gebhart/patrepeval huggingface dataset:
Quantitative High-Resolution Renal Perfusion Imaging Using 3-Dimensional Through-Time Radial Generalized Autocalibrating Partially Parallel Acquisition (2014)

Highly undersampled data were successfully reconstructed with 3D through-time radial GRAPPA to achieve a high-resolution 3-dimensional renal DCE-MRI examination. The acquisition was completely free breathing, and the images were registered to compensate for respiratory motion. This allowed for an accurate high-resolution 3D quantitative renal functional mapping of perfusion and filtration parameters.
A tunable dual-band dual-element MIMO antenna system with compact size (2012)

We present the design and fabrication of a novel dual-band 2-element printed MIMO antenna system for LTE and 4G wireless handsets. It covers a lower band of 840-905 MHz with a -6 dB bandwidth of 55 MHz. The higher band covers 2990-3210 MHz with a -6 dB bandwidth of 220 MHz. The MIMO antenna system is tunable via two control arms. The 2-element MIMO antenna system occupies 67×50×0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> of an FR-4 substrate. The effect of the tuning arms on the resonance frequency as well as the bandwidths of the two bands is investigated. Simulation and measurement results are presented. The maximum measured gain approximately 0 dBi at 880 MHz and 1.5 dBi at 3100 MHz.
Advantages of a single-cycle production assay to study cell culture-adaptive mutations of hepatitis C virus (2008)

The JFH1 strain of hepatitis C virus (HCV) is unique among HCV isolates, in that the wild-type virus can traverse the entire replication cycle in cultured cells. However, without adaptive mutations, only low levels of infectious virus are produced. In the present study, the effects of five mutations that were selected during serial passage in Huh-7.5 cells were studied. Recombinant genomes containing all five mutations produced 3-4 logs more infectious virions than did wild type. Neither a coding mutation in NS5A nor a silent mutation in E2 was adaptive, whereas coding mutations in E2, p7, and NS2 all increased virus production. A single-cycle replication assay in CD81-deficient cells was developed to study more precisely the effect of the adaptive mutations. The E2 mutation had minimal effect on the amount of infectious virus released but probably enhanced entry into cells. In contrast, both the p7 and NS2 mutations independently increased the amount of virus released.
Shigella Outer Membrane Protein PSSP-1 Is Broadly Protective against Shigella Infection (2015)

In developing countries, Shigella is a primary cause of diarrhea in infants and young children. Although antibiotic therapy is an effective treatment for shigellosis, therapeutic options are narrowing due to the emergence of antibiotic resistance. Thus, preventive vaccination could become the most efficacious approach for controlling shigellosis. We have identified several conserved protein antigens that are shared by multiple Shigella serotypes and species. Among these, one antigen induced cross-protection against experimental shigellosis, and we have named it pan-Shigella surface protein 1 (PSSP-1). PSSP-1-induced protection requires a mucosal administration route and coadministration of an adjuvant. When PSSP-1 was administered intranasally, it induced cross-protection against Shigella flexneri serotypes 2a, 5a, and 6, Shigella boydii, Shigella sonnei, and Shigella dysenteriae serotype 1. Intradermally administered PSSP-1 induced strong serum antibody responses but failed to induce protection in the mouse lung pneumonia model. In contrast, intranasal administration elicited efficient local and systemic antibody responses and production of interleukin 17A and gamma interferon. Interestingly, blood samples from patients with recent-onset shigellosis showed variable but significant mucosal antibody responses to other conserved Shigella protein antigens but not to PSSP-1. We suggest that PSSP-1 is a promising antigen for a broadly protective vaccine against Shigella.
Frequent loss of expression of the cyclin-dependent kinase inhibitor p27 in epithelial ovarian cancer. (1999)

p27Kip1 is a member of the Cip1/Kip1 family of cyclin-dependent kinase inhibitors and is a potential tumor suppressor gene. Low levels of p27 are associated with poor prognosis in a variety of tumors, including breast, colon, prostate, and lung carcinomas. In the present study, p27 protein expression was investigated by immunohistochemistry and Western blot analysis in a series of 82 epithelial ovarian tumors [16 classified as low malignant potential (LMP) and 66 classified as primary ovarian adenocarcinomas]. Immunohistochemical analysis revealed frequent loss of p27 expression in primary ovarian adenocarcinomas (33%), with respect to LMP tumors (6%; P = 0.0009). In addition to nuclear staining, cytoplasmic localization of p27 was noted in 45 (55%) of 82 cases. p27 levels inversely correlated with cdk2 kinase activity in a representative subset of tumors. When the clinical outcome of the patients was evaluated in relationship to p27 status, we observed a significant correlation between presence of p27 staining and a longer time to progression (P = 0.032 by log-rank test). These data indicate that loss of p27 is a frequent event in ovarian carcinomas as compared with LMP tumors, suggesting that these tumor types may have different pathogenesis. p27 levels may also represent a useful prognostic marker for predicting disease recurrence in primary ovarian carcinomas.
Effect of phenylglyoxal-modified alpha2-antiplasmin on urokinase-induced fibrinolysis. (1998)

One of the functions of activated blood clotting factor XIII (FXIIIa) is the crosslinking of alpha2-antiplasmin (alpha2AP) to fibrin. This process results in localization and concentration of alpha2AP throughout fibrin, thereby making fibrin more resistant to digestion by plasmin. We reasoned that competition by chemically-modified inactive alpha2AP (mod alpha2AP) with native alpha2AP would diminish the resistance of fibrin to digestion by plasmin. Mod alpha2AP was prepared by treating native alpha2AP with an Arg-specific reagent, phenylglyoxal. An average of four of the total nineteen Arg residues in alpha2AP reacted with phenylglyoxal and resulted in complete loss of plasmin inhibitory activity; however, mod alpha2AP competed effectively with native alpha2AP for becoming crosslinked to fibrin by FXIIIa catalysis. In the presence of mod alpha2AP, urokinase (UK)-induced plasma clot lysis time shortened significantly. Mod alpha2AP enhanced UK-induced clot lysis in a whole blood system as shown by the similarities of rates of clot lysis for a mixture of 20 U/ml UK and 1.5 microM mod alpha2AP versus that induced by 100 U/ml UK without mod alpha2AP. Less fibrinogenolysis occurred in whole blood when mod alpha2AP was present since much lower UK concentrations were needed to achieve the same level of fibrinolysis than when only native alpha2AP was present. Our results indicate that mod alpha2AP enhances UK-induced fibrinolysis by competitive inhibition of factor XIIIa-mediated incorporation of native alpha2AP into fibrin.
Amylodextrins containing beta-glucan from oat flours and bran (1993)

Amylodextrins with soluble beta-glucan contents as high as 10% were prepared from milled oat flours and bran. The level of enzymatic conversion was measured by high performance liquid chromatography and gel permeation chromatography. The large molecular weight amylodextrin fragments containing the beta-glucan from low level amylolytic conversions were measured by gel permeation chromatography. The different elution times of the two separate enzyme conversion mixture components suggest different modes of enzyme actions. Lower molecular weight fractions are produced by the action of Bacillus licheniformis alpha-amylase in contrast to the action of B. stearothermophilus alpha-amylase, due possibly to dissimilar enzyme dosages. Comparisons of the amylodextrin compositions produced by B. stearothermophilus alpha-amylase and B. licheniformis alpha-amylase systems at intermediate conversion levels revealed that the B. stearothermophilus alpha-amylase gave much larger quantities of the maltohexaose component than the B. licheniformis alpha-amylase.
Porous Hollow Fiber Anti-Solvent Crystallization-Based Continuous Method of Polymer Coating on Submicron and Nanoparticles (2020)

Using porous hollow fiber membranes, systems/methods for continuously synthesizing polymer-coated particles by anti-solvent crystallization are provided. The disclosed systems/methods provide for synthesis of polymer-coated drug particles/crystals from solutions of the polymer and the drug particles in suspension by exposing the solution to an anti-solvent through a porous hollow fiber device. A feed solution of a coating polymer with suspended drug particles can be exposed to an anti-solvent through hollow fiber pores, thereby causing the polymer to precipitate on and coat the drug particles. In addition, a feed solution of a coating polymer with drug in solution can be exposed to an anti-solvent through hollow fiber pores, thereby causing the drug to crystallize from the solution and the polymer to precipitate/coat the drug. Results indicate that a uniformly coated, free-flowing product may be developed in this advantageous porous hollow fiber anti-solvent crystallization method. The coated drug particles can be used for controlled release of the drug, and the molecule and the crystal structure are not affected by the process.
Angelman syndrome patient neuron screen identifies a potent and selective clinical ASO targeting <i>UBE3A-ATS</i> with long lasting effect in cynomolgus monkey (2022)

Abstract Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A with no available treatment. Restoring UBE3A levels via downregulation of the paternally cis-acting long non-coding antisense transcript (UBE3A-ATS) is a potential disease modifying. Developing molecules targeting human UBE3A-ATS is challenging because it is expressed only in neurons and lacks animal species sequence conservation. To overcome this, we performed a library screen of locked-nucleic acid (LNA)-modified antisense oligonucleotides (ASOs) on AS patient-derived neurons, identifying initial sequences. Further optimization led to the identification of the ASO, RO7248824, which selectively and potently reduces UBE3A-ATS, while concomitantly upregulating the UBE3A mRNA and protein. These properties held true in both human AS patient- and neurotypical-, as well as cynomolgus monkey-derived neurons. In vivo use of tool molecules in wild-type (WT) and AS Ube3am-/p+ mice, revealed a steep relationship between UBE3A-ATS knock-down and UBE3A mRNA/protein upregulation, whereby an almost 90% downregulation was needed to achieve a 50% upregulation, respectively. This relationship was confirmed in cynomolgus monkeys. Whereby, repeated lumbar intrathecal administrations of RO7248824 was well tolerated without adverse in-life effects or tissue pathology and produced a robust, long lasting (up to 3 months) paternal reactivation of UBE3A mRNA/protein across key monkey brain regions. Our results demonstrate that AS human pluripotent stem cell neurons serve as an excellent translational tool and furthermore LNA-modified ASOs exhibit excellent drug-like properties. Sustained efficacy translated to infrequent, intrathecal dosing and serves as the basis for the ongoing clinical development of RO7248824 for AS. Graphical Abstract Graphical abstract. From AS patient blood to a neuronal screen, identifies clinical ASO with excellent in vivo properties. ( 1 ) Patients were recruited. ( 2 ) Whereby blood was reprogrammed into hIPSC and subsequently differentiated into neurons. ( 3 ) ASOs were designed and screened on human neurons to downregulate the UBE3A-ATS likely via directed RNase H Cleavage of Nascent Transcripts. ( 4a ) RO7248824 was identified that potently and selective reduces UBE3A-ATS, concomitantly with upregulating the UBE3A sense transcript and protein which was used for in vitro pk/pd. ( 4b ) In parallel tool murine ASO were used demonstrate in vivo POC.(5) Pivotal nonhuman primate studies to monitor safety and predict the human dose. (6) RO7248824 is in AS clinical trial . One Sentence Summary From angelman syndrome human neuron screen to cynomolgus monkey proof of concept identifies the clinical molecule RO7248824
Identifying Mood Episodes Using Dialogue Features from Clinical Interviews (2019)

Bipolar disorder, a severe chronic mental illness characterized by pathological mood swings from depression to mania, requires ongoing symptom severity tracking to both guide and measure treatments that are critical for maintaining long-term health. Mental health professionals assess symptom severity through semi-structured clinical interviews. During these interviews, they observe their patients' spoken behaviors, including both what the patients say and how they say it. In this work, we move beyond acoustic and lexical information, investigating how higher-level interactive patterns also change during mood episodes. We then perform a secondary analysis, asking if these interactive patterns, measured through dialogue features, can be used in conjunction with acoustic features to automatically recognize mood episodes. Our results show that it is beneficial to consider dialogue features when analyzing and building automated systems for predicting and monitoring mood.
Demosaicing: heterogeneity projection hard-decision adaptive interpolation using spectral-spatial correlation (2006)

A novel heterogeneity-projection hard-decision adaptive interpolation (HPHD-AI) algorithm is proposed in this paper for color reproduction from Bayer mosaic images. The proposed algorithm aims to estimate the optimal interpolation direction and perform hard-decision interpolation, in which the decision is made before interpolation. To do so, a new heterogeneity-projection scheme based on spectral-spatial correlation is proposed to decide the best interpolation direction from the original mosaic image directly. Exploiting the proposed heterogeneity-projection scheme, a hard-decision rule can be designed easily to perform the interpolation. We have compared this technique with three recently proposed demosaicing techniques: Lu's, Gunturk's and Li's methods, by utilizing twenty-five natural images from Kodak PhotoCD. The experimental results show that HPHD-AI outperforms all of them in both PSNR values and S-CIELab ▵<i>Ε</i>*<sub>ab</sub> measures.
Autoantibodies against platelet membrane glycoproteins in children with acute and chronic immune thrombocytopenic purpura (1989)

The autoimmune nature of chronic immune thrombocytopenic purpura (ITP) in adults is widely accepted. In contrast, the pathogenetic mechanism in acute and chronic ITP in children is not known. In this report, we studied 39 children with destructive thrombocytopenia, 15 patients with acute ITP and 24 patients with chronic ITP. Platelet autoantibodies to platelet glycoprotein IIb/IIIa were detected in 14 of 24 patients (58.3%) in the chronic ITP group and in four of 15 (26.7%) with acute ITP. Binding ratios (+/- SD) of positive patients were significantly greater (P = .01) in chronic ITP (8.0 +/- 9.1) when compared with those of acute ITP where the binding ratios were only slightly above the normal range (1.9 +/- 0.4). The results show that autoantibodies against platelet glycoproteins are present in the majority of children with chronic ITP confirming the autoimmune nature of this disorder. The minimal elevation seen in the positive children with acute ITP suggests a different pathogenetic mechanism. These data suggest that this approach may be useful in differentiating acute from chronic ITP patients.
Thermoacoustic tomography with integrating area and line detectors (2005)

Thermoacoustic (optoacoustic, photoacoustic) tomography is based on the generation of acoustic waves by illumination of a sample with a short electromagnetic pulse. The absorption density inside the sample is reconstructed from the acoustic pressure measured outside the illuminated sample. So far measurement data have been collected with small detectors as approximations of point detectors. Here, a novel measurement setup applying integrating detectors (e.g., lines or planes made of piezoelectric films) is presented. That way, the pressure is integrated along one or two dimensions, enabling the use of numerically efficient algorithms, such as algorithms for the inverse radon transformation, for thermoacoustic tomography. To reconstruct a three-dimensional sample, either an area detector has to be moved tangential around a sphere that encloses the sample or an array of line detectors is rotated around a single axis. The line detectors can be focused on cross sections perpendicular to the rotation axis using a synthetic aperture (SAFT) or by scanning with a cylindrical lens detector. Measurements were made with piezoelectric polyvinylidene fluoride film detectors and evaluated by comparison with numerical simulations. The resolution achieved in the resulting tomography images is demonstrated on the example of the reconstructed cross section of a grape.
Blood-brain barrier transport using a high-affinity, brain-selective VNAR (Variable Domain of New Antigen Receptor) antibody targeting transferrin receptor 1 (2019)

ABSTRACT Transfer across the blood-brain barrier (BBB) remains a significant hurdle for the development of biopharmaceuticals with therapeutic effects within the central nervous system. We established a functional selection method to identify high-affinity single domain antibodies to the transferrin receptor 1 (TfR1) with efficient biotherapeutic delivery across the BBB. Methods A synthetic phage display library based on the variable domain of new antigen receptor (VNAR) was used for in vitro selection against recombinant human TfR1 ectodomain (rh-TfR1-ECD) followed by in vivo selection in mouse for brain parenchyma penetrating antibodies. Phage formatted VNARs cross-reactive to recombinant human and mouse TfR1-ECD were fused to Fc domain of human IgG1 (hFc) and tested for TfR1-ECD binding by ELISA and surface plasmon resonance. The pharmacokinetics and biodistribution of VNAR-hFcs were studied in mice by ELISA and immunolabeling following intravenous (IV) injection and cardiac perfusion. Functional activity was measured by body temperature reduction following the IV injection of neurotensin fused to a TXB2-hFc (TXB2-hFc-NT). Results TXB2 was identified as a high-affinity, species cross-reactive VNAR antibody against TfR1-ECD, that does not to compete with transferrin or ferritin for receptor binding. IV dosing of TXB2-hFc at 25 nmol/kg (1.875 mg/kg) in mice resulted in rapid binding to brain capillaries with subsequent transport into the brain parenchyma and specific uptake into TfR1-positive neurons. Likewise, IV dosing of TXB2-hFc-NT at 25 nmol/kg resulted in a rapid and reversible pharmacological response as measured by body temperature reduction. TXB2-hFc did not elicit any acute adverse reactions, bind or deplete circulating reticulocytes or reduce BBB-expressed endogenous TfR1 in mice. There was no evidence of target-mediated clearance or accumulation in peripheral organs except lung. Conclusions A species cross-reactive and brain-selective VNAR antibody to TfR1 was identified by a combination of in vitro and in vivo phage selection. As a high-affinity, bivalent Fc fusion protein, TXB2 rapidly crossed the BBB and exhibited a favorable pharmacokinetic and safety profile and can be readily adapted to carry a wide variety of biotherapeutics from blood to brain.
Hydramycin, a new antitumor antibiotic. Taxonomy, isolation, physico-chemical properties, structure and biological activity. (1991)

A new antitumor antibiotic hydramycin was isolated from the fermentation broth of Streptomyces violaceus P950-4 (ATCC 53807). It showed potent antibacterial and cytotoxic activity and increased the survival time of mice inoculated with P388 leukemia. A new structure related to the pluramycin group antibiotics was assigned by its spectroscopic experiments.
Nonseparable Radial Frame Multiresolution Analysis in Multidimensions (2003)

Abstract In this article we present a nonseparable multiresolution structure based on frames which is defined by radial frame scaling functions. The Fourier transform of these functions is the indicator (characteristic) function of a measurable set. We also construct the resulting frame multiwavelets, which can be isotropic as well. Our construction can be carried out in any number of dimensions and for a big variety of dilation matrices.
Type inference for datalog with complex type hierarchies (2010)

Type inference for Datalog can be understood as the problem of mapping programs to a sublanguage for which containment is decidable. To wit, given a program in Datalog, a schema describing the types of extensional relations, and a user-supplied set of facts about the basic types (stating conditions such as disjointness, implication or equivalence), we aim to infer an over-approximation of the semantics of the program, which should be expressible in a suitable sublanguage of Datalog. We argue that Datalog with monadic extensionals is an appropriate choice for that sublanguage of types, and we present an inference algorithm. The inference algorithm is proved sound, and we also show that it infers the tightest possible over-approximation for a large class of Datalog programs. Furthermore, we present a practical containment check for a large subset of our type language. The crux of that containment check is a novel generalisation of Quine's procedure for computing prime implicants. The type system has been implemented in a state-of-the-art industrial database system, and we report on experiments with this implementation.
Cytotoxic T‐cell clone against rectal carcinoma induced by stimulation of a patient's peripheral blood mononuclear cells with autologous cultured tumor cells (1997)

In an effort to establish cytolytic T lymphocytes (CTLs) against colorectal carcinoma (CRC) by stimulating patients' lymphocytes with autologous tumor cells, we used peripheral blood mononuclear cells (PBMC) from a patient with minimal residual rectal carcinoma following removal of the primary lesion and involved regional lymph nodes as a source to generate CTLs in culture. A CTL line and clone were established from the patient's PBMC following stimulation of PBMC with autologous, cultured tumor cells and interleukin-2. The CTL line and the clone consisted predominantly of CD4+ lymphocytes. The CTL clone expressed two T-cell receptor variable alpha chains (V alpha11 and V alpha22) and one beta chain (Vbeta14). The cytokine secretion pattern of the CTL line was of the Th1-type. Both the CTL line and the clone lysed the autologous rectal carcinoma cells, but not the allogeneic, partially human lymphocyte antigen (HLA)-matched or nonmatched CRC cells, autologous Epstein-Barr virus-transformed B cells, K562 (natural killer target) cells or Daudi (lymphokine-activated killer target) cells. Lysis of autologous tumor cells most likely was HLA class I-restricted. Our unique success in generating CTLs against this tumor type may rest in the inclusion of a patient with minimal residual, rather than advanced, disease.
An artificial sphincter using shape memory alloy actuators. (2000)

This paper describes the development of an artificial sphincter using shape memory alloy (SMA). With the artificial sphincter it is expected to enable the active bowel movement of patients with the lack of anal sphincters due to inborn intestinal atresia or medical operations of an artificial anus. The SMA actuator has the function of a sphincter muscle; keeping the artificial anus closed at the body temperature and opening it by heating. Investigations on the thermomechanical properties of the actuator have been carried out. Animal experiments have also been done, and the results showed potentially applicability of the artificial sphincter for implantation in living bodies.