gebhart/patrepeval huggingface dataset:
Rapid Multiplexed Immunoassay for Simultaneous Serodiagnosis of HIV-1 and Coinfections (2011)

Diagnosis of opportunistic infections in HIV-infected individuals remains a major public health challenge, particularly in resource-limited settings. Here, we describe a rapid diagnostic system that delivers a panel of serologic immunoassay results using a single drop of blood, serum, or plasma. The system consists of disposable cartridges and a simple reader instrument, based on an innovative implementation of planar waveguide imaging technology. The cartridge incorporates a microarray of recombinant antigens and antibody controls in a fluidic channel, providing multiple parallel fluorescence immunoassay results for a single sample. This study demonstrates system performance by delivering antibody (Ab) reactivity results simultaneously for multiple antigens of HIV-1, Treponema pallidum (syphilis), and hepatitis C virus (HCV) in a collection of clinical serum, plasma, and whole-blood samples. By plotting antibody reactivity (fluorescence intensity) for known positive and negative samples, empirical reactivity cutoff values were defined. The HIV-1 assay shows 100% agreement with known seroreactivity for a collection of 82 HIV Ab-positive and 142 HIV Ab-negative samples, including multiple samples with HCV and syphilis coinfection. The treponema-specific syphilis assay correctly identifies 67 of 68 T. pallidum Ab-positive and 100 of 102 T. pallidum Ab-negative samples, and the HCV assay correctly identifies 59 of 60 HCV Ab-positive and 120 of 121 HCV Ab-negative samples. Multiplexed assay performance for whole-blood samples is also demonstrated. The ability to diagnose HIV and opportunistic infections simultaneously at the point of care should lead to more effective therapy decisions and improved linkage to care.
ROBOTIC CALIBRATION ISSUES: ACCURACY, REPEATABILITY AND CALIBRATION (2000)

The groundwork for a contact calibration methodology using a touch probe is developed for an articulated robot arm. This solution is framed within current calibration and metrology issues in robotics based upon the kinematical mechanical design of a serial link manipulator. Accuracy, repeatability, and resolution are explored and a simplistic approach is taken. This exercise is intended to lay the groundwork for exploring the feasibility of integrating a commercial product such as a force sensor or touch trigger probe on the end of a robot arm. Candidate processes and/or applications are identified. Findings indicate that an in- process contact calibration methodology that is accurate, repeatable, and cost effective would be a desirable solution.
STUDIES ON EXPERIMENTAL HYPERTENSION (1937)

Excision of the thoracic portion of the splanchnic nerves and the lower four dorsal sympathetic ganglia on both sides failed to prevent the development of persistent hypertension which, in dogs, follows the production of renal ischemia by partial clamping of the renal arteries (1). In dogs with this type of experimental renal hypertension existent for varying lengths of time (up to about 4 years), excision of the splanchnic nerves and the lower four dorsal sympathetic ganglia failed to effect any degree of permanent lowering of the blood pressure. For the dog, at least, these results tend to minimize the importance of the splanchnic vasomotor mechanism in the pathogenesis of renal hypertension. This is in agreement with the conclusions of Prinzmetal and Wilson (6) and of Pickering (7) about the part played by the vasomotor system in human hypertension. It is also in agreement with the work of Page (8), and of Collins (9), who showed that in dogs excision of the extrinsic renal nerves alone does not prevent experimental hypertension due to renal ischemia. Although the results of this investigation fail to give experimental support for the operation that is being practised on human beings with hypertension, yet they do not necessarily controvert the reports of beneficial effects in some cases of human hypertension. Further study of the effects on man is necessary before the results of this operation can be adequately evaluated.
Preparation of Cystamine Core Dendrimer and Antibody–Dendrimer Conjugates for MRI Angiography (2011)

Herein we report the preparation along with the in vivo and in vitro MRI characterization of two generation four and five cystamine core dendrimers loaded with thirty and fifty-eight derivatized Gd-DOTA (G4SS30, G5SS58) respectively. Likewise the development and characterization of two half-dendrimers conjugated to the F(ab')(2) fragment of the monoclonal antibody (mAb) panitumumab functionalized with a maleimide conjugation functional group site (Ab-(G4S15)(4), Ab-(G5S29)(4)) are also described. The in vitro molar relaxivity of the Ab-(G4S15)(4) conjugate, measured at pH 7.4, 22 °C, and 3T showed a moderate increase in relaxivity as compared to Magnevist (6.7 vs 4.0 mM(-1) s(-1)) while the Ab-(G5S29)(4) conjugate was 2-fold higher (9.1 vs 4.0 mM(-1) s(-1)). The data showed that only a high injection dose (0.050 mmol Gd(3+)/kg) produced a detectable contrast enhanced contrast for the Ab-(G4S15)(4) conjugate while a lower dose (0.035 mmol Gd(3+)/kg) was sufficient for the Ab-(G5S29)(4) conjugate. The antibody-SMCC conjugate was purified by a Sephadex G-100 column, and the antibody-dendrimer-based agents were purified by spin filtration using a Centricon filter (50,000 MCO). The protein assay coupled with cysteine and Ellman's assay indicated an antibody to dendrimer ratio of 1:4. The in vivo blood clearance half-lives of the four agents measured at the jugular vein were ~12-22 min.
Single nucleus analysis of the chromatin landscape in mouse forebrain development (2017)

ABSTRACT Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes 1–4 . However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin 5 and is optimized for nuclei from flash-frozen primary tissue samples (snATAC-seq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specific cis regulatory sequences and infer potential master transcriptional regulators of each cell population. Our results demonstrate the feasibility of a general approach for identifying cell-type-specific cis regulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals.
Fumaric Acid Therapy in Psoriasis: A Double-Blind Comparison between Fumaric Acid Compound Therapy and Monotherapy with Dimethylfumaric Acid Ester (1990)

In a 4-month double-blind study the effects of dimethylfumaric acid esters (DMFAE-EC) and DMFAE plus salts of monoethylfumaric acid esters (fumaric acid combination, FAC-EC) in enteric-coated tablets were compared in 22 respectively 23 patients with psoriasis. In both groups about 50% showed a considerable improvement, i.e. the initial score was more than halved. The therapeutic effects showed no significant differences in both groups with respect to the total psoriasis score or the different parameters. In the FAC-EC group the effects were obtained more rapidly. Most frequently observed side effects in both groups were flushings, stomachache and diarrhea. Due to these complaints 3 respectively 8 patients discontinued therapy. Eosinophilia, leukopenia and lymphopenia were the most frequently observed differences in lab tests. It was concluded that FAC-EC had no significantly better effect than monotherapy with DMFAE-EC. Moreover, enteric coating of the tablets did not prevent stomach complaints. Until more information has been obtained about the pharmacokinetics, the toxicity and optimal composition of the drug, the fumaric acid therapy in psoriasis should be seen as experimental.
Formation of polarized beams in chains of dielectric spheres and cylinders (2013)

Using numerical modeling, it is shown that chains of dielectric spheres and cylinders act as polarizers. The mechanism is based on gradual filtering of periodically focused modes with a certain polarization propagating with minimal losses due to Brewster angles conditions, whereas orthogonally polarized modes are strongly attenuated. It is shown that chains of cylinders filter linearly polarized beams, whereas chains of spheres filter radially polarized beams. In the geometrical optics limit, we show that in a range of sphere refractive indices 1.68-1.80 a degree of radial polarization in excess of 0.9 can be obtained in 10-sphere-long chains.
High-Level Dystrophin Expression after Adenovirus-Mediated Dystrophin Minigene Transfer to Skeletal Muscle of Dystrophic Dogs: Prolongation of Expression with Immunosuppression (1998)

Replication-deficient adenovirus vectors (AdV) have been successfully used to transfer a truncated human dystrophin cDNA to skeletal muscle of dystrophin-deficient mdx mice. A dystrophin-deficient golden retriever dog model (GRMD) has been identified, which, unlike the mouse model, leads to a clinicopathological phenotype similar to that of Duchenne muscular dystrophy (DMD). We show for the first time that high-level dystrophin expression in skeletal muscle of GRMD dogs can be achieved by AdV-mediated gene transfer. However, a humoral and cellular immune response of the host against antigens of viral and transgene origin (similar to that occurring in mdx mice after AdV-mediated dystrophin gene transfer) leads to a decline of dystrophin expression over a 2-month period. Immunosuppression by cyclosporin significantly prolonged transgene expression. The GRMD model may help to solve the open questions pertaining to dystrophin gene transfer such as systemic delivery and improvement of muscle function before human trials for gene replacement therapy in DMD may be considered.
High-Power Broadly Tunable Electrooptic Frequency Comb Generator (2013)

Broadband traveling-wave electrooptic modulators made of lithium niobate have reached a high level of technological maturity. They can provide simultaneously low Vπ, sustain high power (both optical and RF) and yet provide low propagation loss. By combining together these features, we present a high-power handling, broadly tunable, electrooptic frequency comb generator. The device produces between 60 and 75 lines within -10 dB bandwidth over its full tuning range-from 6 to 18 GHz-and can handle up to 1 W of optical input power. This optical frequency comb platform is very well suited for applications in RF photonics and optical communications that require independent RF and optical tuning as well as high-repetition rates but moderate bandwidth.
Prevention of low density lipoprotein aggregation by high density lipoprotein or apolipoprotein A-I. (1990)

We have shown previously that low density lipoprotein (LDL) subjected to vortexing forms self-aggregates that are avidly phagocytosed by macrophages. That phagocytic uptake is mediated by the LDL receptor. We now show that LDL self-aggregation is strongly inhibited (80-95%) by the presence of high density lipoprotein (HDL) or apolipoprotein (apo) A-I. Another type of LDL aggregation, namely that induced by incubation of LDL with phospholipase C, was also markedly inhibited by HDL or apoA-I. The aggregation of LDL induced by vortexing was not inhibited by 2.5 M NaCl, and apoA-I was still able to block LDL aggregation at this high salt concentration, strongly suggesting hydrophobic interactions as the basis for the effect of apoA-I. The fact that apoA-I protected against LDL aggregation induced by two apparently quite different procedures suggests that the aggregation in these two cases has common features. We propose that these forms of LDL aggregation result from the exposure of hydrophobic domains normally masked in LDL and that the LDL-LDL association occurs when these domains interact. ApoA-I, because of its amphipathic character, is able to interact with the exposed hydrophobic domains of LDL and thus block the intermolecular interactions that cause aggregation.
Low frequency of p16/CDKN2A methylation in sporadic melanoma: comparative approaches for methylation analysis of primary tumors. (1997)

Methylation of the 5' CpG island of the p16 tumor suppressor gene represents one possible mechanism for inactivation of this cell cycle regulatory gene that is also a melanoma predisposition locus. We have investigated the potential contribution of somatic silencing of the p16 gene by DNA methylation in 30 cases of sporadic cutaneous melanoma. The methylation status of the 5' CpG island of p16 was initially determined by Southern analysis and then reevaluated (in a blinded manner) using methylation-specific PCR, methylation-sensitive single nucleotide primer extension, and bisulfite genomic sequencing. All methodologies yielded concordant results, and significant levels of methylation were observed in 3 of the 30 (10%) melanoma DNAs analyzed. Of the three tumors found to be methylated, two were also positive for LOH on 9p21 (where the p16 gene resides), implying that both p16 alleles were inactivated, one via deletion and the other via methylation-associated transcriptional silencing. The association between methylation and transcriptional silencing of p16 was also further supported by inducing p16 expression with a DNA demethylating agent (5-aza-2'-deoxycytidine) in a melanoma cell line known to harbor a methylated p16 allele. Although methylation-associated gene silencing does not represent a common mechanism for p16 inactivation in sporadic melanoma, our findings provide support that PCR-based techniques, such as methylation-specific PCR and methylation-sensitive single nucleotide primer extension, can be reliably used for the accurate detection and quantitation of aberrant levels of DNA methylation in tumor specimens.
Effects of Hibernation or Cryopreservation on the Survival and Integration of Striatal Grafts Placed in the Ibotenate-Lesioned Rat Caudate-Putamen (1995)

Tissue storage prior to intracerebral transplantation would represent a major advantage when conducting clinical transplantation trials in that the procurement of the embryonic donor tissue and the timing of neurosurgery could be planned more efficiently. In the present study, the effects of storing rat embryonic striatal tissue at either +4°C or below freezing temperature prior to grafting to the adult striatum, were assessed with regard to transplant survival, morphology and integration. Eleven days following a unilateral injection of ibotenic acid into the head of the caudate-putamen, a control group of rats received grafts of striatal primordium prepared immediately after dissection from rat embryos (embryonic day 16). A second group of rat embryonic striatal tissue was stored at 4°C (hibernation) for 5 days and then transplanted. A third group of the striatal donor tissue was cryopreserved in liquid nitrogen for 5 days before implantation surgery. Six to seven weeks following transplantation surgery, the grafts were analysed in brain sections processed for acetylcholinesterase histochemistry, DARPP-32 (dopamine and cyclic AMP regulated phosphoprotein with a molecular weight of 32 kDa) and tyrosine hydroxylase (TH) immunocytochemistry. The mean total graft volume and the relative size of the AChE-positive regions were not significantly different between the three groups. Striatal-specific graft regions, positively stained for AChE and DARPP-32, generally exhibited TH immunoreactivity, suggesting that they had received dopaminergic afferents from the host brain. We conclude that embryonic rat striatal tissue can be cryopreserved or hibernated over 5 days without significant impairment in the yield of striatal neurons following intrastriatal implantation and without markedly affecting transplant morphology.
Heterogeneity of Autoantibodies against Thyroid Peroxidase in Autoimmune Thyroid Disease: Evidence against Antibodies Directly Inhibiting Peroxidase Activity as Regulatory Factors in Thyroid Hormone Metabolism (1991)

The close relationship between thyroid microsomal antigen and thyroid peroxidase (TPO) is now well established. The present study evaluates the significance of autoantibodies against TPO (anti-TPO-Abs) in the various forms and stages of autoimmune thyroid disease with respect to a possible heterogeneous nature and particularly to their influence on TPO activity. When measured by a RIA using purified human TPO, anti-TPO-Abs were highly correlated with microsomal antibodies determined by enyzme-linked immunosorbant assay (r = 0.96; P less than 0.0001) and with the results of a TPO immunoprecipitation assay using crude microsomal preparations (r = 0.76; P less than 0.001). Relating the results of these assays to the reactivities of patients' sera with thyroid microsomes in immunoblot under nonreducing and reducing conditions, discordant results could be observed in a few cases. Further analysis of these data indicate a heterogeneous nature of anti-TPO-Abs, which react with at least two antigenic domains of the TPO molecule. The comparative analysis of patients with hyperthyroid Graves' disease, patients with Graves' disease in clinical remission, and patients with hypothyroid Hashimoto's thyroiditis revealed no significant differences in the antibody spectrum. When evaluating the direct influence of anti-TPO-Abs on the activity of TPO under a rigorous methodological approach, we found no significant inhibition of the enzymatic activity by any of the sera investigated from patients with autoimmune thyroid disease compared to that in sera from normal controls. In conclusion, the data indicate a heterogeneous nature of anti-TPO-Abs. The spectrum of antigenic epitopes recognized by anti-TPO-Abs seems not to be significantly different in the various forms and stages of autoimmune thyroid disease. The lack of an inhibitory effect of autoantibodies on TPO activity argues against direct binding of autoantibodies to the enzymatic sites of TPO and indicates that they are not important factors in producing thyroid dysfunction in autoimmune thyroid disease.
Dansylcadaverine inhibits internalization of 125I-epidermal growth factor in BALB 3T3 cells. (1980)

The binding and internalization of 125I-epidermal growth factor (125I-EGF) was studied in cultures of BALB 3T3 cells using a novel method that involved removal of cell-surface hormone by treatment with acetic acid under conditions that did not remove internalized hormone. In control cultures, 125I-EGF initially bound to its receptor on the plasma membrane and then was rapidly internalized. After 30 min, only 15% of the cell-bound hormone remained on the surface. In contrast, cultures treated with dansylcadaverine retained 82% of the cell-bound hormone on the cell surface. We propose that dansylcadaverine inhibits EGF internalization by preventing it from clustering in clathrin-coated pits.
A Lagrangian Slug Capturing Scheme for Gas-Liquid Flows in Pipes (2007)

In this thesis a new Lagrangian numerical scheme for the simulation of gas-liquid flows in pipelines is presented. Based on an approximate two-fluid model, this new scheme, called LASSI (Lagrangian Approximate Scheme for Slug Initiation) is dedicated to the modelling of the transition between stratified and slug flow. It is able to capture directly the slug initiation process and to track the motion of every single slug in the pipe without numerical diffusion. It can thus be qualified as a slug capturing and slug tracking scheme.\n\nThe scheme is based on the decoupling between the fast pressure dynamics governing the motion of the slugs and the much slower liquid transport in the bubbles. The liquid motion in the bubbles is then approximately modelled by a modified version of the shallow water equations, in which the influence of the Bernoulli suction force is subtracted from the traditional hydrodynamical term. The fully Lagrangian structure of the scheme makes it possible to accurately capture the transport of the fast interfacial waves whose growth can eventually result in a slug initiation.\n\nThe model predictions are compared with some experimental results obtained in the NTNU multiphase flow laboratory or taken from the literature. Several flow conditions are considered, in particular the case of hydrodynamic slugging in near-horizontal flows, slugging in an upwards pipe, severe slugging, and slugging triggered by fast transients. Numerical predictions are also compared with theoretical considerations regarding the stability of stratified flow.
Anti-tau oligomers passive vaccination for the treatment of Alzheimer disease (2010)

The aggregation and accumulation of the microtubule-associated protein (Tau) is a pathological hallmark of Alzheimer's disease (AD) and many neurodegenerative diseases. Despite the poor correlation between neurofirillary tangles (NFTs) and disease progression, and evidence showing, that neuronal loss in AD actually precedes NFTs formation research until recently focused on them and other large meta-stable inclusions composed of aggregated hyperphosphorylated tau protein. Lately, the significance and toxicity of NFTs has been challenged and new aggregated tau entity has emerged as the true pathogenic species in tauopathies and a possible mediator of Aβ toxicity in AD. Tau intermediate aggregate (tau oligomers; aggregates of an intermediate that is between monomers and NFTs in size) can cause neurodegeneration and memory impairment in the absence of Aβ. This exciting body of evidence includes results from human brain samples, transgenic mouse and cell-based studies. Despite extensive efforts to develop a safe and efficacious vaccine for AD using Aβ peptide as an immunogen in active vaccination approaches or anti Aβ antibodies for passive vaccination, success has been modest. Nonetheless, these studies have produced a wealth of fundamental knowledge that has potential to application to the development of a tau-based immunotherapy. Herein, I discuss the evidence supporting the critical role of tau oligomers in AD, the potential and challenges for targeting them by immunotherapy as a novel approach for AD treatment.
Algebraic Formulation and Program Generation of Three-Dimensional Hilbert Space-Filling Curves. (2004)

Abstract: We use a tensor product based multi-linear algebra theory to formulate three-dimensional Hilbert space-filling curves. A 3-D Hilbert space-filling curve is specified as a permutation which rearranges three-dimensional 2 n 2 n 2 n data elements stored in the row major order as in C language or the column major order as in FORTRAN language to the order of traversing a 3-D Hilbert space-filling curve. The tensor product formulation of 3-D Hilbert space-filling curves uses stride permutation, reverse permutation, and Gray permutation. We present both recursive and iterative tensor product formulas of 3-D Hilbert space-filling curves. In addition, we derive a tensor product formula of inverse 3-D Hilbert space-filling curve permutation. The tensor product formulas are directly translated into computer programs which can be used in various applications. The process of program generation is explained in the paper.
[Pharmacokinetics of crocetin in rats]. (2002)

This method is quick, precise and reliable. Crocetin was shown to be quickly absorbed in rats.