Cost and power analysis of linkage disequilibrium methods for locating genes influencing quantitative traits in humans

Linkage disequilibrium methods can be used to find genes influencing quantitative trait variation in humans. Linkage disequilibrium methods can require smaller sample sizes than linkage equilibrium methods, such as the variance component approach to find loci with a specific effect size. The increase in power is at the expense of requiring more markers to be typed to scan the entire genome. This thesis compares different linkage disequilibrium methods to determine which factors influence the power to detect disequilibrium. The costs of disequilibrium and equilibrium tests were compared to determine whether the savings in phenotyping costs when using disequilibrium methods outweigh the additional genotyping costs.^ Nine linkage disequilibrium tests were examined by simulation. Five tests involve selecting isolated unrelated individuals while four involved the selection of parent child trios (TDT). All nine tests were found to be able to identify disequilibrium with the correct significance level in Hardy-Weinberg populations. Increasing linked genetic variance and trait allele frequency were found to increase the power to detect disequilibrium, while increasing the number of generations and distance between marker and trait loci decreased the power to detect disequilibrium. Discordant sampling was used for several of the tests. It was found that the more stringent the sampling, the greater the power to detect disequilibrium in a sample of given size. The power to detect disequilibrium was not affected by the presence of polygenic effects.^ When the trait locus had more than two trait alleles, the power of the tests maximized to less than one. For the simulation methods used here, when there were more than two-trait alleles there was a probability equal to 1-heterozygosity of the marker locus that both trait alleles were in disequilibrium with the same marker allele, resulting in the marker being uninformative for disequilibrium.^ The five tests using isolated unrelated individuals were found to have excess error rates when there was disequilibrium due to population admixture. Increased error rates also resulted from increased unlinked major gene effects, discordant trait allele frequency, and increased disequilibrium. Polygenic effects did not affect the error rates. The TDT, Transmission Disequilibrium Test, based tests were not liable to any increase in error rates.^ For all sample ascertainment costs, for recent mutations ($<$100 generations) linkage disequilibrium tests were less expensive than the variance component test to carry out. Candidate gene scans saved even more money. The use of recently admixed populations also decreased the cost of performing a linkage disequilibrium test. ^

Citation analysis of faculty publication: beyond Science Citation Index and Social Science Citation Index.

When evaluated for promotion or tenure, faculty members are increasingly judged more on the quality than on the quantity of their scholarly publications. As a result, they want help from librarians in locating all citations to their published works for documentation in their curriculum vitae. Citation analysis using Science Citation Index and Social Science Citation Index provides a logical starting point in measuring quality, but the limitations of these sources leave a void in coverage of citations to an author's work. This article discusses alternative and additional methods of locating citations to published works.

Community Responsibility for Runaway and Thrownaway Youth--Commentary

The following is a commentary on an article discussing homeless youth and the need for communities to address this issue. It is clear that research is needed to understand more about the extent, causes and consequences of youth homelessness whether the youth has run or been thrown away from home. Drawing on interviews conducted with homeless and runaway youth, this commentary calls for community responsibility directed at locating these youth, acknowledging their presence in communities across the U.S., and developing coordinated multijurisdictional responses that support youth development and build on the strengths that have helped them survive.

Targeted Multistage Delivery of Nanoparticles to the Bone Marrow

Bone marrow is a target organ site involved in multiple diseases including myeloproliferative disorders and hematologic malignancies and metastases from breast and prostate. Most of these diseases are characterized with poor quality of life, and the treatment options are only palliative due to lack of delivery mechanisms for systemically injected drugs which results in dose limitation to protect the healthy hematopoietic cells. Therefore, there is a critical need to develop effective therapeutic strategies that allow for selective delivery of therapeutic payload to the bone marrow. Nanotechnology-based drug delivery systems provide the opportunity to deliver drugs to the target tissue while decreasing exposure to normal tissues. E-selectin is constitutively expressed on the bone marrow vasculature, but almost absent in normal vessels, and therefore, E-selectin targeted drug delivery presents an ideal strategy for the delivery of therapeutic nanoparticles to the bone marrow. The objective of this study was to develop a novel bone marrow targeted multistage vector (MSV) via E-selectin for delivery of therapeutics and imaging agents. To achieve this goal, Firstly, an E-selectin thioaptamer (ESTA) ligand was identified through a two-step screening from a combinatorial thioaptamer library. Next, ESTA-conjugated MSV (ESTA-MSV) were developed and evaluated for their stability and binding to E-selectin expressing endothelial cells. Different types of nanoparticles including liposomes, quantum dots, and iron oxide nanoparticles were loaded into the porous structure of ESTA-MSV. In vivo targeting experiments demonstrated 8-fold higher accumulation of ESTA-MSV in the mouse bone marrow as compared to non-targeted MSV Furthermore, intravenous injection of liposomes loaded ESTA-MSV resulted in a significantly higher accumulation of liposome in the bone marrow space as compared to injection of non-targeted MSV or liposomes alone. Overall this study provides first evidence that E-selectin targeted multistage vector preferentially targets to bone marrow vasculature and delivers larger amounts of nanoparticles. This delivery strategy holds potential for the selective delivery of large amounts of therapeutic payload to the vascular niches in the bone marrow for the treatment of bone marrow associated diseases.

Comparison of alternative methods of contact tracing in a syphilis control program

The purpose of this study was to compare the relative effectiveness of alternative methods of tracing named contacts of syphilis patients. A total of 236 contacts, identified by patients in two City of Houston Department of Health and Human Services clinics during the period April 1 through July 31, 1987, were studied. After contacts were grouped by sex and age, the proportion brought to examination by each of three methods, and by a combination of methods, was determined for each subgroup.^ The study found that 78.4% of all the 236 named sex contacts reported were located and brought to examination by the various methods of contact tracing and that 21.6% were missed. Of the 185 contacts examined, a combination of methods identified 47.7% of the cases, telephone contact, 28.6%, field contact, 16.9%, and patient referral, 11.8%.^ Of the 236 contacts reported, males made up 56.8% and females 43.2%. Contact tracing was more successful among females, with 81.4% of the 102 named female contacts, as compared to 76.1% of the 134 named male contacts being brought to examination. It is not known whether equal efforts were exerted in the follow-up of both male and female contacts. In both female and male subgroups, a combination of methods brought over 40% of sex contacts to examination. Telephone contact among females yielded 27.7% of the cases and field contact 18.1%, whereas in males, telephone contact identified 29.4% of the cases and field contact 15.7%. Patient referral was the least productive method in both sex groups, locating 12.8% in males as compared to 10.8% in females.^ On an age specific basis, a combination of methods was the most effective method in the 15-39 age group, whereas telephone contact was most effective in the 40-44 age group, and field contact in the 50-54 age group. Of all the methods of contact tracing, patient referral was the least productive in most age groups.^ Future studies of contact tracing should incorporate several important variables which were not examined in this study. ^

Investigating the epidemic of heroin use in Dar es Salaam, Tanzania: Recognizing the issues of heroin smokers

Since heroin was introduced to East Africa during the 1980s, heroin use practices have changed rapidly in response to various internal and external pressures. The aim of this study was to identify and describe the population of heroin users and locations of heroin use in Dar es Salaam, Tanzania, in order to understand recent contexts of heroin use. The study took place between June 30 and August 19, 2011, in all three districts (Kinondoni, Ilala, and Temeke) of Dar es Salaam. We mapped sites using a Global Positioning System device, counted numbers of heroin users, and conducted informal interviews with heroin users. The mixed-methods analyses of the data included quantifying the basic demographic and aggregate information about the sites and heroin users, as well as qualitative analysis and coding of fieldnotes from observations and responses to interviews which was used to identify themes and characteristics of heroin users. ^ We identified a total of 150 sites and counted a total of 1046 male and 46 female non-injecting drug users and 78 male and 9 female injecting drug users (IDUs) of heroin. We found that social organization existed at some of the sites, with 31% (n=47) of sites reporting having a leader and 44% (n=66) of sites reporting mutual aid between users frequenting the site. We had difficulty locating IDUs and female drug users, and the majority of users we encountered were heroin smokers of kokteli, a mixture of heroin, cannabis, and/or tobacco which is smoked like a cigarette. ^ This research highlighted heroin smokers’ desire for access to drug treatment services. The current methadone-based medication assisted treatment (MAT) program is funded and operates as an HIV prevention program for IDUs to reduce HIV infection in this population and slow or stop the spread of a second wave of HIV infection in the general population. However, smokers perceived MAT to be primarily a drug use prevention or cessation program and felt unjustly neglected from the intervention, leading to a tense relationship with IDUs. From a public health standpoint, future interventions should include heroin smokers to prevent HIV transmission. ^

Neocortical hyperexcitability defect in a mutant mouse model of spike-wave epilepsy, {\it stargazer}

Single-locus mutations in mice can express epileptic phenotypes and provide critical insights into the naturally occurring defects that alter excitability and mediate synchronization in the central nervous system (CNS). One such recessive mutation (on chromosome (Chr) 15), stargazer(stg/stg) expresses frequent bilateral 6-7 cycles per second (c/sec) spike-wave seizures associated with behavioral arrest, and provides a valuable opportunity to examine the inherited lesion associated with spike-wave synchronization.^ The existence of distinct and heterogeneous defects mediating spike-wave discharge (SWD) generation has been demonstrated by the presence of multiple genetic loci expressing generalized spike-wave activity and the differential effects of pharmacological agents on SWDs in different spike-wave epilepsy models. Attempts at understanding the different basic mechanisms underlying spike-wave synchronization have focused on $\gamma$-aminobutyric acid (GABA) receptor-, low threshold T-type Ca$\sp{2+}$ channel-, and N-methyl-D-aspartate receptor (NMDA-R)-mediated transmission. It is believed that defects in these modes of transmission can mediate the conversion of normal oscillations in a trisynaptic circuit, which includes the neocortex, reticular nucleus and thalamus, into spike-wave activity. However, the underlying lesions involved in spike-wave synchronization have not been clearly identified.^ The purpose of this research project was to locate and characterize a distinct neuronal hyperexcitability defect favoring spike-wave synchronization in the stargazer brain. One experimental approach for anatomically locating areas of synchronization and hyperexcitability involved an attempt to map patterns of hypersynchronous activity with antibodies to activity-induced proteins.^ A second approach to characterizing the neuronal defect involved examining the neuronal responses in the mutant following application of pharmacological agents with well known sites of action.^ In order to test the hypothesis that an NMDA receptor mediated hyperexcitability defect exists in stargazer neocortex, extracellular field recordings were used to examine the effects of CPP and MK-801 on coronal neocortical brain slices of stargazer and wild type perfused with 0 Mg$\sp{2+}$ artificial cerebral spinal fluid (aCSF).^ To study how NMDA receptor antagonists might promote increased excitability in stargazer neocortex, two basic hypotheses were tested: (1) NMDA receptor antagonists directly activate deep layer principal pyramidal cells in the neocortex of stargazer, presumably by opening NMDA receptor channels altered by the stg mutation; and (2) NMDA receptor antagonists disinhibit the neocortical network by blocking recurrent excitatory synaptic inputs onto inhibitory interneurons in the deep layers of stargazer neocortex.^ In order to test whether CPP might disinhibit the 0 Mg$\sp{2+}$ bursting network in the mutant by acting on inhibitory interneurons, the inhibitory inputs were pharmacologically removed by application of GABA receptor antagonists to the cortical network, and the effects of CPP under 0 Mg$\sp{2+}$aCSF perfusion in layer V of stg/stg were then compared with those found in +/+ neocortex using in vitro extracellular field recordings. (Abstract shortened by UMI.) ^