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1.
Ann Oncol ; 27(5): 801-6, 2016 05.
Article in English | MEDLINE | ID: mdl-27022066

ABSTRACT

BACKGROUND: A patient suffering from metastatic colorectal cancer, treatment-related toxicity and resistance to standard chemotherapy and radiation was assessed as part of a personalized oncogenomics initiative to derive potential alternative therapeutic strategies. PATIENTS AND METHODS: Whole-genome and transcriptome sequencing was used to interrogate a metastatic tumor refractory to standard treatments of a patient with mismatch repair-deficient metastatic colorectal cancer. RESULTS: Integrative genomic analysis indicated overexpression of the AP-1 transcriptional complex suggesting experimental therapeutic rationales, including blockade of the renin-angiotensin system. This led to the repurposing of the angiotensin II receptor antagonist, irbesartan, as an anticancer therapy, resulting in the patient experiencing a dramatic and durable response. CONCLUSIONS: This case highlights the utility of comprehensive integrative genomic profiling and bioinformatics analysis to provide hypothetical rationales for personalized treatment options.


Subject(s)
Biphenyl Compounds/administration & dosage , Colorectal Neoplasms/drug therapy , Precision Medicine , Tetrazoles/administration & dosage , Transcription Factor AP-1/genetics , Aged , Angiotensin Receptor Antagonists/administration & dosage , Angiotensins/antagonists & inhibitors , Angiotensins/genetics , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Computational Biology , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Irbesartan , Neoplasm Metastasis , Renin-Angiotensin System/drug effects , Transcriptome/genetics
2.
Int J Clin Pract ; 70(1): 82-8, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26575855

ABSTRACT

OBJECTIVE: To validate the In-hospital Mortality for PulmonAry embolism using Claims daTa (IMPACT) multivariable prediction rule using admission claims data. STUDY DESIGN: Retrospective claims database analysis. METHODS: This analysis was performed using Humana admission claims data from January 2007 to March 2014. We included adult patients admitted for their first PE during this period (International Classification of Diseases, ninth edition, Clinical Modification code of 415.1x in in the primary position or secondary position when accompanied by a primary code for a PE complication). The IMPACT rule, consisting of age plus 11 comorbidities, was used to estimate patients' probability of in-hospital mortality and classify risk. Low risk was defined as in-hospital mortality ≤ 1.5%. IMPACT was evaluated by evaluating prognostic test characteristic values and 95% confidence intervals (CIs). RESULTS: A total of 23,858 patients admitted for PE were included, and 3.3% died in-hospital. The IMPACT prediction rule classified 2371 (9.9%) as low-risk; with a sensitivity of 97.6%, 95% CI: 96.1-98.5, specificity of 10.2%, 95% CI: 9.8-10.6, negative and positive predictive values of 99.2% (95% CI: 98.7-99.5) and 3.5% (95% CI: 3.3-3.8) and c-statistic of 0.70, 95% CI: 0.0.68-0.72, for in-hospital mortality. IMPACT classified 42.7% of patients < 65 years old as low-risk; with a sensitivity, specificity and c-statistic of 85.0%, 95% CI: 77.4-90.5, 43.3%, 95% CI: 42.0-44.7 and 0.74, 95% CI: 0.69-0.78, respectively. CONCLUSION: The IMPACT prediction rule was valid when implemented in a database consisting largely of Medicare claims. Following further external validation and direct comparison to commonly used clinical prediction rules, IMPACT may become a valuable tool for payers and hospitals wishing to retrospectively assess whether their PE patients are being kept hospitalized for the optimal period of time.


Subject(s)
Decision Support Techniques , Hospital Mortality , Pulmonary Embolism/mortality , Administrative Claims, Healthcare/statistics & numerical data , Adult , Age Factors , Aged , Aged, 80 and over , Comorbidity , Female , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Predictive Value of Tests , Retrospective Studies
3.
Int J Clin Pract ; 69(3): 321-7, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25395271

ABSTRACT

BACKGROUND: Venous thromboembolism (VTE), which comprises deep-vein thrombosis (DVT) and pulmonary embolism (PE), is associated with significant morbidity and mortality and represents a considerable economic burden to the US healthcare system. Although it is well established that patients with an initial VTE are at increased risk for recurrent VTE, limited data exist on the clinical burden of a secondary DVT or PE event. The objective of this retrospective observational study was to conduct an epidemiologic evaluation, from a hospital perspective, of patients with an initial DVT or PE who experienced a recurrent event postdischarge requiring hospital readmission. METHODS: Hospital claims containing DVT or PE as a primary diagnosis for hospitalisation during the period October 2009 to April 2013 were identified by retrospective analysis using the MarketScan database. The time to hospital readmission for DVT or PE was assessed using the MarketScan Treatment Pathways tool. RESULTS: Of 214,901 patient admissions identified with a diagnosis of DVT or PE at hospital admission, approximately 4% were subsequently readmitted to the hospital with a diagnosis of PE (8217) or DVT (9138). Of all readmitted patients with a diagnosis of DVT on initial admission, 66% were rehospitalised with a diagnosis of DVT, and 34% were rehospitalised with a diagnosis of PE. Of all readmitted patients with a diagnosis of PE on initial admission, 63% were rehospitalised with a diagnosis of PE and 37% with a diagnosis of DVT. Of all hospital readmissions with a diagnosis of PE or DVT, 62% and 58% occurred within the first 30 days following an initial PE or DVT event, respectively. CONCLUSIONS: The burden of DVT or PE is large, not only because of the initial hospitalisation event but also because of the high number of hospital readmissions, more than half of which occur within 30 days.


Subject(s)
Patient Readmission/trends , Pulmonary Embolism/therapy , Venous Thrombosis/therapy , Adolescent , Adult , Aged , Child , Child, Preschool , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Pulmonary Embolism/diagnosis , Pulmonary Embolism/epidemiology , Retrospective Studies , United States/epidemiology , Venous Thrombosis/diagnosis , Venous Thrombosis/epidemiology , Young Adult
4.
J Clin Pharm Ther ; 39(3): 253-8, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24494931

ABSTRACT

WHAT IS KNOWN AND OBJECTIVES: Venous thromboembolism (VTE), comprising deep vein thrombosis (DVT) and pulmonary embolism (PE), is a serious, life-threatening condition that often complicates treatment of individuals who are already ill and increases in risk with age. The comorbidity burden of VTE can complicate treatment; therefore, treatment should be influenced by the presence of comorbidities (Kearon 2012). The prevalence of common conditions in the VTE population is, therefore, an important subject of research. Prevalence of two common comorbid burdens, prior myocardial infarction (MI) and upper gastrointestinal (GI) conditions, was studied among survey respondents who reported DVT or PE. METHODS: Responses to the 2010 wave of the National Health and Wellness Survey (NHWS), a self-administered, internet-based questionnaire from a nationwide, demographically representative sample of adults, were evaluated. RESULTS AND DISCUSSION: Among the 814 participants reporting a history of VTE, 9·7% (n = 60) of the DVT subpopulation and 13·2% (n = 39) of the PE subpopulation also reported prior MI. In respondents with prior MI, cardiovascular, urological, and pain comorbidities were each reported as additional comorbidities by at least two thirds of respondents in both the PE and DVT subpopulations, with cardiovascular and urological conditions reported significantly (P < 0·05) more often than among respondents with no prior MI. Among the respondents reporting VTE, 48·9% (n = 302) of the subpopulation reporting DVT and 52·2% (n = 154) of those reporting PE also reported upper GI comorbidities. Cardiovascular and pain conditions in the respondents reporting upper GI comorbidities were each reported by more than three quarters of VTE patients in both the DVT and PE subpopulations and were significantly more common (P < 0·05) than among their counterparts without upper GI comorbidities. WHAT IS NEW AND CONCLUSION: The results of the NHWS indicate that VTE patients who have either of two common comorbid burdens, prior MI and concomitant upper GI conditions, also showed high levels of additional, concurrent comorbidities and generally poor health status. Clinicians must be aware of the total comorbidity profile of their patients who have experienced VTE in order to best manage them and prescribe appropriate therapy.


Subject(s)
Gastrointestinal Diseases/epidemiology , Myocardial Infarction/epidemiology , Venous Thromboembolism/epidemiology , Comorbidity , Female , Health Status , Humans , Male , Middle Aged , Prevalence , Risk Factors
5.
J Clin Pharm Ther ; 39(6): 663-72, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25252190

ABSTRACT

WHAT IS KNOWN AND OBJECTIVE: Current guidelines recommend a combination of clopidogrel and aspirin for management of patients who have experienced an acute coronary syndrome (ACS). Additional antiplatelet agents have been recently approved. Few comparative effectiveness studies are available for these new agents. Accordingly, we evaluated effect on time to hospital admission and resource utilization (number of hospitalizations, ER visits and outpatient visits) of prasugrel vs. clopidogrel in prasugrel-treated patients as assessed in a matched cohort. METHODS: Based on the Truven Health Analytics MarketScan database from 01 January 2009 through 31 July 2012, a retrospective prasugrel-clopidogrel matched cohort was created. Inferences for average treatment effect over 1 and 12 months on time to hospitalization and resource utilization were performed by (i) frequentist Kaplan-Meier estimation with a Cox proportional hazard model and Lin's cost history method for censored resource utilization outcomes and (ii) Bayesian discrete-time hazard and negative binomial models. RESULTS AND DISCUSSION: The 10,963 matched pairs were well balanced on baseline characteristics. Frequentist analyses of time to hospital admission over 365 days and mean all-cause resource utilization over 30 and 365 days showed no statistical differences between prasugrel and clopidogrel (P-values > 0·05). Based on Bayesian analysis of time to admission over 12 months, there was positive evidence of equivalence (0·987 probability of equivalence at a 10% equivalence margin and a Bayes factor of 0·611). Although the frequentist analyses for number of all-cause hospitalizations showed a lack of a significant difference at Months 1 and 12, the Bayesian data analysis showed positive evidence of superiority of clopidogrel at Month 1 (Bayes factor: 5·369); however, at Month 12, there was little evidence of superiority of one treatment over the other (Bayes factor: 0·422). WHAT IS NEW AND CONCLUSION: Using frequentist and Bayesian data analyses, in prasugrel-treated patients, clopidogrel was equivalent to prasugrel for time to hospital admission over 12 months and there was positive evidence that it was superior to prasugrel for number of hospitalizations over the first month of treatment.


Subject(s)
Acute Coronary Syndrome/drug therapy , Piperazines/therapeutic use , Platelet Aggregation Inhibitors/therapeutic use , Thiophenes/therapeutic use , Ticlopidine/analogs & derivatives , Aged , Bayes Theorem , Clopidogrel , Cohort Studies , Female , Hospitalization/statistics & numerical data , Humans , Kaplan-Meier Estimate , Male , Middle Aged , Prasugrel Hydrochloride , Proportional Hazards Models , Retrospective Studies , Ticlopidine/therapeutic use , Time Factors , Treatment Outcome
6.
Nat Genet ; 22(3): 265-70, 1999 Jul.
Article in English | MEDLINE | ID: mdl-10391214

ABSTRACT

Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www. stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.


Subject(s)
Arabidopsis/genetics , Genome, Plant , Chromosome Mapping , Chromosomes, Bacterial/genetics , DNA Fingerprinting , DNA, Plant/genetics , DNA, Plant/isolation & purification , Databases, Factual , Genomic Library , Humans , Sequence Analysis, DNA
7.
Nat Commun ; 12(1): 1638, 2021 Mar 12.
Article in English | MEDLINE | ID: mdl-33712576

ABSTRACT

Key insights in materials at extreme temperatures and pressures can be gained by accurate measurements that determine the electrical conductivity. Free-electron laser pulses can ionize and excite matter out of equilibrium on femtosecond time scales, modifying the electronic and ionic structures and enhancing electronic scattering properties. The transient evolution of the conductivity manifests the energy coupling from high temperature electrons to low temperature ions. Here we combine accelerator-based, high-brightness multi-cycle terahertz radiation with a single-shot electro-optic sampling technique to probe the evolution of DC electrical conductivity using terahertz transmission measurements on sub-picosecond time scales with a multi-undulator free electron laser. Our results allow the direct determination of the electron-electron and electron-ion scattering frequencies that are the major contributors of the electrical resistivity.

8.
J Mol Biol ; 306(2): 145-57, 2001 Feb 16.
Article in English | MEDLINE | ID: mdl-11237590

ABSTRACT

Inositol 1,4,5-trisphosphate receptors in Caenorhabditis elegans are encoded by a single gene, itr-1. This provides a powerful system in which to dissect the mechanisms that control the tissue-specific expression of molecules that determine the specificity of calcium signalling. We first identified the Caenorhabditis briggsae orthologue of itr-1, Cbitr-1. Comparison of the two itr-1 genes revealed that the chromosomal organisation, gene structure and predicted cDNA and protein sequences were all conserved. The conserved gene structure supports the hypothesis that the itr-1 gene has three promoters, each of which gives rise to an alternative mRNA and hence unique protein. To test this and to identify the roles of the three putative promoters (pA, pB and pC) in regulating itr-1 expression we fused each promoter to the green fluorescent protein gene and identified their expression patterns. Introduction of these transgenes into C. elegans identified unique and defined patterns of green fluorescent protein expression directed by each promoter: pA directs expression in the pharyngeal terminal bulb, the rectal epithelial cells and vulva; pB directs expression in the motor neurone PDA, the amphid socket cells and the spermatheca; pC directs expression in the spermathecal valve, uterine sheath cells, pharyngeal isthmus and intestine. Thus tissue-specific expression of itr-1 variants is directed by three promoters and this results in adjacent cells in the same tissue containing different inositol trisphosphate receptor isoforms. Within pA, four short regions (pA-A to pA-D) of sequence conservation between C. elegans and C. briggsae were identified. Deletion analysis demonstrated that the region containing pA-C is required for expression in the terminal bulb and rectal epithelial cells and the region containing pA-D is required for expression in the vulva. pA-C includes sequences similar to the binding sites for transcription factors that have been demonstrated to be important in pharyngeal development and gene expression.


Subject(s)
Caenorhabditis elegans/genetics , Calcium Channels/genetics , Gene Expression Regulation , Promoter Regions, Genetic/genetics , Receptors, Cytoplasmic and Nuclear/genetics , Amino Acid Sequence , Animals , Animals, Genetically Modified , Base Sequence , Caenorhabditis/genetics , Calcium Channels/chemistry , Chromosomes/genetics , Consensus Sequence/genetics , Conserved Sequence/genetics , Inositol 1,4,5-Trisphosphate Receptors , Molecular Sequence Data , Organ Specificity , Protein Isoforms/chemistry , Protein Isoforms/genetics , RNA, Messenger/analysis , RNA, Messenger/genetics , Receptors, Cytoplasmic and Nuclear/chemistry , Recombinant Fusion Proteins/analysis , Recombinant Fusion Proteins/genetics , Response Elements/genetics
9.
Neuroscience ; 134(1): 21-32, 2005.
Article in English | MEDLINE | ID: mdl-15953684

ABSTRACT

Death occurs in the homozygous mutant mouse weaver among several classes of neuron in cerebellum and ventral midbrain, because these neurons carry a mutation in the G protein-gated inwardly rectifying potassium channel, Girk2. GIRK2 is expressed in all neuronal types killed by wv in cerebellum and midbrain as well as in neurons elsewhere that suffer lesser consequences. GIRK2(wv) affects neurons postnatally, after proliferation, at the time of final differentiation. To assess the impact of GIRK2(wv) on neuronal development and viability, we introduced cDNA encoding wild-type and mutant channels into a variant of a CNS derived catecholamine cell line (Cath.a) known as Cath.a-differentiated. When cultured in serum-free medium, Cath.a-differentiated cells cease proliferation and undergo morphological differentiation, growing long neurites. Cath.a-differentiated cells do not express endogenous Girk channels. Transfection of GIRK2(wv) resulted in the death of Cath.a-differentiated cells, in a cDNA-concentration dependent manner. The highest concentration of Girk2(wv) cDNA caused loss of about half the cells, the next highest concentration one-third, and the least had no effect on viability. However, even the lowest concentration resulted in disruption of neurite outgrowth and reduced the protein products of co-transfected genes. High concentrations of MK801, which prevent Na(+) influx through the mutant channel, prevented death induced by GIRK2(wv). Cell death and disruption of neurite outgrowth were counteracted in GIRK2(wv)-expressing cells by the presence of an unrelated inwardly rectifying potassium channel, Kir2.3. These results are consistent with wv being a gain-of-function mutation, causing disruption of cellular homeostasis by mechanisms such as increased Na(+) influx and chronic depolarization which may in turn result in an excessive metabolic burden on the cell.


Subject(s)
Central Nervous System/cytology , Gene Expression Regulation/physiology , Neurites/physiology , Neurons/cytology , Animals , Blotting, Western/methods , Cell Count/methods , Cell Cycle/genetics , Cell Differentiation/physiology , Cell Line , Dizocilpine Maleate/pharmacology , Excitatory Amino Acid Antagonists/pharmacology , Green Fluorescent Proteins/biosynthesis , Immunohistochemistry/methods , Mice , Mice, Neurologic Mutants , Neurons/physiology , Potassium Channels, Inwardly Rectifying/metabolism , Time Factors , Transfection/methods
10.
Genetics ; 152(4): 1573-84, 1999 Aug.
Article in English | MEDLINE | ID: mdl-10430584

ABSTRACT

The masculinizing gene her-1 in Caenorhabditis elegans (Ce-her-1) encodes a novel protein, HER-1A, which is required for male development. To identify conserved elements in her-1 we have cloned and characterized two homologous nematode genes: one by synteny from the closely related free-living species C. briggsae (Cb-her-1) and the other, starting with a fortuitously identified expressed sequence tag, from the distantly related parasite Brugia malayi (Bm-her-1). The overall sequence identities of the predicted gene products with Ce-HER-1A are only 57% for Cb-HER-1, which is considerably lower than has been found for most homologous briggsae genes, and 35% for Bm-HER-1. However, conserved residues are found throughout both proteins, and like Ce-HER-1A, both have putative N-terminal signal sequences. Ce-her-1 produces a larger masculinizing transcript (her-1a) and a smaller transcript of unknown function (her-1b); both are present essentially only in males. By contrast, Cb-her-1 appears to produce only one transcript, corresponding to her-1a; it is enriched in males but present also in hermaphrodites. Injection of dsRNA transcribed from Cb-her-1 into C. briggsae hermaphrodites (RNA interference) caused XO animals to develop into partially fertile hermaphrodites. Introducing a Cb-her-1 construct as a transgene under control of the C. elegans unc-54 myosin heavy chain promoter caused strong masculinization of both C. briggsae and C. elegans hermaphrodites. Introduction of a similar Bm-her-1 construct into C. elegans caused only very weak, if any, masculinization. We conclude that in spite of considerable divergence the Cb gene is likely to be a functional ortholog of Ce-her-1, while the function of the distantly related Bm gene remains uncertain.


Subject(s)
Brugia malayi/genetics , Caenorhabditis elegans Proteins , Caenorhabditis elegans/genetics , Caenorhabditis/genetics , Disorders of Sex Development/genetics , Genes, Helminth , Helminth Proteins/genetics , Sex Determination Processes , Amino Acid Sequence , Animals , Animals, Genetically Modified , Cloning, Molecular , DNA, Complementary/genetics , Evolution, Molecular , Helminth Proteins/physiology , Molecular Sequence Data , Promoter Regions, Genetic , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/physiology , Sequence Alignment , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid , Species Specificity
11.
Arch Intern Med ; 158(18): 1977-89, 1998 Oct 12.
Article in English | MEDLINE | ID: mdl-9778197

ABSTRACT

Cardiovascular disease, including coronary heart disease, is the leading cause of death both in men and in women in the United States. The purpose of this review is to describe the effectiveness of lipid-lowering therapy in reducing cardiovascular morbidity and mortality, which has recently been extended to patients with mild to moderate hypercholesterolemia, and the cost of providing therapy, which would be prohibitive if all persons with hypercholesterolemia received treatment. Cost-effectiveness analysis provides a rational means of allocating limited health care resources by allowing the comparison of the costs of lipid-lowering therapy, in particular, therapy with beta-hydroxy-beta-methylglutaryl-CoA (coenzyme A) reductase inhibitors (statins), with the costs of atherosclerosis that could be prevented by lowering cholesterol. To extend the benefits of treatment to the large number of persons not receiving therapy, we need to implement more cost-effective treatment by improving risk assessment, increasing treatment effectiveness, and reducing the cost of therapy.


Subject(s)
Anticholesteremic Agents/economics , Hydroxymethylglutaryl-CoA Reductase Inhibitors/economics , Atorvastatin , Carotid Stenosis/economics , Carotid Stenosis/prevention & control , Cerebrovascular Disorders/economics , Cerebrovascular Disorders/prevention & control , Clinical Trials as Topic , Coronary Disease/economics , Coronary Disease/prevention & control , Cost-Benefit Analysis , Fatty Acids, Monounsaturated/economics , Fluvastatin , Heptanoic Acids/economics , Humans , Indoles/economics , Lovastatin/economics , Pravastatin/economics , Pyrroles/economics , Simvastatin/economics
12.
Gene ; 243(1-2): 67-74, 2000 Feb 08.
Article in English | MEDLINE | ID: mdl-10675614

ABSTRACT

The Caenorhabditis briggsae homologue of the Caenorhabditis elegans pag-3 gene was cloned and sequenced. When transformed into a C. elegans pag-3 mutant, the C. briggsae pag-3 gene rescued the pag-3 reverse kinker and lethargic phenotypes. The C. elegans pag-3 gene fused to lacZ was expressed in the same pattern in C. elegans and C. briggsae. Unlike many gene homologues compared between C. elegans and C. briggsae, extensive sequence conservation was found in the non-coding regions upstream of the pag-3 exons, in several of the introns and in the downstream non-coding region. Furthermore, the splice acceptor and splice donor sites were conserved, and the size of the introns and exons was surprisingly similar. The predicted protein sequence of C. briggsae PAG-3 was 85% identical to the protein sequence of C. elegans PAG-3. Because so much of the non-coding region of pag-3 was conserved, the control of pag-3 may be quite complex, involving the binding of many trans-acting factors. These results suggest the evolutionary conservation of the pag-3 gene sequence, its expression and function.


Subject(s)
Caenorhabditis elegans Proteins , Caenorhabditis elegans/genetics , Caenorhabditis/genetics , DNA-Binding Proteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Caenorhabditis/physiology , Caenorhabditis elegans/physiology , Conserved Sequence , DNA, Helminth/chemistry , DNA, Helminth/genetics , DNA, Helminth/isolation & purification , DNA-Binding Proteins/physiology , Exons , Genetic Complementation Test , Introns , Molecular Sequence Data , Mutation , Recombinant Fusion Proteins/genetics , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid
13.
Cytogenet Genome Res ; 102(1-4): 32-8, 2003.
Article in English | MEDLINE | ID: mdl-14970675

ABSTRACT

We have constructed a medium density physical map of bovine chromosome 19 using a combination of mapping loci on both a bovine bacterial artificial chromosome (BAC) scaffold map and a whole genome radiation hybrid (WGRH) panel. The resulting map contains 70 loci spanning the length of bovine chromosome 19. Three contiguous groups of BACs were identified on the basis of multiple loci mapping to individual BAC clones. Bovine chromosome 19 was found in this study to be comprised almost entirely from regions of human chromosome 17, with a small region putatively assigned to human chromosome 10. Fourteen breakpoints between the bovine and human chromosomes were detected, with a possibility of five more based on ordering of the WGRH map.


Subject(s)
Chromosomes, Artificial, Bacterial/genetics , Chromosomes/genetics , Genome , Physical Chromosome Mapping/methods , Physical Chromosome Mapping/veterinary , Radiation Hybrid Mapping/methods , Radiation Hybrid Mapping/veterinary , Animals , Cattle , Contig Mapping/methods , Contig Mapping/veterinary , Genetic Markers/genetics , Humans , Male , Oligonucleotide Probes/genetics
14.
Biotechniques ; 33(3): 532-4, 536, 538-9, 2002 Sep.
Article in English | MEDLINE | ID: mdl-12238763

ABSTRACT

We are investigating approaches to increase DNA sequencing quality. Since a majorfactor in sequence generation is the cost of reagents and sample preparations, we have developed and optimized methods to sequence directly plasmid DNA isolated from alkaline lysis preparations. These methods remove the costly PCR and post-sequencing purification steps but can result in low sequence quality when using standard resuspension protocols on some sequencing platforms. This work outlines a simple, robust, and inexpensive resuspension protocol for DNA sequencing to correct this shortcoming. Resuspending the sequenced products in agarose before electrophoresis results in a substantial and reproducible increase in sequence quality and read length over resuspension in deionized water and has allowed us to use the aforementioned sample preparation methods to cut considerably the overall sequencing costs without sacrificing sequence quality. We demonstrate that resuspension of unpurified sequence products generated from template DNA isolated by a modified alkaline lysis technique in low concentrations of agarose yields a 384% improvement in sequence quality compared to resuspension in deionized water. Utilizing this protocol, we have produced more than 74,000 high-quality, long-read-length sequences from plasmid DNA template on the MegaBACET 1000 platform.


Subject(s)
DNA, Bacterial/genetics , Plasmids/genetics , Sepharose , Sequence Analysis, DNA/instrumentation , Sequence Analysis, DNA/methods , Cell Fractionation/methods , DNA, Bacterial/isolation & purification , Electrophoresis, Agar Gel/instrumentation , Electrophoresis, Agar Gel/methods , Plasmids/isolation & purification , Quality Control , Reproducibility of Results , Sensitivity and Specificity
15.
Semin Arthritis Rheum ; 30(4): 288-97, 2001 Feb.
Article in English | MEDLINE | ID: mdl-11182029

ABSTRACT

OBJECTIVE: This manuscript identifies characteristics that put people with rheumatoid arthritis (RA) at high risk for osteoporosis or gastrointestinal (GI) disturbances. The manuscript then reviews therapies available for osteoporosis in the United States and makes recommendations about choosing therapies that minimize GI adverse effects in RA patients at high risk for such events. DATA SOURCES: References identified through MEDLINE, abstracts, and prescribing information for individual drugs. DATA EXTRACTION: Characteristics that predispose patients to osteoporosis and GI problems were identified. Data on individual osteoporosis therapies were assessed by risk-benefit analysis and appropriateness for use in patients at risk for GI disturbances. DATA SYNTHESIS: High risk of osteoporosis in people with RA is caused by disease activity, medication effects, physical inactivity, and standard risk factors such as postmenopausal status and increased age. Patients with RA are frequently at high GI risk if they are receiving nonsteroidal anti-inflammatory drugs or corticosteroids. Because of the high potential for erosive esophagitis and other upper GI disorders with alendronate, caution is warranted in prescribing alendronate to RA patients with high GI risk. In such patients, estrogen replacement therapy, selective estrogen receptor modulators, or calcitonin should be considered for treatment, and either estrogen replacement therapy or selective estrogen receptor modulators should be considered for osteoporosis prevention. CONCLUSIONS: Assessment of GI risk is important in patients with RA and osteoporosis. Risk factors should be considered when choosing osteoporosis therapies.


Subject(s)
Arthritis, Rheumatoid/complications , Gastrointestinal Diseases/prevention & control , Osteoporosis/drug therapy , Alendronate/therapeutic use , Anti-Inflammatory Agents, Non-Steroidal/therapeutic use , Arthritis, Rheumatoid/drug therapy , Estrogen Replacement Therapy , Female , Gastrointestinal Diseases/chemically induced , Humans , Osteoporosis/etiology , Postmenopause , Raloxifene Hydrochloride/therapeutic use , Risk Factors
16.
J Clin Psychiatry ; 59 Suppl 3: 3-7, 1998.
Article in English | MEDLINE | ID: mdl-9541331

ABSTRACT

UNLABELLED: The Clozaril National Registry (CNR) was created to help protect patients from developing potentially fatal agranulocytosis secondary to treatment with the antipsychotic medicine clozapine. The CNR, designed and maintained by the manufacturer of the branded Clozaril (clozapine), has the principal goals of (1) prophylaxis-preventing inappropriate retreatment, and (2) quality assurance-overseeing adherence to a "no blood, no drug" policy. This article reviews the estimated impact of the CNR on clozapine-related morbidity and mortality over the first 5 years of commercial experience in the United States. METHOD: Complete data on leukopenia and agranulocytosis, gathered from the CNR database for the period of 1990-1994, were reviewed and compared with data from the pre-CNR period. RESULTS: Use of clozapine in 99,502 patients according to package labeling requirements (distribution of the medicine linked to mandated white blood cell count testing) was associated with a total of 382 cases of agranulocytosis (0.38%) versus an expected cumulative total of 995 cases (based on the pre-CNR rate of 1% to 2%). Based on the expected agranulocytosis rate, up to 149 deaths might have been anticipated. Instead, there were only 12 deaths attributed to complications of agranulocytosis. CONCLUSION: The CNR provides for universal rechallenge protection as well as controlled dispensing of clozapine. It also serves as an early warning system to promote the safe and effective use of clozapine. The CNR includes quality assurance mechanisms designed to enhance compliance. Despite the added logistic requirements this system places upon physician, pharmacist, and manufacturer, the CNR has helped to reduce substantially potential fatal outcomes. The CNR reinforces both patient and treatment system compliance. Based on this favorable experience concerning agranulocytosis and associated fatalities, the Neuropsychopharmacology Advisory Committee to the U.S. Food and Drug Administration has unanimously recommended a reduction in frequency of the white blood cell count testing requirement after 6 months to every 14 days, instead of weekly. Finally, the CNR database containing white blood cell count and demographic data on every patient in the United States who has received the medicine has served as a unique epidemiologic database.


Subject(s)
Clozapine/adverse effects , Drug Information Services/organization & administration , Adverse Drug Reaction Reporting Systems/organization & administration , Agranulocytosis/chemically induced , Agranulocytosis/epidemiology , Agranulocytosis/prevention & control , Clozapine/therapeutic use , Databases, Factual , Drug Approval , Humans , Leukocyte Count , Leukopenia/chemically induced , Leukopenia/epidemiology , Leukopenia/prevention & control , Registries , Schizophrenia/drug therapy , United States/epidemiology
17.
Neurochem Int ; 27(4-5): 385-96, 1995.
Article in English | MEDLINE | ID: mdl-8845739

ABSTRACT

The mature form of cathepsin D (Cat D), purified to homogeneity from postmortem human brain or mouse brain, behaved as a 42-kDa protein in its native state but revealed additional proteolytic processing under denaturing conditions. Human brain Cat D was composed of a 30-32 kDa heavy chain and a protein doublet consisting of 14 and 15 kDa light chains. Mouse Cat D, which closely resembled the human enzyme in amino acid composition, existed mainly as the uncleaved 42-kDa protein, but up to 40% existed as a complex of 30-32 kDa and 12-14 kDa chains. The 3:1 ratio of light to heavy (30-32 kDa) chains suggested processing of some 30-kDa chains. Cleavage of the 42-kDa chain could not be induced autolytically. Human brain Cat D had a 2-3-fold higher specific activity than the mouse enzyme but shared other properties, including similar biphasic pH optima (peaks at pH 3.30 and 4.2), Km values for methemoglobin and inhibitor profiles. Human Cat D displayed the same polypeptide chain composition when purified from brains differing in postmortem interval (3-28 h). Fresh SH-SY5Y human neuroblastoma cells analyzed on Western blots with anti-Cat D antibodies also displayed only cleaved forms of mature Cat D. Furthermore, brain Cat D isolated from mice stored after death for 5, 15 or 30 h at 25 degrees C contained the same molar ratios of cleaved and uncleaved enzyme found in fresh mouse brain . Cat D activity was stable in human brains with postmortem intervals up to 27 h and stored frozen for up to 3 years. Similarly, total Cat D activity was essentially unchanged in brains of mice subjected to stimulated postmortem conditions for 0.5-4.2 h, although 20% of the total soluble brain protein became insoluble during this postmortem interval. These results demonstrate a remarkable postmortem stability of Cat D and strongly suggest that limited proteolytic cleavage of mature brain Cat D is an in vivo event, the extent of which varies markedly in different species.


Subject(s)
Aging/metabolism , Brain/metabolism , Cathepsin D/chemistry , Cathepsin D/metabolism , Peptide Hydrolases/metabolism , Aged , Animals , Drug Stability , Humans , Immunoblotting , Mice , Mice, Inbred C57BL , Neuroblastoma/metabolism , Neuroblastoma/pathology , Postmortem Changes , Time Factors , Tumor Cells, Cultured
18.
J Clin Pharmacol ; 41(3): 239-50, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11269564

ABSTRACT

This article reviews the different treatments currently available for osteoporosis and examines the benefits and adverse events that are associated with each. While emphasizing safety considerations, this review summarizes the following treatments for osteoporosis: calcium supplements, fluoride, hormone replacement therapy, raloxifene, bisphosphonates, salmon calcitonin, and calcitriol. Before prescribing any of these agents, the clinician should review the risk/benefit profile of each drug in the context of the individual patient's history, concomitant diseases, concurrent medications, and general physical condition.


Subject(s)
Bone Remodeling/drug effects , Osteoporosis/drug therapy , Calcitonin/therapeutic use , Calcitriol/therapeutic use , Calcium/therapeutic use , Diphosphonates/therapeutic use , Drug Therapy, Combination , Female , Fluorides/therapeutic use , Hormone Replacement Therapy/adverse effects , Humans , Osteoporosis/epidemiology , Raloxifene Hydrochloride/therapeutic use , Risk Assessment , Selective Estrogen Receptor Modulators
19.
Pharmacoeconomics ; 19(3): 267-79, 2001.
Article in English | MEDLINE | ID: mdl-11303415

ABSTRACT

OBJECTIVES: To estimate component and total costs of treatment and to examine differences in cost and cost effectiveness between oral antifungal medication and local therapy for patients with toenail onychomycosis. DESIGN: Prospective, observational study of patients with onychomycosis who visited dermatologists and podiatrists in the US. Physicians provided data on clinical management, disease severity, nail improvement and resource utilisation. Patients completed questionnaires on resource utilisation and symptoms at base-line, 4 and 9 months. To estimate costs, reported utilisation was multiplied by unit costs expressed in 1997 US dollars ($US) and derived in 2 ways: first, using Medicare fees; and second, using standard physician fees. RESULTS: After adjustment for key demographic and clinical variables, participants receiving oral medication had higher total costs based on standard fees ($US794 vs $US575) and medication costs ($US564 vs $US109), lower procedure costs ($US0 vs $US122) and physician visit costs ($US200 vs $US330), and greater clinical effectiveness as measured by global improvement rating (86 vs 35%) and Toenail Symptom Index (94 vs 49%). For participants receiving oral medication, 90% of total costs were incurred during the first 4 months of follow-up, whereas for those receiving local therapy, costs were more evenly distributed throughout the study period. Incremental cost-effectiveness analysis showed $US304 to $US491 per additional case improved with oral medication over a 9-month timeframe. Extrapolation of these results using 2 time-points (months 4 and 9) suggested that cost equivalence would be reached 17 to 21 months following the initiation of treatment. CONCLUSIONS: During 9 months of follow-up in patients with toenail onychomycosis, the use of oral antifungal medication resulted in superior patient outcomes, but at higher total cost compared with local therapy.


Subject(s)
Health Care Costs , Onychomycosis/drug therapy , Adult , Aged , Antifungal Agents/therapeutic use , Cost-Benefit Analysis , Female , Humans , Male , Middle Aged , Prospective Studies
20.
Am J Manag Care ; 4(10): 1377-82, 1998 Oct.
Article in English | MEDLINE | ID: mdl-10338731

ABSTRACT

CONTEXT: About 1 in 3 women taking alendronate for osteoporosis report gastrointestinal symptoms, a rate much higher than that found during clinical trials. OBJECTIVE: To establish the frequency of outpatient visits and hospital admissions for acid-related upper gastrointestinal disorder (ARD) among women taking alendronate and to identify potential risk factors. METHODS: A retrospective database analysis identified 812 women with osteoporosis who had filled one or more 10-mg alendronate prescriptions from October 1995 through October 1996. RESULTS: One hundred (12.3%) of the 812 women received healthcare for ARD, a clinical encounter rate of 28.5 per 100 person-years. A reference group of 362,109 women from the same health plan had 17.6 ARD encounters per 100 person-years. Excluding women who had ARDs before receiving alendronate, alendronate users were 1.6 (95% CI = 1.2, 2.7) times more likely to have an ARD encounter than nonusers. Risk of having ARD increased with age [users aged 70 years and older had a relative risk of 1.5 (95% confidence interval (CI) 1.0-2.30) compared with younger women] and with concurrent use of nonsteroidal anti-inflammatory drugs (NSAIDS) (relative risk 1.7, 95% CI 1.1-2.6). CONCLUSIONS: Elderly alendronate users or those concurrently taking NSAIDS should be carefully monitored because of their high risk of having ARD. Cost/benefit analyses of alendronate treatment for osteoporosis should include costs of treating ARD.


Subject(s)
Alendronate/adverse effects , Gastroesophageal Reflux/therapy , Health Maintenance Organizations/statistics & numerical data , Office Visits/statistics & numerical data , Osteoporosis/drug therapy , Patient Admission/statistics & numerical data , Aged , California/epidemiology , Female , Gastroesophageal Reflux/chemically induced , Humans , Incidence , Middle Aged , Retrospective Studies
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