Search PubMed⌕ Search

Biomedical subjects

W Miller

Publications and source records attributed to W Miller.

At least 73 records · Page 4Linked to original sources
PubMed1998

A database of experimental results on globin gene expression.

Information on gene expression and regulation is expanding rapidly, and the complexity of the experimental design and data makes unique demands on databases to store the results. We describe a prototype database containing experimental results on the expression of mammalian beta-like globin genes, along with several query methods for accessing the information. The database has tables for DNA transfer experiments, protein-DNA binding results, and positions of DNase hypersensitive sites, which make extensive use of nested data structures. Comparison of data from various mammals is accomplished by providing a common coordinate system via a simultaneous alignment of matching DNA sequences. Interactive access to the database is available at a site called the Globin Gene Server on the World Wide Web (http://globin.cse. psu.edu). This software should be useful for any genetic system in which DNA sequence data are available.

Animals↗
PubMed1998

Protein sequence similarity searches using patterns as seeds.

Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the pattern-hit initiated BLAST (PHI-BLAST) program described here takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence. The random distribution of PHI-BLAST alignment scores is studied analytically and empirically. In many instances, the program is able to detect statistically significant similarity between homologous proteins that are not recognizably related using traditional single-pass database search methods. PHI-BLAST is applied to the analysis of CED4-like cell death regulators, HS90-type ATPase domains, archaeal tRNA nucleotidyltransferases and archaeal homologs of DnaG-type DNA primases.

Adenosine Triphosphatases↗
PubMed1998

The iron chelator L1 potentiates oxidative DNA damage in iron-loaded liver cells.

Iron-mediated carcinogenesis is thought to occur through the generation of oxygen radicals. Iron chelators are used in attempts to prevent the long term consequences of iron overload. In particular, 1,2-dimethyl-3-hydroxypyrid-4-one (L1), has shown promise as an effective chelator. Using an established hepatocellular model of iron overload, we studied the generation of iron-catalyzed oxidative DNA damage and the influence of iron chelators, including L1, on such damage. Iron loading of HepG2 cells was found to greatly exacerbate hydrogen peroxide-mediated DNA damage. Desferrithiocin was protective against iron/hydrogen peroxide-induced DNA damage; deferoxamine had no effect. In contrast, L1 exposure markedly potentiated hydrogen peroxide-mediated oxidative DNA damage in iron-loaded liver cells. However, when exposure to L1 was maintained during incubation with hydrogen peroxide, L1 exerted a protective effect. We interpret this as indicating that L1's potential toxicity is highly dependent on the L1:iron ratio. In vitro studies examining iron-mediated ascorbate oxidation in the presence of L1 showed that an L1:iron ratio must be at least 3 to 1 for L1 to inhibit the generation of free radicals; at lower concentrations of L1 increased oxygen radical generation occurs. In the clinical setting, such potentiation of iron-catalyzed oxidative DNA damage at low L1:iron ratios may lead to long-term toxicities that might preclude administration of L1 as an iron chelator. Whether this implication in fact extends to the in vivo situation will have to be verified in animal studies.

Cell Line↗
PubMed1998

Multiple regulatory elements in the 5'-flanking sequence of the human epsilon-globin gene.

We have previously reported, on the basis of transfection experiments, the existence of a silencer element in the 5'-flanking region of the human embryonic (epsilon) globin gene, located at -270 base pairs 5' to the cap site, which provides negative regulation for this gene. Experiments in transgenic mice suggest the physiological importance of this epsilon-globin silencer, but also suggest that down-regulation of epsilon-globin gene expression may involve other negative elements flanking the epsilon-globin gene. We have now extended the analysis of epsilon-globin gene regulation to include the flanking region spanning up to 6 kilobase pairs 5' to the locus control region using reporter gene constructs with deletion mutations and transient transfection assays. We have identified and characterized other strong negative regulatory regions, as well as several positive regions that affect transcription activation. The negative regulatory regions at -3 kilobase pairs (epsilonNRA-I and epsilonNRA-II), flanked by a positive control element, has a strong effect on the epsilon-globin promoter both in erythroid K562 and nonerythroid HeLa cells and contains several binding sites for transcription factor GATA-1, as evidenced from DNA-protein binding assays. The GATA-1 sites within epsilonNRA-II are directly needed for negative control. Both epsilonNRA-I and epsilonNRA-II are active on a heterologous promoter and hence appear to act as transcription silencers. Another negative control region located at -1.7 kilobase pairs (epsilonNRB) does not exhibit general silencer activity as epsilonNRB does not affect transcription activity when used in conjunction with an epsilon-globin minimal promoter. The negative effect of epsilonNRB is erythroid specific, but not stage-specific as it can repress transcription activity in both K562 erythroid cells as well as in primary cultures of adult erythroid cells. Phylogenetic DNA sequence comparisons with other primate and other mammalian species show unusual degree of flanking sequence homology for the epsilon-globin gene, including in several of the regions identified in these functional and DNA-protein binding analyses, providing alternate evidence for their potential importance. We suggest that the down-regulation of epsilon-globin gene expression as development progresses involves complex, cooperative interactions of these negative regulatory elements, epsilonNRA-I/epsilonNRA-II, epsilonNRB, the epsilon-globin silencer and probably other negative and positive elements in the 5'-flanking region of the epsilon-globin gene.

Animals↗
PubMed1998

Analysis of 9-fluorenylmethoxycarbonyl (FMOC) loading of solid-phase synthesis resins by gas chromatography

Base-catalyzed cleavage of the 9-fluorenylmethoxycarbonyl (FMOC) group and subsequent analysis by UV spectrophotometry is commonly employed to measure the "loading" of functional groups on solid support. Recent work suggests that 1,8-diazabicyclo[5.4. 0]undec-7-ene (DBU) may be superior to piperidine (the most commonly used base for the cleavage) for quantitative analysis by UV. We have compared deprotection of FMOC-bearing compounds by both DBU and piperidine, and have observed by GC-MS the formation of a dibenzofulvene-piperidine adduct (piperidine deprotection), and the formation of unassociated dibenzofulvene (DBU deprotection). We have further been able to use GC analysis of dibenzofulvene produced in the DBU deprotection mixture in a quantitative analysis of resin loading, which gave results comparable to UV methods. Sample preparation for this method has been automated using the Nautilus 2400 organic synthesizer to reduce the amount of operator time and increase throughput of sample analysis. Copyright 1998 John Wiley & Sons, Inc.

Journal Article↗
PubMed1998

A combination of low-dose cyclophosphamide and colony-stimulating factors is more cost-effective than granulocyte-colony-stimulating factors alone in mobilizing peripheral blood stem and progenitor cells.

BACKGROUND: The use of peripheral blood progenitor cells (PBPCs) instead of autologous bone marrow leads to more rapid engraftment following high-dose chemotherapy. Mobilization regimens differ with respect to toxicity, efficiency, and cost. STUDY DESIGN AND METHODS: Two cohorts of patients with breast cancer received one of two mobilization regimens: granulocyte-colony-stimulating factor (G-CSF) at 10 micrograms per kg was given subcutaneously for 5 days, with leukapheresis begun on Day 6, or low-dose cyclophosphamide followed by sequential granulocyte-macrophage-CSF (GM-CSF) at 5 micrograms per kg for 5 days and by G-CSF at 10 micrograms per kg, with leukapheresis begun on Day 11. Results of CD34+ cell collection, engraftment, and costs of mobilization were determined. RESULTS: The combination chemotherapy and growth factor regimen was more efficient in mobilizing CD34+ cells. Sixty-six percent of patients reached a target 4 x 10(6) CD34+ cells per kg in a single leukapheresis session with the combination regimen, compared to 14 percent who received G-CSF alone (p < 0.01). The mean number of leukapheresis sessions required to reach a target of 4 x 10(6) CD34+ cells per kg was 1.3 for the combination regimen and 2.7 for the regimen of G-CSF alone (p < 0.01). One patient in the chemotherapy and growth factor group developed febrile neutropenia. Engraftment was similar in both cohorts of patients. The cost of mobilization, including all supplies and cryopreservation, was $7381 for the G-CSF regimen and $5508 for the chemotherapy regimen (p < 0.05). This reduction was attributed to the lower number of leukapheresis and cryopreservation sessions, which outweighed the slight increase in expense for chemotherapy and growth factor in the combination regimen. CONCLUSION: This combination mobilization regimen allowed the predictable and efficient collection of CD34+ cells from the peripheral blood in a limited number of leukapheresis sessions, which reduced the cost of mobilization by approximately 25 percent.

Adult↗
PubMed1998

Alignments without low-scoring regions.

Given a strong match between regions of two sequences, how far can the match be meaningfully extended if gaps are allowed in the resulting alignment? The aim is to avoid searching beyond the point that a useful extension of the alignment is likely to be found. Without loss of generality, we can restrict attention to the suffixes of the sequences that follow the strong match, which leads to the following formal problem. Given two sequences and a fixed X > 0, align initial portions of the sequences subject to the constraint that no section of the alignment scores below -X. Our results indicate that computing an optimal alignment under this constraint is very expensive. However, less rigorous conditions on the alignment can be guaranteed by quite efficient algorithms. One of these variants has been implemented in a new release of the Blast suite of database search programs.

Algorithms↗
PubMed1998

Use of physician assistants as surgery/trauma house staff at an American College of Surgeons-verified Level II trauma center.

BACKGROUND: Historically, surgical physicians staff trauma centers, which provide trauma patients with improved outcomes. Such benefits fuel the expansion of designated trauma centers. Cutbacks in residency programs of surgical specialties, however, necessitate substitutions for traditional trauma providers. METHODS: A literature and record review was conducted to examine the use of physician assistants in a large community hospital's verified trauma center. Current and historical outcomes were analyzed regarding the trauma surgeon/physician assistant model. RESULTS: Injury Severity Scores increased 19%, transfer time to the operating room decreased 43%, transfer time to the intensive care unit decreased 51%, and transfer time to the floor decreased 20%. The length of stay for admissions decreased 13%, and the length of stay for neurotrauma intensive care unit patients decreased 33%. CONCLUSION: The Hurley Medical Center trauma surgeon/physician assistant model is a viable alternative for verified trauma centers unable to maintain a surgical residency program. Consistency and quality of care indicated by shortened length of stay is a hallmark of such a model providing the highest quality of care.

Adolescent↗
PubMed1998

Effect of topical anesthetic use on initial patient satisfaction and overall success with rigid gas permeable contact lenses.

BACKGROUND: Rigid gas permeable (RGP) contact lenses have numerous benefits; however, RGP lens use is not increasing in the United States. An important factor for this trend has been initial comfort. Studies have demonstrated that how RGPs are presented to patients, in addition to lens design, can play an important role in the initial comfort process. Another important factor could be the use of a topical anesthetic during the fitting and dispensing visits. The purpose of this study was to use a multicenter format to determine if topical anesthetic use increased the likelihood of patient satisfaction and success. METHODS: A total of 80 subjects, with no previous rigid lens wear experience, was entered into this 1-month study, including 20 subjects from each of 4 institutions. Subjects were randomly divided into the following two groups: (A) anesthetic or (B) placebo, with the former group receiving one drop of a topical anesthetic before lens insertion at both the diagnostic fitting and dispensing visits, whereas the latter group received a placebo. Subjects completed a questionnaire on their perception of rigid lens wear both immediately before fitting and at the 1-month visit. After diagnostic fitting with rigid lenses, subjects completed an adaptation questionnaire after 15 min, 1 week, 2 weeks, and 1 month of lens wear. RESULTS: Seventy of the 80 subjects completed the study and, of the 10 subjects who discontinued, 8 were in the placebo group. In all categories evaluated, the anesthetic group experienced a more optimum adaptation experience at each visit vs. the placebo group. Specifically, overall comfort was rated significantly higher at both dispensing and 2 weeks. In addition, the anesthetic group exhibited significantly greater overall satisfaction with rigid lens wear at 2 and 4 weeks. Also, the anesthetic group perceived their adaptation, sensitivity, and adaptation time to be significantly better at the 1-month visit. There was no significant difference in corneal staining between these two groups at each visit, with the exception of a greater amount of staining in the central quadrant for the placebo group at the 1-month visit. CONCLUSIONS: The use of a topical anesthetic at the fitting and dispensing visits for first-time wearers of RGP lenses resulted in significantly fewer dropouts, improved initial comfort, an enhanced perception of the adaptation process, and greater overall satisfaction after 1 month of lens wear as compared to the use of a nonanesthetizing placebo at those visits. This result, in combination with both presenting RGP lenses in a nonthreatening manner and optimizing the lens design and fitting relationship, should result in a positive adaptation process and successful wear of RGP contact lenses.

Adaptation, Physiological↗
PubMed1998

Analysis of the quality and utility of random shotgun sequencing at low redundancies.

The currently favored approach for sequencing the human genome involves selecting representative large-insert clones (100-200 kb), randomly shearing this DNA to construct shotgun libraries, and then sequencing many different isolates from the library. This method, entitled directed random shotgun sequencing, requires highly redundant sequencing to obtain a complete and accurate finished consensus sequence. Recently it has been suggested that a rapidly generated lower redundancy sequence might be of use to the scientific community. Low-redundancy sequencing has been examined previously using simulated data sets. Here we utilize trace data from a number of projects submitted to GenBank to perform reconstruction experiments that mimic low-redundancy sequencing. These low-redundancy sequences have been examined for the completeness and quality of the consensus product, information content, and usefulness for interspecies comparisons. The data presented here suggest three different sequencing strategies, each with different utilities. (1) Nearly complete sequence data can be obtained by sequencing a random shotgun library at sixfold redundancy. This may therefore represent a good point to switch from a random to directed approach. (2) Sequencing can be performed with as little as twofold redundancy to find most of the information about exons, EST hits, and putative exon similarity matches. (3) To obtain contiguity of coding regions, sequencing at three- to fourfold redundancy would be appropriate. From these results, we suggest that a useful intermediate product for genome sequencing might be obtained by three- to fourfold redundancy. Such a product would allow a large amount of biologically useful data to be extracted while postponing the majority of work involved in producing a high quality consensus sequence.

Animals↗
PubMed1998

A computer program for aligning a cDNA sequence with a genomic DNA sequence.

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.

Algorithms↗
PubMed1998

Synthesis and evaluation of some masked phosphate esters of the anti-herpesvirus drug 882C (netivudine) as potential antiviral agents.

A number of symmetric and asymmetric 5'-phosphate esters of the potent anti-varicella-zoster virus (VZV) agent 1-(beta-D-arabinofuranosyl)-5-prop-1-ynyluracil (882C; netivudine) were prepared as potential lipophilic, membrane-soluble prodrugs of the bio-active phosphate forms. The compounds were prepared by the base-catalysed coupling of various phosphorochloridates with the free nucleoside analogue. Compounds were fully characterized by a range of spectroscopic and analytical methods and were studied for their inhibition of several viruses in tissue culture. All of the phosphate esters were inactive against human cytomegalovirus, herpes simplex virus type 2, VZV, human immunodeficiency virus type 1 and influenza A virus (EC50 > 100 microM) except the 5'-(4-nitrophenyl phenyl) phosphate, which inhibited influenza A virus. The relative rate of esterase-mediated hydrolysis of one of the lead target structures was measured in order to rationalize the poor antiviral action, and data were collected on possible metabolites in support of this analysis. Cell-specific esterases are implicated as key determinants of the antiviral potency of prodrugs of this type.

Animals↗
PubMed1998

The Paced Auditory Serial Addition Task (PASAT): norms for age, education, and ethnicity.

The Paced Auditory Serial Addition Task (PASAT) is often used to measure attention, concentration, working memory, and speed of information processing. Using a modified 200-item version of the PASAT with presentation rates of 3.0, 2.4, 2.0, and 1.6 items per second, we analyzed demographic influences on test performance in a large sample (N = 566) of healthy North American adults. We found that age, education, and ethnicity were significant predictors, accounting for nearly 23% of the variance in test performance. We discuss these results in comparison to previous normative studies, and present a formula and tables for computing age, education, and ethnicity-adjusted T scores for performance on the PASAT 200.

Adult↗
PubMed1998

Tirapazamine with cisplatin in patients with advanced non-small-cell lung cancer: a phase II study.

PURPOSE: A phase II study was conducted to evaluate the safety and efficacy of tirapazamine combined with cisplatin for the treatment of patients with advanced non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Forty-four patients with stage IIIB/IV NSCLC were treated with a combination of tirapazamine and cisplatin. Patients received tirapazamine 260 mg/m2 administered intravenously over 2 hours, followed 1 hour later by cisplatin 75 mg/m2 administered over an additional hour, repeated every 21 days. The duration of therapy was meant to be limited to four cycles for nonresponders and eight cycles for responders. RESULTS: Ten of 44 patients (23%) showed a partial response. The estimated median survival for all patients was 37 weeks. Toxicities were treatable and included grade 3 nausea or vomiting (25%), fatigue (27.3%), and muscle cramps (4.5%). No dose reductions were necessary. CONCLUSION: The results show that tirapazamine can safely be added to cisplatin. Both the median survival and response rate observed strongly suggest that tirapazamine with cisplatin is more active than cisplatin alone.

Adult↗
PubMed1998

Caffeine and nicotine use in an addicted population.

This study was undertaken to examine differences in caffeine and nicotine use between the psychiatric population and the addicted population in a private psychiatric inpatient facility. Eighty-six patients on an adult addictive disease inpatient unit and 80 patients on an adult psychiatry unit in a private psychiatric hospital were interviewed with regard to their use of nicotine and caffeine. In addition, demographic information and primary diagnoses were obtained from the psychiatric admission assessment in the medical record as listed by the admitting psychiatrist. Although there was little difference in psychiatric patients vs. chemically dependent patients with regard to the percentage of caffeine users, the chemically dependent individuals drank more coffee, soft drinks, and tea. A much greater percentage of the chemically dependent individuals also smoked cigarettes, although not in a greater amount than the psychiatric patients who smoked. Because group assignment was not random, ordinary least squares (OLS) regression analyses were conducted to determine the independent associations of age, sex, education, and treatment population in predicting levels of caffeine and tobacco use. Even after controlling for demographic differences between the two samples, chemically dependent patients still reported higher levels of daily caffeine and tobacco use than patients on the general psychiatric unit.

Adolescent↗
PubMed1998

Access to a syllabus of human hemoglobin variants (1996) via the World Wide Web.

Information on mutations in human hemoglobin is important in many efforts, including understanding the pathophysiology of hemoglobin diseases, developing therapies, elucidating the dynamics of sequence alterations inhuman populations, and dissecting the details of protein structure/function relationships. Currently, information is available on a large number of mutations and variants, but is distributed among thousands of papers. In an effort to organize this voluminous data set, two Syllabi have been prepared compiling succinct information on human hemoglobin abnormalities. In both of these, each entry provides amino acid and/or DNA sequence alterations, hematological and clinical data, methodology used for characterization, ethnic distribution, and functional properties and stability of the hemoglobin, together with appropriate literature references. A Syllabus of Human Hemoglobin Variants (1996) describes 693 abnormal hemoglobins resulting from alterations in the alpha-, beta-, gamma-, and delta-globin chains, including special abnormalities such as double mutations, hybrid chains, elongated chains, deletions, and insertions. We have converted this resource to an electronic form that is accessible via the World Wide Web at the Globin Gene Server (http://globin.cse.psu.edu). Hyperlinks are provided from each entry in the tables of variants to the corresponding full description. In addition, a simple query interface allows the user to find all entries containing a designated word or phrase. We are in the process of converting A Syllabus of Thalassemia Mutations (1997) to a similar electronic format.

Computer Communication Networks↗