Laboratory and Basic Science Research Commons^™

A Pseudolikelihood Approach For Simultaneous Analysis Of Array Comparative Genomic Hybridizations (Acgh), David A. Engler, Gayatry Mohapatra, David N. Louis, Rebecca Betensky

Harvard University Biostatistics Working Paper Series

DNA sequence copy number has been shown to be associated with cancer development and progression. Array-based Comparative Genomic Hybridization (aCGH) is a recent development that seeks to identify the copy number ratio at large numbers of markers across the genome. Due to experimental and biological variations across chromosomes and across hybridizations, current methods are limited to analyses of single chromosomes. We propose a more powerful approach that borrows strength across chromosomes and across hybridizations. We assume a Gaussian mixture model, with a hidden Markov dependence structure, and with random effects to allow for intertumoral variation, as well as intratumoral clonal …

Application Of A Multiple Testing Procedure Controlling The Proportion Of False Positives To Protein And Bacterial Data, Merrill D. Birkner, Alan E. Hubbard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Simultaneously testing multiple hypotheses is important in high-dimensional biological studies. In these situations, one is often interested in controlling the Type-I error rate, such as the proportion of false positives to total rejections (TPPFP) at a specific level, alpha. This article will present an application of the E-Bayes/Bootstrap TPPFP procedure, presented in van der Laan et al. (2005), which controls the tail probability of the proportion of false positives (TPPFP), on two biological datasets. The two data applications include firstly, the application to a mass-spectrometry dataset of two leukemia subtypes, AML and ALL. The protein data measurements include intensity and …

Test Statistics Null Distributions In Multiple Testing: Simulation Studies And Applications To Genomics, Katherine S. Pollard, Merrill D. Birkner, Mark J. Van Der Laan, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We have developed generally applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for control of a broad class of Type I error rates, defined as tail probabilities and expected values for arbitrary functions of the numbers of false positives and rejected hypotheses (Dudoit and van der Laan, 2005; Dudoit et al., 2004a,b; Pollard and van der Laan, 2004; van der Laan et al., 2005, 2004a,b). As argued in the early article of Pollard and van der …

Alternative Assay Techniques For Protein Kinase A, Justin Brink

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Acute Toxicity Testing Without Animals: More Scientific And Less Of A Gamble, Gillian R. Langley

Application of Alternative Methods Collection

In this report, we argue specifically that acute toxicity data should not be sought from animal tests. The underlying principle of such tests on rats and mice is that the results can be effectively extrapolated to humans. In fact, after nearly 80 years of use of these tests, the predictivity of rodent data for human acute toxic effects has been disputed but never proven.

Multiple Testing Procedures: R Multtest Package And Applications To Genomics, Katherine S. Pollard, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics. The current version of multtest provides MTPs for tests concerning means, differences in means, and regression parameters in linear and Cox proportional hazards models. Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of false positives and rejected hypotheses. These error rates include tail probabilities …

Anatomy And Three-Dimensional Reconstructions Of The Brain Of A Bottlenose Dolphin (Tursiops Truncatus) From Magnetic Resonance Images, Lori Marino, Keith D. Sudheimer, Timothy L. Murphy, Kristina K. Davis, D. Ann Pabst, William A. Mclellan, James K. Rilling, John I. Johnson

Veterinary Science and Medicine Collection

Cetacean (dolphin, whale, and porpoise) brains are among the least studied mammalian brains because of the formidability of collecting and histologically preparing such relatively rare and large specimens. Magnetic resonance imaging offers a means of observing the internal structure of the brain when traditional histological procedures are not practical. Furthermore, internal structures can be analyzed in their precise anatomic positions, which is difficult to accomplish after the spatial distortions often accompanying histological processing. In this study, images of the brain of an adult bottlenose dolphin, Tursiops truncatus, were scanned in the coronal plane at 148 antero-posterior levels. From these scans …

Magnetic Resonance Imaging And Three-Dimensional Reconstructions Of The Brain Of A Fetal Common Dolphin, Delphinus Delphis, Lori Marino, Timothy L. Murphy, Lyad Gozal, John I. Johnson

Veterinary Science and Medicine Collection

To demonstrate the kinds of data that can be obtained non-destructively and non-invasively from preserved museum specimens using modern imaging technology the head region of a whole body fetal specimen of the common dolphin, Delphinus delphis, aged 8–9 months post-conception, was scanned using Magnetic Resonance Imaging (MRI). Series of scans were obtained in coronal, sagittal and horizontal planes. A digital three-dimensional reconstruction of the whole brain was prepared from the coronal series of scans. Sectional areas and three-dimensional volumes were obtained of the cerebral hemispheres and of the brainstemplus-cerebellum. Neuroanatomical features identified in the scans include the major sulci of …

Horticulture Research Report 1994 - 1998, Frank Wise Institute, Kununurra, Department Of Agriculture, Western Australia, D. Robinson, M. Howes, R. Randell

Horticulture research reports

This report summarises horticultural research, development and extension activities undertaken by staff from the Kununurra District Office during the period 1993 to 1998 and reported annually at the Frank Wise Institute Horticultural Research Review. The range and extent of activities presented and supported by Agriculture Western Australia with industry collaboration indicates the importance of horticulture in the economies of the Kimberley Region and Western Australia. Further support by funding bodies and agribusiness, and collaboration with other research organizations is also acknowledged. Since the early 1980's, horticultural output and value of production from the Ord River Irrigation Area (ORIA) have risen …

A Pilot Study Testing A Proprietary Sealant For Plaque Reduction, Jennifer Rowland

Loma Linda University Electronic Theses, Dissertations & Projects

Enamel demineralization due to increased plaque accumulation is a well-recognized problem associated with fixed orthodontic appliances. The purpose of this study was to evaluate the efficacy of a proprietary product to be marketed by 3M Unitek for the reduction of plaque accumulation and thereby reduce enamel demineralization.

Sixty four bovine teeth were divided equally into an untreated control group and a group treated with the proprietary sealant product. Both groups were subsequently immersed in a Streptococcus mutans culture. Plaque deposits from each group were removed, suspended in trypticase soy broth, serially diluted, and plated on trypticase soy agar at 1, …

Western Australian Fisheries - Key Achievements 1997-1998, Fisheries Western Australia

Fisheries Published Reports

The WA fishing community can look back at the past year with considerable satisfaction.

Close partnership arrangements between Government, industry, the community and Fisheries Western Australia have both consolidated and advanced the State's position at the forefront of sustainable management of marine environments and fish resources.

Together, commercial fishing and recreational fishing make 􀁚 annual $1.5 billion contribution to the Western Australian economy. Through a carefully balanced portfolio of policies and initiatives the Coalition is making sure that both sectors continue to prosper, while at the same time ensuring that future generations inherit a marine environment which we are all …

Periodontal Repair In Dogs : Evaluation Of Rhbmp-2 Carriers, Lauralee Nygaard

Loma Linda University Electronic Theses, Dissertations & Projects

This study evaluated candidate carriers for recombinant human bone morphogenic protein-2 (rhBMP-2) in periodontal reconstructive surgery.

Canine demineralized bone matrix (DBM), bovine inorganic crystallene bone matrix (Bio-Oss), bovine derived microfibrillar collagen matrix (Helistat), poly (D,L-lactide-coglycolide) micropaiticles (PLGA), and polylactic acid granules (Drilac) were used with rhBMP-2 (20 (µg/100 µl implant volume) in routine critical size canine supraalveolar periodontal defects. Contralateral defects in six beagle dogs were randomly assigned to receive: DBM/rhBMP-2, DBM-control, Bio-Oss/rhBMP-2, Helistat/rhBMP-2, PLGA/rhBMP-2, or Drilac/rhBMP-2, all with autologous blood except for Helistat and PLGA. Animals were sacrificed eight weeks post-surgery and block sections of the defects were processed …

1991 Catalogue Of The Australian Lupin Collection Including Field Evaluation Data For Wild, Semi-Domesticated And Fully Domesticated Accessions, J. C. Clements, W. A. Cowling

Grain and other field crops research reports

This report lists all wild, semi-domesticated and fully domesticated accessions in the Australian Lupin Collection to 1991. The Collection is composed of 2,264 accessions (Perth Numbers between 20629 and 27067) introduced to Australia or from naturalized populations and breeding programmes within Australia. Several accessions are selections from variable populations which were identified during field trials in South Perth, Western Australia. This catalogue lists the characteristics and field evaluation data for every accession where available. Plant breeders and crop scientists will find this information useful for the selection of lupin genotypes with desired characteristics.

Section A of this catalogue should be …

A Flow Cytometric Analysis Of Immunocyte Populations In Peripheral Blood And Pleural Effusions Of Patients With Cancer, Mandy L. Bohn

Loma Linda University Electronic Theses, Dissertations & Projects

Two-color flow cytometric analysis was performed on paired samples of peripheral blood (PB) and pleural effusions (PE) of patients with metastatic malignancies. The purpose of these analyses was to test the hypothesis that there are significant differences in the distribution of immunocyte populations in the PE compared to that of the PB.

The majority of the pleural fluid immunocytes were CD3+ cells. The ratio of CD4+ to CD8+ cells was higher in the PE compared to PB. Levels of CD8+, CD19+ and CD14+ cells were not significantly different in the PE compared to the levels in the PB. CD16+CD56+ cells …

The Role Of T Cells In The Pathogenesis Of Periapical Lesions, John B. Wallstrom

Loma Linda University Electronic Theses, Dissertations & Projects

The pulps of mandibular molars of 15 athymic and 15 conventional rats were surgically exposed and left open to their oral flora. Each group was divided into 3 subgroups of 5 animals each. The rats were sacrificed after their pulps were exposed for 2, 4, or 8 weeks. After fixing, decalcifying, and embedding, the specimens were sectioned and stained with H and E. They were then examined under a microscopic grid and quantified by percentages of surface areas of bone, connective tissue, bone marrow, intrabony spaces, periapical lesions, and numbers of osteoclasts. This was done using a DataVoice computerized data …

Effect Of Photoperiod On Developmental Morphology And Enolase Isoenzyme Immunohistochemistry In Rat And Djungarian Hamster Superficial Pineal Glands, Chalmer D. Mcclure

Loma Linda University Electronic Theses, Dissertations & Projects

The best understood functional activity of the pineal gland is its diurnal production of melatonin in response to environmental lighting cues. Several enzymes of the melatonin pathway respond to daily photoperiod changes, for example hydroxyindole-O-methyltransferase (HIOMT) and serotonin N-acetyltransferase (SNAT). Increased levels of the glycolytic enzyme neuron-specific enolase (NSE) are thought to reflect increased physiological demands placed on neurons and neuroendocrine tissues. Homodimer non-neuronal enolase isoenzyme (NNE) is immunolocalized to cells, and the hybrid enolase (consisting of subunits from NSE and NNE) has been seen in cerebellar stellate and basket cells. Although not rate limiting, concentrations of both NSE and …

Decreased Triiodothyronine Binding To The Hepatic Nuclear Thyroid Hormone Receptor In The Diabetic Mouse, Thomas J. Dewind

Loma Linda University Electronic Theses, Dissertations & Projects

The diabetic C57BL/KsJ-db m mouse has abnormal thyroid hormone levels and indications of thyroid hormone resistance. To investigate the basis of these abnormalities, the hepatic nuclear thyroid hormone receptor was extracted with 0.4 M KCl, 1.1 mM MgCl₂, 20 mM Tris/HCl, pH 7.9 from hepatocyte nuclei of normal C57BL/KsJ, heterozygous C57BL/KsJ-db m (db/m), and diabetic C57BL/KsJ-db m (db/db) mice. Normal and heterozygous mice were grouped together as the controls. Triiodothyronine (T₃) binding studies at 4°C using nitrocellulose filtration to separate free T₃ from receptor bound T₃ demonstrated an …

Estimation Of Food Limitation In Daphnia Pulex From Boulder Basin, Lake Mead, Thomas Mark Bartanen

Publications (WR)

In February, 1982 I began a year-long study to determine if growth and reproduction in Daphnia Pulex were limited by the amount of food available in Boulder Basin, Lake Mead. To determine this, I made monthly collections of Daphnia Pulex and natural lake seston from an already established station in Boulder Basin. I cultured the Daphnia Pulex under simulated field conditions in a flow-through feeding apparatus using four different food regimes; 1-natural lake seston filtered through 80 um mesh to remove other zooplankton, 2-lake seston (as above) with an enrichment of 10³ cells-ml^-1 of Chlamydomonas reinhardti, 3-lake …

The Effect Of Dietary Fat Level On Tumor Development And Immunity In Balb/C Mice Fed Casein Of Wheat Gluten As Protein And Challenged With Herpes Type 2-Transformed Cells, Helen Drakou

Loma Linda University Electronic Theses, Dissertations & Projects

A high percentage of fat in the diet has been implicated through epidemiological studies in several human cancers. Studies in experimental animals have produced evidence that increasing the fat in the diet decreases the animal’s ability to restrict tumor development and growth. In previous work done in this laboratory with BALB/c mice injected with herpes simplex Type 2-transformed mouse cells (H238), the effects of a diet which greatly enhanced tumor growth was compared with one which restricted tumor growth. The latter, a low (5%) fat, low protein diet, in which the protein was casein, was also found to produce a …

The Significance Of Alternative Techniques In Biomedical Research: An Analysis Of Nobel Prize Awards, Martin Stephens

Experimentation Collection

No abstract provided.

The Effect Of Dietary Alpha - Linolenic Acid On Apparent Risk Factors Of Cardiovascular Disease, Kelvin D. Lindbeck

Loma Linda University Electronic Theses, Dissertations & Projects

Eight healthy male lacto-ovo-vegetarian subjects averaging 28.0 ± 3.6 years of age (22 to 53 years) were fed a diet rich in α-linolenic acid (18:3 ω 3) for four weeks. Arterial blood pressure and body weight were recorded each week. Plasma 6-keto-prostaglandin F_1α (6-keto- PGF_1α ), thromboxane B₂ (TXB₂), total cholesterol, triglyceride, and total phospholipid fatty acid composition were analyzed at 0, 2 and 4 weeks.

Systolic blood pressure increased significantly between weeks 0 and 1 (106.5 ± 2.7 mmHg to 114.0 ± 3.7 mmHg; p < 0.003), but decreased to 107.3 t 2.6 mrHg (p < 0.02) at week 2. There was an insignificant increase in both systolic and diastolic blood pressures after four weeks. There was no significant change in either total cholesterol or triglyceride levels during the four weeks.

Plasma 6-keto-PGF_1α levels increased significantly from 60.13 ± …

Protection Of Animals And Animal Experimentation: A Survey Of Scientific Experts, Norbert Lagoni, Joachim Fiebelkorn, Hans-Joachim Wormuth

Experimentation Collection

This article summarizes information from a survey of biomedical scientists, specifically pharmacologists and toxicologists, on the use of laboratory animals and the potential for replacing their use with alternative methods for the development and evaluation of pharmaceutical substances. The majority of those surveyed felt that the alternatives could supplement or complement animal tests, but not replace the tests altogether. However, most favored the use of nonsentient material in safety tests.

The Effect Of Hypercholesterolemia On The Membrane Lipids, 3-0-[¹⁴C] Methylglucose Transport, And 2,3-Diphosphoglycerate Levels In Rat Erythrocytes, Edwin J. Lester Jr.

Loma Linda University Electronic Theses, Dissertations & Projects

An increase in dietary cholesterol and cholic acid will produce hypercholesterolemia in rats. For ten months, two groups of rats (six in each group) were fed commercial rat pellets (control group) or rat pellets plus cholesterol (1%) and cholic acid (0.25%) (experimental group). A blood sample from each animal was divided into three aliquots for three separate experiments on the erythrocytes: a membrane cholesterol and phospholipid determination, a 3-0-[¹⁴C] methylglucose (30MG) transport determination, and a 2,3-diphosphoglycerate (2,3 DPG) determination. The 30MG transport and 2,3 DPG aliquots were each incubated in the same five concentrations of 30MG and glucose …

A Morphometrical Analysis Of The Guinea Pig Placenta After Chronic Exposure To Carbon Monoxide, Marcella J. Woolsey

Loma Linda University Electronic Theses, Dissertations & Projects

We used morphometric analysis to determine if placental structure is modified by carbon monoxide, Camm-Hartley guinea pigs were exposed throughout gestation to chronic conditions of carbon monoxide (averaging about 180 parts per million). Maternal weight, placental weight, fetal weight, and fetal length were recorded at the time of placental fixation. Using a computerized image analyzer on photomicrographs obtained through light microscopy, we measured maternal and fetal percent vessel volumes, surface areas, and vessel numbers. Maternal vessel numbers and surface area remained basically unchanged but decreased slightly. Maternal percent volume decreased 15%. However, fetal capillary number increased 35% (p < 0.01) from a control value of 2325 ± 184 per mm² (SE …

The Effect Of Periapical Inflammation On Cellular Cementum : A Scanning Electron Microscope Study, Gary S. Yonemoto

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of this study was to obtain information on the morphologic changes that occur in cellular cementum exposed to periapical inflammation.

Ten single rooted human teeth were collected. There were five specimens of normal cellular cementum and five specimens of diseased cellular cementum, which had been exposed to periapical inflammation. Each specimen was fractured longitudinally through the apical foramen, leaving the organic component intact. The cross-sectional morphology of cellular cementum was then examined using an ARM Model 1000 scanning electron microscope. Energy dispersive x-ray spectrometry was also conducted on samples representative of the two test groups.

A methodology was …

Grain Crop Variety Trials Western Australia 1978-1979, H. M. Fisher, G. B. Crosbie

Grain and other field crops research reports

The regional crop variety testing programme conducted by the Western Australian Department of Agriculture covers the final two stages of a four stage process of evaluating locally produced crossbreds and introduced material comprising:-

Plant Breeder Trials

Stage 1: Initial small plot yield tests on early generation material - 1 to 3 sites. Stage 2: Small plot yield tests on selected material (F5 derived) - 3 to 4 sites.

Regional Testing Programme

Stage 3: Large scale preliminary trials - 9 to 10 sites. Stage 4: Large scale final yield trials - 40 to 50 sites.

The basis of the regional programme …

Ultrasonic Versus Hand Filing Of The Human Root Canal System, Howard W. Scholz Jr.

Loma Linda University Electronic Theses, Dissertations & Projects

A comparison was made of ultrasonic filing versus hand filing using three solutions to flood the canals of 24 extracted human maxillary central incisors. A modified PR-30 Cavitron insert was used in a Cavitron 1010 unit for the ultrasonic filing. The clinical crown was removed with a diamond saw and water spray at the cemento-enamel junction. The two major groups were ultrasonic filing versus hand filing; the three subgroups were solution/solvents - 10% EDTA, 2.0% NaOCl, and distilled water.

After filing, the roots were grooved longitudinally with a high speed bur and cracked opened with a mallet and chisel. The …

Apical Closure Induction Using Bone Growth Factors And Mineral Trioxide Aggregate, Kenneth W. Tittle

Loma Linda University Electronic Theses, Dissertations & Projects

This study compared the ability of three different bone growth factor combinations with that of Ca(OH)₂ to stimulate apical closure as well as the effectiveness of Mineral Trioxide Aggregate (MTA) as an apical barrier. Fifty-six roots of second and fourth mandibular premolars of seven six- month old beagle dogs were used. Periradicular lesions were created over a four week period. The canals were cleaned and shaped and filled with Ca(OH)₂ for one week. They were then irrigated and received one of seven different treatments in a balanced design. Growth factors were placed in a carboxymethylcellulose carrier and delivered …

Effects Of Cocaine, Nicotine And Diet On Voluntary Alcohol Consumption In Rats, Zaida Raquel Cordero Loayza

Loma Linda University Electronic Theses, Dissertations & Projects

The consumption of alcohol is a problem not only in this country (U.S.), but also in many other places in the world. Thus we find the Indians in Peru, Bolivia and other neighboring countries (Ecuador and northern part of Argentina) consuming alcohol to the point that they become alcoholics, in addition to this they also chew coca leaves, plant from which cocaine is extracted.

In an effort to establish the cause for this behavior, we put Sprague-Dawley albino rats on either a poor or good basal diet. Once every other day the rats were injected with a solution of cocaine. …

Vibrational Analysis Of Octahedral Molecules, Magdi Aziz Girgis

Archived Theses and Dissertations

No abstract provided.