cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/usctheses-c3-204649
title: Oligomeric Aβ alters transport of GluR2 mRNA

description: Alzheimer’s disease (AD) is characterized by loss of memory and learning deficits caused by synaptic damage secondary to toxic oligomeric beta-amyloid (oAβ) deposition. Several glutamate receptors regulate transmission at the synapse, including the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, composed of the four subunits, GluR1-4. The GluR2 subunit has been found to contribute to Ca2+ regulation by rendering the AMPA receptor impermeable to it. oAβ may directly affect synaptic function by interacting with the AMPA receptor, which was found to have a binding site for Aβ  (Tozaki et al., 2002). ❧ GluR2 mRNA is thought to be transported to the synapse via the dendrite where it is locally translated (Grooms et al., 2006). We hypothesize that oAβ causes a shift in the transport of GluR2 mRNA, resulting in aberrant local expression of the receptor. Since Ca2+ dysregulation is thought to be involved in the pathogenesis of AD, the effect of oAβ on GluR2 may directly contribute to synaptic dysfunction. ❧ Using organotypic rat cortical cultures exposed to nanomolar levels of oAβ for 7 to 21 days, we examined the distribution of GluR2 subunit protein and GluR2 mRNA using fluorescent immunohistochemical and in situ hybridization techniques. In control (untreated) tissue, the GluR2 subunit colocalizes with the scaffold protein PSD-95, indicating its presence at the postsynaptic endings, whereas there is minimal or no colocalization in the oAβ-treated tissue. ❧ Next, we analyzed two splice variants of GluR2 mRNA: flip and flop. The distribution of GluR2 mRNA also appears to be affected by oAβ treatment. In untreated rat cortical tissue, mRNA has a diffuse appearance and is visible in the neuropil and dendritic projections, and with less frequency in the cytoplasm around the soma. In the oAβ -treated tissue, GluR2 mRNA appears to be present in lesser amounts in the neuropil, clustering mostly around the soma, and assuming a punctate appearance when visible in dendritic projections. This effect is evident in both the flip and flop splice variants after 2 weeks of oAβ treatment. ❧ Our findings suggest that oAβ may influence localization of GluR2 mRNA, inducing it to assemble into granules which remain primarily in the soma. These results suggest that oAβ may cause a shift in the transport of GluR2 mRNA, resulting in aberrant expression in the soma. These results may be an early step in the disease pathogenesis, and the consequences of this alteration may contribute to the synaptic changes.
DOI: 10.23725/5f84-7f89
title: NWD285363.recab.cram.crai

description: TOPMed: NWD285363 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.23725/azka-c182
title: NWD290849.recab.cram.crai

description: TOPMed: NWD290849 <br>HapMap_1000G: NA19238 <br>Seq Ctr: NYGC <br>File:  CRAI index file
DOI: 10.23725/b6wm-r292
title: NWD263474.recab.cram

description: TOPMed: NWD263474 <br>HapMap_1000G: NA19238 <br>Seq Ctr: NYGC <br>File:  CRAM file
DOI: 10.23725/n6gw-6b06
title: NWD296991.recab.cram.crai

description: TOPMed: NWD296991 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Baylor <br>File:  CRAI index file
DOI: 10.23725/nmvb-jm80
title: NWD290849.recab.cram

description: TOPMed: NWD290849 <br>HapMap_1000G: NA19238 <br>Seq Ctr: NYGC <br>File:  CRAM file
DOI: 10.23725/qx0h-2r91
title: NWD293295.recab.cram

description: TOPMed: NWD293295 <br>HapMap_1000G: NA19238 <br>Seq Ctr: NYGC <br>File:  CRAM file
DOI: 10.23725/tvcd-yj32
title: NWD285363.recab.cram

description: TOPMed: NWD285363 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.25549/usctheses-c3-141475
title: Page 208
DOI: 10.25549/usctheses-c3-160556
title: Page 38
DOI: 10.23725/25t4-hv33
title: NWD298195.recab.cram

description: TOPMed: NWD298195 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.23725/87ym-s365
title: NWD315403.recab.cram

description: TOPMed: NWD315403 <br>HapMap_1000G: HG01249 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.23725/8rmj-d025
title: NWD315195.recab.cram

description: TOPMed: NWD315195 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/b7ck-wg13
title: NWD315403.recab.cram.crai

description: TOPMed: NWD315403 <br>HapMap_1000G: HG01249 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.23725/bcbn-6b23
title: NWD298195.recab.cram.crai

description: TOPMed: NWD298195 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.23725/gk4r-n566
title: NWD316026.recab.cram.crai

description: TOPMed: NWD316026 <br>HapMap_1000G: HG01249 <br>Seq Ctr: WashU <br>File:  CRAI index file
DOI: 10.23725/qdhf-0w55
title: NWD293295.recab.cram.crai

description: TOPMed: NWD293295 <br>HapMap_1000G: NA19238 <br>Seq Ctr: NYGC <br>File:  CRAI index file
DOI: 10.23725/r1hs-mf74
title: NWD296991.recab.cram

description: TOPMed: NWD296991 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Baylor <br>File:  CRAM file
DOI: 10.23725/xj4k-ba74
title: NWD315195.recab.cram.crai

description: TOPMed: NWD315195 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.25549/usctheses-c3-177081
title: Page 86
DOI: 10.25549/usctheses-c3-177114
title: Page 119
DOI: 10.25549/usctheses-c3-205339
title: Public-private partnerships in freight-rail capacity improvement

description: Public-private partnerships, or PPPs, are a central-development component for U.S. freight railroads. As growth drives the need to increase capacity, these partnerships are seen as a key component in addressing track capacity, terminal expansion, and port-related development projects outside of traditional frameworks in direct public investment or complete privatization. As important as these arrangements are for the rail enterprise, their use varies from project to project, and there is great disparity for implementation depending on the parties and goals. In most cases, success and profitability are not often measured, and there are few studies demonstrating how they were successful. ❧ This paper proposes to identify the tools for success in PPPs and how to use them in the freight-rail industry. As part of this effort, the study seeks to help rail-focused development professionals understand the best practices for implementation of these partnerships in their companies and with public entities. The tools for success outlined include the various business structures, finance requirements, contract elements, and management techniques necessary for successful performance. Additionally, the study will describe specific practices that must be used by professionals to promote measurable success. ❧ This study is created to define the role of PPPs in rail-freight-capacity expansion and what skills are required to successfully assist, manage, and promote their use in the railroad enterprise. The study will demonstrate through specific railroad-related PPPs what is required for partnerships to be formed and managed for successful development. In the end, the study seeks to refine and train the planning-and-development professional in railroad-capacity expansion by teaching the process for successful PPPs.
DOI: 10.25549/usctheses-c3-336378
title: Regulation of neuronal function by the conserved SKN-1/Nrf stress response pathway in Caenorhabditis elegans

description: Improvisation, or the ability to adapt to changing environmental conditions, is a defining pillar of life, and evolutionarily conserved mechanisms exist to promote survival and mitigate damage during stress from a cellular to organismal level. Improvisation may be achieved in part through changes in neuronal function, causing behavioral adaptation. The goal of this dissertation is to determine mechanisms by which neuronal function is regulated by cellular stress pathways and how activation of these pathways in neurons promotes survival. Using the model Caenorhabditis elegans, I ask 1) how the conserved stress response transcription factor SKN-1, homologous to the mammalian Nrf family of transcription factors, is regulated by WDR-23, 2) how SKN-1 is regulated by stress, and 3) how SKN-1-mediated transcriptional programs regulate synaptic function. ❧ During normal conditions, SKN-1 is constitutively degraded; I show that SKN-1 is negatively regulated by the WD40 repeat protein WDR-23. wdr-23 encodes two isoforms, and while both isoforms are capable of completely rescuing defects associated with wdr-23 mutants, one isoform localizes to mitochondrial membranes, while the other localizes exclusively to nuclei. Through mitochondrial stressors and genetic mutations, I show that increased SKN-1 activity in the intestine results in reduced synaptic vesicle release. I predict that a soluble factor might be released from the intestine and acts hormonally on neurons to regulate behavior. I then use whole transcriptome RNA sequencing from whole worm lysate, and I identify over 2,000 genes to be regulated by SKN-1. While the majority of transcriptional targets are antioxidants and detoxificants or genes involved in metabolism and signaling, a handful of secreted neuropeptides are also up-regulated, indicating one or more of these peptides might be responsible for regulating neuronal function. ❧ Interestingly, from the RNA sequencing results I also identify approximately 800 genes affected by SKN-1 activity in neurons. Of these, I examine in depth the neuronally expressed cell adhesion molecule nlg-1/neuroligin. In the presence of mitochondrial stressors, the expression of nlg-1 increases, and this increase is dependent on the presence of skn-1. Using translational fusion proteins, I show that NLG-1 localizes to synapses, and increased SKN-1 activity increases the synaptic abundance of NLG-1. Furthermore, pharmacologic toxicity studies indicate that increasing the abundance of NLG-1 protects animals from death, while animals lacking nlg-1 are highly sensitive. These results indicate that SKN-1 may act in neurons to initiate transcription of targets that promote organismal survival during stress.
DOI: 10.23725/5b2p-ej23
title: NWD373853.recab.cram

description: TOPMed: NWD373853 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/n1ac-jg33
title: NWD422016.recab.cram

description: TOPMed: NWD422016 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/q4ek-w392
title: NWD319341.recab.cram.crai

description: TOPMed: NWD319341 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.23725/rcpf-dd19
title: NWD428511.recab.cram

description: TOPMed: NWD428511 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Illumina <br>File:  CRAM file
DOI: 10.23725/re2q-xj33
title: NWD319341.recab.cram

description: TOPMed: NWD319341 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/syyz-7x09
title: NWD422016.recab.cram.crai

description: TOPMed: NWD422016 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.23725/t0v8-sy60
title: NWD316026.recab.cram

description: TOPMed: NWD316026 <br>HapMap_1000G: HG01249 <br>Seq Ctr: WashU <br>File:  CRAM file
DOI: 10.23725/v2ae-0q76
title: NWD373853.recab.cram.crai

description: TOPMed: NWD373853 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.25549/usctheses-c3-160528
title: Page 10
DOI: 10.25549/usctheses-c3-194583
title: Molecular mechanism of transforming growth factor-beta signaling in skin wound healing

description: TGF-beta is a secreted cytokine, which plays an important role in cell development, differentiation, and homeostasis in both physiologic and pathologic conditions, such as tumorigenesis, abnormal wound healing and skin cancer. TGF-beta transmit signal from the extracellular environment to intracellular signaling networks via its cell surface receptor complex, the TGF-beta type II/ I receptor (TbetaRII/TbetaRI) heterodimer. TGF-beta ligand binds to TbetaRII, which in turn recruits and activates TbetaRI, resulting in activation of downstream signaling complex, receptor Smads (R-Smads) and common Smad4. TGF-beta stimulation is also known to activate R-Smad-independent signaling pathways, such as the extracellular signal-regulated kinase (ERK1/2) pathway. However, two long-standing questions remained: 1) why TGF-beta activates ERK depends on the cell context and 2) whether or not TbetaRII is able to mediate the TGF-beta signaling without the participation of TbetaRI. In the chapter two, it is shown that TGF-beta activates ERK in human dermal fibroblasts (DFs) and inhibits ERK in human keratinocytes (HKs). While the TbetaRI expression remains similar in both cell types, the expression level of TbetaRII in DFs is more than seven fold higher than that in HKs. Down-regulation of TbetaRII in DFs blocked TGF-beta-stimulated ERK activation. In contrast, up-regulation of TbetaRII in HKs to the similar level in DFs resulted in activation of ERK rather than inhibition by TGF-beta. Most intriguingly, the TbetaRII-mediated TGF-beta-stimulated ERK activation or inactivation in these cells did not require any participation of TbetaRI. Thus, this study illustrates that the vii expression levels of TbetaRII determine how TGF-beta regulates ERK in various cell types and provides direct evidence for the TbetaRI-independent signaling by TbetaRII. ❧ In wound healing, TGF-beta controls cell proliferation and migration. In the chapter three, the mechanism of TGF-beta's anti-motility was revealed. Anti-migration is one of the primary effects of TGF-beta on non-transformed cell types. We previously reported that TGF-beta3 inhibits PDGF-BB-induced dermal cell migration during wound healing. However, it was not clear what the underlying mechanism was. In this study, it is shown that TGF-beta3 activates PKA pathway through R-Smads/Smad4 complex. Activation of PKA led to over-expression and phosphorylation of paxillin, a focal adhesion molecule. As a result, polarization by PDGF-bb was disrupted and migration rate was decreased. This study elucidates the new mechanism of TGF-beta3 for inhibition of cell migration.
DOI: 10.23725/0h6f-we97
title: NWD444824.recab.cram.crai

description: TOPMed: NWD444824 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Baylor <br>File:  CRAI index file
DOI: 10.23725/0hgj-c856
title: NWD433038.recab.cram.crai

description: TOPMed: NWD433038 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.23725/e97z-er71
title: NWD434806.recab.cram.crai

description: TOPMed: NWD434806 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Baylor <br>File:  CRAI index file
DOI: 10.23725/ktbz-dh31
title: NWD444824.recab.cram

description: TOPMed: NWD444824 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Baylor <br>File:  CRAM file
DOI: 10.23725/msya-ep07
title: NWD434806.recab.cram

description: TOPMed: NWD434806 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Baylor <br>File:  CRAM file
DOI: 10.23725/tk0e-bk23
title: NWD433038.recab.cram

description: TOPMed: NWD433038 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.23725/yh1j-ch78
title: NWD428511.recab.cram.crai

description: TOPMed: NWD428511 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Illumina <br>File:  CRAI index file
DOI: 10.25549/usctheses-c3-160555
title: Page 37
DOI: 10.25549/usctheses-c3-160565
title: Page 47
DOI: 10.25549/usctheses-c3-170655
title: Page 145
DOI: 10.25549/usctheses-c3-177112
title: Page 117
DOI: 10.25549/usctheses-c3-206250
title: Protective factors against the clinical onset of Alzheimer's disease: a case for cognitive reserve

description: Cognitive reserve refers to the fact that some people are better able to compensate for compromised brain structures than others (Stern, 2009).  This ability to respond differentially to brain damage can be measured using different proxies, such as education, occupation and leisure activities.  The aim of this study is to investigate if cognitive reserve moderates the relationship between dementia severity, dementia duration, and age of onset with the amount of atrophy in the brain.  This study involved 193 individuals (123 females; 70 males) from the Swedish Twin Registry.  CT scans were rated using linear measurements to measure atrophy in various parts of the brain.  The results found that cognitive reserve does moderate the relationship between dementia severity, dementia duration and age of onset with the amount of atrophy in the brain.  Those who have higher cognitive reserve have more brain damage at a given level of dementia severity and at a given level of dementia duration.  Individuals who have higher cognitive reserve have a later age of onset than those who have less reserve. Specific parts of the brain, like the temporal ventricle area, frontal lobe and third ventricle are especially affected by this relationship.
DOI: 10.25549/usctheses-c3-208402
title: Developing strong board relationships during the first 90 days: Strategies for aspiring superintendents

description: Federal, state, and local accountability mandates (i.e., No Child Left Behind Act of 2001) and declining fiscal resources have put increasing pressure on school boards to find the “right” superintendent that can lead their district through this tumultuous period in public education. With over 50% of the current superintendents planning retirement in 2015 according to Kowalski, McCord, Peterson, Young, and Ellerson (2011), the time to prepare the next generation of aspiring superintendents is now. The purpose of this study was to identify the behaviors and strategies successful superintendents used to build strong relationships with their board during the entry period.  This study was conducted by a cohort of nine researchers from the Rossier School of Education at the University of Southern California.  Using a qualitative research design approach that included data from 64 superintendent surveys and 48 board member surveys as well as one-to-one interviews with a superintendent and his board president, this researcher conducted an in-depth case study.  Data analysis revealed that the entry period was a critically important time that successful superintendents used to implement strategies that cultivated strong relationships with their boards. These strategies included: (a) having an entry plan, (b) relentless open and transparent communication, and (c) alignment and use of a variety of leadership efforts which met the goals and/or needs of the district.  The data also revealed that interpersonal skills was an important factor that led to the hiring and ultimate success of superintendents during the entry period.
DOI: 10.25549/usctheses-c3-278442
title: Gender, learning, and trafficking: helping vulnerable Thai women through NGO and government non-formal education programs
DOI: 10.23725/1baw-rk48
title: NWD446684.recab.cram

description: TOPMed: NWD446684 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Illumina <br>File:  CRAM file
DOI: 10.23725/4s3f-7s52
title: NWD455342.recab.cram.crai

description: TOPMed: NWD455342 <br>HapMap_1000G: NA19238 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.23725/7b09-w840
title: NWD463423.recab.cram

description: TOPMed: NWD463423 <br>HapMap_1000G: HG01249 <br>Seq Ctr: NYGC <br>File:  CRAM file
DOI: 10.23725/8adg-fp62
title: NWD465900.recab.cram

description: TOPMed: NWD465900 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/bxf1-gm52
title: NWD446684.recab.cram.crai

description: TOPMed: NWD446684 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Illumina <br>File:  CRAI index file
DOI: 10.23725/fayj-r870
title: NWD463423.recab.cram.crai

description: TOPMed: NWD463423 <br>HapMap_1000G: HG01249 <br>Seq Ctr: NYGC <br>File:  CRAI index file
DOI: 10.23725/kb6x-1j49
title: NWD455342.recab.cram

description: TOPMed: NWD455342 <br>HapMap_1000G: NA19238 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.23725/shhv-vt24
title: NWD465900.recab.cram.crai

description: TOPMed: NWD465900 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.25549/usctheses-c3-160547
title: Page 29
DOI: 10.25549/usctheses-c3-177106
title: Page 111
DOI: 10.25549/usctheses-c3-205022
title: Formal and informal networks of successful female superintendents in California

description: This study examined the networking and mentoring practices of female superintendents in California. Through a mixed-methods approach, quantitative data was collected from a survey using electronic questionnaires, and qualitative data was collected from open-ended questions on the survey and interviews. The survey response rate was 50%.  Of the respondents, nine superintendents were selected and interviewed. Data from these sources, along with that from available research, were triangulated in order to find convergent and divergent themes. ❧ Key findings of female superintendents in this study included the following: (1) formal networks provided support for female superintendents, especially locally-based and county-sponsored networks; (2) informal networks included local groups who met frequently over a meal; (3) gender identity and voice were an issue for some female superintendents in formal networks; however, no respondents felt this was an issue in the informal networks; (4) networking supported the women while they were already in the position of superintendent, and the benefits included gaining information related to the role of the superintendency as well as social and emotional support; (5) mentoring provided primary support while the individual was pursuing the superintendency and through the first year in the position; (6) women were mentored by their direct supervisors, who took the initiative to intentionally mentor the individual. ❧ Findings were interpreted through the lens of social network theory and the framework of communities of practice. Implications of these findings as well as recommendations for future research were identified.
DOI: 10.23725/01x2-7y75
title: NWD470340.recab.cram.crai

description: TOPMed: NWD470340 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.23725/2dte-7k29
title: NWD490850.recab.cram

description: TOPMed: NWD490850 <br>HapMap_1000G: NA19238 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.23725/5h21-kd39
title: NWD480514.recab.cram

description: TOPMed: NWD480514 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/a408-qr02
title: NWD479955.recab.cram

description: TOPMed: NWD479955 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.23725/f9jt-7f46
title: NWD480514.recab.cram.crai

description: TOPMed: NWD480514 <br>HapMap_1000G: NA19238 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.23725/g7xc-gw10
title: NWD479955.recab.cram.crai

description: TOPMed: NWD479955 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.23725/xtkd-6767
title: NWD470340.recab.cram

description: TOPMed: NWD470340 <br>HapMap_1000G: NA12878 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.25549/usctheses-c3-141482
title: Page 215
DOI: 10.25549/usctheses-c3-177077
title: Page 82
DOI: 10.25549/usctheses-c3-177082
title: Page 87
DOI: 10.25549/usctheses-c3-177113
title: Page 118