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PubMed2003

Numerical simulations of multiconjugate adaptive optics wave-front reconstruction on giant telescopes.

We present sample Monte Carlo simulation results to illustrate the trends in multiconjugate adaptive optics (MCAO) performance as the telescope aperture diameter increases from 8 to 32 m with all other first-order system parameters held constant. The MCAO system considered includes three deformable mirrors, a 1-arc min square field of view, and five wave-front-sensing references consisting of either natural guide stars or laser guide stars at a range of either 30 or 90 km. The rms residual wave-front error decreases slowly with increasing aperture diameter with natural guide stars, whereas performance degrades significantly with increasing aperture diameter for laser guide stars at 30 km if the number of guide stars is held fixed. Performance with laser guide stars at 90 km is a weak function of telescope aperture diameter in the range from 8 to 32 m, with rms wave-front errors no more than 20% greater than the corresponding natural guide-star case for the same level of wave-front sensor's measurement noise.

Journal Article↗

PubMed1997

Fixed archival tissue. Purify DNA and primers for good PCR yield!

The analysis of archival formalin-fixed, paraffin-embedded tissue samples becomes increasingly important for molecular biology studies. As fixation and paraffin-embedding cause alterations of proteins and nucleic acids, archival sources of DNA must be handled with care. To address the need for specificity and reproducibility, we developed an improved protocol for semi-automated DNA extraction adapted to fixed, embedded tissue samples, and a PCR approach using HPLC-purified primers.

DNA↗

PubMed2005

Experimental force definition system for a new orthodontic retraction spring.

A new geometry of orthodontic retraction spring was experimentally studied through an electronic device (platform for measuring forces), using strain gauges that were adapted to cantilever beams. The sample consisted of 36 titanium-molybdenum springs, divided into three groups of 12 springs each. The springs were produced with different cross sections of 0.016 x 0.022 inch and 0.017 x 0.025 inch and with different angles between the extremities (120 degrees and 130 degrees). The springs were adapted to the platform in three different positions so that the force system developed by them could be known (horizontal forces, vertical forces, alpha-beta moments, and moment-to-force ratio M:F). The analysis of factorial variance and the Tukey honestly significant difference test were applied to verify the differences between the averages caused by three possible variation sources and the interactions between them. Regression analysis was also performed to obtain the spring rate. The results show the interactions between the three geometric variables, force magnitudes, and also the spring rates, which are compatible with the ones mentioned in the literature related to the subject. The spring rate was within the levels that are appropriate for clinical use (varying from beta = 33.1 gf/mm to beta = 43.9 gf/mm).

Dental Stress Analysis↗

PubMed1988

Computer system for quantitative evaluation of an electrotactile vocoder for artificial hearing.

A computer-controlled experimental electrotactile vocoder system is designed to evaluate quantitatively the transmission of speech information and to test various design options for tactual vocoders. The system is composed of a digital speech synthesizer, a digital vocoder, a computer-driven electrotactile display, and an adaptive controller for psychophysical experimentation. Samples of continua representing speech contrast types occurring in natural languages are synthesized by systematically manipulating selected subphonemic features. The synthesized speech stimuli are processed using a programmable vocoder and presented to the skin with an electrotactile display belt worn on the abdomen. Transmission of significant speech parameters is quantitatively evaluated using adaptive psychophysical techniques and labeling tests. The system is used to assess the potential of speech transmission through the skin and to evaluate different vocoder configurations and processing techniques for tactual vocoders to be used as artificial hearing devices by the deaf.

Adult↗

PubMed2001

Group sequential test strategies for superiority and non-inferiority hypotheses in active controlled clinical trials.

In a group sequential active controlled clinical trial, the study hypothesis may be a superiority hypothesis that an experimental treatment is more effective than the active control therapy or a non-inferiority hypothesis that the treatment is no worse than the active control within some non-inferiority range. When it is necessary to plan for testing the superiority and the non-inferiority hypotheses, we propose an adaptive group sequential closed test strategy by which the sample size is planned for testing superiority and is to be increased for showing non-inferiority given that it is deemed more plausible than superiority based on the observed sample path during the course of the trial. The proposed adaptive test strategy is valid in terms of having the type I error probability maintained at the targeted alpha level for both superiority and non-inferiority. It has power advantage or sample size saving over the traditional group sequential test designed for testing either superiority only or non-inferiority only.

Controlled Clinical Trials as Topic↗

PubMed2005

Nurse aide empowerment strategies and staff stability: effects on nursing home resident outcomes.

PURPOSE: This study examines the moderating effect of staff stability on the relationship between management practices used to empower nurse aides and resident outcomes in a multistate sample of nursing homes. An adaptation of Kanter's theory of structural power in organizations guided the framework for the model used in this study. DESIGN AND METHODS: Management practices and nurse aide staff stability measures were taken from a survey of directors of nursing (n = 156) and day-shift charge nurses (n = 430) in a stratified random sample of nursing facilities in Maine, Mississippi, New York, and Ohio (n = 156). Facility risk-adjusted pressure ulcer incidence rates and social engagement scores, taken from the Minimum Data Set, served as resident outcome measures. A hierarchical linear regression model was used to test the moderating effect of staff stability. RESULTS: The situation in which higher numbers of rewards were given to nurse aide staff was associated with lower incidence of pressure ulcers, whereas the situation in which nurse aides had more influence in resident care decisions was associated with higher aggregate social engagement scores. The inclusion of nurse aide staff stability in the regression model provided additional explanatory information for the relationship between management practices and resident outcomes. Facilities experiencing low turnover and high retention were associated with lower pressure ulcer incidence, whereas facilities with high turnover and high retention were associated with higher social engagement scores. IMPLICATIONS: This study suggests that certain management practices used to empower nurse aides can influence resident outcomes. Further, effects of nurse aide staff stability vary with respect to the physical versus psychosocial nature of the outcome.

Nursing Assistants↗

PubMed1995

The measurement of growth hormone bioactivity in patient serum using an eluted stain assay.

We have adapted the MTT-ESTA bioassay for human GH (hGH) to measure the lactogenic bioactivity of the hormone in human serum. This highly quantitative in vitro colorimetric bioassay is based upon the reduction of a tetrazolium salt, 3-[4,5-dimethyl-thiazol-2-yl]2,5-diphenyl tetrazolium bromide (MTT), to its formazan by lactogen-activated Nb2 cells. Relatively high concentrations of human serum (1-10%) modified responses to the hormone in a complex manner. As the serum effects varied between samples, it proved impossible to adapt the bioassay by the conventional approach of using a lactogen-depleted serum as a representative matrix. However, as the Nb2 cells were exceptionally sensitive to hGH, the serum effects could be diluted out. We adopted a dilution strategy by which all samples of human serum were included in the bioassay at a concentration of 0.625% or less. A valid assay was obtained, as judged by the criteria of parallelism between diluted samples and hGH standards, and recoveries of spiked samples that were close to 100%. Hormonal specificity was achieved with the use of a highly specific anti-PRL antiserum. A within-assay precision of between 2-5% over the dose range of 0.03-0.96 microgram hGH/L was attained. As only highly diluted samples could be used, the sensitivity of the clinical bioassay was 1.2-2.4 micrograms hGH/L. The between-assay precision was estimated to be 11% and 9% at initial hGH concentrations in serum of 4.8 and 19.2 micrograms hGH/L, respectively. By exploiting the high sample capacity of the eluted stain bioassay system, we followed the changes in bioactivity and immunoactivity of hGH in multiple timed samples after stimulation of hGH secretion in an adult by GHRH. Systematic and progressive changes were observed in the bioactive/immunoactive ratios. Analogous changes were observed after insulin-induced hypoglycemia in a child with short stature. We speculate that the changes in the bioactive/immunoactive ratios reflect alterations in the proportions of the isoforms of hGH in the circulation after acute stimulation.

Animals↗

PubMed1994

The AAMD Adaptive Behavior Scale--School Edition, Part Two: Test-retest reliability and parent-teacher agreement in a behavior disordered sample.

Test-retest reliability and parent-teacher agreement were estimated for Part Two of the AAMD Adaptive Behavior Scale--School Edition. Test-retest reliability was based on a subgroup of 20 students selected randomly from the total sample of 66; these were 7 students classified as Behavior Disordered, 7 students referred for behavior problems but not classified, and 6 students not referred or classified. Parent-teacher agreement was investigated for a subgroup of 25 students classified as Behavior Disordered. Test-retest reliability of .83 was significant, while parent-teacher agreement coefficients were nonsignificant. Such results are consistent with previous research using similar instruments. The implications are discussed and suggestions for research are presented.

Adaptation, Psychological↗

PubMed2025

LYCEUM: learning to call copy number variants on low-coverage ancient genomes.

MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions. RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection. AVAILABILITY AND IMPLEMENTATION: LYCEUM is available at https://github.com/ciceklab/LYCEUM.

DNA Copy Number Variations↗

PubMed2005

Profiling oligosaccharidurias by electrospray tandem mass spectrometry: quantifying reducing oligosaccharides.

A method to semiquantify urinary oligosaccharides from patients suffering from oligosaccharidurias is presented. 1-Phenyl-3-methyl-5-pyrazolone has been used to derivatize urinary oligosaccharides prior to analysis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Disease-specific oligosaccharides were identified for several oligosaccharidurias, including GM1 gangliosidosis, GM2 gangliosidosis, sialic acid storage disease, sialidase/neuraminidase deficiency, galactosialidosis, I-cell disease, fucosidosis, Pompe and Gaucher diseases, and alpha-mannosidosis. The oligosaccharides were referenced against the internal standard, methyl lactose, to produce ratios for comparison with control samples. Elevations in specific urinary oligosaccharides were indicative of lysosomal disease and the defective catabolic enzyme. This method has been adapted to enable assay of large sample numbers and could readily be extended to other oligosaccharidurias and to monitor oligosaccharide levels in patients receiving treatment. It also has immediate potential for incorporation into a newborn screening program.

Carbohydrate Sequence↗

PubMed1996

Future research directions to study genetic damage in germ cells and estimate genetic risk.

The late Frits Sobels developed a parallelogram model to estimate genetic risk to humans based on experimental data in somatic cells (peripheral blood) of exposed animals and humans and on data from progeny studies of exposed animals (mice). Recently, an extension to the original parallelogram model was proposed to bridge the gap of extrapolation between rodent and human germ cells by studying sperm samples. The comparison in the parallelogram of rodent/human sperm data with data from rodent progeny tests to derive at an estimate of human progeny at risk is more promising. Therefore, data on all possible end points, DNA adducts, mutations, chromosomal aberrations, and aneuploidy, should be obtained in sperm of exposed rodents and humans. The technology from somatic cell studies is available or adaptable to sperm studies. Sperm samples lend themselves to automated analyses because they are a homogeneous cell population. By flow cytometry or image analysis, large cell samples can be studied per individual. Animal experiments could be conducted in the actual range of chronic human exposure to low doses. The acceptability of extrapolation from the high acute doses so far used in animal experiments to low chronic doses of human exposure could be assessed. Proof could be obtained in human germ cells for the assumption that data from animal experiments can be extrapolated to humans. Data from transgenic rodent systems may play an important role in the extension of the parallelogram approach to genetic risk estimation by providing a link between cancer and genetic risk estimates.

Aneuploidy↗

PubMed1989

Diagnostic test for mucopolysaccharidosis. II. Rapid quantification of glycosaminoglycan in urine samples collected on a paper matrix.

The direct 1,9-dimethylmethylene blue (DMB) method for quantifying sulfated glycosaminoglycan (GAG) in urine (Clin Chem 1989; 35:374-9) has been adapted to a convenient means for sample collection and transport as a test to identify individuals with mucopolysaccharidosis (MPS) storage diseases. Results correlated moderately well (r = 0.85) with those of a commonly used, but more laborious, quantitative method. In studying factors to maximize differentiation of pathological from normal values, we found that GAG excretion (expressed as milligrams GAG per gram creatinine) fits a logarithmic function with respect to age and varies markedly below age five years. This must be considered in developing normative values and forming diagnoses. Of 112 separate urine specimens obtained from 41 MPS patients representing the major MPS diseases, glycosaminoglycan excretion by all exceeded that for age-matched normal individuals. The convenience of this method allowed us to establish the first normative values for three-week-old infants (n = 435) found to have a mean glycosaminoglycan excretion of 179 (SD 86.3) mg of GAG per gram of creatinine. This method improves the diagnostic capability for those MPS diseases that have been particularly difficult to identify (Sanfilippo's syndrome and Morquio's syndrome), and may also provide a test for other disorders with previously unrecognized abnormal excretion of glycosaminoglycan (e.g., mucolipidosis and acromesomelic dysplasia). Most importantly, this MPS diagnostic test is unique in its suitability for mass screening of newborn infants.

Adolescent↗

PubMed2002

Inactivation of acid-adapted and nonadapted Escherichia coli O157:H7 during drying and storage of beef jerky treated with different marinades.

The inactivation of both acid-adapted and unadapted Escherichia coli O157:H7 during the processing of beef jerky was studied. Following inoculation with the pathogen, beef slices were subjected to different predrying marinade treatments, dried at 60 degrees C for 10 h, and stored at 25 degrees C for 60 d. The predrying treatments evaluated were as follows: (i) no treatment (C), (ii) traditional marinade (TM), (iii) double-strength TM modified with added 1.2% sodium lactate, 9% acetic acid, and 68% soy sauce with 5% ethanol (MM), (iv) dipping into 5% acetic acid for 10 min followed by application of TM (AATM), and (v) dipping into 1% Tween 20 for 15 min and then into 5% acetic acid for 10 min followed by TM (TWTM). Bacterial survivors were determined during drying and storage using tryptic soy agar with 0.1% pyruvate, modified eosin methylene blue agar, and sorbitol MacConkey agar. Results indicated that bacterial populations decreased during drying in the order of TWTM (4.9 to 6.7 log) > AATM > MM > C > or = TM (2.8 to 4.9 log) predrying treatments. Populations of acid-adapted E. coli O157:H7 decreased faster (P < 0.05) in AATM and TWTM than nonadapted cells during drying, whereas no significant difference was found in inactivation of acid-adapted and nonadapted inocula in C and TM samples. MM was more effective in inactivating the nonadapted than the adapted inoculum. Bacterial populations continued to decline during storage and dropped below the detection limit (-0.4 log10 CFU/cm2) as early as day 0 (after drying) or as late as day 60, depending on acid adaptation, predrying treatment, and agar medium. The results indicated that acid adaptation may not increase resistance to the hurdles involved in jerky processing and that use of additional antimicrobial chemicals or preservatives in jerky marination may improve the effectiveness of drying in inactivating E. coli O157:H7.

Acetic Acid↗

PubMedDate not supplied

Homogeneous enzyme immunoassay for theophylline with a centrifugal analyzer.

A rapid homogeneous enzyme immunoassay for theophylline has been adapted to a centrifugal analyzer. The sample volume used was 10 microliter and sera from as many as 28 patients could be measured in 180 seconds. The assay temperature was 30 degrees and the absorbance rates were measured at 340 nm. Within-run and run-to-run precision showed a coefficient of variation of less than 2.6 and 7.5 percent, respectively, for theophylline concentrations of 2.5 to 40 mg per liter. The method was linear to 50 mg per liter and the analytical recovery was quantitative. A comparison between high pressure liquid chromatography (X) and the centrifugal analyzer enzyme immunoassay method (Y) for 51 patient samples revealed a correlation coefficient of 0.976 with a regression line of Y = 1.07 X -1.05 mg per liter. Reagent costs were reduced three-fold by adapting the enzyme immunoassay procedure from a semi-automatic spectrophotometer to a centrifugal analyzer. An absorbance rate for each theophylline sample was obtained by a multipoint kinetic rate computer program by the centrifugal analyzer. Severe hemolysis and lipemia interfered in this assay.

Autoanalysis↗

PubMed1976

Enhancement studies on algae and isolated chloroplasts. Part II. Enhancement of oxygen evolution in intact chloroplasts.

Intact isolated chloroplasts were shown to exhibit a characteristic three-phase pattern of development of oxygen evolution activity. The first phase, Phase I, appeared to be an equilibration phase in which the isolated chloroplasts adapted to the conditions on the electrode surface. It was characterised by a rapidly increasing rate of oxygen evolution accompanied by decreasing enhancement signals. The second phase, Phase II, was an intermediate phase in which the rate of oxygen evolution was maximal and no enhancement was observed. In the last phase, Phase III, the rate of oxygen fell again, normal enhancement was still missing, but the samples appeared to undergo slow adaptive changes closely related to the State I-State II changes previously reported for whole cell systems. The concentrations of Mg2+ within the chloroplast were shown to play an important role in the control of the development of both the oxygen evolution and enhancement signals. It was shown how these signals could be explained in terms of a model that was consistent with that developed in Part I of this investigation to account for the variability of enhancement of the alga Chlorella pyrenoidosa.

Chlorella↗

PubMed2002

Performance of a Brazilian population sample in the Boston Diagnostic Aphasia Examination: a pilot study.

Brazilian researchers and health professionals often face the challenge of having to use tests developed in foreign languages and standardized for populations of other countries, especially in the fields of Neuropsychology and Neurolinguistics. This fact promotes a feeling that some scoring systems may be inadequate for our sociocultural reality. In the present study, we describe the performance of a Brazilian population sample submitted to a translated and adapted version of the Boston Diagnostic Aphasia Examination (BDAE). Sixty normal volunteers (21 men and 39 women), all Portuguese native speakers, ranging in age from 15 to 78 years (average 43.7) and with an educational level of 2 to 16 years (average 9.9), were tested using a translated and adapted Portuguese version of the BDAE. Cut-off scores are suggested for our population and the performance of the Brazilian sample is compared to that of American and Colombian samples, with the results being closely similar in all tasks. We also performed a correlation analysis between age, gender and educational level and the influence of these variables on the performance of the subjects. We found no statistically significant differences between genders. Educational level correlated positively with performance, especially in the subtests involving reading and writing. There was a negative correlation between age and performance in two subtests (Visual Confrontation Naming and Sentences to Dictation), but a coexisting effect of educational level could not be ruled out.

Achievement↗

PubMed1987

Laboratory and field microassay of cholinesterases in whole blood, plasma, and erythrocytes.

A straightforward method is described for determination of the activities of erythrocyte acetylcholinesterase and plasma cholinesterase from single 10-mul samples of highly diluted whole blood. The procedure is a spectrophotometric microassay adapted for use with microtitration plates. The use of an enzyme immunoassay reader facilitates the rapid analysis of large numbers of samples. An inexpensive adaptation of the method was also devised that requires no instrumentation and was evaluated under field conditions in Haiti. Either the field or laboratory versions of the method can accurately determine increments of 10% or less in the level of inhibition of acetylcholinesterase or cholinesterase in whole blood, plasma, or erythrocytes.

Acetylcholinesterase↗

PubMed1996

Intestinal base excretion in the seawater-adapted rainbow trout: a role in acid-base balance?

A potential role for the intestine of seawater-adapted teleosts in acidbase regulation was investigated following earlier reports of highly alkaline rectal fluids in the gulf toadfish Opsanus beta. Rectal samples taken from starved seawater-adapted rainbow trout had a high fluid pH (8.90±0.03; mean ± s.e.m., N=13) and base (HCO3-+2CO32-) content of 157±26 mequiv kg-1 (N=11). In trout fitted with rectal catheters, rectal fluid was voided at a rate of 0.47±0.11 ml kg-1 h-1 (N=8), giving a net base excretion rate of 114±15 µequiv kg-1 h-1 (N=7). Drinking rates averaged 3.12±0.48 ml kg-1 h-1 (N=8), and accounted for only 6 % of the base excreted via the intestine, indicating substantial net transport of endogenously derived base into the intestine. Rectally excreted base was approximately balanced by an equivalent efflux of net acid from non-rectal sources (possibly as NH4+ excretion via the gills). Samples taken from four sites along the intestine revealed that the most anterior region (the pyloric intestine) was responsible for the majority of HCO3-+2CO32- accumulation. The pyloric intestine was subsequently perfused in situ to investigate possible mechanisms of base secretion. Net base fluxes were found to be dependent on luminal Cl-, 76 % stimulated by amiloride, 20 % inhibited by 10(-4) mol l-1 acetazolamide, but unaffected by either 10(-4) mol l-1 SITS or 2x10(-5) mol l-1 DIDS. This suggests that the mechanism of base secretion within the pyloric intestine may involve a Cl-/HCO3--ATPase. It is speculated that intestinal base secretion may play a role in facilitating osmoregulation of seawater-adapted teleosts.

Journal Article↗