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PubMed2026

ALPINE: a scalable pipeline for comprehensive classification of gene-editing outcomes from long-read amplicon sequencing.

SUMMARY: CRISPR genome editing has enabled precise genetic modification for gene and cell therapies, but edits often produce heterogeneous on-target outcomes, including homology-directed repair (HDR) knock-ins, DNA repair template integrations, and structural variants. Existing tools are frequently limited to short reads or lack viral vector-specific integration categories needed for therapeutic development. Here, we present ALPINE (Amplicon Long-read Pipeline for INtegration Evaluation), a scalable and reproducible pipeline for classifying and quantifying gene-editing outcomes from long-read amplicon sequencing supporting both PacBio HiFi and Oxford Nanopore platforms. ALPINE classifies reads into 10+ categories, including DNA repair vector integration subtypes, and performs variant calling near the gene-edited site with batch, multi-sample reporting. Uniquely, ALPINE can distinguish between cells treated with multiple DNA repair vectors and identify distinct molecular features, such as inverted terminal repeats (ITRs), enabling comprehensive characterization of complex gene editing outcomes. Dual-target benchmarking on simulated datasets demonstrated high accuracy for transgene integration events. Independent validation on public crosslinked-HDR dataset confirmed ALPINE's integration detection capabilities, and application to edited T cell samples demonstrated comprehensive gene-editing outcome profiling. AVAILABILITY: ALPINE is available under MIT license at https://github.com/Maggi-Chen/ALPINE and https://doi.org/10.5281/zenodo.20272510. All analysis scripts and visualization code used in this manuscript are available at https://github.com/Maggi-Chen/ALPINE-manuscript-analysis. Simulated datasets are deposited at Zenodo (https://doi.org/10.5281/zenodo.20260865). Public dataset PRJNA913199 is available through NCBI SRA.

Gene Editing↗

PubMed2005

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries.

MOTIVATION: T-cell response to peptides bound on MHC Class I or Class II molecules is essential for immune recognition of pathogens. T-cells are activated by specific peptide epitopes that are determined within the antigen processing pathways and presented on the surface of other cells bound to MHC molecules. To determine which part of allergenic or pathogenic proteins can stimulate T-cells is important for the treatment of diseases. We sought to take advantage of the falling cost of synthetic, screening grade peptides, and devise a comprehensive, non-hypothesis-driven screen for T-cell epitopes. We were interested in the study of celiac disease (CD) and used the ELISPOT technique to perform a large number of T-cell assays. We therefore needed to compensate for the lack of statistical data analysis methods for ELISPOT assays. RESULTS: We describe a method to comprehensively screen for T-cell epitopes within a family or a group of proteins. We have implemented an algorithm to generate a set of unique short peptide sequences that incorporate all possible epitopes within a group of proteins. T-cell assays were performed in 96-well plates using the ELISPOT assay to screen for responses in CD patients against any epitopes in glutens. We describe a statistical model to fit the data and an Expectation Maximization algorithm to estimate the parameters of interest and analyze the resulting data. AVAILABILITY: Implementations of our algorithms in R or Perl are available at http://bioinf.wehi.edu.au/folders/immunol.

Algorithms↗

PubMed1993

Comprehension deficits elicited by electrical stimulation of Broca's area.

We report on three patients with intractable focal seizures arising from the language-dominant left hemisphere. In the work-up prior to surgical treatment, arrays of subdural electrodes were placed over the left temporal lobe and adjacent supra-Sylvian region. Electrical stimulation of the inferior frontal cortex language region ('Broca's area') produced marked interference with language output functions including speech arrest, slowing of oral reading, paraphasia and anomia. At some cortical language sites in this region cortical stimulation also produced language comprehension deficits, particularly in response to more complex auditory verbal instructions and visual semantic material. The severe impairment of comprehension verbal information was in clear contrast with ability to process non-verbal material, which was not affected.

Adolescent↗

PubMed1998

Distinct time courses of word and context comprehension in the left temporal cortex.

The time course and cortical basis of reading comprehension were studied using magnetoencephalography. The cortical structures implicated most consistently with comprehension were located in the immediate vicinity of the left auditory cortex, where final words totally inappropriate to the overall sentence context evoked enduring activation starting approximately 250 ms and lasting up to 600 ms after word onset. Contextually appropriate but unexpected words produced weaker activation which terminated earlier. Highly anticipated words totally failed to activate this area, suggesting that the conceptual network became involved only if unexpected information was detected during the primary word identification process. We propose that the point in time (350 ms after word onset) where the response to appropriate but unexpected endings started to diverge from those to contextually inappropriate endings reflects the boundary between understanding a single word and the meaning of a whole sentence.

Adult↗

PubMed1999

Electrophysiological manifestations of open- and closed-class words in patients with Broca's aphasia with agrammatic comprehension. An event-related brain potential study.

This paper presents electrophysiological data on the on-line processing of open- and closed-class words in patients with Broca's aphasia with agrammatic comprehension. Event-related brain potentials were recorded from the scalp when Broca patients and non-aphasic control subjects were visually presented with a story in which the words appeared one at a time on the screen. Separate waveforms were computed for open- and closed-class words. The non-aphasic control subjects showed clear differences between the processing of open- and closed-class words in an early (210-375 ms) and a late (400-700 ms) time-window. The early electrophysiological differences reflect the first manifestation of the availability of word-category information from the mental lexicon. The late differences presumably relate to post-lexical semantic and syntactic processing. In contrast to the control subjects, the Broca patients showed no early vocabulary class effect and only a limited late effect. The results suggest that an important factor in the agrammatic comprehension deficit of Broca's aphasics is a delayed and/or incomplete availability of word-class information.

Adult↗

PubMed2001

Comprehension of metaphors and idioms in patients with Alzheimer's disease: a longitudinal study.

Language in patients with Alzheimer's disease has been extensively studied, with the exception of non-literal language comprehension. However, in our speech, we often make use of expressions, which are not necessarily interpreted on a literal ground. Comprehension of metaphors and idioms was examined in 39 patients with probable early Alzheimer's disease. The results showed that the decline of figurative language is not an early symptom of dementia and can occur independently from the impairment of propositional language. It was also found that metaphors and idioms differ as far as the predominant kind of error is concerned.

Aged↗

PubMed2003

A comparative study of rehabilitation outcomes of elderly hip fracture patients: the advantage of a comprehensive orthogeriatric approach.

BACKGROUND: The optimal setting and design of a comprehensive treatment for elderly hip fracture patients is unknown. The aims of this study were to compare the functional outcomes associated with an innovative comprehensive single-step (geriatric-based) and classic double-step (orthopedic-based) treatment of such patients. METHODS: This is a partially concurrent prospective study, taking place in the orthogeriatric unit of a department of geriatric rehabilitation, in a large urban academic freestanding hospital. The participants were 336 consecutive elderly people, admitted for surgery of extracapsular or intracapsular hip fracture. 204 patients were admitted to the department of orthopedic surgery and transferred, shortly after surgery, to the orthogeriatric ward for ongoing rehabilitation (ORT group). Another 116 patients were admitted directly to a geriatric-based orthogeriatric ward, and they received surgical, medical, and rehabilitation treatment within the same facility (ORTGER group). The main outcome measures were length of stay, absolute functional gains of the motor functional independence measure (FIM), and relative functional motor gains according to the Montebello rehabilitation factor score. Successful rehabilitation was defined as relative functional gain >.5. RESULTS: 320 patients were included in the final analysis. The two groups were similar, yet ORT-group patients were somewhat younger (p <.02) and were cognitively better preserved (p <.01). Admission cognitive FIM was the strongest positive predictive factor associated with successful rehabilitation (odds ratio = 2.45, 95% confidence interval 1.89-3.31, and p <.001). Significant improvement of total FIM scores occurred during rehabilitation in both groups. The relative functional gain was similar in the two groups, but total hospital length of stay was 5 days shorter in the ORTGER group (p <.01). After the effect of age, sex, length of stay, fracture type, and cognition at onset of the rehabilitation period were adjusted for, patients of the ORTGER group had a twofold chance for successful rehabilitation, compared with ORT-group patients (odds ratio = 1.97, 95% confidence interval 1.09-3.65, and p =.03). CONCLUSIONS: The functional outcome of elderly hip fracture patients is better for those treated in the orthogeriatric setting, as compared with the common two-steps model of orthopedic surgery followed by transfer to a geriatric rehabilitation facility.

Aged↗

PubMed1980

Sentence comprehension abilities throughout the adult life span.

Sentence comprehension abilities of adults ranging in age from 18 to 80 years were compared as they enacted, through an object-manipulation task, the meanings of spoken sentences containing relative clauses. A decline in performance was observed beginning with subjects in their 60s. Those in their 70s not only erred more frequently than younger subjects, but also made errors of a more serious nature. Great variability was observed within age groups, some of which was accounted for by Vocabulary and Digit Span scores and by educational level. Even after adjustment for the relevant variables, scores for the older groups were bimodally distributed. These results are discussed in terms of cognitive factors underlying sentence comprehension.

Adolescent↗

PubMed1983

Comprehension and retention of television programs by 20- and 60-year olds.

Two experiments were conducted to examine age differences in adults' comprehension and retention of television programs; in both studies content (level of information) and learner (vocabulary level) variables were explored. Fifty older and 50 younger adults participated in each study. Results from Experiment I measures of free recall, probe recall, and recognition showed a significant age by vocabulary interaction; only older low-verbal adults were consistently poorer than their younger counterparts. Experiment II demonstrated that the locus of this interaction may be at initial program comprehension rather than solely at retrieval. The results were interpreted as demonstrating the importance of considering learner characteristics in adult cognitive developmental research.

Adolescent↗

PubMed1984

Development of indicator scales for the Comprehensive Assessment and Referral Evaluation (CARE) interview schedule.

The objective of this research was to develop indicator scales for major health and social problems of individuals aged 65 or over who live in the community. A semistructured interview technique, the Comprehensive Assessment and Referral Evaluation (CARE), was used in two large surveys in London and New York City. Twenty-two indicator scales were developed by using items that met certain clinical and statistical criteria. These indicator scales are intended for use in developing a general taxonomy of the problems of older individuals, for clinical assessment and referral of such individuals, and for use in geriatric epidemiological research. The scales were developed to be comprehensive with regard to the CARE, to be relatively independent of one another, and to have satisfactory content, clinical, and face validities, and interrater and internal consistency reliabilities.

Activities of Daily Living↗

PubMed1990

Effects of labeling techniques on memory and comprehension of prescription information in young and old adults.

We conducted a study to determine the effects of presenting prescription information in a pictorial compared to a verbal format on comprehension and memory in young and old adults. Both comprehension and memory for drug information were studied as a function of age and presentation method. Participants received prescription instructions on actual medicine bottles in one of two formats: verbal instructions only, or verbal instructions mixed with pictorial representations. Results indicated that (a) younger adults' memory for prescription information was facilitated by the mixed instructions, but that mixed instructions appeared to hamper older adults' memory for prescription information; (b) younger adults recalled more information overall relative to older adults across both presentation conditions; and (c) older adults were less able to comprehend prescription information relative to younger adults. Results suggest that well-organized verbal prescription labels are more facilitative for the elderly and that additional efforts must be undertaken to improve the clarity of labeling on prescription drugs.

Adult↗

PubMed2025

PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility.

Self-incompatibility (SI) is an important genetic mechanism in angiosperms that prevents inbreeding and promotes outcrossing, with significant implications for crop breeding, including genetic diversity, hybrid seed production, and yield optimization. In eudicots, SI is typically governed by a single S-locus containing tightly linked pistil and pollen S-determinant genes. Despite major advances in SI research, a centralized, comprehensive resource for SI-related genomic data remains lacking. To address this gap, we developed the Plant Self-Incompatibility Atlas (PSIA), a systematically curated knowledgebase providing an extensive compilation of plant SI, including genomic resources for SI species, S gene annotations, molecular mechanisms, phylogenetic relationships, and comparative genomic analyses. The current release of PSIA includes over 500 genome assemblies from 469 SI species. Using known S genes as queries, we manually identified and rigorously curated 3700 S genes. PSIA provides detailed S-locus information from assembled genomes of SI species and offers an interactive platform for browsing, BLAST searches, S gene analysis, and data retrieval. Additionally, PSIA serves as a unique platform for comparative genomic studies of S-loci, facilitating exploration of the dynamic processes underlying the origin, loss, and regain of SI. As a comprehensive and user-friendly resource, PSIA will greatly advance our understanding of angiosperm SI and serve as a valuable tool for crop breeding and hybrid seed production. PSIA is freely available at http://www.plantsi.cn.

Self-Incompatibility in Flowering Plants↗

PubMed2026

cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers.

Cancer is a major global health threat, and early detection is crucial for improving patient outcomes. DNA methylation in circulating cell-free DNA (cfDNA) has emerged as a promising biomarker for non-invasive cancer diagnosis. However, the integration and utilization of existing cfDNA methylation data have been limited, hindering comprehensive research efforts, particularly in the discovery of cfDNA methylation biomarkers. To address this challenge, we introduced cfMethDB, a comprehensive database dedicated to cfDNA methylation in cancer that encompasses 4828 publicly available datasets. Through standardized analysis, we identified 1,048,770 differentially methylated cytosines (DMCs) as candidate biomarkers across seven cancer types. With cfMethDB, we not only identified known cfDNA methylation biomarkers, but also discovered several genes, such as ZIC4, that could be novel biomarkers. Moreover, cfMethDB offers a suite of user-friendly tools, including biomarker evaluation, pan-cancer search, and end motif analysis. We hope that cfMethDB will serve as a valuable platform for the discovery of novel cancer cfDNA methylation biomarkers and facilitate cancer research and clinical applications. cfMethDB is publicly available at https://cfmethdb.hzau.edu.cn/home.

Humans↗

PubMed2004

Effect evaluation of a comprehensive community intervention aimed at reducing socioeconomic health inequalities in The Netherlands.

To date, comprehensive community health projects have not been evaluated in terms of their effect at the individual level, because outcomes are usually not defined at this level. In a community health project in The Netherlands, evaluation outcome mapping, a technique derived from intervention mapping, was used to identify distal as well as proximal programme objectives from which outcome measures could be derived. The intervention took place in a deprived area, where community members themselves defined stress, lack of area safety and parenting problems as the health-related problems they wanted to see addressed in the project. Local organizations wrote and implemented an action plan. The effects among residents were studied in a quasi-experimental design. Although no significant effects on improved perceived health or health-related problems were found at the level of the residents, the problems identified and their assumed causes showed significant coherence. This study is believed to be of relevance to evidence-based health promotion theory and practice as it demonstrates that it is possible to conduct an individual effect evaluation in a comprehensive community approach without jeopardizing the process of the intervention.

Adult↗

PubMed2004

The content and comprehensiveness of hepatitis C education in methadone maintenance and drug-free treatment units.

Although drug users are at elevated risk for hepatitis C virus (HCV) infection, many are uniformed or misinformed about the virus. Drug treatment programs are uniquely situated to provide comprehensive risk-modifying educational programs for decreasing HCV transmission, a strategy advocated in the most recent National Institutes of Health Consensus Development Conference Statement on the Management of Hepatitis C. Given the large proportion of patients that inject drugs in methadone maintenance treatment programs and the high prevalence of HCV among drug injectors, we compared a nationwide sample (N = 246) of methadone maintenance treatment programs and drug-free programs regarding the content and comprehensiveness of HCV education. All of these programs provide HCV education to at least some of their patients. Results indicated that, compared to drug-free programs, methadone maintenance treatment programs cover a significantly greater number of HCV-related topics, and that a significantly greater proportion of the methadone programs cover specific topics (e.g., how to avoid transmitting HCV, the importance of testing for HCV, treatment options if HCV positive). Of special concern is that fewer than three quarters of the drug-free programs address what to do if co-infected with human immunodeficiency virus (HIV) and HCV and how to maintain health if HCV positive, and only about half of the drug-free and methadone maintenance treatment programs educate HCV-positive patients about the importance of obtaining vaccinations for hepatitis A and B. Drug treatment programs need to educate patients about the proactive steps these individuals can take to deal with HCV, provide critically needed HCV services, and encourage patients to make full use of these services.

Analgesics, Opioid↗

PubMed1986

Methylation blockage and other improvements to a comprehensive DNA analysis program.

A comprehensive DNA analysis computer program was described in the second special issue of Nucleic Acids Research on the applications of computers to research on nucleic acids by Stone and Potter (1). Criteria used in designing the program were user friendliness, ability to handle large DNA sequences, low storage requirement, migratability to other computers and comprehensive analysis capability. The program has been used extensively in an industrial-research environment. This paper talks about improvements to that program. These improvements include testing for methylation blockage of restriction enzyme recognition sites, homology analysis, RNA folding analysis, integration of a large DNA database (GenBank), a site specific mutagenesis analysis, a protein database and protein searching programs. The original design of the DNA analysis program using a command executive from which any analytical programs can be called, has proven to be extremely versatile in integrating both developed and outside programs to the file management system employed.

Base Sequence↗

PubMed2001

iProClass: an integrated, comprehensive and annotated protein classification database.

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200,000 non-redundant PIR and SWISS-PROT proteins organized with more than 28,000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetown.edu/iproclass/.

Databases, Factual↗

PubMed2001

Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe.

In order to isolate meiosis-specific genes in Schizosaccharomyces pombe, we have constructed a subtracted cDNA library enriched in clones whose expression is enhanced during meiosis induced by nitrogen starvation. Using northern blot analysis, we isolated 31 kinds of clones whose expression was induced in a meiosis/sporulation-specific manner. We comprehensively named them meu after meiotic expression upregulated. The transcription of 20 meu genes was found to be dependent on the mei4(+) gene, which encodes a transcription factor required for the progression of meiosis. DNA sequencing indicated that most of the meu genes encode novel proteins. Notably, five of the meu genes harbor no apparent protein coding sequences, and the transcripts form stable hairpin structures, suggesting that they may generate non-coding RNAs or antisense RNAS: The results presented here imply that RNAs are also important for the comprehensive characterization of genomic expression.

Base Sequence↗