gebhart/patrepeval huggingface dataset:
A Bayesian Nonparametric Model for Disease Subtyping: Application to Emphysema Phenotypes (2016)

We introduce a novel Bayesian nonparametric model that uses the concept of disease trajectories for disease subtype identification. Although our model is general, we demonstrate that by treating fractions of tissue patterns derived from medical images as compositional data, our model can be applied to study distinct progression trends between population subgroups. Specifically, we apply our algorithm to quantitative emphysema measurements obtained from chest CT scans in the COPDGene Study and show several distinct progression patterns. As emphysema is one of the major components of chronic obstructive pulmonary disease (COPD), the third leading cause of death in the United States [1], an improved definition of emphysema and COPD subtypes is of great interest. We investigate several models with our algorithm, and show that one with age , pack years (a measure of cigarette exposure), and smoking status as predictors gives the best compromise between estimated predictive performance and model complexity. This model identified nine subtypes which showed significant associations to seven single nucleotide polymorphisms (SNPs) known to associate with COPD. Additionally, this model gives better predictive accuracy than multiple, multivariate ordinary least squares regression as demonstrated in a five-fold cross validation analysis. We view our subtyping algorithm as a contribution that can be applied to bridge the gap between CT-level assessment of tissue composition to population-level analysis of compositional trends that vary between disease subtypes.
Low-Latency Tracking of Multiple Permanent Magnets (2019)

Magnetic target tracking is a low-cost, portable, and passive method for tracking materials wherein magnets are physically attached or embedded without the need for line of sight. Traditional magnet tracking techniques use optimization algorithms to determine the positions and orientations of permanent magnets from magnetic field measurements. However, such techniques are constrained by high latencies, primarily due to the numerical calculation of the gradient. In this study, we derive the analytic gradient for multiple-magnet tracking and show a dramatic reduction in tracking latency. We design a physical system comprising an array of magnetometers and one or more spherical magnets. To validate the performance of our tracking algorithm, we compare the magnet tracking estimates with state-of-the-art motion capture measurements for each of four distinct magnet sizes. We find comparable position and orientation errors to state-of-the-art magnet tracking, but demonstrate increased maximum bandwidths of 336%, 525%, 635%, and 773% for the simultaneous tracking of 1, 2, 3, and 4 magnets, respectively. We further show that it is possible to extend the analytic gradient to account for disturbance fields, and we demonstrate the simultaneous tracking of 1 to 4 magnets with disturbance compensation. These findings extend the use of magnetic target tracking to high-speed, real-time applications requiring the tracking of one or more targets without the constraint of a fixed magnetometer array. This advancement enables applications such as low-latency augmented and virtual reality interaction, volitional or reflexive control of prostheses and exoskeletons, and simplified multi-degree-of-freedom magnetic levitation.
Finite Temperature Dynamical Correlations in Massive Integrable Quantum Field Theories (2016)

We consider the finite-temperature frequency and momentum dependent two-point functions of local operators in integrable quantum field theories. We focus on the case where the zero temperature correlation function is dominated by a delta-function line arising from the coherent propagation of single particle modes. Our specific examples are the two-point function of spin fields in the disordered phase of the quantum Ising and the O(3) nonlinear sigma models. We employ a Lehmann representation in terms of the known exact zero-temperature form factors to carry out a low-temperature expansion of two-point functions. We present two different but equivalent methods of regularizing the divergences present in the Lehmann expansion: one directly regulates the integral expressions of the squares of matrix elements in the infinite volume whereas the other operates through subtracting divergences in a large, finite volume. Our central results are that the temperature broadening of the line shape exhibits a pronounced asymmetry and a shift of the maximum upwards in energy ("temperature dependent gap"). The field theory results presented here describe the scaling limits of the dynamical structure factor in the quantum Ising and integer spin Heisenberg chains. We discuss the relevance of our results for the analysis of inelastic neutron scattering experiments on gapped spin chain systems such as CsNiCl3 and YBaNiO5.
Prader-Willi Syndrome: The Disease that Opened up Epigenomic-Based Preemptive Medicine (2016)

Prader-Willi syndrome (PWS) is a congenital neurodevelopmental disorder caused by loss of function of paternally expressed genes on chromosome 15 due to paternal deletion of 15q11-q13, maternal uniparental disomy for chromosome 15, or an imprinting mutation. We previously developed a DNA methylation-based PCR assay to identify each of these three genetic causes of PWS. The assay enables straightforward and rapid diagnosis during infancy and therefore allows early intervention such as nutritional management, physical therapy, or growth hormone treatment to prevent PWS patients from complications such as obesity and type 2 diabetes. It is known that various environmental factors induce epigenomic changes during the perinatal period, which increase the risk of adult diseases such as type 2 diabetes and intellectual disabilities. Therefore, a similar preemptive approach as used in PWS would also be applicable to acquired disorders and would make use of environmentally-introduced "epigenomic signatures" to aid development of early intervention strategies that take advantage of "epigenomic reversibility".
Detecting Dementia: Novel Neuropsychological Markers of Preclinical Alzheimer’s Disease (2003)

The results of a previous study have suggested that impaired performance on one neuropsychological test, CANTAB Paired Associates Learning (PAL), may serve as a marker for preclinical Alzheimer's disease (AD). In a group of individuals with 'questionable dementia', the baseline PAL performance was found to correlate significantly with subsequent deterioration in global cognitive function over an 8-month period. The present paper reports diagnostic outcome data for the same individuals 32 months after the first assessment and evaluates the predictive diagnostic utility of baseline neuropsychological measures. Thirty-two months after joining the study, 11 of the 43 'questionable dementia' patients met the criteria for probable AD diagnosis ('converters') and 29 remained free from AD ('non-converters'). Logistic regression analysis revealed that two tests of memory, in combination, could be used to predict a later diagnosis of probable AD with a high level of accuracy [chi(2)(3) = 47.054, p < 0.0001]. As predicted, these tests are measures of visuospatial learning (CANTAB PAL) and, also, semantic memory (Graded Naming Test). These two tests in combination appear to be highly accurate in detecting cognitive dysfunction characteristic of preclinical AD. Using these tests, a simple algorithm is described for calculating, with 100% accuracy for this sample of 40 patients, the probability that an individual with mild memory impairments will go on to receive a diagnosis of probable AD.
Prevention of migraine attacks through the use of dihydroergotamine. (1986)

A strictly controlled clinical trial on a group of 20 patients treated with a time-release preparation of dihydroergotamine compared with 20 on a placebo for the prevention of migraine attacks confirmed that dihydroergotamine was very effective and considered satisfactory by 65% of the patients treated.
Effective sampling and learning for mallows models with pairwise-preference data (2014)

Learning preference distributions is a critical problem in many areas (e.g., recommender systems, IR, social choice). However, many existing learning and inference methods im-pose restrictive assumptions on the form of user preferences that can be admitted as ev-idence. We relax these restrictions by considering as data arbitrary pairwise comparisons of alternatives, which represent the fundamental building blocks of ordinal rankings. We develop the first algorithms for learning Mallows models (and mixtures thereof) from pair-wise comparison data. At the heart of our technique is a new algorithm, the generalized repeated insertion model (GRIM), which allows sampling from arbitrary ranking distribu-tions, and conditional Mallows models in particular. While we show that sampling from a Mallows model with pairwise evidence is computationally difficult in general, we develop approximate samplers that are exact for many important special cases—and have provable bounds with pairwise evidence—and derive algorithms for evaluating log-likelihood, learn-ing Mallows mixtures, and non-parametric estimation. Experiments on real-world data sets demonstrate the effectiveness of our approach.1
Fast Synopsis for Moving Objects Using Compressed Video (2014)

With the increasing volume of video data, how to analyze and browse video in a fast and effective way has become an urgent problem in applications. This letter proposes a novel video synopsis method in compressed domain for browsing video captured by static cameras. Synopsis video is a video abstraction, which displays moving objects from different periods simultaneously on the primary background contents of original video. To overcome the low efficiency of traditional video synopsis for compressed video, our method presents a new graph cut algorithm to extract objects tubes and meanwhile gives a fast solution to minimize energy function in compressed domain. Experimental results in H.264 video have demonstrated the high-efficiency of this new video synopsis scheme for massive video browsing.
The effects of hydrostatic pressure on matrix synthesis in articular cartilage (1991)

The direct effects of hydrostatic pressure on matrix synthesis in articular cartilage can be studied independently of the other factors that change during loading. We have found that the influence of hydrostatic pressure on incorporation rates of 35SO4 and [3H]proline into adult bovine articular cartilage slices in vitro depends on the pressure level and on the time at pressure. Pressures in the "physiological" range (5-15 MPa) applied for 20 s or for 5 min could stimulate tracer incorporation (30-130%) during the following 2 h, but higher pressures (20-50 MPa) had no effect on incorporation rates. The degree of stimulation in cartilage obtained from different animals was found to vary; in some animals none was seen. Stimulation also varied with position along the joint. Physiological pressures (5-10 MPa) applied continuously for the 2-h incubation period also stimulated incorporation rates, but pressures greater than 20 MPa always produced a decrease that was related to the applied pressure and that was reversible. These results suggests that the hydrostatic pressure that occurs during loading is a signal that can stimulate matrix synthesis rates in articular cartilage.
Fanca-/- hematopoietic stem cells demonstrate a mobilization defect which can be overcome by administration of the Rac inhibitor NSC23766 (2009)

Fanconi anemia is a severe bone marrow failure syndrome resulting from inactivating mutations of Fanconi anemia pathway genes. Gene and cell therapy trials using hematopoietic stem cells and progenitors have been hampered by poor mobilization of HSC to peripheral blood in response to G-CSF. Using a murine model of Fanconi anemia (Fanca(-/-) mice), we found that the Fanca deficiency was associated with a profound defect in hematopoietic stem cells and progenitors mobilization in response to G-CSF in absence of bone marrow failure, which correlates with the findings of clinical trials in Fanconi anemia patients. This mobilization defect was overcome by co-administration of the Rac inhibitor NSC23766, suggesting that Rac signaling is implicated in the retention of Fanca(-/-) hematopoietic stem cells and progenitors in the bone marrow. In view of these data, we propose that targeting Rac signaling may enhance G-CSF-induced HSC mobilization in Fanconi anemia.
Transformer Tank Vibration Modeling as a Method of Detecting Winding Deformations—Part II: Experimental Verification (2005)

In Part I of the paper, a tank vibration model was proposed as a method to detect the winding deformations in power transformers. This model is incorporated in a model-based monitoring system for power transformers. In this paper, the experimental verification of the proposed model that calculates vibration on the transformer tank is reported. The model was validated in a 1500-kVA experimental transformer constructed as a reduced scale model of a 60-MVA 220-kV unit. In order to load the test transformer, the opposition method described in IEC 60076-2 Standard was used allowing to vary the load and power factor over a wide range. Sensors to measure vibrations and temperature were installed in the test transformer. The model was validated under different test transformer operating conditions. In order to verify the model's ability to detect failures, a deformation was provoked in the test transformer winding. Model predictions were compared with the measured vibration in that situation. The model has also been applied to four (30-40 MVA) grid transformers. Some results of this field validation are presented in this paper.
Mechanisms, Kinetics, and Dynamics of Oxidation and Reactions on Oxide Surfaces Investigated by Scanning Probe Microscopy (2010)

Advances in scanning probe microscopies (SPM) have allowed the mechanisms and rates of adsorption, diffusion and reactions on surfaces to be characterized by directly observing the motions of the individual atoms and molecules involved. The importance of oxides as thermal and photocatalysts, chemical sensors, and substrates for epitaxial growth has motivated dynamical SPM studies of oxide surfaces and their formation. Work on the TiO(2) (110) surface is reviewed as an example of how dynamic SPM studies have revealed unexpected interactions between adsorbates and defects that influence macroscopic reaction rates. Studies following diffusion, adsorption and phase transitions on bulk and surface oxides are also discussed. A perspective is provided on advanced SPM techniques that hold great promise for yielding new insights into the mechanisms and rates of elemental processes that take place either during oxidation or on oxide surfaces, with particular emphasis on methods that extend the time and chemical resolution of dynamical SPM measurements.
A synthesis of the C6,C11-dideoxyanthracyclinone skeleton via Hassall cyclization and oxidative desilylation (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA synthesis of the C6,C11-dideoxyanthracyclinone skeleton via Hassall cyclization and oxidative desilylationE. V. Vedejs and J. R. PribishCite this: J. Org. Chem. 1988, 53, 8, 1593–1599Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://doi.org/10.1021/jo00243a001Request reuse permissionsArticle Views569Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (960 KB) Get e-Alertsclose Get e-Alerts
Discrete effects of the acylamino proton in a chymotrypsin substrate on different processes in catalysis (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiscrete effects of the acylamino proton in a chymotrypsin substrate on different processes in catalysisMichael Caplow and Curtis HarperCite this: J. Am. Chem. Soc. 1972, 94, 18, 6508–6512Publication Date (Print):September 1, 1972Publication History Published online1 May 2002Published inissue 1 September 1972https://pubs.acs.org/doi/10.1021/ja00773a039https://doi.org/10.1021/ja00773a039research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Action from Still Image Dataset and Inverse Optimal Control to Learn Task Specific Visual Scanpaths (2013)

Human eye movements provide a rich source of information into the human vi-sual information processing. The complex interplay between the task and the visual stimulus is believed to determine human eye movements, yet it is not fully understood, making it difficult to develop reliable eye movement prediction sys-tems. Our work makes three contributions towards addressing this problem. First, we complement one of the largest and most challenging static computer vision datasets, VOC 2012 Actions, with human eye movement recordings collected un-der the primary task constraint of action recognition, as well as, separately, for context recognition, in order to analyze the impact of different tasks. Our dataset is unique among the eyetracking datasets of still images in terms of large scale (over 1 million fixations recorded in 9157 images) and different task controls. Sec-ond, we propose Markov models to automatically discover areas of interest (AOI) and introduce novel sequential consistency metrics based on them. Our methods can automatically determine the number, the spatial support and the transitions between AOIs, in addition to their locations. Based on such encodings, we quan-titatively show that given unconstrained read-world stimuli, task instructions have significant influence on the human visual search patterns and are stable across subjects. Finally, we leverage powerful machine learning techniques and com-puter vision features in order to learn task-sensitive reward functions from eye movement data within models that allow to effectively predict the human visual search patterns based on inverse optimal control. The methodology achieves state of the art scanpath modeling results. 1
Formation of Silica Nanoparticles in Microemulsions (2007)

Silica nanoparticles for controlled release applications have been produced by the reaction of tetramethylorthosilicate (TMOS) inside the water droplets of a water-in-oil microemulsion, under both acidic (pH 1.05) and basic (pH 10.85) conditions. In-situ FTIR measurements show that the addition of TMOS to the microemulsion results in the formation of silica as TMOS, preferentially located in the oil phase, diffuses into the water droplets. Once in the hydrophilic domain, hydrolysis occurs rapidly as a result of the high local concentration of water. Varying the pH of the water droplets from 1.05 to 10.85, however, considerably slows the hydrolysis reaction of TMOS. The formation of a dense silica network occurs rapidly under basic conditions, with IR indicating the slower formation of more disordered silica in acid. SAXS analysis of the evolving particles shows that approximately 11 nm spheres are formed under basic conditions; these are stabilized by a water/surfactant layer on the particle surface during formation. Under acidic conditions, highly uniform approximately 5 nm spheres are formed, which appear to be retained within the water droplets (approximately 6 nm diameter) and form an ordered micelle nanoparticle structure that exhibits sufficient longer-range order to generate a peak in the scattering at q approximately equal to 0.05 A-1. Nitrogen adsorption analysis reveals that high surface area (510 m2/g) particles with an average pore size of 1 nm are formed at pH 1.05. In contrast, base synthesis results in low surface area particles with negligible internal porosity.
Characteristics of Serum Antibody in Enteric Septicemia of Catfish (1995)

The Falcon Assay Screen Test enzyme-linked immunosorbent assay was used to determine the characteristics of antibody directed against Edwardsiella ictaluri exoantigen and the antibody's relationship to E. ictaluri in channel catfish suffering from enteric septicemia of catfish (ESC). This antibody was detected in the serum of channel catfish 5 d after fish were exposed to live E. ictaluri by bath immersion. A significant (P < 0.05) specific antibody response was stimulated between 14 and 21 d postexposure (DPE) which then declined at 28 DPE. Mortality resulting from E. ictaluri first occurred at 5 DPE and peaked at 21 DPE. Following reexposure, the specific memory antibody response peaked at 21 DPE, but at a level lower than that of the primary infection, and declined at 84 DPE. The reexposed catfish were protected against mortality resulting from E. ictaluri infection. Serum and antibody harvested from channel catfish protected against ESC-related mortality failed to passively immunize channel catfish against ESC. However, the channel catfish passively immunized with immune serum and antibody had significant (P < 0.05) circulating specific antibody immediately before E. ictaluri exposure. We conclude that channel catfish infected with E. ictaluri mount substantial primary and memory antibody responses to E. ictaluri exoantigen. The present results suggest that reexposure fails to stimulate a memory antibody response that was greater than the primary antibody response to E. ictaluri exoantigen. Antibodies to E. ictaluri exoantigen alone were not protective in the channel catfish experimental model of ESC.