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Biomedical subjects

L J Allen

Publications and source records attributed to L J Allen.

At least 19 recordsLinked to original sources
PubMed2001

Atomic scattering factors for K-shell electron energy-loss spectroscopy.

Atomic scattering factors for K-shell electron energy-loss spectroscopy (EELS) have been calculated for elements in the range Z = 6 (carbon) to Z = 50 (tin). The calculations are based on relativistic Hartree-Fock wave functions for the atomic bound states and Hartree-Slater wave functions for the continuum states. The results are presented in parameterized form so that accurate values of the scattering factors can be obtained for incident electron energies between 50 and 400 keV, collection semi-angles between 10 and 40 mrad, and energy windows between 25 and 100 eV. The parameterizations are for scattering vectors with magnitude s = sin theta/lambda up to 2.5 A(-1) (2 theta is the scattering angle and lambda is the wavelength of the incident electrons).

Journal Article↗
PubMed2001

Computational aberration correction for an arbitrary linear imaging system.

We show that aberration corrections can be made in any arbitrary linear imaging system provided the aberrations are well characterized and at least one of these aberrations can be independently varied in a well-controlled manner. We derive a generalization of the Schrödinger equation for wave propagation in aberration space assuming forward scattering. Transport equations in aberration space are derived. A general iterative algorithm which can retrieve the phase, and is robust in the presence of noise, is also derived. This is demonstrated using simulated data pertinent to electron microscopy, from a series of images with differing spherical aberration.

Journal Article↗
PubMed2001

Phase retrieval from images in the presence of first-order vortices.

We discuss retrieval of the phase of quantum-mechanical and classical wave fields in the presence of first-order vortices. A practical method of phase retrieval is demonstrated which is robust in the presence of noise. Conditions for the uniqueness of the retrieved phase are discussed and we show that determination of the phase in a given plane requires a series of at least three two-dimensional intensity images at different propagation distances. The method is applicable to a wide range of scenarios such as the imaging of imperfect crystals, quantitative determination of the strength of vortex filaments in high-temperature superconductors, and x-ray and electron holography.

Journal Article↗
PubMed2001

Phase retrieval and aberration correction in the presence of vortices in high-resolution transmission electron microscopy.

We discuss phase retrieval and the correction of images for aberrations, in particular defocus and spherical aberration, in high-resolution transmission electron microscopy. Non-interferometric phase retrieval requires at least two intensity measurements in different planes. Vortices in the phase may occur in the image plane or the other planes involved in the phase retrieval. We discuss the performance of various methods of phase retrieval in that case. After retrieval of the phase, the aberrations can be corrected in the Fraunhofer diffraction space (the wave function in the diffraction space is related to that in the image space by a Fourier transform). The aberration-corrected image is obtained from the aberration-corrected wave function in the diffraction plane by inverse Fourier transformation.

Journal Article↗
PubMed2001

Structure determination at the atomic level from dynamical electron diffraction data under systematic row conditions.

We discuss a method to obtain structural information on crystals at the atomic level in high-resolution transmission electron microscopy from dynamical diffraction data under systematic row conditions. Working at a fixed incident energy and within an N-beam approximation, data is required at a well defined set of N incident beam orientations to determine the scattering matrix, one orientation for each column in the matrix. At each orientation the corresponding column of the scattering-matrix is obtained by Fourier transformation of the exit surface wave function. Thus, in addition to each exit surface image, we must recover the phase of the wave function for that orientation in the image plane. We show that retrieval of the phase using algorithms based on conservation of flux, which assume continuity of the phase, can yield incorrect solutions for the phase. This is because singularities can occur in the phase of the wave field at points where the intensity is zero, which can lead to edge dislocations in the phase. We demonstrate, using a model example, how these edge dislocations arise. We will show that phase retrieval from a through focal series of measurements or using the Gerchberg-Saxton algorithm (starting from measurements of an image and the corresponding diffraction pattern), correctly retrieves the phase and hence the exit surface wave function for all the orientations required to obtain the scattering-matrix. The dynamical (multiple) scattering can then be inverted to uniquely obtain the projected potential.

Journal Article↗
PubMed2000

Population extinction and quasi-stationary behavior in stochastic density-dependent structured models.

Density-independent and density-dependent, stochastic and deterministic, discrete-time, structured models are formulated, analysed and numerically simulated. A special case of the deterministic, density-independent, structured model is the well-known Leslie age-structured model. The stochastic, density-independent model is a multitype branching process. A review of linear, density-independent models is given first, then nonlinear, density-dependent models are discussed. In the linear, density-independent structured models, transitions between states are independent of time and state. Population extinction is determined by the dominant eigenvalue lambda of the transition matrix. If lambda < or = 1, then extinction occurs with probability one in the stochastic and deterministic models. However, if lambda > 1, then the deterministic model has exponential growth, but in the stochastic model there is a positive probability of extinction which depends on the fixed point of the system of probability generating functions. The linear, density-independent, stochastic model is generalized to a nonlinear, density-dependent one. The dependence on state is in terms of a weighted total population size. It is shown for small initial population sizes that the density-dependent, stochastic model can be approximated by the density-independent, stochastic model and thus, the extinction behavior exhibited by the linear model occurs in the nonlinear model. In the deterministic models there is a unique stable equilibrium. Given the population does not go extinct, it is shown that the stochastic model has a quasi-stationary distribution with mean close to the stable equilibrium, provided the population size is sufficiently large. For small values of the population size, complete extinction can be observed in the simulations. However, the persistence time increases rapidly with the population size.

Age Factors↗
PubMed2000

Comparison of deterministic and stochastic SIS and SIR models in discrete time.

The dynamics of deterministic and stochastic discrete-time epidemic models are analyzed and compared. The discrete-time stochastic models are Markov chains, approximations to the continuous-time models. Models of SIS and SIR type with constant population size and general force of infection are analyzed, then a more general SIS model with variable population size is analyzed. In the deterministic models, the value of the basic reproductive number R0 determines persistence or extinction of the disease. If R0 < 1, the disease is eliminated, whereas if R0 > 1, the disease persists in the population. Since all stochastic models considered in this paper have finite state spaces with at least one absorbing state, ultimate disease extinction is certain regardless of the value of R0. However, in some cases, the time until disease extinction may be very long. In these cases, if the probability distribution is conditioned on non-extinction, then when R0 > 1, there exists a quasi-stationary probability distribution whose mean agrees with deterministic endemic equilibrium. The expected duration of the epidemic is investigated numerically.

Disease Outbreaks↗
PubMed1996

Alterations in blood lymphocyte subpopulations and hematologic values in neonatal calves after administration of a combination of multiple-antigen vaccines.

OBJECTIVE: To evaluate alterations in lymphocyte subpopulations, CBC results, and clinical signs in neonatal calves inoculated with 3 commercially available proprietary multiple-antigen vaccines containing known quantities of endotoxin. DESIGN: Prospective, randomized controlled field trial. ANIMALS: 36 healthy Holstein heifer calves between 3 and 31 days old. PROCEDURE: Vaccines were administered to 18 calves according to label instructions, except for the recommended age of administration. The 18 other calves served as unvaccinated controls. Two weeks after entry into the study, calves were given secondary doses of the same vaccines. Calves in both groups were examined and blood samples were collected for determination of lymphocyte subpopulations and hematological parameters once daily for 5 days beginning on the day that both the primary and the secondary vaccinations were given. Lymphocyte subpopulations, including BoCD2+, BoCD4+, BoCD8+, B cells, and gamma/delta T cells, were determined by use of flow cytometry, using monoclonal antibodies as markers. RESULTS: Vaccinated calves did not develop clinical signs of illness. There were no significant differences in absolute numbers of lymphocyte subpopulations between vaccinated and unvaccinated calves. Vaccinated calves had significantly higher rectal temperatures, total WBC counts, and absolute neutrophil counts than did control calves. These differences persisted for 3 to 4 days after vaccination. CLINICAL IMPLICATIONS: Findings confirm empirical observations that vaccination with multiple products at the same time may induce evidence of an inflammatory response in most calves. Additional research is indicated to further evaluate the safety of using multiple vaccines simultaneously.

Animals↗
PubMed1996

Environmentally driven epizootics.

Environmental conditions can be the driving force behind an epizootic. Environmental changes may favor growth of a particular species, which results in increased contact rates and spread of a disease. We examine this particular phenomenon in SI and SIS models and use it to explain the possible disease outbreaks in nature. Either infected individuals recover from the disease (SIS model) or suffer disease fatalities (SI model). Epizootic models for a single population are examined where contact rate depends on population size. A reproductive number R is defined that depends on environmental carrying capacity. The single-population models are coupled to form three different two-species models with intra- and interspecies contact rates that depend on the population sizes of both populations. The stability results show that it is possible for the disease to drive one of the populations to extinction, the one with disease fatalities. The surviving species serves as a reservoir for the disease. Single- and two-species epizootic models are examined in a particular case where the contact rates are assumed to be constant. This leads to a new definition for the contact rate. A complete global analysis is possible in these latter cases. The results are compared and contrasted with the models with variable contact rates. The prototype for the models is the spread of disease in wildlife populations, which includes such diseases as plague or Lyme disease.

Animals↗
PubMed1995

Effect of penicillin or penicillin and dexamethasone in cattle with infectious bovine keratoconjunctivitis.

To evaluate the efficacy of penicillin or penicillin and dexamethasone for treatment of infectious bovine keratoconjunctivitis, 6- to 8-month-old beef heifers with clinical signs of infectious bovine keratoconjunctivitis were randomly assigned to 1 of 3 treatment groups: penicillin only, penicillin and dexamethasone, or control. Cattle assigned to the penicillin group (n = 18) were treated with 3 daily subconjunctival injections of procaine penicillin G. Cattle assigned to the penicillin/dexamethasone group (n = 13) were treated with 3 daily subconjunctival injections of procaine penicillin G and dexamethasone sodium phosphate. Control cattle (n = 14) were not treated. Healing times and frequency of recurrence for corneal ulcers; severity, diameter, and surface area measurements of corneal ulcers; and clinical scores did not differ among the 3 groups. Frequency of Moraxella bovis isolation from specimens of ocular secretions from ulcerated and non-ulcerated eyes was similar in all groups. Minimum inhibitory concentration of penicillin G for 95 of the 102 tested M bovis isolates was 0.3 U/ml, and for 7 others was 0.03 U/ml. When first and last specimens from 42 of 45 calves with isolation of M bovis on serial microbial cultures were compared, the susceptibility of each last isolate was similar to that of the corresponding first isolate.

Animals↗
PubMed1994

Some discrete-time SI, SIR, and SIS epidemic models.

Discrete-time models, or difference equations, of some well-known SI, SIR, and SIS epidemic models are considered. The discrete-time SI and SIR models give rise to systems of nonlinear difference equations that are similar in behavior to their continuous analogues under the natural restriction that solutions to the discrete-time models be positive. It is important that the entire system be considered since the difference equation for infectives I in an SI model has a logistic form which can exhibit period-doubling and chaos for certain parameter values. Under the restriction that S and I be positive, these parameter values are excluded. In the case of a discrete SIS model, positivity of solutions is not enough to guarantee asymptotic convergence to an equilibrium value (as in the case of the continuous model). The positive feedback from the infective class to the susceptible class allows for more diverse behavior in the discrete model. Period-doubling and chaotic behavior is possible for some parameter values. In addition, if births and deaths are included in the SI and SIR models (positive feedback due to births) the discrete models exhibit periodicity and chaos for some parameter values. Single-population and multi-population, discrete-time epidemic models are analyzed.

Epidemiologic Methods↗
PubMed1994

Perce the permissive pathologist: a cautionary tale of one who misdiagnosed a pseudosarcoma, killed the patient and was found out.

Perce, a promising young trainee pathologist, correctly recognizes a biopsy of a benign pseudosarcoma but his diagnosis is overruled by the less well read Head of Pathology. Acting under instructions from his Chief, Perce knowingly and without protest 'signs out' this benign condition as a sarcoma. The surgeon accepts the diagnosis without question and performs radical surgery, which is complicated by postoperative haemorrhage from which the patient dies. The Coroner orders a review of the slides and the misdiagnosis is discovered. Perce's defense that he did as he was told is rejected; he is forced to quit pathology and becomes an administrator. This unfortunate tale, which is related in verse, is intended to stress the importance of such benign but uncommon pseudosarcomas as nodular fasciitis, proliferative myositis, myositis ossificans, postoperative spindle cell nodule, pseudosarcoma of the bladder and juxta-articular myxoma. The poem also implies that surgeons should not carry out radical surgery based on an uncommon pathological diagnosis without checking on the adequacy of consultation and informed review of the sections.

Diagnostic Errors↗
PubMed1993

Analysis of a measles epidemic.

In January, February and March of 1989 an epidemic of rubeola occurred on the campus of Texas Tech University. A vaccination programme was initiated as soon as the epidemic was confirmed. Extensive case histories of all confirmed cases were collected by the Lubbock City Health Department and given an exhaustive statistical analysis by a group from the Department of Mathematics at Texas Tech University. The data and statistical analysis were used to formulate stochastic and deterministic models of the measles epidemic based on the standard SEIR model. The analysis and the simulations indicate that in order to prevent a measles outbreak on a university campus a high rate of immunity may be required (> 98 per cent). The assumptions in the models raise some interesting questions regarding social contacts which require further investigation.

Antibody Formation↗
PubMed1993

Use of contingency contracting to increase on-task behavior with primary students.

The effectiveness of contingency contracting to improve the on-task behavior of 3 primary-age students was evaluated using an ABABA single-subject replication design. The contract was developed by the teacher and the consequences were selected by the students. Increases in on-task behavior were observed each time that the contingency contracts were in effect. This study has important implications for the use of contracting with primary school children.

Attention↗
PubMed1992

Chromosomal localization of three human D5 dopamine receptor genes.

It is currently thought that genetic predisposition to imbalances in dopaminergic transmission may underlie several neurological disorders, including schizophrenia, manic depression, Tourette syndrome, Parkinson disease, Huntington disease, and alcohol abuse. Originally two receptors, D1 and D2, were thought to account for all of the pharmacological actions of dopamine. However, through homology screening three additional genes, D3, D4, and D5, and two pseudogenes closely related to D5 have been characterized. To begin our genomic and evolutionary analyses of the human D5 dopamine receptor gene and its two pseudogenes, we have mapped each of them to their respective chromosomes. By combining in situ hybridization results with sequence analysis of PCR products from microdissected chromosomes, somatic cell hybrids, and radiation hybrids, we have assigned DRD5 (the locus containing the functional human D5 receptor gene) to chromosome 4p16.1, DRD5P1 (the locus containing D5 pseudogene 1) to chromosome 2p11.1-p11.2, and DRD5P2 (the locus of D5 pseudogene 2) to chromosome 1q21.1.

Base Sequence↗
PubMed1991

A discrete-time model with vaccination for a measles epidemic.

A discrete-time, age-independent SIR-type epidemic model is formulated and analyzed. The effects of vaccination are also included in the model. Three mathematically important properties are verified for the model: solutions are nonnegative, the population size is time-invariant, and the epidemic concludes with all individuals either remaining susceptible or becoming immune (a property typical of SIR models). The model is applied to a measles epidemic on a university campus. The simulated results are in good agreement with the actual data if it is assumed that the population mixes nonhomogeneously. The results of the simulations indicate that a rate of immunity greater than 98% may be required to prevent an epidemic in a university population. The model has applications to other contagious diseases of SIR type. Furthermore, the simulated results of the model can easily be compared to data, and the effects of a vaccination program can be examined.

Adolescent↗
PubMed1990

Comparison of the 15q deletions in Prader-Willi and Angelman syndromes: specific regions, extent of deletions, parental origin, and clinical consequences.

It has recently been shown that apparently similar deletions of chromosome 15q occur commonly in the Prader-Willi and Angelman syndromes. The distinctness of the syndromes suggests that the deletions are not identical. To address this possibility, the specific bands involved and the sizes of the deletions were compared in seven patients with Prader-Willi syndrome and 10 patients with Angelman syndrome using high-resolution G-, Q-, and fluorescent R-banding techniques. The parental origin of the nine cases of Angelman syndrome for which parents were available for study was determined. The same proximal band was deleted (q11.2) in both syndromes. In general, the deletion in patients with Angelman syndrome was larger, though variable, and included bands q12 and part of q13. All of the studied deletions in patients with Angelman syndrome were of maternal origin. This contrasts with the predominant paternal origin of the deletion in patients with Prader-Willi syndrome. Two possible reasons for these observations are postulated: 1) the deleted regions are different at the cytologic and/or molecular level because of different exchange points in meiosis in males and females or to different mechanisms of breakage in males and females, resulting in differing breakpoints; 2) the deleted regions are essentially the same, but differential expression of the genes in the homologous chromosome 15 has occurred (imprinting).

Adolescent↗