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Results for “Unique interface”

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At least 19 recordsLinked to original sources

PubMed2026

An atlas of non-redundant sequences and structures of transcription factor assemblies across domains of life.

Transcription factors (TFs) regulate gene expression by controlling the recruitment of transcriptional machinery to regulatory regions of the genome. Nearly 10% of the human genome encodes TFs, making them one of the largest protein families. Despite their central roles in gene regulation, TFs are historically considered challenging therapeutic targets due to their complex interactions with DNA, RNA and associated proteins. Although recent progress in studying TFs both at molecular and structural level excels our understanding on their function, yet a universal rule decoding their recognition process remains elusive. Here, we present a curated non-redundant dataset of TFs with 3570 sequences and 377 structures. We further characterize "unique interfaces" by quantifying interface identity across interacting chains in TF assemblies. Surprisingly, our data shows that the "unique interfaces" have optimal size ranging from 2000 Å2 to 4000 Å2 irrespective of their quaternary assembly. To understand the functional diversity, we integrate sequence motifs, structural domains, subcellular localization and functional enrichment of TFs. We have also catalogued association of TFs with various human diseases. Our dataset provides a comprehensive platform to perform large scale analysis of TF-assemblies and aid in computational methods for their prediction across domains of life.

Gene regulation↗

PubMed1977

[Comparative experimental investigations with bioglass (L. L. Hench), Al2O3-ceramic and Al2O3-ceramic coated with a mod. Bioglass. I. Results of experiments under non-loaded conditions (author's transl)].

This report deals with comparative results obtained with unloaded intra-osseous implants of bioglass (L. L. Hench), Al2O3-ceramic and Al2O3-ceramic coated with a mod. bioglass. Al2O3-ceramic and bone form a direct bony interface without fibrous tissue interposition, this resulting in a pure mechanic fixation of the implant through frictional forces of the surface roughed ceramic. Pure bioglass (45S5) and bone form a unique persisting direct interface by means of physico-chemical or biochemical phaenomena stabilizing the implant. Interface stability seams to be higher than the fatique strenth of the glass itself. This interface is developed as a consequence of solubility of some of the glass constituents within a surface layer of up to 200 microns, running parallel with a reduction of strength of this surface glass layer. The boronoxide containing bioglass, flame-sprayed onto Al2O3-ceramic samples seams to be less soluble and therefore seams to have lesser bonding capability to bone. The stability of the interface bioglass coating-Al2O3-ceramic was low.

Aluminum↗

PubMed1975

The utilization of dental skills in non-dental situations.

The development of electronic control systems has enabled severely physically handicapped people to revolutionize their lives by using any minimal residual movements they may have to operate micro-switches linking them with typewriters and other environmetal controls. Technical skills of a high order are required in making the unique splint or interface which links the switches with these residual movements whether of the tongue, lips, chin, eyebrow, finger or toe. Through the initiative of the Cordent Trust and generous financial support from the Leverhulme Trust a mobile laboratory was designed and built and a dental technician appointed for a three-year development project in the use of these switches as it was felt that his experience was particularly appropriate to the work and would also demonstrate how dental skills can be used to bring about a degree of rehabilitation far beyond the oral environment.

Electronics, Medical↗

PubMed1977

Protein thiol-disulfide interchange and interfacing with biological systems.

Disulfide-containing proteins offer unique advantages for mechanistic studies of the formation of native three-dimensional structure from unordered, reduced precursors. The main advantage is that covalent intermediates are formed; by characterizing these intermediates, one obtains substantial information about the reaction pathway. Thiol-disulfide interchange is a major component of most oxidative mechanisms carrying thiol to disulfide; thus, it required some attention in its own right. Afinsen's descriptions of a "shuffle-ase" enzyme led us to examine the rates of the uncatalyzed exchange under physiologically plausible conditions. Somewhat surprisingly, we found that the rates for formation of several native proteins in uncatalyzed systems containing GSSG and GSH are as great as with the "shuffle-ase" enzyme, suggesting that a substantial portion of biological thiol oxidations proceed by uncatalyzed exchange. While thiol-disulfide exchange of course results in no net change in the oxidation level of a system, catalytic linkage of thiol or disulfide to other redox systems provides a mechanism for achieving net changes.

Chemical Phenomena↗

PubMed2026

PubMind: literature-based genetic variant extraction and functional annotation using large language models.

Biomedical literature contains extensive functional knowledge on genetic variants, but much remains inaccessible in unstructured text. Existing resources such as ClinVar and HGMD remain limited by coverage, submission bias, update frequency, and sparse annotation. We develop PubMind, an artificial intelligence (AI) framework that uses large language models (LLMs) to triage and extract variant-function-disease associations and supporting evidence from biomedical text. PubMind captures single-nucleotide, copy-number, structural, and gene-fusion variants, and normalizes records to genomic and transcriptomic coordinates. Benchmarking shows >90% accuracy for variant recognition and 99% precision for disease extraction. Applied to >41 million PubMed abstracts and >5 million full-text articles, PubMind generates PubMind-DB, a database of ~1.3 million unique variants with contextual annotations, accessible via web interface and API. Only ~10% of PubMind variants overlap with ClinVar, and >80% of them show concordant pathogenicity labels. PubMind transforms unstructured biomedical text into structured genomic knowledge, advancing variant interpretation for precision medicine.

Large Language Models↗

PubMed1977

Ultrasonic diagnosis of renal and retroperitoneal lesions.

The unique ability of ultrasound to detect soft tissue interfaces makes it a prime tool for at least one major diagnostic approach to soft tissue lesions. Systematic ultrasonic examination of suspected masses in the abdomen should be performed early in the course of investigation. It will help direct additional studies and often result in cost savings by making the diagnostic process more efficient. The method is painless, to the best of our knowledge harmless and can be repeated at will for early study or late follow-up. The ultrasonic look into the body has provided us with a major tool for obtaining far more information on internal structures than was possible even a few years ago. Ultrasonic scans, radioisotope examinations and computerized x-ray tomography are leading us into an era of much increased anatomic knowledge about lesions which heretofore were obscure and difficult to evaluate.

Abdominal Neoplasms↗

PubMed1992

An extracellular matrix infrastructure provides support for murine secondary palatal shelf remodelling.

A crucial part of secondary palate morphogenesis is the movement of the palatal shelves from an initial vertical position on either side of the tongue to a final horizontal one above it to achieve palate closure. The immunocytochemical localization of extracellular matrix (ECM) molecules in the palatal shelf during this remodelling and reorientation revealed the existence of an ECM infrastructure within the mesenchyme. The major components of this infrastructure were collagen III, fibronectin, and hyaluronate (HA). With remodelling, HA's domain within the mesenchyme was expanded, whereas those of fibronectin and collagen III became more circumscribed. The expansion of an HA-rich matrix within the mesenchyme is thought to be crucial for palatal reorientation. The results of this study suggest that, as this expansion occurs, it is modulated by collagen and fibronectin components of the ECM infrastructure. Prior to shelf remodelling, this infrastructure may be anchored by a specialized region of the midoral epithelial-mesenchymal interface and the subjacent mesenchyme which is characterized by the unique distribution of collagen III, fibronectin, and tenascin. The midoral palatal epithelium also may play a role in directing shelf expansion. This epithelial region undergoes changes in cell packing and epithelial cell layering that correlate with shelf remodelling. These changes occur concomitantly with changes in the expression of collagen III, collagen IV, and laminin within the underlying basement membrane. The localization and patterning of tenascin within the developing palate suggests that it not only contributes to the postulated anchoring structure of the midoral epithelial-mesenchymal region, but also plays a role in the determining the fate of the medial edge epithelial cells during the final stage of palate closure.

Animals↗

PubMed1979

Child psychiatry education for general residents.

There is continuing debate about what child psychiatry experiences should be included in a general residency. The author describes the program at the University of Michigan in an effort to provide some insights into the interface between child psychiatry and general residency training. This program is unique in several respects: a 12-month rotation in child psychiatry is offered, and the faculty size and budget of the youth services are comparable to those of the adult services. A survey of all residents and faculty pointed up numerous disagreements as to the length of the rotation and priorities in curriculum. The author discusses the influence of the various competitive processes on the educational program.

Adolescent↗

PubMed1976

Resonance ultrasonic measurements of microscopic gas bubbles.

The positive identification and location of stationary or moving bubbles in human tissue is a persisting problem in the study and management of dysbarism. Since bubbles are resonant scatterers of ultrasound, while structures such as red-cell clumps and tissue interfaces are not, it is possible in principle to identify bubbles uniquely and to determine their position and size. A pulsed, ultrasonic echo-ranging system was expressly designed to exploit the principle of bubble resonance, and was evaluated for bubble identification and location in two experiments. Echos from bubbles in a water bath were computer-processed to reveal a distinct "line-narrowing" in the Fourier domain, which is diagnostic of gas bubbles. An increase in echo signal from a dog's jugular vein upon distal bubble injecton was obtained as evidence for in vivo bubble detection. We conclude that the exploitation of the bubble resonance principle can offer a safe, noninvasive technology for micro-bubble identification, location, and size determination in many tissues. This technology appears capable of measuring stationary bubbles in tissue spaces or impacted in blood vessels as well as those moving in the vascular system.

Air↗

PubMed1975

The interaction of phospholipase A2 with micellar interfaces. The role of the N-terminal region.

The localization of the previously postulated interface recognition site (IRS) in porcine pancreatic phospholipase A2, required for a specific interaction between the enzyme and organized lipid-water interfaces, was investigated by ultraviolet difference spectroscopy, by measurements of the intrinsic fluorescence of the unique Trp residue, and by protection experiments against specific tryptic hydrolysis. Using the enzymically nondegradable substrate analogues: CnH(2n+1)(0-)OOCH2CH2N+(CH3)3-(H,OH), it is shown that the rather hydrophobic N-terminal sequence of the enzyme, viz., Ala-Leu-Trp-Gln-Phe-Arg, is directly involved in the interaction with the lipid-water interface. Besides hydrophobic probably also polar interactions contribute to the binding process. At neutral or acidic pH the presence of a salt bridge between the N-terminal alpha-NH3+ group and a negatively charged side chain stablizes the interface recognition site and allows the enzyme to penetrate micellar surfaces, even in the absence of metal ion. At alkaline pH, interaction of the enzyme with micellar interfaces requires the presence of Ca2+ (Ba2+) ions.

Amines↗

PubMed1978

Interactive computer surface graphics approach to study of the active site of bovine trypsin.

A descriptive medium for the presentation of protein structure has been developed and used to evaluate the structure of the active site of bovine trypsin (EC 3.4.21.4). This technique, involving advanced computer graphics technology, permits the facile display of a representation of the molecular surface of proteins of known structure and employs color to code the structural or chemical features of this surface. Benzamidine derivatives were inserted into the benzamidine-binding site of trypsin and the binary inhibitor-trypsin complex was evaluated by using the computer-generated structure. On the basis of qualitative assessments of the contribution of electrostatic and hydrophobic forces to the binding energy associated with complex formation, we made predictions concerning the effects of interaction of benzamidine substituents and amino acid side chains upon the binding energy associated with inhibitor-protein binding. The computer display of the molecular surfaces of the binary complex of substituted benzamidines and trypsin permitted unique insight into the identity and chemical properties of the atoms that participate at the interface of the molecular surfaces of the inhibitor and the protein. The computer-generated molecular surface display can potentially be combined with quantitative definition of the physical forces involved in the interaction of molecular surfaces. This technology should facilitate the study of the structure-activity relationship of substrates, inhibitors, and drugs that bind to proteins of known three-dimensional structure.

Animals↗

PubMed1976

Issues at the clinical-research interface: placebo effect control groups.

At the clinical-research interface, controls are a significant issue in group therapy evaluation. The authors describe and analyze their unique experience with placebo effect control groups conducted prior to brief, group psychotherapy for married couples. Procedures are outlined and participant reactions noted. Solicited ratings and spontaneous comments provide assessment data. The evidence suggests the feasibility of placebo effect control groups in the context studied. Proposed methodological refinements and clinical implications may be useful for future research efforts.

Adult↗

PubMed1977

Environment and the skin.

The skin is an important interface between man and his environment; it is an important portal of entry for hazardous agents and a vulnerable target tissue as well. It is a uniquely accessible model system for detecting hazards and for studying mechanisms of a wide variety of biologic funcitons. Environmental causes of skin reactions comprise a vast array of physical, chemical and biological agents. To appreciate the role of the skin as an interface with man's environment, it is necessary to understand the multiple adaptive mechanisms, and the defenses of the skin against the environmental stresses. The skin is endowed with a versatile group of defenses against penetration, fluid loss from the body, thermal stress, solar radiation, physical trauma and microbial agents. Patterns of adverse response range in quality and intensity from uncomplicated itching to metastatic neoplasia. Environmental problems comprise a large segment of disabling skin disease. Although critical epidemiologic data is limited, cutaneous illnesses comprise a significant segment of occupational disease. This represents a significant loss in productivity and a major cause of disability. The most serious research needs include the development of surveillance systems for identifying skin hazards and determining frequency of environmental skin disease; the development of new models for studying cutaneous penetration; the elucidation of the mechanisms of nonallergic inflammatory reactions (primary irritation) and of the accommodation phenomenon; the development of more sensitive models for predicting adverse responses to marginal irritants; the utilization of modern skills of immunobiology and immunochemistry to elucidate mechanisms of allergic responses; the launching of epidemiologic studies to determine the long term effects of PCBs and associated compounds such as dioxins; and the expansion of research in the mechanisms of skin cancer in relation to susceptibility, genetic and metabolic considerations, ultraviolet light, and phototoxic agents.

Dermatitis, Contact↗

PubMed2026

Structural insights into histone mimicry by the small hepatitis delta antigen.

Hepatitis delta virus (HDV) is a satellite RNA virus that requires hepatitis B virus (HBV) for propagation but replicates its genome independently in the nucleus. The small form of the hepatitis delta antigen (S-HDAg) is essential for replication and is regulated by post-translational modifications. Acetylation at lysine 72 (K72ac) enables S-HDAg to interact with the bromodomain (BRD) of the host chromatin remodeler bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) to promote viral replication. However, the structural basis for this interaction has remained elusive. Here, we provide structural and biophysical insights into this interaction through quantitative binding assays and X-ray crystallography. Isothermal titration calorimetry revealed that BRDs of BAZ2B and its close homolog BAZ2A bind to the viral peptide weakly, with BAZ2A-BRD exhibiting a modestly higher affinity. The crystal structure of BAZ2A-BRD in complex with the S-HDAg-K72ac peptide demonstrates an inverted binding orientation relative to canonical histone ligands, rationalizing the weak interaction. Mutagenesis studies confirmed the critical binding interface both in vitro and in cells. These findings elucidate the molecular mechanism by which HDV co-opts host BAZ2 bromodomains via a unique, weak-affinity interaction, providing a structural framework for understanding viral replication.

Hepatitis delta Antigens↗

PubMed2026

EPIC: multi-objective guided diffusion for epitope design in TCR-pMHC complexes.

MOTIVATION: T cell receptor (TCR) recognition of peptide-major histocompatibility complex (pMHC) complexes is central to adaptive immunity, yet rational design of immunogenic epitopes remains elusive due to complex triplet binding constraints and data scarcity. No existing method can generate epitopes satisfying simultaneous requirements for antigenicity, MHC presentation, and TCR specificity. RESULTS: We present EPIC, a multi-objective diffusion framework that decomposes TCR-pMHC binding into three biologically grounded sub-tasks, enabling training-free gradient guidance without end-to-end retraining. By integrating ESM-based classifiers with a peptide diffusion generator, EPIC leverages heterogeneous immunological interaction datasets to generate diverse, context-aware epitopes. EPIC-designed top-three epitopes achieve lower predicted interface energies compared to ground-truth epitopes in 78.31% of test cases, while maintaining 80.1% sequence novelty and comparable structural confidence. Generated epitopes exhibit 100% uniqueness, high diversity (64.05%), and high antigenicity scores (0.4723). To our knowledge, EPIC is the first computational framework capable of de novo epitope design while explicitly integrating the triplet constraints of TCR-pMHC binding. This paradigm shift from discovery to design unlocks new potential for personalized cancer vaccines, precision adoptive T cell therapy, and rapid response to emerging infectious diseases. AVAILABILITY AND IMPLEMENTATION: The source code of EPIC is available at https://github.com/Octopus125/EPIC and archived on Zenodo (DOI: 10.5281/zenodo.18537646).

Receptors, Antigen, T-Cell↗

PubMed2026

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.

MOTIVATION: Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. RESULTS: We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. AVAILABILITY AND IMPLEMENTATION: The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

DNA methylation↗

PubMed1975

Community mental health and the community college.

This paper represents one solution to the present mental health dilemma facing today's colleges and universities--static or declining services in the face of increased student needs. What is unique to this solution is that it developed out of a collaborative interaction between a community college and a prototype of a community mental health center in the same geographical area. Multiple interfaces between systems and various members within these systems were established in an effort to provide improved mental health services and the training of all personnel so involved to a higher level of professional functioning.

Community Mental Health Services↗

PubMed2026

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

MOTIVATION: The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. RESULTS: We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. AVAILABILITY AND IMPLEMENTATION: The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). SUPPLEMENTARY INFORMATION: A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Phenotype↗