gebhart/patrepeval huggingface dataset:
Fractal analysis of radiographs: Assessment of trabecular bone structure and prediction of elastic modulus and strength (1999)

The purpose of this study was to determine whether fractal dimension of radiographs provide measures of trabecular bone structure which correlate with bone mineral density (BMD) and bone biomechanics, and whether these relationships depend on the technique used to calculate the fractal dimension. Eighty seven cubic specimen of human trabecular bone were obtained from the vertebrae and femur. The cubes were radiographed along all three orientations--superior-inferior (SI), medial-lateral (ML), and anterior-posterior (AP), digitized, corrected for background variations, and fractal based techniques were applied to quantify trabecular structure. Three different techniques namely, semivariance, surface area, and power spectral methods were used. The specimens were tested in compression along three orientations and the Young's modulus (YM) was determined. Compressive strength was measured along the SI direction. Quantitative computed tomography was used to measure trabecular BMD. High-resolution magnetic-resonance images were used to obtain three-dimensional measures of trabecular architecture such as the apparent bone volume fraction, trabecular thickness, spacing, and number. The measures of trabecular structure computed in the different directions showed significant differences (p<0.05). The correlation between BMD, YM, strength, and the fractal dimension were direction and technique dependent. The trends of variation of the fractal dimension with BMD and biomechanical properties also depended on the technique and the range of resolutions over which the data was analyzed. The fractal dimension showed varying trends with bone mineral density changes, and these trends also depended on the range of frequencies over which the fractal dimension was measured. For example, using the power spectral method the fractal dimension increased with BMD when computed over a lower range of spatial frequencies and decreased for higher ranges. However, for the surface area technique the fractal dimension increased with increasing BMD. Fractal measures showed better correlation with trabecular spacing and number, compared to trabecular thickness. In a multivariate regression model inclusion of some of the fractal measures in addition to BMD improved the prediction of strength and elastic modulus. Thus, fractal based texture analysis of radiographs are technique dependent, but may be used to quantify trabecular structure and have a potentially valuable impact in the study of osteoporosis.
Continuous Regional Cerebral Cortical Blood Flow Monitoring in Head-injured Patients (1995)

Continuous regional cerebral cortical blood flow (rCoBF) was monitored with thermal diffusion flowmetry in 56 severely head-injured patients. Adequate, reliable data were accumulated from 37 patients (21 acute subdural hematomas, 10 cerebral contusions, 4 epidural hematomas, and 2 intracerebral hematomas). The thermal sensor was placed at the time of either craniotomy or burr hole placement. In 15 patients, monitoring was initiated within 8 hours of injury. One-third of the comatose patients monitored within 8 hours had rCoBF measurements of 18 ml per 100 g per minute or less, consistent with previous reports of significant ischemia in the early postinjury period. Initial rCoBF measurements were similar in the patients with Glasgow Coma Scale scores of 3 to 7 and in those with scores of 8 or greater. In patients with poor outcomes, rCoBF measurements did not change significantly from initial measurements; however, in those patients who had better outcomes, final rCoBF measurements were higher than initial rCoBF measurements. The patients who had better outcomes experienced normalization of rCoBF during the period of monitoring, and patients with poor outcomes had markedly reduced final rCoBF. These changes were statistically significant. When management was based strictly upon the intracranial pressure, examples of inappropriate treatment were found. For example, hyperemia and increased intracranial pressure treated with mannitol caused further rCoBF increase, and elevated intracranial pressure with low cerebral blood flow treated with hyperventilation increased the severity of ischemia. In 3 (5%) of 56 patients, wound infections developed. Continuous rCoBF monitoring in head-injured patients offers new therapeutic and prognostic insights into their management.
Retinoic Acid and the Histone Deacetylase Inhibitor Trichostatin A Inhibit the Proliferation of Human Renal Cell Carcinoma in a Xenograft Tumor Model (2005)

The combination of ATRA and the histone deacetylase inhibitor TSA elicits an additive inhibition of cell proliferation in RCC cell lines. These results indicate that ATRA and histone deacetylase inhibitor therapies should be explored for the treatment of advanced RCC.
Feature extraction from spectro-temporal signals using dynamic synapses, recurrency, and lateral inhibition (2010)

This paper presents a spiking neural network-based investigation of the issues associated with extraction of onset, offset, and coincidental firing features from spectro-temporal data. Speech samples containing spoken isolated digits from the TI46 database are employed to demonstrate the way in which these features can be extracted using leaky integrate-and-fire spiking neurons with dynamic synapses. The flexibility that the additional synaptic parameters in the neuron model provides, is demonstrated to be essential for onset, offset and coincidental firing extraction. Recurrency and the interaction between excitation and inhibition together with latency is demonstrated to be a viable means of extracting offset features. The effects of lateral inhibition and in particular its ability to induce transient synchrony in spike firing is evaluated. In particular, by defining a connection length parameter, and hence a neighbourhood size, synchronous firing is shown to gradually develop as connection length and neighbourhood size increases. Finally, the implications for this connectivity in spiking neural networks and its potential for learning spectral and spatio-temporal patterns via the formation of receptive fields is discussed.
Autosomal recessive Sorsby fundus dystrophy revisited: molecular evidence for dominant inheritance. (1997)

Sorsby fundus dystrophy (SFD) originally was characterized as an autosomal dominant disorder in which patients lose central vision during the 4th or 5th decade of life. Since Sorsby's initial description, interfamilial phenotypic variations have been noted and have given rise to controversy as to whether SFD constitutes more than one nosologic entity. In addition, several reports have proposed the existence of a recessively inherited form of SFD. The recent identification of the tissue inhibitor of metalloproteinases-3 (TIMP3) as the disease-causing gene in SFD has made it possible to address the questions of clinical and genetic heterogeneity. In this study, we reinvestigated a large, highly consanguineous Finnish family previously diagnosed as having early-onset autosomal recessive SFD. We identified a novel heterozygous Gly166Cys mutation in TIMP3 in all affected individuals and provide strong evidence for an autosomal dominant inheritance of the SFD phenotype in this family. Our results, in conjunction with a critical review of the reported cases, render the existence of a recessive mode of inheritance in SFD questionable. Considering all available data, we suggest that SFD is a genetically homogeneous, autosomal dominant condition.
Semienzymatic Cyclization of Disulfide-rich Peptides Using Sortase A (2014)

Disulfide-rich cyclic peptides have generated great interest in the development of peptide-based therapeutics due to their exceptional stability toward chemical, enzymatic, or thermal attack. In particular, they have been used as scaffolds onto which bioactive epitopes can be grafted to take advantage of the favorable biophysical properties of disulfide-rich cyclic peptides. To date, the most commonly used method for the head-to-tail cyclization of peptides has been native chemical ligation. In recent years, however, enzyme-mediated cyclization has become a promising new technology due to its efficiency, safety, and cost-effectiveness. Sortase A (SrtA) is a bacterial enzyme with transpeptidase activity. It recognizes a C-terminal penta-amino acid motif, LPXTG, and cleaves the amide bond between Thr and Gly to form a thioacyl-linked intermediate. This intermediate undergoes nucleophilic attack by an N-terminal poly-Gly sequence to form an amide bond between the Thr and N-terminal Gly. Here, we demonstrate that sortase A can successfully be used to cyclize a variety of small disulfide-rich peptides, including the cyclotide kalata B1, α-conotoxin Vc1.1, and sunflower trypsin inhibitor 1. These peptides range in size from 14 to 29 amino acids and contain three, two, or one disulfide bond, respectively, within their head-to-tail cyclic backbones. Our findings provide proof of concept for the potential broad applicability of enzymatic cyclization of disulfide-rich peptides with therapeutic potential.
Improved Enumeration of Lactic Acid Bacteria in Mesophilic Dairy Starter Cultures by Using Multiplex Quantitative Real-Time PCR and Flow Cytometry-Fluorescence In Situ Hybridization (2006)

Nucleic acid-based assays were developed to enumerate members of the three taxa Lactococcus lactis subsp. cremoris, L. lactis subsp. lactis, and Leuconostoc spp. in mesophilic starter cultures. To our knowledge the present is the first study to present a multiplex quantitative PCR (qPCR) strategy for the relative enumeration of bacteria. The multiplex qPCR strategy was designed to quantify the target DNA simultaneously relative to total bacterial DNA. The assay has a high discriminatory power and resolves concentration changes as low as 1.3-fold. The methodology was compared with flow cytometric fluorescence in situ hybridization (FLOW-FISH) and 5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside (X-Gal)-calcium citrate agar-based plate counting. For enumeration by FLOW-FISH, three new probes having the same specificity as the qPCR assay were designed and established. A combination with flow cytometry greatly reduced the time consumed compared to manual enumeration. Both qPCR and FLOW-FISH yielded similar community compositions for 10 complex starter cultures, with all detected subpopulations being highly significantly correlated (P < 0.001). Correlations between X-Gal-calcium citrate agar-based CFU and qPCR-derived counts were highly significant (P < 0.01 and P < 0.001, respectively) for the number of acidifiers versus L. lactis subsp. cremoris and for Leuconostoc spp. as quantified by the two techniques, respectively. This confirmed that most acidifiers in the studied PROBAT cultures are members of L. lactis subsp. cremoris. Quantitative real-time PCR and FLOW-FISH were found to be effective and accurate tools for the bacterial community analysis of complex starter cultures.
Treatment with intranasal fluticasone propionate significantly improves ocular symptoms in patients with seasonal allergic rhinitis (2004)

Patients treated with intranasal FP had clinically and statistically significant decreases in ocular symptom scores compared with vehicle placebo. Data also suggest that FP reduced ocular symptoms more than or comparable with oral LOR. Patients experiencing ocular symptoms associated with allergic rhinitis may benefit from monotherapy with intranasal FP.
The Read Channel (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, we provide a survey of the novel read channel technologies that found their implementation in products over the past decade, and we outline possible technology directions for the future of read channels. Recently, magnetic recording read channels have undergone several changes. In addition to switching from longitudinal to perpendicular recording channels, detectors tuned to media noise sources are now readily implemented in read channel chips. Powerful numerical techniques have emerged to evaluate the capacity of the magnetic recording channel. Further, improved coding/decoding methods have surfaced both for the incumbent Reed–Solomon codes and the promising low-density parity-check codes. The paper is a tutorial-like survey of these emerging technologies with the aim to propel the reader to the forefront of research and development in the areas of signal processing and coding for magnetic recording channels. </para>
Combining the Tape-Lift Method and Fourier Transform Infrared Spectroscopic Imaging for Forensic Applications (2006)

Conventional Fourier transform infrared (FT-IR) spectroscopy and microscopy have been widely used in forensic science. New opportunities exist to obtain chemical images and to enhance the spatial resolution using attenuated total reflection (ATR) FT-IR spectroscopy coupled with a focal-plane array (FPA) detector. In this paper, the sensitivity limits of FT-IR imaging using three different ATR crystals (Ge, ZnSe, and diamond) in three different optical arrangements for the detection of model particles is discussed. Model systems of ibuprofen and paracetamol particles having sizes below 32 mum were studied. The collection of drug particles was achieved with the aid of two different tapes: common adhesive tape and a film of polydimethylsiloxane (PDMS). The surface of the film with collected particles was measured directly via ATR-FT-IR imaging. Since the removal of tape from porous surfaces can be difficult, the application of micro ATR-FT-IR imaging directly to the surface of a newspaper contaminated with particles of model drugs is also discussed. In order to assess the feasibility of the chosen method in a forensic case study, the detection of diacetylmorphine hydrochloride traces in PDMS matrix and the finger surface is investigated. The scenarios considered were that of the detection of evidence collected at a crime scene with the tape lift method and the analysis of the finger of an individual after drug handling. The results show broad implications in the detection of drugs of abuse.
Recombinant Soluble, Multimeric HA and NA Exhibit Distinctive Types of Protection against Pandemic Swine-Origin 2009 A(H1N1) Influenza Virus Infection in Ferrets (2010)

ABSTRACT The emergence and subsequent swift and global spread of the swine-origin influenza virus A(H1N1) in 2009 once again emphasizes the strong need for effective vaccines that can be developed rapidly and applied safely. With this aim, we produced soluble, multimeric forms of the 2009 A(H1N1) HA (sHA 3 ) and NA (sNA 4 ) surface glycoproteins using a virus-free mammalian expression system and evaluated their efficacy as vaccines in ferrets. Immunization twice with 3.75-μg doses of these antigens elicited strong antibody responses, which were adjuvant dependent. Interestingly, coadministration of both antigens strongly enhanced the HA-specific but not the NA-specific responses. Distinct patterns of protection were observed upon challenge inoculation with the homologous H1N1 virus. Whereas vaccination with sHA 3 dramatically reduced virus replication (e.g., by lowering pulmonary titers by about 5 log 10 units), immunization with sNA 4 markedly decreased the clinical effects of infection, such as body weight loss and lung pathology. Clearly, optimal protection was achieved by the combination of the two antigens. Our observations demonstrate the great vaccine potential of multimeric HA and NA ectodomains, as these can be easily, rapidly, flexibly, and safely produced in high quantities. In particular, our study underscores the underrated importance of NA in influenza vaccination, which we found to profoundly and specifically contribute to protection by HA. Its inclusion in a vaccine is likely to reduce the HA dose required and to broaden the protective immunity.
Host Immunity Following Near-Infrared Photoimmunotherapy Is Enhanced with PD-1 Checkpoint Blockade to Eradicate Established Antigenic Tumors (2019)

Near-infrared photoimmunotherapy (NIR-PIT) induces immunogenic cell death but has mostly failed to induce durable antitumor responses in syngenic tumor mouse models. We hypothesized that adaptive immune resistance could be limiting durable responses after treatmemt with NIR-PIT. We investigated the effects of combining NIR-PIT targeting cell-surface CD44 and PD-1 blockade in multiple syngeneic tumor models. In two of three models, NIR-PIT monotherapy halted tumor growth, enhanced dendritic cell tumor infiltration, and induced <i>de novo</i> tumor antigen-specific T-cell responses absent at baseline. The addition of PD-1 blockade reversed adaptive immune resistance, resulting in both enhanced preexisting tumor antigen-specific T-cell responses and enhanced <i>de novo</i> T-cell responses induced by NIR-PIT. Enhanced immune responses correlated with shared tumor antigen expression, suggesting that antigenicity is a major determinant of response to combination NIR-PIT and PD-1 blockade. Combination treatment induced complete rejection of MC38 tumors treated with NIR-PIT, as well as untreated, distant tumors. Accordingly, tumor antigen-specific T-cell responses were measured in both treated and untreated tumors, validating the development of systemic antitumor immunity. Mice that cleared tumors resisted subsequent tumor challenge, indicating the presence of systemic immune memory. Cumulatively, these results demonstrate reversal of adaptive immune resistance following induction of innate and adaptive immunity by NIR-PIT, resulting in high rates of tumor rejection and/or significant tumor growth control in antigenic syngeneic models of cancer.
Human Papillomavirus mRNA and p16 Detection as Biomarkers for the Improved Diagnosis of Cervical Neoplasia (2008)

PubMed and OVID were interrogated with search terms "HPV RNA;" "HPV mRNA;" "HPV transcript-detection, testing, and methods;" "p16" AND "cervical cancer;" "p16" AND "CIN;" "p16" AND "histology"; "p16" AND "cytology;" "p16;" and "screening."
NGS-based deep bisulfite sequencing (2015)

We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.
Microemulsions of Perfluorinated and Semifluorinated Compounds (1994)

Perfluorocarbons combine high gas dissolving capacities with extreme chemical and biological inertness: they are good oxygen carriers in artificial blood and in liquid breathing. However fluorocarbons are highly hydrophobic molecules. To solve the problem of their transport, it is necessary to use the perfluorocarbons as an oil-in water emulsion (O/W). To avoid harsh treatment to form such emulsions and in order to have injectable "blood substitutes", microemulsions seem particularly attractive since they are fluid, transparent, thermodynamically stable microheterogeneous systems. Microemulsions, contrarily to classical emulsions, are formed spontaneously by adding suitable surfactants (or a surfactant+a cosurfactant) in appropriate proportions to a non miscible mixture of water and oil. Biocompatible O/W microemulsions are difficult to obtain because of: 1) the existing segregation between perfluorinated and hydrogenated chains, resulting, in some cases in heterogeneities or gelation phases; 2) the toxicity of some components; 3) the possible harmfulness of the dispersed system, etc... We'll discuss all the parameters involved of the microemulsification process, the nature of products, the phase diagrams, and the phase behaviors. This study will outline certain guidelines necessary for the formation of microemulsions of perfluorinated (or almost completely fluorinated) oils with perfluorinated (or partially fluorinated) surfactants.
Molecular cloning, cDNA sequence, and bacterial expression of human glutamine:fructose-6-phosphate amidotransferase. (1992)

Glutamine:fructose-6-phosphate amidotransferase (GFAT) has recently been shown to be an insulin-regulated enzyme that plays a key role in the induction of insulin resistance in cultured cells. As a first step in understanding the molecular regulation of this enzyme the human form of this enzyme has been cloned and the functional protein has been expressed in Escherichia coli. A 3.1-kilobase cDNA was isolated which contains the complete coding region of 681 amino acids. Expression of the cDNA in E. coli produced a protein of approximately 77 kDa and increased GFAT activity 4.5-fold over endogenous bacterial levels. Recombinant GFAT activity was inhibited 51% by UDP-GlcNAc whereas bacterial GFAT activity was insensitive to inhibition by UDP-GlcNAc. On the basis of these results we conclude that: 1) functional human GFAT protein was expressed, and 2) the cloned human cDNA encodes both the catalytic and regulatory domains of GFAT since the recombinant GFAT was sensitive to UDP-GlcNAc. Overall, the development of cloned GFAT molecular probes should provide new insights into the development of insulin resistance by allowing quantitation of GFAT mRNA levels in pathophysiological states such as non-insulin-dependent diabetes mellitus and obesity.
Process Analytical Chemistry (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProcess Analytical ChemistryJames B. Callis, Deborah L. Illman, and Bruce R. KowalskiCite this: Anal. Chem. 1987, 59, 9, 624A–637APublication Date (Print):May 1, 1987Publication History Published online30 May 2012Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/ac00136a723https://doi.org/10.1021/ac00136a723research-articleACS PublicationsRequest reuse permissionsArticle Views319Altmetric-Citations121LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts