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At least 343 records · Page 19Linked to original sources
PubMed2026

Fine-grained structural classification of biosynthetic gene cluster-encoded products.

MOTIVATION: Biosynthetic gene clusters (BGCs) are responsible the biosynthesis of many natural products, including a multitude of effective therapeutics and their precursors. Advances in genomic data collection as well as computational techniques have made it possible to identify BGCs at scale. However, accurately determining the types of BGC-encoded products from genomic content remains elusive. RESULTS: Here, we introduce BGC annotation tool (BGCat), a machine learning method for fine-grained structural classification of BGC-encoded products, leveraging the NPClassifier natural product nomenclature. Our method leverages a pre-trained protein language model for creating meaningful gene representations and a deep neural network for class label prediction. We show the method outperforms state-of-the-art approaches in coarse-grained product classification and is effective for detailed classification. We implement a clustering-based augmentation strategy for BGC-product relationships, addressing a crucial gap in the available datasets. We then introduce the concept of product class profiles of gene cluster families (GCFs), associating each GCF with a probabilistic distribution of product types and offering a new perspective on GCF functions. Lastly, we use BGCat to provide new product class labels for over 100k BGCs in antiSMASH DB that presently have minimal information about their products. AVAILABILITY AND IMPLEMENTATION: The source code and trained model weights are freely available at https://github.com/HassounLab/BGCat.

Multigene Family↗
PubMed2002

Missing data: our view of the state of the art.

Statistical procedures for missing data have vastly improved, yet misconception and unsound practice still abound. The authors frame the missing-data problem, review methods, offer advice, and raise issues that remain unresolved. They clear up common misunderstandings regarding the missing at random (MAR) concept. They summarize the evidence against older procedures and, with few exceptions, discourage their use. They present, in both technical and practical language, 2 general approaches that come highly recommended: maximum likelihood (ML) and Bayesian multiple imputation (MI). Newer developments are discussed, including some for dealing with missing data that are not MAR. Although not yet in the mainstream, these procedures may eventually extend the ML and MI methods that currently represent the state of the art.

Databases as Topic↗
PubMed2006

Agents in bioinformatics, computational and systems biology.

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.

Artificial Intelligence↗
PubMed2004

Preparing the singing voice specialist revisited.

In review of singing voice specialist preparation, discussion can be chronicled prior to the establishment of Arts Medicine in 1987. Although discussion began in 1984 (and earlier), no formal academic program currently exists to train the singing voice specialist. The need now is greater than ever for a formal program of study to prepare a person who seeks to be a singing voice specialist. The question of adequate preparation continues to be in need of an appropriate answer because no formal training programs or fellowships are available. It is essential to first define the role of singing voice specialists and the populations that they will encounter. To meet the needs of a diverse population, care of the professional voice demands cross-disciplinary training. Knowledge from the fields of music, science, medicine and communication disorders and experience/observation, clinical preparation, and research would provide for optimal preparation. To meet this need, development of a Masters degree program seems highly desirable. The structure of such a program is proposed, along with specific requirements outlined from the music and singing voice pathology components for a Masters Degree in Arts Medicine with a concentration in voice.

Curriculum↗
PubMed1996

Treatment efficacy: stuttering.

The purpose of this article is to review the state of the art regarding treatment efficacy for stuttering in children, teenagers, and adults. Available evidence makes it apparent that individuals who stutter benefit from the services of speech-language pathologists, but it is also apparent that determining the outcome of stuttering treatment is neither easy nor simple. Whereas considerable research has documented the positive influence of treatment on stuttering frequency and behavior, far less attention has been paid to the effects of treatment on the daily life activities of people who stutter and their families. Although it seems reasonable to assume that ameliorating the disability of stuttering lessens the handicap of stuttering, considerably more evidence is needed to confirm this assumption. Despite such concerns, it also seems reasonable to suggest that the outcomes of treatment for many people who stutter are positive and should become increasingly so with advances in applied as well as basic research.

Activities of Daily Living↗
PubMedDate not supplied

The use of gaming strategies in a transcultural setting.

Saudi Arabia's vast economic resources have enabled the development of state-of-the-art hospitals. Nurses recruited from around the world staff these hospitals creating one of the most multicultural practice settings in the world. Ethnic, educational, and experiential diversity; language and communication barriers; and alternative ways of knowing and learning challenge nurse educators to be more creative and explore opportunities for greater participation and learning among various cultural groups. Gaming, as a teaching-learning strategy for multicultural participants, affords the necessary flexibility and nonthreatening atmosphere which facilitates positive interactions among different, and often competing, communication patterns and learning styles. This article explores how and why gaming is as an effective educational strategy in a transcultural setting.

Communication Barriers↗
PubMed1980

Culture and deafness in a Maya Indian village.

Over the years, the question of psychosocial adjustment among the deaf has attracted a great deal of attention. Pioneer work by Levine (1960, 1963); Rainer, Altshuler, and Kallmann (1963); Myklebust (1964); Rainer and Altshuler (1968); Grinker (1969); Mindel and Vernon (1971); and Schlesinger and Meadow (1972), to mention but a few, has aided our understanding of how the deaf adjust to the stress which their handicap imposes upon them. We know a great deal less, however, about the deaf in other societies. Altable (1947); Altshuler, Vollenweider, and Rainer (1971); Youniss (1974); and Sarfaty and Katz (1978) are among the handful of references which appear, and they all deal with urban populations. Kuschel (1973) considers a single deaf man on Rennell Island, in Polynesia, but his concern is primarily the sign language devised by this ingenious man. As far as I am aware, only Woodward (1978) and his associates have an ongoing program for the investigation of deafness in a nonurban society (Washabaugh, Woodward, and DeSantis, 1978). To neglect the way in which other societies handle these problems is to deprive ourselves of a rich source of comparative data. It is also to avoid a strenuous challenge, for the methodology that is appropriate for use in literate, urban societies may have little applicability in a tribal or peasant group. The purpose of this paper, therefore, is to present preliminary data on a group of profoundly, congenitally deaf Maya Indians of southeastern Mexico, with the aim of suggesting hypotheses which may be investigated by future research. The fieldwork upon which the report is based, however, was not part of a purposeful attempt to study the deaf of the village in question; rather, the village was selected as part of the Maya Film Project, directed by Hubert Smith, and at the time the project took to the field the fieldworkers had no idea that the village eventually chosen would contain a high number of deaf inhabitants.

Adolescent↗
PubMed2026

Agentomics: an agentic system that autonomously develops novel state-of-the-art solutions for biomedical machine learning tasks.

MOTIVATION: Extracting knowledge from biomedical data is crucial for advancing our understanding of biological systems and developing novel therapeutics. The quantity, quality, and resolution of biomedical data constantly evolves, requiring the automation of biomedical machine learning (ML). Existing Automated ML tools lack flexibility, while large language models (LLMs) struggle to consistently deliver reproducible machine learning codebases, and existing LLM Agent-powered solutions lag behind human-engineered ML models. RESULTS: Here, we introduce Agentomics, an autonomous LLM-powered agentic system for end-to-end ML experimentation. Given a biomedical dataset, Agentomics implements various ML modeling strategies, and produces a ready-to-use ML model. Agentomics introduces strict validation checkpoints for standard ML development steps, allowing gradual development on top of working code with defined interfaces and validated artifacts. Further, it offers native support for biomedical foundation models that can be leveraged during experimentation. The generic nature of Agentomics allows the user to create ML solutions for a large variety of datasets and use various LLMs. We evaluate Agentomics across 20 datasets from the domains of Protein Engineering, Drug Discovery, and Regulatory Genomics. When benchmarked against other agentic systems, Agentomics outperformed them in all tested domains. When benchmarked against human expert solutions, Agentomics generated novel state-of-the-art models for 11/20 established benchmark datasets. AVAILABILITY AND IMPLEMENTATION: Agentomics is implemented in Python. Source code and documentation are freely available at: https://github.com/BioGeMT/Agentomics-ML.

Machine Learning↗
PubMed2005

The language of loss when a baby dies prior to birth: cocreating human experience.

When a baby dies prior to birth, a woman and her family begin a life long journey of living and transforming with loss. The language used with families during times of devastating loss is important to reflect upon since, language has the potential to either intensify suffering or enhance the family's experience of grieving. Words that affirm the meaning the baby holds for the family can provide comfort as families engage with the reality of lost hopes and dreams. Recognizing that healthcare professionals do not intend to harm families whose babies die prior to birth, the current authors offer this column as a vehicle for reflecting on the meanings of words used during this particular time of loss and grief. The authors further explore the role that the arts have to play in expressing loss and in helping others to understand.

Attitude to Death↗
PubMed2002

Representation of practice guidelines with XML--modeling with XML schema.

OBJECTIVES: Data and information in medicine are mainly represented in slightly structured or even unstructured, narrative text documents. It is nearly impossible to detect and handle relationships between data elements within narrative documents or to retrieve parts of documents that contain specific information. But information access and retrieval are essential to serve the delivery and application of evidence-based medicine. METHODS: The eXtensible Markup Language (XML) provides a standard means to explicitly describe a document's structure and to identify meaningful elements inside textual narrations. Information about the state-of-the-art medical care can be delivered to the physician by different means and media. Clinical practice guidelines are thought to be one possible solution to summarize and present current medical evidence. RESULTS: The structuring of resources containing medical information with XML can facilitate the provision of problem-specific medical information at the point of care by improving content retrieval and presentation. In our project, the XML Schema is used for the electronic representation in order to structure guidelines (and other text-based resources) in a standardized way. CONCLUSION: The transition from unstructured textual data towards structured and coded data will be a migration process. One of the premises of our approach is that the structure that is defined by the information model doesn't restrict the content of the documents. This approach may fill the gap between computerized, algorithmic guideline recommendations and text-based guideline distributions.

Computer Systems↗
PubMed2002

Using a multi-user desktop-based virtual reality system to recreate the São Miguel das Missões ruins.

This paper presents a project initiated back in 1999, in which Virtual Reality is applied in order to create a virtual community over the Internet. The desktop-based multi-user virtual reality system recreates a three-dimensional environment based on photogrammetric maps from the São Miguel das Missões church ruins. The ruins correspond to one of the Jesuit Mission (settlement) which was active in the south of Brazil in the 17th and 18th centuries. It has a great importance to the local region in terms of cultural, historic, and tourist aspects. It has also been inscribed in the UNESCO's world heritage list since 1983. This electronic mock-up allows several interactive operations such as community chats, electronic message exchanging, message boards, walking-through, discussion groups, and embedding of other media such as movies, sound, and html pages. The only requirement necessary to access the community is a web browser powered with any Virtual Reality Modeling Language (VRML) plug-in freely available over the Internet. It is expected that such a solution improves the conservation and dissemination of the Brazilian historic patrimony, congregating history, art, and tourist information in one place on the Internet.

Humans↗
PubMed1985

[Orientation of art, orientation of writing and visual field dominance. An experimental and cultural historical study].

Investigations have shown that 75% of children aged 3-6 years, who have not as yet acquired the ability to write, tend to draw and sketch from the left to the right side. The same tendency has also been found in adults with regard to drawing, which indicates a dominance of the left field of vision when the cerebral optical analysis is used, as it invariably is for the appreciation of three-dimensional figures. The tendency to draw from the left to the right side can be traced back to works of art that date from as far back as the 6th century B.C. Before the 6th century B.C. and way back into the prehistoric period, the direction seems to have been the reverse, i.e. there was a tendency to draw from the right to the left side. Evidence showing that this was true in up to 80% of cases can be found on vase paintings with either geometric shapes or animals. These findings, together with those of earlier publications, are interpreted as evidence that a shift of dominance has taken place during the history of mankind. It is assumed that together with the increasing significance of language and writing, associated with the left cerebral hemisphere, there was also a development toward a right-sided dominance as regards optical analysis.

Art↗
PubMed1996

[The prospects for the use of computers in dentistry].

A universal soft-art complex tentatively named Arm-Stomatolog, covering all sections of dentistry, has been developed. It is based on individual programs in dentistry, making use of high-level algorithmic languages fitted to modern operation systems and permitting block-to-block fitting of individual programs to unite them in a complex.

Algorithms↗