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At least 325 records · Page 18Linked to original sources
PubMed2002

Acoustic identification of female Steller sea lions (Eumetopias jubatus).

Steller sea lion (Eumetopias jubatus) mothers and pups establish and maintain contact with individually distinctive vocalizations. Our objective was to develop a robust neural network to classify females based on their mother-pup contact calls. We catalogued 573 contact calls from 25 females in 1998 and 1323 calls from 46 females in 1999. From this database, a subset of 26 females with sufficient samples of calls was selected for further study. Each female was identified visually by marking patterns, which provided the verification for acoustic identification. Average logarithmic spectra were extracted for each call, and standardized training and generalization datasets created for the neural network classifier. A family of backpropagation networks was generated to assess relative contribution of spectral input bandwidth, frequency resolution, and network architectural variables to classification accuracy. The network with best overall generalization accuracy (71%) used an input representation of 0-3 kHz of bandwidth at 10.77 Hz/bin frequency resolution, and a 2:1 hidden:output layer neural ratio. The network was analyzed to reveal which portions of the call spectra were most influential for identification of each female. Acoustical identification of distinctive female acoustic signatures has several potentially important conservation applications for this endangered species, such as rapid survey of females present on a rookery.

Animals↗
PubMed1998

Assessing chance variability in treatment trials.

Chance variability hampers the interpretation of treatment trials. There are two main ways in which we can be misled: spurious findings may be produced by chance alone, or real effects may be hidden. P values and confidence intervals can help us to avoid these pitfalls when interpreting the findings from clinical trials.

Bias↗
PubMed1992

Interassay variability of immunometric methods for thyrotropin in an external quality assessment survey: evidence that functional sensitivity is not always adequate for clinical decisions.

We investigated the ability of current immunometric methods for thyrotropin (TSH; thyroid-stimulating hormone) to distinguish between low-normal and subnormal hormone concentrations by using the data from an external quality assessment (EQA) survey in 1990. We computed the interassay (between-run) precision profiles from results from 101 laboratories, which used the five most popular kits in the survey; during the control period (one year) each laboratory assayed 4 EQA pools distributed (as hidden replicates) in five occasions. The interassay CV was relatively low (9-13%) for three pools in the normal TSH range (greater than 0.8 milli-int. unit/L) but markedly higher (30-40%, except for one more precise kit) in the subnormal range (0.2 milli-int. unit/L). We calculated the effect of the between-run variability on the diagnostic accuracy (discrimination between normal and subnormal values) for three representative TSH concentrations: 0.2, 0.4, and 0.5 milli-int. unit/L (0.3 milli-int. unit/L was considered the lower normal limit). The three concentrations were reasonably discriminated (P less than or equal to 5%), and only one kit showed a between-run CV less than 18% at 0.2 milli-int. unit/L. For the other four less-precise kits, only the higher TSH value (0.5 milli-int. unit/L) could be classified with an acceptable diagnostic reliability. With the most precise kit, one can distinguish two TSH concentrations in the 0.3-0.5 milli-int. unit/L range that differ by at least 30%; with the other kits, differences greater than 50-60% are needed for reliable discrimination. Thus many laboratories fail to achieve the functional sensitivity of a second-generation assay, even if they use immunometric methods. TSH assays with a better interassay precision in the low concentration range are needed.

Humans↗
PubMed1991

A molecular phylogeny of dinoflagellate protists (pyrrhophyta) inferred from the sequence of 24S rRNA divergent domains D1 and D8.

The sequence of two divergent domains (D1 and D8) from dinoflagellate 24S large subunit rRNA was determined by primer extension using total RNA as template. Nucleotide sequence alignments over 401 bases have been analyzed in order to investigate phylogenetic relationships within this highly divergent and taxonomically controversial group of protists of the division Pyrrhophyta. Data are provided confirming that dinoflagellates represent a monophyletic group. For 11 out of the 13 investigated laboratory grown species, an additional domain (D2) could not be completely sequenced by reverse transcription because of a hidden break located near its 3'-terminus. Two sets of sequence alignments were used to infer dinoflagellate phylogeny. The first [199 nucleotides (nt)] included conservative sequences flanking the D1 and D8 divergent domains. It was used to reconstruct a broad evolutionary tree for the dinoflagellates, which was rooted using Tetrahymena thermophila as the outgroup. To confirm the tree topology, and mainly the branchings leading to closely related species, a second alignment (401 nt) was considered, which included the D1 and D8 variable sequences in addition to the more conserved flanking regions. Species that showed sequence similarities with other species lower than 60% on average (Knuc values higher than 0.550) were removed from this analysis. A coherent and convincing evolutionary pattern was obtained for the dinoflagellates, also confirmed by the position of the hidden break within the D2 domain, which appears to be group specific. The reconstructed phylogeny indicates that the early emergence of Oxyrrhis marina preceded that of most Peridiniales, a large order of thecate species, whereas the unarmored Gymnodiniales appeared more recently, along with members of the Prorocentrales characterized by two thecal plates. In addition, the emergence of heterotrophic species preceded that of photosynthetic species. These results provide new perspectives on proposed evolutionary trees for the dinoflagellates based on morphology, biology, and fossil records.

Animals↗
PubMed1995

Time course of visual extrapolation accuracy.

In two experiments, we examined the extrapolation of a constant-velocity motion along a fixed circular path in the frontal plane. A target moved over an arc of 90 deg and then disappeared. Observers were to assume that the motion continued at the original velocity. After a variable time, a line appeared at another point on the circle to mark the end of the (invisible) 'motion'. Observers decided whether or not the target would have passed this end line, and gave a pass/no-pass response. In Experiment 1, a time course was established for the observed loss in accuracy with increasing duration of invisible motion. Two models of accuracy loss were constructed and tested. Both models assume that (1) extrapolation is performed by 'tracking' the position of the hidden target, and (2) there is no systematic velocity error in tracking, only random variation in tracker velocity. Both models predicted changes in hit and false alarm rates well, except in a condition where response asymmetries were present. In Experiment 2, the hypothesis that observers were tracking the hidden target was assessed by presenting a moving distractor during part of the trial. The presence of the distractor reduced performance under some conditions, suggesting that target tracking was occasionally disrupted. Grossly unequal distributions of pass/no-pass responses were observed for the fastest (8 deg/sec) and slowest (4 deg/sec) target velocities. However, the variable tracker models, using the parameter values from the first experiment, made accurate predictions for the 6 deg/sec condition, in which response distribution was nearly equal. Thus, there may be no need to posit systematic velocity error in motion tracking during extrapolation. The time course of accuracy decline can be accounted for by random variation in tracker velocity when response bias is absent.

Female↗
PubMed2025

Annotation of RxLR Effectors in Oomycete Genomes.

Pathogens have evolved effector proteins to suppress host immunity and facilitate plant infections. RxLR effectors are small, secreted effector proteins with conserved RxLR and dEER amino acid motifs at the N terminus and highly variable C termini and are commonly found in oomycete species. We provide computational approaches to annotate RxLR candidate effector genes in a genome assembly in FASTA format with an available GFF file. Hidden Markov Modeling (HHM) is used in combination with regular expressions to search for RxLR and EER amino acid patterns.

Oomycetes↗
PubMed2001

Intra- and intercellular distribution of mitochondrial probes and changes after treatment with MDR modulators.

Fluorescent probes are currently used to evaluate the mitochondrial transmembrane potential in situ. However, in parallel experiments using the probes JC-1 and TMRM in different cell types (human astrocytes, HEp-2, Vero, KB, and HeLa cells), we found that the distribution of JC-1 and TMRM is highly variable not only in different cell types but also in different cells of the same cell type, a condition that has never been documented until our work. This phenomenon depends on a hidden, widespread multidrug resistance (MDR) phenotype that can be recognized only by comparative assays with MDR inhibitors (progesterone, verapamil, and cyclosporin A) and represents a serious risk of error in the evaluation of the mitochondrial potential.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1979

Effects of some social variables on field dependence.

The effects of socio-economic status, father's absence, family size, and birth order on the field dependence of Grade 6 elementary school children in Jamaica, West Indies, were examined. To 206 boys and 212 girls from 5 urban schools the Hidden Figures Test and a questionnaire were administered. For girls, but not for boys, field independence correlated significantly and positively with socio-economic status, but significantly and negatively with father's absence. No significant relation existed for the boys. Field dependence had no significant relation with family size and birth order.

Birth Order↗
PubMed2007

Optimizing the monitoring strategy of wastewater treatment plants by multiobjective neural networks approach.

This paper applies artificial neural network (ANN) to model the observed effluent quality data. The ANN's structure, involving the number of hidden layer and node and their connection, is determined endogenously by resorting to the compromise of data cost minimization and prediction accuracy maximization. To obtain the best compromise possible, the model introduces an aspiration variable (micro) that represents the level of aspiration achieved in one objective and the conjugate of micro, (1 - micro), represents level of aspiration achieved in the other objective. Because a massive amount of calculation is required, the model applies genetic algorithm (GA) for its computational flexibility and capability to ensure global solution. Feasibility and practicality of the model is tested by a case study with a set of 150 daily observations on 17 operational variables and quality parameters at an industrial wastewater treatment plant (WTP) located in southern Taiwan. Of these 17 variables open to selection, only 6 variables, wastewater flow rate (Q), CN(-), SS, MLSS, pH and COD are selected by the model to achieve the maximum accuracy of prediction, 0.94, with a total cost of 5,950 NT$. By constraining budget availability, the variables included in the model are reduced in number, causing a concomitant reduction in prediction accuracy, that is, by varying micro (aspiration level of accuracy), a trajectory of cost and accuracy is generated. The calculation results a cost of 3,650 NT$ and 0.54 accuracy for the case with variables including flow rate, SCN(-) and SS in equalization basin; aeration tank hydraulic retention time (HRT) and percentage of returned sludge (R%) are selected for building the prediction model when the importance of required budget is equal to the accuracy of prediction model. In addition, when required cost for building ANN model is between 3,650 NT$ and 3,900 NT$, the marginal return of budget input is highest in the entire range of calculation.

Algorithms↗
PubMedDate not supplied

Dissociating performance and learning deficits on spatial navigation tasks in rats subjected to cholinergic muscarinic blockade.

The spatial navigation abilities of rats, subject to muscarinic blockade with atropine sulfate (50 mg/kg), were examined with the object of dissociating putative performance and learning deficits. A number of aspects of performance were not disrupted by the drug treatments, including development of position responses, cue responses, nonspatial discriminations, and the retention of place responses. Acquisition of place navigation was disrupted in a variety of tasks including: dry-land tasks in which rats searched for a hole from which to escape or searched for buried food and swimming pool tasks in which rats searched for a hidden platform on which to escape from the water. Task acquisition as well as motor performance was changed by the drug treatments in each task. Priming animals with experience on a subset of task variables did not significantly improve subsequent place performance. Priming animals with all motoric and spatial demands of a task, except the use of a specific set of distal cues aided performance, whereas priming animals with the use of a specific set distal cues but not motor experience produced little improvement in performance. The results indicate that impairments in the use of motoric skills contribute significantly to the deficits produced by cholinergic muscarinic blockade in spatial navigation tasks.

Animals↗
PubMed2000

Evaluation of neural network models with generalized sensitivity analysis

A sensitivity analysis method for discovering characteristic features of the input data using neural network classification models has been devised. The sensitivity is the gradient of the neural network model response function, and because neural network models are nonlinear, the gradient depends on the point where it is evaluated. Two criteria are used for measuring the sensitivity. The first criterion calculates the sensitivity or gradient of the neural network output with respect to the average of the objects that comprise each class. The second criterion measures the average sensitivity of the class objects. The sensitivity analysis was applied to temperature-constrained cascade correlation network models and evaluated with sets of synthetic data and experimental mobility spectra. The neural network models were built using temperature-constrained cascade correlation networks (TCCCNs). A weight constraint was devised for the output units of the network models. This method implements weight decay with conjugate gradient training and yields more sensitive neural network models. Temperature-constrained hidden units furnish more sensitive network models than networks without constraints. By comparing the sensitivities of the class mean input and the mean sensitivity for all the inputs of a class, the individual input variables may be assessed for linearity. If these two sensitivities for an input variable differ by a constant factor, then that variable is modeled by a simple linear relationship. If the two sensitivities vary by a nonconstant scale factor, then the variable is modeled by higher order functions in the network. The sensitivity method was used to diagnose errors in the training data, and the test for linearity indicated a TCCCN architecture that had better predictability.

Journal Article↗
PubMed2026

Analyzing the impact of subcutaneous injection needle, device, and administration characteristics on patient pain, anxiety, and safety: a systematic literature review.

The subcutaneous (SC) injection route is a commonly used and important method for therapeutic delivery of a wide range of compounds, and needle characteristics have a significant influence on patient pain, anxiety, safety, and other outcomes. This systematic review evaluates the evidence on how needle-specific characteristics (e.g. gauge, length, tip design, wall thickness, concealment) and administration- or device-related factors can affect patient-reported outcomes and clinical safety indicators during and following SC injections. A comprehensive search was conducted in MEDLINE, PubMed, Embase, and ClinicalTrials.gov in June 2024. Studies were included if they assessed the relationship between needle characteristics and pain, anxiety, safety, or related outcomes in individuals receiving SC injections. A dual-reviewer process was used for study selection, data extraction, and quality assessment. Sixty-two studies met inclusion criteria. Evidence consistently indicated that thinner and shorter needles reduced patient-reported pain and adverse events such as bruising and bleeding. Tapered and lubricated needles, hidden or retractable needle designs, and use of autoinjectors or prefilled syringes also contributed to reduced anxiety and improved user satisfaction. However, results were heterogeneous, and many studies lacked sufficient power or single-variable evaluation of individual needle parameters, limiting definitive conclusions. Needle characteristics significantly influence patient experience and safety with SC delivery. While both clinical evidence and practical experience clearly favor thinner, shorter, and concealed needles, further standardized, high-quality research is needed to isolate and quantify the specific contributions of individual needle characteristics to optimize injection practices and support patient-centered device design.

Humans↗
PubMedDate not supplied

Peeling off the hidden genetic heterogeneities of cancers based on disease-relevant functional modules.

Discovering molecular heterogeneities in phenotypically defined disease is of critical importance both for understanding pathogenic mechanisms of complex diseases and for finding efficient treatments. Recently, it has been recognized that cellular phenotypes are determined by the concerted actions of many functionally related genes in modular fashions. The underlying modular mechanisms should help the understanding of hidden genetic heterogeneities of complex diseases. We defined a putative disease module to be the functional gene groups in terms of both biological process and cellular localization, which are significantly enriched with genes highly variably expressed across the disease samples. As a validation, we used two large cancer datasets to evaluate the ability of the modules for correctly partitioning samples. Then, we sought the subtypes of complex diffuse large B-cell lymphoma (DLBCL) using a public dataset. Finally, the clinical significance of the identified subtypes was verified by survival analysis. In two validation datasets, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Then, for the notoriously heterogeneous DLBCL, we demonstrated that two partitioned subtypes using an identified module ("cellular response to stress") had very different 5-year overall rates (65% vs. 14%) and were highly significantly (P < 0.007) correlated with the clinical survival rate. Finally, we built a multivariate Cox proportional-hazard prediction model that included 4 genes as risk predictors for survival over DLBCL. The proposed modular approach is a promising computational strategy for peeling off genetic heterogeneities and understanding the modular mechanisms of human diseases such as cancers.

Databases, Genetic↗
PubMedDate not supplied

Construction of chimaeric processed immunoglobulin genes containing mouse variable and human constant region sequences.

The specificity of monoclonal antibodies provides a powerful diagnostic and therapeutic tool in investigating human neoplasia. Radiological scanning and immunotherapy with mouse tumour-specific monoclonal antibodies have been applied to patients with some success, but a major problem is the neutralization of the mouse antibody induced by repeated administration of heterologous antibodies. To avoid or reduce such immune reactions, chimaeric immunoglobulins consisting of mouse variable (V) and human constant (C) regions can be synthesized. We have constructed a recombinant retrovirus DNA carrying genomic heavy-chain (H) variable-diversity joining (VH-D-JH) and C gamma 1 genes from different species and show here that the chimaeric intervening sequences are spliced out precisely. This procedure provides a useful method to construct the chimaeric mouse-human immunoglobulin gene to be expressed in Escherichia coli, yeast and animal cells. Unexpectedly, a hidden splice donor site in the 5'-flanking region of a human VH gene is used in place of the donor site of the leader sequence exon, resulting in the formation of the V region without the leader sequence.

Animals↗
PubMedDate not supplied

Atrial septal defect with failure to thrive in infancy: hidden pulmonary vascular disease?

Atrial septal defects are usually asymptomatic, and are closed surgically or by a catheter implanted device in preschool age children. Rarely, they may cause symptoms in infancy, and management at this age is debated. We report our experience of six infants who underwent surgical closure, with variable outcomes. Five of these had significant extracardiac pathology. Our data suggest the need to exclude other causes of symptoms, both cardiac and non-cardiac. The question should be asked as to whether surgery is of benefit in these children, and particularly whether they may have underlying primary pulmonary vascular disease.

Failure to Thrive↗
PubMed1996

Radial Basis Function Network Configuration Using Mutual Information and the Orthogonal Least Squares Algorithm.

Input nodes of neural networks are usually predetermined by using a priori knowledge or selected by trial and error. For example, in pattern recognition applications the input nodes are usually the given pattern features and in system identification applications the past input and output data are often used as inputs to the network. Some of the input variables may be irrelevant to the task in hand and therefore may cause a deterioration in network performance. Some may be redundant and may increase the complexity of the network and consume expensive computation time. In the present study, the mutual information between the input variables and the output of the network is used to select a suboptimal set of input variables for the network. The variables are selected according to the information content relevant to the output. Variables which have a higher mutual information with the output and lower dependence on other selected variables are used as network inputs. The algorithms are derived based on heuristics and performance is assessed by using radial basis function (RBF) networks trained with the orthogonal least squares algorithm (OLS), which selects the hidden layer nodes of the network according to the error reduction ratios on the network output. Both real and simulated data sets are used to demonstrate the effectiveness of the new algorithms. Copyright 1996 Elsevier Science Ltd.

Journal Article↗
PubMed2024

Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows.

Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ~3500 proteins at a spatial resolution of 50 &#xb5;m and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.

Journal Article↗
PubMed2005

Spiritual influences on ability to engage in self-care activities among older African Americans.

The influence of spiritual factors on the ability of African-American elders to carry out instrumental activities of daily living (IADL) independent of age, gender, education, and self-rated health is explored using the religion-health explanatory model in a cross-sectional sample of 96 African-American community dwelling adults 62 to 93 years of age. The Reed spiritual perspective (SPS) and self-transcendence (STS) scales are used to study spiritual factors (Reed, 1991). The typical respondent was 75 years of age, female, widowed with 10.4 years of education. Self-rated health and age are strongly related to IADL in models that include the other variables (R2 = 0.41, p < 0.01). Those who are younger and those who self-report better health have higher IADL scores than those without these characteristics. Spiritual factors are significantly related to IADL in a model that includes an interaction of STS with education (R2= 0.50). Among the least educated, STS is associated with higher scores of IADL. Addition of the interaction to the model resulted in a significant positive association of both STS and education with IADL. SPS was unrelated to IADL. Caregivers concerned with functional ability may want to consider interventions based on increasing a sense of self-transcendence, and to consider educational level as a potential moderator of this relationship. Criticism of the religion-health literature has suggested that putative health effects of religion may be exaggerated, because of failure to take confounding variables into account (Sloan, Bagiella, & Powell, 1999). However, this study and a recent survey by Musick, House, and Williams (2004) are evidence that it is just as likely that health benefits of religion would be hidden by confounders as that they would be exaggerated by them.

Activities of Daily Living↗