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At least 271 records · Page 15Linked to original sources

Adaptive BCI based on variational Bayesian Kalman filtering: an empirical evaluation.

This paper proposes the use of variational Kalman filtering as an inference technique for adaptive classification in a brain computer interface (BCI). The proposed algorithm translates electroencephalogram segments adaptively into probabilities of cognitive states. It, thus, allows for nonstationarities in the joint process over cognitive state and generated EEG which may occur during a consecutive number of trials. Nonstationarities may have technical reasons (e.g., changes in impedance between scalp and electrodes) or be caused by learning effects in subjects. We compare the performance of the proposed method against an equivalent static classifier by estimating the generalization accuracy and the bit rate of the BCI. Using data from two studies with healthy subjects, we conclude that adaptive classification significantly improves BCI performance. Averaging over all subjects that participated in the respective study, we obtain, depending on the cognitive task pairing, an increase both in generalization accuracy and bit rate of up to 8%. We may, thus, conclude that adaptive inference can play a significant contribution in the quest of increasing bit rates and robustness of current BCI technology. This is especially true since the proposed algorithm can be applied in real time.

Algorithms↗

Model dependence in quantification of spike interdependence by joint peri-stimulus time histogram.

Multineuronal recordings have enabled us to examine context-dependent changes in the relationship between the activities of multiple cells. The joint peri-stimulus time histogram (JPSTH) is a much-used method for investigating the dynamics of the interdependence of spike events between pairs of cells. Its results are often taken as an estimate of interaction strength between cells, independent of modulations in the cells' firing rates. We evaluate the adequacy of this estimate by examining the mathematical structure of how the JPSTH quantifies an interaction strength after excluding the contribution of firing rates. We introduce a simple probabilistic model of interacting point processes to generate simulated spike data and show that the normalized JPSTH incorrectly infers the temporal structure of variations in the interaction parameter strength. This occurs because, in our model, the correct normalization of firing-rate contributions is different than that used in Aertsen, Gerstein, Habib, and Palm's (1989) effective connectivity model. This demonstrates that firing-rate modulations cannot be corrected for in a model-independent manner, and therefore the effective connectivity does not represent a universal characteristic that is independent of modulation of the firing rates. Aertsen et al.'s (1989) effective connectivity may still be used in the analysis of experimental data, provided we are aware that this is simply one of many ways of describing the structure of interdependence. We also discuss some measure-independent characteristics of the structure of interdependence.

Brain↗

Longitudinal coherence measurements of a transient collisional x-ray laser.

We present what is to our knowledge the first longitudinal coherence measurement of a transient inversion collisional x-ray laser. We investigated the picosecond output of a Ni-like Pd x-ray laser at 14.68 nm generated by the COMET laser facility at the Lawrence Livermore National Laboratory. Interference fringes were generated with a Michelson interferometer setup in which a thin multilayer membrane was used as a beam splitter. We determined the longitudinal coherence for the 4d1S0 --> 4p1P1 lasing transition to be approximately 400 microm (1/e half-width) by changing the length of one interferometer arm and measuring the resultant variation in fringe visibility. The inferred gain-narrowed linewidth of approximately 0.29 pm is a factor of 4 less than previously measured in quasi-steady-state x-ray laser schemes.

Journal Article↗

Quantitative structure--activity relationship (QSAR) studies on non steroidal anti-inflammatory drugs (NSAIDs).

Different chemical structures have been found to possess different anti-inflammatory activities. Inflammation is a normal and essential response to any noxious stimulus which threatens the host and may vary from a localized response to a more generalized one. In view of the complexity and multitude of biochemical factors involved in inflammatory events, few general correlations of chemical structures and physicochemical properties with biological activities would be expected. Nevertheless some general features seem to be commonly associated with a large number of active drugs. However, these main features are not sufficient, but they could reflect certain physicochemical requirements for in vivo efficacy. QSAR is a useful means for maximizing the potency of a new lead compound. In the lead optimization phase of the synthetic project various QSAR procedures with the aid of computer-technology have been proposed. Among them, the classical Hansch approach has been widely used leading to quite a few successful examples. In the QSAR approaches, the prescription to optimise the lead structure is inferred from mathematical equations correlating variations in the potency of a certain biological activity with physicochemical and structural descriptors among congeneric molecules. The QSAR procedures are based on physical organic concepts and involve calculational operations. In the last years, quantum-chemical descriptors have been used in QSAR studies, because of the large physical information content encoded in many of the descriptors. Several anti-inflammatory receptor site models have been proposed. Since inflammation is a complex phenomenon involving interrelationships between humoral and cellular reactions through a number of inflammatory mediators, there is not much evidence on QSAR studies. Several QSAR studies have been reported obtaining only partial results. It was found that substituents which contribute to the high lipophilicity, were favourable to the activity. Substituents of short length (H, CH3) have also a favourable effect. Satisfactory relationships between the in vivo activities and deprotonation energies, the HOMO energies and lipophilicities were found.

Animals↗

Validation of bioassays for quality control.

For a biological assay to be useful for quality control it should fail bad lots, pass good lots, and estimate relative potency with high accuracy and precision. To fail a lot we rely most heavily on the test for parallelism. For the parallelism test and other preliminary tests as well as for inference, appropriate estimates of assay variation are crucial. Location effects on 96 well plates and serial dilution of samples using multichannel pipettes make it difficult to obtain good estimates of assay variation. This paper develops the use of a split-block design and analysis where blocks are reasonably consistent regions of a plate; this approach removes some location effects, allows other location effects to be treated as assay variation and provides appropriate measures of assay variation. Randomization, even within the split-block design, is difficult without robots to reduce the likelihood of procedural errors. There are hardware, software, and validation obstacles to implementation of robots in the bioassay laboratory. More generally, validation of a bioassay should be reported on log relative potency and must address between- and within-assay variation. When between assay variation is not small, the usual weighted approach to combining relative potency estimates (which ignores between-assay variation) is inappropriate; a simple sampling average and standard deviation is a better solution.

Biological Assay↗

The effect of postural changes on the inferred pressures within the nucleus pulposus during lumbar discography.

By observing the variation of intradiscal pressure occurring at different body postures, it is possible to infer a functional hydrostatic behavior of a lumbar disc. Results from such observations on normal discs are already available. However, observations on degenerate discs are largely restricted to in vitro studies. The authors are now able to report a series of recordings taken from discographically degenerate lumbar discs in patients presenting with low-back pain. In this study of twenty patients, pressure observations were made on 21 normal and 19 abnormal discs. From the results that the authors have obtained, they can reaffirm that normal discs behave predictably and as previously described. The abnormal discs, however, did not behave as a single group. They showed patterns of pressure changes in different postures often dissimilar from that shown by the normal discs both in the absolute values recorded and the sequential changes that occur during the postural change. Unfortunately, the authors were unable to correlate either the extent or character of disc degeneration with the observed variation in pressure changes.

Back Pain↗

SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.

Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant public health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analysed intra-host variation in SARS-CoV-2 genome sequences from Boston University's testing mandate. Focusing on intra-host single nucleotide variants (iSNVs), we inferred transmission events and assessed the selective forces shaping within-host viral evolution. To minimize false-positive iSNVs resulting from systematic biases, we implemented stringent data filtering and developed a heuristic to exclude contamination-derived artefacts arising from batched sequencing. We find that intra-host variation is limited and infrequently transmitted during acute infections, suggesting that shared iSNVs serve as highly specific but insensitive markers of transmission. We also observed incomplete purifying selection shaping within-host diversity, with the loci most affected changing among variants of concern. Finally, we identified a highly recurrent iSNV (G11083T) which may represent a site of positive selection. Our results highlight that within-host variation provides insight into within-host pathogen evolution, in spite of its limited use in genomic epidemiology.

SARS-CoV-2↗

The role of gender-related information and self-endorsement of traits in preadolescents' inferences and judgments.

The major purpose of this study was to examine the effects of a target child's gender typicality on different aspects of preadolescents' inferences and judgments. The secondary purpose of the study was to investigate the relation between children's self-endorsement of traits and their inferences and judgments. Fifth and sixth graders were shown a video film, portraying a child playing either a gender-appropriate game with members of the same sex or a gender-inappropriate game with members of the other sex. In addition, subjects completed an adapted version of the BSRI and were categorized into sex-typed, androgynous, and undifferentiated subjects. Subjects made a number of different types of judgments and inferences about the target, including inferences about traits, popularity, choice of gift and name, and willingness to engage in activities with the target. All types of inferences and judgments were affected by the variations in the targets' gender-related behaviors, whereas self-endorsement of traits was not related to the inferences and judgments. The results suggest that the gender typicality of the target behavior is salient to preadolescents, regardless of their sex-role orientation.

Adolescent↗

Inferring the conformation of RNA base pairs and triples from patterns of sequence variation.

The success of comparative analysis in resolving RNA secondary structure and numerous tertiary interactions relies on the presence of base covariations. Although the majority of base covariations in aligned sequences is associated to Watson-Crick base pairs, many involve non-canonical or restricted base pair exchanges (e.g. only G:C/A:U), reflecting more specific structural constraints. We have developed a computer program that determines potential base pairing conformations for a given set of paired nucleotides in a sequence alignment. This program (ISOPAIR) assumes that the base pair conformation is maintained through sequence variation without significantly affecting the path of the sugar-phosphate backbone. ISOPAIR identifies such 'isomorphic' structures for any set of input base pair or base triple sequences. The program was applied to base pairs and triples with known structures and sequence exchanges. In several instances, isomorphic structures were correctly identified with ISOPAIR. Thus, ISOPAIR is useful when assessing non-canonical base pair conformations in comparative analysis. ISOPAIR applications are limited to those cases where unusual base pair exchanges indeed reflect a non-canonical conformation.

Base Composition↗

Genomic insights into positive selection.

The traditional way of identifying targets of adaptive evolution has been to study a few loci that one hypothesizes a priori to have been under selection. This approach is complicated because of the confounding effects that population demographic history and selection have on patterns of DNA sequence variation. In principle, multilocus analyses can facilitate robust inferences of selection at individual loci. The deluge of large-scale catalogs of genetic variation has stimulated many genome-wide scans for positive selection in several species. Here, we review some of the salient observations of these studies, identify important challenges ahead, consider the limitations of genome-wide scans for selection and discuss the potential significance of a comprehensive understanding of genomic patterns of selection for disease-related research.

Animals↗

Cranial metric and discrete trait variation and biological differentiation in the terminal Late Archaic of Ohio: the Duff site cemetery.

Cranial metric and discrete traits were collected from adult individuals of the terminal Late Archaic Duff site cemetery (33 LO 111). Comparisons of cranial metric traits among eight terminal Late Archaic samples including the Duff site sample showed that all samples shared the same generalized variance and by inference the same pattern of shape variation. Some significant size differences were found but these were interpreted as reflecting only minor differences in the underlying polygenic system or differences in environmental interactions. The overall similarity in cranial metrics among the terminal Late Archaic samples strongly suggests that they represent populations that, at least, shared a recent common ancestor. Analysis of discrete trait variation in all the terminal Late Archaic samples showed that the biological distances between samples are associated significantly with the between-sample geographical distances. This association accounts for approximately 25% of the variation in discrete trait frequencies. These results along with the results of the analysis of cranial metrics indicate that all of the terminal Late Archaic samples considered here are related, but geographically nearer samples are more closely related than distant ones.

Analysis of Variance↗

Influence of supervision, therapist's competence, and patient's ego level on the effects of time-limited psychotherapy.

The effects of time-limited psychotherapy, of the Mann (1973) type, were followed-up in a patient sample during 22 months. The effect ratings were highly reliable and showed a strikingly large variation. A path analysis was performed on the data and a causal model inferred that accounts for over 50% of the effect variation. The effect remained stable over time and was primarily influenced (positively) by patient's ego level and (negatively) by therapist's competence. Supervision had, if anything, a negative influence.

Clinical Competence↗

Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations.

Noncoding regions are usually less subject to natural selection than coding regions and so may be more useful for studying human evolution. The recent surveys of worldwide DNA variation in four 10-kb noncoding regions revealed many interesting but also some incongruent patterns. Here we studied another 10-kb noncoding region, which is in 6p22. Sixty-six single-nucleotide polymorphisms were found among the 122 worldwide human sequences, resulting in 46 genotypes, from which 48 haplotypes were inferred. The distribution patterns of DNA variation, genotypes, and haplotypes suggest rapid population expansion in relatively recent times. The levels of polymorphism within human populations and divergence between humans and chimpanzees at this locus were generally similar to those for the other four noncoding regions. Fu and Li's tests rejected the neutrality assumption in the total sample and in the African sample but Tajima's test did not reject neutrality. A detailed examination of the contributions of various types of mutations to the parameters used in the neutrality tests clarified the discrepancy between these test results. The age estimates suggest a relatively young history in this region. Combining three autosomal noncoding regions, we estimated the long-term effective population size of humans to be 11,000 +/- 2800 using Tajima's estimator and 17,600 +/- 4700 using Watterson's estimator and the age of the most recent common ancestor to be 860,000 +/- 258,000 years ago.

Africa↗

Characterizing the response of PET and fMRI data using multivariate linear models.

This paper presents a new method for characterizing brain responses in both PET and fMRI data. The aim is to capture the correlations between the scans of an experiment and a set of external predictor variables that are thought to affect the scans, such as type, intensity, or shape of stimulus response. Its main feature is a Canonical Variates Analysis (CVA) of the estimated effects of the predictors from a multivariate linear model (MLM). The advantage of this over current methods is that temporal correlations can be incorporated into the model, making the MLM method suitable for fMRI as well as PET data. Moreover, tests for the presence of any correlation, and inference about the number of canonical variates needed to capture that correlation, can be based on standard multivariate statistics, rather than simulations. When applied to an fMRI data set previously analyzed by another CVA method, the MLM method reveals a pattern of responses that is closer to that detected in an earlier non-CVA analysis.

Analysis of Variance↗

HFE based re-evaluation of heterozygous hemochromatosis.

Homozygosity for the C282Y mutation in the HFE gene is strongly associated with hereditary hemochromatosis. More than one subject out of 10 in the general population is a heterozygote for the C282Y mutation. In this study, we address whether or not conclusions drawn from HLA-based family studies regarding the expression of heterozygous hemochromatosis are applicable to C282Y heterozygotes. The correlation between HLA-inferred and HFE genotypes and the variation of serum iron tests according to HFE genotype and other factors were studied in persons from well-characterized hemochromatosis pedigrees. Subjects were tested for both C282Y and H63D mutations. The following factors were studied: age, sex, alcohol consumption, body mass index, liver function tests, serum lipids and glucose, serum iron, transferrin saturation, and ferritin. HLA-inferred heterozygotes were C282Y heterozygotes in only 70% and compound heterozygotes (i.e., heterozygotes for both C282Y and H63D) in 20%. C282Y heterozygotes did not differ from wild type homozygotes in terms of serum iron tests. Only compound heterozygotes presented with slightly increased transferrin saturation. On the other hand, increased serum ferritin was strongly associated with overweight or lipidic or glucose abnormalities. C282Y heterozygotes selected from family studies do not have greater serum iron tests than wild type homozygotes, except for compound heterozygotes, and therefore should not require special followup. The discovery of abnormal iron tests in a C282Y heterozygote should lead to workup for other causes of iron overload.

Amino Acid Substitution↗

Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance.

Range-wide variation of maritime pine was studied at maternally inherited and paternally inherited markers (mitochondrial DNA and chloroplast DNA). While chloroplast DNA exhibits the highest diversity, phylogeographic inferences from this marker are blurred by homoplasy and extensive pollen flow. In contrast, the only three mitochondrial haplotypes found provide a clear picture of nonoverlapping areas colonized from different refugia, with no single population having a mixed composition (GST = 1). Comparison of the genetic structure inferred from both organelle genomes allows the investigation of differential seed and pollen dispersal, pointing to pollen, but not seed, dispersal across the Strait of Gibraltar (from Morocco into Iberia). A comparison with already available genetic information, especially that of one of the maritime pine's most threatening insect pests, the bast scale Matsucoccus feytaudi, further completes the picture.

DNA Primers↗

Population-scale detection of methylation outliers from long-read genome sequencing.

BACKGROUND: Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. METHODS: We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. RESULTS: METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. CONCLUSIONS: METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

DNA methylation↗

Genetic characteristic of high molecular weight glutenin subunits in somatic hybrid wheat lines -- potential application to wheat breeding.

Analysis of 17 derivatives from a somatic fusion between common wheat (Triticum aestivum) and tall wheat grass (Thinopyrum ponticum) showed a diversity of high molecular weight glutenin subunit (HMW-GS) compositions. On the basis of the inheritance of HMW-GS patterns, the derivatives were either (i) bred true over four successive generations, (ii) generated a few novel HMW-GS combinations at each generation, or (iii) showed highly unstable HMW-GS compositions. HMW-GS analysis of F(5) seed and each single seed-generated F(6) progenies further revealed that most of the HMW-GS had genetic stability. The variations of HMW-GS were inferred to occur in early generations and were maintained thereafter. Low molecular weight glutenin subunits (LMW-GS) in hybrid lines with high or low bread-making quality, classified into the first pattern, were compared. The result showed that hybrid lines with the uniform HMW-GS patterns also have identical LMW-GS patterns. The Glu-1 quality score was inferred to be relatively significant to the sodium dodecyl dulfate sedimentation value, as well as to correlate with the gluten exponent and contents of dry gluten and proteins. Sexual hybridization between high-quality somatic hybrid progeny II-12 and Chinese Spring (CS) showed that these high-quality HMW-GS genes could entail progenies. There was not subunit variation in the progenies of II-12 x CS. Therefore, sexual hybridization between somatic hybrid line and cultivars can transfer novel high-quality HMW-GS of somatic hybrids and benefit wheat breeding.

Breeding↗