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PubMed1993

A conceptual model for information retrieval with UMLS.

Information retrieval in large information databases is a non-deterministic process which needs a sequence of search steps generally. One of the main problems to which the end-users are faced is to parse efficiently their questions into the query language that the computer systems allow. Conceptual graphs were initially designed for natural language analysis and understanding. Due to their closeness to semantic networks, their expressiveness is powerful enough to be applied to knowledge representation and use by computer systems. This work demonstrates that conceptual graphs are a suitable means to model the end-users querieson the basis of the thesaurus and the semantic network of the UMLS project.

Information Storage and Retrieval↗
PubMed2025

Design of highly functional genome editors by modelling CRISPR-Cas sequences.

Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native environments, such as human cells1. Artificial-intelligence-enabled design provides a powerful alternative with the potential to bypass evolutionary constraints and generate editors with optimal properties. Here, using large language models2 trained on biological diversity at scale, we demonstrate successful precision editing of the human genome with a programmable gene editor designed with artificial intelligence. To achieve this goal, we curated a dataset of more than 1 million CRISPR operons through systematic mining of 26 terabases of assembled genomes and metagenomes. We demonstrate the capacity of our models by generating 4.8× the number of protein clusters across CRISPR-Cas families found in nature and tailoring single-guide RNA sequences for Cas9-like effector proteins. Several of the generated gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector, while being 400 mutations away in sequence. Finally, we demonstrate that an artificial-intelligence-generated gene editor, denoted as OpenCRISPR-1, exhibits compatibility with base editing. We release OpenCRISPR-1 to facilitate broad, ethical use across research and commercial applications.

CRISPR-Cas Systems↗
PubMed1989

Pleiotropy and preadaptation in the evolution of human language capacity.

The capacity for spoken language in the human is a genetic trait, but the information communicated by this means is to a large extent culturally determined. Using a gene-culture coevolutionary approach, we model the hypothesis that speech evolved as a channel for the communication of adaptive cultural traits from parent to offspring. The motivation for this paper is a condition obtained previously that initial increase of communication would require at least a two-fold advantage for the transmitted trait. Here, we show that under reasonable assumptions the invasion condition becomes less stringent. In Model 1, we assume that two adaptive cultural traits can be transmitted. A gene which permits communication of the second adaptive trait. In Model 2, we assume that a related function such as greater memory capacity is a prerequisite for speech, and that this function confers an advantage independent of its association with speech. In both models we assume haploid sexual genetics and a simple scheme of vertical transmission. The stability properties of all corner and edge equilibria of the models are analyzed. The two models taken together suggest a possible scenario for the initial stages of the evolution of speech.

Adaptation, Biological↗
PubMed1997

[Intercultural communication in general practice].

What is the reason for possible communication problems between physicians and immigrants from the third world? How is the interaction between the two groups regulated? To answer such questions, 15 doctors and 10 immigrants were interviewed about their experience of the doctor-patient interaction in unstructured open-ended interviews. Culturally based verbal and non-verbal expressions were particularly difficult to interpret, being based on different thought models and language. Owing to the world wide generalisation of the doctor-patient roles the gap between the two "partners" in the communication has been to some extent bridged. Largely independent of the doctors' will, the immigrants assigned considerable authority to the doctors. Thus the power of the doctor is based on the institutionalisation of the more universal doctor-patient role.

Communication↗
PubMed1992

GOFCOX: a computer program for the goodness-of-fit analysis of the Cox proportional hazards model.

GOFCOX is a user-friendly FORTRAN program for assessing the adequacy of the Cox proportional hazards model. The underlying methodology is based on the comparison of the maximum partial likelihood estimator and a weighted parameter estimator. The latter is the root to an estimation equation that assigns varying weights to the individual contributions to the partial likelihood score function. The weighted and unweighted parameter estimators have the same expectation under the Cox model, but tend to differ when the model is inappropriate. The GOFCOX program computes a rich class of weighted parameter estimators and corresponding goodness-of-fit test statistics. The program runs on both mainframe computers and microcomputers. The running time is minimal even for large data sets. A simple example is provided to illustrate the features of the program.

Computers, Mainframe↗
PubMed1984

Computer programs as theories in biology.

Complex theories in biology may be developed, refined, and tested by the use of computer programmed simulations. The computer is recognized as a powerful tool for theory development; it is, in fact, the only means of thoroughly testing and examining a large and intricate theory. A program as a text is a statement of a theory and when run on the computer it is model of that theory. As the program's behavior is then the major argument for the credibility of a large and complex theory, the program itself is the only irrefutable statement of the theory. Bur programs written in the currently available programming languages tend to be incomprehensible. We argue that the program should be the definitive statement of the theory. In addition, the program plus a series of abstractions is a vehicle for effective communication of complex theories in biology. Several techniques of computer science are borrowed, for the purpose of developing a methodology for abstraction and a language for representing abstractions. The arguments are fully illustrated with a recently published biological theory.

Communication↗
PubMed1991

Finite dose percutaneous drug absorption: a BASIC program for the solution of the diffusion equation.

A BASIC program to obtain the solution for the diffusion equation describing the finite dose percutaneous absorption pharmacokinetics is shown. Drug amount in the solution matrix, Av, that in the skin which is regarded as a simple diffusion membrane. As, and the drug flux from the skin which is provided by the local circulation per unit area, J, and the blood drug concentration. C, expressed as functions of time are obtained using Fourier series. Usually, a small number (less than 10) of series is enough to obtain the accurate values for Av, As, J, and C. It is also shown that the solution of the diffusion equation reported previously for the specific case where both the diffusion coefficient of a drug through the vehicle and skin-capillary clearance are very large is expressed as a limit.

Administration, Cutaneous↗
PubMed1978

Speech development in hearing-impaired children.

Many hearing-impaired children are unable to speak intelligibly. Research indicates, however, that patterns of errors typically found in the speech of such children could be largely avoided by systematic teaching. The purpose of this paper is to present and discuss a model for the progressive development of speech skills to the levels of automaticity required for fluent spoken language.

Child↗
PubMed1994

Emergence of visual-graphic symbol combinations by youth with moderate or severe mental retardation.

Research and practice on augmentative communication for persons with moderate or severe mental retardation have primarily targeted the acquisition and use of single symbols. Symbol combinations, however, provide insight into how augmented communicators use individual symbols to build more complex communications. In Study 1, untaught symbol combinations produced during natural communication interactions by 7 subjects with mental retardation were examined for their semantic, ordering, and generalization patterns. The symbol combinations largely resembled those produced by young speaking language learners, suggesting that the augmented communicators were following typical patterns of communication in generating their symbol combinations. In Study 2, we examined the symbol combinations modeled for subjects by their partners. The structure of the modeled combinations did not resemble the children's productions, indicating that the children could not have relied on simple rote imitation for their combination production. These results suggest that augmented communicators with mental retardation may use their symbols as speaking children use oral words in the development of complex communications.

Adolescent↗
PubMed1996

Variation in the application of natural processes: language-dependent constraints in the phonological acquisition of bilingual children.

This paper studies phonological processes and constraints on early phonological and lexical development, as well as the strategies employed by a young Spanish-, Portuguese-, and Hebrew-speaking child-Nurit (the author's niece)-in the construction of her early lexicon. Nurit's linguistic development is compared to that of another Spanish-, Portuguese-, and Hebrew-speaking child-Noam (the author's son). Noam and Nurit's linguistic development is contrasted to that of Berman's (1977) English- and Hebrew-speaking daughter (Shelli). The simultaneous acquisition of similar (closely related languages) such as Spanish and Portuguese versus that of nonrelated languages such as English and Hebrew yields different results: Children acquiring similar languages seem to prefer maintenance as a strategy for the construction of their early lexicon, while children exposed to nonrelated languages appear to prefer reduction to a large extent (Faingold, 1990). The Spanish- and Portuguese-speaking children's high accuracy stems from a wider choice of target words, where the diachronic development of two closely related languages provides a simplified model lexicon to the child.

Child Language↗
PubMed1997

Context-free evolutionary grammars and the structural language of nucleic acids.

This paper introduces and investigates a generative mechanism based on some operations inspired by the large-scale mutations in genomes (deletion, inversion, transposition, duplication). Basic questions regarding these devices and their generated languages are investigated: generative capacity, closure properties, decidability. We also briefly discuss a few problems concerning our model with respect to some structural features of the nucleic acids.

Evolution, Molecular↗
PubMed2026

Evidence supporting the role of GIGYF2 in synapse development and autism.

Autism spectrum disorder (ASD) is a heterogeneous condition in which genetically defined subtypes offered insights into underlying biological mechanisms and potential targeted treatments. Here, we investigate the clinical and pathogenic significance of GIGYF2 variants in ASD through an integrated approach combining clinical genetics, conditional knockout (cKO) mouse models, neurobiology, and molecular studies. Through targeted sequencing, large-scale genomic data analysis of neurodevelopmental disorder cohorts, and international collaborations, we identified ten affected individuals from eight families harboring de novo or dominantly inherited likely gene-disruptive (LGD) variants and 13 affected individuals from 13 families with de novo missense variants in GIGYF2. Clinical characterization of 16 probands with GIGYF2 variants revealed common features, including ASD, language problems, intellectual disability, and anxiety. In a Gigyf2 cKO mouse model, we observed pronounced autistic-like behaviors, cognitive deficits, and anxiety-like behaviors, mirroring phenotypes observed in affected individuals. Mechanistically, Gigyf2 deficiency disrupted synaptic homeostasis, as evidenced by altered spine density and miniature excitatory postsynaptic currents, and impaired IGF-1R/mTOR signaling, along with dysregulation of synapse-related genes such as Nrp2. Pharmacological inhibition of mTOR with rapamycin or Torin1, as well as Nrp2 knockdown rescued synaptic defects in Gigyf2 KO neurons. These findings define a novel ASD subtype associated with GIGYF2 variants and establish GIGYF2 as a key regulator of synaptic development and function, implicating GIGYF2 dysfunction in ASD pathogenesis and highlighting the IGF-1R/mTOR pathway as a potential therapeutic target for GIGYF2-related ASD subtype.

Journal Article↗
PubMed1996

Methodology for using the UMLS as a background knowledge for the description of surgical procedures.

The Unified Medical Language System (UMLS) contains and organizes a large number of terms from a variety of biomedical terminology systems. This study examines the relevance of the UMLS content and structures to the specific purpose of the conceptual representation of medical procedures. The MAOUSSC modelling is a compositional formalism with a description of elementary procedures in terms of elementary concept entities and combinations of such descriptions into more complex ones. The UMLS knowledge base is expected to provide semantically categorized medical concepts and interconcept relations. A method to reuse the UMLS has been developed. Quantitative and qualitative results are presented. Some difficulties in reusing the UMLS as a background knowledge are related to the preeminence of some terminology sources and to the instanciation of interconcept links. Other ones suggest that purpose-independence in categorization cannot be achieved.

Artificial Intelligence↗
PubMed2025

Novel approaches and applications in identifying DNA methylation markers of cardio-kidney-metabolic disease.

Cardio-kidney-metabolic (CKM) diseases represent a major public health challenge, accounting for a large proportion of global burden of morbidity and mortality. These conditions share risk factors, including genetic predisposition, environmental exposures, and lifestyle influences, which collectively drive disease development and progression. Epigenetic modifications, particularly DNA methylation (DNAm), serve as key mediators and biomarkers between these risk factors and disease phenotypes by regulating gene expression without altering the DNA sequence. Epigenome-wide association studies have identified DNAm markers associated with CKM diseases and related phenotypes, highlighting both shared pathways and disease-specific epigenetic signatures in inflammation, metabolic dysfunction, and aging-related processes. Longitudinal studies further demonstrate the dynamic nature of DNAm changes over time, offering insights into disease trajectories. Additionally, methylation risk scores integrating multiple epigenetic markers show promise in improving disease prediction and risk stratification beyond traditional clinical factors. To synthesize the current evidence, we conducted a targeted literature search in PubMed for English-language, peer-reviewed articles published between 2014 and the present. Future research leveraging large, well-phenotyped cohorts, advanced statistical methods, and innovative study designs will be critical for uncovering novel biomarkers, refining risk prediction models, and developing targeted epigenetic therapies to mitigate the global burden.

Humans↗
PubMed1977

The development of language-like communication without a language model.

Deaf children who are unable to acquire oral language naturally and who are not exposed to a standard manual language can spontaneously develop a structured sign system that has many of the properties of natural spoken language. This communication system appears to be largely the invention of the child himself rather than of the caretakers.

Child, Preschool↗
PubMedDate not supplied

A system that facilitates the orientation within procedure nomenclatures through a semantic approach.

The representation of medical concepts should provide the flexibility required to support several purposes. We have implemented a model in which medical terms are represented in a standard format based on a semantic description of the terms. We have focused on the description of procedures. Underlying this project is the assumption that information about medical procedures is crucial in the healthcare system. A prototype has been developed for urology. Because of the large number of terms in the Unified Medical Language System (UMLS) and the abundance of links between them, we have experimented in the use of the UMLS as the foundation for our concept base. We assess the usefulness of this approach and discuss its improvements.

Algorithms↗
PubMed1997

Simulators in clinical surgery.

Simulators are no replacement for patients in surgical learning. Live patients are required for teaching clinical signs and skills. Large numbers of students, a relative lack of motivation, a decreasing number of common cases, unwilling patients, differences in language, etc., make clinical teaching in India a bitter problem. Because patient-related problems are important, surgical training using models can help students to gain effective control over surgical signs and skills.

Education, Medical, Undergraduate↗