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	g=new Ch(head++);
		g.dl='';g.tit = "Viral Host Specific Evolution: A Case of the Honeybee Virus";
		g.author="Panuwan Chantawannakul and Robert W Cutler";
		g.year = "2009";g.ab="The interactions between a host and parasite are one phenomena which can be observed at the genetic level. Specifically, in host parasite system there are evolutionary forces which act at synonymous codon positions. In our study, we demonstrate that host specific viral genomes can optimize codon usage to successfully parasitize their preferred host. The codon usage co-evolution of host specific honeybee viruses towards the codon usage of the honeybee described in this chapter is evidence for codon usage correlation between an insect host and a single stranded RNA virus. Similar relationships have also been reported in other group of viruses. Such mechanisms could well-explain the host specificity of some virus families and their specificity of disease transmission.";
		g.journal="Nova Press. Chapter: Host-Pathogen Interactions: Genetics, Immunology and Physiology";
		g.page="in press.";
	JOURSUB[JOURSUB.length++]=g;

	
	
	g=new Ch(head++);
		g.dl='';g.tit = "Prediction of the Disulfide Bonding State of Cysteines in Proteins Using Conditional Random Fields Method";
		g.author="Watshara Shoombuatong, Piyarat Nimmanpipug, Pattrinee Traisathit, Sukon Prasitwattanaseree, Chatchai Tayapiwatana, Robert Cutler, and Jeerayut Chaijaruwanich";
		g.year = "2009";g.ab="The formation of disulfide bonding between cysteines plays a major role in protein folding, structure, function, and evolution which conveys important information about protein conformation and folding. There have been a number of studies in the prediction of disulfide bond state of cysteines from protein sequences using computational approaches. Previously proposed methods for predicting the cysteine-bonding state in proteins have used local context and global protein descriptors. In our work, we have developed a novel method based on conditional random fields to predict the disulfide bonding state from protein primary sequence, secondary structures, and relative solvent accessibilities. Our experimental results achieve a simultaneous overall prediction accuracy, precision, and recall as high as 92.6 %, 93%, and 94.5 %, respectively using a dataset of 1,018 proteins containing 9,662 cysteines.";
		g.journal="The 13<sup>th</sup> Pacific-Asia Conference on Knowledge Discovery and Data Mining";g.page="";
	JOURSUB[JOURSUB.length++]=g;

	

		
	var JOURS = new Array();JOURS.length=0;var head=1;	
	g=new Ch(head++);g.dl='';g.tit = "Ion-beam-induced gene transfer in <i>Saccharomyces cerevisiae</i>";g.author="S. Anuntalabhochai, R. Chandej, M. Sanguansermsri, S. Ladpala, R.W. Cutler and T. Vilaithong";g.year = "2009";g.ab="In this paper we present a novel method to induce gene transfer in yeast (<i>Saccharomyces cerevisiae</i>) using a low-energy ion beam. By accelerating nitrogen ions to the 50-60 keV energy range with ions fluences of 1-100 x 10<sup>15</sup> ions/cm<sup>2</sup>, yeast cells were bombarded to characterize the decrease in survival with increasing energy level. Using bombardment conditions optimized for yeast cell survival (50 keV with ion fluences of 1 and 2 x 10<sup>15</sup> ions/cm<sup>2</sup>), a compatible plasmid vector (pYES2) was successfully introduced into the yeast cell with higher concentrations of the plasmid providing improved plasmid transfer. To investigate expression of exotic genes in yeast, two marker genes - <i>GFP</i> and <i>lipoic acid synthetase</i> from <i>Bacillus licheniformis</i> - were chosen to subclone into pYES2 (designed pYGFP and pYlip respectively), and subsequently transformed into the cells. After 10 hours of induction, the expression levels of these genes were analyzed. The pYGFP transformed yeast exhibited a high intensity of <i>GFP</i> protein in the yeast cells and the pYLip showed the expected additional protein-band at 34 kDa detected by SDS-polyacrylamide gel electrophoresis. As a method to transform yeast, low-energy ion beam bombardment is both highly efficient and since yeast can be transformed in less than ten minutes, much more rapid than other yeast transformation methods.";g.journal="Surface and Coatings Technology 203";g.page="2521-2524";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2008)_Hypomethylation_ajas62361-367';g.tit = "Detection of DNA Hypomethylation Mediated Floral Induction in Longan and Spinach Using the HAT-RAPD Technique";g.author="Anuntalabhochai, S., Chundet, R., Buapong, N. and Cutler, R.W.";g.year = "2009";g.ab="In this study, the HAT-RAPD technique was used to detect DNA methylation in the four plant species, rice (<i>Oryza sativa</i>), petunia (<i>Petunia hybrida</i>), spinach (<i>Spinacea oleracea L.</i>) and longan (<i>Dimocarpus longan </i>Lour.), which were induced using 5-azacytidine, potassium chlorate (KClO<sub>3</sub>) and a low temperature stress. Rice and petunia were chosen to be induced because in these species it is known that 5-azacytidine is able to reduce methylation levels in their genomes leading to morphological changes, in particular floral induction, in the developing plants. Using the RAPD technique, DNA methylation was detected using the restriction enzymes <i>Hpa</i>II and <i>Msp</i>I in rice and petunia (as expected), and in spinach, but was found to be absent in Longan., which suggests that floral induction in longan is induced by a different non-methylation dependent pathway.";g.journal="American Journal of Applied Sciences 6(2)";g.page="361-367";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='';g.tit = "Synonymous codon usage bias dependent on local nucleotide context in the class <i>Deinococci</i>";g.author="Robert W. Cutler and Panuwan Chantawannakul";g.year = "2008";g.ab="To study the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patterns in the <i>Deinococcus radiodurans</i>, <i>D. geothermalis</i>, and <i>Thermus thermophilus</i> genomes for nucleotide replacement dependent on the surrounding nucleotide context. Nucleotides on the third codon site were found to be strongly correlated with nucleotide sites at most six nucleotides away in all three species, where abundance patterns were dependent on whether two nucleotides share the same purine(R)/pyrimidine(Y) status. In the class <i>Deinococci</i> adjacent third site nucleotides were strongly correlated, where NNR|NNR and NNY|NNY codon pairs were over abundant while NNR|NNY and NNY|NNR codon pairs were underabundant. By far the largest deviations in all three species occur for NN(YR)|(YR)NN codon pairs. In the <i>Thermus</i> species, the NNY|YNN and NNR|RNN codon pairs were overabundant versus the underabundant NNY|RNN and NNR|YNN codon pairs, whereas in the <i>Deinococcus</i> species the opposite over/under-abundance relationship held for adjacent (GC) bases. We also observed a weaker overabundance of NNR|NRN and NNY|NYN codon pairs versus the underabundant NNR|NYN and NNY|NRN codon pairs. The perfect purine/pyrimidine symmetry of each of these cases, plus the lack of significant deviations for nucleotide pairs on other length scales up to 20 codons apart demonstrates that a pervasive pattern of nucleotide replacement dependent on local nucleotide context, and not codon bias, has occurred in these species. This nucleotide replacement has lead to modified synonymous codon usage within the class <i>Deinococci</i> that affects which codons are positioned at particular codon sites dependent on the local nucleotide context.";g.journal="Journal of Molecular Evolution";g.page="in press.";JOURS[JOURS.length++]=g;
    g=new Ch(head++);g.dl='(2008)_Ficus_TOAJ';g.tit = "Phylogenetic Diversity of <i>Ficus</i> Species Using HAT-RAPD Markers as a Measure of Genomic Polymorphism";g.author="Anuntalabhochai S, Phromthep W, Sitthiphrom S, Chundet R and Cutler RW";g.year = "2008";g.ab="To create a molecular marker characterization for twenty species of <i>Ficus</i>, eight decamer primers were used to randomly amplify these species genomic DNA producing a total of 172 distinct polymorphic band patterns. One band was chosen to be converted into the more robust sequence characterized amplified region (SCAR) marker format to provide a unique molecular marker characterization for the variety of <i>Ficus</i> hirta. This technique for species identification and characterization provides a morphologically independent test to verify relatedness and provide species information particularly for cases where such identification was previously untenable such as in the case of morphologically indistinguishable plant cuttings.";g.journal="The Open Agriculture Journal, 2";g.page="62-67";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2008)_hotspring_SciAsia_0707-875';g.tit = "Morphological and Phylogenic Diversity of Cyanobacterial Populations in Six Hot Springs of Thailand";g.author="Udomluk Sompong, Richard W. Castenholz, Robert W. Cutler, Somboon Anuntalabhochai, and Yuwadee Peerapornpisal";g.year = "2008";g.ab="To characterize the phylogenetic and morphological diversity of Cyanobacteria in Thailand, Cyanobacteria were collected from mats in six hot springs with water temperatures ranging from 40 to 75&#176;C. Samples were collected for culture isolation, microscopic morphological examination and molecular analysis of the 16S rRNA sequence to establish the levels of morphological versus genomic diversity. Fourteen cyanobacterial morphotypes were investigated using microscopy with the dominant species of cyanobacteria being Synechococcus spp., Phormidium cf. boryanum and Leptolyngbya spp.. A total of 20  distinct isolates of cyanobacteria were grown in culture medium, and an additional 79 samples were examined using denaturing gradient gel electrophoresis and DNA sequence analysis to establish phylogenetic relationships. The observed decrease in morphological diversity with increasing water temperature was found to be compensated for by an increase in molecular sequence diversity of the morphologically indistinguishable cyanobacterial species. Molecular clines were found to span both temperature and geophysical boundaries for samples from the Northern and Southern Thailand regions.";g.journal="Science Asia 34";g.page="153-162";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2008)_viralhoneybee_JIP';g.tit = "Convergent host-parasite codon usage between honey bee and bee associated viral genomes";g.author="Panuwan Chantawannakul and Robert W. Cutler";g.year = "2008";g.ab="By correlating the codon usage in four insects (the honey bee, red flour beetle, mosquito and fruit fly) with six honey bee host specific viruses, we found that the codon usage patterns of the bee viruses were strongly related to that of the honey bee and only weakly related to the red flour beetle. The insects shared varying degrees of codon usage similarity which roughly follow the known phylogenetic relatedness.  All of the codon usage similarity can be described by relatedness-by-descent except for the high codon usage similarity between the honey bee and honey bee associated viruses. This evidence for the convergent evolution of the honey bee viruses toward the codon usage of the honey bee suggests that small host specific viral genomes have the freedom to quickly optimize codon usage to successfully parasitize their preferred host. The codon usage coevolution of the six host specific honey bee viruses towards the codon usage of the honey bee described in this paper is the first evidence for codon usage correlation between an insect host and a single stranded RNA virus.";g.journal="Journal of Invertebrate Pathology, 98(2)";g.page="206-210";JOURS[JOURS.length++]=g;	
	g=new Ch(head++);g.dl='';g.tit="The Effect of Local Nucleotides on Synonymous Codon Usage in the Honeybee (<i>Apis mellifera</i> L.) Genome";g.author="Robert W. Cutler and Panuwan Chantawannakul";g.year = "2007";g.ab="Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine - <i>A</i> or thyamine - <i>T</i>) versus strong (guanine - <i>G</i> or cytosine - <i>C</i>) status, to nucleotides on the first codon site which are dependent on their purine (<i>A/G</i>) versus pyrimidine (<i>C/T</i>) status. In particular, for adjacent 3<sup>rd</sup> and 1<sup>st</sup> site nucleotides, weak/pyrimidine and strong/purine nucleotide combinations occur much more frequently than the under-abundant weak/purine and strong/pyrimidine nucleotide combinations. Since a similar effect is also found in the non-coding regions, but is present for all adjacent nucleotides, this coding effect is most likely due to a genome wide context dependent mutation error correcting mechanism in combination with selective constraints on adjacent 1<sup>st</sup> and 2<sup>nd</sup> nucleotide pairs within codons. The position dependent relationship of synonymous codon usage is evidence for a novel form of codon position bias which utilizes the redundancy in the genetic code to minimize the effect of nucleotide mutations within coding regions.";g.page="637-645";g.journal="Journal of Molecular Evolution 64(6)";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2007)_Antrhracnose_AJAB';g.tit="Control of Anthracnose caused by <i>Colletotrichum musae</i> on <i>Curcuma alismatifolia</i> Gagnep. using Antagonistic <i>Bacillus</i> spp.";g.author="Supuk Mahadtanapuk, Mondhon Sanguansermsri, Robert W. Cutler, Vicha Sardsud and Somboon Anuntalabhochai";g.year = "2007";g.ab="Over 400 bacterial strains, isolated from leaf surfaces of <i>Curcuma alismatifolia</i> Gagnep. and hot springs in the Chiang Mai province of northern Thailand, were screened <i>in vitro</i> for antagonistic activity against <i>Colletotrichum musae</i>, an anthracnose fungus. Three isolates provided greater than 75% growth inhibition of the fungus <i>in vitro</i> and were identified as <i>Bacillus licheniformis, B. amyloliquefaciens</i> and <i>B. subtilis</i>. Using in planta tests, <i>B. amyloliquefaciens</i> and <i>B. subtilis</i> were shown to efficiently colonize the curcuma bracts, provide a statistically significant growth suppression of <i>C. musae</i> over that of <i>B. licheniformis</i>, and all three isolates could provide 100% inhibition of conidial fungal germination. When <i>B. licheniformis</i> was co-inoculated in combination with either of the other two bacteria, the ability of <i>B. amyloliquefaciens</i> and <i>B. subtilis</i> to suppress the fungal disease was dramatically reduced. Both <i>B. amyloliquefaciens</i> and <i>B. subtilis</i> were found to contain an isoform of iturin A with antifungal activity against <i>C. musae</i>. As a preventative measure to control the spread of <i>C. musae</i> and reduce the severity of fungal infections, <i>B. amyloliquefaciens</i> could be used to inoculate curcuma flowers cost effectively and reduce the need for the toxic synthetic fungicides currently in use.";g.journal="American Journal of Agricultural and Biological Sciences 2(2)";g.page="54-61";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2007)_Hybrid_Detection_Lychee_ScienceAsia';g.tit="Hybrid detection in lychee (Litchee chinensis Sonn.) cultivars using HAT-RAPD markers";g.author="Ruttaporn Chundet, Robert W. Cutler, and Somboon Anuntalabhochai";g.year = "2007";g.ab="In this paper we present a method to detect hybrids obtained from open-pollinated seeds in lychee cultivars (Litchi chinensis Sonn.) using the high annealing temperature random amplified polymorphic DNA (HAT-RAPD) methodology. A series of 10 arbitrary random primers were used to amplify polymorphic bands ranging from 200 to 2,300 bp. These bands were tracked from parent to hybrid offspring for crosses of four economically important varieties (Chacrapat, KimJeng, Hong Huey and O-Hia) of interest and both gender and variety specific band transmission rates were assessed. Respective of lychee variety, all hybrids showed a significant loss of parental bands with the largest losses occurring between male parent and offspring. Variety specific bands were characterized for each lychee variety and hybrid band transmission rates were determined such that hybrids could be detected to any level of desired significance given enough initial banding data. This molecular marker technique provides a clear and compelling way to ascertain hybrid status of new plants without having to wait for six to seven year for the plants to mature. As such it should provide a powerful tool to lychee breeders in the propagation of current lychee varieties and allow the tracking of polymorphisms between hybrids to determine possible genomic regions responsible for the transmission of high quality fruit.";g.page=" 307-311";g.journal="Science Asia 33";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2007)_Mutation_Blichen';g.tit="Mutation of <i>Bacillus licheniformis</i> using low-energy ion beam bombardment";g.author="S. Mahadtanapuk, R. Cutler, L.D. Yu, T. Vilaithong and S. Anuntalabhochai";g.year = "2007";g.ab="Anthracnose, caused by the fungus <i>Colletotrichum</i> sp., is an important disease affecting a wide range of flowers.  To control this fungus various methods including the use of natural antagonists have been used for biological control. In this study, <i>Bacillus licheniformis</i>, isolated from hot springs in the Chiang Mai province, was shown to suppress conidia germination of the fungus and reduce symptoms caused by the disease <i>in planta</i>. To induce mutations in <i>B. licheniformis</i>, a low energy ion beam was applied to the bacteria using N-ions to bombard the bacteria under  vacuum conditions at an energy of 28-50 keV with a fluence range of 1-10 x 10<sup>15</sup> ions/cm<sup>2</sup>.  After this treatment, one mutant was found which had lost its antagonistic property. To try to characterize this mutation, the HAT-RAPD technique was used to produce band patterns for both the bombarded bacteria and the original wild type. From these polymorphic band patterns, differences were found which were induced by the ion beam. These polymorphism bands were subcloned into a pGEM-T vector and sequenced.  One band fragment conserved in the wild type and lost in the mutant bacteria was found to code for the lipase gene.  Further research will focus on other genes and gene functions which may be involved in the observed antipathogenicity.";g.page = "doi:10.1016/j.surfcoat.2006.08.148";g.journal="Surface & Coatings Technology";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2007)_CurcumaHyrbidDetection_HORTI';g.tit="Hybrid detection and characterization of <i>Curcuma</i> spp. using sequence characterized DNA markers";g.author="Somboon Anuntalabhochai, Supranee Sitthiphrom, Wipada Thongtaksin, Mondhon Sanguansermsri and Robert W. Cutler, PhD";g.year = "2007";g.ab="The tropical flower Curcuma alismatifolia of the family Zingiberaceae is widely valued as a cut flower and potted plant due to its range of vibrant colors and large long-lasting inflorescences. Much of this diversity has been cultivated through extensive hybridization of wild varieties since hybrids often exhibit dramatic phenotypic differences from the parents. This phenotypic diversity though has led to difficulties identifying and classifying the relatedness of Curcuma varieties particularly between hybrids. To overcome these difficulties we characterized a molecular marker which can distinguish \"Patumma\" varieties and hybrids formed with crosses of this variety. Patumma is one of the founding Curcuma varieties from which many hybrid crosses and induced mutation varieties were developed. Using a set of eleven unique decamer primers, polymorphic bands ranging from 100 to 2,900 base pairs were used to examine twenty Curcuma varieties from which banding patterns of interest were selected for conversion to the more reproducible and robust sequence characterized amplified region (SCAR) markers. In particular, one SCAR marker amplified a region 600 bp in length which was conserved in all Patumma varieties and hybrids and as an independent test did not amplify an additional series of twenty four distinct Curcuma varieties. Since new varieties of Curcuma are often dissimilar from their progenitors, this genomic analysis allows a cost-effective morphologically independent characterization of Curcuma hybrids.";g.page="389-393";g.journal="Scientia Horticulturae, 111";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2007)_LongonTemperature_JAC';g.tit="Development of sequence characterized DNA markers linked to a temperature insensitivity for fruit production in Longan (<i>Dimocarpus longan</i> Lour.) cultivars";g.author="Cutler, R.W., Sitthiphrom, S., Marha, J., and Anuntalabhochai S.";g.year = "2007";g.ab="In this paper we characterize a temperature dependence in longan (Dimocarpus longan Lour.) cultivars using the high annealing temperature random amplified polymorphic DNA (HAT-RAPD) methodology. This form of genomic analysis allows a random sampling of the complete genome to provide information about phenotypic traits of interest. Using a set of eighteen unique decamer primers, polymorphic bands ranging from 100 to 2,500 base pairs were examined for fourteen longan varieties from which banding patterns of interest were selected for conversion to the more reproducible and robust sequence characterized amplified region (SCAR) markers. In particular, one SCAR marker produced an electrophoresis banding pattern which could distinguish between longan varieties requiring a sustained interval at low temperatures for fruit production versus those that do not. When sequenced, the initial 90 nucleotides of this band were >85% identical to the 12-oxophytodienoic acid (OPDA) reductase gene. OPDA is an immediate precursor to Jasmonic acid which has been described as the \"master switch\" for lipid-derived environmental signaling to factors such as flowering and osmotic stress. Both water deficit and cold acclimation use the same Jamonic acid mediated signaling mechanism which could explain the recent success of potassium chlorate to induce off-season flowering and fruit formation.";g.page="74-78";g.journal="Agronomy and Crop Science, 193";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2006)_LycheeTemperature';g.tit="Development of sequence characterized DNA markers linked to a temperature dependence for flower induction in lychee (<i>Litchi chinensis </i>Sonn.) cultivars";g.author="Cutler, R.W., Chundet R, Handa T, and Anuntalabhochai S";g.ab="In this paper, we present a method to find DNA markers for traits of interest in lychee cultivars (Litchi chinensis Sonn.) using high annealing temperature random amplified polymorphic DNA (HAT-RAPD) as an initial screening method. Using 5 arbitrary random primers, a wide range of polymorphic bands ranging from 200 to 5200 bp were produced. Bands of interest were then selected for sequencing and conversion to the more reproducible and robust sequence characterized amplified region (SCAR) markers. Specifically, SCAR markers were found that distinguished lychee varieties requiring a sustained interval at low temperatures for flower induction versus those varieties that do not require such an environment, and another SCAR marker was found that amplified only the economically important Kom cultivar. These sequences shared similarity to known transposons suggesting a mechanism by which the temperature insensitivity may have initially developed.";g.year = "2006";g.page="264-270";g.journal="Scientia Horticulturae, 107";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='';g.tit="A Model for Creative Undergraduate Bioinformatics Research Within the Liberal Arts Biology Curriculum";g.author="Robert W. Cutler";g.ab="Due to the recent advances in sequencing technology and the corresponding increase in the availability of genomic data, the field of bioinformatics has become an area of critical importance. This field is also an area that can play to the strengths of a liberal arts education because it requires a breadth of skills and ability for critical thinking. With that said, there are real challenges to implementing a bioinformatics program within the framework of a liberal arts college - mainly time constraints due to these same interdisciplinary requirements. In this article I describe a model in which creative undergraduate research can be implemented within the constraints of a liberal arts biology curriculum.";g.year = "2005";g.page="1-5";g.journal="Transformations, 2:2";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2005)_SciAsiaDatabase';g.tit="DNA Fingerprint Database of Some Economically Important Thai Plants: Litchi chinensis Sonn, Dimocarpus longan Lour, and Peuraria spp.";g.page="145-149";g.journal="ScienceAsia, 31";g.ab="The high annealing temperature random amplified polymorphic DNA (HAT-RAPD) method can be used to generate highly polymorphic data from PCR amplification of DNA samples to determine relatedness in plant cultivars. Using the HAT-RAPD method, we created a fingerprint database of tropical plants for fourteen subspecies of Dimocarpus longan Lour., twelve subspecies of Litchi chinensis Sonn., and seven distinct varieties of the genus Peuraria, two of which were previously uncharacterized. Out of a total of 22 distinct primer sets, a subset of primers with reproducible DNA band patterns was characterized for each species. From this data, we developed a web-accessible database which both graphically and quantitatively depicts the existent bands and species phylogenies using character state data generated from the banding patterns. Using historical and geographic data for these plant species and subspecies, the generated phylogenies support the currently accepted species relationships for D. longan and L. chinensis and characterize the unidentified varieties of Peuraria. The HAT-RAPD experimental method combined with band pattern recognition is a cost effective and easily characterized methodology that can be used to identify plant varieties, as well as to advance the knowledge of biodiversity in previously uncharacterized species.";g.author="Rungrach Wangspa, Robert W. Cutler, Supranee Sitthiprom, Ruttaporn Chundet, Nadtaya Dumampai, and Somboon Anuntalabhochai";g.year = "2005";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2004)_ApisExon';g.tit="A Genomic-wide analysis of Apis mellifera: Insights into diverse high copy number ORFs";g.page="172-175";g.journal="Journal of Apicultural Research, 43:4";g.ab="This paper develops a frequency-based analysis of every open reading frame (ORF) in the honey bee (Apis mellifera) genome using a set of PERL algorithms which were developed to identify novel exonic regions. Using the actual amino acid abundances for these regions, this ORF profiles approach found a background Poisson distribution of randomly arranged regions. On top of this background, significant overabundances of small ORF regions greater than 16 amino acids were found. Some of these regions share similarity to known sequences such as the ribosomal proteins, but several families of these regions shared no similarity to any other nucleotide or amino acid sequence. This frequency analysis was developed to search for the odorant binding proteins which are expected to occur with a high copy number yet share little sequence similarity to any other known sequence.";g.author="Supriya Munshaw, Robert W. Cutler, Siriwatwongsiri and Panuwan Chantawannakul";g.year = "2004";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='';g.tit="Cartesian Product and Edge Domination";g.page="129-133";g.journal="Ars. Combinatoria, 70";g.ab="A set of edges D in a graph G is a dominating set of edges if every edge not in D is adjacent to at least one edge in D. The minimum cardinality of an edge dominating set of G is the edge domination number of G, denoted D<sub>E</sub>(G). In this paper we investigate the edge domination number for the cartesian product of an n-colorable graph G and the complete graph Kn.";g.author="Robert W. Cutler, III and Mark D. Halsey";g.year = "2004";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='';g.tit="Edge Domination Critical Graphs";g.page="97-108";g.journal="JCMCC, 41";g.ab="A set of edges D in a graph G is a dominating set of edges if every edge not in D is adjacent to at least one edge in D. The minimum cardinality of an edge dominating set of G is the edge domination number of G, denoted D<sub>E</sub>(G). A graph G is edge domination critical, or EDC, if for any vertex v in G we have D<sub>E</sub>(G-v) = D<sub>E</sub>(G) - 1. Every graph G must have an induced subgraph F such that F is EDC and D<sub>E</sub>(G) = D<sub>E</sub>(F). In this paper we prove that no tree with more than 2 vertices is EDC, develop a forbidden subgraph characterization for the edge domination number of a tree, and we develop a construction that conserves the EDC property.";g.author="Robert W. Cutler, III and Mark D. Halsey";g.year = "2002";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(2000)_Group_G2_JMP';g.tit="A relation between anomaly coefficients and the group G<sub>2</sub>";g.page="2295-2298";g.journal="Journal of Mathematical Physics, 41:4";g.ab="We show that in 4D the anomaly coefficients for SU(3) irreps are equal to the dimensions of G<sub>2L</sub> irreps. This allows the direct calculation of 4D anomalies for any group in terms of the Weyl dimension formula for G<sub>2</sub>. We also give results for 6D and comment on the D > 6 case.";g.author="R.W. Cutler, III and T.W. Kephart";g.year = "2000";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(1999)_2loop';g.tit="The constraints on N=1 supergravities and type I superstrings from 2-loop chiral anomalies";g.page="73-77";g.journal="Physics Letters B, 467";g.ab="N=1 supergravities with SO(2<sup>2n+1</sup>) gauge groups are local chiral anomaly free at 1-loop in D=4n+2 dimensions (n>=0), as are SO(32) type I superstrings in 10D. We show that at 2-loops only D=6 and D=10 theories remain anomaly free, so a generalized Adler-Bardeen theorem continues to hold in these cases when the Green-Schwarz mechanism is used to cancel subleading and mixed anomalies.";g.author="R.W. Cutler, III and T.W. Kephart";g.year = "1999";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(1995)_ncube';g.tit="Edge Domination of G x Q<sub>n</sub>";g.page="69-79";g.journal="Bull. Inst. Combin. Appl., 15";g.ab="An edge dominating set E of a graph G is a subset of the edge set of G such that every edge not in E is adjacent to at least one edge in E. The edge domination number of G is the cardinality of a minimum edge dominating set of G. A lower-bound for the edge domination number of any graph G crossed with the n-dimensional cube Q<sub>n</sub> is found to be 1/3 the number of vertices in G x Q<sub>n</sub>. Several families of graphs with this minimum edge domination number are presented.";g.author="R.W. Cutler, III";g.year = "1995";JOURS[JOURS.length++]=g;
	g=new Ch(head++);g.dl='(1995)_Diffraction';g.tit="Diffraction from reconstructed surfaces with incommensurate domain walls";g.page="258-264";g.journal="Surface Science, 340";g.ab="The kinematic approximation method has shown that the peak intensity and the full width at half maximum (FWHM) of stepped surfaces exhibit an oscillatory behavior for changing incident energy. This paper generalizes the kinematic approximation to an (N x 1) reconstructed surface with a distribution of various types of lateral displacements at a step. A particular solution of this model we call the fixed point solution, yields a clear intuitive understanding of these oscillations as well as an exact solution for the step density of any surface. The specific examples of (5 X 1) and (2 x 1) reconstruction are examined to show the striking differences between the reconstructed surface diffraction patterns. These differences make an examination of the half-maximum (HM) intensity position a powerful tool to determine the surface structure for any incommensurate stepped surface.";g.author="R.W. Cutler, III G.-C. Wang, and T.-M. Lu";g.year = "1995";JOURS[JOURS.length++]=g;


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		f=new Ch(chap++);f.titl = "The Fisherman";f.talk="One of my favorite pastimes is hiking and backpacking. On one 5 day trip I took by myself, I met a homeless man from Louisiana. He was staying in the shelter I had planned to use. After a long day hiking 15+ miles I was beat and couldn't wait to sit down and rest. I was immediately set upon by this schizophrenic man. After listening to his increasingly disjointed and disturbing talk, I got up and hiked another couple of miles away from him. I had the distinct feeling that sleeping under the clear sky was much more comfortable and safer then if I had stayed at that shelter. The 'fisherman' in this mood piece has much in common with my memory of this experience.";f.file = "fishing";g.data[g.data.length++]=f;
		f=new Ch(chap++);f.titl = "Love's Flight";f.talk="Sometimes there's not much to say. This story has to stand on it's own, but one word of warning, it's not a happy story.";f.file = "flight";g.data[g.data.length++]=f;
		f=new Ch(chap++);f.titl = "Eyes";f.talk="During my time as an EMT I worked in several emergency rooms, volunteered in a pediatric cancer ward, was a summer camp medic and did CPR on 5 people. This piece came about due to my reflections on some of these experiences.";f.file = "eyes";g.data[g.data.length++]=f;
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		f=new Ch(chap++);f.talk="";f.titl = "Multiple Personality Disorder";f.file = "MPD";g.data[g.data.length++]=f;
		f=new Ch(chap++);f.talk="";f.titl = "Open Fourm 2: Biotechnology";f.file = "forum2";g.data[g.data.length++]=f;
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	t+='<span class="black2" onclick="PAGE=2;setPage()">Publications</span><br><p>';
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    t+='Since my first trip to Thailand in 2001 and a subsequent Fulbright Fellowship to do research at Chiang Mai University, I have spent a great deal of time first travelling to and now living in Chiang Mai Thailand.<br><P><br>';
    t+='The images which can be reached using the menu to the left are from several of these trips and other places I have travelled. If you click on a thumbnail image, a new window will appear with a larger image.<br><P><br>';
	t+='Feel free to e-mail me at <span class=sub2 onClick="parent.location=\'mailto:cutler121@gmail.com\'\">cutler121@gmail.com</span> if you have any comments or questions about my travels.<br><P><br>';
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function onloadfunction(){}


if (window.addEventListener)		window.addEventListener("load", onloadfunction, false)
else if (window.attachEvent) 		window.attachEvent("onload", onloadfunction)
else if (document.getElementById) 	window.onload=onloadfunction


	textLyr = new layerObject('textLayer','absolute',-150,25,'hidden');


//	setMain();

image1 = new Image();
image1.src = "melow.gif";

image2 = new Image();
image2.src = "mesh.gif";

//	textLyr = new layerObject('textLayer','absolute',-150,25,'visible');
	
function SetDOPICS(){
	var t='<EM><big><span class=title>Images</span></big></em><br><p>';
	
	for (var k=0; k<PICSNAME.length; k++){
		t+='<div class="menutitle" onclick="SwitchMenu('+"'sub"+k+"'"+')"><b>'+PICSNAME[k].titl+'</b></div>';
		t+='<span class="submenu" id="sub'+k+'">';
		for(var j=0;j<PICSNAME[k].name2.length;j++){
			if(PICSNAME[k].num[j] == '0'){
				t+='<div class=sub><b>-</b> '+PICSNAME[k].name2[j]+'</div>';
				var l;
				for(l=0;l<PICSNAME[k].tit[j];l++){
					t+='<div class=sub onclick="FLAGP='+(k+2)+';FLAGP1='+(j+l+1)+';DOPICS()">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'+PICSNAME[k].name2[j+l+1]+'</div>';
				}
				j+=l;
			}
			else{t+='<div class=sub onclick="FLAGP='+(k+2)+';FLAGP1='+(j)+';DOPICS()"><b>-</b> '+PICSNAME[k].name2[j]+'</div>';}
		}
		t+="\n</span>";
	}	

	t+='<br><p><EM><big><span class=u onclick="imgHome();">Home</span></big></em>';
	WriteLayer('textLayer',null,t);
	
}


function SetDOWRITE(){
	var t='<EM><big><span onclick="PictP=0;setPage();" class=t>Writing<br>Samples</span></big></em><br><p><br>';
	var ot=0;
	
	for (var k=0; k<POEM.length; k++){
		t+='<p><span onclick="PictP='+(k+1)+';setPage();" class=red>'+POEM[k].titl+'<br>';
//		t+='<p><span onclick="DOSTORY('+(k+1)+');" class=red>'+POEM[k].titl+'<br>'+(k+1);
			
	}

	t+='<br><p><EM><big><span class=u onclick="imgHome();">Home</span></big></em>';
	WriteLayer('textLayer',null,t);
	
	
	
}




function DOSTORY(PP){
	
	//	f.titl = "";f.file = "";f.date = "";g.data[g.data.length++]=f;

	PictP = PP;
	
	var i=2;
	var wid=page_width-340;
	if(wid>500){wid=500;}
	var t='<div id=pubsto valign=center align=center style="height:'+(page_height-120)+';width:'+(page_width-340)+';border:0;overflow:auto;padding:0;margin:0;valign:center;"><img src=invis.gif height=25 width=25>';
	if(PictP == 0){
		t+='<table border=0 cellpadding=0 cellspacing=0 width='+wid+'><tr><td valign=center align=center>';
	
		t+='<br><p></p><span class="red" onclick="PAGE=3;setPage();">Main Writing Page</span><br><p>';


		t+='<span class="black">All of the documents in this area are stored as<br>Adobe PDF files.  <br><p>';


		t+='If a PDF viewer is not installed on your machine, the following link will take you to the main Adobe page where you can get a free copy of the Adobe Acrobat Viewer.<br></p><p></p><center><a href="http://www.adobe.com/products/acrobat/readstep.html" _base_target="main"><img src="getacro.gif" _base_target="main"></a></center><br><p> Feel free to e-mail me at <span class=sub2 onClick="parent.location=\'mailto:cutler121@gmail.com\'\">cutler121@gmail.com</span> if you have any comments or questions about my work.</p></span>	';
		t+='</td></tr></table>';
	
	}
	else{
		k=PictP-1;

		t+='<table border=0 valign=center cellpadding=0 cellspacing=0 height='+(page_height-150)+' width='+wid+'><tr><td ';
		if(POEM[k].left.match(/1/)){t+='align=left';}else{t+='align=center';}
		t+='><span class="tred">'+POEM[k].titl+'</span><br><p>';

		for (var j=0; j<POEM[k].data.length; j++){
			if(POEM[k].left.match(/1/)){t+='<u>';}
			t+='<br><p><span onclick="window.open(\'writing/'+POEM[k].data[j].file+'.pdf\',\'_blank\')" target="_blank" class=black>'+POEM[k].data[j].titl;
			if(POEM[k].left.match(/1/)){t+='</u>'+POEM[k].data[j].talk;}
			t+='</span>';
		}
//		if(POEM[k].left.match(/1/)){
		t+='</td></tr></table>';//}
		
	}

	t+='</div>';	
//	var t= 'HELLO';
	WriteLayer('middle',null,t);
	return;
}