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Search Results: 1 - 10 of 2025 matches for " Geoffrey Siwo "
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Viral Organization of Human Proteins
Stefan Wuchty,Geoffrey Siwo,Michael T. Ferdig
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011796
Abstract: Although maps of intracellular interactions are increasingly well characterized, little is known about large-scale maps of host-pathogen protein interactions. The investigation of host-pathogen interactions can reveal features of pathogenesis and provide a foundation for the development of drugs and disease prevention strategies. A compilation of experimentally verified interactions between HIV-1 and human proteins and a set of HIV-dependency factors (HDF) allowed insights into the topology and intricate interplay between viral and host proteins on a large scale. We found that targeted and HDF proteins appear predominantly in rich-clubs, groups of human proteins that are strongly intertwined among each other. These assemblies of proteins may serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. Particular transcription factors and protein kinases facilitate indirect interactions between HDFs and viral proteins. Discerning the entanglement of directly targeted and indirectly interacting proteins may uncover molecular and functional sites that can provide novel perspectives on the progression of HIV infection and highlight new avenues to fight this virus.
A statistical approach to finding overlooked genetic associations
Andrew K Rider, Geoffrey Siwo, Nitesh V Chawla, Michael Ferdig, Scott J Emrich
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-526
Abstract: We propose an alternative method to identify eQTLs that builds on traditional approaches. In contrast to genome-wide techniques, our method determines the significance of an association between an expression trait and a locus with respect to the set of all associations to the expression trait. The use of this specific information facilitates identification of expression traits that have an expression profile that is characterized by a single exceptional association to a locus.Our approach identifies expression traits that have exceptional associations regardless of the genome-wide significance of those associations. This property facilitates the identification of possible false negatives for genome-wide significance. Further, our approach has the property of prioritizing expression traits that are affected by few strong associations. Expression traits identified by this method may warrant additional study because their expression level may be affected by targeting genes near a single locus.We demonstrate our method by identifying eQTL hotspots in Plasmodium falciparum (malaria) and Saccharomyces cerevisiae (yeast). We demonstrate the prioritization of traits with few strong genetic effects through Gene Ontology (GO) analysis of Yeast. Our results are strongly consistent with results gathered using genome-wide methods and identify additional hotspots and eQTLs.New eQTLs and hotspots found with this method may represent regions of the genome or biological processes that are controlled through few relatively strong genetic interactions. These points of interest warrant experimental investigation.eQTL studies use gene expression data and genetic variation between individuals to calculate the association between expression traits and genotypes. In the context of eQTL studies an 'expression trait' refers to the quantity of labeled (c)DNA hybridizing to a single probe on a microarray. An eQTL is a strong association between one locus in the genome and one expression trait.
Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum
Heather B Reilly Ayala, Mark A Wacker, Geoffrey Siwo, Michael T Ferdig
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-577
Abstract: Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle.We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c), a Zinc finger transcription factor (PFL0465c) both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c).Malaria is one of the deadliest infectious diseases in the world with the most lethal form, Plasmodium falciparum, infecting more than 500 million people each year, two to three million of whom die [1]. The characteristic malarial fevers occur in multiples of 24 hr due to synchronous parasite development and proliferation in the host's red blood cells (RBC), corresponding to cell lysis and massive liberation of new parasites and toxins into the host's bloodstream [2,3]. Clinical studies in South east Asia have demonstrated that parasite lines which proliferate at an increased rate in RBC are more virulent than those with low multiplication rates,
Ten Simple Rules for Organizing a Virtual Conference—Anywhere
Nelson N. Gichora,Segun A. Fatumo,Mtakai V. Ngara,Noura Chelbat,Kavisha Ramdayal,Kenneth B. Opap,Geoffrey H. Siwo,Marion O. Adebiyi,Amina El Gonnouni,Denis Zofou,Amal A. M. Maurady,Ezekiel F. Adebiyi,Etienne P. de Villiers,Daniel K. Masiga,Jeffrey W. Bizzaro,Prashanth Suravajhala,Sheila C. Ommeh ,Winston Hide
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000650
Matrices That Commute with Their Conjugate and Transpose  [PDF]
Geoffrey Goodson
Advances in Linear Algebra & Matrix Theory (ALAMT) , 2013, DOI: 10.4236/alamt.2013.33005

It is known that if A∈Mn is normal (AA*=A*A) , then AA ̄=A ̄A if and only if AAT=ATA. This leads to the question: do both AA ̄=A ̄A and AAT=ATA imply that A is normal? We give an example to show that this is false when n=4, but we show that it is true when n=2 and n=3.

Groups Having Elements Conjugate to Their Squares and Connections with Dynamical Systems  [PDF]
Geoffrey R. Goodson
Applied Mathematics (AM) , 2010, DOI: 10.4236/am.2010.15055
Abstract: In recent years, dynamical systems which are conjugate to their squares have been studied in ergodic theory. In this paper we study the consequences of groups having elements which are conjugate to their squares and consider examples arising from topological dynamics and more general dynamical systems
Pharmacological Adjuvants to Limit Erythropoietin Stimulating Agents Exposure  [PDF]
Iqbal Masood, Geoffrey Teehan
Open Journal of Nephrology (OJNeph) , 2012, DOI: 10.4236/ojneph.2012.24015
Abstract: Anemia in chronic kidney disease (CKD) is common, causing morbidity and mortality, and is primarily due to reduced erythropoietin (EPO) release and, to a lesser degree, shortened red cell survival. Erythropoietin Stimulating Agents like epoetin Alfa and darbepoetin alpha are used commonly to treat this form of anemia. Recent evidence suggests increased morbidity and mortality associated with higher hemoglobin in the setting of these agents use. Whether these complications are due to higher dose of erythropoietin or its resistance (i.e. inflammation), or achieving a higher hemoglobin remains unclear. Tightening restrictions on these agents has led to increase interest in the use of non-ESA adjuvants to improve erythropoiesis. This review will highlight the most promising of these agents.
A Case of Type I Hepatorenal Syndrome Treated with Vasopressin  [PDF]
Laura Connor, Geoffrey Teehan
Open Journal of Nephrology (OJNeph) , 2013, DOI: 10.4236/ojneph.2013.33025

Hepatorenal syndrome (HRS) is a grave complication of end-stage liver disease and is associated with a very high mortality. This case report described a 42-year-old female with advanced alcohol-induced cirrhosis who developed HRS that was initially treated with Midodrine and Octreotide but renal function continued to deteriorate. Vasopressin therapy was added and HRS was successfully reversed. There are few data available on the use of vasopressin for HRS and this case supports its use in treatment of HRS, particularly in countries where the more widely studied Terlipressin is unavailable. This case also demonstrates that a patient failing one medical therapy for HRS may respond to an alternative or adjunctive therapy. Therefore, this should be attempted to increase the patient’s chance of survival.

Forensic odontostomatology  [PDF]
Geoffrey H. Sperber
Forensic Medicine and Anatomy Research (FMAR) , 2013, DOI: 10.4236/fmar.2013.14019
Abstract: Teeth are the most durable and enduring structures of human anatomy, surviving fragmentation, partial incineration and severe decomposition. The role of teeth in identification is manifested as significant specifiers of deceased or living individuals. The characteristics of dentalmorphology are genetically-inherited and ascribable to racial or familial ancestry. Dental age identification is attributable to young individuals. The chemical composition of teeth identifies diets during life, as attritional wear patterns do. Bite marks transiently relate to the perpetrator of attacks. Dental restorations and prostheses are evidence of economic, cultural and social status of deceased individuals. Palatal rugae patterns are unique to individuals. The DNA identification of postmortem dental pulp tissue relating to a deceased individual or a living relative is the ultimate criterion of positive association of forensic recognition, as other means of identification become less effective, forensic dental identification increases in importance.
Letter to the Editor  [PDF]
Geoffrey H. Sperber
Forensic Medicine and Anatomy Research (FMAR) , 2013, DOI: 10.4236/fmar.2013.14012
Abstract: Letter to the Editor; Forensic Medicine and Anatomy Research
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