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Articles 61 - 85 of 85
Full-Text Articles in Genetics and Genomics
Bioconductor: Open Software Development For Computational Biology And Bioinformatics, Robert C. Gentleman, Vincent J. Carey, Douglas J. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Guenther Sawitzki, Colin Smith, Gordon K. Smyth, Luke Tierney, Yee Hwa Yang, Jianhua Zhang
Bioconductor: Open Software Development For Computational Biology And Bioinformatics, Robert C. Gentleman, Vincent J. Carey, Douglas J. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Guenther Sawitzki, Colin Smith, Gordon K. Smyth, Luke Tierney, Yee Hwa Yang, Jianhua Zhang
Bioconductor Project Working Papers
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have …
Minnesota Banded Darters (Etheostoma Zonale) Exhibit A High Degree Of Genetic Similarity In Mitochondrial Dna Sequences Occurrence, Jean Porterfield, Molly Fee, Jessica Theorin
Minnesota Banded Darters (Etheostoma Zonale) Exhibit A High Degree Of Genetic Similarity In Mitochondrial Dna Sequences Occurrence, Jean Porterfield, Molly Fee, Jessica Theorin
Journal of the Minnesota Academy of Science
Hylogeography, or the historical interpretation of population genetic data, is a useful tool for addressing historical processes like the colonization history of organisms. North American freshwater fishes have experienced glacial ebb and flow in their relatively recent past (as little as 10,000 years before present in Minnesota), and studies of variation in intraspecific DNA sequences of these fishes can shed light on their radiations into previously glaciated areas. This study assessed intraspecific variation in two mitochondrial genes of the banded darter (Etheostoma zonale) from seven Minnesota localities. A high degree of similarity was found among all individuals in the study. …
New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, Daniel C. Ciobanu, John W. M. Vleck, S. M. Lonergan, H. Thomsen, J. C. M. Dekkers, G. S. Plastows, M. F. Rothschild
New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, Daniel C. Ciobanu, John W. M. Vleck, S. M. Lonergan, H. Thomsen, J. C. M. Dekkers, G. S. Plastows, M. F. Rothschild
Department of Animal Science: Faculty Publications
Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and …
Smart Sequence Similarity Search (S⁴) System, Zhuo Chen
Smart Sequence Similarity Search (S⁴) System, Zhuo Chen
Theses Digitization Project
Sequence similarity searching is commonly used to help clarify the biochemical and physiological features of newly discovered genes or proteins. An efficient similarity search relies on the choice of tools and their associated subprograms and numerous parameter settings. To assist researchers in selecting optimal programs and parameter settings for efficient sequence similarity searches, the web-based expert system, Smart Sequence Similarity Search (S4) was developed.
Multigene Metabolic Engineering Via The Chloroplast Genome, Oscar Nemesio Ruiz
Multigene Metabolic Engineering Via The Chloroplast Genome, Oscar Nemesio Ruiz
Electronic Theses and Dissertations
The vast majority of valuable agronomic traits are encoded polygenetically. Chloroplast genetic engineering offers an alternate approach to multigene engineering by allowing the insertion of entire pathways in a single transformation event, while being an environmentally friendly approach. Stable integration into the chloroplast genome and transcription of the phaA gene coding for β-ketothiolase was confirmed by Southern and northern blots. Coomassie-stained gel and western blots confirmed hyperexpression of β-ketothiolase in leaves and anthers, with high enzyme activity. The transgenic lines were normal except for the male sterile phenotype, lacking pollen. Scanning electron microscopy revealed a collapsed morphology of the pollen …
Effects Of Index Selection On The Performance And Carcass Composition Of Sheep Given Foods Of Different Protein Concentrations Ad Libitum., R. M. Lewis, G. C. Emmans, G. Simm
Effects Of Index Selection On The Performance And Carcass Composition Of Sheep Given Foods Of Different Protein Concentrations Ad Libitum., R. M. Lewis, G. C. Emmans, G. Simm
Department of Animal Science: Faculty Publications
Sheep of a line selected on an index to increase carcass lean content at 150 days of age (selected (S); no. = 90), and an unselected control line (control (C); no. = 90), were given ad libitum foods of three different protein concentrations (192, 141 and 120 g/kg dry matter). Growth was measured from about 21 to 114 kg live weight. The carcasses of each line were analysed for lean, fat and bone at three widely varying weights in both males and females. Level of protein did not affect the extent to tohidi S was superior to C in the …
Effects Of Two Dried Forages, And A Choice Between Them, On Intake, Growth And Carcass Composition In Lambs Of Two Breeds And Their Cross, R. M. Lewis, J. M. Macfarlane, G. C. Emmans
Effects Of Two Dried Forages, And A Choice Between Them, On Intake, Growth And Carcass Composition In Lambs Of Two Breeds And Their Cross, R. M. Lewis, J. M. Macfarlane, G. C. Emmans
Department of Animal Science: Faculty Publications
The effects of for age type, breed type and sex on lamb growth and carcass composition, and their changes throughout growth, were measured. The three breed types were Scottish Blackface (no. =31), Suffolk (no. =28) and their reciprocal cross (no. =30). The lambs were given ad libitum a pelleted rye grass alone, pelleted lucerne alone or a choice of both. Each lamb was scanned using X-ray computed tomography to measure the weights of fat, lean and bone in the carcass at three proportions of mature body weight (0-30, 0·45 and 0·65). Live weights and food intake data were recorded weekly. …
Predicting Population Gene Frequency From Sample Data, R. M. Lewis, B. Grundy, L. A. Kuehn
Predicting Population Gene Frequency From Sample Data, R. M. Lewis, B. Grundy, L. A. Kuehn
Department of Animal Science: Faculty Publications
With an increase in the number of candidate genes for important traits in livestock, effective strategies for incorporating such genes into selection programmes are increasingly important. Those strategies in part depend on the frequency of a favoured allele in a population. Since comprehensive genotyping of a population is seldom possible, we investigate the consequences of sampling strategies on the reliability of the gene frequency estimate for a bi-allelic locus. Even within a subpopulation or line, often only a proportion of individuals will be genotype tested. However, through segregation analysis, probable genotypes can be assigned to individuals that themselves were not …
Soil Characterization Using Textural Features Extracted From Gpr Data, Lameck O. Odhiambo, Robert S. Wright, Ronald E. Yoder
Soil Characterization Using Textural Features Extracted From Gpr Data, Lameck O. Odhiambo, Robert S. Wright, Ronald E. Yoder
Department of Animal Science: Faculty Publications
Soils can be non-intrusively mapped by observing similar patterns within ground-penetrating radar (GPR) profiles. We observed that the intricate and often indiscernible textural variability found within a complex GPR image possesses important parameters that help delineate regions of similar soil characteristics. Therefore, in this study, we examined the feasibility of using textural features extracted from GPR data to automate soil characterizations. The textural features were matched to a "fingerprint" database of previous soil classifications of GPR textural features and the corresponding ground truths of soil conditions. Four textural features (energy, contrast, entropy, and homogeneity) were selected for inputs into a …
Evaluation Of Procedures To Predict Fat-Free Lean In Swine Carcasses, Rodger K. Johnson, E. P. Johnson, R. Goodwin, J. W. Mabry, R. K. Miller, O. W. Robison, H. Sellers, M. D. Tokach
Evaluation Of Procedures To Predict Fat-Free Lean In Swine Carcasses, Rodger K. Johnson, E. P. Johnson, R. Goodwin, J. W. Mabry, R. K. Miller, O. W. Robison, H. Sellers, M. D. Tokach
Department of Animal Science: Faculty Publications
The objectives were to develop equations for predicting fat-free lean in swine carcasses and to estimate the prediction bias that was due to genetic group, sex, and dietary lysine level. Barrows and gilts (n = 1,024) from four projects conducted by the National Pork Board were evaluated by six procedures, and their carcass fat-free lean was determined. Pigs of 16 genetic groups were fed within weight groups one of four dietary regimens that differed by 0.45% in lysine content and slaughtered at weights between 89 and 163 kg. Variables in equations included carcass weight and measures of backfat depth and …
Effects Of Food Quality On Growth And Carcass Composition In Lambs Of Two Breeds And Their Cross, R. M. Lewis, J. M. Macfarlane, G. Simm, G. C. Emmans
Effects Of Food Quality On Growth And Carcass Composition In Lambs Of Two Breeds And Their Cross, R. M. Lewis, J. M. Macfarlane, G. Simm, G. C. Emmans
Department of Animal Science: Faculty Publications
The effects offood quality, breed type and sex (ram and ewe) on Iamb growth and carcass composition, and their changes throughout growth, were measured. The three breed typeswereScottish Blackface (B; no. = 24), Suffolk (S; no. = 28) and their reciprocal crosses (X; no. 33). The lambs had free access to a nutritionally non-limiting food, H, or a bulky food, L. Each lamb was scanned using X-ray computed tomography to measure the weights offat, lean and bone in the carcass at three degrees of maturity (0·30, 0·45 and 0·65) in live weight. Live weight and food intake data were recorded …
Exogenous Estrogen Boosts Circulating Estradiol Concentrations And Calcium Uptake By Duodenal Tissue In Heat-Stressed Hens, K.K. Hansen, M.M. Beck, S.E. Scheideler, Erin E. Blankenship
Exogenous Estrogen Boosts Circulating Estradiol Concentrations And Calcium Uptake By Duodenal Tissue In Heat-Stressed Hens, K.K. Hansen, M.M. Beck, S.E. Scheideler, Erin E. Blankenship
Department of Animal Science: Faculty Publications
In the hen, heat stress (HS) disrupts shell calcification and reproductive processes, including hormone synthesis and egg production. Two studies were conducted to investigate palliative effects of exogenous estrogen or dietary vitamin D3 on Ca homeostasis and reproductive physiology during HS. Study 1: Hy-Line W36 hens were randomly assigned to thermoneutral (TN) or HS treatments and to 1 of 7 estrogen treatments: zero (control) or one Compudose 200 implant given 1, 2, 3, 8, 9, or 10 d before onset of HS. With no implant, HS reduced plasma estradiol (E2) and total Ca absorbed (CaT) by duodenal cells (P < 0.05). In TN hens with implants, plasma E2 tripled within 24 h (P < 0.05) and remained elevated (P < 0.05) through d 9. In HS hens with implants, plasma E2 rose 6-fold (P < 0.05) to equal TN+E2 concentrations and remained elevated through d 10. In TN and HS hens with implants, the rate of Ca absorption (CaTR) and CaT increased dramatically; the responses were quadratic and essentially identical. Study 2: Hy-Line W36 hens were provided diets formulated either according to NRC requirements (NRC, 1994), or with the addition of 22,000 IU/kg vitamin D3 (+VD hens). A 24-h HS episode was imposed 2 wk after initiation of the dietary regimen. Duodenal samples were collected for Ca absorption assays after the 24-h HS episode. Both CaTR and CaT in +VD hens were approximately 3-fold higher than in hens in the NVD group (P = 0.102). The results lead to the conclusion that exogenous estrogen, high levels of dietary vitamin D, or both, before a HS episode, are efficacious in alleviating at least some of the effects of HS and should be further investigated.
Long-Term Environmental Effects Of Conifer Removal To Achieve Aspen Release In Near-Stream Areas Within The Northern Sierras, Kenneth W. Tate, Bobette Jones, Melanie Mcfarland, Tom Rickman, Al Vasquez
Long-Term Environmental Effects Of Conifer Removal To Achieve Aspen Release In Near-Stream Areas Within The Northern Sierras, Kenneth W. Tate, Bobette Jones, Melanie Mcfarland, Tom Rickman, Al Vasquez
Aspen Bibliography
The advanced state of conifer encroachment in aspen stands in the Sierra Nevada and southern Cascades is retarding aspen regeneration, putting an estimated 70 plus percent of stands at immediate risk of extinction with a significant percentage of stands already lost.
Executive Summary The Role Of Ungulate Herbivory And Management On Ecosystem Patterns And Processes: A Problem Analysis, John G. Kie, Martin Vavra
Executive Summary The Role Of Ungulate Herbivory And Management On Ecosystem Patterns And Processes: A Problem Analysis, John G. Kie, Martin Vavra
Aspen Bibliography
No abstract provided.
National Pork Producers Council Maternal Line Genetic Evaluation: A Comparison Of Growth And Carcass Traits In Terminal Progeny, J. D. Cassady, O. W. Berg, Rodger K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller, R. N. Goodwin
National Pork Producers Council Maternal Line Genetic Evaluation: A Comparison Of Growth And Carcass Traits In Terminal Progeny, J. D. Cassady, O. W. Berg, Rodger K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller, R. N. Goodwin
Department of Animal Science: Faculty Publications
The objective of this study was to compare growth and carcass traits of 1,252 progeny of six commercially available dam lines included in the National Pork Producers Council Maternal Line Evaluation Project. Lines compared included one maternal line supplied by each of American Diamond Swine Genetics (ADSG), Danbred NA (DB), two lines supplied by Monsanto Choice Genetics (DK and GPK347), Newsham Hybrids (NH), and Landrace × Large White females supplied by the National Swine Registry (NSR). All females were mated to DB, Duroc-Hampshire terminal sires. Traits analyzed were ADG from 56 to 115 kg live weight, days to 115 kg, …
Glycosyltransferases Encoded By Viruses, Nicolas Markine-Goriaynoff, Laurent Gillet, James L. Van Etten, Haralambos Korres, Naresh Verma, Alain Vanderplasschen
Glycosyltransferases Encoded By Viruses, Nicolas Markine-Goriaynoff, Laurent Gillet, James L. Van Etten, Haralambos Korres, Naresh Verma, Alain Vanderplasschen
James Van Etten Publications
Studies of cellular biology in recent decades have highlighted the crucial roles of glycans in numerous important biological processes, raising the concept of glycomics that is now considered as important as genomics, transcriptomics and proteomics. For millions of years, viruses have been co-evolving with their hosts. Consequently, during this co-evolution process, viruses have acquired mechanisms to mimic, hijack or sabotage host processes that favour their replication, including mechanisms to modify the glycome. The importance of the glycome in the regulation of host–virus interactions has recently led to a new concept called ‘glycovirology’. One fascinating aspect of glycovirology is the study …
Hsp70 Promotes Tnf-Mediated Apoptosis By Binding Ikkγ And Impairing Nf-Κb Survival Signaling, Ruiqiong Ran, Aigang Lu, Lu Zhang, Yang Tang, Hongyan Zhu, Huichun Xu, Benjamin Feng, Chun Han, Guoping Zhou, Alan C. Rigby, Frank R. Sharp
Hsp70 Promotes Tnf-Mediated Apoptosis By Binding Ikkγ And Impairing Nf-Κb Survival Signaling, Ruiqiong Ran, Aigang Lu, Lu Zhang, Yang Tang, Hongyan Zhu, Huichun Xu, Benjamin Feng, Chun Han, Guoping Zhou, Alan C. Rigby, Frank R. Sharp
Peer Reviewed Articles
The major heat shock protein, Hsp70, can protect against cell death by directly interfering with mitochondrial apoptosis pathways. However, Hsp70 also sensitizes cells to certain apoptotic stimuli like TNF. Little is known about how Hsp70 enhances apoptosis. We demonstrate here that Hsp70 promotes TNF killing by specifically binding the coiled-coil domain of IκB kinase γ (IKKγ) to inhibit IKK activity and consequently inhibit NF-κB-dependent antiapoptotic gene induction. An IKKγ mutant, which interacts with Hsp70, competitively inhibits the Hsp70–IKKγ interaction and relieves heat-mediated NF-κB suppression. Depletion of Hsp70 expression with RNA interference rescues TNF-mediated cell death. Although TNF may or may …
Morphological Characteristics And Species Separation Of Hawaiian Postlarval Amphidromous Fishes, M. Eric Benbow, Albert J. Burky, Carl M. Way
Morphological Characteristics And Species Separation Of Hawaiian Postlarval Amphidromous Fishes, M. Eric Benbow, Albert J. Burky, Carl M. Way
Biology Faculty Publications
There are five Hawaiian amphidromous fishes (Gobiidae: Lentipes concolor, Awaous guamensis, Sicyopterus stimpsoni, Stenogobius hawaiiensis; Eleotridae: Eleotris sandwicensis). Amphidromous adults deposit eggs on the stream bottom. After hatching, larvae drift to the ocean for growth followed by postlarval migration back into the streams. Postlarvae were collected to construct a dichotomous identification key based on 12 morphological measures and ray counts from four fins. Overall, the presense of fused pelvic fins, standard length (SL), and fin ray numbers were the most useful in species separation. Gobies were separated from the eleotrid by the former having fused …
Human Genetic Variation And Health: New Assessment Approaches Based On Ethnogenetic Layering, Fatimah Linda Collier Jackson
Human Genetic Variation And Health: New Assessment Approaches Based On Ethnogenetic Layering, Fatimah Linda Collier Jackson
Department of Biology Faculty Publications
Human genetic variation is often biologically relevant, particularly when it influences (or is influenced by) health outcomes. For example, human genetic variation can modulate disease aetiology as in the case ofhomozygous beta sickle gene (βS/βS or sickle cell) pathology. Conversely, health outcomes, such as the frequency and duration of homozygous sickle cell pathology, can change affected group gene frequencies by selectively targeting and culling specific genotypes in a group, such as clinically more severe βS Bantu/βS Bantu versions of the βS gene, thereby changing future patterns of genetic variation in this gene.
Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.
Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.
Mathematics & Statistics Faculty Publications
Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.
Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …
Demographic Estimates From Y Chromosome Microsatellite Polymorphisms: Analysis Of A Worldwide Sample, J. Michael Macpherson, Sohini Ramachandran, Lisa Diamond, Marcus W. Feldman
Demographic Estimates From Y Chromosome Microsatellite Polymorphisms: Analysis Of A Worldwide Sample, J. Michael Macpherson, Sohini Ramachandran, Lisa Diamond, Marcus W. Feldman
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions …
A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson
A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson
PCOM Scholarly Works
Transcriptional regulatory cascades during epicardial and coronary vascular development from proepicardial progenitor cells remain to be defined. We have used immunohistochemistry of human embryonic tissues to demonstrate that the TBX5 transcription factor is expressed not only in the myocardium, but also throughout the embryonic epicardium and coronary vasculature. TBX5 is not expressed in other human fetal vascular beds. Furthermore, immunohistochemical analyses of human embryonic tissues reveals that unlike their epicardial counterparts, delaminating epicardial-derived cells do not express TBX5 as they migrate through the subepicardium before undergoing epithelial-mesenchymal transformation required for coronary vasculogenesis. In the chick, Tbx5 is expressed in the …
Cd46-Mediated Transduction Of A Species D Adenovirus Vaccine Improves Mucosal Vaccine Efficacy, Zenaido T. Camacho, Mallory A. Turner, Michael A. Barry, Eric A. Weaver
Cd46-Mediated Transduction Of A Species D Adenovirus Vaccine Improves Mucosal Vaccine Efficacy, Zenaido T. Camacho, Mallory A. Turner, Michael A. Barry, Eric A. Weaver
Nebraska Center for Virology: Faculty Publications
The high levels of preexisting immunity against Adenovirus type 5 (Ad5) have deemed Ad5 unusable for translation as a human vaccine vector. Low seroprevalent alternative viral vectors may be less impacted by preexisting immunity, but they may also have significantly different phenotypes from that of Ad5. In this study we compare species D Ads (26, 28, and 48) to the species C Ad5. In vitro transduction studies show striking differences between the species C and D viruses. Most notably, Ad26 transduced human dendritic cells much more effectively than Ad5. In vivo imaging studies showed strikingly different transgene expression profiles. The …
Phylogenetic Analyses Of Texas Isolates Indicate An Evolving Subtype Of The Clade B Feline Immunodeficiency Viruses, Eric A. Weaver, Ellen W. Collisson, Margaret Slater, Guan Zhu
Phylogenetic Analyses Of Texas Isolates Indicate An Evolving Subtype Of The Clade B Feline Immunodeficiency Viruses, Eric A. Weaver, Ellen W. Collisson, Margaret Slater, Guan Zhu
Nebraska Center for Virology: Faculty Publications
Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.
Detection Of Five Common Cftr Mutations By Rapid-Cycle Real Time Amplification Refractory Mutation System Pcr., Eugene Dempsey, David Barton, Fergus Ryan
Detection Of Five Common Cftr Mutations By Rapid-Cycle Real Time Amplification Refractory Mutation System Pcr., Eugene Dempsey, David Barton, Fergus Ryan
Articles
No abstract provided.