gebhart/patrepeval huggingface dataset:
Esophagin and proliferating cell nuclear antigen (PCNA) are biomarkers of human esophageal neoplastic progression (2004)

PCNA and esophagin have been implicated in the multistep process of carcinogenesis, but simultaneous characterization of these proteins in the early stages of esophageal neoplastic progression has yet to be undertaken. In morphologically normal esophageal epithelium, esophagin stains the granular layer cells, principally in their cell membrane portions. PCNA, in contrast, stains the nuclei of cells in the parabasal and basal layers. We examined 201 regions from 47 patients that represented different stages of esophageal neoplasia, comprising 34 areas of normal mucosa, 18 of dysplasia in squamous epithelium (DYS/SC), 39 squamous cell carcinoma (SCCA), 29 areas of Barrett's esophagus, 48 of Barrett's dysplasia (DYS/BAR) and 33 areas of adenocarcinoma (AC). The immunostaining patterns of esophagin and PCNA were evaluated and graded for level of expression. There was loss of esophagin expression in the high- and low-grade dysplasias compared to normal epithelia. In the squamous dysplasias, there was more intense staining (of esophagin) in the atypical nuclei and superficial squamous epithelial cells than in the basal cells. PCNA staining was increased in intensity in the high-grade dysplasias relative to normal basal layer cells. Combined analysis of esophagin and PCNA appears to reveal an inverse relationship between proliferation and differentiation during esophageal neoplastic progression. Moreover, this combined staining approach also offers promise for detecting esophageal cancer in early, precancerous stages.
The influence of antiscatter grids on soft‐tissue detectability in cone‐beam computed tomography with flat‐panel detectors (2004)

The influence of antiscatter x-ray grids on image quality in cone-beam computed tomography (CT) is evaluated through broad experimental investigation for various anatomical sites (head and body), scatter conditions (scatter-to-primary ratio (SPR) ranging from approximately 10% to 150%), patient dose, and spatial resolution in three-dimensional reconstructions. Studies involved linear grids in combination with a flat-panel imager on a system for kilovoltage cone-beam CT imaging and guidance of radiation therapy. Grids were found to be effective in reducing x-ray scatter "cupping" artifacts, with heavier grids providing increased image uniformity. The system was highly robust against ring artifacts that might arise in CT reconstructions as a result of gridline shadows in the projection data. The influence of grids on soft-tissue detectability was evaluated quantitatively in terms of absolute contrast, voxel noise, and contrast-to-noise ratio (CNR) in cone-beam CT reconstructions of 16 cm "head" and 32 cm "body" cylindrical phantoms. Imaging performance was investigated qualitatively in observer preference tests based on patient images (pelvis, abdomen, and head-and-neck sites) acquired with and without antiscatter grids. The results suggest that although grids reduce scatter artifacts and improve subject contrast, there is little strong motivation for the use of grids in cone-beam CT in terms of CNR and overall image quality under most circumstances. The results highlight the tradeoffs in contrast and noise imparted by grids, showing improved image quality with grids only under specific conditions of high x-ray scatter (SPR> 100%), high imaging dose (Dcenter> 2 cGy), and low spatial resolution (voxel size > or = 1 mm).
The clinical evaluation of new drugs for sepsis. A prospective study design based on survival analysis (1993)

<h3>Objective.</h3> —To develop a survival model and severity assessment method to estimate the 28-day mortality risk for patients with sepsis syndrome entering phase 2 and 3 drug evaluations. <h3>Design.</h3> —Retrospective analysis of intensive care unit admissions with sepsis syndrome by means of log-normal regression to identify risk factors for 28-day mortality. Prospective application of the model to patients with gram-negative infection meeting sepsis syndrome criteria from separate data collection (validation group). <h3>Patients.</h3> —A total of 58 737 intensive care unit admissions at 107 hospitals in the United States and Western Europe screened to yield 1195 patients meeting entry criteria for the sepsis syndrome study for the original model; 295 hospitalized patients with gram-negative infection meeting criteria for sepsis syndrome for validation. <h3>Main Outcome Measures.</h3> —Survival time and mortality at 28 days after fulfillment of the sepsis syndrome criteria. <h3>Results.</h3> —Acute physiologic abnormalities were the most important prognostic factors influencing outcome (82% of total χ<sup>2</sup>). Specific disease resulting in intensive care unit admission and the time the patient was in the hospital and intensive care unit before qualification were also independent risks, as were age and a clinical history of cirrhosis. The model's overall classification accuracy was a Somers' Dyx of .52 (rank correlation between predicted risk and 28-day mortality) (receiver operating characteristic area, 0.76), with equal accuracy (Dyx=.59; receiver operating characteristic area, 0.80) in the independent group of patients. <h3>Conclusions.</h3> —We created an accurate independent estimate for 28-day mortality risk for patients with sepsis syndrome (severe sepsis). This estimate could improve the evaluation of new drugs by investigating whether the drug's benefit varies by patient risk and then determining the amount of benefit for individual patients. (<i>JAMA</i>. 1993;270:1233-1241)
Potential of silver nanoparticle‐coated polyurethane foam as an antibacterial water filter (2005)

Silver nanoparticles can be coated on common polyurethane (PU) foams by overnight exposure of the foams to nanoparticle solutions. Repeated washing and air-drying yields uniformly coated PU foam, which can be used as a drinking water filter where bacterial contamination of the surface water is a health risk. Nanoparticles are stable on the foam and are not washed away by water. Morphology of the foam was retained after coating. The nanoparticle binding is due to its interaction with the nitrogen atom of the PU. Online tests were conducted with a prototypical water filter. At a flow rate of 0.5 L/min, in which contact time was of the order of a second, the output count of Escherichia coli was nil when the input water had a bacterial load of 10(5) colony-forming units (CFU) per mL. Combined with the low cost and effectiveness in its applications, the technology may have large implications to developing countries.
Pseudomorphic synthesis of mesoporous zeolite Y crystals (2010)

A simple method for the conception of mesoporous zeolite Y crystals with a narrow intracrystalline mesopore size distribution is reported. It involves the pseudomorphic transformation of parent zeolite crystals by recrystallisation in the presence of surfactants, and leads to two interconnected pore systems in the zeolite crystals.
Design of quadrature modulator for digital FM signaling with digital signal processing (1982)

Abstract To introduce digital transmission into mobile communications, various digital FM methods with a modulation index of 0.5, such as TFM and GMSK, have been studied. Stable operation of these transmission systems requires high accuracy in setting the modulation index and carrier frequency in the modulator. This paper describes a quadrature modulator that provides accurate phase control using digital signal processing (DSP). GMSK is used as a modulation scheme, and its characteristics are discussed in detail. In general, the output of a modulator adapting DSP contains deviations from the ideal analog waveforms attributable to sampling, quantization and truncation errors. These errors are superposed as noise on the modulating waves and cause degradation in signal transmission. The relation between the noise spectra and the circuit parameters is first analyzed and the design procedure is then made clear in a form of a flowchart. An example of circuit parameters yielding a ratio of the signal‐to‐noise spectra of 60 dB is given. We fabricated a DPS orthogonal modulator using these parameters and confirmed that the desired modulation characteristics could be obtained.
Using real-time recognition of human-robot interaction styles for creating adaptive robot behaviour in robot-assisted play (2009)

This paper presents an application of the Cascaded Information Bottleneck Method for real-time recognition of Human-Robot Interaction styles in robot-assisted play. This method, that we have developed, is implemented here for an adaptive robot that can recognize and adapt to children's play styles in real time. The robot rewards well-balanced interaction styles and encourages children to engage in the interaction. The potential impact of such an adaptive robot in robot-assisted play for children with autism is evaluated through a study conducted with seven children with autism in a school. A statistical analysis of the results shows the positive impact of such an adaptive robot on the children's play styles and on their engagement in the interaction with the robot.
IBM Research and Columbia University TRECVID-2012 Multimedia Event Detection (MED), Multimedia Event Recounting (MER), and Semantic Indexing (SIN) Systems (2012)

For this year’s TRECVID Multimedia Event Detection task, our team studied high-level visual and audio semantic features, midlevel visual attributes, and sophisticated low-level features. In addition, a range of new modeling strategies were studied, including those that take into account temporal dynamics of event semantics, optimize fusion of system components, provide linear approximations of non-linear kernels, and generate synthetic data for the limited exemplar condition. For the Pre-Specified task, we submitted 4 runs: Run 1 involved the fusion of a broad array of sophisticated low-level features. Run 2 involved the same set of low-level features to model the events under the limited exemplar condition. Run 3 involved the fusion of all our semantic system components. Run 4 was composed of the fusion of all low-level and semantic features used in Runs 1-3, in addition to event models built from techniques for linear approximation of non-linear kernels. For Ad Hoc, we submitted 2 runs: Run 5, which was the fusion of Linear Temporal Pyramids of visual semantics, fused with event models built directly on low-level features. Run 6 was our limited exemplar run, which used both Linear Temporal Pyramids of visual semantics, as well as a method for generating synthetic training data. Our experiments suggest the following: 1) Semantic modeling improves the event modeling performance of the low-level features they are based on. 2) Mid-level visual attributes contribute complimentary information. 3) Event videos demonstate temporal patterns. 4) Linear approximation methods to nonlinear kernels perform similarly to the original non-linear ker
Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci (2017)

Open chromatin provides access to DNA-binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS). Most of the identified open chromatin regions (OCRs) are differentially accessible between neurons and non-neurons, and show enrichment with known cell type markers, promoters and enhancers. Relative to those of non-neurons, neuronal OCRs are more evolutionarily conserved and are enriched in distal regulatory elements. Transcription factor (TF) footprinting analysis identifies differences in the regulome between neuronal and non-neuronal cells and ascribes putative functional roles to a number of non-coding schizophrenia (SCZ) risk variants. Among the identified variants is a Single Nucleotide Polymorphism (SNP) proximal to the gene encoding SNX19. In vitro experiments reveal that this SNP leads to an increase in transcriptional activity. As elevated expression of SNX19 has been associated with SCZ, our data provide evidence that the identified SNP contributes to disease. These results represent the first analysis of OCRs and TF-binding sites in distinct populations of postmortem human brain cells and further our understanding of the regulome and the impact of neuropsychiatric disease-associated genetic risk variants.
Vitamin D analogues and psoriasis (1992)

Topical vitamin D analogues offer a new, effective, more convenient and generally well-tolerated option for the treatment of psoriasis. Only psoriasis vulgaris has been intensively studied, but other forms of the disease may also respond. Both calcitriol and calcipotriol have been shown to be effective in numerous clinical trials, and the latter has compared well with betamethasone valerate and short-contact dithranol in controlled studies. Their mechanism of action is not yet fully understood and may prove complex. The most important effect may be a direct regulation of keratinocyte proliferation and differentiation. However, these compounds also have potent immunological properties, and may act by inhibition of cytokine production by keratinocytes or lymphocytes. Topical application of vitamin D analogues appears generally to be remarkably safe, but hypercalcaemia and hypercalciuria may develop if large quantities are used.
Arsenic Removal from Groundwater and Its Safe Containment in a Rural Environment: Validation of a Sustainable Approach (2008)

Of all the naturally occurring groundwater contaminants, arsenic is by far the most toxic. Any large-scale treatment strategy to remove arsenic from groundwater must take into consideration safe containment of the arsenic removed with no adverse ecological impact. Currently, 175 well-head community-based arsenic removal units are in operation in remote villages of the Indian subcontinent. Approximately 150,000 villagers collect arsenic-safe potable water everyday from these units. The continued safe operation of these units has amply demonstrated that use of regenerable arsenic-selective adsorbents is quite viable in remote locations. Upon exhaustion, the adsorbents are regenerated in a central facility by a few trained villagers and reused. The process of regeneration reduces the volume of disposable arsenic-laden solids by nearly 2 orders of magnitude. Finally, the arsenic-laden solids are contained on well-aerated coarse-sand filters with minimum arsenic leaching. This disposal technique is scientifically more appropriate than dumping arsenic-loaded adsorbents in the reducing environment of landfills as currently practiced in developed countries including the United States.
Ductal carcinoma in situ of the male breast (1994)

Although the sample size was small, our patients and a review of the literature suggest that most DCIS in men is of the papillary type and that mastectomy without axillary dissection is the preferred treatment.
Efficacy and safety of avocado/soybean unsaponifiables in the treatment of symptomatic osteoarthritis of the knee and hip. A prospective, multicenter, three-month, randomized, double-blind, placebo-controlled trial. (1997)

One of the objectives of symptomatic slow-acting drugs for osteoarthritis is to reduce the need for drugs with a less favorable safety profile, mainly analgesics and nonsteroidal antiinflammatory drugs (NSAIDs). We conducted a three-month, prospective, randomized, double-blind, placebo-controlled, parallel-group trial to evaluate the efficacy of avocado/soybean unsaponifiables in terms of NSAID use reduction. Patients with primary femorotibial or hip osteoarthritis (OA) (ACR criteria and Kellgren-Lawrence radiological stage IB, II, or III) of at least six months' duration with regular pain for more than three months requiring therapy with NSAID (visual analog scale score > or = 25 mm and Lequesne's index on therapy > or = 4) were given one capsule per day of avocado/soybean unsaponifiables or a placebo for three months. During the first 45 days, patients in both groups were also given one of seven predefined NSAIDs. The primary efficacy criteria was the rate of patients taking back a NSAID and the delay before re-intake. Secondary efficacy criteria were the total dose of NSAID, overall ratings by the patient and by the physician, the visual analog scale pain score and the functional index. Of the 164 included patients, 163 were evaluable, 80 in the active drug group and 83 in the placebo group. Mean age was 62.9 +/- 8.8 years. The diagnosis was femorotibial OA in 101 patients and hip OA in 62. Data were collected on day 45 in 153 patients (77 on the active drug and 76 on the placebo). The number of patients who took back NSAID therapy was significantly smaller in the group treated by avocado/soybean unsaponifiables (33; 43.4%) than in the placebo group (53; 69.7%) (P < 0.001). Also, beyond day 54, the time spent off NSAID therapy was shorter in the placebo group. The functional index showed a significantly greater improvement in the active drug group (-2.3 +/- 2.6) than in the placebo group (-1.0 +/- 2.6) (P < 0.01). Pain scores over time were similar in the two groups. Overall patient ratings were significantly better in the active drug group (P < 0.01). Safety was oggd in both groups. After six weeks, avocado/soybean unsaponifiables reduced the need for NSAID in patients with lower limb OA.
Ultrafast dynamics of coherent optical phonons and nonequilibrium electrons in transition metals (2005)

The femtosecond optical pump-probe technique was used to study dynamics of photoexcited electrons and coherent optical phonons in transition metals Zn and Cd as a function of temperature and excitation level. The optical response in time domain is well fitted by linear combination of a damped harmonic oscillation because of excitation of coherent ${E}_{2g}$ phonon and a subpicosecond transient response due to electron-phonon thermalization. The electron-phonon thermalization time monotonically increases with temperature, consistent with the thermomodulation scenario, where at high temperatures the system can be well explained by the two-temperature model, while below $\ensuremath{\approx}50\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ the nonthermal electron model needs to be applied. As the lattice temperature increases, the damping of the coherent ${E}_{2g}$ phonon increases, while the amplitudes of both fast electronic response and the coherent ${E}_{2g}$ phonon decrease. The temperature dependence of the damping of the ${E}_{2g}$ phonon indicates that population decay of the coherent optical phonon due to anharmonic phonon-phonon coupling dominates the decay process. We present a model that accounts for the observed temperature dependence of the amplitude assuming the photoinduced absorption mechanism, where the signal amplitude is proportional to the photoinduced change in the quasiparticle density. The result that the amplitude of the ${E}_{2g}$ phonon follows the temperature dependence of the amplitude of the fast electronic transient indicates that under the resonant condition both electronic and phononic responses are proportional to the change in the dielectric function.
Planning and Optimization of Cellular Heterogeneous Networks (2016)

A Thesis Submitted to the Faculty of Graduate Studies and Research In Partial Ful llment of the Requirements For the Degree of Doctor of Philosophy in Electronic Systems Engineering University of Regina. xv, 199 p.
Identification of Mouse Hepatitis Virus Papain-Like Proteinase 2 Activity (2000)

Mouse hepatitis virus (MHV) is a 31-kb positive-strand RNA virus that is replicated in the cytoplasm of infected cells by a viral RNA-dependent RNA polymerase, termed the replicase. The replicase is encoded in the 5'-most 22 kb of the genomic RNA, which is translated to produce a polyprotein of >800 kDa. The replicase polyprotein is extensively processed by viral and perhaps cellular proteinases to give rise to a functional replicase complex. To date, two of the MHV replicase-encoded proteinases, papain-like proteinase 1 (PLP1) and the poliovirus 3C-like proteinase (3CLpro), have been shown to process the replicase polyprotein. In this report, we describe the cloning, expression, and activity of the third MHV proteinase domain, PLP2. We show that PLP2 cleaves a substrate encoding the first predicted membrane-spanning domain (MP1) of the replicase polyprotein. Cleavage of MP1 and release of a 150-kDa intermediate, p150, are likely to be important for embedding the replicase complex in cellular membranes. Using an antiserum (anti-D11) directed against the C terminus of the MP1 domain, we verified that p150 encompasses the MP1 domain and identified a 44-kDa protein (p44) as a processed product of p150. Pulse-chase experiments showed that p150 is rapidly generated in MHV-infected cells and that p44 is processed from the p150 precursor. Protease inhibitor studies revealed that unlike 3CLpro activity, PLP2 activity is not sensitive to cysteine protease inhibitor E64d. Furthermore, coexpression studies using the PLP2 domain and a substrate encoding the MP1 cleavage site showed that PLP2 acts efficiently in trans. Site-directed mutagenesis studies confirmed the identification of cysteine 1715 as a catalytic residue of PLP2. This study is the first to report enzymatic activity of the PLP2 domain and to demonstrate that three distinct viral proteinase activities process the MHV replicase polyprotein.
Dielectrophoresis of microbioparticles in water with planar and capillary quadrupole electrodes (2003)

Dielectrophoresis of single microbioparticles was measured in a planar quadrupole microelectrode (50 mum or 65 mum in working area radius) with a microscope. Carbon and polystyrene microparticles, yeast cells and DNA molecules (about 40 kbp) were adopted as a sample. Their dielectrophoretic mobilities were analysed quantitatively with their intrinsic and surface conductivity, their permittivities and their sizes as well as the conductivity and permittivity of aqueous media. Using the dielectrophoretic mobilities obtained with the planar quadrupole microelectrode, some instances of the separation performance between the microparticles were demonstrated with a fabricated capillary quadrupole microelectrode (82.5 mum in bore radius) under the field flow fractionation regime.
Halogeno‐substituted 2‐ and 3‐methylbenzo[<i>b</i>]thiophenes: Use of <sup>1</sup>H NMR spectral analysis and <sup>1</sup>H{<sup>1</sup>H} nuclear Overhauser effect for locating the halogen substituent (1985)

Abstract Thirty‐seven halogeno‐substituted 2‐ and 3‐methyl‐(or halogenomethyl)‐benzo [ b ]thiophenes, including 17 new compounds, were prepared. The constitution of 14 of these was confirmed by full analysis (LAOCOON) of their 80 MHz 1 HNMR spectra and by 1 H{ 1 H} NOE measurements. In this way a by‐product from the preparation of 4‐ and 6‐bromo‐3‐bromomethylbenzo[ b ]thiophenes was shown conclusively to be 5‐bromo‐3‐bromomethylbenzo[ b ]thiophene. The 3‐substituted benzo[ b ]thiophenes showed greater NOE enhancement factors at H‐4 than at H‐2 when the 3‐methyl or halogenomethyl substituent was irradiated.