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PubMed1996

Generalizability of in-shoe peak pressure measures using the F-scan system.

In-shoe pressure analysis can be useful in the management of a variety of foot and ankle problems, but guidelines are needed to determine the practical limitations of the measures. The primary purpose of this study was to determine the reliability of peak plantar pressures taken with the F-Scan system over multiple steps, sensors, and days, and using a force platform for additional calibration. Data were collected on 10 healthy subjects as they walked across a force platform for a minimum of three trials on four separate sessions that were 1 week apart. Using a mean of three steps with a single sensor on 1 day, generalizability coefficients were 0.75 for manufacturer calibration and 0.82 with force platform calibration; reliability coefficients for absolute decisions (index of dependability) were 0.60 for manufacturer calibration and 0.76 with force platform calibration. Force measures from the F-Scan and force platform were highly correlated (r = 0.93), but the absolute difference between the measures varied between sensors and over time. RELEVANCE:--Peak pressure measures taken from a mean of three steps with procedures outlined by the F-Scan manufacturer provide pressure values that demonstrate adequate reliability for clinical and research purposes when rank ordering of measures is indicated. If measures are to be used for making absolute decisions (e.g., identifying a threshold for injury), calibration from a stable source such as a force platform is recommended.

Journal Article↗
PubMed2004

Translational benefits from research on rare genodermatoses.

Significant new discoveries about many of the genodermatoses have been made recently through an improved knowledge of the human genome, advances in molecular screening strategies and also through more comprehensive Internet DNA databases. By 2003, over 350 single gene skin disorders had been characterized at a molecular level. These new data provide more detailed information for patients, allow for more accurate diagnoses, and help improve genetic counselling. Other benefits include the feasibility of carrier screening and DNA-based prenatal testing, as well as a platform for devising new treatments, including somatic gene therapy. Research on rare single gene disorders also provides new insight into more common skin conditions. For example, new ideas about photosensitivity are emerging from discoveries of mutations in a novel component of the actin cytoskeleton (kindlin-1) in the rare inherited poikiloderma disorder, Kindler syndrome. Likewise, new clues to understanding disease pathology in lichen sclerosus have been gleaned from the discovery of pathogenic mutations in the skin protein, extracellular matrix protein 1, in the rare sclerosing inherited skin disorder, lipoid proteinosis. Finally, new insight into what can cause exuberant granulation tissue in chronic wounds has been provided by the discovery of specific mutations in the basement membrane protein, laminin 5, in the rare inherited condition, laryngo-onychocutaneous syndrome. It is clear that a precise research focus on the rare genodermatoses is providing practical benefits for sufferers of these disorders, as well as new lessons and ideas about more common acquired skin conditions.

Databases, Nucleic Acid↗
PubMed2025

Association of AGER genetic variants with chronic obstructive pulmonary disease susceptibility in Southern Chinese Han populations.

OBJECTIVE: Chronic obstructive pulmonary disease (COPD) remains a leading cause of disability and mortality among elderly populations. Studies indicate that AGER plays a critical regulatory role in the pathogenesis of respiratory disorders. However, the genetic variations in AGER to COPD susceptibility remain incompletely understood. This study employs a case-control design to investigate associations between AGER genetic variants and COPD risk in the Southern Chinese Han population. METHODS: This study enrolled 270 COPD patients and 271 healthy controls. AGER single-nucleotide polymorphisms (SNPs) were analysed using the MassARRAY iPLEX platform. Logistic regression models evaluated associations between AGER polymorphisms and COPD susceptibility, with false discovery rate (FDR) correction applied to mitigate multiple testing errors. SNP-SNP interactions were investigated through multifactor dimensionality reduction (MDR) analysis. Expression quantitative trait locus (eQTL) data from the GTEx database were further analysed to assess regulatory relationships between SNPs and AGER gene expression levels. RESULTS: This study showed that rs3134941 (G allele, OR = 0.21, 95% CI = 0.10-0.41, p (FDR) = 0.001) and rs3131300 (G allele, OR = 0.32, 95% CI = 0.20-0.49, p (FDR) = 0.0001) were significantly associated with a reduced susceptibility to COPD. MDR indicated that rs3131300 was the optimal predictive model for COPD risk. Additionally, initial mechanistic investigations utilizing the GTEx database identify rs3134941 (C > G) and rs3131300 (A > G) as significant expression quantitative trait loci for AGER mRNA in cell-cultured fibroblasts and whole blood. CONCLUSION: Our study demonstrated that AGER genetic variants might play a protective role in the progression of COPD.

Aged↗
PubMed2006

DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing.

A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.

Base Sequence↗
PubMed2005

The use of scFv-displaying yeast in mammalian cell surface selections.

Yeast surface display has proven to be a powerful tool for the directed evolution of immunological proteins when soluble ligands are available (Cho, B.K., Kieke, M.C., Boder, E.T., Wittrup, K.D., Kranz, D.M., 1998. A yeast surface display system for the discovery of ligands that trigger cell activation. J. Immunol. Methods 220, 179; Boder, E.T., Midelfort, K.S., Wittrup, K.D., 2000. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc. Natl. Acad. Sci. U. S. A. 97, 10701; Shusta, E.V., Holler, P.D., Kieke, M.C., Kranz, D.M., Wittrup, K.D., 2000. Directed evolution of a stable scaffold for T-cell receptor engineering. Nat. Biotechnol. 18, 754; Esteban, O., Zhao, H., 2004. Directed evolution of soluble single-chain human class II MHC molecules. J. Mol. Biol. 340, 81). This investigation extends the utility of this display platform by demonstrating its capacity for use in cell panning selections. This was accomplished by employing a model single-chain antibody (scFv)-hapten system that allowed for detailed investigation of the factors governing panning success. Yeast displaying anti-fluorescein scFv (4-4-20) exhibited specific interactions with the fluoresceinated endothelial cells and could be recovered from large backgrounds of irrelevant yeast in just three rounds. Successful selections required as few as 1700 fluorescein ligands per cell, and a three-round enrichment ratio of 10(6) was possible. These results indicate that yeast surface display is a viable option for use in cell or tissue-based selections.

Animals↗
PubMed2026

Optimization of a Semi-nested PCR Protocol for Amplifying the Entire Spike Protein Region to Identify SARS-CoV-2 Variants in Wastewater.

Wastewater-based monitoring of SARS-CoV-2 and other pathogens is a widely adopted tool for assessing epidemic dynamics. While quantitative assays are commonly used to estimate infection levels in catchment populations, phylogenetic information-such as identifying circulating variants-is also crucial for public health. However, applying the widely used ARTIC protocol for full-genome sequencing to wastewater samples has proven challenging, likely due to the limited specificity and sensitivity of multiplex RT-PCR in such complex matrices. In this study, we developed and optimized a semi-nested RT-PCR assay targeting the full S-protein coding region (~4000 bases) for phylogenetic characterization of SARS-CoV-2 in wastewater. By reducing multiplexing and using single-plex reactions for both RT and PCR steps, we successfully amplified ~2000&#xa0;bp fragments. Amplicons were sequenced using the Flongle Flow Cell platform. The optimized method-consisting of reverse transcription with specific primers followed by three parallel single-plex semi-nested PCRs-yielded over 1,000 SARS-CoV-2-like reads per primer set in 30 out of 39 wastewater samples in treatment plants in Japan, including those with <10 copies per analyte. Variant proportions were estimated using a newly developed approach based on single-nucleotide variant pattern matrix, revealing the presence of multiple co-circulating variants, including XBB lineages, JN.1, and notably BA.2.75, which was undetected in domestic clinical surveillance. These results highlight the effectiveness of our approach for detecting temporal shifts in SARS-CoV-2 variants, even at low RNA concentrations.

Polymerase Chain Reaction↗
PubMed2000

X-ray structure of simian immunodeficiency virus integrase containing the core and C-terminal domain (residues 50-293)--an initial glance of the viral DNA binding platform.

The crystal structure of simian immunodeficiency virus (SIV) integrase that contains in a single polypeptide the core and the C-terminal deoxyoligonucleotide binding domain has been determined at 3 A resolution with an R-value of 0.203 in the space group P2(1)2(1)2(1). Four integrase core domains and one C-terminal domain are found to be well defined in the asymmetric unit. The segment extending from residues 114 to 121 assumes the same position as seen in the integrase core domain of avian sarcoma virus as well as human immunodeficiency virus type-1 (HIV-1) crystallized in the absence of sodium cacodylate. The flexible loop in the active site, composed of residues 141-151, remains incompletely defined, but the location of the essential Glu152 residue is unambiguous. The residues from 210-218 that link the core and C-terminal domains can be traced as an extension from the core with a short gap at residues 214-215. The C(alpha) folding of the C-terminal domain is similar to the solution structure of this domain from HIV-1 integrase. However, the dimeric form seen in the NMR structure cannot exist as related by the non-crystallographic symmetry in the SIV integrase crystal. The two flexible loops of the C-terminal domain, residues 228-236 and residues 244-249, are much better fixed in the crystal structure than in the NMR structure with the former in the immediate vicinity of the flexible loop of the core domain. The interface between the two domains encompasses a solvent-exclusion area of 1500 A(2). Residues from both domains purportedly involved in DNA binding are narrowly distributed on the same face of the molecule. They include Asp64, Asp116, Glu152 and Lys159 from the core and Arg231, Leu234, Arg262, Arg263 and Lys264 from the C-terminal domain. A model for DNA binding is proposed to bridge the two domains by tethering the 228-236 loop of the C-terminal domain and the flexible loop of the core.

Amino Acid Sequence↗
PubMed2026

Hotgenes: an R package for reducing bottlenecks in bulk omics data exploration and collaboration.

SUMMARY: A critical part of omics analysis is the transition from early data exploration to final interpretation, often including different analytical platforms and the proliferation of figures, tables, and files. To minimize potential errors and delays that can occur during this process, we have developed an R package called "Hotgenes" that contains a wide range of flexible utilities available in a single modular Shiny application. With Hotgenes, differential expression results generated from bulk omics platforms can be imported and shared among collaborators with minimal coding. Furthermore, the modular Hotgenes user interface can be customized by advanced users to fit the needs of their evolving pipelines. AVAILABILITY AND IMPLEMENTATION: Hotgenes is implemented in R and is freely available at https://github.com/pfizer-opensource/Open-Hotgenes. A permanent archived version is available at https://doi.org/10.5281/zenodo.20129460.

Software↗
PubMed2004

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

Alleles↗
PubMed2026

Imaging-Guided Omics Technologies for Resolving Rare Cancer States and Advancing Nanomedicine.

The ability to resolve rare and transient cellular states is critical for understanding metastasis, immune evasion, and therapy resistance in cancer, yet these dynamic processes often escape detection by conventional sequencing and imaging approaches. Recent advances at the interface of nanotechnology, high-resolution live-cell imaging, and single-cell/spatial multiomics methods have enabled functional profiling of cells with unprecedented precision within their native microenvironment. In this Mini-Review, we highlight emerging nanoscale platforms that couple real-time phenotypic imaging with molecular readouts, such as FUNseq and CIN-seq, to directly link functional heterogeneity to transcriptomic, proteomic, and epigenomic information. By integrating nanoscale optical imaging, microengineered perturbation tools, and AI-driven computational analysis, these technologies open up new avenues for dissecting rare metastatic, therapy-resistant, or immune-evasive subpopulations. We further discuss how these next-generation imaging-guided single-cell and spatial omics platforms not only advance fundamental cancer biology but also create opportunities to accelerate the development of nanomedicine applications.

Humans↗
PubMed1997

Internet-enabled solutions for health care business problems.

Many health care delivery organizations have built, installed, or made use of Nets. As single entities merge with others, and independent institutions become part of much larger delivery networks, the need for collaboration is critical. With the formation of such partnerships, existing platforms will become increasingly available from which it will be possible to build disparate technologies that must somehow be part of a single working "system." Nets can enable this leveraging, allowing access from multiple technological platforms. The collaboration, distribution, application integration, and messaging possibilities with the Nets are unprecedented. We believe that meeting a health care delivery organization's needs without these benefits will soon be unthinkable. While Nets are not the answer to the challenges facing health care delivery today, they certainly are a large contributor to the solution.

Computer Communication Networks↗
PubMed2005

Analysis of the factors affecting the accuracy of detection for single base alterations by oligonucleotide microarray.

The oligonucleotide microarray, a high-throughput polymorphism detection technology, holds great promise for the characterization of complex genetic variance. To achieve greater sensitivity and specificity for it to be an effective platform technology we present results and discuss some of the factors influencing signal intensities and single-mismatch discrimination in array-based mutation/SNP detection. Probes with a series of concentrations were spotted onto the slide in order to find the optimal concentration with the identifiable satisfying signals and the stable ratios between matched and mismatched probes. It was found that under our experimental conditions, when the initial probe concentration is higher than the maximum immobilization capability of the slide (7.5 microM), the hybridization signal will be saturated and the ratio between matched and mismatched probes will be more stable than at a lower probe concentration. Considering the cost of probes and the systematic stability, a constant spotting concentration of 10 microM was selected. The stability of different types of mismatched oligo-DNA duplexes on the glass surface was also confirmed. The results show that the order of stability of mismatched oligo-DNA duplexes on a glass surface is in general agreement with previous reports conducted using liquid and polyacrylamide gel pads. This suggests that the influence of the mismatched base pair on the stability of the duplex in a solid hybridization system is similar to that in the solution hybridization environment.

Nucleic Acid Heteroduplexes↗
PubMed1979

Sources of variation in locomotor activity and stereotypy in rats treated with d-amphetamine.

Rats injected with doses of d-amphetamine 0--5.0 mg/kg were observed continuously in either an enclosed Y-maze or on an elevated Y-shaped platform. Patterns of increased walking and stereotypy were unaffected by the type of apparatus, but rearing remained totally suppressed at all dose levels on the elevated platform. In the second experiment, groups of rats where given single short tests in the enclosed Y-maze, which was novel to them. The stimulant actions of d-amphetamine on locomotion were obscured by high baseline levels of motor activity induced by the novel environment. Continuous measurements of habituated rats may provide a more sensitive means of evaluating stimulant actions of drugs in screening tests. The observed changes in patterns of onset and offset of increased locomotion and of stereotypy were consistent with the view that these types of behaviour are, to some extent, independently, mediated.

Animals↗
PubMed2001

Combining speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on a Microsoft Windows platform.

This presentation describes our experience in combining speech recognition software, clinical review software, and other software products on a single computer. Different processor speeds, random access memory (RAM), and computer costs were evaluated. We found that combining continuous speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on the same platform is feasible and can lead to substantial savings of hardware cost. This combination optimizes use of limited workspace and can improve radiology workflow.

Humans↗
PubMed2005

Bilateral chronic constriction of the sciatic nerve: a model of long-term cold hyperalgesia.

UNLABELLED: Effects of chronic constriction injury (CCI) and sham surgery of both sciatic nerves were evaluated for reflex lick/guard (L/G) and operant escape responses to thermal stimulation of rats. Experiment 1 compared L/G and escape responses to 0.3 degrees C, 43 degrees C, and 47 degrees C stimulation during a period of 60 days after CCI. Experiment 2 evaluated escape from 44 degrees C, 47 degrees C, and 10 degrees C for 100 days after CCI. The rats escaped from heat or cold stimulation of the paws in a dark compartment by climbing on a thermally neutral platform in a brightly lit compartment. For reflex testing, a single compartment provided no escape option. There was no significant effect of bilateral CCI on reflex or escape responses to nociceptive heat. However, there were long-term increases in the duration of L/G responding during trials of 0.3 degrees C stimulation and in the duration of escape responding to 10 degrees C. Hyperalgesia for cold was confirmed by a preference test, with a 2-compartment shuttle box with one floor heated (45 degrees C) and the other floor cooled (10 degrees C). Occupancy of the heated compartment was significantly increased by CCI (indicating a relative aversion for cold). PERSPECTIVE: For preclinical testing of treatments for allodynia/hyperalgesia after nerve injury, it is crucial to use methods of testing that are sensitive to effects on nociception throughout the neuraxis. Operant escape testing satisfies this criterion and is sensitive to bilateral CCI of rats, which avoids asymmetric postural/motor influences of unilateral CCI.

Animals↗
PubMed2005

Current practice relating to equine castration in the UK.

This study aimed to characterise current practice relating to equine castration in the UK. A questionnaire was posted to all 655 veterinary practices specified to provide veterinary care for horses, or classified as specialist equine practices. Respondents were asked to cite the number of equine castrations performed annually by the practice, describe techniques used for castration, outline anaesthetic/sedative/analgesic drug protocols used and provide details of post-operative medication. There was a 43% response rate to the questionnaire. Considerable variation in techniques and analgesia provision was identified, with the majority of respondents using a number of sedation/anaesthetic protocols rather than a single technique. This characterisation of current practice provides a useful platform from which subsequent investigations into welfare implications of current equine castration techniques can be directed.

Analgesics↗
PubMed2003

Optical imaging fiber-based live bacterial cell array biosensor.

A live cell array biosensor was fabricated by immobilizing bacterial cells on the face of an optical imaging fiber containing a high-density array of microwells. Each microwell accommodates a single bacterium that was genetically engineered to respond to a specific analyte. A genetically modified Escherichia coli strain, containing the lacZ reporter gene fused to the heavy metal-responsive gene promoter zntA, was used to fabricate a mercury biosensor. A plasmid carrying the gene coding for the enhanced cyan fluorescent protein (ECFP) was also introduced into this sensing strain to identify the cell locations in the array. Single cell lacZ expression was measured when the array was exposed to mercury and a response to 100nM Hg(2+) could be detected after a 1-h incubation time. The optical imaging fiber-based single bacterial cell array is a flexible and sensitive biosensor platform that can be used to monitor the expression of different reporter genes and accommodate a variety of sensing strains.

Adenosine Triphosphatases↗