gebhart/patrepeval huggingface dataset:
P2‐054: Predicting the progression of Alzheimer's disease by plasma‐based biomarkers (2012)

Alzheimer's disease (AD) is the most common form of dementia, at present there remains a need for accurate biomarkers that can predict disease progression. In recent years markers of prediction, early diagnosis and progression have been identified in plasma by our group. We have therefore selected a multiplexing approach using the immuno-based MILLIPLEX® MAP assays to validate our previously discovered biomarkers with the aim to identify a combination of markers that can predict disease progression. 430 Alzheimer's disease subjects, 395 cognitively normal and 173 mild cognitively impairment subjects were recruited from 2 large multi-centre cohorts. EDTA plasma was collected and evaluated for 45 analytes, using immuno-based MILLIPLEX® MAP assays. Samples were randomized, blinded to the clinical information and measured in duplicate. The intra-assay precision was calculated as the coefficient of variation (%) for each analyte and was <10% across the 45 analytes. The inter-assay precision was <15% for 40 out of the 45 analytes. The results from our study have identified 32 analytes that significantly correlate with changes in Clinical Dementia Rating (CDR), mini-mental state examination (MMSE), Alzheimer's disease Assessment Scale-Cognitive Subscale (ADAS-cog) and Global Detoriation Scale (GDS) in our Alzheimer's disease subjects. This univariate analysis will be followed by multivariate analysis to identify which combination of analytes may be able to predict disease progression. Plasma-based biomarkers have the potential to successfully predict disease progression. Results from previous studies along with this qualification study, strengthen the notion that multiplexing plasma biomarkers improve accuracy and may have a useful clinical application.
Laguerre nonparametric deconvolution technique of time-resolved fluorescence data: application to the prediction of concentrations in a mixture of biochemical components (2004)

To estimate the intrinsic fluorescence intensity decay of a compound, the excitation light pulse must be deconvolved from the measured fluorescence pulse trace. The most commonly used deconvolution method is the multiexponential least-square iterative reconvolution (LSIR) technique. A variant of LSIR in which the intrinsic fluorescence intensity decay is expressed as an expansion on the discrete time Laguerre basis, was recently introduced. In this study, the performance of the Laguerre deconvolution technique was successfully tested with simulated and fluorescence standard data. It was also demonstrated that the Laguerre deconvolution presents a number of advantages over the classical multiexponential LSIR, including less expensive computational resolution, and the property to generate a unique set of expansion coefficients highly correlated with the intrinsic lifetimes. A novel method for concentration estimation based on the analysis of the Laguerre expansion coefficients was also proposed and successfully applied to different fluorescence standard mixtures, performing even better (error<2%) than more traditional methods of spectral analysis, such as PCR (error<7%) and PLS (error<10%). These findings suggest that the use of Laguerre expansion coefficients represents an alternative nonparametric approach to characterize and discriminate biological systems, in terms of their spectral and lifetime characteristics.
Conformation-Dependent High-Affinity Monoclonal Antibodies to Prion Proteins (2010)

Prion diseases are fatal, neurodegenerative illnesses caused by the accumulation of PrP(Sc), an aberrantly folded isoform of the normal, cellular prion protein. Detection of PrP(Sc) commonly relies on immunochemical methods, a strategy hampered by the lack of Abs specific for this disease-causing isoform. In this article, we report the generation of eight mAbs against prion protein (PrP) following immunization of Prnp-null mice with rPrP. The eight mAbs exhibited distinct differential binding to cellular prion protein and PrP(Sc) from different species as well as PrP-derived synthetic peptides. Five of the eight mAbs exhibited binding to discontinuous PrP epitopes, all of which were disrupted by the addition of 2-ME or DTT, which reduced the single disulfide bond found in PrP. One mAb F20-29 reacted only with human PrP, whereas the F4-31 mAb bound bovine PrP; the K(D) values for mAbs F4-31 and F20-29 were ~500 pM. Binding of all five conformation-dependent mAbs to PrP was inhibited by 2-ME in ELISA, Western blots, and histoblots. One conformation-dependent mAb F4-31 increased the sensitivity of an ELISA-based test by nearly 500-fold when it was used as the capture Ab. These new conformation-dependent mAbs were found to be particularly useful in histoblotting studies, in which the low backgrounds after treatment with 2-ME created unusually high signal-to-noise ratios.
A New Method for Rapid In Vitro Propagation of Apple and Pear (2001)

Improved in vitro clonal propagation methods are valuable tools for nurseries and growers, and are essential for manipulation and improvement of tree fruit germplasm using the tools and techniques of biotechnology. We have developed a rapid shoot multiplication procedure for clonal propagation of apple, Malus × domestica cv. Gale Gala and pear, Pyrus communis L. cv. Bartlett. Rapid clonal multiplication was achieved after the following series of steps: pre-conditioning of micropropagated shoots, sectioning pre-treated stems into thin slices, placing slices onto shoot induction medium and incubating directly under cool-white fluorescent lights or after a brief dark incubation. Multiple induction of shoots recovered from stem slice explants within three weeks of culture. A maximum of 37% of cultured apple stem slices, and 97% of pear stem slices, showed induction of shoots. More shoots were recovered on phytagel solidified shoot induction medium than on agar. Cultured stem slices of both apple and pear showed maximum recovery of shoots from shoot induction medium supplemented with thidiazuron (TDZ) compared to medium supplemented with BAP and kinetin. Under ideal conditions, pear stems generated four times the shoots as the same quantity or length of apple shoots. Micropropagated shoots were rooted and transferred to the greenhouse and field nursery for further evaluation. Chemical names used: N -phenyl -N ′-1,2,3-thidiazol-5-ylurea (thidiazuron or TDZ); 6-benzylaminopurine (BAP).
STOCHASTIC BARCODING FOR SINGLE-CELL TRACKING (2013)

We present stochastic barcoding (SB), a method for tracking cell identity across analytical platforms. SB uses a randomly generated code based on number, color and position of beads encapsulated together with a set of cells of interest. We demonstrate SB use in an application where cells are transferred from a microwell array into a microtitre plate while keeping their identity, and obtain an average identification accuracy of 96% for transfer of 100 blocks. Finally, we model scaling of the method up to 1000 blocks and show that SB is able to achieve ~90% accuracy.
A Translatable Predictor of Human Radiation Exposure (2014)

Terrorism using radiological dirty bombs or improvised nuclear devices is recognized as a major threat to both public health and national security. In the event of a radiological or nuclear disaster, rapid and accurate biodosimetry of thousands of potentially affected individuals will be essential for effective medical management to occur. Currently, health care providers lack an accurate, high-throughput biodosimetric assay which is suitable for the triage of large numbers of radiation injury victims. Here, we describe the development of a biodosimetric assay based on the analysis of irradiated mice, ex vivo-irradiated human peripheral blood (PB) and humans treated with total body irradiation (TBI). Interestingly, a gene expression profile developed via analysis of murine PB radiation response alone was inaccurate in predicting human radiation injury. In contrast, generation of a gene expression profile which incorporated data from ex vivo irradiated human PB and human TBI patients yielded an 18-gene radiation classifier which was highly accurate at predicting human radiation status and discriminating medically relevant radiation dose levels in human samples. Although the patient population was relatively small, the accuracy of this classifier in discriminating radiation dose levels in human TBI patients was not substantially confounded by gender, diagnosis or prior exposure to chemotherapy. We have further incorporated genes from this human radiation signature into a rapid and high-throughput chemical ligation-dependent probe amplification assay (CLPA) which was able to discriminate radiation dose levels in a pilot study of ex vivo irradiated human blood and samples from human TBI patients. Our results illustrate the potential for translation of a human genetic signature for the diagnosis of human radiation exposure and suggest the basis for further testing of CLPA as a candidate biodosimetric assay.
Birefringence of solid-state laser media: broadband tuning discontinuities and application to laser line narrowing (1989)

Spectral consequences that result from using birefringent media with broadband gain inside of laser cavities containing polarizing elements are described. We show that the laser intensity is modulated as a function of the output frequency unless the cavity elements are carefully aligned so that their polarization axis coincides with a principal optical axis of the gain medium. Analysis of the tuning characteristics of a birefringent polarizationdependent gain medium is exploited to provide a simple method for line narrowing the laser output. By introduction of an intracavity birefringent compensator the narrow-band output can be continuously tuned. Experimental results for alexandrite lasers are presented.
Assembly and alignment of Proximity Communication enabled multi-chip packages using elastomeric bump interposers (2012)

A MCM enabled by Proximity Communication (P×C) includes a two-dimensional array of facing chips, including island chips and bridge chips that communicate with each other using P×C I/Os placed in the overlapping regions. In order to maintain the relative vertical spacing of these P×C I/O pads as well as to allow Ball-in-Pit self-alignment technology to work, elastomeric bump interposers are placed in cavities in a substrate, which house the bridge chips, to provide a compressive force on the back surfaces of the bridge chips. These interposers contain compressible structures which are precisely placed to make sure that sufficient and symmetric amount of force is applied to the bridge chip to ensure that facing surfaces of the island chips and the bridge chips, as well as connectors on these surfaces, are held securely and reliably and are approximately coplanar without bending the bridge chips. At the same time, the interposer must also allow the bridge chip to be lowered sufficiently to disengage the ball-pit sites during the reflow process of the island chips. In this paper, the design and fabrication of such compliant mechanical interposers are discussed.
Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting Middle East Respiratory Syndrome Coronavirus Spike Protein: An In Silico Approach (2019)

There is no effective therapeutic or vaccine for Middle East Respiratory Syndrome and this study attempts to find therapy using peptide by establishing a basis for the peptide-protein interactions through in silico docking studies for the spike protein of MERS-CoV. The antimicrobial peptides (AMPs) were retrieved from the antimicrobial peptide database (APD3) and shortlisted based on certain important physicochemical properties. The binding mode of the shortlisted peptides was measured based on the number of clusters which forms in a protein-peptide docking using Piper. As a result, we identified a list of putative AMPs which binds to the spike protein of MERS-CoV, which may be crucial in providing the inhibitory action. It is observed that seven putative peptides have good binding score based on cluster size cutoff of 208. We conclude that seven peptides, namely, AP00225, AP00180, AP00549, AP00744, AP00729, AP00764, and AP00223, could possibly have binding with the active site of the MERS-CoV spike protein. These seven AMPs could serve as a therapeutic option for MERS and enhance its treatment outcome.
A mathematical model approach quantifying patients’ response to changes in mechanical ventilation: Evaluation in volume support (2015)

This paper presents a mathematical model-approach to describe and quantify patient-response to changes in ventilator support. The approach accounts for changes in metabolism (V̇O2, V̇CO2) and serial dead space (VD), and integrates six physiological models of: pulmonary gas-exchange; acid-base chemistry of blood, and cerebrospinal fluid; chemoreflex respiratory-drive; ventilation; and degree of patients' respiratory muscle-response. The approach was evaluated with data from 12 patients on volume support ventilation mode. The models were tuned to baseline measurements of respiratory gases, ventilation, arterial acid-base status, and metabolism. Clinical measurements and model simulated values were compared at five ventilator support levels. The models were shown to adequately describe data in all patients (χ(2), p > 0.2) accounting for changes in V̇CO2, VD and inadequate respiratory muscle-response. F-ratio tests showed that this approach provides a significantly better (p < 0.001) description of measured data than: (a) a similar model omitting the degree of respiratory muscle-response; and (b) a model of constant alveolar ventilation. The approach may help predict patients' response to changes in ventilator support at the bedside.
<title>Microlens - Ended Fibres: A New Fabrication Technique</title> (1984)

The formation of spherical or elliptical terminations on optical fibres by heating produces an integral microlens element which can be used to improve the coupling efficiency between a laser diode and a fibre or between two fibres, or to focus the output beam for biome-dical applications. A novel fabrication technique is outlined, which uses the laser light energy delivered by the fibre itself. The method is easy and reliable, and is applicable to all types of multimode fibres, even of large core diameter.
Information preserving XML schema embedding (2005)

A fundamental concern of information integration in an XML context is the ability to embed one or more source documents in a target document so that (a) the target document conforms to a target schema and (b) the information in the source document(s) is preserved. In this paper, information preservation for XML is formally studied, and the results of this study guide the definition of a novel notion of schema embedding between two XML DTD schemas represented as graphs. Schema embedding generalizes the conventional notion of graph similarity by allowing an edge in a source DTD schema to be mapped to a path in the target DTD. Instance-level embeddings can be defined from the schema embedding in a straightforward manner, such that conformance to a target schema and information preservation are guaranteed. We show that it is NP-complete to find an embedding between two DTD schemas. We also provide efficient heuristic algorithms to find candidate embeddings, along with experimental results to evaluate and compare the algorithms. These yield the first systematic and effective approach to finding information preserving XML mappings.
A new genetic linkage map of tomato based on a<i>Solanum lycopersicum</i> ×<i>S. pimpinellifolium</i>RIL population displaying locations of candidate pathogen response genes (2009)

The narrow genetic base of the cultivated tomato, Solanum lycopersicum L., necessitates introgression of new variation from related species. Wild tomato species represent a rich source of useful genes and traits. Exploitation of genetic variation within wild species can be facilitated by the use of molecular markers and genetic maps. Recently we identified an accession (LA2093) within the red-fruited wild tomato species Solanum pimpinellifolium L. with exceptionally desirable characteristics, including disease resistance, abiotic stress tolerance, and high fruit lycopene content. To facilitate genetic characterization of such traits and their exploitation in tomato crop improvement, we developed a new recombinant inbred line (RIL) population from a cross between LA2093 and an advanced tomato breeding line (NCEBR-1). Furthermore, we constructed a medium-density molecular linkage map of this population using 294 polymorphic markers, including standard RFLPs, EST sequences (used as RFLP probes), CAPS, and SSRs. The map spanned 1091 cM of the tomato genome with an average marker spacing of 3.7 cM. A majority of the EST sequences, which were mainly chosen based on the putative role of their unigenes in disease resistance, defense-related response, or fruit quality, were mapped onto the tomato chromosomes for the first time. Co-localizations of relevant EST sequences with known disease resistance genes in tomato were also examined. This map will facilitate identification, genetic exploitation, and positional cloning of important genes or quantitative trait loci in LA2093. It also will allow the elucidation of the molecular mechanism(s) underlying important traits segregating in the RIL population. The map may further facilitate characterization and exploitation of genetic variation in other S. pimpinellifolium accessions as well as in modern cultivars of tomato.
Learning a saliency map using fixated locations in natural scenes (2011)

Inspired by the primate visual system, computational saliency models decompose visual input into a set of feature maps across spatial scales in a number of pre-specified channels. The outputs of these feature maps are summed to yield the final saliency map. Here we use a least square technique to learn the weights associated with these maps from subjects freely fixating natural scenes drawn from four recent eye-tracking data sets. Depending on the data set, the weights can be quite different, with the face and orientation channels usually more important than color and intensity channels. Inter-subject differences are negligible. We also model a bias toward fixating at the center of images and consider both time-varying and constant factors that contribute to this bias. To compensate for the inadequacy of the standard method to judge performance (area under the ROC curve), we use two other metrics to comprehensively assess performance. Although our model retains the basic structure of the standard saliency model, it outperforms several state-of-the-art saliency algorithms. Furthermore, the simple structure makes the results applicable to numerous studies in psychophysics and physiology and leads to an extremely easy implementation for real-world applications.
Performance and Thermal Characterization of the NASA-300MS 20 kW Hall Effect Thruster (2013)

NASA's Space Technology Mission Directorate is sponsoring the development of a high fidelity 15 kW-class long-life high performance Hall thruster for candidate NASA technology demonstration missions. An essential element of the development process is demonstration that incorporation of magnetic shielding on a 20 kW-class Hall thruster will yield significant improvements in the throughput capability of the thruster without any significant reduction in thruster performance. As such, NASA Glenn Research Center and the Jet Propulsion Laboratory collaborated on modifying the NASA-300M 20 kW Hall thruster to improve its propellant throughput capability. JPL and NASA Glenn researchers performed plasma numerical simulations with JPL's Hall2De and a commercially available magnetic modeling code that indicated significant enhancement in the throughput capability of the NASA-300M can be attained by modifying the thruster's magnetic circuit. This led to modifying the NASA-300M magnetic topology to a magnetically shielded topology. This paper presents performance evaluation results of the two NASA-300M magnetically shielded thruster configurations, designated 300MS and 300MS-2. The 300MS and 300MS-2 were operated at power levels between 2.5 and 20 kW at discharge voltages between 200 and 700 V. Discharge channel deposition from back-sputtered facility wall flux, and plasma potential and electron temperature measurements made on the inner and outer discharge channel surfaces confirmed that magnetic shielding was achieved. Peak total thrust efficiency of 64% and total specific impulse of 3,050 sec were demonstrated with the 300MS-2 at 20 kW. Thermal characterization results indicate that the boron nitride discharge chamber walls temperatures are approximately 100 C lower for the 300MS when compared to the NASA- 300M at the same thruster operating discharge power.
Temperature Compensated Sapphire Resonator for Ultra-Stable Oscillator Capability (1994)

We report on the design and test of a whispering gallery sapphire resonator for which the dominant microwave mode family shows frequency-stable, compensated operation for temperatures above 77 kelvin.
Confidence measures for voice search applications (2007)

Abstract Voice search is the technology underlying many spoken dialog applications that enable users to access information using spoken queries. This paper reviews voice search technology, and proposes a new and effective method for computing semantic confidence measures. It explores the use of maximum entropy classifiers as confidence models, and investigates a feature selection algorithm that leads to an effective subset of prominent features for the classifier. The experimental results on a directory assistance application show that the reduced feature set not only makes the model more effective in handling different recognition and search engine combinations, but also results in a very informative confidence measure that is closely correlated with the actual voice search accuracy. Index Terms : voice search, directory assistance, confidence measure, Tf-Idf vector space model, maximum entropy model. 1. Introduction
Fluorine substitution influence on benzo[2,1,3]thiadiazole based polymers for field-effect transistor applications (2016)

Four conjugated copolymers with a donor/acceptor architecture comprising 4,4-dihexadecyl-4H-cyclopenta[1,2-b:5,4-b']dithiophene as the donor structural unit and benzo[2,1,3]thiadiazole fragments with varying degrees of fluorination as the acceptor structural units have been synthesized and characterized. It has been shown that the energy levels were decreased after the fluorine substitution. The field-effect charge carrier mobility was similar for all polymers with less than an order of magnitude difference between different acceptor units.