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At least 109 records · Page 6Linked to original sources

PubMed2025

scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.

MOTIVATION: Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge. RESULTS: Here, we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting. AVAILABILITY AND IMPLEMENTATION: The source code, and detailed documentation are freely available at https://github.com/nf-core/scnanoseq and https://nf-co.re/scnanoseq under the MIT License. Documentation for the version of nf-core/scnanoseq used for this paper, including default parameters and descriptions of output files are available at https://nf-co.re/scnanoseq/1.1.0.

Single-Cell Analysis↗

PubMed1986

Computing with neural circuits: a model.

A new conceptual framework and a minimization principle together provide an understanding of computation in model neural circuits. The circuits consist of nonlinear graded-response model neurons organized into networks with effectively symmetric synaptic connections. The neurons represent an approximation to biological neurons in which a simplified set of important computational properties is retained. Complex circuits solving problems similar to those essential in biology can be analyzed and understood without the need to follow the circuit dynamics in detail. Implementation of the model with electronic devices will provide a class of electronic circuits of novel form and function.

Action Potentials↗

PubMed2025

A dataset of estimated heterozygous individual and carrier couple frequencies for pan-ancestry carrier screening.

The data described in this publication supported the development and evaluation of pan-ancestry reproductive carrier screening panels for autosomal recessive (AR) and X-linked (XL) conditions. Raw data included combined sets of DNA variants in 1,350 AR/XL genes obtained from the ClinVar and gnomAD databases. The dataset enabled calculations of positive yield for individuals and couples across both ancestry-specific and pan-ancestry, optimised "Goldilocks"-ranked gene panels, addressing population-specific variations in the frequencies of heterozygous individuals and carrier couples. The positive yield analysis offered a performance metric for carrier screening panels, facilitating the modeling of screening performance for panels of varying sizes and composition and providing resources for optimizing panel content to ensure equity across underrepresented genetic ancestries The dataset can support ongoing research into the equitable application of carrier screening and offers significant reuse potential for refining population genetic screening practices, validating computational models, and developing frameworks to update carrier screening panels in alignment with evolving genomic data, including in underrepresented and minority populations.

Carrier screening↗

PubMed1992

[Acute abdominal pain--standardized findings as diagnostic support. Results of a prospective multicenter intervention study and testing of a computer-assisted diagnosis system].

Despite powerful diagnostic tools (e.g. ultrasound, special laboratory investigations), the diagnosis of acute abdominal pain is still a considerable problem. Several studies in the UK have shown that the diagnostic accuracy can be improved by structured and standardized history taking and clinical examination and by computer-aided diagnosis. In the framework of a concerted action of the European Community we have conducted a prospective multicenter interventional trial comparing two consecutive phases: a) a baseline phase in clinical routine without additional intervention, b) a test phase with structured and standardized history and clinical examination (questionnaire, documentation programme). In addition, a computer-aided diagnostic system developed in the UK was applied to the cases in the test phase. Outcome criteria were the diagnostic accuracy of the initial and the final examiner, the perforated appendix rate, the negative appendectomy rate, the negative laparotomy rate and the rates of diagnostic errors with missing indication to operation and of delayed urgent operations. No differences could be found between the phases with respect to the outcome criteria. In the baseline phase (test phase) diagnostic accuracy was 59% (59%), diagnostic accuracy after investigation (senior examiner) was 77% (78%), perforated appendix rate was 11% (16%), negative appendectomy rate was 13% (15%), negative laparotomy rate was 7% (8%), the rate of missed urgent indications to operation was 1.1% (1.9%) and the rate of delayed urgent operations was 3.4% (2.4%). Major differences between the centers were recorded. Computer-aided diagnosis resulted in a diagnostic accuracy of 51%. The introduction of structured and standardized history taking and clinical examination has not brought any improvement of the good results in clinical routine. It is doubtful, whether existing systems of computer-aided diagnosis are able to significantly decrease the still remaining error rate of 20%.

Abdomen, Acute↗

PubMed2026

Endothelial cell-specific DNA methylation alterations in breast cancer.

DNA methylation alterations are well-established contributors to carcinogenesis, yet, in the tumor microenvironment (TME), patterns of lineage and cell-specific methylation alterations are not well understood. Single-cell DNA methylation profiling in the TME is limited by technical challenges and high costs. Here, we use bulk DNA methylation, cell type deconvolution (HiTIMED), and an interaction testing framework (CellDMC) to identify reproducible, computationally inferred lineage-specific epigenetic alterations in the TME supported by orthogonal data sources. Tumor endothelial cells (TECs), critical regulators of angiogenesis, vascular permeability, and immune cell trafficking, acquire structural and functional abnormalities that promote tumor growth. We hypothesize that TECs have altered DNA methylation compared with endothelial cells in non-tumor tissues. In genome-scale methylation data from discovery and validation datasets (tumor n = 1071; non-tumor n = 415), we identify and validate >4500 TEC-specific CpGs with altered methylation, many mapping to genes involved in angiogenesis and endothelial function. Integration with gene expression data indicates that TEC-specific methylation alterations may reprogram transcriptional networks controlling angiogenesis. High-resolution, cell lineage-specific epigenetic landscapes can be inferred from bulk methylation data, implicating TEC-specific DNA methylation alterations as potential drivers of cancer angiogenesis and vascular dysfunction and providing a framework for future mechanistic and translational studies of the tumor vasculature.

DNA Methylation↗

PubMed1992

A computational model of the amplitude and implicit time of the b-wave of the human ERG.

To improve the usefulness of the ERG in identifying the sites and mechanisms of adaptation, development, and disease processes, a theoretical framework based upon Granit's analysis of the ERG was evaluated. The framework assumes that the ERG is the sum of two potentials, one, P3, generated by the receptors and the other, P2, generated by the cells of the INL. Hood and Birch (1990a, b) demonstrated that the leading edge of the a-wave can be quantitatively described by a model used to describe the response from single rod receptors. This model provides P3(t), a theoretical receptor response as a function of time, for any given flash intensity. The ERGs from normal observers and patients with retinal diseases were analyzed in this framework, first by deriving P2 by computer subtracting the predicted P3(t) responses. This analysis was successful and a computational model of the ERG was then derived. The model of P2(t) was constructed with linear filters and a static nonlinearity and using P3(t) as the input. The ERG for any given flash intensity is then P3(t) + P2(t). The model describes (1) the change both in implicit times and in trough-to-peak b-wave amplitudes with flash intensity for the normal, dark-adapted observers; and (2) the changes in b-wave implicit times and amplitudes for three patients with retinal diseases. Among the implications drawn from these analyses were as follows: (1) The fits of the Naka-Rushton equation to trough-to-peak b-wave amplitudes must be interpreted with great care. (2) When the INL is affected by retinal disease, the b-wave may be a very poor reflection of INL activity. (3) The implicit time of the b-wave can provide a measure of receptor sensitivity.

Adult↗

PubMed1992

An approach to evaluating heuristics in abduction: a case study using RedSoar--an abductive system for red blood cell antibody identification.

Abduction, or inference to a best explanation, is a ubiquitous type of inference that is frequently used by humans in a wide range of tasks. However, many realistic domains have properties that make abduction computationally intractable (i.e., where the time to reach a solution increases exponentially with the number of possible explanations). We present a domain task analysis and performance evaluation of RedSoar, a plausible cognitive computational model of abduction, that accomplishes the antibody identification task in immunohematology. The task analysis reveals how a computationally intractable abductive problem, where one is seeking optimal solutions, can be reformulated to be a computationally tractable abductive problem, by seeking satisfactory rather then optimal solutions. From the satisfactory perspective, our evaluation framework of RedSoar's performance explores the computational benefits and costs of having directly available abstract hypothesis formation knowledge, and how a strong causal constraint between hypotheses and data reduces the combinatorial explosion of constructing a best explanation.

Antibodies↗

PubMed2025

Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms.

MOTIVATION: Modern single-cell omics data are key to unraveling the complex mechanisms underlying risk for complex diseases revealed by genome-wide association studies (GWAS). Phenotypic screens in model organisms have several important parallels to GWAS which the author explores in this essay. RESULTS: The author provides the historical context of such screens, comparing and contrasting similarities to association studies, and how these screens in model organisms can teach us what to look for. Then the author considers how the results of GWAS might be exhaustively interrogated to interpret the biological mechanisms underpinning disease processes. Finally, the author proposes a general framework for tackling this problem computationally, and explore the data, mechanisms, and technology (both existing and yet to be invented) that are necessary to complete the task. AVAILABILITY AND IMPLEMENTATION: There are no data or code associated with this article.

Genome-Wide Association Study↗

PubMed1985

[Value of computer tomographic determination of spleen size for the elucidation of splenic involvement within the framework of primary lymph node neoplasms].

The splenic index was determined in 155 persons, without evidence of splenic disease, in order to obtain a simple measure of splenic size. Subsequently 36 patients with malignant lymphomas and who then had their spleens removed were examined by CT. A comparison of the CT and pathological-anatomical findings showed that it is a valuable non-invasive method for diagnosing splenic involvement, having a specificity of 86%, sensitivity of 77% and accuracy of 83%.

Adolescent↗

PubMed1992

Chimeric and humanized antibodies with specificity for the CD33 antigen.

L and H chain cDNAs of M195, a murine mAb that binds to the CD33 Ag on normal and leukemic myeloid cells, were cloned. The cDNAs were used in the construction of mouse/human IgG1 and IgG3 chimeric antibodies. In addition, humanized antibodies were constructed which combined the complementarity-determining regions of the M195 antibody with human framework and constant regions. The human framework was chosen to maximize homology with the M195 V domain sequence. Moreover, a computer model of M195 was used to identify several framework amino acids that are likely to interact with the complementarity-determining regions, and these residues were also retained in the humanized antibodies. Unexpectedly, the humanized IgG1 and IgG3 M195 antibodies, which have reshaped V regions, have higher apparent binding affinity for the CD33 Ag than the chimeric or mouse antibodies.

Amino Acid Sequence↗

PubMed1985

Computer-based information systems models. Perspectives for nursing.

A synthesis of theories from the management information systems (MIS) field provided the conceptual framework to describe how to design and develop effective computer-based information systems. An analysis of activities and interviews with nurse managers in a tertiary care medical center provided the basis for describing five major nursing department functions and the information requirements arising from those functions. The MIS framework was applied to the nursing department information requirements in order to derive MNIS, a normative model of a nursing information system, which was then used to "bench mark" the current status of commercially available nursing information systems. The researchers compared the MNIS with 28 nursing information systems that vendors are currently developing or marketing. The comparison revealed large gaps between nursing department needs and vendor-provided solutions.

Commerce↗

PubMedDate not supplied

A computer-based AIDS education program for nursing students.

A multidisciplinary team has developed a computer-based software program for educating nursing students and other college students about six sexually transmitted diseases (STDs). The program for educating about Acquired Immune Deficiency Syndrome (AIDS) is the first of the six "Smartbooks" to be completed, using the Hypercard Expert System shell on the Macintosh computer. Information is organized within a framework known as a concept map, and the student user progresses through the program in a self-directed way by "clicking" on the portion of the concept map that is of interest. Thus, the knowledge base can be accessed in many different ways, and is not restricted to a linear format. Comparative quantitative analysis using a control program shows consistently better student retention of information presented within the program that features concept maps. Qualitative results indicate that students find the conceptually-arranged knowledge base implicitly easy to understand, "fun" to use, and interesting to explore. Educational theory suggests that the success of such a format may be related to the schematic nature of memory.

Acquired Immunodeficiency Syndrome↗

PubMed1989

Computer applications for staff development and patient education.

The changing and evolving profession of nursing necessitates extensive staff development activities on the part of nursing management. This ongoing responsibility is essential to maintaining the currency and competence of practicing nurses and facilitating their professional growth. Simultaneously there are economic constraints coinciding with increased consumer demands for patient education. The purpose of this paper is to explore an innovative teaching method, the use of instructional computing for staff development and patient education programs. The theoretical frameworks for this instructional modality are identified and general advantages and disadvantages of instructional computing applications are described. Specific examples of programs from the literature are briefly discussed.

Attitude to Computers↗

PubMed2025

SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis.

Spatial transcriptomics (ST) integrates spatial information into genomics, yet methods for generating spatially-informed gene representations are limited and computationally intensive. We present SIGEL, a cost-effective framework that derives gene manifolds from ST data by exploiting spatial genomic context. The resulting SIGEL-generated gene representations (SGRs) are context-aware, biologically meaningful, and robust across samples, making them highly effective for key downstream tasks, including imputing missing genes, detecting spatial expression patterns, identifying disease-related genes and interactions, and improving spatial clustering. Extensive experiments across diverse ST datasets validate SIGEL's effectiveness and highlight its potential in advancing spatial genomics research.

Genomics↗

PubMed1992

Modelling of intersegmental coordination in the lamprey central pattern generator for locomotion.

Rhythmic motor activity requires coordination of different muscles or muscle groups so that they are all active with the same cycle duration and appropriate phase relationships. The neural mechanisms for such phase coupling in vertebrate locomotion are not known. Swimming in the lamprey is accomplished by the generation of a travelling wave of body curvature in which the phase coupling between segments is so controlled as to give approximately one full wavelength on the body at any swimming speed. This article reviews work that has combined mathematical analysis, biological experimentation and computer simulation to provide a conceptual framework within which intersegmental coordination can be investigated. Evidence is provided to suggest that in the lamprey, ascending coupling is dominant over descending coupling and controls the intersegmental phase lag during locomotion. The significance of long-range intersegmental coupling is also discussed.

Animals↗

PubMed1986

Role of electrical interactions in synchronization of epileptiform bursts.

Four general mechanisms can hypothetically contribute to or mediate localized synchronization of neuronal activity: (a) recurrent excitatory chemical synapses, (b) electrotonic coupling via gap junctions, (c) electrical field effects (ephaptic interactions), and (d) changes in the concentration of extracellular ions (e.g., K+). It has generally been believed that synchronization of epileptiform bursts derives primarily, if not exclusively, from recurrent excitatory chemical synapses. Dual intracellular recordings from the CA3 area of the hippocampus have been used to demonstrate the existence of recurrent synaptic excitation, and computer simulations have provided a theoretical framework for the idea that relatively sparse interactions through recurrent excitatory chemical synapses can generate synchronized bursting after inhibitory pathways are blocked with convulsant agents. Additional experimental studies have supported the hypothesis that a model for seizure discharge, the penicillin-induced paroxysmal depolarization shift (PDS), is associated with a large increase in excitatory synaptic conductance. However, recent studies have suggested that electrical interactions are also likely to play an important role in spike synchronization during epileptic discharges. Several research groups have used in vitro preparations to show that afterdischarges and spontaneous bursts of population spikes (which represent synchronized action potentials) can occur after chemical synaptic transmission has been blocked in solutions containing low [Ca2+]. Although this result was first observed in the CA1 area, it has recently been confirmed in other regions of the hippocampus. These experiments indicate that mechanisms other than chemical synaptic transmission are capable of synchronizing action potentials in the hippocampus. In this chapter, two forms of electrical interaction that could mediate synchronization will be considered: (a) electrotonic coupling through gap junctions and (b) electrical field effects through extracellular space. Changes in the concentration of extracellular ions are another mechanism not involving chemical synapses. However, it seems unlikely that ionic changes act on the rapid time scale of electrical interactions, and their contribution is discussed elsewhere in this volume. We review evidence for the existence of electrotonic coupling and electrical field effects in the hippocampus and neocortex, and discuss their possible involvement in the synchronization of epileptiform events.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2026

Secure bioinformatics: privacy-preserving federated analytics using homomorphic encryption.

MOTIVATION: Large-scale bioinformatics analyses increasingly require collaboration across multiple cohorts and institutions, yet existing workflows often rely on data co-localization, which is slow, difficult to scale, and raises privacy concerns. We present a privacy-preserving federated analytics framework that enables secure statistical analysis across distributed datasets without transferring raw data, by performing all computations on encrypted data via cryptographic methods. RESULTS: We evaluate the framework by validating polygenic risk scores and conducting meta-analyses on two real-world cohorts. The proposed solution achieves over 99.9% accuracy relative to plaintext analyses, while maintaining scalable runtime performance with increasing data size and number of participating sites. These results demonstrate the feasibility of secure federated analytics for practical bioinformatics applications involving sensitive data.

Computational Biology↗

PubMed1992

Continuum electrostatics of the C-peptide: anatomy of the problem.

A computational study of the role of all ionizable groups of the C-peptide in its helix-coil transition is performed within the framework of continuum electrostatics. The method employed in our computations involves a numeric solution of the Poisson equation with the Boundary Element Method. Our calculations correctly predict the experimentally observed trends in the helix-coil equilibrium of the C-peptide, and suggest that the mechanisms involved are more complex than usually presumed in the literature. Our results suggest that electrostatic interactions in the unfolded conformation are often more important than in the helix, total electrostatic contribution to the helix-coil transition due to the side chains of the C-peptide destabilizes the helix, changes in the helix stability produced by the changes in the ionization state of the side chains are dominated by side chain effects, the effect of the helix dipole on the energetics of the helix-coil transition of the C-peptide is either minor or similar to other contributions in magnitude; while the formation of a salt bridge is electrostatically favorable, formation of the hydrogen bond between a charged and a polar side chains is not. Factors limiting the accuracy of the computations are discussed.

C-Peptide↗