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At least 199 records · Page 11Linked to original sources
PubMed2024

Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data.

UNLABELLED: Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor-type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole-genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a data set of 39,787 solid tumors sequenced using a clinically targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivaling the performance of WGS-based methods. GDD-ENS can also guide diagnoses of rare type and cancers of unknown primary and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows could provide clinically relevant tumor-type predictions to guide treatment decisions in real time. SIGNIFICANCE: We describe a highly accurate tumor-type prediction model, designed specifically for clinical implementation. Our model relies only on widely used cancer gene panel sequencing data, predicts across 38 distinct cancer types, and supports integration of patient-specific nongenomic information for enhanced decision support in challenging diagnostic situations. See related commentary by Garg, p. 906. This article is featured in Selected Articles from This Issue, p. 897.

Humans↗
PubMed2006

One novel and one recurrent mutation in the PROS1 gene cause type I protein S deficiency in patients with pulmonary embolism associated with deep vein thrombosis.

We investigated the molecular basis of type I protein S (PS) deficiency in two unrelated Japanese families, in which both probands developed pulmonary embolism associated with deep vein thrombosis. Nucleotide sequencing of amplified DNA revealed distinct point mutations in the PROS1 gene of the probands, which were designated protein S Sapporo 1 and protein S Sapporo 2. Additional mutations in the PROS1 gene were excluded by DNA sequencing of all exons and intron/exon boundaries. In the 25-year-old Japanese male patient who carried protein S Sapporo 1, we identified a heterozygous A-to-T change in the invariant ag dinucleotide of the acceptor splice site of intron f of the PROS1 gene. This mutation is a novel splice site mutation that impairs normal mRNA splicing, leading to exon 7 skipping, which was confirmed by platelet mRNA analysis. Translation of this mutant transcript would result in a truncated protein that lacks the entire epidermal growth factor-like domain 3 of the PS molecule. In a 31-year-old Japanese male and his younger brother who each carried protein S Sapporo 2, we detected a previously described heterozygous T-to-C transition at nucleotide position 1147 in exon 10 of the PROS1 gene, which predicts an amino acid substitution of tryptophan by arginine at residue 342 in the laminin G1 domain of the PS molecule. Both mutations would cause misfolding of the PS protein, resulting in the impairment of secretion, which is consistent with the type I PS deficiency phenotype.

Adult↗
PubMed2004

Nuclear integrations of mitochondrial DNA in gorillas.

Great ape systematics, particularly at the species level and below, is currently under debate, due in part to the recent influx of molecular data. The phylogenies of previously published mitochondrial control region (or D-loop) DNA sequences in gorillas show deep splits within West African gorillas (Gorilla gorilla gorilla), and very high levels of nucleotide diversity in this subspecies. Here we demonstrate that several previously reported D-loop haplotypes from West African gorillas are in all likelihood nuclear integrations of mitochondrial DNA. Revised estimates of the amount and pattern of mitochondrial DNA diversity in gorillas are provided, revealing two reciprocally monophyletic and highly divergent groups of gorillas, concurrent with their geographic distribution.

Animals↗
PubMed2000

Kinetic modeling of ATP synthesis by ATP synthase and its mechanistic implications.

Based on the torsional mechanism of ATP synthesis by ATP synthase, a kinetic scheme has been developed in this work. The scheme considers adenine nucleotide transport, binding of substrates ADP and P(i), unbinding of product ATP, and ATP synthesis. This kinetic scheme has been analyzed mathematically, and a kinetic model has been obtained to explain the experimentally observed hyperbolic Michaellian dependence of the rate of ATP synthesis on the ADP concentration by ATP synthase under physiological steady-state operating conditions. The principal results of the kinetic model have been compared with the experimental data and an estimate of the enzymological kinetic parameters V(max), K(M), and K(I) has been determined. Mechanistic implications arising from further analysis of the kinetic model have been discussed. These biological implications provide deep insight into the sequence of events leading to ATP synthesis.

Adenosine Diphosphate↗
PubMed2002

Mutational analysis of a mammalian reovirus mRNA capping enzyme.

The amino-terminal 42-kDa region of the 144-kDa mammalian reovirus lambda 2 protein is a guanylyltransferase. It catalyzes the transfer of GMP from GTP to the 5' end of 5' -diphosphorylated mRNA via a phosphoamide with Lys-190. This amino acid is located at the base of a deep cleft. Based on sequence comparisons, the Kx[V/L/I]S motif is present in all known and proposed guanylyltransferases of the family Reoviridae. The requirement for this conserved sequence and other regions of the enzyme was analyzed by site-directed mutagenesis. Based on the enzymatic activity of the mutants, Lys-190 and Asp-191 are the only amino acids of the (190)KDLS sequence that are necessary for enzymatic activity. Since Asp-191 has its side chain oriented away from the cleft, most likely it plays an indirect role in forming a functional guanylyltransferase.

Alanine↗
PubMed1983

Penicillin-induced epileptic foci in the motor cortex: vertical inhibition.

Neuronal mechanisms responsible for a vertical restriction of focal seizure activity in the motor cortex were analysed. For this purpose intracellular recording from neurones in superficial (50-300 microns below cortical surface), middle (300-800 microns) and deep cortical layers (800-1300 microns) was performed. As a model of foci of various vertical extensions the spread of seizure activity from superficial to deeper cortical laminae following epicortical penicillin application was used. The appearance of characteristic epileptiform potentials in the surface record with a focus restricted to upper cortical laminae was accompanied (i) in superficial neurones by the development of paroxysmal depolarization shifts (PDS), (ii) in middle neurones by depolarization often followed by hyperpolarization, and (iii) in deep neurones by a sequence of membrane potential changes. The latter consisted of an initial depolarization, an early hyperpolarization, an intermediate depolarization, a late hyperpolarization and a final depolarization. The hyperpolarizing components led to complete suppression of action potentials (vertical inhibition). The early hyperpolarization and the first part of the late hyperpolarization were reduced in amplitude when the intracellular chloride activity was elevated. The intermediate depolarization was replaced by PDS with the enlargement of the epileptic focus into the cortex. The actual effect of the vertical inhibition may in part be responsible for the variability in epileptic motor phenomena coinciding with epileptiform potentials in the surface EEG.

Animals↗
PubMedDate not supplied

Evaluation of diaphragmatic movement with MR fluoroscopy in chronic obstructive pulmonary disease.

The aim of this study was to show reduction of the diaphragmatic excursion with MR fluoroscopy in patients with chronic obstructive pulmonary disease (COPD) and to compare the results with pulmonary function test (PFT). The study included 13 men and 10 women (average age 56.2) with COPD, and 9 men and 6 women (average age 55.8) as a control group. MR fluoroscopy images with Spoiled Gradient-echo pulse sequence was obtained during deep inspiration and expiration. After examination, over cine-loop display, the highest and lowest positions of the diaphragm were identified and the distance of excursion was measured. Differences in the diaphragmatic excursion between patient and healthy subjects were compared. We have also compared MR fluoroscopy results with PFT. In each person of both groups, excursion of the diaphragm was demonstrated clearly in cine-loop display. Differences of excursion between deepest and highest point of diaphragm were on average 26 and 20 mm, respectively, in the right and left side in patients and 69 and 56 mm in healthy group. Significant correlation was found between expiratory volume in 1 s and MR fluoroscopy results. MR fluoroscopy study showed that there were significant statistical differences in diaphragmatic excursion between patients with COPD and healthy subjects. Expiratory volume in 1 s is closely associated with the diaphragmatic excursion. MR fluoroscopy would seem to be a useful method for showing diaphragmatic excursion.

Adult↗
PubMed1999

Creutzfeldt-Jakob disease: magnetic resonance imaging findings.

Rapidly progressive dementia in an adult with findings of bilateral, symmetric high signal intensity on T2-weighted sequences and normal findings on T1-weighted sequences predominantly in the deep grey matter is suggestive of Creutzfeldt-Jakob disease (CJD). The peripheral cortex may be involved, as it was in the present case. The absence of subcortical periventricular white matter high signal intensity suggests that symmetric high signal intensities within the basal ganglia and cortical grey matter are more likely to be due to a degenerative process rather than due to ischaemia, infection or tumour.

Creutzfeldt-Jakob Syndrome↗
PubMed2001

Dynamics of subjective contour formation in the early visual cortex.

To elucidate the roles of visual areas V1 and V2 and their interaction in early perceptual processing, we studied the responses of V1 and V2 neurons to statically displayed Kanizsa figures. We found evidence that V1 neurons respond to illusory contours of the Kanizsa figures. The illusory contour signals in V1 are weaker than in V2, but are significant, particularly in the superficial layers. The population averaged response to illusory contours emerged 100 msec after stimulus onset in the superficial layers of V1, and around 120--190 msec in the deep layers. The illusory contour response in V2 began earlier, occurring at 70 msec in the superficial layers and at 95 msec in the deep layers. The temporal sequence of the events suggests that the computation of illusory contours involves intercortical interaction, and that early perceptual organization is likely to be an interactive process.

Animals↗
PubMed2005

Different splicing defects lead to differential effects downstream of the lipid and protein phosphatase activities of PTEN.

PTEN, encoding a dual phosphatase tumor suppressor, is mutated in 85 and 65% of individuals with Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome (BRRS), respectively. Approximately 23 germline mutations in putative splice sites have been published, but resulting downstream outcome data are limited. We determined splicing defects in PTEN in 40 germline PTEN mutation positive cases and 33 mutation negative cases with classic CS, BRRS and CS- or BRRS-like features. Altered splicing was observed in 4/40 mutation positive probands and 2/33 mutation negative probands. We then sought to characterize the transcriptional and biochemical outcomes of the five distinct splice-site mutations, which led to the skipping of exon 3, 4 or 6. Two mutation negative BRRS patients also showed exon 3 skipping, and later, genomic sequencing revealed a mutation deep in intron 2. The splice-site mutations leading to the deletions of exon 3, 4 or 6 resulted in reduced dual phosphatase activities of PTEN. Deletion of exon 4 was associated with severely reduced lipid phosphatase activity, whereas exon 3 skipping resulted in markedly reduced protein phosphatase activity. In addition, exon 3 deleted transcript and protein were stable and localized to the nucleus more efficiently than the wild-type PTEN. In contrast, exon 4 skipping resulted in unstable transcripts and severely truncated unstable PTEN protein lacking its phosphatase domain. We have not only described for the first time, the effect of a deep intronic/branch-site mutation on exon skipping in PTEN but also found that different splice-site mutations resulting in the deletion of different exons lead to distinct outcomes.

Breast Neoplasms↗
PubMed2023

Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.

Large single-cell RNA datasets have contributed to unprecedented biological insight. Often, these take the form of cell atlases and serve as a reference for automating cell labeling of newly sequenced samples. Yet, classification algorithms have lacked the capacity to accurately annotate cells, particularly in complex datasets. Here we present SIMS (Scalable, Interpretable Machine Learning for Single-Cell), an end-to-end data-efficient machine learning pipeline for discrete classification of single-cell data that can be applied to new datasets with minimal coding. We benchmarked SIMS against common single-cell label transfer tools and demonstrated that it performs as well or better than state of the art algorithms. We then use SIMS to classify cells in one of the most complex tissues: the brain. We show that SIMS classifies cells of the adult cerebral cortex and hippocampus at a remarkably high accuracy. This accuracy is maintained in trans-sample label transfers of the adult human cerebral cortex. We then apply SIMS to classify cells in the developing brain and demonstrate a high level of accuracy at predicting neuronal subtypes, even in periods of fate refinement, shedding light on genetic changes affecting specific cell types across development. Finally, we apply SIMS to single cell datasets of cortical organoids to predict cell identities and unveil genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. When cell types are obscured by stress signals, label transfer from primary tissue improves the accuracy of cortical organoid annotations, serving as a reliable ground truth. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.

Brain organoids↗
PubMed2005

Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis.

Helicolenus dactylopterus is an Atlantic benthopelagic fish species inhabiting high-energy habitats on continental slopes, seamounts and islands. Partial sequences of the mitochondrial control region (D-loop) and cytochrome b (cyt b) were used to test the hypothesis that H. dactylopterus disperses between continental margin, island and seamount habitats on intraregional, regional and oceanic scales in the North Atlantic. Individuals were collected from five different geographical areas: Azores, Madeira, Portugal (Peniche), Cape Verde and the northwest Atlantic. D-loop (415 bp) and cyt b (423 bp) regions were partially sequenced for 208 and 212 individuals, respectively. Analysis of variation among mitochondrial DNA sequences based on pairwise F-statistics and AMOVA demonstrated marked genetic differentiation between populations in different geographical regions specifically the Mid-Atlantic Ridge (Azores)/northeast Atlantic (Portugal, Madeira) compared to populations around the Cape Verde Islands and in the northwest Atlantic. Some evidence of intraregional genetic differentiation between populations was found. Minimum-spanning network analysis revealed star-shaped patterns suggesting that populations had undergone expansion following bottlenecks and/or they have been colonized by jump dispersal events across large geographical distances along pathways of major ocean currents. Mismatch distribution analysis indicated that Azores and northwest Atlantic populations fitted a model of historical population expansion following a bottleneck/founder event estimated to be between 0.64 and 1.2 million years ago (Ma).

Analysis of Variance↗
PubMed1994

Synaptic physiology of horizontal afferents to layer I in slices of rat SI neocortex.

Layer I is a dense synaptic zone ubiquitous in cerebral cortex. Here we describe a novel in vitro preparation of rat somatosensory (SI) neocortical slices that isolates the fibers that extend horizontally through layer I, and allows intracellular and extracellular analysis of synaptic input to dendrites in layer I. Current source-density analysis of this isolated horizontal layer I input reveals monophasic current sinks restricted to layer I and the most superficial part of layer II. The layer I synaptic response of each neuron was correlated with its morphology by filling penetrated cells with biocytin. All filled cells that responded to horizontal layer I inputs were pyramidal neurons in layers II, III, or V with distal apical dendrites in layer I. There was no evidence of antidromic activation from isolated layer I stimulation, and HRP injected into layer I was not transported via the isolated layer I pathway to cortical neurons within the slice. Therefore, this preparation provides a unique way to study an extrinsic synaptic input localized to the most distal apical dendrites of many pyramidal neurons. In contrast to the EPSP-IPSP sequence characteristically evoked by deep layer stimulation, horizontal layer I inputs evoked long-lasting EPSPs (approximately 50 msec); IPSPs were observed only rarely, in the most superficial neurons. Horizontal layer I-evoked EPSPs were blocked by the non-NMDA glutamate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione. Consistent with the very distal site of layer I inputs to layer V pyramidal neurons, the amplitudes of initial EPSPs were insensitive to manipulations of the somatic membrane potential. However, these distal EPSPs were greatly attenuated when combined with IPSPs evoked by deep layer stimulation, indicating that the proximal inputs may modulate distal EPSPs with shunting inhibition. In many layer V neurons, the initial EPSP evoked by horizontal layer I stimulation was followed by a variable late depolarization that was blocked by the NMDA receptor antagonist 2-amino-5-phosphonovaleric acid. Since these late depolarizations were enhanced by somatic depolarization and abolished by hyperpolarization, they appeared to be generated postsynaptically at a site more proximal than the initial EPSP that was insensitive to these manipulations. Synaptic inputs to the distal tufts of pyramidal neurons may trigger active currents along the apical dendrites that amplify the EPSP on its way to the soma.

2-Amino-5-phosphonovalerate↗
PubMed2003

Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria.

A novel Gram-positive bacterial strain was isolated from forest soil. According to its 16S rRNA sequence, this strain is a deep-rooting member of the class Actinobacteria. The 16S rRNA sequence is most closely related (approximately 94% identity) to clones of uncultured bacteria detected in different terrestrial environments, while showing only a remote relationship (approximately 90% identity or less) to sequences of cultured species. Cells of the first cultured representative of this phylogenetic cluster are small, short rods that are motile by peritrichous flagella, catalase- and oxidase-positive and grow under aerobic conditions. In liquid culture, flagella from different cells can aggregate to form networks, clearly visible under the light microscope. The peptidoglycan contains meso-diaminopimelic acid and is directly cross-linked (type A1gamma). Mycolic acids are not present. The polar lipids are phosphatidylinositol and an unidentified phospholipid. Menaquinone MK-7(H4) was detected as the predominant isoprenoid quinone. Oleic, 14-methylpentadecanoic, hexadecanoic and omega6c-heptadecenoic acids are the predominant components of the cellular fatty acid profile. The DNA G + C content is 71 mol%. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics justify the proposal of a new genus and species, Conexibacter woesei gen. nov., sp. nov., with the type strain ID131577T (=DSM 14684T =JCM 11494T).

Actinobacteria↗
PubMed2025

G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration.

MOTIVATION: G-quadruplexes (G4s) are non-canonical nucleic acid structures formed in guanine-rich regions that modulate gene regulation and genomic stability. The thermodynamic stability of G4s directly influences their biological functions and potential as therapeutic targets. However, current quantitative frameworks for predicting G4 stability rely on predetermined structural features, limiting their effectiveness for diverse G4 topologies, and fail to account for environmental factors such as ion concentration and pH that significantly modulate G4 stability in cellular contexts. RESULTS: We present G4STAB, a multi-input deep learning neural network that accurately predicts DNA G4 melting temperatures based on sequence features, salt concentration, and pH. Trained on 2382 diverse DNA G4 sequences, our model achieves high accuracy (R 2=0.8) without relying on predetermined G4 structural features. G4STAB successfully captures established G4 stability determinants and proposes previously unobserved sequence-stability relationships. Analysis of 391 502 experimentally validated G4s reveals that cancer-like ionic environments alter G4 stability profiles, with a 13.5-fold increase in the number of structures exhibiting physiological melting temperatures (36-42°C). These findings suggest systematic genomic patterns in G4 stability responses across chromosomes and gene types. AVAILABILITY AND IMPLEMENTATION: G4STAB is available at https://github.com/donn-liew/G4STAB; G4STAB web database interface is available at https://donn-liew.github.io/g4stab-web-database/.

G-Quadruplexes↗
PubMed2001

Sequence-sensitive subcomponents of P300: topographical analyses and dipole source localization.

P300 amplitude and reaction time (RT) are strongly affected by the sequence of events preceding the eliciting stimulus. Sommer, Leuthold and Soetens (1999) found that robust sequential effects in P300 amplitude could be dissociated from more variable sequential effects in RTs. However, global changes in P300 amplitude and topography gave rise to the suggestion that sequential effects are specific for a subcomponent of P300 that is separate from and anterior to the classical parietal P300. Here, confirming evidence for dissociable subcomponents of P300 is reported from two experiments. Independent component analysis separated a centrally distributed sequence-sensitive subcomponent from a more parietal subcomponent. Subsequent dipole source analysis indicated a deep mesial source for the sequence-sensitive subcomponent. Overlap with reafferent somatosensory activity appears to be responsible for an apparent lateralization of this component towards the hemisphere ipsilateral to the responding hand.

Adolescent↗
PubMed1999

Normal myelination of the pediatric brain imaged with fluid-attenuated inversion-recovery (FLAIR) MR imaging.

BACKGROUND AND PURPOSE: As in adult imaging, FLAIR can be applied to pediatric brain imaging, and this requires an appreciation of the normal pediatric brain appearance by FLAIR imaging. The purpose of this study was to describe the MR appearance of the brain in normal infants and young children as demonstrated by fluid-attenuated inversion-recovery (FLAIR) MR imaging. METHODS: We retrospectively examined MR brain studies, interpreted as normal by pediatric radiologists, from 29 patients (aged 1 to 42 months) to catalog the appearance of myelination in multiple brain areas. RESULTS: On T2-weighted images, white matter progressed from hyperintense to hypointense relative to adjacent gray matter over the first 2 years of life. An analogous, although slightly delayed sequence was observed on FLAIR images with the exception of the deep cerebral hemispheric white matter, which followed a triphasic sequence of development. On FLAIR images, the deep cerebral white matter was heterogeneously hypointense relative to gray matter in the young infant, became hyperintense early in the first few months of life, and then reverted to hypointense during the second year of life. CONCLUSION: The normal appearance and development of brain white matter must be taken into account when interpreting FLAIR images of infants and young children.

Adult↗