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Search Results: 1 - 10 of 402017 matches for " Donna M Cassidy-Hanley "
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Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
Robert S Coyne, Mathangi Thiagarajan, Kristie M Jones, Jennifer R Wortman, Luke J Tallon, Brian J Haas, Donna M Cassidy-Hanley, Emily A Wiley, Joshua J Smith, Kathleen Collins, Suzanne R Lee, Mary T Couvillion, Yifan Liu, Jyoti Garg, Ronald E Pearlman, Eileen P Hamilton, Eduardo Orias, Jonathan A Eisen, Barbara A Methé
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-562
Abstract: We addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified.We report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes.Tetrahymena thermophila is a well studied model organism for molecular and cellular biology. Telomerase, self-splicing RNA, and the function of histone acetylation are some of the major discoveries made with this unicellular ciliated protozoan (reviewed in [1,2]). It was also the first member of the phylum Ciliophora to have its complete somatic (macronuclear, or MAC) genome sequenced [3]. Like other ciliates, T. thermophila's MAC genome is a highly processed version of the germline (micronuclear, or MIC) genome, which is transcriptionally silent and responsible for direct transmission of genetic material to future sexual generations [4].
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-10-r100
Abstract: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.The ciliates are an ancient and diverse phylogenetic group related to the largely parasitic apicomplexans, but consisting mostly of free-living heterotrophs. Some ciliates, however, have adopted a parasitic lifestyle. By far the most important of these is Ichthyophthirius multifiliis (which we will refer to by its common name of Ich), an endoparasite that causes white spot disease in freshwater fish [1,2]. With an extremely broad host-range, Ich is responsible for large-scale die-offs in natural populations and poses a significant threat to the growing worldwide aquaculture industry. Ich has a simple life cycle with no intermediate hosts (Figure 1). The free-swimming theront form invades the epidermis of susceptible fish, feeding on host tissue and growing up to 0.5 mm in diameter. Host-associated trophonts become visible as individual white spots for which this disease is n
Nonlinearity in Quantum Theory and Closed Timelike Curves
M. J. Cassidy
Physics , 1994, DOI: 10.1103/PhysRevD.52.5676
Abstract: We examine consequences of the density matrix approach to quantum theory in the context of a model spacetime containing closed timelike curves and find that in general, an initially pure state will evolve in a nonlinear way to a mixed quantum state. CPT invariance and the implications of this nonlinearity for the statistical interpretation of quantum theory are discussed.
Divergences in the Effective Action for Acausal Spacetimes
M. J. Cassidy
Physics , 1997, DOI: 10.1088/0264-9381/14/11/006
Abstract: The 1--loop effective Lagrangian for a massive scalar field on an arbitrary causality violating spacetime is calculated using the methods of Euclidean quantum field theory in curved spacetime. Fields of spin 1/2, spin 1 and twisted field configurations are also considered. In general, we find that the Lagrangian diverges to minus infinity at each of the nth polarised hypersurfaces of the spacetime with a structure governed by a DeWitt-Schwinger type expansion.
Family Background and Environment, Psychological Distress, and Juvenile Delinquency  [PDF]
Tony Cassidy
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.29142
Abstract: The relationship between youth offending and family background is still unclear in the literature. This study explored the role of family factors and psychological distress in relation to delinquency and youth offending to try and explicate the relative importance of family structure, family relations, and psychological distress. The study used the Brief Symptom Inventory, the Family Environment Scale, and the Delinquency Scale in a structured interview format to measure psychological distress, family structure and relations, and levels of youth offending, in 219 older children and adolescents aged between 12-17 years living in areas associated with high levels of youth offending in the UK. Analysis involved correlations, hierarchical multiple regression and analysis of variance. Family relations were the best predictors of delinquency and were also correlated with psychological distress. The relationship between delinquency and psychological distress indicated that participants with more psychological distress were less likely to be involved in criminal behaviour. The study supports the conclusion that youth offending and psychological distress are both influenced by a range of factors in the family, but may be unrelated to each other.
Crustal Magnetization of Mars: Terra Meridiani and Terra Sirenum  [PDF]
Renee A. French, Donna M. Jurdy
Journal of Modern Physics (JMP) , 2017, DOI: 10.4236/jmp.2017.88083
Abstract: We examine the crustal magnetization of Terra Meridiani and Terra Sirenum, the region representing the strongest magnetization in the Southern Hemisphere, by downward continuing mapping level data (400 km altitude) from the Mars Global Surveyor (MGS) Magnetometer and Electron Reflectometer (MAG/ER). We find that the surface magnetization in both regions can be fit with a small number of sources, with the positive sources stronger than negative ones in both regions. The ratio of the strongest positive to strongest negative source for the regions matches within 2%. For both regions, the locations of strong sources are positioned at the outer rings of ancient impact features. We employ two approaches of source depth estimation. One method employs downward continuation of positive and negative sources from mapping level into the subsurface to extrapolate the depth to magnetization. With this approach, source depths generally range from 80 ± 20 km in Terra Meridiani and 65 ± 25 km in Terra Sirenum. A graphical approach uses the contour map of surface magnetization to estimate depths ranging from 125 km for thick sources in Terra Meridiani and from 82 km for thick sources in Terra Sirenum. These depths require a low (≤∼20 mW/m2) Martian heat flux to permit magnetite, hematite, and/or pyrrhotite (although limited) as carriers through 100 km or more. The upcoming InSight mission will provide invaluable seismic constraints on both crustal and core structure, in addition to the first Martian heat flow measurements that will constrain magnetization.
Advance Directives in the Context of Uncertain Prognosis for Residents of Nursing Homes  [PDF]
Beryl E. Cable-Williams, Donna M. Donna M. Wilson, Norah Keating
Open Journal of Nursing (OJN) , 2014, DOI: 10.4236/ojn.2014.44037

This report documents the findings of a mixed-methods study focused on the advanced directives of 182 residents of three LTC facilities in southern Ontario, Canada. Although almost all had a completed advance directive within 3 months of death, most did not have a palliative designation or directive until a few days before they died. Each facility’s written Progress Notes revealed staff members usually sought additional confirmation of care preferences from residents’ substitute decision-makers within a few days of the death. It was thus common for advance directives to change from a more interventionist approach to the least interventionist approach near death. This change indicates that the meaning and significance of advance care planning and resulting advance directives must be considered in light of the processes and temporal factors involved in their completion and use within this distinct population. The relational nature of advance care planning and concern about ageism as a factor for withholding or withdrawing life support for LTC residents are considered as possible explanatory factors. These findings and their implications are described in relation to end-of-life care policies and practices in LTC facilities.

System-on-Chip Design Using High-Level Synthesis Tools  [PDF]
Erdal Oruklu, Richard Hanley, Semih Aslan, Christophe Desmouliers, Fernando M. Vallina, Jafar Saniie
Circuits and Systems (CS) , 2012, DOI: 10.4236/cs.2012.31001
Abstract: This paper addresses the challenges of System-on-Chip designs using High-Level Synthesis (HLS). HLS tools convert algorithms designed in C into hardware modules. This approach is a practical choice for developing complex applications. Nevertheless, certain hardware considerations are required when writing C applications for HLS tools. Hence, in order to demonstrate the fundamental hardware design concepts, a case studyis presented. Fast Fourier Transform (FFT) implementation in ANSI C is examined in order to explore the important design issues such as concurrency, data recurrences and memory accesses that need to be resolved before generating the hardware using HLS tools. There are additional language constraints that need to be addressed including use of pointers, recursion and floating point types.
Models for Chronology Selection
M. J. Cassidy,S. W. Hawking
Physics , 1997, DOI: 10.1103/PhysRevD.57.2372
Abstract: In this paper, we derive an expression for the grand canonical partition function for a fluid of hot, rotating massless scalar field particles in the Einstein universe. We consider the number of states with a given energy as one increases the angular momentum so that the fluid rotates with an increasing angular velocity. We find that at the critical value when the velocity of the particles furthest from the origin reaches the speed of light, the number of states tends to zero. We illustrate how one can also interpret this partition function as the effective action for a boosted scalar field configuration in the product of three dimensional de Sitter space and $S^1$. In this case, we consider the number of states with a fixed linear momentum around the $S^1$ as the particles are given more and more boost momentum. At the critical point when the spacetime is about to develop closed timelike curves, the number of states again tends to zero. Thus it seems that quantum mechanics naturally enforces the chronology protection conjecture by superselecting the causality violating field configurations from the quantum mechanical phase space.
Neuroinflammation in the Aging Down Syndrome Brain; Lessons from Alzheimer's Disease
Donna M. Wilcock
Current Gerontology and Geriatrics Research , 2012, DOI: 10.1155/2012/170276
Abstract: Down syndrome (DS) is the most genetic cause of mental retardation and is caused by the triplication of chromosome 21. In addition to the disabilities caused early in life, DS is also noted as causing Alzheimer's-disease-like pathological changes in the brain, leading to 50–70% of DS patients showing dementia by 60–70 years of age. Inflammation is a complex process that has a key role to play in the pathogenesis of Alzheimer's disease. There is relatively little understood about inflammation in the DS brain and how the genetics of DS may alter this inflammatory response and change the course of disease in the DS brain. The goal of this review is to highlight our current understanding of inflammation in Alzheimer's disease and predict how inflammation may affect the pathology of the DS brain based on this information and the known genetic changes that occur due to triplication of chromosome 21. 1. Introduction Down syndrome (DS) is the most common chromosomal anomaly among live-born infants and is the most frequent genetic cause of mental retardation [1, 2], with an incidence of one per 733 live births in the United States [3]. DS is caused by a triplication of chromosome 21 (a full list of genes located on chromosome 21 can be found in [4]). Due to the extensive number of genes triplicated, there is an extremely high incidence of congenital cardiac and gastrointestinal abnormalities [5]. DS is usually detected during pregnancy through first-trimester screening tests followed up by confirmation through amniocentesis, chorionic villus sampling, or percutaneous umbilical blood sampling [6]. Alzheimer’s disease (AD) is the leading cause of dementia and is characterized clinically by a progressive loss of memory and cognition. An absolute diagnosis of AD can only occur after pathological analysis is performed on the brain tissue. There are two signature pathological lesions required for diagnosis; neuritic plaques composed of aggregated amyloid-β (Aβ) peptides, and neurofibrillary tangles composed of hyperphosphorylated, aggregated tau protein [7]. AD is usually considered a disease of aging, where currently 1 in 8 Americans over the age of 65 have AD yet half of those over 85 years have AD (data obtained from the Alzheimer’s Association; www.alz.org). In DS, Aβ deposits begin to accumulate in childhood and increase progressively with age [8]. There is an acceleration of this pathology between the ages of 35–45 years when other AD pathologies begin to occur, most importantly neurofibrillary tangles and inflammation [9]. Despite the certainty of developing
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