gebhart/patrepeval huggingface dataset:
Dynamic-SCFlip Decoding of Polar Codes (2018)

This paper proposes a generalization of the recently introduced successive cancellation flip (SCFlip) decoding of polar codes, characterized by a number of extra decoding attempts, where one or several positions are flipped from the standard SC decoding. To make such an approach effective, we first introduce the concept of higher order bit flips and propose a new metric to determine the bit flips that are more likely to correct the trajectory of the SC decoding. We then propose a generalized SCFlip decoding algorithm, referred to as dynamic-SCFlip (D-SCFlip), which dynamically builds a list of candidate bit flips, while guaranteeing that the next attempt has the highest probability of success among the remaining ones. Simulation results show that D-SCFlip is an effective alternative to SC-list decoding of polar codes, by providing very good error correcting performance, with an average computation complexity close to the one of the SC decoder.
Source description and sampling techniques in PEREGRINE Monte Carlo calculations of dose distributions for radiation oncology (1997)

We outline the techniques used within PEREGRINE, a 3D Monte Carlo code calculation system, to model the photon output from medical accelerators. We discuss the methods used to reduce the phase-space data to a form that is accurately and efficiently sampled.
CD34+AC133+VEGFR-2+ Cells Are Primitive Hematopoietic Progenitors, Not Functional Endothelial Progenitor Cells. (2006)

Abstract Endothelial progenitor cells (EPCs) are currently used for angiogenic therapies or as biomarkers to assess cardiovascular disease risk and progression. However, there is no uniform definition of an EPC, which complicates interpretation of prior EPC studies. EPCs are primarily defined by expression of cell surface antigens. The most widely cited definition of an EPC is a cell which co-expresses CD34, AC133 and VEGFR-2. Importantly, these antigens are also expressed on the most primitive population of hematopoietic progenitor cells (HPCs), including high proliferative potential- (HPP-) and low proliferative potential-colony forming cells (LPP-CFCs). Remarkably, CD34+AC133+VEGFR-2+ cells have never been isolated and plated in endothelial cell (EC) or hematopoietic cell clonogenic assays to determine what cell progeny can be derived from a CD34+AC133+VEGFR-2+ cell. Utilizing human umbilical cord blood (CB), an enriched source of both EPCs and HPCs, we isolated and purified CD34+AC133+VEGFR-2+ cells by FACS and assayed for the presence of clonogenic endothelial CFCs (ECFCs) plus HPP- and LPP-CFCs. Surprisingly, CD34+AC133+VEGFR-2+ cells do not form ECFCs under any culture conditions previously described for outgrowth of EPCs. However, consistent with a HPC phenotype, CD34+AC133+VEGFR-2+ cells formed both HPP- and LPP-CFCs in multiple independent assays. In addition, all CD34+AC133+VEGFR-2+ cells were shown to co-express the specific hematopoietic cell surface antigen, CD45, which is not present on ECs. Based on this information, we plated CD34+CD45+ or CD34+CD45− cells to determine if EPCs could be separated from HPCs on the basis of CD45 expression. In multiple independent assays, CD34+CD45+ cells consistently formed both HPP- and LPP-CFCs but not EC colonies. In contrast, CD34+CD45− cells form EC colonies but not hematopoietic cell colonies. Taken together, these data demonstrate that circulating CD34+AC133+VEGFR-2+ cells are HPCs and the biologic mechanism for their correlation with cardiovascular disease needs to be re-examined. Furthermore, studies focused on determining the angiogenic potential of CD34+CD45− cells are needed given that this cell population harbors ECFCs.
Novel Quinazoline-Based Compounds Impair Prostate Tumorigenesis by Targeting Tumor Vascularity (2007)

Previous evidence showed the ability of the quinazoline-based alpha(1)-adrenoreceptor antagonist doxazosin to suppress prostate tumor growth via apoptosis. In this study, we carried out structural optimization of the chemical nucleus of doxazosin and a subsequent structure-function analysis toward the development of a novel class of apoptosis-inducing and angiogenesis-targeting agents. Our lead compound, DZ-50, was effective at reducing endothelial cell viability via a nonapoptotic mechanism. Treatment with DZ-50 effectively prevented in vitro tube formation and in vivo chorioallantoic membrane vessel development. Confocal microscopy revealed a significantly reduced ability of tumor cells to attach to extracellular matrix and migrate through endothelial cells in the presence of DZ-50. In vivo tumorigenicty studies using two androgen-independent human prostate cancer xenografts, PC-3 and DU-145, showed that DZ-50 treatment leads to significant suppression of tumorigenic growth. Exposure to the drug at the time of tumor cell inoculation led to prevention of prostate cancer initiation. Furthermore, DZ-50 resulted in a reduced formation of prostate-tumor derived metastatic lesions to the lungs in an in vivo spontaneous metastasis assay. Thus, our drug discovery approach led to the development of a class of lead (quinazoline-based) compounds with higher potency than doxazosin in suppressing prostate growth by targeting tissue vascularity. This new class of quinazoline-based compounds provides considerable promise as antitumor drugs for the treatment of advanced prostate cancer.
Automatic stent strut detection in intravascular OCT images using image processing and classification technique (2013)

Intravascular OCT (iOCT) is an imaging modality with ideal resolution and contrast to provide accurate in vivo assessments of tissue healing following stent implantation. Our Cardiovascular Imaging Core Laboratory has served >20 international stent clinical trials with >2000 stents analyzed. Each stent requires 6-16hrs of manual analysis time and we are developing highly automated software to reduce this extreme effort. Using classification technique, physically meaningful image features, forward feature selection to limit overtraining, and leave-one-stent-out cross validation, we detected stent struts. To determine tissue coverage areas, we estimated stent “contours” by fitting detected struts and interpolation points from linearly interpolated tissue depths to a periodic cubic spline. Tissue coverage area was obtained by subtracting lumen area from the stent area. Detection was compared against manual analysis of 40 pullbacks. We obtained recall = 90±3% and precision = 89±6%. When taking struts deemed not bright enough for manual analysis into consideration, precision improved to 94±6%. This approached inter-observer variability (recall = 93%, precision = 96%). Differences in stent and tissue coverage areas are 0.12 ± 0.41 mm<sup>2</sup> and 0.09 ± 0.42 mm<sup>2</sup>, respectively. We are developing software which will enable visualization, review, and editing of automated results, so as to provide a comprehensive stent analysis package. This should enable better and cheaper stent clinical trials, so that manufacturers can optimize the myriad of parameters (drug, coverage, bioresorbable versus metal, etc.) for stent design.
Gadolinium-loaded Plastic Scintillators for Thermal Neutron Detection using Compensation (2016)

Plastic scintillator loading with gadolinium-rich organometallic complexes shows a high potential for the deployment of efficient and cost-effective neutron detectors. Due to the low-energy photon and electron signature of thermal neutron capture by Gd-155 and Gd-157, alternative treatment to pulse-shape discrimination has to be proposed in order to display a count rate. This paper discloses the principle of a compensation method applied to a two-scintillator system: a detection scintillator interacts with photon and fast neutron radiation and is loaded with gadolinium organometallic compound to become a thermal neutron absorber, while a not-gadolinium loaded compensation scintillator solely interacts with the fast neutron and photon part of incident radiation. After the nonlinear smoothing of the counting signals, a hypothesis test determines whether the resulting count rate post-background response compensation falls into statistical fluctuations or provides a robust indication of neutron activity. Laboratory samples are tested under both photon and neutron irradiations, allowing the authors to investigate the performance of the overall detection system in terms of sensitivity and detection limits, especially with regards to a similar-active volume He-3 based commercial counter. The study reveals satisfactory figures of merit in terms of sensitivity and directs future investigation toward promising paths.
Fluorogenic Probes with Substitutions at the 2 and 7 Positions of Cephalosporin are Highly BlaC‐Specific for Rapid <i>Mycobacterium tuberculosis</i> Detection (2014)

Current methods for the detection of Mycobacterium tuberculosis (Mtb) are either time consuming or require expensive instruments and are thus are not suitable for point-of-care diagnosis. The design, synthesis, and evaluation of fluorogenic probes with high specificity for BlaC, a biomarker expressed by Mtb, are described. The fluorogenic probe CDG-3 is based on cephalosporin with substitutions at the 2 and 7 positions and it demonstrates over 120,000-fold selectivity for BlaC over TEM-1 Bla, the most common β-lactamase. CDG-3 can detect 10 colony-forming units of the attenuated Mycobacterium bovis strain BCG in human sputum in the presence of high levels of contaminating β-lactamases expressed by other clinically prevalent bacterial strains. In a trial with 50 clinical samples, CDG-3 detected tuberculosis with 90% sensitivity and 73% specificity relative to Mtb culture within one hour, thus demonstrating its potential as a low-cost point-of-care test for use in resource-limited areas.
Mesenchymal stem cells as a novel vaccine platform (2012)

Vaccines are the most efficient and cost-effective means of preventing infectious disease. However, traditional vaccine approaches have thus far failed to provide protection against human immunodeficiency virus (HIV), tuberculosis, malaria, and many other diseases. New approaches to vaccine development are needed to address some of these intractable problems. In this report, we review the literature identifying stimulatory effects of mesenchymal stem cells (MSC) on immune responses and explore the potential for MSC as a novel, universal vaccination platform. MSC are unique bone marrow-derived multipotent progenitor cells that are presently being exploited as gene therapy vectors for a variety of conditions, including cancer and autoimmune diseases. Although MSC are predominantly known for anti-inflammatory properties during allogeneic MSC transplant, there is evidence that MSC can actually promote adaptive immunity under certain settings. MSC have also demonstrated some success in anti-cancer therapeutic vaccines and anti-microbial prophylactic vaccines, as we report, for the first time, the ability of modified MSC to express and secrete a viral antigen that stimulates antigen-specific antibody production in vivo. We hypothesize that the unique properties of modified MSC may enable MSC to serve as an unconventional but innovative, vaccine platform. Such a platform would be capable of expressing hundreds of proteins, thereby generating a broad array of epitopes with correct post-translational processing, mimicking natural infection. By stimulating immunity to a combination of epitopes, it may be possible to develop prophylactic and even therapeutic vaccines to tackle major health problems including those of non-microbial and microbial origin, including cancer, or an infectious disease like HIV, where traditional vaccination approaches have failed.
Switchable circular beamsplitter using a dual-frequency cholesteric liquid crystal (1998)

The cholesteric liquid crystal (LC) has a chiral structure defined by pitch length. This unique structure reflects one handedness of circularly polarized light and is used as a circular polarizer. This polarizer can be actively switched between a state that is transparent to light of all polarizations and another state that in only transmissive to one handedness of circularly polarized light. The dual- frequency material is used to reduce the relaxation time. The dual-frequency circular polarizer can be switched from the transparent homeotropic texture by a low frequency driving signal, and switched to the reflecting planar texture by a high frequency signal. This polarizer functions as a switchable shutter for which we have characterized switching process, relaxation time, polarization purity, and extinction ratio.
Abstract 019: Oxidized LDL and AGE-LDL in Circulating Immune Complexes Strongly Predict Progression of Carotid IMT in Type 1 Diabetes (2012)

Many studies have demonstrated a relationship between modified LDL and cardiovascular disease. Nonetheless, few studies have examined the relationship between modified LDL immune complexes (IC) and cardiovascular disease, even though the majority of modified LDL in circulation is bound to IC. We report the relationship between circulating concentrations of IC of oxidized LDL (oxLDL-IC), malondialdehyde-LDL (MDA-LDL-IC) and advanced glycation end products-LDL (AGE-LDL-IC) and progression of atherosclerosis over a 12 year period in individuals with type 1 diabetes. OxLDL-IC, AGE-LDL-IC and MDA-LDL-IC levels were measured in a subgroup of 459 patients participating in the Diabetes Control and Complications Trial (DCCT) and it’s follow up study the Epidemiology of Diabetes Interventions and Complications (EDIC). Internal carotid intima-medial thickness (IMT) was measured at EDIC follow-up years 1, 6 and 12. Levels of oxLDL-IC, AGE-LDL-IC and MDA-LDL-IC were moderately correlated with lipid levels [i.e., rho<0.32], but not with age. Modified LDL-IC significantly predicted having elevated internal carotid IMT (i.e., IMT ≥1.00 mm) as well as progression of IMT defined as being in the upper quintile of change from EDIC year 1 to 12 after adjusting for DCCT treatment group [intensive vs. conventional], retinopathy cohort [primary prevention vs. secondary intervention], age, gender, diabetes duration, albumin excretion rate, LDL, HDL, SBP, smoking status and IMT reader (Table). Relative to those in the lowest quartile, individuals in the upper quartile of oxLDL-IC had a 3.7-fold increased odds (CI: 1.72, 7.94) of having IMT ≥ 1.00 mm and had a 6.1-fold increased odds (CI: 2.57, 14.6) of having significant IMT progression. Parallel odds ratios for AGE-LDL-IC were 3.26 (CI: 1.57, 6.79) and 5.31 (CI: 2.23, 12.6), while results for MDA-LDL-IC were not as strong. Our study indicates that high levels of oxLDL-IC and AGE-LDL-IC are important predictors of carotid intima-medial thickening in patients with type 1 diabetes.
Identification of Novel High-Frequency DNA Methylation Changes in Breast Cancer (2007)

Recent data have revealed that epigenetic alterations, including DNA methylation and chromatin structure changes, are among the earliest molecular abnormalities to occur during tumorigenesis. The inherent thermodynamic stability of cytosine methylation and the apparent high specificity of the alterations for disease may accelerate the development of powerful molecular diagnostics for cancer. We report a genome-wide analysis of DNA methylation alterations in breast cancer. The approach efficiently identified a large collection of novel differentially DNA methylated loci (approximately 200), a subset of which was independently validated across a panel of over 230 clinical samples. The differential cytosine methylation events were independent of patient age, tumor stage, estrogen receptor status or family history of breast cancer. The power of the global approach for discovery is underscored by the identification of a single differentially methylated locus, associated with the GHSR gene, capable of distinguishing infiltrating ductal breast carcinoma from normal and benign breast tissues with a sensitivity and specificity of 90% and 96%, respectively. Notably, the frequency of these molecular abnormalities in breast tumors substantially exceeds the frequency of any other single genetic or epigenetic change reported to date. The discovery of over 50 novel DNA methylation-based biomarkers of breast cancer may provide new routes for development of DNA methylation-based diagnostics and prognostics, as well as reveal epigenetically regulated mechanism involved in breast tumorigenesis.
A Novel Non-Linear Ion Mirror with Only Three Elements (2000)

A novel tubular ion mirror has been designed for reflectron time-of-flight mass spectrometry (TOF-MS). This design consists of only three cylindrical elements. With this mirror, an electric field is achieved that is non-linear along the mirror axis and has improved off-axis homogeneity compared with conventional simple geometry ion mirrors. The practical operation of this mirror is simpler than that of conventional diaphragm ion mirrors. Design parameters, including the relative lengths and voltages of the three elements, can be determined empirically. Once the mirror depth dimensions have been implemented, the voltages of the middle and rear elements are the only adjustable parameters. The electric field achieved by the mirror deviates only slightly from a linear mirror with constant field strength. The second-order deviation curve reveals two regions of curvature; all ions are turned around in the second curvature region. A plot of arrival time vs ion kinetic energy has a flattened “S” shape. The aspects of this shape are affected by the voltages of the middle and rear elements. SIMION 7 simulation demonstrates that this new non-linear ion mirror can perform second-order kinetic energy correction for large kinetic energy variation (33%) and substantial beam dimensions. Both the ion kinetic energy variation and the mirror element voltages affect the mass resolution obtained with the mirror. Ion trajectory simulations with a 10 mm diameter beam from a standard, two-field source predict that baseline resolution can be 16,000, 7600 and 1200 for 15%, 26% and 33% kinetic energy variations, respectively.
Resonant Second-Order Nonlinear Optical Processes in Quantum Cascade Lasers (2003)

We demonstrate an efficient intracavity nonlinear interaction of laser modes in a specially adapted quantum cascade laser. A two-wavelength quantum cascade laser structure emitting at wavelengths of 7.1 and 9.5 micrometer included cascaded resonant optical intersubband transitions in an intracavity configuration leading to resonantly enhanced sum-frequency and second-harmonic generation at wavelengths of 4.1, 3.6, and 4.7 micrometer respectively. Laser peak optical powers of 60 and 80 mW resulted in 30 nW of sum-frequency signal and 10-15 nW of second-harmonic signal, both in good agreement with theoretical calculations.
Sialosylated Lewisx in the sera of cancer patients detected by a cell-binding inhibition assay. (1985)

A new cell-binding inhibition assay to detect tumor-associated antigens in sera was developed. This assay determined that sialosylated Lewisx, as detected by the CSLEX1 monoclonal antibody, is present in the sera of 95% of patients with advanced lung adenocarcinomas. Sera with inhibition titers of 1:16 or higher were presumed to contain sialosylated Lewisx. Tests of over 900 sera samples from both malignant and benign disease patients yielded the following percentages of positive inhibition: lung cancers, 43.8%; stomach cancer, 26.0%; colon cancer, 44.4%; gall bladder and bile duct cancers, 47.8%; pancreas cancer, 37.5%; breast cancer, 26.7%; cancers of the hematopoietic system, 2.9%; benign diseases, 0.9% (332 sera); and normal healthy donors, 0.7% (280 sera). Within the lung cancer group, 95% of the sera from 21 advanced (Stages III and IV) nontreated adenocarcinoma patients gave positive results with high inhibition titers, whereas only 27% of sera from treated advanced adenocarcinoma patients yielded positive results. The sensitivity of the cell-binding inhibition assay is similar to those of the solid-phase radioimmunosandwich and reverse passive-hemagglutination assays. Reproducibility tests yielded an r value of 0.90. These results suggest that this simple cell-binding inhibition assay could be applied with monoclonal antibodies, such as CSLEX1, to monitor cancer.
Apparatus and method for determining a likely word sequence from labels generated by an acoustic processor (1990)

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Mining Hardware Assertions With Guidance From Static Analysis (2013)

We present GoldMine, a methodology for generating assertions automatically in hardware. Our method involves a combination of data mining and static analysis of the register transfer level (RTL) design. The RTL design is first simulated to generate data about the design's dynamic behavior. The generated data is then mined for “candidate assertions” that are likely to be invariants. The data mining algorithm is a decision-tree-based supervised learning algorithm. These candidate assertions are then passed through a formal verification engine to filter out the spurious candidates. The assertions that are attested as true by the formal engine are system invariants. These are then evaluated by a process of designer ranking that is provided as feedback to the data mining engine. We demonstrate the scalability of GoldMine by showing assertion generation of the RTL of Sun's OpenSparc T2 many-threaded processor. Our results show that GoldMine can generate complex, high coverage assertions for sequential as well as combinational designs in RTL, thereby minimizing human effort in this process. GoldMine assertions distill the random input stimulus space and can be used for calibrating directed tests. They can be used in a regression test suite of an evolving RTL. They are also useful in providing differing perspectives from the designer, as well as hints to designers for manually writing assertions.
Liposome-Encapsulated Amphotericin B for Treatment of Disseminated Candidiasis in Neutropenic Mice (1984)

The relative efficacies of free amphotericin B (Amp B) and liposome-encapsulated Amp B (L-AmpB) in the treatment of established Candida albicans infection in mice rendered neutropenic with cyclophosphamide were studied. AmpB was entrapped in multilamellar liposomes composed of dimyristoyl phosphatidylcholine and dimyristoyl phosphatidylglycerol in a molar ratio of 7:3. Infected mice treated with single doses of 3 mg L-AmpB/kg of body weight had an increased survival time compared with those injected with either single (dose, 0.8 mg/kg) or multiple doses (dose, 0.8 mg/kg daily for five days) of free AmpB. When treatment was delayed beyond three days postinfection, neither single nor multiple doses of free AmpB resulted in increased survival, whereas treatment with single-dose L-AmpB (dose, 4 mg/kg) showed efficacy when delayed as much as four days postinfection. Five days postinfection only higher doses (dose, 5.6 mg-11.2 mg/kg) of L-AmpB improved survival time and the renal impairment present in the infected animals. These data provided a rational basis for using high-dose L-AmpB to treat fungal diseases in humans, particularly in neutropenic patients.