gebhart/patrepeval huggingface dataset:
SU-FF-T-198: A Comprehensive MLC Dose Model: Use in Dynamic IMRT Verification Using An EPID (2009)

Purpose: To report on our development of a comprehensive MLC model that incorporates interleaf leakage, transmission, and tongue-and-groove effects, which can be used to accurately predict the a-Si electronic portal imaging device's (EPID's) dose image for use in pretreatment IMRT verification. This would remedy the fact that our current clinical TPS (Eclipse v 8.1) only models a portion of the MLC's dose effects which can lead to large verification errors. Method and Materials: EPID images were acquired using Varian's Varis Portal (aS500) Vision's service monitor (IAS3) using a 6 MV beam at 400 MU/min and ‘integrated image’ mode. Images from sweeping-window and closed-MLC fields were used to determine MLC interleaf leakage and transmission. Sweeping-checker fields were used to characterize the shape of the MLC penumbra perpendicular to the travel direction, which was used to model the MLC's tongue-and-groove effects. In-house software (MATLAB) was used to generate a 2D correction map which, when multiplied by the original predicted TPS images produces a corrected predicted image, which was then used for IMRT verification. Results: Dynamic IMRT EPID verifications with and without correction maps applied were performed. Verification of a worst-case test field yielded a gamma-map for the uncorrected case where 42.8% of the pixels had gamma-values of > 1 (3mm and 3%). After correcting for MLC effects, only 4.2% of the pixels have gamma-values > 1. After applying the correction to a clinical head-and neck IMRT field, the percentage of pixels failing the gamma analysis was reduced from 3.6% to 0.25%. Conclusion: By implementing a correction map for the predicted EPID image, an accurate prediction of the measured EPID image can be generated. Therefore, this technique may significantly help the interpretation of verifications yielding marginal or unacceptable gamma-map results by isolating the source of the discrepancies between predicted and measured images.
Helicobacter pylori and Antibiotic Resistance, A Continuing and Intractable Problem (2016)

Helicobacter pylori, a human pathogen with a high global prevalence, is the causative pathogen for multiple gastrointestinal diseases, especially chronic gastritis, peptic ulcers, gastric mucosa-associated lymphoid tissue lymphoma, and gastric malignancies. Antibiotic therapies remain the mainstay for H. pylori eradication; however, this strategy is hampered by the emergence and spread of H. pylori antibiotic resistance. Exploring the mechanistic basis of this resistance is becoming one of the major research questions in contemporary biomedical research, as such knowledge could be exploited to devise novel rational avenues for counteracting the existing resistance and devising strategies to avoid the development of a novel anti-H. pylori medication. Encouragingly, important progress in this field has been made recently. Here, we attempt to review the current state and progress with respect to the molecular mechanism of antibiotic resistance for H. pylori. A picture is emerging in which mutations of various genes in H. pylori, resulting in decreased membrane permeability, altered oxidation-reduction potential, and a more efficient efflux pump system. The increased knowledge on these mechanisms produces hope that antibiotic resistance in H. pylori can ultimately be countered.
Current Practices in Safety Pharmacology (2010)

Abstract Safety pharmacology is branch of study that attempts to understand the human risk posed by exposure to the promising new drug. The field of safety pharmacology allows for the study of new and marketed therapeutic agents aimed at identifying their pharmacodynamic properties. This article offers an overview of existing practices in safety pharmacology, including ionic current assays and repolarization (APD) assays.
Enterprise services (2002)

Examining the emerging field of Web Services and how it is integrated into existing enterprise infrastructures.
Lignin-derived phenolic compounds in different types of peat profiles in Hokkaido, Japan (1995)

Abstract How is the composition of organic matter of peat related to the environment of the peatland? How does it change with the process of peat formation? How does it change when the peatland is affected by the lowering of the ground water table? What are the relationships between the organic matter composition of peat and peatland plants? These are problems which we attempted to address in this study. Peat samples were collected layer-wise from four different peat profiles formed under different environments in Hokkaido, Japan, The basic properties of the peat profiles, i.e. major peat-forming plants, contents of carbon and nitrogen, C/N ratio, pH, degree of humification analyzed by several methods, were described and compared. As one of the keys to answer the above-mentioned questions, we selected lignin-derived phenolic compounds that are released by CuO-NaOH oxidation. The composition of the phenolic compounds varied remarkably among the peat layers differing in peat-forming plants and in the mode of accumulation. The classification into high-moor, transitional moor, and low-moor peat was not sufficient to explain the composition of the phenolic compounds of peat. Differences in major peat-forming plants, i.e. sphagnum moss or sedges in high-moor peat, and Phragmites or Alnus in low-moor peat exerted significant effects on the phenolic composition.
Vibrational spectroscopy: a clinical tool for cancer diagnostics (2009)

Vibrational spectroscopy techniques have demonstrated potential to provide non-destructive, rapid, clinically relevant diagnostic information. Early detection is the most important factor in the prevention of cancer. Raman and infrared spectroscopy enable the biochemical signatures from biological tissues to be extracted and analysed. In conjunction with advanced chemometrics such measurements can contribute to the diagnostic assessment of biological material. This paper also illustrates the complementary advantage of using Raman and FTIR spectroscopy technologies together. Clinical requirements are increasingly met by technological developments which show promise to become a clinical reality. This review summarises recent advances in vibrational spectroscopy and their impact on the diagnosis of cancer.
Responsive copolymers for enhanced petroleum recovery. Quarterly technical progress report, June 23--September 21, 1994 (1994)

Summaries are given on the technical progress on three tasks of this project. Monomer and polymer synthesis discusses the preparation of 1(7-aminoheptyloxymethyl)naphthalene and poly(maleic anhydride-alt-ethyl vinyl ether). Task 2, Characterization of molecular structure, discusses terpolymer solution preparation, UV analysis, fluorescence analysis, low angle laser light scattering, and viscometry. The paper discusses the effects of hydrophobic groups, the effect of pH, the effect of electrolyte addition, and photophysical studies. Task 3, Solution properties, describes the factorial experimental design for characterizing polymer solutions by light scattering, the light scattering test model, orthogonal factorial test design, linear regression in coded space, confidence level for coded space test mode coefficients, coefficients of the real space test model, and surface analysis of the model equations.
Whole Bladder Mechanics during Filling (1999)

In addition to molecular and cellular properties, elemental and whole bladder properties are important to the function of the bladder during filling. The bladder pressure volume filling relation is dependent on all aspects of bladder tissue. Elemental mechanics properties include elasticity, viscoelasticity, and plastic deformation of bladder tissue. Whole bladder properties include bladder shape, mass, and distension. This paper reviews work on mathematical model aimed at determining the effect of whole bladder properties on bladder filling mechanics and outlines directions for the future.
Expression of gelatinases A and B, and TIMPs 1 and 2 during corneal wound healing. (1998)

Unlike gelatinase A, gelatinase B is expressed exclusively by migrating basal epithelial cells after wounding. The matrix metalloproteinase-tissue inhibitor of metalloproteinase (MMP)/TIMP systems may play an important role in the early stages of corneal wound healing after excimer laser keratectomy.
Speech Emotion Recognition using Gaussian Mixture Vector Autoregressive Models (2007)

It is believed that modeling temporal structure of the speech data may be useful for the problem of speech emotion recognition (T. Nwe et al., 2003). In this paper, Gaussian mixture vector autoregressive model is proposed as a statistical classifier for this task. The main motivation behind using such a model is its ability to model the dependency among extracted speech feature vectors as well as the multi-modality in their distribution. When applied to the Berlin emotional speech database, the proposed technique provides a classification accuracy of 76% versus 71% for the hidden Markov model, 67% for the k-nearest neighbors, 55% for feed-forward neural networks. The model gives also better discrimination between high-arousal, low arousal, and neutral emotions than the HMM.
Automated lung segmentation in magnetic resonance images (2005)

Segmentation of the lungs within magnetic resonance (MR) scans is a necessary preprocessing step in the computerized analysis of thoracic MR images. This task is complicated by potentially significant cardiac and pulmonary motion artifacts, partial volume effect, and morphological deformation from disease. We have developed an automated segmentation method to account for these complications. First, the thorax is segmented using a threshold obtained from analysis of the cumulative gray-level histogram constructed along a diagonal line through the center of the image. Next two separate lung-thresholded images are created. The first lung-thresholded image is created using histogram-based gray-level thresholding techniques applied to the segmented thorax. To include lung areas that may be adversely affected by artifact or disease, a second lung-thresholded image is created by applying a grayscale erosion operator to the first lung-thresholded image. After a rolling ball filter is applied to the lung contour to eliminate non-lung pixels from the thresholded lung regions, a logical OR operation is used to combine the two lung-thresholded images into the final segmented lung regions. Modifications to this approach were required to properly segment sections in the lung bases. In a preliminary evaluation, the automated method was applied to 10 MR scans, an observer evaluated the segmented lung regions using a five-point scale (“highly accurate segmentation” to “highly inaccurate segmentation”). Eighty-five percent of the segmented lung regions were rated as highly or moderately accurate.
Data from Fine-Mapping <i>IGF1</i> and Prostate Cancer Risk in African Americans: The Multiethnic Cohort Study (2023)

&lt;div&gt;Abstract&lt;p&gt;Genetic variation at insulin-like growth factor 1 (&lt;i&gt;IGF1&lt;/i&gt;) has been linked to prostate cancer risk. However, the specific predisposing variants have not been identified. In this study, we fine-mapped the &lt;i&gt;IGF1&lt;/i&gt; locus for prostate cancer risk in African Americans. We conducted targeted Roche GS-Junior 454 resequencing of a 156-kb region of &lt;i&gt;IGF1&lt;/i&gt; in 80 African American aggressive prostate cancer cases. Three hundred and thirty-four &lt;i&gt;IGF1&lt;/i&gt; SNPs were examined for their association with prostate cancer risk in 1,000 African American prostate cancer cases and 991 controls. The top associated SNP in African Americans, rs148371593, was examined in an additional 3,465 prostate cancer cases and 3,425 controls of non-African American ancestry—European Americans, Japanese Americans, Latinos, and Native Hawaiians. The overall association of 334 &lt;i&gt;IGF1&lt;/i&gt; SNPs and prostate cancer risk was assessed using logistic kernel-machine methods. The association between each SNP and prostate cancer risk was evaluated through unconditional logistic regression. A false discovery rate threshold of &lt;i&gt;q&lt;/i&gt; &lt; 0.1 was used to determine statistical significance of associations. We identified 8 novel &lt;i&gt;IGF1&lt;/i&gt; SNPs. The cumulative effect of the 334 &lt;i&gt;IGF1&lt;/i&gt; SNPs was not associated with prostate cancer risk (&lt;i&gt;P&lt;/i&gt; = 0.13) in African Americans. Twenty SNPs were nominally associated with prostate cancer at &lt;i&gt;P&lt;/i&gt; &lt; 0.05. The top associated SNP among African Americans, rs148371593 [minor allele frequency (MAF) = 0.03; &lt;i&gt;P&lt;/i&gt; = 0.0014; &lt;i&gt;q&lt;/i&gt; &gt; 0.1], did not reach our criterion of statistical significance. This polymorphism was rare in non-African Americans (MAF &lt; 0.003) and was not associated with prostate cancer risk (&lt;i&gt;P&lt;/i&gt; = 0.98). Our findings do not support the role of &lt;i&gt;IGF1&lt;/i&gt; variants and prostate cancer risk among African Americans. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 23(9); 1928–32. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
On surrogate methods for detecting lateral gene transfer (2001)

Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees.
Soil nitrate nitrogen levels as an index of nitrogen fertilizer needs of sugarbeets (1971)

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Sparse Bayesian infinite factor models (2011)

We focus on sparse modelling of high-dimensional covariance matrices using Bayesian latent factor models. We propose a multiplicative gamma process shrinkage prior on the factor loadings which allows introduction of infinitely many factors, with the loadings increasingly shrunk towards zero as the column index increases. We use our prior on a parameter-expanded loading matrix to avoid the order dependence typical in factor analysis models and develop an efficient Gibbs sampler that scales well as data dimensionality increases. The gain in efficiency is achieved by the joint conjugacy property of the proposed prior, which allows block updating of the loadings matrix. We propose an adaptive Gibbs sampler for automatically truncating the infinite loading matrix through selection of the number of important factors. Theoretical results are provided on the support of the prior and truncation approximation bounds. A fast algorithm is proposed to produce approximate Bayes estimates. Latent factor regression methods are developed for prediction and variable selection in applications with high-dimensional correlated predictors. Operating characteristics are assessed through simulation studies, and the approach is applied to predict survival times from gene expression data.
Vibration Control using Neural Network with Adaptively Rearranging Structure (2004)

The neural network has been applied to many engineering problems such as pattern recognition, optimization, system identification and control because of its nonlinear mapping capability. Although the network has a great ability to acquire solution for given problems through learning, several problems are known such as the convergence to a local minimum solution and the empirical tuning of network parameter to obtain desired accuracy. Such an instability may be overcome by finding suitable network structure. The optimized network structure with minimum connection can be obtained by employing optimization techniques such as Genetic Algorithms. However, it is hardly applicable to time-varying systems in view of computation efficiency. In the present paper, we deal with the adaptive neural network controller which rearranges its connection structure suitably according to the given problems. The network is applied to vibration control problem of single degree of freedom nonlinear system, and the performance of the controller is discussed by numerical investigation.
The effect of peer counseling on quality of life following diagnosis of breast cancer: an observational study (2006)

Women with breast cancer express the greatest need for counseling at the time of diagnosis and report that the intervention they want is to be able to speak with someone who has the same cancer, but has lived through the crisis of treatment and is leading a ‘normal’ life. We conducted an observational study of a 6-month peer-counseling intervention testing outcomes for both newly diagnosed women (Sojourners) and peer counselors (Navigators) as a first step toward the goal of validating a peer navigator program. Significant improvement in the Sojourners was observed in trauma symptoms, emotional well-being, cancer self-efficacy, and desire for information on breast cancer resources. Navigators maintained baseline levels of the outcome variables, but increased in dissatisfaction with their interactions with their medical team and increased emotional suppression. Our findings indicate that peer navigation may halt a decline in quality of life that is commonly found in the first year following breast cancer diagnosis. In addition, Navigators were not adversely affected by their experience; however, careful training and supervision of Navigators is crucial to overall success. Randomized clinical trials are needed to demonstrate the efficacy of peer navigator programs. Copyright © 2006 John Wiley & Sons, Ltd.
ChemInform Abstract: Asymmetric Activation/Deactivation of Racemic Ru Catalysts for Highly Enantioselective Hydrogenation of Ketonic Substrates. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Tuning the selectivity of light hydrocarbons in natural gas in a family of isoreticular MOFs (2017)

The kinetic adsorption selectivity of methane <italic>versus</italic> other light hydrocarbons, present in natural gas, is tuned in a rationally synthesized family of isoreticular MOFs.
Etude du mode de répartition du courant dans un contact électrique glissant multifilamentaire (1985)

Après avoir décrit une version moderne de contact électrique glissant multifilamentaire, on montre pour quelle raison le courant peut se répartir inégalement entre les différents filaments constituant un balai. On présente ensuite une modélisation dans laquelle la région de partage du courant est assimilée à un assemblage de couches co-axiales de conductivités différentes. On montre, grâce à ce modèle, que la répartition du courant est analogue à celle due à l'effet de peau, dans un matériau massif parcouru par du courant alternatif. On décrit enfin une expérience dont les résultats sont en bon accord avec les résultats tirés de la modélisation.
Cellular and molecular mechanisms of neural repair after stroke: Making waves (2006)

Stroke is associated with a limited degree of functional recovery. Imaging studies in humans have shown that reorganization in periinfarct and connected cortical areas most closely correlates with functional recovery after stroke. On a cellular level, two major regenerative events occur in periinfarct cortex: axons sprout new connections and establish novel projection patterns, and newly born immature neurons migrate into periinfarct cortex. Stroke induces a unique microenvironment for axonal sprouting in periinfarct cortex, in which growth-inhibitory molecules are reduced for 1 month after the infarct. During this period, neurons activate growth-promoting genes in successive waves. Neurogenesis also occurs through waves of migration of immature neurons from their origin in the subventricular zone into periinfarct cortex. This migration is mediated, in part, by the cytokine erythropoietin. These data indicate that the cellular environment after stroke is far from one of just death and destruction, but rather involves a longer evolving process of neuronal regeneration. Poststroke neuronal regeneration is characterized by waves of specific cellular and molecular events. Manipulating these waves of regeneration may provide for novel therapies that will improve recovery after stroke.
Quantitative Determination of Constituents in Various Licorice Roots by Means of High Performance Liquid Chromatography (1998)

During the course of our studies on the chemical constituents of botanically identified Chinese licorice roots of various origins, we have identified 15 kinds of saponins and 49 kinds of flavonoids (including flavonoid glycosides). With these chemical constituents at hand, we have carried out the chemical evaluation studies of licorice roots available in Japan by means of high performance liquid chromatography (HPLC). In the HPLC analysis using an ODS reversed-phase column, a combination of 1% aqueous acetic acid and acetonitrile was used as the mobile phase in a gradient solvent system, and the eluate was monitored with UV absorption at 254 nm (for saponins with a diene or a conjugated carbonyl moiety, liquiritin, and liquiritin apioside) or at 350 nm (for other flavonoid constituents). By our analytical method described here, quantitative analyses of saponin and flavonoid constituents were effected simultaneously. We have found an interesting piece of information concerning the origin of parent plants and their characteristic constituents such as saponins and flavonoids.
Correlation Analysis with Neutron Count Distributions in Randomly or Signal Triggered Time Intervals for Assay of Special Fissile Materials (1985)

A mathematical model is derived for the probability distribution of neutron signal multiples inside randomly and signal triggered time intervals for a generalized time response function of the neutron detector assembly. The theory is applied to assemblies with an exponential time decay of its neutron population. The probability distributions, their factorial moments, and moments are expressed as a function of the spontaneous fission rate, (α-n) reaction rate, neutron detection probability, probability that a neutron generates a fast fission, and nuclear data. Measurements with a plutonium sample are analyzed to check the derived algorithms for the factorial moments of the two probability distributions.
Sections des fibrés vectoriels sur une courbe (1982)

Soit X une courbe algbrique propre et lisse de genre g ^2. Si E est un fibre vectoriel semi-stable sur X, de rang r, de degr rfe-1) (de sorte que x()0), on peut se demander si H(X, I.)=0, lorsque L est un faisceau inversible gnrique de degr 0. La rponse est non en gnral; elle est positive pour les petites valeurs de r et, en caractristique p>0, lorsque est le faisceau des diffrentielles localement exactes, ce qui implique que les p-sous-groupcs de Sylow de ti (X) sont gros .