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Peter S White

Publications and source records attributed to Peter S White.

At least 19 recordsLinked to original sources
PubMed2006

Arylthiolate-protected silver quantum dots.

This paper describes a new, organic-soluble 4-tert-butylbenzyl mercaptan (BBT) monolayer-protected silver cluster (AgBBT MPC) as the first example of a dissolved silver nanoparticle that exhibits quantized one-electron double layer charging (QDL) voltammetry. Polydisperse AgBBT MPCs made by two different synthetic protocols, but with similar average core diameters (2.1 nm), exhibit sharply differing electrochemistry and optical absorbance spectra. A two-phase procedure (organic/aqueous, termed Prep A-AgBBT) produced MPCs exhibiting a 475 nm surface plasmon absorbance and QDL voltammetry. Neither property was seen for MPCs made by a single-phase procedure, termed Prep B-AgBBT. The difference is thought to reflect poor passivation to oxide formation in the latter Prep B procedure, which is supported by X-ray photoelectron spectroscopy results. Thermogravimetry, mass spectra, and electrochemistry results suggest an average stoichiometric formula of Ag140BBT53, but transmission electron microscopy shows that the products are also polydisperse and include polycrystalline aggregates. Dry, cast films of both Ag MPC preparations on interdigitated array electrodes exhibit low electron hopping conductivity, compared to Au MPCs.

Gold↗
PubMed2006

Automated recognition of malignancy mentions in biomedical literature.

BACKGROUND: The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction procedures can assist in the acquisition and management of this knowledge. Previous efforts in biomedical text mining have focused primarily upon named entity recognition of well-defined molecular objects such as genes, but less work has been performed to identify disease-related objects and concepts. Furthermore, promise has been tempered by an inability to efficiently scale approaches in ways that minimize manual efforts and still perform with high accuracy. Here, we have applied a machine-learning approach previously successful for identifying molecular entities to a disease concept to determine if the underlying probabilistic model effectively generalizes to unrelated concepts with minimal manual intervention for model retraining. RESULTS: We developed a named entity recognizer (MTag), an entity tagger for recognizing clinical descriptions of malignancy presented in text. The application uses the machine-learning technique Conditional Random Fields with additional domain-specific features. MTag was tested with 1,010 training and 432 evaluation documents pertaining to cancer genomics. Overall, our experiments resulted in 0.85 precision, 0.83 recall, and 0.84 F-measure on the evaluation set. Compared with a baseline system using string matching of text with a neoplasm term list, MTag performed with a much higher recall rate (92.1% vs. 42.1% recall) and demonstrated the ability to learn new patterns. Application of MTag to all MEDLINE abstracts yielded the identification of 580,002 unique and 9,153,340 overall mentions of malignancy. Significantly, addition of an extensive lexicon of malignancy mentions as a feature set for extraction had minimal impact in performance. CONCLUSION: Together, these results suggest that the identification of disparate biomedical entity classes in free text may be achievable with high accuracy and only moderate additional effort for each new application domain.

Algorithms↗
PubMed2006

Bis(acetylacetonato)tricarbonyl tungsten(II): a convenient precursor to chiral bis(acac) tungsten(II) complexes.

Two equivalents of acetylacetonate (acac) have been successfully introduced into a monomeric tungsten(II) coordination sphere. With the tetracarbonyltriiodotungsten(II) anion as a precursor, the formation of a tungsten(II) bis(acac) tricarbonyl complex, W(CO)3(acac)2, 1, has been accomplished. The addition of PMe3 or PMe2Ph to tricarbonyl complex 1 formed tungsten(II)bis(acac)dicarbonylphosphine complexes 2a and 2b, respectively. Single-crystal X-ray diffraction studies of the parent tricarbonyl complex, 1, and dicarbonyl trimethylphosphine complex 2a confirmed seven-coordinate geometries for both complexes. Variable-temperature 1H and 13C{1H} NMR spectroscopy revealed fluxional behavior for these seven-coordinate molecules: rapid exchange of the three carbon monoxide ligands in 1 was observed, and movement of the phosphine ligand through a mirror plane in a C(S) intermediate species was observed for both 2a and 2b. Tricarbonyl complex 1 reacted readily with alkyne reagents to form bis(acac)monocarbonylmonoalkynetungsten(II) complexes 3a (PhC(triple bond)CH) and 3b (MeC(triple bond)CMe). Variable-temperature 1H NMR spectroscopy was used to probe rotation of the alkyne ligand in 3a and 3b. The introduction of two alkyne ligands was accomplished thermally using excess PhC(triple bond)CPh to form bis(alkyne) complex 4 which was characterized crystallographically, as well as by 1H and 13C NMR spectroscopy. The availability of W(CO)3(acac)2 as a source of the W(acac)2 d4 moiety lies at the heart of the chemistry reported here.

Journal Article↗
PubMed2006

Metallophosphite-catalyzed asymmetric acylation of alpha,beta-unsaturated amides.

The l-menthone-derived TADDOL phosphite 6b catalyzes highly enantioselective conjugate additions of acyl silanes to alpha,beta-unsaturated amides. p-Methoxybenzoyl cyclohexyldimethylsilane adds to a variety of N,N-dimethyl acrylamide derivatives in the presence of the lithium salt of 6b. In many instances the alpha-silyl-gamma-ketoamide product undergoes facile enantioenrichment (to 97-99% ee) upon recrystallization. Desilylation with HF.pyr affords the formal Stetter addition products. Baeyer-Villiger oxidation of the desilylated gamma-ketoamides affords useful ester products. An X-ray diffraction study of 6b reveals that the isopropyl group of the menthone ketal influences the position of the syn-pseudoaxial phenyl group in the TADDOL structure. Through a crossover experiment, the silicon migration step in the reaction mechanism is shown to be strictly intramolecular.

Acylation↗
PubMed2006

Carbon monoxide promoted reductive elimination of hydrogen from Tp' platinum complexes.

Acid-assisted reductive elimination of hydrogen from Tp'PtH(3) and of methane and hydrogen from Tp'PtMeH(2) (Tp' = hydridotris(3,5-dimethylpyrazolyl)borate) is examined herein. Loss of H(2) is observed from solutions containing platinum(IV) complexes of the type Tp'Pt(R)(H)(2) (R = Me, H) upon protonation and addition of a ligand such as CO. Results of kinetic studies on reductive elimination of H(2) and formation of [kappa(2)-(HTp')Pt(R)(L)][BAr'(4)] products from intermediates derived from Tp'Pt(R)(H)(2) precursors are described. Elimination appears to occur from cationic 6-coordinate [kappa(2)-(HTp')Pt(R)(H)(2)(L)][BAr'(4)] species.

Journal Article↗
PubMed2006

An automated procedure to identify biomedical articles that contain cancer-associated gene variants.

The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing information regarding genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing "relevant" from "not relevant" abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or sets of documents.

Computational Biology↗
PubMed2005

Synthesis and ligand exchange reactions of P2Pd(II) and P2Pt(II) salicylaldimates.

Reaction of (dppe)MCl(2)(dppe = 1,2-bis(diphenylphosphino)ethane) with 2-(N-phenyliminomethyl)phenol leads to air-stable (dppe)M(N,O) chelates (M = Pd, 1a; M = Pt, 1b). The N-4-methylphenyl derivative of 1a has been characterized by X-ray analysis. The N,O ligands are kinetically labile and exchange occurs in solution in the presence of other salicylaldimines. In the presence of anilines, a metal-mediated imine exchange process occurs. Hammett analysis reveals that the platinum complexes are sensitive to the electronics at N but not at O. Electron donating groups on the N-aryl ring stabilize the metal complex.

Chelating Agents↗
PubMed2005

Definition and characterization of a region of 1p36.3 consistently deleted in neuroblastoma.

Substantial genomic and functional evidence from primary tumors and cell lines indicates that a consistent region of distal chromosome 1p is deleted in a sizable proportion of human neuroblastomas, suggesting that this region contains one or more tumor suppressor genes. To determine systematically and precisely the location and extent of 1p deletion in neuroblastomas, we performed allelic loss studies of 737 primary neuroblastomas and genotype analysis of 46 neuroblastoma cell lines. Together, the results defined a single region within 1p36.3 that was consistently deleted in 25% of tumors and 87% of cell lines. Two neuroblastoma patients had constitutional deletions of distal 1p36 that overlapped the tumor-defined region. The tumor- and constitutionally-derived deletions together defined a smallest region of consistent deletion (SRD) between D1S2795 and D1S253. The 1p36.3 SRD was deleted in all but one of the 184 tumors with 1p deletion. Physical mapping and DNA sequencing determined that the SRD minimally spans an estimated 729 kb. Genomic content and sequence analysis of the SRD identified 15 characterized, nine uncharacterized, and six predicted genes in the region. The RNA expression profiles of 21 of the genes were investigated in a variety of normal tissues. The SHREW1 and KCNAB2 genes both had tissue-restricted expression patterns, including expression in the nervous system. In addition, a novel gene (CHD5) with strong homology to proteins involved in chromatin remodeling was expressed mainly in neural tissues. Together, these results suggest that one or more genes involved in neuroblastoma tumorigenesis or tumor progression are likely contained within this region.

Chromosome Deletion↗
PubMed2005

Reactions of vinyl acetate and vinyl trifluoroacetate with cationic diimine Pd(II) and Ni(II) alkyl complexes: identification of problems connected with copolymerizations of these monomers with ethylene.

Vinyl acetate (VA) and vinyl trifluoroacetate (VA(f)) react with [(NwedgeN)Pd(Me)(L)][X] (M = Pd, Ni, (NwedgeN) = N,N'-1,2-acenaphthylenediylidene bis(2,6-dimethyl aniline), Ar(f) = 3,5-trifluoromethyl phenyl, L = Ar(f)CN, Et2O; X = B(Ar(f))4-, SbF6-) to form pi-adducts 3 and 5 at -40 degrees C. Binding affinities relative to ethylene have been determined. Migratory insertion occurs in a 2,1 fashion (DeltaG++ = 19.4 kcal/mol, 0 degrees C for VA, and 17.4 kcal/mol, -40 degrees C for VA(f)) to yield five-membered chelate complexes [(NwedgeN)Pd(kappa2-CH(Et)(OC(O)-CH3))]+, 4, and [(NwedgeN)Pd(kappa2-CH(Et)(OC(O)CF3))]+, 6. When VA is added to [(NwedgeN)Ni(CH3)]+, an equilibrium mixture of an eta2 olefin complex, 8c, and a kappa-oxygen complex, 8o, results. Insertion occurs from the eta2 olefin complex, 8c (DeltaG++ = 15.5 kcal/mol, -51 degrees C), in both a 2,1 and a 1,2 fashion to generate a mixture of five- and six-membered chelates, 9(2,1) and 9(1,2). VA(f) inserts into the Ni-CH3 bond (-80 degrees C) to form a five-membered chelate with no detectable intermediate. Thermolysis of the Pd chelates results in beta-acetate elimination from 4 (DeltaG++ = 25.5 kcal/mol, 60 degrees C) and beta-trifluoroacetate elimination from 6 (DeltaG = 20.5 kcal/mol, 10 degrees C). The five-membered Ni chelate, 9(2,1), is quite stable at room temperature, but the six-membered chelate, 9(1,2), undergoes beta-elimination at -34 degrees C. Treatment of the OAc(f) containing Pd chelate 6 with ethylene results in complete opening to the pi-complex [(NwedgeN)Pd(kappa2-CH(Et)(OAc(f)))(CH2CH2)]+ (OAc(f) = OC(O)CF3), 18, while reaction of the OAc containing Pd chelate 4 with ethylene establishes an equilibrium between 4 and the open form 16, strongly favoring the closed chelate 4 (DeltaH = -4.1 kcal/mol, DeltaS = -23 eu, K = 0.009 M(-1) at 25 degrees C). The open chelates undergo migratory insertion at much slower rates relative to those of the simple (NwedgeN)Pd(CH3)(CH2CH2)+ analogue. These quantitative studies provide an explanation for the behavior of VA and VA(f) in attempted copolymerizations with ethylene.

Journal Article↗
PubMed2005

Genomic structure and organization of the high grade Myopia-2 locus (MYP2) critical region: mutation screening of 9 positional candidate genes.

PURPOSE: Myopia is a common complex eye disorder, with implications for blindness due to increased risk of retinal detachment, chorioretinal degeneration, premature cataracts, and glaucoma. A genomic interval of 2.2 centiMorgans (cM) was defined on chromosome band 18p11.31 using 7 families diagnosed with autosomal dominant high myopia and was designated the MYP2 locus. To characterize this region, we analyzed 9 known candidate genes localized to within the 2.2 cM interval by direct sequencing. METHODS: Using public databases, a physical map of the MYP2 interval was compiled. Gene expression studies in ocular tissues using complementary DNA library screens, microarray experiments, reverse transcription techniques, and expression data identified in external databases aided in prioritizing gene selection for screening. Coding regions, intron-exon boundaries and untranslated exons of all known genes [Clusterin-like 1 (CLUL1), elastin microfibril interfacer 2 (EMILIN2), lipin 2 (LPIN2), myomesin 1 (MYOM1), myosin regulatory light chain 3 (MRCL3), myosin regulatory light chain 2 (MRLC2), transforming growth beta-induced factor (TGIFbeta), large Drosophila homolog associated protein 1 (DLGAP1), and zinc finger protein 161 homolog (ZFP161)] were sequenced using genomic DNA samples from 9 affected and 6 unaffected MYP2 pedigree members, and from 5 external controls (4 unaffected and 1 affected). Gene sequence changes were compared to known variants from public single nucleotide polymorphism (SNP) databases. RESULTS: In total, 103 polymorphisms were found by direct sequencing; 10 were missense, 14 were silent, 26 were not translated, 49 were intronic, 1 insertion, and 3 were homozygous deletions. Twenty-seven polymorphisms were novel. Novel SNPs were submitted to the public database; observed frequencies were submitted for known SNPs. No sequence alterations segregated with the disease phenotype. CONCLUSIONS: Mutation analysis of 9 encoded positional candidate genes on MYP2 loci did not identify sequence alterations associated with the disease phenotype. Further studies of MYP2 candidate genes, including analysis of putative genes predicted in silico, are underway.

Chromosomes, Human, Pair 18↗
PubMed2005

Oxidative dissolution of copper and zinc metal in carbon dioxide with tert-butyl peracetate and a beta-diketone chelating agent.

A series of beta-diketone ligands, R(1)COCH(2)COR(2) [tmhdH (R(1) = R(2) = C(CH(3))(3)); tfacH (R(1) = CF(3); R(2) = CH(3)); hfacH (R(1) = R(2) = CF(3))], in combination with tert-butyl peracetate (t-BuPA), have been investigated as etchant solutions for dissolution of copper metal into carbon dioxide solvent. Copper removal in CO(2) increases in the order tfacH < tmhdH < hfacH. A study of the reactions of the hfacH/t-BuPA etchant solution with metallic copper and zinc was conducted in three solvents: scCO(2) (supercrical CO(2)); hexanes; CD(2)Cl(2). The etchant solution/metallic zinc reaction produced a diamagnetic Zn(II) complex, which allowed NMR identification of the t-BuPA decomposition products as tert-butyl alcohol and acetic acid. Gravimetric analysis of the amount of zinc consumed, together with NMR studies, confirmed the 1:1:2 Zn:t-BuPA:hfacH reaction stoichiometry, showing t-BuPA to be an overall two-electron oxidant for Zn(0). The metal-containing products of the copper and zinc reactions were characterized by elemental analysis, IR spectroscopy, and, as appropriate, NMR spectroscopy and single-crystal X-ray diffraction [trans-M(hfac)(2)(H(2)O)(CH(3)CO(2)H) (1, M = Cu; 2, M = Zn)]. On the basis of the experimental results, a working model of the oxidative dissolution reaction is proposed, which delineates the key chemical variables in the etching reaction. These t-BuPA/hfacH etchant solutions may find application in a CO(2)-based chemical mechanical planarization (CMP) process.

Journal Article↗
PubMed2005

Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform.

Many cancers are characterized by chromosomal aberrations that may be predictive of disease outcome. Human neuroblastomas are characterized by somatically acquired copy number changes, including loss of heterozygosity (LOH) at multiple chromosomal loci, and these aberrations are strongly associated with clinical phenotype including patient outcome. We developed a method to assess region-specific LOH by genotyping multiple SNPs simultaneously in DNA from tumor tissues. We identified informative SNPs at an average 293-kb density across nine regions of recurrent LOH in human neuroblastomas. We also identified SNPs in two copy number neutral regions, as well as two regions of copy number gain. SNPs were PCR-amplified in 12-plex reactions and used in solution-phase single-nucleotide extension incorporating tagged dideoxynucleotides. Each extension primer had 5' complementarity to one of 2000 oligonucleotides on a commercially available tag-array platform allowing for solid-phase sorting and identification of individual SNPs. This approach allowed for simultaneous detection of multiple regions of LOH in six human neuroblastoma-derived cell lines, and, more importantly, 14 human neuroblastoma primary tumors. Concordance with conventional genotyping was nearly absolute. Detection of LOH in this assay may not require comparison to matched normal DNAs because of the redundancy of informative SNPs in each region. The customized tag-array system for LOH detection described here is rapid, results in parallel assessment of multiple genomic alterations, and may speed identification of and/or assaying prognostically relevant DNA copy number alterations in many human cancers.

Humans↗
PubMed2004

An entity tagger for recognizing acquired genomic variations in cancer literature.

VTag is an application for identifying the type, genomic location and genomic state-change of acquired genomic aberrations described in text. The application uses a machine learning technique called conditional random fields. VTag was tested with 345 training and 200 evaluation documents pertaining to cancer genetics. Our experiments resulted in 0.8541 precision, 0.7870 recall and 0.8192 F-measure on the evaluation set.

Abstracting and Indexing↗
PubMed2004

Fine mapping of the Schnyder's crystalline corneal dystrophy locus.

Schnyder's crystalline corneal dystrophy (SCCD) is a rare autosomal dominant eye disease with a spectrum of clinical manifestations that may include bilateral corneal clouding, arcus lipoides, and anterior corneal crystalline cholesterol deposition. We have previously performed a genome-wide linkage analysis on two large Swede-Finn families and mapped the SCCD locus to a 16-cM interval between markers D1S2633 and D1S228 on chromosome 1p36. We have collected 11 additional families from Finland, Germany, Turkey, and USA to narrow the critical region for SCCD. Here, we have used haplotype analysis with densely spaced microsatellite markers in a total of 13 families to refine the candidate interval. A common disease haplotype was observed among the four Swede-Finn families indicating the presence of a founder effect. Recombination results from all 13 families refined the SCCD locus to 2.32 Mbp between markers D1S1160 and D1S1635. Within this interval, identity-by-state was present in all 13 families for two markers D1S244 and D1S3153, further refining the candidate region to 1.58 Mbp.

Chromosome Mapping↗
PubMed2004

Genomic annotation of the meningioma tumor suppressor locus on chromosome 1p34.

Meningioma is a frequently occurring tumor of the meninges surrounding the central nervous system. Loss of the short arm of chromosome 1 (1p) is the second most frequent chromosomal abnormality observed in these tumors. Previously, we identified a 3.7 megabase (Mb) region of consistent deletion on 1p33-p34 in a panel of 157 tumors. Loss of this region was associated with advanced disease and predictive for tumor relapse. In this report, a high-resolution integrated map of the region was constructed (CompView) to identify all markers in the smallest region of overlapping deletion (SRO). A regional somatic cell hybrid panel was used to more precisely localize those markers identified in CompView as within or overlapping the region. Additional deletion mapping using microsatellites localized to the region narrowed the SRO to approximately 2.8 Mb. The 88 markers remaining in the SRO were used to screen genomic databases to identify large-insert clones. Clones were assembled into a physical map of the region by PCR-based, sequence-tagged site (STS) content mapping. A sequence from clones was used to validate STS content by electronic PCR and to identify transcripts. A minimal tiling path of 43 clones was constructed across the SRO. Sequence data from the most current sequence assembly were used for further validation. A total of 59 genes were ordered within the SRO. In all, 17 of these were selected as likely candidates based on annotation using Gene Ontology Consortium terms, including the MUTYH, PRDX1, FOXD2, FOXE3, PTCH2, and RAD54L genes. This annotation of a putative tumor suppressor locus provides a resource for further analysis of meningioma candidate genes.

Chromosomes, Human, Pair 1↗
PubMed2004

me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements.

We have adapted the originally described electronic PCR (e-PCR) algorithm to perform string searches more accurately and much more rapidly than previously possible. Our implementation [multithreaded e-PCR (me-PCR)] runs sufficiently fast to allow even desktop machines to query quickly large genomes with very large genomic element sets. In addition, me-PCR is multithreaded, interprets all IUPAC nucleotide symbols, allows searches with elements specified by long sequences (such as SNPs), accepts ranges in the expected PCR size input field, requires substantially less memory for analysis of large sequences and corrects a number of minor flaws causing misreporting of hits in exceptional cases. Thus, me-PCR provides increased annotation capabilities for complex genomes to non-expert laboratories.

Algorithms↗
PubMed2004

Synthesis of Pt(dpk)Cl(4) and the reversible hydration to Pt(dpk-O-OH)Cl(3).H-phenCl: X-ray, spectroscopic, and electrochemical characterization.

We report on the synthesis of a platinum(IV) compound containing a di-2-pyridyl ketone (dpk) ligand that is stable both in its anhydrous form [Pt(dpk)Cl(4)] (1) and in its hydrated form [Pt(dpk-O-OH)Cl(3)].H-phenCl (2). The crystal structure of the hydrated form shows that one of the hydroxide groups from the resulting gem-diol has undergone a cyclometalation/condensation reaction resulting in an oxygen atom directly coordinated to the Pt(IV) center and the formation of H-phenCl. We correlate our physical data with predictions made by molecular modeling, and we propose an explanation for the unusual activity found for this dpk ketone. Spectroscopic and solubility studies are presented here, as well. Electrochemical studies of 1 indicate that it undergoes a highly irreversible reduction at a potential of about -0.45 V vs Ag(+)/Ag in CH(3)CN and that the irreversibility is likely due to an EC mechanism, the nature of which is currently under further investigation. Another distinct redox pair, apparently reversible, appears at a potential of about -1.1 V vs Ag(+)/Ag.

Journal Article↗