The interpretation of oligonucleotide maps. A theoretical study of nucleic acid digests with special reference to repeated diverged sequences.
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Animals↗
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Results for “reference mapping”
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Genome analysis of species 3 adenoviruses isolated during summer outbreaks of conjunctivitis and pharyngoconjunctival fever in the Glasgow and London areas in 1981.
Genome analysis was performed on 125 adenovirus isolates from conjunctival swabs of patients with conjunctivitis obtained in Glasgow between 1981 and 1984. A summer outbreak in 1981 was mainly due to species 3 adenoviruses, of which genotype 3GB and five different genotypic variants cocirculated. Three species 3 variants were also observed in 1982. The genome changes of variants were located on physical maps of the Ad3 reference strain and found to be clustered near the ends of the adenovirus DNA (including the fiber area), whereas the hexon coding region was unaltered. In contrast to the genome heterogeneity observed among the species 3 adenoviruses collected in Glasgow in 1981 it was found that all 69 Ad3 isolates obtained from an outbreak of pharyngoconjunctival fever in a boarding school near London during the summer of 1981 possessed the 3GB genotype.
Adenoviridae Infections↗
Comparison of ATPase activities and heavy chains of rabbit atrial and thyrotoxic ventricular myosin subfragment-1.
Subfragment-1 of rabbit atrial and thyrotoxic ventricular myosin (V1 isomyosin) has been prepared and purified by DEAE-cellulose column chromatography. Pyrophosphate-polyacrylamide gel electrophoretic patterns and column chromatographic profile of the atrial subfragment differ from those of thyrotoxic ventricular myosin subfragment-1. On the other hand, Ca2+, Mg2+ and actin-activated ATPase activities of these subfragments are identical. Comparison of the peptide mapping by limited proteolysis in the presence of sodium dodecyl sulfate of the heavy and the light subunits of these subfragments reveals that the patterns for the heavy chain peptides of these subfragments are substantially similar but their light chain peptide patterns differ. The results suggest that the enzymatic and structural similarities that have been recognized between these isoenzymes using intact myosin hold true for the myosin subfragment-1. The differences between these subfragments are due to the differences in the light chains associated with them.
Animals↗
The value of closely spaced scalp electrodes in the localization of epileptiform foci: a study of 26 patients with complex partial seizures.
Twenty-seven patients with complex partial seizures were studied electrographically utilizing a large number of closely spaced scalp electrodes around the epileptogenic focus. Skull roentgenograms were made with the electrodes in place in order to relate the electrode positions to underlying brain anatomy. Field distribution maps were constructed from reference montages employing the closely spaced electrode set. Electrodes other than 10-20 were maximal most often and the single electrodes most often maximal were D9-D10, anterior temporal in location. This method of localization is of help in the evaluation of patients with complex partial seizures who may be surgical candidates.
Adolescent↗
Identification of maxicircle DNA sequences in Leishmania Tarentolae that are homologous to sequences of specific yeast mitochondrial structural genes.
Sequences homologous to the yeast mitochondrial structural genes for cytochrome oxidase subunits I and II, ATPase 6 and cytochrome b were identified on the kinetoplast DNA maxicircle molecule by low stringency hybridization of maxicircle blots with heterologous probes derived from mitochondrial DNA of yeast petite mutants. No hybridization was observed with the yeast ATPase 9 gene probe. The relative extent of base sequence mismatch was determined by melting of the heterologous hybrids. Candidates for the transcripts of these presumptive structural genes were proposed with reference to the transcriptional map of the maxicircle of Leishmania tarentolae. These results provide the first indication that maxicircle DNA specifies information for a limited number of conserved mitochondrial gene products similar to those already described for other eukaryotic cells.
Adenosine Triphosphatases↗
Nasopharyngeal recordings of somatosensory evoked potentials document the medullary origin of the N18 far-field.
Because the nasopharyngeal electrode provides non-invasive access to the ventral brain-stem at the medullo-pontine level we used it for recording somatosensory evoked potentials (SEPs) to median nerve stimulation (non-cephalic reference). After the P9 and P11 far-fields, the nasopharyngeal SEPs disclosed a negative-going component which was interpreted as the near-field equivalent of the P14 scalp far-field generated in the caudal part of the medial lemniscus. Nasopharyngeal SEPs also revealed a large N18 with voltage and features strikingly similar to those of the scalp-recorded N18 far-field. These results suggest that N18 is generated in the medulla and not more rostrally in the brain-stem. The use of a nasopharyngeal electrode as reference for topographic brain mapping is discussed. The paper documents the feasibility and relevance of nasopharyngeal recordings for non-invasive analysis of short-latency SEPs.
Adult↗
Staining of serum concanavalin A-binding proteins after micro two-dimensional electrophoresis and blotting.
Human serum proteins separated by micro two-dimensional electrophoresis in the absence of denaturants were electrophoretically transferred to nitrocellulose sheets (blots), and glycoproteins on the blots were stained by sequential incubation with the lectin concanavalin A, the glycoprotein horseradish peroxidase and the substrates of peroxidase diaminobenzidine-hydrogen peroxide. The stained serum concanavalin A-binding glycoproteins were identified by referring to the "identification map" of human plasma proteins, which we have prepared by immunochemical staining of the proteins on the blots. The concanavalin A-peroxidase method applied for the blots after two-dimensional electrophoresis provided information on the location of serum concanavalin A-binding glycoproteins, and showed greater sensitivity than Coomassie Brilliant blue R-250 staining for several serum proteins.
Electrophoresis, Polyacrylamide Gel↗
Mapping neuropeptide-containing pathways in the brain with special reference to data obtained from the rat limbic system.
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Animals↗
Computer-aided optimisation of drug enantiomer separation in chiral high-performance liquid chromatography.
The advent of several new column materials for the resolution of chiral compounds in high-performance liquid chromatography has opened up new possibilities for the analysis of drug enantiomers both in the dosage form and in bioanalytical studies. The utility of simplex optimisation, modified simplex and response surface mapping are considered with reference to the antischistosomal drug, oxamniquine, separated on an alpha 1-acid glycoprotein column. The resolution of the enantiomers of three closely related benzodiazepines, temazepam, oxazepam and lorazepam, is attempted on three new column systems: cellulose triacetate, beta-cyclodextrin and the reversed-phase column porous graphitic carbon with beta-cyclodextrin as a mobile phase additive.
Chromatography, High Pressure Liquid↗
The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8.
White is a widespread coat color among domestic pig breeds and is controlled by an autosomal dominant gene I. The segregation of this gene was analyzed in a reference pedigree for gene mapping developed by crossing the European wild pig and a Large White domestic breed. The gene for dominant white color was shown to be closely linked to the genes for albumin (ALB) and platelet-derived growth factor receptor alpha (PDGFRA) on chromosome 8. An unexpected phenotype with patches of colored and white coat was observed among the F1 and F2 animals. The segregation data indicated that the phenotype was controlled by a third allele, denoted patch (Ip), most likely transmitted by one of the Large White founder animals. It is shown that the ALB, PDGFRA, I linkage group shares homologies with parts of mouse chromosome 5, human chromosome 4, and horse linkage group II, all of which contain dominant genes for white or white spotting. Candidate genes for the dominant white and patch mutations in the pig are proposed on the basis on these linkage homologies and the recent molecular definition of the dominant white spotting (W) and patch (Ph) mutations in the mouse.
Albumins↗
Distinct antibody specificities to a 64-kD islet cell antigen in type 1 diabetes as revealed by trypsin treatment.
Type 1 diabetes is associated with antibodies that immunoprecipitate a 64-kD islet cell membrane protein from detergent extracts of pancreatic islets. In this study we have determined whether mild trypsin treatment of islet membranes can release fragments of the antigen that bind antibodies in the serum of Type 1 diabetic patients. Partial tryptic proteolysis of [35S]methionine-labeled 64-kD antigen immunoprecipitated from detergent extracts of rat islets resulted in the formation of 50-, 40-, and 37-kD fragments. Similar sized fragments were recovered when sera from diabetic patients were employed to immunoprecipitate polypeptides solubilized by mild trypsin treatment of a particulate fraction of radiolabeled rat islets. Of 27 diabetic patients, 22 possessed antibodies to the 50-kD polypeptide and 21 to the 40- and 37-kD polypeptides. A positive association was found between 64k antibodies and antibodies to the 50-kD fragment but not between 64k antibodies and antibodies to the 40- or 37-kD fragments. Some 64k antibody negative patients possessed antibodies that efficiently immunoprecipitated the latter fragments. Serum from 25 of 27 (93%) diabetic patients immunoprecipitated at least one of the three tryptic polypeptides. One of 20 nondiabetic controls immunoprecipitated a 50-kD polypeptide and all controls were negative for antibodies to 40- and 37-kD fragments. Thus, Type 1 diabetes is associated with the presence of at least two antibody reactivities to distinct determinants of the 64-kD antigen, and some patients may possess antibodies to a cryptic epitope on the detergent-solubilized molecule. These data suggest that the detection of antibodies (present in 93% of patients) to epitopes on tryptic polypeptides of the 64-kD antigen may be of even greater diagnostic value for the onset of Type 1 diabetes than analyses of antibodies reactive with the intact 64-kD antigen.
Adolescent↗
NoisyFlow: differentially private optimal transport using neural networks for secure biomedical data sharing across multiple institutions.
MOTIVATION: Biomedical models improve when trained on data pooled across institutions, but sensitive patient records (e.g. genomics, clinical data, and medical images) are difficult to share due to privacy constraints. Moreover, data collected at different sites often have shifted distributions because of covariate differences (including batch effects), so privacy-preserving sharing alone cannot simply resolve cross-site mismatch. Methods that protect individuals while explicitly aligning distributions are needed to enable reliable multi-institutional analyses. RESULTS: We present NoisyFlow, a three-stage differentially private framework for cross-institutional harmonization under distribution shift. In stage I, each site learns a differentially private flow-based generator of its local labeled distribution. In stage II, it learns a neural optimal transport map to a shared reference distribution. In stage III, a central server composes the released models to generate reference-aligned pseudo-data for downstream analysis without accessing raw records. Across four biomedical settings spanning single-cell genomics, histopathology, neurogenomics, and wearable sensing, NoisyFlow reduces distribution shift while preserving downstream utility under formal differential privacy guarantees. AVAILABILITY AND IMPLEMENTATION: The implementation of NoisyFlow is available at https://github.com/gersteinlab/NoisyFlow.
Information Dissemination↗
A complete diploid human genome benchmark for personalized genomics.
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental duplications, and satellite repeats, including 39,144 protein-coding genes across both haplotypes. To facilitate application of the benchmark, we developed tools for measuring the accuracy of sequencing reads, phased variant call sets, and genome assemblies against a diploid reference. Genome-wide analyses show that state-of-the-art de novo assembly methods resolve 2-7% more sequence and outperform variant calling accuracy by an order of magnitude, yielding just one error per 100 kb across 99.9% of the benchmark regions. Adoption of genome-based benchmarking is expected to accelerate the development of cost-effective methods for complete genome sequencing, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.
Journal Article↗
Tissue compensator fabrication using a simple photographic technique.
A simple method of fabricating photon beam tissue compensators is described. A plaster cast of the patient's surface contours is partially immersed in a mixture of India ink and water to obtain a topographic map relative to a reference plane which is perpendicular to the photon beam. The contours are photographed, and successive contours corresponding to different missing tissue thicknesses are used to fabricate a compensator from lead sheets cut to the same shape with the proper magnification.
Humans↗
Computer correction of projective distortions in dental radiographs.
Distortions in radiographic images caused by changes in shape and position of the film relative to the x-ray beam can result in registration artifacts which interfere with interpretation of subtracted images. A warping transformation is described which maps known points of reference in one image into homologous points in another. The corrected image pair can then be superimposed and subtracted with significantly-reduced differences in registration to facilitate the detection of localized changes of diagnostic interest.
Computers↗
WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp.
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
Journal Article↗
Principles and physics of Doppler.
This article reviews the available Doppler instrumentation and application to assessment of blood flow velocity. A review of the basis of quantitative measurements such as volume flow, modified Bernoulli and continuity equations, and pressure half-time are discussed. A brief technical description of Doppler color-flow mapping is presented with reference to data acquisition and display.
Blood Flow Velocity↗
Blood clotting factor IX BM Nagoya. Substitution of arginine 180 by tryptophan and its activation by alpha-chymotrypsin and rat mast cell chymase.
Factor IX BM Nagoya (IX Nagoya) is a natural mutant of factor IX responsible for severe hemophilia B. A patient with this mutant is characterized by a markedly prolonged ox brain prothrombin time. IX Nagoya was purified from the patient's plasma by immunoaffinity chromatography with an anti-factor IX monoclonal antibody column. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that treatment of IX Nagoya with factor XIa/Ca2+ resulted in cleavage only at the Arg145-Ala146 bond. Reversed-phase high performance liquid chromatography of a trypsin digest of IX Nagoya showed an aberrant peptide, which was further digested with proteinase Asp-N. Primary structure analysis of one of the Asp-N peptides revealed that Arg180 is replaced by Trp. An essentially complete (99%) amino acid sequence of IX Nagoya was obtained by sequencing fragments derived from a lysyl endopeptidase digest in which no other substitutions in the catalytic triad or substrate binding site were found. We also found that IX Nagoya is activated by alpha-chymotrypsin or rat mast cell chymase by monitoring the rate of factor X activation using a fluorogenic peptide substrate in the presence of factor VIII, phospholipids, and Ca2+. These results indicate that the substitution of Arg180 by Trp impairs the cleavage by factor XIa required for activation of this zymogen and that the substitution causes hemophilia BM.
Amino Acid Sequence↗