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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↗

PubMed1990

2.2 A resolution structure analysis of two refined N-acetylneuraminyl-lactose--wheat germ agglutinin isolectin complexes.

The crystal structures of complexes of isolectins 1 and 2 of wheat germ agglutinin (WGA1 and WGA2) with N-acetylneuraminyl-lactose (NeuNAc-alpha(2-3)-Gal-beta(1-4)-Glc) have been refined on the basis of data in the 8 to 2.2 A resolution range to final crystallographic R-factors of 17.2% and 15.3% (Fo greater than 1 sigma), respectively. Specific binding interactions and water association, as well as changes in conformation and mobility of the structure upon ligand binding, were compared in the two complexes. The temperature factors (B = 16.3 A2 and 18.4 A2) were found to be much lower compared with those of their respective native structures (19 to 22 A2). Residues involved in sugar binding, dimerization and in lattice contacts exhibit the largest decreases in B-value, suggesting that sugar binding reduces the overall mobility of the protein molecules in the crystal lattice. The binding mode of this sialyl-trisaccharide, an important cell receptor analogue, has been compared in the two isolectins. Only one of the two unique binding sites (4 per dimer), located in the subunit/subunit interface, is occupied in the crystals. This site, termed the "primary" binding site, contains one of the five amino acid substitutions that differentiate WGA1 and WGA2. Superposition of the refined models in each of the independent crystallographic environments indicates a close match only of the terminal non-reducing NeuNAc residue (root-mean-square delta r of 0.5 to 0.6 A). The Gal-Glc portion was found to superimpose poorly, lack electron density, and possess high atomic thermal factors. In both complexes NeuNAc is stabilized through contact with six amino acid side-chains (Ser114 and Glu115 of subunit 1 and Ser62, Tyr64, Tyr(His)66 and Tyr73 of subunit 2), involving all NeuNAc ring substituents. Refinement has allowed accurate assessment of the contact distances for four hydrogen bonds, a strong buried non-polar contact with the acetamido CH3 group and a large number of van der Waals' interactions with the three aromatic side-chains. The higher affinity of N-acetylneuraminyl-lactose observed by nuclear magnetic resonance studies for WGA1 can be explained by the more favorable binding interactions that occur when residue 66 is a Tyr. The tyrosyl side-chain provides a larger surface for van der Waals' stacking against the NeuNAc pyranose ring than His66 and a hydrogen bond contact with Gal (C2-OH), not possible in WGA2.(ABSTRACT TRUNCATED AT 400 WORDS)

Binding Sites↗

PubMed1991

Tubal pregnancy. Associated histopathology.

Endometrial histologic characteristics are of little value in predicting ectopic pregnancy. The growing tubal gestation does not have any unique characteristics as far as the maternal-fetal tissue interface is concerned. The placentation is relatively superficial, and the growth is intraluminal. Tubal rupture occurs as a result of progressive tubal distention with focal hemorrhagic necrosis. Persistence is a reflection of incomplete evacuation combined with the noncyclic shedding of the tubal epithelium. The evacuated implantation site and conservative surgical incisions are not directly related to the recurrence of ipsilateral tubal pregnancies. The most common histologic finding related to tubal pregnancy is that of prior tubal disease.

Embryo Implantation↗

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↗

PubMed1991

Coordinate developmental regulation of purine catabolic enzyme expression in gastrointestinal and postimplantation reproductive tracts.

Using histochemical detection, we have visualized in situ the complete metabolic pathway for the degradation of purine nucleotides. From the tongue to the ileum, diverse epithelial cell types lining the lumen of the mouse gastrointestinal (GI) tract strongly coexpress each of the five key purine catabolic enzymes. Dramatic increases in the expression of each enzyme occurred during postnatal maturation of the GI tract. Using in situ hybridization, an intense accumulation of adenosine deaminase (ADA) mRNA was detected only within GI epithelial cells undergoing postmitotic differentiation. In a similar manner, at the developing maternal-fetal interface, high level expression of the purine catabolic pathway also occurred in a unique subset of maternal decidual cells previously known to express high levels of alkaline phosphatase and ADA. This induction occurred almost immediately after implantation in the periembryonic maternal decidual cells, shortly thereafter in antimesometrial decidual cells, and later in cells of the placental decidua basalis: all of which contain cell types thought to be undergoing programmed cell death. The expression of the pathway at the site of embryo implantation appears to be critical because its pharmacologic inhibition during pregnancy has been found to be embryolethal or teratogenic. Purine destruction at these nutritional interfaces (placenta and gastrointestinal tract) seem to override any potential economy of purine salvage, and may represent biochemical adaptation to nucleic acid breakdown occurring in the context of dietary digestion or extensive programmed cell death.

5'-Nucleotidase↗

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↗

PubMed1992

Shape distributions of protein topography.

A method is presented for measuring protein surface shape. It is an improvement of an earlier method that intersects a sphere with the solvent-excluded volume of a protein molecule. The new method, called a shape distribution, produces a more sophisticated description of the region of the sphere inside the protein than is provided by simply measuring the region's area or solid angle. This method is applied to the prediction of molecular complexes in three systems: the hemoglobin nonallosteric interface, trypsin and trypsin inhibitor, and heme and apomyoglobin. It does not uniquely predict the correct structure, even though the individual structures are taken from the experimentally determined complex structure. However, it does provide a list of several hundred predicted complexes, one of which is correct, and from which the correct complex might be extracted by a subsequent chemical filter.

Algorithms↗

PubMed1990

[Dental sac and its role in periodontal development].

The present study examined the role of the innermost layer of dental sac tissue in periodontal development. Empty bony crypts were filled with Hydroxylapatite ceramic granules of porous consistency in 5-day-old rats. After 4.5 and 24 weeks the specimens were processed for light and transmission electron microscopy. Only 4 weeks later cement regeneration was seen on ceramic surfaces with bundles of oriented collagen fibers inserting in the cementoid matrix. Ultrastructurally the newly formed cementum-like tissue was in intimate contact to the synthetic hydroxylapatite crystals. A consistent finding was the presence of an interface between cementum and the ceramic surface. The present findings question the unique role of the "investing layer" in periodontal development and the existence of cement-inducting properties of dentin.

Animals↗

PubMedDate not supplied

Liquid chromatographic-atomic absorption spectrophotometric method for determination of methyl mercury in seafood: collaborative study.

A previously developed method that uses a simplified sample preparation procedure and atomic absorption detection of liquid chromatographic eluates for the determination of methyl mercury in seafood has been collaboratively studied. The unique feature of the method involves the use of a specially designed interface for the generation of mercury vapor. Methyl mercury is isolated from the blended sample by chloroform elution from a diatomaceous earth-hydrochloric acid column. The organomercury compound is then extracted into a small volume of 0.01M sodium thiosulfate solution. An aliquot of this solution is injected onto a Zorbax ODS column and eluted with methanol-ammonium acetate solution (3 + 2), pH 5.7, containing 0.01% mercaptoethanol. Mercury is detected by flameless atomic absorption spectrophotometry using the interface. The samples analyzed in the study were unspiked swordfish, unspiked and spiked lobster, and unspiked and spiked tuna. The spiked samples contained methyl mercury both above and below the U.S. Food and Drug Administration guideline level of 1 microgram Hg/g. Reproducibility relative standard deviations ranged from 10.5% at 1 microgram Hg/g to 18.2% at about 0.1 microgram Hg/g. Accuracy, measured by comparison to reference values obtained by the Associate Referee, ranged from 94.4 to 99.6%. The method has been adopted official first action.

Animals↗

PubMed1990

Magnetic resonance imaging simulator: a teaching tool for radiology.

The increasing use of magnetic resonance imaging (MRI) as a clinical modality has put an enormous burden on medical institutions to cost effectively teach MRI scanning techniques to technologists and physicians. Since MRI scanner time is a scarce resource, it would be ideal if the teaching could be effectively performed off-line. In order to meet this goal, the radiology Department at the University of Pennsylvania has designed and developed a Magnetic Resonance Imaging Simulator. The simulator in its current implementation mimics the General Electric Signa (General Electric Magnetic Resonance Imaging System, Milwaukee, WI) scanner's user interface for image acquisition. The design is general enough to be applied to other MRI scanners. One unique feature of the simulator is its incorporation of an image-synthesis module that permits the user to derive images for any arbitrary combination of pulsing parameters for spin-echo, gradient-echo, and inversion recovery pulse sequences. These images are computed in 5 seconds. The development platform chosen is a standard Apple Macintosh II (Apple Computer, Inc, Cupertino, CA) computer with no specialized hardware peripherals. The user interface is implemented in HyperCard (Apple Computer Inc, Cupertino, CA). All other software development including synthesis and display functions are implemented under the Macintosh Programmer's Workshop 'C' environment. The scan parameters, demographics, and images are tracked using an Oracle (Oracle Corp, Redwood Shores, CA) data base. Images are currently stored on magnetic disk but could be stored on optical media with minimal effort.

Computer Simulation↗

PubMed1989

Ordered disruption of subunit interfaces during the stepwise reversible dissociation of Escherichia coli phosphofructokinase with KSCN.

The reversible inactivation and dissociation of the allosteric phosphofructokinase from Escherichia coli has been studied in relatively mild conditions, i.e., in the presence of the chaotropic agent KSCN. At moderate KSCN concentration, the loss of enzymatic activity involves two separated phases: first, a rapid dissociation of part of the tetramer into dimers, second, a slower displacement of the dimer-tetramer equilibrium upon further dissociation of the dimer into monomers. These two reactions can no longer be distinguished above 0.3 M KSCN since complete inactivation occurs in a single reaction. Different changes are observed for the fluorescence and the activity of the enzyme in KSCN: the fluorescence is not affected by the dissociation into dimers which is responsible for inactivation. The decrease in fluorescence reflects the change in environment of the unique tryptophan residue, Trp 311, during the dimer to monomer dissociation. This residue belongs to the interface containing the regulatory site, and its native fluorescence indicates that this interface is still present in the dimer. The substrate fructose 6-phosphate protects phosphofructokinase from inactivation by binding to the tetramer and prevents its dissociation into dimers. The presence of phosphoenolpyruvate prevents the slow dissociation of the dimer into monomers, which shows the ability of the dimer to bind the inhibitor. Two successive processes can be observed during reassociation of the protein upon KSCN dilution. First, a fast reaction (k1 = 2 x 10(5) M-1.s-1) is accompanied by a fluorescence increase and results in the formation of the dimeric species.(ABSTRACT TRUNCATED AT 250 WORDS)

Allosteric Regulation↗

PubMed1988

Endothelial communication. State of the art lecture.

By virtue of its location at the interface of flowing blood and vascular tissue, the endothelial cell monolayer is in a unique position for interactions with soluble and cellular elements of the blood on one side and with component cells of the vascular tissue on the other. This brief review outlines humoral and contact-mediated endothelial communication with other cells, particularly the resident cells of the vessel wall. Evidence for gap junctional communication channels between endothelium and vascular cells is summarized and discussed in relation to endothelial ion channel activity. Myoendothelial gap junctional communication is proposed as a mechanism involved in vasorelaxation, either independent of or in concert with secreted endothelium-derived relaxing factor(s).

Acetylcholine↗

PubMed1992

The major piscine liver alcohol dehydrogenase has class-mixed properties in relation to mammalian alcohol dehydrogenases of classes I and III.

The major alcohol dehydrogenase of cod liver has been purified, enzymatically characterized, and structurally analyzed in order to establish original functions and relationships among the deviating classes of the enzyme in mammalian tissues. Interestingly, the cod enzyme exhibits mixed properties--many positional identities with a class III protein, but functionally a class I enzyme--blurring the distinction among the classes of alcohol dehydrogenase. The two domain interfaces, affected by movements upon coenzyme binding, both exhibit substitutions in a manner thus far unique to the cod enzyme. In contrast, coenzyme-binding residues are highly conserved. At the active site, inner and outer parts of the substrate pocket show different extents of amino acid replacement. In total, no less than 7-10 residues of 11 in the substrate binding pocket differ from those of all the mammalian classes, explaining the substrate specificities. However, the inner part of the substrate pocket is very similar to that of the class I enzymes, which is compatible with the observed characteristics of the cod enzyme: ethanol is an excellent substrate (Km = 1.2 mM) and 4-methylpyrazole is a strong inhibitor (Ki = 0.1 microM). These values are about as low as those typical for the ethanol-active class I mammalian enzyme and do not at all resemble those for class III, for which ethanol is hardly a substrate and pyrazole is hardly an inhibitor. Further out in the substrate pocket, several residues differ from the mammalian classes, affecting large substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcohol Dehydrogenase↗

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↗

PubMed1992

A graphical user interface for quantitative imaging and analysis of electrophoretic gels and autoradiograms.

DNA/GUI (DNA Graphical User Interface) is an interactive software system for rapid and efficient analysis of images of the types used in genome mapping, such as autoradiograms and electrophoretic gels. Images are digitized using a commercially available charge-coupled-device (CCD) camera system and analyzed on a graphics workstation using a menu-driven user interface. DNA/GUI features automatic lane and band detection, simultaneous display of multiple images and a unique spatial-normalization algorithm. Images and their associated data are archived and easily available for later recall. Preliminary results indicate that DNA/GUI is a useful tool in the analysis and comparison of images used in a variety of applications such as genetic-linkage analysis and DNA restriction mapping. The interactive display software is based on the X Window System and is therefore readily portable to a variety of graphics workstations.

Autoradiography↗