) the variation of the subunit dissociation constant xK2 with ligand concentration (X) and (c) the correlations between changes in dimer-dimer contact energy and the sequential ligand binding steps. Sensitivity of the linkage function has been explored by numerical simulation. It is shown that subunit dissociation may appreciably affect oxygenation curves under usual conditions of measurement and that relying solely on either xK2 or Ȳ may lead to incorrect picutres of the energetics, whereas the combination defines the system much more exactly. PMID:4530985

  3. Linkage study between manic-depressive illness and chromosome 21

    SciTech Connect

    Ewald, H.; Mors, O.; Flint, T.

    1996-04-09

    Chromosome 21, of interest as potentially containing a disease gene for manic-depressive illness as possible evidence for a gene predisposing to affective disorder, has recently been reported in a single large family as well as samples of families. The present study investigates for linkage between manic-depressive illness and markers covering the long arm of chromosome 21 in two manic-depressive families, using ten microsatellite polymorphisms as markers. No conclusive evidence for a disease gene on the long arm of chromosome 21 was found. Assuming either a dominant or recessive mode of inheritance, close linkage to the marker PFKL, which has been reported as possibly linked to affective disorder, seems unlikely in the families studied here. PFKL and more telomeric markers yielded small positive lod scores at higher recombination fractions in the largest family, and small positive lod scores at lower recombination fractions in the affecteds-only analyses in the smallest family. 32 refs., 2 figs., 3 tabs.

  4. An improved recommendation algorithm via weakening indirect linkage effect

    NASA Astrophysics Data System (ADS)

    Chen, Guang; Qiu, Tian; Shen, Xiao-Quan

    2015-07-01

    We propose an indirect-link-weakened mass diffusion method (IMD), by considering the indirect linkage and the source object heterogeneity effect in the mass diffusion (MD) recommendation method. Experimental results on the MovieLens, Netflix, and RYM datasets show that, the IMD method greatly improves both the recommendation accuracy and diversity, compared with a heterogeneity-weakened MD method (HMD), which only considers the source object heterogeneity. Moreover, the recommendation accuracy of the cold objects is also better elevated in the IMD than the HMD method. It suggests that eliminating the redundancy induced by the indirect linkages could have a prominent effect on the recommendation efficiency in the MD method. Project supported by the National Natural Science Foundation of China (Grant No. 11175079) and the Young Scientist Training Project of Jiangxi Province, China (Grant No. 20133BCB23017).

  5. The effect of pedigree complexity on quantitative trait linkage analysis.

    PubMed

    Dyer, T D; Blangero, J; Williams, J T; Göring, H H; Mahaney, M C

    2001-01-01

    Due to the computational difficulties of performing linkage analysis on large complex pedigrees, most investigators resort to simplifying such pedigrees by some ad hoc strategy. In this paper, we suggest an analytical method to compare the power of various pedigree simplification schemes by using the asymptotic distribution of the likelihood-ratio statistic. We applied the method to the large Hutterine pedigree. Our results indicate that the breaking and reduction of inbreeding loops can greatly diminish the power to localize quantitative trait loci. We also present an efficient Monte Carlo method for estimating identity-by-descent allele sharing in large complex pedigrees. This method is used to facilitate a linkage analysis of serum IgE levels in the Hutterites without simplifying the pedigree.

  6. Parametric and nonparametric linkage analysis: A unified multipoint approach

    SciTech Connect

    Kruglyak, L.; Daly, M.J.; Reeve-Daly, M.P.; Lander, E.S.

    1996-06-01

    In complex disease studies, it is crucial to perform multipoint linkage analysis with many markers and to use robust nonparametric methods that take account of all pedigree information. Currently available methods fall short in both regards. In this paper, we describe how to extract complete multipoint inheritance information from general pedigrees of moderate size. This information is captured in the multipoint inheritance distribution, which provides a framework for a unified approach to both parametric and nonparametric methods of linkage analysis. Specifically, the approach includes the following: (1) Rapid exact computation of multipoint LOD scores involving dozens of highly polymorphic markers, even in the presence of loops and missing data. (2) Nonparametric linkage (NPL) analysis, a powerful new approach to pedigree analysis. We show that NPL is robust to uncertainty about mode of inheritance, is much more powerful than commonly used nonparametric methods, and loses little power relative to parametric linkage analysis. NPL thus appears to be the method of choice for pedigree studies of complex traits. (3) Information-content mapping, which measures the fraction of the total inheritance information extracted by the available marker data and points out the regions in which typing additional markers is most useful. (4) Maximum-likelihood reconstruction of many-marker haplotypes, even in pedigrees with missing data. We have implemented NPL analysis, LOD-score computation, information-content mapping, and haplotype reconstruction in a new computer package, GENEHUNTER. The package allows efficient multipoint analysis of pedigree data to be performed rapidly in a single user-friendly environment. 34 refs., 9 figs., 2 tabs.

  7. Linkage Of Laser And Handling Systems In Multi Station Operation

    NASA Astrophysics Data System (ADS)

    Petschke, U.; Kramer, R.; Wolff, Udo W.; Beyer, Eckhard

    1989-03-01

    Special requirements are needed for highly flexible, multi station laser processing. Linkage of several lasers with various handling stations causes different kinds of tasks to be solved in the fields of optics, electro mechanics, laser technology and opto electro-nics. A new design for flexible high power CO2 laser beam handling has been developed, including self-checking security systems, laser beam diagnostics, easily adjustable high power beam bending mirrors, high precision motorized mechanics and computer controlled user guidance.

  8. Linkage of carbohydrate to hydroxyamino acids in mucopolysaccharides and mucoproteins

    PubMed Central

    Adams, J. B.

    1965-01-01

    1. Glycosidic linkage of carbohydrate to the primary hydroxyl groups of threonine and serine has been established in human blood-group A and Lea substances, bovine submaxillary-gland mucin and human pseudomyxomatous mucin. 2. Treatment of these substances in 0·09n-lithium hydroxide at 100° for 1hr. led to β-elimination at these glycosidic linkages with the resultant formation of α-oxobutyric acid and glycine from threonine linkages, and pyruvic acid from serine linkages. Though most of the threonine was destroyed in every case, about one-third to one-half of the serine residues resisted alkaline cleavage. Such results, indicative of the presence of unbound serine residues, allow, in submaxillary mucin, for a close correlation between the remaining serine, threonine, glutamic acid and aspartic acid and the available sialyl-(2→6)-N-acetylgalactosamine prosthetic groups. 3. The stoichiometry of the β-eliminations has been demonstrated for pseudomyxomatous mucin. The α-oxo acids were separated and determined as their quinoxalinol derivatives by thin-layer chromatography on silica gel. Reaction at the threonine centres favoured α-oxobutyric acid formation (70%, via the intermediary dehydropeptide) over the alternative pathway to glycine (30%). 4. 100% of the hexosamine was destroyed in submaxillary-gland mucin, 85% in pseudomyxomatous mucin and about 60% in the blood-group substances. In the latter cases, the glucosamine/galactosamine ratio was increased from about 4:1 to 8–10:1, suggesting a preferential destruction of galactosamine. Evidence was obtained, however, for a further destruction of hexosamine, in addition to that which could be theoretically attached to peptide at possible known binding sites. 5. The major part of the alkali-resistant hexosamine in the blood-group substances was non-diffusible and was accompanied by the constituent carbohydrates in similar molar proportions to the native materials. ImagesFig. 1. PMID:16749136

  9. Genome scan for linkage to Gilles de la Tourette syndrome

    SciTech Connect

    Barr, C.L.; Livingston, J.; Williamson, R.

    1994-09-01

    Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

  10. A sequence-tagged linkage map of Brassica rapa.

    PubMed

    Kim, Jung Sun; Chung, Tae Young; King, Graham J; Jin, Mina; Yang, Tae-Jin; Jin, Yong-Moon; Kim, Ho-Il; Park, Beom-Seok

    2006-09-01

    A detailed genetic linkage map of Brassica rapa has been constructed containing 545 sequence-tagged loci covering 1287 cM, with an average mapping interval of 2.4 cM. The loci were identified using a combination of 520 RFLP and 25 PCR-based markers. RFLP probes were derived from 359 B. rapa EST clones and amplification products of 11 B. rapa and 26 Arabidopsis. Including 21 SSR markers provided anchors to previously published linkage maps for B. rapa and B. napus and is followed as the referenced mapping of R1-R10. The sequence-tagged markers allowed interpretation of the pattern of chromosome duplications within the B. rapa genome and comparison with Arabidopsis. A total of 62 EST markers showing a single RFLP band were mapped through 10 linkage groups, indicating that these can be valuable anchoring markers for chromosome-based genome sequencing of B. rapa. Other RFLP probes gave rise to 2-5 loci, inferring that B. rapa genome duplication is a general phenomenon through 10 chromosomes. The map includes five loci of FLC paralogues, which represent the previously reported BrFLC-1, -2, -3, and -5 and additionally identified BrFLC3 paralogues derived from local segmental duplication on R3.

  11. The first doubled haploid linkage map for cultivated oat.

    PubMed

    Tanhuanpää, Pirjo; Kalendar, Ruslan; Schulman, Alan H; Kiviharju, Elina

    2008-08-01

    To date, all linkage maps of hexaploid oat (Avena sativa L.) have been constructed using recombinant inbred lines (RILs). Doubled haploids (DHs), however, have the advantage over RILs of their comprehensive homozygosity. DHs have been used for mapping in several cereal species, but in oats the production of large DH populations has only recently become an option. A linkage map of hexaploid oat was constructed using an anther culture-derived DH population (137 individuals) from the F1 individuals of a cross between the Finnish cultivar 'Aslak' and the Swedish cultivar 'Matilda'. The map is composed of 28 linkage groups containing 625 DNA markers: 375 AFLPs (amplified fragment length polymorphisms), 3 IRAPs (inter-retrotransposon amplified polymorphisms), 12 ISSRs (inter simple sequence repeats), 12 microsatellites, 57 RAPDs (random amplified polymorphic DNAs), 59 REMAPs (retrotransposon-microsatellite amplified polymorphisms), 105 SRAPs (sequence-related amplified polymorphisms), and 2 SNPs (single-nucleotide polymorphisms). The total map size is 1526 cM. Over half of the markers in the map showed distorted segregation, with alleles from 'Aslak' usually prevailing. This is explained by the better performance of 'Aslak' in anther culture. Quantitative trait loci affecting some important quality and agronomic traits are being localized on the map.

  12. Displacements and segment linkage in strike-slip fault zones

    NASA Astrophysics Data System (ADS)

    Peacock, D. C. P.

    Small-scale, well exposed strike-slip fault zones near Kirkcudbright, Scotland, cut sub-vertical bedding, so that mapped bed separations allow the displacements, linkage and evolution of fault segments to be assessed. Displacement variations along the segments can be related to lithologic variations, conjugate relationships, offsets, segment linkage and fault bends. High displacement gradients at the tips of conjugate and offset faults produce convex-upwards ( E-type) displacement-distance ( d-x) profiles. Contractional fault bends and linkage points are marked by a decrease in fault displacement, producing partially concave-upwards ( D-type) d-x profiles. Where fault displacement gradients are steep, wallrocks are marked by structures such as synthetic faults, normal drag folding, ductile strain and veining, which transfer displacement. The faults studied tend to have lower r/ dMAX ratios (where r = distance between the point of maximum displacement and the fault tip on a particular profile, and dMAX = maximum displacement on the profile) than are shown by normal faults in map view. This may be because r is measured parallel to the displacement direction and/or because of lithologic variations.

  13. Allelic loss and linkage studies in prostate cancer

    SciTech Connect

    Johnson, D.R.; Bale, A.E.; Lytton, B.

    1994-09-01

    Prostate cancer is the most common malignancy in U.S. males. Many examples of familial aggregation have been reported, and segregration analysis suggests that an autosomal dominant gene with a penetrance of 88% by age 85 accounts for 9% of all cases. Because many dominant cancer predisposition syndromes are related to germline mutations in tumor suppressor genes, we analyzed a series of sporadic and hereditary tumors for allelic loss. High grade sporadic, paraffin-embedded, primary prostate tumors were obtained from the archival collection in the Department of Pathology at Yale and hereditary tumors from three families were obtained by an advertisement in the New York Times and from referrals by urologists. PCR analysis showed loss in 4/7 informative sporadic prostate tumors with NEFL (8p21), in 8/22 informative tumors with D10S169 (10q26-qter), in 2/8 informative tumors with D10S108 (10q) and in 4/23 informative tumors with D10S89 (10p) in agreement with previous studies. PYGM on chromosome 11 and D9S127 on chromosome 9 showed no loss. Linkage analysis with NEFL in 3 prostate cancer families gave strongly negative results for close linkage (Z=-2.1 at {theta}=0.01) but LOD scores were very dependent on parameters, e.g. gene frequency, phenocopy rate, and penetrance. Linkage analysis with chromosome 10 markers and systematic analysis of the genome for other area of allelic loss are underway.

  14. Glycosidic linkage conformation of methyl-α-mannopyranoside

    NASA Astrophysics Data System (ADS)

    Coskuner, Orkid; Bergeron, Denis E.; Rincon, Luis; Hudgens, Jeffrey W.; Gonzalez, Carlos A.

    2008-07-01

    We study the preferred conformation of the glycosidic linkage of methyl-α-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-α-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.

  15. Linkage analysis of the Nail-patella syndrome

    SciTech Connect

    Campeau, E.; Watkins, D.; Rouleau, G.A.; Babul, R.; Der Kaloustian, V.M.; Buchanan, J.A.; Meschino, W.

    1995-01-01

    Nail-patella syndrome (NPS) is an autosomal dominant disorder characterized by dysplasia of nails and patella, decreased mobility of the elbow, iliac horns, and, in some cases, nephropathy. The disorder has been mapped to the long arm of chromosome 9, but the precise localization and identity of the NPS gene are unknown. Linkage analysis in three NPS families, using highly informative dinucleotide repeat polymorphisms on 9q33-q34, confirmed linkage of NPS to this chromosome. Recombinations were detected, by two-point linkage analysis, between NPS and the centromeric markers D9S60 and the gelsolin gene and the telomeric markers D9S64 and D9S66, in one of the families. Haplotype analysis suggested an additional recombination between NPS and the argininosuccinate synthetase (ASS) gene. These results localize the NPS gene to an interval on 9q34.1, distal to D9S60 an proximal to ASS, comprising a genetic distance of {approximately}9 cM. This represents a significant refinement in the localization of the NPS gene. 25 refs., 2 figs., 1 tab.

  16. Linkage mechanics and power amplification of the mantis shrimp's strike.

    PubMed

    Patek, S N; Nowroozi, B N; Baio, J E; Caldwell, R L; Summers, A P

    2007-10-01

    Mantis shrimp (Stomatopoda) generate extremely rapid and forceful predatory strikes through a suite of structural modifications of their raptorial appendages. Here we examine the key morphological and kinematic components of the raptorial strike that amplify the power output of the underlying muscle contractions. Morphological analyses of joint mechanics are integrated with CT scans of mineralization patterns and kinematic analyses toward the goal of understanding the mechanical basis of linkage dynamics and strike performance. We test whether a four-bar linkage mechanism amplifies rotation in this system and find that the rotational amplification is approximately two times the input rotation, thereby amplifying the velocity and acceleration of the strike. The four-bar model is generally supported, although the observed kinematic transmission is lower than predicted by the four-bar model. The results of the morphological, kinematic and mechanical analyses suggest a multi-faceted mechanical system that integrates latches, linkages and lever arms and is powered by multiple sites of cuticular energy storage. Through reorganization of joint architecture and asymmetric distribution of mineralized cuticle, the mantis shrimp's raptorial appendage offers a remarkable example of how structural and mechanical modifications can yield power amplification sufficient to produce speeds and forces at the outer known limits of biological systems. PMID:17921168

  17. Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).

    PubMed

    Olson, Matthew S; Robertson, Amanda L; Takebayashi, Naoki; Silim, Salim; Schroeder, William R; Tiffin, Peter

    2010-04-01

    *Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.

  18. Genetic linkage analysis in the age of whole-genome sequencing.

    PubMed

    Ott, Jurg; Wang, Jing; Leal, Suzanne M

    2015-05-01

    For many years, linkage analysis was the primary tool used for the genetic mapping of Mendelian and complex traits with familial aggregation. Linkage analysis was largely supplanted by the wide adoption of genome-wide association studies (GWASs). However, with the recent increased use of whole-genome sequencing (WGS), linkage analysis is again emerging as an important and powerful analysis method for the identification of genes involved in disease aetiology, often in conjunction with WGS filtering approaches. Here, we review the principles of linkage analysis and provide practical guidelines for carrying out linkage studies using WGS data. PMID:25824869

  19. Enrollment in HIV Care Two Years after HIV Diagnosis in the Kingdom of Swaziland: An Evaluation of a National Program of New Linkage Procedures

    PubMed Central

    MacKellar, Duncan A.; Williams, Daniel; Storer, Nosipho; Okello, Velephi; Azih, Charles; Drummond, Jennifer; Nuwagaba-Biribonwoha, Harriet; Preko, Peter; Morgan, Rebecca L.; Dlamini, Makhosazana; Byrd, Johnita; Agolory, Simon; Baughman, Andrew L.; McNairy, Margaret L.; Sahabo, Ruben; Ehrenkranz, Peter

    2016-01-01

    To improve early enrollment in HIV care, the Swaziland Ministry of Health implemented new linkage procedures for persons HIV diagnosed during the Soka Uncobe male circumcision campaign (SOKA, 2011–2012) and the Swaziland HIV Incidence Measurement Survey (SHIMS, 2011). Abstraction of clinical records and telephone interviews of a retrospective cohort of HIV-diagnosed SOKA and SHIMS clients were conducted in 2013–2014 to evaluate compliance with new linkage procedures and enrollment in HIV care at 92 facilities throughout Swaziland. Of 1,105 clients evaluated, within 3, 12, and 24 months of diagnosis, an estimated 14.0%, 24.3%, and 37.0% enrolled in HIV care, respectively, after adjusting for lost to follow-up and non-response. Kaplan-Meier functions indicated lower enrollment probability among clients 14–24 (P = 0.0001) and 25–29 (P = 0.001) years of age compared with clients >35 years of age. At 69 facilities to which clients were referred for HIV care, compliance with new linkage procedures was low: referral forms were located for less than half (46.8%) of the clients, and few (9.6%) were recorded in the appointment register or called either before (0.3%) or after (4.9%) their appointment. Of over one thousand clients newly HIV diagnosed in Swaziland in 2011 and 2012, few received linkage services in accordance with national procedures and most had not enrolled in HIV care two years after their diagnosis. Our findings are a call to action to improve linkage services and early enrollment in HIV care in Swaziland. PMID:26910847

  20. Enrollment in HIV Care Two Years after HIV Diagnosis in the Kingdom of Swaziland: An Evaluation of a National Program of New Linkage Procedures.

    PubMed

    MacKellar, Duncan A; Williams, Daniel; Storer, Nosipho; Okello, Velephi; Azih, Charles; Drummond, Jennifer; Nuwagaba-Biribonwoha, Harriet; Preko, Peter; Morgan, Rebecca L; Dlamini, Makhosazana; Byrd, Johnita; Agolory, Simon; Baughman, Andrew L; McNairy, Margaret L; Sahabo, Ruben; Ehrenkranz, Peter

    2016-01-01

    To improve early enrollment in HIV care, the Swaziland Ministry of Health implemented new linkage procedures for persons HIV diagnosed during the Soka Uncobe male circumcision campaign (SOKA, 2011-2012) and the Swaziland HIV Incidence Measurement Survey (SHIMS, 2011). Abstraction of clinical records and telephone interviews of a retrospective cohort of HIV-diagnosed SOKA and SHIMS clients were conducted in 2013-2014 to evaluate compliance with new linkage procedures and enrollment in HIV care at 92 facilities throughout Swaziland. Of 1,105 clients evaluated, within 3, 12, and 24 months of diagnosis, an estimated 14.0%, 24.3%, and 37.0% enrolled in HIV care, respectively, after adjusting for lost to follow-up and non-response. Kaplan-Meier functions indicated lower enrollment probability among clients 14-24 (P = 0.0001) and 25-29 (P = 0.001) years of age compared with clients >35 years of age. At 69 facilities to which clients were referred for HIV care, compliance with new linkage procedures was low: referral forms were located for less than half (46.8%) of the clients, and few (9.6%) were recorded in the appointment register or called either before (0.3%) or after (4.9%) their appointment. Of over one thousand clients newly HIV diagnosed in Swaziland in 2011 and 2012, few received linkage services in accordance with national procedures and most had not enrolled in HIV care two years after their diagnosis. Our findings are a call to action to improve linkage services and early enrollment in HIV care in Swaziland. PMID:26910847

  1. Student Records

    ERIC Educational Resources Information Center

    Morshavitz, Helen

    1974-01-01

    Pupil files are accumulating increasing amounts of sensitive data. Yet parents have been barred from seeing their children's files while law enforcement officials and other public agencies have been given virtually free access. However, a national law in regard to student records is a real possibility. (Author/WM)

  2. Student Records

    ERIC Educational Resources Information Center

    Fields, Cheryl

    2005-01-01

    Another topic involving privacy has attracted considerable attention in recent months--the "student unit record" issue. The U.S. Department of Education concluded in March that it would be feasible to help address lawmakers' concerns about accountability in higher education by constructing a database capable of tracking students from institution…

  3. Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.).

    PubMed

    Ecke, Wolfgang; Clemens, Rosemarie; Honsdorf, Nora; Becker, Heiko C

    2010-03-01

    Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies >or=0.1 were used for the analysis of linkage disequilibrium in a population of 85 canola quality winter rapeseed genotypes. A low overall level of linkage disequilibrium was found with a mean r (2) of only 0.027 over all 356,590 possible marker pairs. At a significance threshold of P = 2.8 x 10(-7), which was derived by a Bonferroni correction from a global alpha-level of 0.1, only 0.78% of the marker pairs were in significant linkage disequilibrium. Among physically linked marker pairs, the level of linkage disequilibrium was about five times higher with more than 10% of marker pairs in significant linkage disequilibrium. Linkage disequilibrium decayed rapidly with distance between linked markers with high levels of linkage disequilibrium extending only for about 2 cM. Owing to the rapid decay of linkage disequilibrium with distance association analyses in canola quality rapeseed will have a significantly higher resolution than QTL analyses in segregating populations by interval mapping, but much larger number of markers will be necessary to cover the whole genome. A major impact of the recent breeding history of rapeseed on linkage disequilibrium could not be observed.

  4. Genetic linkage heterogeneity in the fragile X syndrome.

    PubMed

    Brown, W T; Gross, A C; Chan, C B; Jenkins, E C

    1985-01-01

    Genetic linkage between a factor IX DNA restriction fragment length polymorphism (RFLP) and the fragile X chromosome marker was analyzed in eight fragile X pedigrees and compared to eight previously reported pedigrees. A large pedigree with apparently full penetrance in all male members showed a high frequency of recombination. A lod score of -7.39 at theta = 0 and a maximum score of 0.26 at theta = 0.32 were calculated. A second large pedigree with a nonpenetrant male showed tight linkage with a maximum lod score of 3.13 at theta = 0, a result similar to one large pedigree with a nonpenetrant male previously reported. The differences in lod scores seen in these large pedigrees suggested there was genetic heterogeneity in linkage between families which appeared to relate to the presence of nonpenetrant males. The combined lod score for the three pedigrees with nonpenetrant males was 6.84 at theta = 0. For the 13 other pedigrees without nonpenetrant males the combined lod score was -21.81 at theta = 0, with a peak of 0.98 at theta = 0.28. When lod scores from all 16 families were combined, the value was -15.14 at theta = 0 and the overall maximum was 5.13 at theta = 0.17. To determine whether genetic heterogeneity was present, three statistical tests for heterogeneity were employed. First, a "predivided-sample" test was used. The 16 pedigrees were divided into two classes, NP and P, based upon whether or not any nonpenetrant males were detected in the pedigree. This test gave evidence for significant genetic heterogeneity whether the three large pedigrees with seven or more informative males (P less than 0.005), the eight pedigrees with three informative males (P less than 0.001), or all 16 pedigrees (P less than 0.001) were included in the analysis. Second, Morton's large sample test was employed. Significant heterogeneity was present when the analysis was restricted to the three large pedigrees (P less than 0.025), or to the eight pedigrees with informative males

  5. Records Reaching Recording Data Technologies

    NASA Astrophysics Data System (ADS)

    Gresik, G. W. L.; Siebe, S.; Drewello, R.

    2013-07-01

    The goal of RECORDS (Reaching Recording Data Technologies) is the digital capturing of buildings and cultural heritage objects in hard-to-reach areas and the combination of data. It is achieved by using a modified crane from film industry, which is able to carry different measuring systems. The low-vibration measurement should be guaranteed by a gyroscopic controlled advice that has been , developed for the project. The data were achieved by using digital photography, UV-fluorescence photography, infrared reflectography, infrared thermography and shearography. Also a terrestrial 3D laser scanner and a light stripe topography scanner have been used The combination of the recorded data should ensure a complementary analysis of monuments and buildings.

  6. Linkage and linkage disequilibrium in chromosome band 1p36 in American Chaldeans with inflammatory bowel disease.

    PubMed

    Cho, J H; Nicolae, D L; Ramos, R; Fields, C T; Rabenau, K; Corradino, S; Brant, S R; Espinosa, R; LeBeau, M; Hanauer, S B; Bodzin, J; Bonen, D K

    2000-05-22

    The idiopathic inflammatory bowel diseases (IBDs), consisting of Crohn's disease and ulcerative colitis, are complex genetic disorders involving chronic inflammation of the intestines. Multiple genetic loci have been implicated through genome-wide searches, but refinement of localization sufficient to undertake positional cloning efforts has been problematic. This difficulty can be obviated through identification of ancestrally shared regions in genetic isolates, such as the Chaldean population, a Roman Catholic group from Iraq. We analyzed four multiply affected American Chaldean families with inflammatory bowel disease not known to be related. We observed evidence for linkage and linkage disequilibrium in precisely the same region of chromosome band 1p36 reported previously in an outbred population. Maximal evidence for linkage was observed near D1S1597 by multipoint analysis (MLOD = 3.01, P = 6.1 x 10(-5)). A shared haplotype (D1S507 to D1S1628) was observed over 27 cM between two families. There was homozygous sharing of a 5 cM portion of that haplotype in one family and over a <1 cM region in the second family. Homozygous sharing of this haplotype near D1S2697 and D1S3669 was observed in one individual in a third multiply affected family, with heterozygous sharing in a fourth family. Linkage in outbred families as well as in this genetic isolate indicates that a pathophysiologically crucial IBD susceptibility gene is located in 1p36. These findings provide a unique opportunity to refine the localization and identify a major susceptibility gene for a complex genetic disorder.

  7. Results of the independent radiological verification survey of the remedial action performed at 525 S. Main Street, Oxford, Ohio, (OXO002)

    SciTech Connect

    Kleinhans, K.R.; Rice, D.E.; Murray, M.E.; Carrier, R.F.

    1996-04-01

    Between October 1952 and February 1957, National Lead of Ohio (NLO), a primary contractor for the Atomic Energy Commission (AEC), subcontracted certain uranium machining operations to Alba Craft Laboratory, Incorporated, located at 10-14 West Rose Avenue, Oxford, Ohio. In 1992, personnel from Oak Ridge National Laboratory (ORNL) confirmed the presence of residual radioactive materials from the AEC-related operations in and around the facility in amounts exceeding the applicable Department of Energy (DOE) guidelines. Above-guideline radiation levels were also found both indoors and outdoors at 525 S. Main Street, a private residential property in the immediate vicinity of the Alba Craft site. This document reports the findings at this private residence. Although the amount of uranium found on the properties posed little health hazard if left undisturbed, the levels were sufficient to require remediation to bring radiological conditions into compliance with current guidelines, thus ensuring that the public and the environment are protected. A team from ORNL conducted a radiological verification survey of the property at 525 S. Main Street, between November 1993 and December 1994. The survey was conducted at the request of DOE and included directly measured radiation levels, the collection and analysis of soil samples to determine concentrations of uranium and certain other radionuclides, and comparison of these data to the guidelines.

  8. Computer-Based Internet-Hosted Assessment of L2 Literacy: Computerizing and Administering of the Oxford Quick Placement Test in ExamView and Moodle

    NASA Astrophysics Data System (ADS)

    Meurant, Robert C.

    Sorting of Korean English-as-a-Foreign-Language (EFL) university students by Second Language (L2) aptitude allocates students to classes of compatible ability level, and was here used to screen candidates for interview. Paper-and-pen versions of the Oxford Quick Placement Test were adapted to computer-based testing via online hosting using FSCreations ExamView. Problems with their online hosting site led to conversion to the popular computer-based learning management system Moodle, hosted on www.ninehub.com. 317 sophomores were tested online to encourage L2 digital literacy. Strategies for effective hybrid implementation of Learning Management Systems in L2 tertiary education include computer-based Internet-hosted L2 aptitude tests. These potentially provide a convenient measure of student progress in developing L2 fluency, and offer a more objective and relevant means of teacher- and course-assessment than student evaluations, which tend to confuse entertainment value and teacher popularity with academic credibility and pedagogical effectiveness.

  9. Introducing the Oxford Vocal (OxVoc) Sounds database: a validated set of non-acted affective sounds from human infants, adults, and domestic animals

    PubMed Central

    Parsons, Christine E.; Young, Katherine S.; Craske, Michelle G.; Stein, Alan L.; Kringelbach, Morten L.

    2014-01-01

    Sound moves us. Nowhere is this more apparent than in our responses to genuine emotional vocalizations, be they heartfelt distress cries or raucous laughter. Here, we present perceptual ratings and a description of a freely available, large database of natural affective vocal sounds from human infants, adults and domestic animals, the Oxford Vocal (OxVoc) Sounds database. This database consists of 173 non-verbal sounds expressing a range of happy, sad, and neutral emotional states. Ratings are presented for the sounds on a range of dimensions from a number of independent participant samples. Perceptions related to valence, including distress, vocalizer mood, and listener mood are presented in Study 1. Perceptions of the arousal of the sound, listener motivation to respond and valence (positive, negative) are presented in Study 2. Perceptions of the emotional content of the stimuli in both Study 1 and 2 were consistent with the predefined categories (e.g., laugh stimuli perceived as positive). While the adult vocalizations received more extreme valence ratings, rated motivation to respond to the sounds was highest for the infant sounds. The major advantages of this database are the inclusion of vocalizations from naturalistic situations, which represent genuine expressions of emotion, and the inclusion of vocalizations from animals and infants, providing comparison stimuli for use in cross-species and developmental studies. The associated website provides a detailed description of the physical properties of each sound stimulus along with cross-category descriptions. PMID:25009511

  10. Results of the independent radiological verification survey of the remedial action performed at the former Alba Craft Laboratory site, Oxford, Ohio, (OXO001)

    SciTech Connect

    Kleinhans, K.R.; Murray, M.E.; Carrier, R.F.

    1996-04-01

    Between October 1952 and February 1957, National Lead of Ohio (NLO), a primary contractor for the Atomic Energy Commission (AEC), subcontracted certain uranium machining operations to Alba Craft Laboratory, Incorporated, located at 10-14 West Rose Avenue, Oxford, Ohio. In 1992, personnel from Oak Ridge National Laboratory (ORNL) confirmed the presence of residual radioactive materials from the AEC-related operations in and around the facility in amounts exceeding the applicable Department of Energy (DOE) guidelines. Although the amount of uranium found on the property posed little health hazard if left undisturbed, the levels were sufficient to require remediation to bring radiological conditions into compliance with current guidelines, thus ensuring that the public and the environment are protected. A team from ORNL conducted a radiological verification survey of the former Alba Craft Laboratory property between December 1994 and February 1995. The survey was conducted at the request of DOE and included directly measured radiation levels, the collection and analysis of soil samples to determine concentrations of uranium and certain other radionuclides, and comparison of these data to the guidelines. This document reports the findings of this survey. The results of the independent verification survey of the former Alba Craft Laboratory property demonstrate that all contaminated areas have been remediated to radionuclide concentrations and activity levels below the applicable guideline limits set by DOE.

  11. Data linkage in an established longitudinal cohort: the Western Australian Pregnancy Cohort (Raine) Study.

    PubMed

    Mountain, Jenny A; Nyaradi, Anett; Oddy, Wendy H; Glauert, Rebecca A; de Klerk, Nick H; Straker, Leon M; Stanley, Fiona J

    2016-01-01

    The Western Australian Data Linkage System is one of a few comprehensive, population-based data linkage systems worldwide, creating links between information from different sources relating to the same individual, family, place or event, while maintaining privacy. The Raine Study is an established cohort study with more than 2000 currently active participants. Individual consent was obtained from participants for information in publicly held databases to be linked to their study data. A waiver of consent was granted where it was impracticable to obtain consent. Approvals to link the datasets were obtained from relevant ethics committees and data custodians. The Raine Study dataset was subsequently linked to academic testing data collected by the Western Australian Department of Education. Examination of diet and academic performance showed that children who were predominantly breastfed for at least 6 months scored higher academically at age 10 than children who were breastfed for less than 6 months. A further study found that better diet quality at ages 1, 2 and 3 years was associated with higher academic scores at ages 10 and 12 years. Examination of nutritional intake at 14 years of age found that a better dietary pattern was associated with higher academic performance. The detailed longitudinal data collected in the Raine Study allowed for adjustment for multiple covariates and confounders. Data linkage reduces the burden on cohort participants by providing additional information without the need to contact participants. It can give information on participants who have been lost to follow-up; provide or complement missing data; give the opportunity for validation studies comparing recall of participants with administrative records; increase the population sample of studies by adding control participants from the general population; and allow for the adjustment of multiple covariates and confounders. The Raine Study dataset is extensive and detailed, and can be

  12. Linkage between acoustic parameters and seabed sediment properties in the south-western Baltic Sea

    NASA Astrophysics Data System (ADS)

    Endler, Michael; Endler, Rudolf; Bobertz, Bernd; Leipe, Thomas; Arz, Helge W.

    2015-04-01

    Acoustic profiling methods are widely used to provide a rapid view into geological structures. For the interpretation of acoustic profiling results (single- and multi-beam), reliable geo-acoustic models are needed. Suitable geo-acoustic models covering a wide range of sediment types do not exist to date for the Baltic Sea. Based on surface sediment datasets, geo-acoustic models have been set up for the prediction of acoustical parameters derived from sedimentological data for south-western Baltic Sea surface sediments. Empirical relationships were created to predict key in situ parameters (p-wave velocity, wet bulk density) from sedimentological core data, notably grain density and water content. The Gassmann-Hamilton equations were used to set up a more generic physically based model. For the first time semi-empirical equations for the calculation of the elastic frame modulus and the solid sediment particle modulus were established by an iterative Gassmann-Hamilton fitting procedure. The resulting models have a remarkably good performance with, for example, a calculated sound velocity accuracy of about 17-32 m s-1 depending on model input data. The acoustic impedance of seafloor sediments can be estimated from single-beam echosounding if the contribution of seafloor reflectivity is extracted from the total acoustic signal. The data reveal a strong linkage between acoustic impedance and selected sediment properties (e.g. grain size, water content). This underlines the potential for effective mapping of seafloor sediment properties (e.g. habitat mapping). Furthermore, these geo-acoustic models can be used by marine geologists for a precise linkage between sediment facies identified in longer cores and corresponding acoustic facies recorded by high-resolution seismic profiling in future work.

  13. Greenland Blocking As a Mechanism for Recent Arctic/Mid-Latitude Weather Linkages

    NASA Astrophysics Data System (ADS)

    Overland, J. E.; Hanna, E.; Wang, M.

    2014-12-01

    High-latitude blocking (HLB) located near and west of Greenland and in northeastern Siberia is a process that links Arctic processes to mid-latitude weather. HLB lies north of the jet stream and tends to bifurcate or divert the jet stream southward, rather than providing a complete block to the westerly flow. It is differentiated from mid-latitude blocking located in the central Atlantic to Europe and the western Pacific along eddy-driven jet streams. It is important to identify and understand an increase in recent HLB in early winter during the last five years relative to time series since 1948, even though this length is too short to robustly distinguish the influence of Arctic forcing from random events. In the last five early winters (December-January 2009-10 through 2013-14), two record and four other negative Arctic Oscillation atmospheric circulation index events have been observed, with positive Greenland Blocking Indices (GBI, greater 500 hPa geopotential heights) and increased geopotential thickness west of Greenland. Cold air penetrated into the southeastern United States in December 2009 and 2010 and January 2014 related to amplification in the long-wave upper-level atmospheric wind pattern. Northward air flow over Davis Strait acts as a positive feedback to maintain the Greenland air temperature anomalies. Extreme negative GBI were observed in December 2011-January 2012. Increased thickness associated with positive GBI can be a response to external (local sea ice loss, Greenland surface warming, or even equatorial teleconnections) or internal (advection and orientation of the long wave patterns) processes. A similar blocking feature is observed in Siberia/eastern Asia. A Bayesian approach to an Arctic/mid-latitude weather linkage emphasizes the nearly irresolvable uncertainty surrounding causation of recent major weather events; yet it drives scientific understanding of linkages and potential impacts on seasonal forecasting.

  14. The Québec BCG Vaccination Registry (1956–1992): assessing data quality and linkage with administrative health databases

    PubMed Central

    2014-01-01

    Background Vaccination registries have undoubtedly proven useful for estimating vaccination coverage as well as examining vaccine safety and effectiveness. However, their use for population health research is often limited. The Bacillus Calmette-Guérin (BCG) Vaccination Registry for the Canadian province of Québec comprises some 4 million vaccination records (1926-1992). This registry represents a unique opportunity to study potential associations between BCG vaccination and various health outcomes. So far, such studies have been hampered by the absence of a computerized version of the registry. We determined the completeness and accuracy of the recently computerized BCG Vaccination Registry, as well as examined its linkability with demographic and administrative medical databases. Methods Two systematically selected verification samples, each representing ~0.1% of the registry, were used to ascertain accuracy and completeness of the electronic BCG Vaccination Registry. Agreement between the paper [listings (n = 4,987 records) and vaccination certificates (n = 4,709 records)] and electronic formats was determined along several nominal and BCG-related variables. Linkage feasibility with the Birth Registry (probabilistic approach) and provincial Healthcare Registration File (deterministic approach) was examined using nominal identifiers for a random sample of 3,500 individuals born from 1961 to 1974 and BCG vaccinated between 1970 and 1974. Results Exact agreement was observed for 99.6% and 81.5% of records upon comparing, respectively, the paper listings and vaccination certificates to their corresponding computerized records. The proportion of successful linkage was 77% with the Birth Registry, 70% with the Healthcare Registration File, 57% with both, and varied by birth year. Conclusions Computerization of this Registry yielded excellent results. The registry was complete and accurate, and linkage with administrative databases was highly feasible. This

  15. Development of the Oxford Hills Healthy Moms Project using a social marketing process: a community-based physical activity and nutrition intervention for low-socioeconomic-status mothers in a rural area in Maine.

    PubMed

    Dharod, Jigna M; Drewette-Card, Rebecca; Crawford, David

    2011-03-01

    A physical activity and nutrition community intervention called the Oxford Hills Healthy Moms (OHHM) Project was developed using a multifaceted social marketing process, including review of state surveillance results, key informant interviews, and a survey and focus group discussions with low-socioeconomic-status (low-SES) mothers. This formative work was used to make key decisions on the selection of the intervention region, segmentation of the audience, and design of intervention strategies addressing multiple levels of the socioecological model. The OHHM Project aims to increase fruit and vegetable consumption and physical activity levels among low-SES mothers in the Oxford Hills region of Maine. The OHHM Project includes five components: (a) physical activity buddy program, (b) cooking club with education, (c) fruit and vegetable discount buying club with education, (d) increased access to produce vendors, and (e) increased access to places for physical activity.

  16. Linkage mapping in sheep and deer identifies a conserved pecora ruminant linkage group orthologous to two regions of HSA16 and a portion of HSA7Q

    SciTech Connect

    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 that this linkage pattern was present in the genome of the common ancestor of the pecora ruminants. 35 refs., 1 fig., 2 tabs.

  17. McCrillisite, NaCs(Be,Li)Zr2(PO4)4.1-2H2O, a new mineral species from Mount Mica, Oxford County, Maine, and new data for gainesite

    USGS Publications Warehouse

    Foord, E.E.; Brownfield, M.E.; Lichte, F.E.; Davis, A.M.; Sutley, S.J.

    1994-01-01

    McCrillisite, a member of the gainesite group, occurs in the Mount Mica granitic pegmatite, South Paris, Oxford County, Maine. The mineral is a product of late-stage hydrothermal alteration and is associated with approximately 20 other silicate, oxide, carbonate, arsenite and phosphate minerals. Crystals occur in mm- to cm-sized cavities, and individuals are up to 1.2 mm in maximum dimension. The crystallography and mineral chemistry of McCrillisite are described. -from Authors

  18. Meta-analysis of genome-wide linkage scans for renal function traits

    PubMed Central

    Rao, Madhumathi; Mottl, Amy K.; Cole, Shelley A.; Umans, Jason G.; Freedman, Barry I.; Bowden, Donald W.; Langefeld, Carl D.; Fox, Caroline S.; Yang, Qiong; Cupples, Adrienne; Iyengar, Sudha K.; Hunt, Steven C.

    2012-01-01

    Background. Several genome scans have explored the linkage of chronic kidney disease phenotypes to chromosomic regions with disparate results. Genome scan meta-analysis (GSMA) is a quantitative method to synthesize linkage results from independent studies and assess their concordance. Methods. We searched PubMed to identify genome linkage analyses of renal function traits in humans, such as estimated glomerular filtration rate (GFR), albuminuria, serum creatinine concentration and creatinine clearance. We contacted authors for numerical data and extracted information from individual studies. We applied the GSMA nonparametric approach to combine results across 14 linkage studies for GFR, 11 linkage studies for albumin creatinine ratio, 11 linkage studies for serum creatinine and 4 linkage studies for creatinine clearance. Results. No chromosomal region reached genome-wide statistical significance in the main analysis which included all scans under each phenotype; however, regions on Chromosomes 7, 10 and 16 reached suggestive significance for linkage to two or more phenotypes. Subgroup analyses by disease status or ethnicity did not yield additional information. Conclusions. While heterogeneity across populations, methodologies and study designs likely explain this lack of agreement, it is possible that linkage scan methodologies lack the resolution for investigating complex traits. Combining family-based linkage studies with genome-wide association studies may be a powerful approach to detect private mutations contributing to complex renal phenotypes. PMID:21622988

  19. Development of a black gram [Vigna mungo (L.) Hepper] linkage map and its comparison with an azuki bean [Vigna angularis (Willd.) Ohwi and Ohashi] linkage map.

    PubMed

    Chaitieng, B; Kaga, A; Tomooka, N; Isemura, T; Kuroda, Y; Vaughan, D A

    2006-11-01

    The Asian Vigna group of grain legumes consists of six domesticated species, among them black gram is widely grown in South Asia and to a lesser extent in Southeast Asia. We report the first genetic linkage map of black gram [Vigna mungo (L.) Hepper], constructed using a BC(1)F(1) population consisting of 180 individuals. The BC(1)F(1) population was analyzed in 61 SSR primer pairs, 56 RFLP probes, 27 AFLP loci and 1 morphological marker. About 148 marker loci could be assigned to the 11 linkage groups, which correspond to the haploid chromosome number of black gram. The linkage groups cover a total of 783 cM of the black gram genome. The number of markers per linkage group ranges from 6 to 23. The average distance between adjacent markers varied from 3.5 to 9.3 cM. The results of comparative genome mapping between black gram and azuki bean show that the linkage order of markers is highly conserved. However, inversions, insertions, deletions/duplications and a translocation were detected between the black gram and azuki bean linkage maps. The marker order on parts of linkage groups 1, 2 and 5 is reversed between the two species. One region on black gram linkage group 10 appears to correspond to part of azuki bean linkage group 1. The present study suggests that the azuki bean SSR markers can be widely used for Asian Vigna species and the black gram genetic linkage map will assist in improvement of this crop.

  20. Structures and apoprotein linkages of phycoerythrobilin and phycocyanobilin

    PubMed Central

    Killilea, S. Derek; O'Carra, Padraig; Murphy, Richard F.

    1980-01-01

    Phycoerythrobilin and phycocyanobilin are covalently attached to the apoproteins of phycoerythrins and phycocyanins. One linkage consists of an ester bond between the hydroxy group of a serine residue and the propionate side chain on one of the inner pyrrole rings (probably ring C). The other linkage is a labile thioether bond between a cysteine residue and the two-carbon side chain on pyrrole ring A. This side chain and both of the α-positions of the ring A are in the reduced state. This constitutes an important structural revision, since, in the structures currently accepted for the phycobilins, the two-carbon side chain on ring A is depicted as an ethylidene grouping and this has been regarded not only as a very characteristic feature of the phycobilins, but also as a probable structural feature of the chromophore of phytochrome, largely on the basis of other analogies with the phycobilins. The ethylidene-containing structures apply instead to artefact forms of the pigments released from the apoproteins by treatment with hot methanol. Cleavage of the ring-A linkage involves an elimination reaction releasing the cysteine residue and generating a double bond in the ring-A side chain. During cleavage in methanol the direction of the elimination is towards the ring, generating the ethylidene double bond. Since this is linked to the conjugated system, the methanol-released pigments differ spectrally from the native phycobilins. During acid-catalysed release of the pigments, the elimination apparently goes in the opposite direction, generating a double bond at the outer position of the side chain. Since this double bond is not linked to the conjugated system, the acid-released pigments remain spectrally identical with their protein-bound counterparts. PMID:7396852

  1. Structures and apoprotein linkages of phycoerythrobilin and phycocyanobilin.

    PubMed

    Killilea, S D; O'Carra, P; Murphy, R F

    1980-05-01

    Phycoerythrobilin and phycocyanobilin are covalently attached to the apoproteins of phycoerythrins and phycocyanins. One linkage consists of an ester bond between the hydroxy group of a serine residue and the propionate side chain on one of the inner pyrrole rings (probably ring C). The other linkage is a labile thioether bond between a cysteine residue and the two-carbon side chain on pyrrole ring A. This side chain and both of the alpha-positions of the ring A are in the reduced state. This constitutes an important structural revision, since, in the structures currently accepted for the phycobilins, the two-carbon side chain on ring A is depicted as an ethylidene grouping and this has been regarded not only as a very characteristic feature of the phycobilins, but also as a probable structural feature of the chromophore of phytochrome, largely on the basis of other analogies with the phycobilins. The ethylidene-containing structures apply instead to artefact forms of the pigments released from the apoproteins by treatment with hot methanol. Cleavage of the ring-A linkage involves an elimination reaction releasing the cysteine residue and generating a double bond in the ring-A side chain. During cleavage in methanol the direction of the elimination is towards the ring, generating the ethylidene double bond. Since this is linked to the conjugated system, the methanol-released pigments differ spectrally from the native phycobilins. During acid-catalysed release of the pigments, the elimination apparently goes in the opposite direction, generating a double bond at the outer position of the side chain. Since this double bond is not linked to the conjugated system, the acid-released pigments remain spectrally identical with their protein-bound counterparts. PMID:7396852

  2. A genetic linkage map of red drum, Sciaenops ocellatus.

    PubMed

    Portnoy, D S; Renshaw, M A; Hollenbeck, C M; Gold, J R

    2010-12-01

    Second-generation, sex-specific genetic linkage maps were generated for the economically important estuarine-dependent marine fish Sciaenops ocellatus (red drum). The maps were based on F(1) progeny from each of two single-pair mating families. A total of 237 nuclear-encoded microsatellite markers were mapped to 25 linkage groups. The female map contained 226 markers, with a total length of 1270.9 centiMorgans (cM) and an average inter-marker interval of 6.53 cM; the male map contained 201 markers, with a total length of 1122.9 cM and an average inter-marker interval of 6.03 cM. The overall recombination rate was approximately equal in the two sexes (♀:♂=1.03:1). Recombination rates in a number of linkage intervals, however, differed significantly between the same sex in both families and between sexes within families. The former occurred in 2.4% of mapped intervals, while the latter occurred in 51.2% of mapped intervals. Sex-specific recombination rates varied within chromosomes, with regions of both female-biased and male-biased recombination. Original clones from which the microsatellite markers were generated were compared with genome sequence data for the spotted green puffer, Tetraodon nigroviridis; a total of 43 matches were located in 17 of 21 chromosomes of T. nigroviridis, while seven matches were in unknown portions of the T. nigroviridis genome. The map for red drum provides a new, useful tool for aquaculture, population genetics, and comparative genomics of this economically important marine species. PMID:20477786

  3. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    PubMed

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  4. The use of the MOD score in linkage analysis

    SciTech Connect

    Rice, J.P.; Neuman, R.J.; Burroughs, T.E.

    1994-09-01

    The detection of genes for complex diseases through linkage analysis has become feasible now that a dense genetic map is available. However, the best analytic approach to use is unclear when the mode of inheritance is unknown. In prior work, we simulated traits determined by 2, 4, or 6 loci with different degrees of heritability. Approaches which maximized the likelihood under a single-locus model (i.e. the wrong model) performed poorly both in terms of the expected lod score (ELOD) and an upward bias in the estimate of {theta}. MOD scores (lod scores maximized over genetic parameters) have been suggested by Risch (1984) and Clerget-Darpoux (1986) as a way to obviate difficulties due to unspecified ascertainment. The MOD score method is equivalent to maximizing the likelihood of the marker data conditional on all phenotypic data. In cases were segregation analysis under the wrong model would lead to {open_quotes}meaningless{close_quotes} parameter estimates, conditioning on the phenotypic information has intuitive appeal. We have modified the program ILINK of the LINKAGE package to allow maximization of the LOD score. The use of the MOD score gave the best results in the simulated oligogenic data sets. We estimated the three penetrances, and found the heterozygote penetrance to be close to the arithmetic mean of the homozygote penetrances, and reflected the underlying additive oligogenic model. It should be emphasized that without linkage data, there will be no information to estimate these parameters. We have derived analytic results in some special two-locus cases to indicate why the MOD worked in the simulation experiment. One useful feature of the MOD score statistic is that computations are done under the single-locus model, so, unlike the use of the two-trait locus model, the computations are feasible.

  5. Genetic linkage studies in autosomal recessive retinitis pigmentosa

    SciTech Connect

    Mansfield, D.C.; Teague, P.W.; Barber, A.

    1994-09-01

    Autosomal recessive retinitis pigmentosa (arRP) is a severe retinal dystrophy characterized by night blindness, progressive constriction of the visual fields and loss of central vision in the fourth or fifth decades. The frequency of this form of retinitis pigmentosa (RP) varies in different populations. Mutations within the rhodopsin, cyclic GMP phosphodiesterase-{beta} subunit and cGMP-gated channel genes have been reported in some arRP families. The genetic loci responsible for the majority of cases have yet to be identified. Genetic heterogeneity is likely to be extensive. In order to minimize the amount of genetic heterogenity, a set of arRP families was ascertained within the South-Central Sardinian population, in which 81% of families with a known mode of inheritance show an autosomal recessive form of RP. The Sardinian population is an ethnic {open_quotes}outlier{close_quotes}, having remained relatively isolated from mainland and other cultures. Genetic linkage data has been obtained in a set of 11 Sardinian arRP kindreds containing 26 affected members. Under the assumption of genetic homogeneity, no evidence of linkage was found in the arRP kindreds using 195 markers, which excluded 62% of the genome (Z<-2). Positive lod scores were obtained with D14S80 which showed no recombination in a subset of 5 families. Heterogeneity testing using D14S80 and arRP showed no significant evidence of heterogeneity (p=0.18) but evidence of linkage ({chi}{sup 2}=3.64, p=0.028). We are currently screening the neural retina-specific leucine zipper gene (NRL) in 14q11 for mutations as a candidate locus.

  6. Geometric design of mechanical linkages for contact specifications

    NASA Astrophysics Data System (ADS)

    Robson, Nina Patarinsky

    2008-10-01

    This dissertation focuses on the kinematic synthesis of mechanical linkages in order to guide an end-effortor so that it maintains contact with specified objects in its workspace. Assuming the serial chain does not have full mobility in its workspace, the contact geometry is used to determine the dimensions of the serial chain. The approach to this problem, is to use the relative curvature of the contact of the end-effector with one or more objects to define velocity and acceleration specifications for its movement. This provides kinematic constraints that are used to synthesize the dimensions of the serial chain. The mathematical formulation of the geometric design problem, leads to systems of multivariable polynomial equations, which are solved exactly using sparse matrix resultants and polynomial homotopy methods. The results from this research yield planar RR and 4R linkages that match a specified contact geometry, spatial TS, parallel RRS and perpendicular RRS linkages that have a required acceleration specification. A new strategy for a robot recovery from actuator failures is demonstrated for the Mars Exploratory Rover Arm. In extending this work to spatial serial chains, a new method based on sparse matrix resultants was developed, which solves exact synthesis problems with acceleration constraints. Further the research builds on the theoretical concepts of contact relationships for spatial movement. The connection between kinematic synthesis and contact problems and its extension to spatial synthesis are developed in this dissertation for the first time and are new contributions. The results, which rely upon the use of surface curvature effects to reduce the number of fixtures needed to immobilize an object, find applications in robot grasping and part-fixturing. The recovery strategy, presented in this research is also a new concept. The recognition that it is possible to reconfigure a crippled robotic system to achieve mission critical tasks can guide

  7. Linkage heterogeneity among 59 Dutch hereditary breast cancer families

    SciTech Connect

    Cornelis, R.S.; Vliet, M. van; Leeuwen, I. van

    1994-09-01

    We have investigated 59 Dutch kindreds with at least three first-degree relatives with breast and/or ovarian cancer for linkage to BRCA1 on 17q12-q21, using at least 4 microsatellite markers flanking BRCA1 on either side. Assuming no heterogeneity, the overall multipoint lod score in this group of families was -7.59. A marked clustering of lod scores >0.5 was observed among the 13 families with a mean age of onset lower than 45 (total lod score: +3.36). Among the 8 kindreds with a mean age of onset lower than 45 and {ge}3 cases diagnosed under 45, the lod score was +4.43. Interestingly, most of the evidence against linkage was found in 17 families with a mean age of onset between 45 and 54 (total lod score of -8.72). It was estimated that 28% of the breast-only families might be caused by BRCA1. Over the 16 breast-ovarian cancer families a lod score of -3.78 was obtained under homogeneity. The highest lod score was +0.57, assuming heterogeneity with 33% of the families being linked to BRCA1. One family gave a multipoint lod score of -2.01 and thereby satisfies the conventional criterion of an unlinked family. Our results support the conclusions from earlier work by others, namely that BRCA1 predisposes particularly to early-onset breast cancer. The proportion of breast-ovarian cancer families we found linked to BRCA1 is much lower than that found by the Breast Cancer Linkage Consortium. This might be caused by the single unlinked family against an insufficient number of families able to give conclusive positive lod scores.

  8. Prioritizing Tiger Conservation through Landscape Genetics and Habitat Linkages

    PubMed Central

    Yumnam, Bibek; Jhala, Yadvendradev V.; Qureshi, Qamar; Maldonado, Jesus E.; Gopal, Rajesh; Saini, Swati; Srinivas, Y.; Fleischer, Robert C.

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km2 of forest habitat was found to be only 21,290 km2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status to

  9. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    PubMed

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  10. Linkage of preaxial polydactyly type 2 to 7q36

    SciTech Connect

    Hing, A.V.; Slaugh, R.; Dowton, S.B.

    1995-08-28

    We have characterized a 6-generation North American Caucasian kindred segregating one form of preaxial polydactyly type 2 (PPD-2). We demonstrate linkage to the 7q36 region and describe a submicroscopic telomeric chromosomal deletion in phase with the PPD-2 phenotype. Recently, several kindreds segregating triphalangeal thumb (TPT) with and without associated hand anomalies (syndactyly and/or postaxial polydactyly) have also been linked to the subtelomeric region of chromosome 7q. We demonstrate by haplotype analysis that our North American pedigree represents a PPD allele that is independent of the founder PPD allele present in the previously described kindreds. 23 refs., 5 figs., 2 tabs.

  11. Linkages between aromatic structures in the Argonne Premium Coal Samples

    SciTech Connect

    Winans, R.E.; Tomczyk, N.A.

    1997-04-01

    The objective of this study is to elucidate the nature of the important linkages between aromatic clusters and variations of these links with coal rank. From studies using methods such as NMR and mass spectrometry, the authors have considerable information on the size and types of aromatic clusters in the Argonne coals. In this study, extracts, model polymers, extracted coals, and modified coals are examined by temperature resolved high resolution mass spectrometry. There is evidence that strong bond cleavage may be very important for volatile release in pyrolysis of higher rank coals.

  12. The Reduction of Aileron Operating Force by Differential Linkage

    NASA Technical Reports Server (NTRS)

    Jones, Robert T; Nerken, Albert I

    1936-01-01

    It is shown that the control force of ordinary ailerons may be reduced to zero over a range of deflections and at a given flight condition by the use of an appropriate differential movement. Approximations to the ideal motion obtainable with a simple linkage are discussed and a chart that enables the selection of an appropriate crank arrangement is presented. Various aspects of the practical application of the system are discussed and it is concluded that a small fixed tab, deflected to trim both ailerons upward, would be advantageous.

  13. Linkage disequilibrium, haplotype analysis and Werner`s syndrome

    SciTech Connect

    Wijsman, E.M.; Goddard, K.A.B.; Martin, G.M.

    1994-09-01

    Werner`s syndrome (WS) is a rare, autosomal, recessive disorder of premature aging. Although the underlying defect is unknown, the gene for the disorder, WRN, has been mapped to the 8p11.1-21.1 region. We have assembled a sample of 30 Japanese and 24 non-Japanese (primary Caucasian) WS patients, as well as a control sample from each population. 25 of the Japanese patients and 10 of the Caucasian patients are from consanguineous marriages. We recently presented evidence from these families which places WRN in the 10.2 cM interval between D8S87 and D8S137. However, because WS is so rare and because many patients are from consanguineous marriages, fine localization of the gene by traditional meiotic mapping methods is unlikely to succeed. The existence of linkage disequilibrium is now recognized as a key piece of evidence in defining a small region (typically under 1-2 cM) containing a gene of interest. Thus an alternative approach for refining the location of WRN may be to identify linked markers which are in linkage disequilibrium with the disease. We recently suggested that WRN may be close to D8S339 and GSR in the above interval because of the presence of statistically significant evidence of linkage disequilibrium in the Japanese sample. In addition, there was evidence in both populations that a limited number of haplotypes was associated with the disease. Here we report an extension of this study to include a number of additional markers. We present additional evidence that there is linkage disequilibrium between many of these markers and WRN in both the Japanese and Caucasian samples. In addition, the additional markers do not markedly subdivide the disease haplotypes defined by D8S339 and GSR, while at the same time they introduce substantial numbers of new haplotypes into the control populations. These results suggest that the haplotypes associated with WS may be used to further define the limits of WRN.

  14. Atmospheric Blocking as a Mechanism for Arctic-Subarctic Linkages

    NASA Astrophysics Data System (ADS)

    Overland, J. E.; Francis, J. A.; Hanna, E.

    2012-12-01

    Evidence for the existence of an atmospheric linkage between recent Arctic change and mid-latitude climate and extreme weather events, and their physical processes, are controversial. Local forcing mechanisms are clear: loss of sea ice and snow cover on land shift the albedo allowing increased heat storage which in turn results in increases of lower troposphere temperatures. Stratification is reduced allowing more vertical mixing, and higher temperatures increase the geopotential thickness and create an upward bowing of geopotential heights into the mid-troposphere. Regional circulation changes are in response to horizontal temperature gradients via the thermal wind. Further, recent mid-latitude weather extremes such as snow events in Europe, eastern Asia and northeastern North America during winters 2009-2010 and 2010-2011, and heat waves in 2010-2012, show high amplitude meridional flow patterns that connect with Arctic latitudes. In opposition, despite similar Arctic conditions in the last half decade, mid-latitude intra-seasonal and interannual differences are large, suggesting large contributions from natural chaotic variability. Several studies using climate models are helpful by showing widely different impacts in multiple ensemble runs with the same sea ice loss, but appear not to show major linkages compared to statistical and case studies-perhaps due to deficiencies in capturing baroclinic-planetary wave interactions. All of the above information point to the complexity of Arctic linkages and that different outcomes are to be expected for each event. Evaluating a potential shift in mid-latitude weather frequencies associated with well expected Arctic change over the next decades would be a major accomplishment for the Arctic and climate communities. Atmospheric blocking, with increased meridional flow, appears to be a reasonable conceptual model for such linkages at the current level of understanding. Blocking is a transient phenomenon at sub-monthly time

  15. Cardiovascular disease treatment among patients with severe mental illness: a data linkage study between primary and secondary care

    PubMed Central

    Woodhead, Charlotte; Ashworth, Mark; Broadbent, Matthew; Callard, Felicity; Hotopf, Matthew; Schofield, Peter; Soncul, Murat; Stewart, Robert J; Henderson, Max J

    2016-01-01

    Background Suboptimal treatment of cardiovascular diseases (CVD) among patients with severe mental illness (SMI) may contribute to physical health disparities. Aim To identify SMI characteristics associated with meeting CVD treatment and prevention guidelines. Design and setting Population-based electronic health record database linkage between primary care and the sole provider of secondary mental health care services in south east London, UK. Method Cardiovascular disease prevalence, risk factor recording, and Quality and Outcomes Framework (QOF) clinical target achievement were compared among 4056 primary care patients with SMI whose records were linked to secondary healthcare records and 270 669 patients without SMI who were not known to secondary care psychiatric services, using multivariate logistic regression modelling. Data available from secondary care records were then used to identify SMI characteristics associated with QOF clinical target achievement. Results Patients with SMI and with coronary heart disease and heart failure experienced reduced prescribing of beta blockers and angiotensin-converting enzyme inhibitor/angiotensin receptor blockers (ACEI/ARB). A diagnosis of schizophrenia, being identified with any indicator of risk or illness severity, and being prescribed with depot injectable antipsychotic medication was associated with the lowest likelihood of prescribing. Conclusion Linking primary and secondary care data allows the identification of patients with SMI most at risk of undertreatment for physical health problems. PMID:27114210

  16. Are Routinely Collected NHS Administrative Records Suitable for Endpoint Identification in Clinical Trials? Evidence from the West of Scotland Coronary Prevention Study

    PubMed Central

    Barry, Sarah J. E.; Dinnett, Eleanor; Kean, Sharon; Gaw, Allan; Ford, Ian

    2013-01-01

    Background Routinely collected electronic patient records are already widely used in epidemiological research. In this work we investigated the potential for using them to identify endpoints in clinical trials. Methods The events recorded in the West of Scotland Coronary Prevention Study (WOSCOPS), a large clinical trial of pravastatin in middle-aged hypercholesterolaemic men in the 1990s, were compared with those in the record-linked deaths and hospitalisations records routinely collected in Scotland. Results We matched 99% of fatal study events by date. We showed excellent matching (97%) of the causes of fatal endpoint events and good matching (>80% for first events) of the causes of nonfatal endpoint events with a slightly lower rate of mismatching of record linkage than study events (19% of first study myocardial infarctions (MI) and 4% of first record linkage MIs not matched as MI). We also investigated the matching of non-endpoint events and showed a good level of matching, with >78% of first stroke/TIA events being matched as stroke/TIA. The primary reasons for mismatches were record linkage data recording readmissions for procedures or previous events, differences between the diagnoses in the routinely collected data and the conclusions of the clinical trial expert adjudication committee, events occurring outside Scotland and therefore being missed by record linkage data, miscoding of cardiac events in hospitalisations data as ‘unspecified chest pain’, some general miscoding in the record linkage data and some record linkage errors. Conclusions We conclude that routinely collected data could be used for recording cardiovascular endpoints in clinical trials and would give very similar results to rigorously collected clinical trial data, in countries with unified health systems such as Scotland. The endpoint types would need to be carefully thought through and an expert endpoint adjudication committee should be involved. PMID:24058681

  17. Linkage of autosomal recessive lamellar ichthyosis to chromosome 14q

    SciTech Connect

    Russell, L.J.; Compton, J.G.; Bale, S.J.; DiGiovanna, J.J.; Hashem, N.

    1994-12-01

    The authors have mapped the locus for lamellar ichthyosis (LI), an autosomal recessive skin disease characterized by abnormal cornification of the epidermis. Analysis using both inbred and outbred families manifesting severe LI showed complete linkage to several markers within a 9.3-cM region on chromosome 14q11. Affected individuals in inbred families were also found to have striking homozygosity for markers in this region. Linkage-based genetic counseling and prenatal diagnosis is now available for informative at-risk families. Several transcribed genes have been mapped to the chromosome 14 region containing the LI gene. The transglutaminase 1 gene (TGM1), which encodes one of the enzymes responsible for cross-linking epidermal proteins during formation of the stratum corneum, maps to this interval. The TGM1 locus was completely linked to LI (Z = 9.11), suggesting that TGM1 is a good candidate for further investigation of this disorder. The genes for four serine proteases also map to this region but are expressed only in hematopoietic or mast cells, making them less likely candidates.

  18. Genetic by environment interactions affect plant–soil linkages

    PubMed Central

    Pregitzer, Clara C; Bailey, Joseph K; Schweitzer, Jennifer A

    2013-01-01

    The role of plant intraspecific variation in plant–soil linkages is poorly understood, especially in the context of natural environmental variation, but has important implications in evolutionary ecology. We utilized three 18- to 21-year-old common gardens across an elevational gradient, planted with replicates of five Populus angustifolia genotypes each, to address the hypothesis that tree genotype (G), environment (E), and G × E interactions would affect soil carbon and nitrogen dynamics beneath individual trees. We found that soil nitrogen and carbon varied by over 50% and 62%, respectively, across all common garden environments. We found that plant leaf litter (but not root) traits vary by genotype and environment while soil nutrient pools demonstrated genotype, environment, and sometimes G × E interactions, while process rates (net N mineralization and net nitrification) demonstrated G × E interactions. Plasticity in tree growth and litter chemistry was significantly related to the variation in soil nutrient pools and processes across environments, reflecting tight plant–soil linkages. These data overall suggest that plant genetic variation can have differential affects on carbon storage and nitrogen cycling, with implications for understanding the role of genetic variation in plant–soil feedback as well as management plans for conservation and restoration of forest habitats with a changing climate. PMID:23919173

  19. Ubiquitin Chain Editing Revealed By Polyubiquitin Linkage-Specific Antibodies

    SciTech Connect

    Newton, K.; Matsumoto, M.L.; Wertz, I.E.; Kirkpatrick, D.S.; Lill, J.R.; Tan, J.; Dugger, D.; Gordon, N.; Sidhu, S.S.; Fellouse, F.A.; Komuves, L.; French, D.M.; Ferrando, R.E.; Lam, C.; Compaan, D.; Yu, C.; Bosanac, I.; Hymowitz, S.G.; Kelley, R.F.; Dixit, V.M.

    2009-05-22

    Posttranslational modification of proteins with polyubiquitin occurs in diverse signaling pathways and is tightly regulated to ensure cellular homeostasis. Studies employing ubiquitin mutants suggest that the fate of polyubiquitinated proteins is determined by which lysine within ubiquitin is linked to the C terminus of an adjacent ubiquitin. We have developed linkage-specific antibodies that recognize polyubiquitin chains joined through lysine 63 (K63) or 48 (K48). A cocrystal structure of an anti-K63 linkage Fab bound to K63-linked diubiquitin provides insight into the molecular basis for specificity. We use these antibodies to demonstrate that RIP1, which is essential for tumor necrosis factor-induced NF-{kappa}B activation, and IRAK1, which participates in signaling by interleukin-1{beta} and Toll-like receptors, both undergo polyubiquitin editing in stimulated cells. Both kinase adaptors initially acquire K63-linked polyubiquitin, while at later times K48-linked polyubiquitin targets them for proteasomal degradation. Polyubiquitin editing may therefore be a general mechanism for attenuating innate immune signaling.

  20. Linkage studies on chromosome 22 in familial schizophrenia

    SciTech Connect

    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 of 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.

  1. Tropical glaciers and climate dynamics: Resolving the linkages

    NASA Astrophysics Data System (ADS)

    Mölg, Thomas

    2013-04-01

    Large-scale atmosphere/ocean circulation and mountain glaciers represent two entirely different scales in the climate system. Therefore, statistical linkages between the two mask a cascade of processes that act on different temporal and spatial dimensions. Low-latitude glaciers are particularly well suited for studying such processes, since these glaciers are situated in the "heart" of the global climate system (the tropics). This presentation gives an overview of a decade of research on tropical climate and glaciers on Kilimanjaro (East Africa), which is, to our knowledge, the only case where space/time linkages between high-altitude glaciers and climate dynamics have been investigated systematically throughout the main scales. This includes the complex modification of atmospheric flow when air masses impinge on high mountains, an aspect that has been widely neglected from a cryospheric viewpoint. The case of Kilimanjaro demonstrates (1) the great potential of learning about climate system processes and their connections, (2) advances in our understanding of the importance of moisture for glaciers that lie far above the mean freezing level, and (3) methodological advances in combining atmospheric and cryospheric modelling.

  2. A Node Linkage Approach for Sequential Pattern Mining

    PubMed Central

    Navarro, Osvaldo; Cumplido, René; Villaseñor-Pineda, Luis; Feregrino-Uribe, Claudia; Carrasco-Ochoa, Jesús Ariel

    2014-01-01

    Sequential Pattern Mining is a widely addressed problem in data mining, with applications such as analyzing Web usage, examining purchase behavior, and text mining, among others. Nevertheless, with the dramatic increase in data volume, the current approaches prove inefficient when dealing with large input datasets, a large number of different symbols and low minimum supports. In this paper, we propose a new sequential pattern mining algorithm, which follows a pattern-growth scheme to discover sequential patterns. Unlike most pattern growth algorithms, our approach does not build a data structure to represent the input dataset, but instead accesses the required sequences through pseudo-projection databases, achieving better runtime and reducing memory requirements. Our algorithm traverses the search space in a depth-first fashion and only preserves in memory a pattern node linkage and the pseudo-projections required for the branch being explored at the time. Experimental results show that our new approach, the Node Linkage Depth-First Traversal algorithm (NLDFT), has better performance and scalability in comparison with state of the art algorithms. PMID:24933123

  3. Linkage and mutation analysis of Thomsen and Becker myotonia families

    SciTech Connect

    Koty, P.P.; Pegoraro, E.; Hoffman, E.P.

    1994-09-01

    Thomsen (autosomal dominant) and Becker (autosomal recessive) myotonias are characterized by the inability for muscle relaxation after voluntary, mechanical, or electrical stimulation. Families with both diseases have been linked to the skeletal muscle chloride channel (CLC1) on chromosome 7q35; however, only 2 gene mutations have been identified, and the reasons underlying the alternative dominant or recessive inheritance are not clear. We used linkage analysis and SSCP of 23 exons to screen 8 families (56 individuals) and 7 isolated cases with the diagnosis of Thomsen/Becker myotonia. A novel mutation (1290M) in exon 8 was detected in a family with Thomsen disease. Three additional families showed the previously described G230E change. Thus, chloride channel mutations could be identified in 4/5 families showing dominant inheritance. We were able to exclude linkage to the CLC1 gene in the fifth family. In patients with recessive Becker disease, an isolated case had two unique conformers, one causing a novel A437T change in exon 12. We also identified the previously reported F413C change in a second family. We found significant differences in the clinical picture between families with different mutations but also in families with the same mutation. Our data indicates that DNA studies are critical for correct diagnosis of the myotonias.

  4. A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter].

    PubMed

    Yu, Ju-Kyung; Kantety, Ramesh V; Graznak, Elizabeth; Benscher, David; Tefera, Hailu; Sorrells, Mark E

    2006-10-01

    Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. Ninety-four F(9) recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis tef cv. Kaye Murri x Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST-SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops.

  5. Extracellular rigidity sensing by talin isoform–specific mechanical linkages

    PubMed Central

    Austen, Katharina; Ringer, Pia; Mehlich, Alexander; Chrostek-Grashoff, Anna; Kluger, Carleen; Klingner, Christoph; Sabass, Benedikt; Zent, Roy; Rief, Matthias; Grashoff, Carsten

    2015-01-01

    The ability of cells to adhere and sense differences in tissue stiffness is crucial for organ development and function. The central mechanisms by which adherent cells detect extracellular matrix compliance, however, are still unknown. Using two single-molecule–calibrated biosensors that allow the analysis of a previously inaccessible but physiologically highly relevant force regime in cells, we demonstrate that the integrin activator talin establishes mechanical linkages upon cell adhesion, which are indispensable for cells to probe tissue stiffness. Talin linkages are exposed to a range of piconewton (pN) forces and bear, on average, 7–10 pN during cell adhesion depending on their association with f-actin and vinculin. Disruption of talin’s mechanical engagement does not impair integrin activation and initial cell adhesion but prevents focal adhesion reinforcement and thus extracellular rigidity sensing. Intriguingly, talin mechanics are isoform-specific so that expression of either talin-1 or talin-2 modulates extracellular rigidity sensing. PMID:26523364

  6. Assigning linkage haplotypes from parent and progeny genotypes

    SciTech Connect

    Nejati-Javaremi, A.; Smith, C.

    1996-04-01

    Given the genotypes of parents and progeny, their haplotypes over several or many linked loci can be easily assigned by listing the allele type at each locus along the haplotype known to be from each parent. Only a small number (5-10) of progeny per family is usually needed to assign the parental and progeny haplotypes. Any gaps left in the haplotypes may be filled in from the assigned haplotypes of relatives. The process is facilitated by having multiple alleles at the loci and by using more linked loci in the haplotype and with more progeny from the mating. Crossover haplotypes in the progeny can be identified by their being unique or uncommon, and the crossover point can often be detected if the locus linkage map order is known. The haplotyping method applies to outbreeding populations in plants, animals, and man, as well as to traditional experimental crosses of inbred lines. The method also applies to half-sib families, whether the genotype of the mates are known or unknown. The haplotyping procedure is already used in linkage analysis but does not seem to have been published. It should be useful in teaching and in genetic applications of haplotypes. 15 refs., 5 tabs.

  7. Multivariate linkage analysis of specific language impairment (SLI).

    PubMed

    Monaco, Anthony P

    2007-09-01

    Specific language impairment (SLI) is defined as an inability to develop appropriate language skills without explanatory medical conditions, low intelligence or lack of opportunity. Previously, a genome scan of 98 families affected by SLI was completed by the SLI Consortium, resulting in the identification of two quantitative trait loci (QTL) on chromosomes 16q (SLI1) and 19q (SLI2). This was followed by a replication of both regions in an additional 86 families. Both these studies applied linkage methods to one phenotypic trait at a time. However, investigations have suggested that simultaneous analysis of several traits may offer more power. The current study therefore applied a multivariate variance-components approach to the SLI Consortium dataset using additional phenotypic data. A multivariate genome scan was completed and supported the importance of the SLI1 and SLI2 loci, whilst highlighting a possible novel QTL on chromosome 10. Further investigation implied that the effect of SLI1 on non-word repetition was equally as strong on reading and spelling phenotypes. In contrast, SLI2 appeared to have influences on a selection of expressive and receptive language phenotypes in addition to non-word repetition, but did not show linkage to literacy phenotypes.

  8. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.

    PubMed

    Newton, Kim; Matsumoto, Marissa L; Wertz, Ingrid E; Kirkpatrick, Donald S; Lill, Jennie R; Tan, Jenille; Dugger, Debra; Gordon, Nathaniel; Sidhu, Sachdev S; Fellouse, Frederic A; Komuves, Laszlo; French, Dorothy M; Ferrando, Ronald E; Lam, Cynthia; Compaan, Deanne; Yu, Christine; Bosanac, Ivan; Hymowitz, Sarah G; Kelley, Robert F; Dixit, Vishva M

    2008-08-22

    Posttranslational modification of proteins with polyubiquitin occurs in diverse signaling pathways and is tightly regulated to ensure cellular homeostasis. Studies employing ubiquitin mutants suggest that the fate of polyubiquitinated proteins is determined by which lysine within ubiquitin is linked to the C terminus of an adjacent ubiquitin. We have developed linkage-specific antibodies that recognize polyubiquitin chains joined through lysine 63 (K63) or 48 (K48). A cocrystal structure of an anti-K63 linkage Fab bound to K63-linked diubiquitin provides insight into the molecular basis for specificity. We use these antibodies to demonstrate that RIP1, which is essential for tumor necrosis factor-induced NF-kappaB activation, and IRAK1, which participates in signaling by interleukin-1beta and Toll-like receptors, both undergo polyubiquitin editing in stimulated cells. Both kinase adaptors initially acquire K63-linked polyubiquitin, while at later times K48-linked polyubiquitin targets them for proteasomal degradation. Polyubiquitin editing may therefore be a general mechanism for attenuating innate immune signaling.

  9. Health governance: principal-agent linkages and health system strengthening.

    PubMed

    Brinkerhoff, Derick W; Bossert, Thomas J

    2014-09-01

    Governance is increasingly recognized as an important factor in health system performance, yet conceptually and practically it remains poorly understood and subject to often vague and competing notions of both what its role is and how to address its weaknesses. This overview article for the symposium on health governance presents a model of health governance that focuses on the multiplicity of societal actors in health systems, the distribution of roles and responsibilities among them and their ability and willingness to fulfil these roles and responsibilities. This focus highlights the principal-agent linkages among actors and the resulting incentives for good governance and health system performance. The discussion identifies three disconnects that constitute challenges for health system strengthening interventions that target improving governance: (1) the gap between the good governance agenda and existing capacities, (2) the discrepancy between formal and informal governance and (3) the inattention to sociopolitical power dynamics. The article summarizes the three country cases in the symposium and highlights their governance findings: health sector reform in China, financial management of health resources in Brazilian municipalities and budget reform in hospitals in Lesotho. The concluding sections clarify how the three cases apply the model's principal-agent linkages and highlight the importance of filling the gaps remaining between problem diagnosis and the development of practical guidance that supports 'best fit' solutions and accommodates political realities in health systems strengthening.

  10. Linkage disequilibrium interval mapping of quantitative trait loci

    PubMed Central

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

    2006-01-01

    Background 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. Results 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. Conclusion 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. PMID:16542433

  11. Post-Miocene extension in Central Anatolia; It's linkage to Aegean extension

    NASA Astrophysics Data System (ADS)

    Rojay, Bora; Özsayın, Erman

    2013-04-01

    Post-Miocene extension in Central Anatolia; It's linkage to Aegean extension Anatolian Plate, -where Central Anatolia situated on-, escapes westward onto African plate along Eastern Mediterranean-Cyprus subduction zone, sliding by North and East Anatolian faults. Central Anatolia is bounded by dextral North Anatolian Fault from north, Taurides from south and it is fragmented by strike slip faults evolving under N-S compression in east and by Aegean horst and grabens evolving under N-S extension in west. To be able to delineate and understand the deformational order in Central Anatolia and its linkage to Aegean region, various sectors with the Anatolia are chosen, namely, Ankara region (Beypazarı to Kazan Miocene basins), Eskişehir region (Mihallıçık to İnönü Miocene basins) in Central Anatolia, Gediz-Alaşehir Graben and Efes areas in Western Anatolia are selected. To sum up, in a wide region from Central Anatolia to Western Anatolia, i. Unconformities btw uppermost Late Miocene and Plio-Quaternary, and btw Plio-Quaternary and Quaternary are clearly identified in both regions, ii) ENE-WSW to N-S compression (intense post-Late Miocene - pre-Pliocene folding) with almost E-W extension operates during post-Miocene (during Pliocene) is followed by a short lived strike slip deformation during Early Pliocene, and finally by NW-SE to WNW-ESE oriented multi directional extension during post-Plio-Quaternary. And in Gediz-Alaşehir Graben and Efes (western Anatolia); a continuous NNE-SSW to NE-SW multi directed extension since post-Late Miocene following almost N-S compression (post-Early Miocene) operated. Dextral strike slip faulting with normal components and normal faulting with right lateral strike slip components are recorded on same fault planes, iii) Quaternary normal faulting post dates folding, reverse and strike slip faulting in both regions. However, right lateral strike slip faulting is recorded to the NW tip of the normal faults like Efes, Manisa and

  12. From DNA to protein: Transformations and their possible role in linkage learning

    SciTech Connect

    Kargupta, H.; Stafford, B.

    1997-04-01

    This paper first extends the traditional perspective of linkage using the basic concepts developed in the SEARCH framework and identifies the fundamental objectives of linkage learning. It then explores the computational role of gene-expression (DNA{r_arrow}RNA{r_arrow}Protein transformations) in evolutionary linkage learning, using group representation theory. It offers strong evidence to support the hypothesis that the transformations in gene-expression define a group of symmetry transformations that leaves the fitness invariant; however, they change the eigen functions leading to identifying independent subspaces of the search space (a major objective of linkage learning) using irreducible representations of such transformations.

  13. Failure to find a chromosome 18 pericentric linkage in families with schizophrenia

    SciTech Connect

    De Lisi, L.E.; Shields, G.; Lehner, T.

    1995-12-18

    A recent report of a possible linkage of bipolar affective disorder to a pericentric region of chromosome 18 initiated the present investigation to search for a similar linkage in 32 families with schizophrenia. The results of a study using 5 markers mapped to this region show negative lod scores and only weak evidence for any linkage by nonparametric analyses. If the previously reported finding is a true positive linkage for bipolar disorder, then either it is unlikely to be related to the genetics of schizophrenia, or the proportion of families linked to this region is small. 12 refs., 4 tabs.

  14. Genetic Linkage Map of Fishes of the Genus Xiphophorus (Teleostei: Poeciliidae)

    PubMed Central

    Morizot, D. C.; Slaugenhaupt, S. A.; Kallman, K. D.; Chakravarti, A.

    1991-01-01

    Analysis of genotypes of 76 polymorphic loci in more than 2600 backcross hybrid individuals derived from intra- and interspecific genetic crosses of fishes of the genus Xiphophorus (Poeciliidae) resulted in the identification of 17 multipoint linkage groups containing 55 protein-coding loci and one sex chromosome-linked pigment pattern gene. Multipoint linkage analyses identified highly probable gene orders for 10 linkage groups. The total genome length was estimated to be ~18 Morgans. Comparisons of the Xiphophorus linkage map with those of other fishes, amphibians and mammals suggested that fish gene maps are remarkably similar and probably retain many syntenic groups present in the ancestor of all vertebrates. PMID:2004711

  15. How home HIV testing and counselling with follow-up support achieves high testing coverage and linkage to treatment and prevention: a qualitative analysis from Uganda

    PubMed Central

    Ware, Norma C; Wyatt, Monique A; Asiimwe, Stephen; Turyamureeba, Bosco; Tumwesigye, Elioda; van Rooyen, Heidi; Barnabas, Ruanne V; Celum, Connie L

    2016-01-01

    Introduction The successes of HIV treatment scale-up and the availability of new prevention tools have raised hopes that the epidemic can finally be controlled and ended. Reduction in HIV incidence and control of the epidemic requires high testing rates at population levels, followed by linkage to treatment or prevention. As effective linkage strategies are identified, it becomes important to understand how these strategies work. We use qualitative data from The Linkages Study, a recent community intervention trial of community-based testing with linkage interventions in sub-Saharan Africa, to show how lay counsellor home HIV testing and counselling (home HTC) with follow-up support leads to linkage to clinic-based HIV treatment and medical male circumcision services. Methods We conducted 99 semi-structured individual interviews with study participants and three focus groups with 16 lay counsellors in Kabwohe, Sheema District, Uganda. The participant sample included both HIV+ men and women (N=47) and HIV-uncircumcised men (N=52). Interview and focus group audio-recordings were translated and transcribed. Each transcript was summarized. The summaries were analyzed inductively to identify emergent themes. Thematic concepts were grouped to develop general constructs and framing propositional statements. Results Trial participants expressed interest in linking to clinic-based services at testing, but faced obstacles that eroded their initial enthusiasm. Follow-up support by lay counsellors intervened to restore interest and inspire action. Together, home HTC and follow-up support improved morale, created a desire to reciprocate, and provided reassurance that services were trustworthy. In different ways, these functions built links to the health service system. They worked to strengthen individuals’ general sense of capability, while making the idea of accessing services more manageable and familiar, thus reducing linkage barriers. Conclusions Home HTC with follow

  16. Health Disparities in Hepatitis C Screening and Linkage to Care at an Integrated Health System in Southeast Michigan

    PubMed Central

    Brar, Indira; Baker-Genaw, Kimberly

    2016-01-01

    With recommended screening for hepatitis C among the 1945–1965 birth cohort and advent of novel highly effective therapies, little is known about health disparities in the Hepatitis C care cascade. Our objective was to evaluate hepatitis C screening rates and linkage to care, among patients who test positive, at our large integrated health system. We used electronic medical records to retrospectively identify patients, in the birth cohort, who were seen in 21 Internal Medicine clinics from July 2014 to June 2015. Patients previously screened for hepatitis C and those with established disease were excluded. We studied patients’ sociodemographic and medical conditions along with provider-specific factors associated with likelihood of screening. Patients who tested positive for HCV antibody were reviewed to assess appropriate linkage to care and treatment. Of 40,561 patients who met inclusion criteria, 21.3% (8657) were screened, 1.3% (109) tested positive, and 30% (30/100) completed treatment. Multivariate logistic regression showed that African American race, male gender, electronic health engagement, residency teaching clinic visit, and having more than one clinic visit were associated with higher odds of screening. Patients had a significant decrease in the likelihood of screening with sequential interval increase in their Charlson comorbidity index. When evaluating hepatitis C treatment in patients who screened positive, electronic health engagement was associated with higher odds of treatment whereas Medicaid insurance was associated with significantly lower odds. This study shows that hepatitis C screening rates and linkage to care continue to be suboptimal with a significant impact of multiple sociodemographic and insurance factors. Electronic health engagement emerges as a tool in linking patients to the hepatitis C care cascade. PMID:27525983

  17. Health Disparities in Hepatitis C Screening and Linkage to Care at an Integrated Health System in Southeast Michigan.

    PubMed

    Bourgi, Kassem; Brar, Indira; Baker-Genaw, Kimberly

    2016-01-01

    With recommended screening for hepatitis C among the 1945-1965 birth cohort and advent of novel highly effective therapies, little is known about health disparities in the Hepatitis C care cascade. Our objective was to evaluate hepatitis C screening rates and linkage to care, among patients who test positive, at our large integrated health system. We used electronic medical records to retrospectively identify patients, in the birth cohort, who were seen in 21 Internal Medicine clinics from July 2014 to June 2015. Patients previously screened for hepatitis C and those with established disease were excluded. We studied patients' sociodemographic and medical conditions along with provider-specific factors associated with likelihood of screening. Patients who tested positive for HCV antibody were reviewed to assess appropriate linkage to care and treatment. Of 40,561 patients who met inclusion criteria, 21.3% (8657) were screened, 1.3% (109) tested positive, and 30% (30/100) completed treatment. Multivariate logistic regression showed that African American race, male gender, electronic health engagement, residency teaching clinic visit, and having more than one clinic visit were associated with higher odds of screening. Patients had a significant decrease in the likelihood of screening with sequential interval increase in their Charlson comorbidity index. When evaluating hepatitis C treatment in patients who screened positive, electronic health engagement was associated with higher odds of treatment whereas Medicaid insurance was associated with significantly lower odds. This study shows that hepatitis C screening rates and linkage to care continue to be suboptimal with a significant impact of multiple sociodemographic and insurance factors. Electronic health engagement emerges as a tool in linking patients to the hepatitis C care cascade. PMID:27525983

  18. The age of human mutation: Genealogical and linkage disequilibrium analysis of the CLN5 mutation in the Finnish population

    SciTech Connect

    Varilo, T; Savukoski, M.; Peltonen, L.

    1996-03-01

    Variant late infantile neuronal ceroid lipofuscinosis (vLINCL) is an autosomal recessive progressive encephalopathy of childhood enriched in the western part of Finland, with a local incidence of 1/1,500. We recently assigned the locus for vLINCL, CLN5, to 13q21.1-q32. In the present study, the haplotype analysis of Finnish CLN5 chromosomes provides evidence that one single mutation causes vLINCL in the Finnish population. Eight microsatellite markers closely linked to the CLN5 gene on chromosome 13q were analyzed, to study identity by descent by shared haplotype analysis. One single haplotype formed by flanking markers D13S160 and D13S162 in strong linkage disequilibrium (P < .0001) was present in 81% of disease-bearing chromosomes. Allele 4 at the marker locus D13S162 was detected in 94% of disease-bearing chromosomes. To evaluate the age of the CLN5 mutation by virtue of its restricted geographical distribution, church records were used to identify the common ancestors for 18 vLINCL families diagnosed in Finland. The pedigrees of the vLINCL ancestors merged on many occasions, which also supports a single founder mutation that obviously happened 20-30 generations ago (i.e., {approximately}500 years ago) in this isolated population. Linkage disequilibrium was detected with seven markers covering an extended genetic distance of 11 cM, which further supports the young age of the CLN5 mutation. When the results of genealogical and linkage disequilibrium studies were combined, the CLN5 gene was predicted to lie {approximately}200-400 kb (total range 30-1,360 kb) from the closest marker D13S162. 29 refs., 2 figs., 5 tabs.

  19. The Linkage Outcomes of a Large-scale, Rapid Transfer of HIV-infected Patients From Hospital-based to Community-based Clinics in South Africa

    PubMed Central

    Cloete, Christie; Regan, Susan; Giddy, Janet; Govender, Tessa; Erlwanger, Alison; Gaynes, Melanie R.; Freedberg, Kenneth A.; Katz, Jeffrey N.; Walensky, Rochelle P.; Losina, Elena; Bassett, Ingrid V.

    2014-01-01

    Background  President's Emergency Plan for AIDS Relief (PEPFAR) funding changes have resulted in human immunodeficiency virus (HIV) clinic closures. We evaluated linkage to care following a large-scale patient transfer from a PEPFAR-funded, hospital-based HIV clinic to government-funded, community-based clinics in Durban. Methods  All adults were transferred between March and June 2012. Subjects were surveyed 5–10 months post-transfer to assess self-reported linkage to the target clinic. We validated self-reports by auditing records at 8 clinics. Overall success of transfer was estimated using linkage to care data for both reached and unreached subjects, adjusted for validation results. Results  Of the 3913 transferred patients, 756 (19%) were assigned to validation clinics; 659 (87%) of those patients were reached. Among those reached, 468 (71%) had a validated clinic record visit. Of the 46 who self-reported attending a different validation clinic than originally assigned, 39 (85%) had a validated visit. Of the 97 patients not reached, 59 (61%) had a validated visit at their assigned clinic. Based on the validation rates for reached and unreached patients, the estimated success of transfer for the cohort overall was 82%. Conclusions  Most patients reported successful transfer to a community-based clinic, though a quarter attended a different clinic than assigned. Validation of attendance highlights that nearly 20% of patients may not have linked to care and may have experienced a treatment interruption. Optimizing transfers of HIV care to community sites requires collaboration with receiving clinics to ensure successful linkage to care. PMID:25734128

  20. Physiological linkage in couples and its implications for individual and interpersonal functioning: A literature review.

    PubMed

    Timmons, Adela C; Margolin, Gayla; Saxbe, Darby E

    2015-10-01

    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: (a) coactivation of the sympathetic nervous system or the hypothalamic-pituitary adrenal axis is "bad," (b) moderate physiological linkage is "just right," (c) physiological linkage is problematic if the individual or couple is overloaded, and (d) 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

  1. Spin Transfer in Polymer Degradation of Abnormal Linkage

    NASA Astrophysics Data System (ADS)

    Yu, Tianrong; Tian, Chuanjin; Liu, Xizhe; Wang, Jia; Gao, Yang; Wang, Zhigang

    2016-09-01

    The degradation of polymer materials plays an important role in production and life. In this work, the degradation mechanism of poly-α-methylstyrene (PAMS) tetramers with abnormal linkage was investigated by using density functional theory (DFT). Calculated results indicate that the head-to-head and the tail-to-tail reactions needed to overcome the energy barriers are about 0.15 eV and about 1.26 eV, respectively. The broken C-C bond at the unsaturated end of the chain leads to the dissociation of alpha-methylstyrene (AMS) monomers one by one. Furthermore, the analyses of bond characteristics are in good agreement with the results of energy barriers. In addition, the spin population analysis presents an interesting net spin transfer process in depolymerization reactions. We hope that the current theoretical results provide useful help to understand the degradation mechanism of polymers.

  2. HIV testing and linkage to services for youth

    PubMed Central

    Kurth, Ann E; Lally, Michelle A; Choko, Augustine T; Inwani, Irene W; Fortenberry, J Dennis

    2015-01-01

    Introduction HIV testing is the portal to serostatus knowledge that can empower linkage to care for HIV treatment and HIV prevention. However, young people's access to HIV testing is uneven worldwide. The objective of this paper is to review the context and concerns faced by youth around HIV testing in low- as well as high-income country settings. Discussion HIV testing is a critical entry point for primary and secondary prevention as well as care and treatment for young people including key populations of vulnerable youth. We provide a framework for thinking about the role of testing in the continuum of prevention and care for young people. Brief case study examples from Kenya and the US illustrate some of the common barriers and issues involved for young people. Conclusions Young people worldwide need more routine access to HIV testing services that effectively address the developmental, socio-political and other issues faced by young women and men. PMID:25724506

  3. Flow and Noise Control: Toward a Closer Linkage

    NASA Technical Reports Server (NTRS)

    Thomas, Russell H.; Choudhari, Meelan M.; Joslin, Ronald D.

    2002-01-01

    Motivated by growing demands for aircraft noise reduction and for revolutionary new aerovehicle concepts, the late twentieth century witnessed the beginning of a shift from single-discipline research, toward an increased emphasis on harnessing the potential of flow and noise control as implemented in a more fully integrated, multidisciplinary framework. At the same time, technologies for developing radically new aerovehicles, which promise quantum leap benefits in cost, safety and performance benefits with environmental friendliness, have appeared on the horizon. Transitioning new technologies to commercial applications will also require coupling further advances in traditional areas of aeronautics with intelligent exploitation of nontraditional and interdisciplinary technologies. Physics-based modeling and simulation are crucial enabling capabilities for synergistic linkage of flow and noise control. In these very fundamental ways, flow and noise control are being driven to be more closely linked during the early design phases of a vehicle concept for optimal and mutual noise and performance benefits.

  4. Re-identification of DNA through an automated linkage process.

    PubMed Central

    Malin, B.; Sweeney, L.

    2001-01-01

    This work demonstrates how seemingly anonymous DNA database entries can be related to publicly available health information to uniquely and specifically identify the persons who are the subjects of the information even though the DNA information contains no accompanying explicit identifiers such as name, address, or Social Security number and contains no additional fields of personal information. The software program, REID (Re-Identification of DNA), iteratively uncovers unique occurrences in visit-disease patterns across data collections that reveal inferences about the identities of the patients who are the subject of the DNA. Using real-world data, REID established identifiable linkages in 33-100% of the 10,886 cases explicitly surveyed over 8 gene-based diseases. PMID:11825223

  5. Linkage and association analysis in pedigrees from different populations.

    PubMed

    Beyene, Joseph; Yan, Jun; Greenwood, Celia M T

    2005-01-01

    Using the Genetic Analysis Workshop 14 simulated datasets we carried out nonparametric linkage analyses and applied a log-linear method for analysis of case-parent-triad data with stratification on parental mating type. We proposed and applied a random effect modelling approach to explore the impact of population heterogeneity on tests of association between genetic markers and disease status. The estimated genetic effect may appear to be strongly significant in one population but nonsignificant in another population, leading to confusion about interpretation. However, when results are interpreted in the light of a random effects model, both studies may be making similar statements about a genetic effect that varies depending on environment and background. PMID:16451671

  6. Extensional hard linkages, eastern Gulf of Suez, Egypt

    NASA Astrophysics Data System (ADS)

    McClay, Ken; Khalil, Samir

    1998-06-01

    The Araba Abu Durba area on the eastern margin of the Gulf of Suez exhibits two superb outcrop examples of extensional hard linkages in a rift basin. Here, three large, domino-style, basement-cored, northeast-dipping fault blocks are formed by a series of major northwest-trending normal faults. These are offset by two north-northeast trending sinistral oblique-slip transfer faults that terminate in horsetail normal fault splays. The transfer faults do not extend across the entire rift basin. Detailed mapping and structural analysis show that they developed by breakage of initial low-strain relay ramps along reactivated north-northeast trending basement fabrics between overlapping northwest-trending normal fault segments. Paleostrain analysis of fault-slip indicators shows that both the normal and the sinistral oblique-slip transfer faults were formed synchronously in response to northeast-southwest extension, perpendicular to the main northwest rift trend.

  7. Rga (Rodgers) and the HLA region: linkage and associations.

    PubMed

    Giles, C M; Gedde-Dahl, T; Robson, E B; Thorsby, E; Olaisen, B; Arnason, A; Kissmeyer-Nielsen, F; Schreuder, I

    1976-08-01

    In 19 families with 97 children the segregation of Rga (Rodgers) was found to be compatible with Mendelian inheritance and five backcross and 14 intercross families were found among HLA and Bf typed families. Close linkage (lods + 17.82) without recombination was found between Rg and the HLA region, with a direct count of 96 nonrecombinant meioses for Rg-HLA-B. Rg- was strongly associated with HLA-B8 (29 of 30 haplotypes) and probably associated with Bw40, but did occur on other HLA-B haplotypes. By inference Rg- is negatively associated with Ch- (Chido). The Rg-Ch- haplotype has not been observed. Rga and Cha may or may not be coded for by different sites of the same cistron closely linked to HLA-B:C and cannot as yet be excluded from being parts of B or C.

  8. Close genetic linkage between HLA and renal glycosuria.

    PubMed

    De Marchi, S; Cecchin, E; Basile, A; Proto, G; Donadon, W; Jengo, A; Schinella, D; Jus, A; Villalta, D; De Paoli, P

    1984-01-01

    Renal glycosuria is an inherited disorder of renal tubule function in which significant amounts of glucose are excreted in the urine in the simultaneous presence of normal blood glucose levels. Renal glucose titration analyses and HLA genotypes were performed in 5 unrelated affected families with a total of 25 patients and 40 healthy relatives. In each family the gene responsible for renal glycosuria segregates with the HLA complex suggesting a close genetic linkage. 2 cases carry intra-HLA recombinant haplotypes; in these subjects our findings indicate that the abnormal gene is closer to the HLA-A locus than the HLA-B locus. No HLA-A, HLA-B or HLA-C specific antigen is selectively increased among the 5 unrelated families affected with renal glycosuria.

  9. Linkages of plant–soil feedbacks and underlying invasion mechanisms

    PubMed Central

    Inderjit; Cahill, James F.

    2015-01-01

    Soil microbial communities and processes have repeatedly been shown to impact plant community assembly and population growth. Soil-driven effects may be particularly pronounced with the introduction of plants to non-native ranges, as introduced plants are not typically accompanied by transference of local soil communities. Here we describe how the mechanisms by which soil community processes influence plant growth overlap with several known and well-described mechanisms of plant invasion. Critically, a given soil community process may either facilitate or limit invasion, depending upon local conditions and the specific mechanisms of soil processes involved. Additionally, as soil communities typically consist of species with short generation times, the net consequences of plant–soil feedbacks for invasion trajectories are likely to change over time, as ecological and evolutionary adjustments occur. Here we provide an overview of the ecological linkages of plant–soil feedbacks and underlying mechanisms of invasion. PMID:25784668

  10. The social ecology of health: leverage points and linkages.

    PubMed

    Grzywacz, J G; Fuqua, J

    2000-01-01

    The authors demonstrate the usefulness of social ecology theory for improving the treatment and prevention of poor health. The social ecology of health, unlike the topics of previous triptychs in Behavioral Medicine, is a field without a clearly defined body of literature. We begin with an overview of the ecological perspective and ecological theory as outlined by Bronfenbrenner and colleagues, provide examples of how ecological concepts have been demonstrated to influence health, and discuss how these concepts can be used by health professionals. We present a heuristic model illustrating leverage points and linkages (i.e., socioeconomic status, family, work, and school), for health, and we conclude with a consideration of the benefits of social ecology to health professionals and a summary of the limitations of the ecological model.

  11. Linkage of ocean and fjord dynamics at decadal period

    NASA Astrophysics Data System (ADS)

    Ebbesmeyer, Curtis C.; Coomes, Carol A.; Cannon, Glenn A.; Bretschneider, Dale E.

    At decadal period (10-20 years), dynamic linkage was evident between atmospheric low pressure systems over the North Pacific Ocean and circulation in a Pacific Northwest fjord (Puget Sound). As the Aleutian low pressure center shifts, storms arriving from the North Pacific Ocean deposit varying amounts of precipitation in the mountains draining into the estuarine system; in turn, the fluctuating addition of fresh water changes the density distribution near the fjord basin entrance sill, thereby constraining the fjord's vertical velocity structure. The linkage was examined using time series of 21 environmental parameters which covaried between the 2 regimes associated with cycling of the Aleutian Low between its eastern and westernmost winter positions. Observations from 1899 to 1987 suggest that, in the 20th century, approximately 5 cycles may have occurred between these regimes. Covariation in all but one of the time series (Puget Sound's main basin salinity) occurred because of the high degree of correlation between parameters and the strong decadal cycles compared with long-term averages, interannual variability, and seasonal cycles. Basin salinity was relatively steady due to opposing influences of oceanic source/water salinity and the addition of fresh water in each regime. However, the decadal signal for the other parameters characterizing Puget Sound water are apparently amplified twofold compared with that of the atmosphere over the North Pacific Ocean. "As to Holmes, I observed that he sat frequently for half an hour on end, with knitted brows and an abstracted air, but he swept the matter away with a wave of his hand when I mentioned it". "Data! data! data!" he cried impatiently. "I can't make bricks without clay." A. Conan Doyle The Adventure of the Copper Beeches

  12. Exploiting semantic linkages among multiple sources for semantic information retrieval

    NASA Astrophysics Data System (ADS)

    Li, JianQiang; Yang, Ji-Jiang; Liu, Chunchen; Zhao, Yu; Liu, Bo; Shi, Yuliang

    2014-07-01

    The vision of the Semantic Web is to build a global Web of machine-readable data to be consumed by intelligent applications. As the first step to make this vision come true, the initiative of linked open data has fostered many novel applications aimed at improving data accessibility in the public Web. Comparably, the enterprise environment is so different from the public Web that most potentially usable business information originates in an unstructured form (typically in free text), which poses a challenge for the adoption of semantic technologies in the enterprise environment. Considering that the business information in a company is highly specific and centred around a set of commonly used concepts, this paper describes a pilot study to migrate the concept of linked data into the development of a domain-specific application, i.e. the vehicle repair support system. The set of commonly used concepts, including the part name of a car and the phenomenon term on the car repairing, are employed to build the linkage between data and documents distributed among different sources, leading to the fusion of documents and data across source boundaries. Then, we describe the approaches of semantic information retrieval to consume these linkages for value creation for companies. The experiments on two real-world data sets show that the proposed approaches outperform the best baseline 6.3-10.8% and 6.4-11.1% in terms of top five and top 10 precisions, respectively. We believe that our pilot study can serve as an important reference for the development of similar semantic applications in an enterprise environment.

  13. Linkage map of Escherichia coli K-12, edition 8.

    PubMed Central

    Bachmann, B J

    1990-01-01

    The linkage map of Escherichia coli K-12 depicts the arrangement of genes on the circular chromosome of this organism. The basic units of the map are minutes, determined by the time-of-entry of markers from Hfr into F- strains in interrupted-conjugation experiments. The time-of-entry distances have been refined over the years by determination of the frequency of cotransduction of loci in transduction experiments utilizing bacteriophage P1, which transduces segments of DNA approximately 2 min in length. In recent years, the relative positions of many genes have been determined even more precisely by physical techniques, including the mapping of restriction fragments and the sequencing of many small regions of the chromosome. On the whole, the agreement between results obtained by genetic and physical methods has been remarkably good considering the different levels of accuracy to be expected of the methods used. There are now few regions of the map whose length is still in some doubt. In some regions, genetic experiments utilizing different mutant strains give different map distances. In other regions, the genetic markers available have not been close enough to give accurate cotransduction data. The chromosome is now known to contain several inserted elements apparently derived from lambdoid phages and other sources. The nature of the region in which the termination of replication of the chromosome occurs is now known to be much more complex than the picture given in the previous map. The present map is based upon the published literature through June of 1988. There are now 1,403 loci placed on the linkage group, which may represent between one-third and one-half of the genes in this organism. PMID:2194094

  14. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    PubMed

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-01-01

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations. PMID:27525897

  15. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    PubMed

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-07-29

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

  16. Exploring Linkages Between Gulf of Mexico Sea Surface Conditions and North American Hydroclimate during the Holocene

    NASA Astrophysics Data System (ADS)

    Richey, J. N.; Thirumalai, K.; Quinn, T. M.; Poore, R. Z.

    2015-12-01

    The Gulf of Mexico is part of the Atlantic Warm Pool, a feature that drives oceanic moisture flux to the surrounding continent. It is connected to the North Atlantic Ocean via the loop current, which transports salt and heat from the Caribbean and Gulf of Mexico poleward via the Gulf Stream. As such, variations in Gulf of Mexico sea surface temperature (SST) and salinity (SSS) are linked to changes in North Atlantic Ocean circulation and North American hydroclimate. Although SST and SSS variability in the Gulf of Mexico are well understood on inter-annual and glacial-interglacial timescales, little is known about centennial scale variability in these sea surface parameters through the Holocene. We present here the first continuous multi-decadal resolution time series of SST and SSS spanning the entire Holocene from the Gulf of Mexico. This proxy reconstruction is based on paired measurements of Mg/Ca and δ18O in the planktic foraminifer, Globigerinoides ruber (white variety) in the Garrison Basin. Using these data, in combination with additional Gulf of Mexico SST and SSS records from the late Holocene, we explore linkages between North American precipitation patterns and ocean circulation on centennial timescales.

  17. Exploited species impacts on trophic linkages along reef-seagrass interfaces in the Florida Keys.

    PubMed

    Valentine, John F; Heck, Kenneth L; Blackmon, Derrick; Goecker, Margene E; Christian, Juliet; Kroutil, Ryan M; Peterson, Bradley J; Vanderklift, Mathew A; Kirsch, Kevin D; Beck, Mike

    2008-09-01

    The removal of fish biomass by extensive commercial and recreational fishing has been hypothesized to drastically alter the strength of trophic linkages among adjacent habitats. We evaluated the effects of removing predatory fishes on trophic transfers between coral reefs and adjacent seagrass meadows by comparing fish community structure, grazing intensity, and invertebrate predation potential in predator-rich no-take sites and nearby predator-poor fished sites in the Florida Keys (USA). Exploited fishes were more abundant at the no-take sites than at the fished sites. Most of the exploited fishes were either omnivores or invertivores. More piscivores were recorded at no-take sites, but most (approximately 95%) were moderately fished and unexploited species (barracuda and bar jacks, respectively). Impacts of these consumers on lower trophic levels were modest. Herbivorous and smaller prey fish (< 10 cm total length) densities and seagrass grazing diminished with distance from reefs and were not negatively impacted by the elevated densities of exploited fishes at no-take sites. Predation by reef fishes on most tethered invertebrates was high, but exploited species impacts varied with prey type. The results of the study show that, even though abundances of reef-associated fishes have been reduced at fished sites, there is little evidence that this has produced cascading trophic effects or interrupted cross-habitat energy exchanges between coral reefs and seagrasses.

  18. 75 FR 64317 - Advisory Committee on Interdisciplinary, Community-Based Linkages; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-19

    ... HUMAN SERVICES Health Resources and Service Administration Advisory Committee on Interdisciplinary... Interdisciplinary, Community-Based Linkages (ACICBL). Dates and Times: December 1, 2010, 11 a.m. to 3 p.m., EST... subject as the HRSA Advisory Committee on Interdisciplinary, Community-Based Linkages. FOR...

  19. 77 FR 70169 - Advisory Committee on Interdisciplinary, Community-Based Linkages; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-23

    ... HUMAN SERVICES Health Resources and Service Administration Advisory Committee on Interdisciplinary... Interdisciplinary, Community-Based Linkages (ACICBL). Dates and Times: December 7, 2012, 1:00 p.m.-5:00 p.m. EST... subject as the HRSA Advisory Committee on Interdisciplinary, Community-Based Linkages. For...

  20. Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

    PubMed Central

    Liu, Min; Liu, Hui; Zeng, Huaping; Deng, Dejing; Xin, Huaigen; Song, Jun; Xu, Chunhua; Sun, Xiaowen; Hou, Xilin; Wang, Xiaowu; Zheng, Hongkun

    2014-01-01

    Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/. PMID:24905985