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PubMed2026

Efforts towards a precision medicine approach in juvenile idiopathic arthritis.

Juvenile idiopathic arthritis (JIA) is the commonest group of childhood arthritides. Despite the availability of advanced therapeutics, many children and young people (CYP) with JIA experience disease flares, and in some, chronic joint damage. Tailoring treatment based on unique biological profiles would benefit CYP with JIA given their variable clinical presentation and disease course. To date, biomarkers to predict treatment response are lacking. With advances in single cell technologies, we are now able to profile the genes and proteins of target tissues at unprecedented resolution to define the biological basis of disease and guide novel treatment approaches. The complex analyses and combination of biological and clinical outcome data from large datasets across disease phenotypes have become possible with the development of computational and machine learning methods. Here, we summarize the strategies to integrate data through multimodal based approaches to maximize precision medicine and research priorities for CYP with JIA.

Humans↗
PubMed2000

A performance adequate computational model for auditory localization.

A computational model of auditory localization resulting in performance similar to humans is reported. The model incorporates both the monaural and binaural cues available to a human for sound localization. Essential elements used in the simulation of the processes of auditory cue generation and encoding by the nervous system include measured head-related transfer functions (HRTFs), minimum audible field (MAF), and the Patterson-Holdsworth cochlear model. A two-layer feed-forward back-propagation artificial neural network (ANN) was trained to transform the localization cues to a two-dimensional map that gives the direction of the sound source. The model results were compared with (i) the localization performance of the human listener who provided the HRTFs for the model and (ii) the localization performance of a group of 19 other human listeners. The localization accuracy and front-back confusion error rates exhibited by the model were similar to both the single listener and the group results. This suggests that the simulation of the cue generation and extraction processes as well as the model parameters were reasonable approximations to the overall biological processes. The amplitude resolution of the monaural spectral cues was varied and the influence on the model's performance was determined. The model with 128 cochlear channels required an amplitude resolution of approximately 20 discrete levels for encoding the spectral cue to deliver similar localization performance to the group of human listeners.

Humans↗
PubMed2004

Biofunctionalization of carbon nanotubes for atomic force microscopy imaging.

The study of biological processes relies increasingly on methods for probing structure and function of biochemical machinery (proteins, nucleic acids, and so on) with submolecular resolution. Atomic force microscopy (AFM) has recently emerged as a promising approach for imaging biological structures with resolution approaching the nanometer scale. Two important limitations of AFM in biological imaging are (1) resolution is constrained by probe tip dimensions, and (2) typical probe tips lack chemical specificity to differentiate between functional groups in biological structures. Single-walled carbon nanotubes (SWNTs) offer an intriguing possibility for providing both high resolution and chemical selectivity in AFM imaging, thus overcoming the enumerated limitations. Procedures for generating SWNT tips for AFM will be described. Carboxylic acid functional groups at the SWNT ends can be functionalized using covalent coupling chemistry to attach biological moieties via primary amine groups. Herein, the focus will be on describing methods for attaching biotin to SWNT tips and probing streptavidin on surfaces; importantly, this same coupling chemistry can also be applied to other biomolecules possessing primary amine groups. Underivatized SWNT tips can also provide high-resolution AFM images of DNA. Biofunctionalization of SWNT AFM tips offers great potential to enable high-resolution, chemically selective imaging of biological structures.

Biotin↗
PubMed1998

The effect of sample freezing on proton magic-angle spinning NMR spectra of biological tissue.

Magic-angle spinning (MAS) has recently been shown to enhance spectral resolution in NMR examinations of intact biological tissue ex vivo. This work demonstrates that freezing certain tissue samples before examination by 1H MAS NMR can have a marked effect on their spectra. Spectra of rat kidney after freezing in liquid nitrogen, compared with spectra before freezing, showed a significant increase in signal intensities from alanine (>100%), glutamine (>40%), and glycine (>100%), and a decrease in signals assigned to lipids and other macromolecules. Some resonances--such as from leucine, valine, isoleucine, and aspartate--only became visible after freezing the tissue. These observations suggest that low temperature storage of tissue necropsies or biopsies might affect the results of a MAS NMR analysis, possibly resulting in the misinterpretation of metabolite changes to pathogen or disease effects.

Animals↗
PubMed2003

Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.

Bacteriophage P22 is a prototypical biological machine used for studying protein complex assembly and capsid maturation. Using cryo-EM, we solved the structures of P22 before and after the capsid maturation at 8.5 A and 9.5 A resolutions, respectively. These structures allowed visualization of alpha-helices and beta-sheets from which the capsid protein fold is derived. The capsid fold is similar to that of the coat protein of HK97 bacteriophage. The cryo-EM shows that a large conformational change of the P22 capsid during maturation transition involves not only the domain movement of individual subunits, but also refolding of the capsid protein.

Bacteriophage P22↗
PubMed1996

New method for the resolution of the enantiomers of 5,6-dihydroxy-2-methyl-aminotetralin by selective derivatization and HPLC analysis: application to biological fluids.

A new chiral derivatization procedure for the HPLC resolution of chiral catecholamines and structurally related compounds is described. The homochiral reagent, (+)-(R)-1-phenylethyl isocyanate (RPEIC), was added to separate and quantitate the enantiomers of rac-5,6-dihydroxy-2-methyl-aminotetralin, the main metabolite of rac-5, 6-diisobutyryl-2-methyl-aminotetralin, a potent dopamine agonist, by reversed-phase HPLC analysis. To avoid catecholamine degradation in the basic reaction medium and to obtain the selective and quantitative derivatization of the amino group of the compound, the reversible complex formation between diphenylborinic acid (DPBA) and the catechol group, in alkaline medium, was performed before homochiral isocyanate addition. The RPEIC derivatization was completed in 30 min and then the DPBA complex was dissociated by adding dilute acid. The structure of intermediates and urea derivatives was confirmed by mass spectometry. The use of an electrochemical detector, operating in redox mode, allowed HPLC quantitation of enantiomers at the nanogram level in plasma and urine. The derivatization procedure is also suitable for other catecholamine-related compounds.

Animals↗
PubMed2004

Characterisation of low, medium and high responders following FSH stimulation prior to ultrasound-guided transvaginal oocyte retrieval in cows.

In human IVF, the concept of 'low responders' is well known and generally defined as women with poor-response to gonadotrophin stimulation in a previous induction cycle. The objective of this retrospective study is to describe and characterise the concepts of 'low-, medium-, and high-response' and 'low, medium, and high responders' in bovine-assisted reproduction by analysing the OPU-IVF results obtained following 665 gonadotrophin-stimulated sessions conducted in 112 animals, nearly all of which were previously unsuccessful in traditional multiple ovulation and embryo transfer (MOET) programs. They were submitted to OPU and IVP between 1999 and 2003. In reference to these 665 OPU sessions, categories of response were defined based on the overall mean+/-S.D. follicles aspirated and COC obtained i.e., for follicles 14.7+/-9.8 and for COCs 11.7+/-8.1. So arbitrary cut-off values to define the categories of sessions were for follicles 5 and 25, and for COC 4 and 20. The three categories for follicles punctured in one session were therefore follicle low-response (FLR) or=25 follicles and for COCs recovered in one session COC low-response (CLR) or=20 COC. In addition, four categories of animals were also defined: (1) a low responder animal (LRA) had at least one OPU session in which FLR and CLR were observed (genuine low-response, see Section ); these animals did not have any high-response sessions, (2) a medium responder animal (MeRA) had only medium-responses, (3) a high responder animal (HRA) had at least one OPU session in which FHR and CHR were observed; these animals did not have any low-response sessions, and (4) mixed responder animals (MiRA) had both low and high-responses. Finally, we distinguished biological (animals) and technical (recovery rate and ultrasound resolution) causes of response differences. In 'low, high, medium and mixed reponders,' different results were obtained (p<0.05): mean follicle numbers (8.8+/-4.8a, 22.4+/-10.5c, 13.2+/-5.2b,15.1+/-10.2d), COC numbers (6.3+/-3.9a, 18.5+/-8.2c, 10.4+/-4b, 12.0+/-8.3d), embryo numbers (1.8+/-2.1a, 5.6+/-4.9c, 2.5+/-2.7b, 3.5+/-3.8d) and also for recovery rate (72%a, 83%b,79%, 79%) and percentage embryo development (29%, 30%a, 24%b, 29%). In conclusion, the results of this study demonstrate that variability in OPU results has technical (ultrasound resolution and recovery rate) as well as biological (animal) aspects. Selection of animals with extreme (high or low) follicle and COC production results allows us to distinguish three populations: 'low, medium, and high responders' to FSH stimulation.

Animals↗
PubMed2006

High-resolution ab initio three-dimensional x-ray diffraction microscopy.

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

Algorithms↗
PubMed2002

Voxx: a PC-based, near real-time volume rendering system for biological microscopy.

Confocal and two-photon fluorescence microscopy have advanced the exploration of complex, three-dimensional biological structures at submicron resolution. We have developed a voxel-based three-dimensional (3-D) imaging program (Voxx) capable of near real-time rendering that runs on inexpensive personal computers. This low-cost interactive 3-D imaging system provides a powerful tool for analyzing complex structures in cells and tissues and encourages a more thorough exploration of complex biological image data.

Animals↗
PubMed2004

Multidimensional separations in the pharmaceutical arena.

The introduction of novel, powerful and rapid multidimensional separation and characterization methods has produced revolutionary global changes at the genome, proteome and metabolome level, bringing about a radical transition in our views of living systems, at the molecular level. The age of proteomics and metabolomics demands high-resolution multidimensional separation techniques. Multidimensional gas and liquid chromatography techniques, in addition to capillary and microchip electrophoresis methods, offer increased resolution and sensitivity, while also affording adequate throughput and reproducibility to meet the demands of the modern pharmaceutical industry. Coupled with MS, these techniques provide not only separation but also reliable identification of the sample components. The resolving power of these methods has proved to be superior over individual one-dimensional approaches, enabling the comprehensive separation of complex biological mixtures, with excellent resolution and reproducibility. High capacity computer systems that are capable of rigorous qualitative and quantitative analysis of the separation profiles allow the establishment and mining of large databases. Examples of various modern multidimensional separation techniques, and their integration with MS, are reviewed, here, with respect to pharmaceutical analysis.

Chromatography, Gas↗
PubMed2025

Sparse deconvolution of cell type medleys in spatial transcriptomics.

Mapping cell distributions across spatial locations with whole-genome coverage is essential for understanding cellular responses and signaling However, current deconvolution models aim to estimate the proportions of distinct cell types in each spatial transcriptomics spot by integrating reference single-cell data. These models often assume strong overlap between the reference and spatial datasets, neglecting biology-grounded constraints such as sparsity and cell-type variations, as well as technical sparsity. As a result, these methods rely on over-permissive algorithms that ignore given constraints leading to inaccurate predictions, particularly in heterogeneous or unmatched datasets. We introduce Weight-Induced Sparse Regression (WISpR), a machine learning algorithm that integrates spot-specific hyperparameters and sparsity-driven modeling. Unlike conventional approaches that neglect biology-grounded constraints, WISpR accurately predicts cell-type distributions while preserving biological coherence, i.e., spatially and functionally consistent cell-type localization, even in unmatched datasets. Benchmarking against five alternative methods across ten datasets, WISpR consistently outperformed competitors and predicted cellular landscapes in both normal and cancerous tissues. By leveraging sparse cell-type arrangements, WISpR provides biologically informed, high-resolution cellular maps. Its ability to decode tissue organization in both healthy and diseased states highlights WISpR's practical utility for spatial transcriptomics, particularly in challenging settings involving noise, sparsity, or reference mismatches.

Humans↗
PubMed1996

Electron holographic observation for biological specimens: electron holography of bio-specimens.

Electron holography has been applied to the observation of biological filaments. The technique has some advantages over conventional imaging for observing weak-phase objects such as small unstained biological structures. To avoid artificial structural transformation of the sample owing to the interaction with the supporting film, a holey carbon film was used to support the filaments. A tobacco mosaic virus bridged over a hole was observed as a cylindrical shape; the contrast distribution across the filament represents its actual shape, which is difficult to obtain with conventional transmission electron microscopy. A number of technical limitations which at present prevent high-resolution structure analysis of biological macromolecules by electron holography are discussed in this report.

Electrons↗
PubMed2003

Micro- and nanotechnologies for studying cellular function.

The study of complex biological systems requires methods to perturb the system in complex yet controlled ways to elucidate mechanisms and dynamic interactions, and to recreate in vivo conditions in flexible in vitro set-ups. This paper reviews recent advances in the use of micro- and nanotechnologies in the study of complex biological systems and the advantages they provide in these two areas. Particularly useful for controlling the chemical and mechanical microenvironments of cells is a set of techniques called soft lithography, whereby elastomeric materials are used to transfer and generate micro- and nanoscale patterns. Examples of some of the capabilities of soft lithography include the use of elastomeric stamps to generate micropatterns of protein and the use of elastomeric channels to localize chemicals with subcellular spatial resolutions. These types of biological micro- and nanotechnologies combined with mathematical modeling will propel our understandings of cellular and subcellular physiology to new heights.

Animals↗
PubMed1999

A gas chromatography/electron capture/negative chemical ionization high-resolution mass spectrometry method for analysis of endogenous and exogenous N7-(2-hydroxyethyl)guanine in rodents and its potential for human biological monitoring.

A gas chromatography/electron capture/negative chemical ionization high-resolution mass spectrometry (GC/EC/NCI-HRMS) method was developed for quantitating N7-(2-hydroxyethyl)guanine (N7-HEG) with excellent sensitivity and specificity. [4,5,6,8-(13)C(4)]-N7-HEG was synthesized, characterized, and quantitated using HPLC/electrospray ionization mass spectrometry (HPLC/ESI-MS) so it could serve as an internal standard. After being converted to its corresponding xanthine and derivatized with pentafluorobenzyl (PFB) bromide twice, the PFB derivative of N7-HEG was characterized using GC/EC/NCI-HRMS carried out at full scan mode. The most abundant fragment was at m/z 555, with a molecular formula of C(21)H(9)N(4)O(3)F(10), resulting from the loss of one PFB group. By monitoring m/z 555.0515 (analyte) and m/z 559.0649 (internal standard), this assay demonstrated a linear relationship over a range of 1 fmol to 1 pmol of N7-HEG versus 20 fmol of [(13)C(4)]-N7-HEG on column. The limit of detection (LOD) for the complete assay was 600 amol (S/N = 5) injected on column. The variation of this assay was within 15% from 1 to 20 fmol of N7-HEG versus 2 fmol of [(13)C(4)]-N7-HEG with four replications for each calibration standard. Two hundred to three hundred micrograms of spleen DNA of control rats and mice and 100 microg of spleen DNA of rats and mice exposed to 3000 ppm ethylene for 6 h/day for 5 days were analyzed using GC/EC/NCI-HRMS. The amounts of N7-HEG varied from 0.2 to 0.3 pmol/micromol of guanine in tissues of control rats. Ethylene-exposed animals had 5-15-fold higher N7-HEG levels than controls. This assay was able to quantitate N7-HEG in 25-30 microg of DNA from human lymphocytes with excellent specificity. This was due in part to human tissues having 10-15-fold higher amounts of endogenous N7-HEG than rodents. These results show that this GC/EC/NCI-HRMS method is highly sensitive and specific and can be used in biological monitoring and molecular dosimetry and molecular epidemiology studies.

Animals↗
PubMed1978

Compartmentalizing the S period.

In order to increase the resolution of interphase analysis we have developed a method which is an alternative to cytofluometric techniques for tissues where cell flow is not applicable. The method combines the estimation of cell frequency in G1, S, G2 and mitosis after a 3H-thymidine pulse with the grouping of interphase cells according to their DNA content, as estimated by cytophotometry in Feulgen stained nuclei. By superimposing both sets of data we get three different artificial compartments within the S period. As a biological test of the resolution reached, the method readily confirmed that hydroxyurea, after one cycle time, accumulates cycling cells of Allium cepa L. root meristems in early S.

Cell Compartmentation↗
PubMed1994

The analysis of fluorophore-labeled glycans by high-resolution polyacrylamide gel electrophoresis.

Many important biological processes are mediated by the carbohydrate moieties of glycoconjugates. Their structural determination presents considerable difficulties because of both their complex structures and the small quantities which are available from biological sources. In order to address some of the problems in this field a new method of glycan analysis has been developed in which saccharides having a reducing end group are labeled covalently with a fluorophore and the derivatives separated with high resolution by polyacrylamide gel electrophoresis. Fluorophores have been used that enable the electrophoretic separation of positional isomers, anomers, and epimers of a variety of saccharides. Mixtures of complex glycans obtained by enzymatic cleavage from glycoproteins yield electrofluorograms showing high-resolution oligosaccharide profiles. Techniques for obtaining saccharide sequence information from isolated oligosaccharides have been developed. Subpicomolar quantities of individual saccharides can be detected using an imaging system based on a cooled charge-coupled device. The method enables rapid, simultaneous, parallel analyses of multiple samples. The analytical and clinical applications and potential of the system are discussed.

Carbohydrate Sequence↗
PubMed2003

Use of mobile phase 18-crown-6 to improve peak resolution between mono- and divalent metal and amine cations in ion chromatography.

It is difficult to quantify NH4+ by ion chromatography in the presence of high concentrations of Na+ due to peak overlap. The Dionex IonPac CS15 column, which contains phosphonate, carboxylate, and 18-crown-6 functional groups, was originally developed to overcome this problem. We have found that the addition of 18-crown-6 to the eluent promotes improved peak resolution between Na+ and NH4+ even at concentrations as high as 60,000 to 1 using this column. Its use also improves the separation of alkali and alkaline earth metal and amine cations. Mobile phase 18-crown-6 increased the retention times of CH3NH3+, NH4+, and K+, and decreased the retention time of Sr2+. The retention times of Li+, Na+, Mg2+, Ca2+, (CH3)2NH2+, and (CH3)3NH+ were not affected. This method makes possible the direct analysis of ammonia from nitrogenase, the enzyme responsible for biological nitrogen fixation. The resolution of the NH4+ peak from the Na+ and Mg2+ peaks improved from zero resolution to values of 6.19 and 5.65, respectively. This technique considerably reduces the analysis time of NH4+ in the presence of high concentrations of Mg2+ and Na+ over traditional indophenol measurements.

Amines↗
PubMed1983

Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples.

The preparation and high resolution observation of frozen hydrated thin sections has been studied by transmission electron microscopy (TEM and STEM) on model systems, including pure water, protein solutions, catalase crystals, myelin sheath and various tissues. The state of the ice is determined by electron diffraction. Mass measurement in the electron microscope is used to determine section thickness and control hydration. An adequate depth of vitrified material for sectioning can be obtained from many biological suspensions or untreated tissues. Frozen hydrated sections around 100 nm thick can be produced under optimal conditions from vitreous ice or from vitrified biological samples. Sectioning, transfer and observation in the electron microscope is feasible without alteration of the sample hydration or its initial vitrification. Biological structures can be preserved and observed down to 10 nm. Under favourable working conditions, specimen compression during sectioning and electron beam damage are the factors limiting high resolution observations.

Animals↗