gebhart/patrepeval huggingface dataset:
Disruptive Innovation in Laboratory Medicine (2015)

Over the last 5 decades, laboratory medicine has witnessed a remarkable wave of innovations that transformed the field from a peripheral to a central player in healthcare delivery. These advances enabled the introduction and performance of new tests on a large scale, some in a decentralized setting, in an accurate and a precise manner, thus leading to better diagnosis, more accurate prediction of disease prognosis, and improved patient management. This evolution was the result of both sustaining and disruptive innovation, the latter being a new concept, technology, product, or process that is at first inferior to an existing one but with time it improves, becomes superior to it, and eventually replaces it. Some examples of disruptive innovation in laboratory medicine include continuous flow analysis, dry reagents on dipsticks, pregnancy home testing, PCR, point-of-care testing, and use of MALDI-TOF mass spectrometry for pathogen identification. Although sustaining innovation steadily drives progress, paradigm shifts usually occur only with disruptive thinking. With the escalating cost of healthcare and the prediction that it will soon reach 20% of the annual GDP in the US, bold measures and disruptive approaches in delivering effective and economical clinical laboratory testing are more needed than ever. In this Q&A, a group of inventors, entrepreneurs, and cutting-edge scientists share their views on sustaining and disruptive innovation in laboratory medicine.

Describe briefly the core technology or concept of your innovation. 



Eric Topol: Smartphones as the hub of medicine going forward, capable of performing routine laboratories (with suitable hardware additions), real-time, real-world biosensor data of most physiologic metrics, capability of doing a substantial part of the physical examination, and ultimately, assembly of a virtual medical assistant to process these multilayered medical data for each individual. All of this data collection and analytics would be supported by cloud computing and validated algorithms.



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Eugene …
Synthesis of 9-[5-(alkylthio)-5-deoxy-.beta.-D-erythro-pent-4-enofuranosyl)adenines as potential inhibitors of transmethylation (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 9-[5-(alkylthio)-5-deoxy-.beta.-D-erythro-pent-4-enofuranosyl)adenines as potential inhibitors of transmethylationG. Wayne Craig, Ethan D. Sternberg, Gordon H. Jones, and John G. MoffattCite this: J. Org. Chem. 1986, 51, 8, 1258–1264Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/jo00358a017https://doi.org/10.1021/jo00358a017research-articleACS PublicationsRequest reuse permissionsArticle Views284Altmetric-Citations12LEARN 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
ChemInform Abstract: Phosphorus‐Containing Macrocycles. A Game of Building Blocks (1992)

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.
Electronic control of stereoselectivity. 22. Crossover in .pi.-facial stereoselection during [4 + 2] cycloaddition of triazolinediones to isodicyclopentadiene and its dehydro derivatives (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic control of stereoselectivity. 22. Crossover in .pi.-facial stereoselection during [4 + 2] cycloaddition of triazolinediones to isodicyclopentadiene and its dehydro derivativesLeo A. Paquette, Kenneth E. Green, and Leh Yeh HsuCite this: J. Org. Chem. 1984, 49, 19, 3650–3652Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://doi.org/10.1021/jo00193a042RIGHTS & PERMISSIONSArticle Views32Altmetric-Citations13LEARN 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 (428 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
No Involvement of Antidiuretic Hormone in Acute Antidiuresis During PEEP Ventilation in Humans (1987)

Decreased urinary output (Vu ml/min) after institution of PEEP is attributed to a variety of mechanisms including decreased cardiac output and renal blood flow (RBF), activation of neurohormonal reflexes, increased catecholamines, plasma renin activity (PRA), and antidiuretic hormone (ADH) release. To evaluate these factors, seven normovolemic patients (36 yr +/- 13 SD), free of preexisting lung, cardiac, or renal disease, requiring continuous mandatory ventilation for neurologic reasons were studied. The authors measured or calculated: total blood volume (TBV) (51Cr); right atrial, pulmonary arterial, pulmonary wedge, and systemic pressures, cardiac index (CI); renal plasma flow (RPF) (iodohippurate sodium 131I [131I PAH] clearance); glomerular filtration rate (GFR) (creatinine clearance), free water clearance (CH2O), osmolal clearance (Cosm), fractional excretion of sodium (FENa+) and potassium (FEK+); and plasma renin activity (PRA) (ng X ml-1 X h-1), plasma ADH (pg/ml; radioimmunoassay), epinephrine (E in pg/ml), and norepinephrine (NE in pg/ml) (double-isotope radioenzymatic assay). Two conditions were studied after 90-min steady state: 1) zero PEEP (ZEEP); and 2) 15 cmH2O PEEP. PEEP caused a significant decrease in CI (-21%; P less than 0.01) and RPF (-19%; P less than 0.05) without significant decrease in GFR. A significant decrease in Vu (-55%; P less than 0.05), FENa+ (-39%; P less than 0.05) and Cosm (-36%; P less than 0.25) occurred without modification in CH2O. Plasma ADH remained in the normal range and did not increase when PEEP was applied.(ABSTRACT TRUNCATED AT 250 WORDS)
Modeling Imperative String Operations with Transducers (2010)

We present a domain-specific imperative language, Bek, that directly models low-level string manipulation code featuring boolean state, search operations, and substring substitutions. We show constructively that Bek is reversible through a semantics-preserving translation to symbolic finite state transducers, a novel representation for transducers that annotates transitions with logical formulae. Symbolic finite state transducers give us a new way to marry the classic theory of finite state transducers with the recent progress in satisfiability modulo theories (SMT) solvers. We exhibit an efficient well-founded encoding from symbolic finite state transducers into the higher-order theory of algebraicdatatypes.Weevaluatethepracticalutilityof Bekasa constraint language in the domain of web application sanitization code. We demonstrate that our approach can address real-world queries regarding, for example, the idempotence and relative strictness of popular sanitization functions.
An Inequality between Energy and Intersection (1990)

We prove that the identity map on a closed Riemannian manifold without conjugate points is energyminimizing in its homotopy class. For this we introduce a quantity called intersection and we establish an inequality between energy and intersection.
A comprehensive water tunnel test of a horizontal axis marine hydrokinetic turbine for model validation and verification (2014)

As interest in waterpower technologies has increased over the last few years, there has been a growing need for a public database of measured data for these devices. This would provide a basic understanding of the technology and means to validate analytic and numerical models. Through collaboration between Sandia National Laboratories, Penn State University Applied Research Laboratory, and University of California, Davis, a new marine hydrokinetic turbine rotor was designed, fabricated at 1:8.7-scale, and experimentally tested to provide an open platform and dataset for further study and development. The water tunnel test of this three-bladed, horizontal-axis rotor recorded power production, blade loading, near-wake characterization, cavitation effects, and noise generation. Additionally, preliminary comparisons are mode from unsteady CFD for the flow fields measured.
Inversion Analysis of Distribution of Energy Radiated from an Earthquake Fault Based on the Seismic Intensity Data (2003)

The method of the inversion analysis to evaluate the distribution of seismic energy radiated from an earthquake fault plane based on seismic intensity distribution data has been developed. The fault plane is divided into small sub-faults. The optimized seismic energy distribution of each sub-fault is calculated using the least square method to minimize the error between evaluated and observed seismic intensities.The energy distribution of a seismic fault is related to seismic intensity using the attenuation formula with equivalent hypocentral distance. The parameters of the attenuation formula are obtained from a regression analysis with measured seismic intensity data of recent moderate earthquakes.The forward analyses using an assumed model are performed to verify the accuracy of the inversion analysis and to evaluate the effect of factors such as the standard deviation of seismic intensity, constraint condition of inversion analysis and configuration of observation stations.Finally, the method is applied to the Showa Tonankai earthquake in 1944 and the Showa Nankai earthquake in 1946 and the result is compared with the tsunami and strong motion waveform inversion results to confirm the efficiency and applicability of the method.
γδ T cells in EAE: Early trafficking events and cytokine requirements (2009)

We have previously shown that gammadelta T cells traffic to the CNS during EAE with concurrently increased expression of beta(2)-integrins and production of IFN-gamma and TNF-alpha. To extend these studies, we transferred bioluminescent gammadelta T cells to WT mice and followed their movement through the acute stages of disease. We found that gammadelta T cells rapidly migrated to the site of myelin oligodendrocyte glycoprotein peptide injection and underwent massive expansion. Within 6 days after EAE induction, bioluminescent gammadelta T cells were found in the spinal cord and brain, peaking in number between days 10 and 12 and then rapidly declining by day 15. Reconstitution of gammadelta T cell(-/-) mice with gammadelta T cells derived from beta(2)-integrin-deficient mice (CD11a, -b or -c) demonstrated that gammadelta T-cell trafficking to the CNS during EAE is independent of this family of adhesion molecules. We also examined the role of gammadelta T-cell-produced IFN-gamma and TNF-alpha in EAE and found that production of both cytokines by gammadelta T cells was required for full development of EAE. These results indicate that gammadelta T cells are critical for the development of EAE and suggest a therapeutic target in demyelinating disease.
Face detection technique based on rotation invariant wavelet features (2004)

A rotation and scale invariant face detection algorithm based on the texture of a human face is proposed. Wavelet packet analysis is performed on the test image to get the coefficients. It is observed that wavelet packet decomposition until third level is sufficient enough to get the necessary frequencial components essential for classifying faces and nonfaces. Rotation invariant textural features are extracted from the wavelet coefficients. A scale invariant distance measure between the feature vectors of each of the candidate faces and the prototype face image is proposed to classify the candidate faces into faces and nonfaces. The detection process implements a nonlinear luminance based lighting compensation method, which is very efficient in enhancing and restoring the natural colors into the images taken in darker and varying lighting environments. The novel detection process proposed is highly efficient in terms of speed and accuracy in detecting frontal view faces in a complex background. The face detection performance of the proposed system is comparable to other reported leading systems.
System-theoretical model reduction for reservoir simulation and optimization (2009)

This thesis is concerned with low-order modelling of heterogeneous reservoir systems for the purpose of efficient simulation and optimization of flooding processes with multiple injection and production (smart) wells. Typically, one is initially equipped with a physics-based ('white-box') model consisting of O(103-106) equations and parameters representing a (coupled) system of discretized PDEs defined on a geometric grid. The model-order reduction (MOR) methodology undertaken in this research is fundamentally different from the traditional, 'grid-coarsing' approximation methods, in that no coarse-grid approximation of the fine-grid problem is employed at all. Instead, the reduced-order models are here based on 'system-theoretic' and dynamically intrinsic properties of the fine-scale system. In single-phase flow problems that can be modelled as linear time-invariant state-space systems these properties are, e.g., the system's transfer function in the Laplace domain, the eigenstructure of the system matrix, or controllability and observability of the (particular state-space realization of the) system. For multi-phase flow problems resulting in nonlinear state-space models, intrinsic information needs to be sought in data obtained by simulating the fine-scale model. The contribution of this thesis can be divided into three themes: 1) Standard 'projection-based' MOR: assessment of the performance of modal truncation, singular perturbation, balanced truncation, transfer function moments maching (inc. Krylov-subspaces), and proper orthogonal decomposition (POD), 2) Acceleration of solving the fine-scale problem: use of MOR as a 'shadow simulation' to determine an improved fine-scale initial guess, and 3) Acceleration of waterflooding optimization: use of POD in the inner-loop of an adjoint-based optimization scheme.
Dissociative ionization and angular distributions of CS[sub 2] and its ions (1998)

The dissociative ionization of CS2 has been investigated at several different wavelengths (375, 750, 395, and 790 nm), for pulse-widths as short as 50fs, and laser intensities in the range of (2.2×1013−3×1016) W/cm2. It is found from the various mass spectra that fragmentation is relatively more pronounced at shorter wavelengths, whilst at longer wavelengths, the parent dominates. Another interesting feature, occurring in the data and literature, is the presence of an S2+ ion at wavelengths less than about 532 nm, and near total absence at wavelengths longer than this. Angular distributions are presented for both 395 and 790 nm. Sn+-ions fragment along the polarization direction, while the Cn+-ions fragment perpendicularly to it, providing a way of distinguishing the different fragments produced in the coulomb explosion process. Finally, distribution widths decrease with higher charge states of the ions, implying that they are more aligned with the field.
Material surfaces affect the protein expression patterns of human macrophages: A proteomics approach (2006)

Monocyte-derived macrophages (MDM) are key inflammatory cells and are central to the foreign body response to implant materials. MDM have been shown to exhibit changes in actin cytoskeleton, multinucleation, cell size, and function in response to small alterations in polycarbonate-urethane (PCNU) surface chemistry. Although PCNU chemistry has an influence on de novo protein synthesis, no assessments of the protein expression profiles of MDM have yet been reported. The rapid emerging field of expression proteomics facilitates the study of changes in cellular protein profiles in response to their microenvironment. The current study applied proteomic techniques, 2-dimensional electrophoresis (2-DE) combined with MALDI-ToF (matrix assisted laser desorption ionization-time of flight) mass spectrometry, to determine differences in MDM protein expression influenced by PCNU. Results indicated that MDM responded to material chemistry by modulation of structural proteins (i.e. actin, vimentin, and tubulin). Additionally, intracellular protein modulation which requires proteins responsible for trafficking (i.e. chaperone proteins) and protein structure modification (i.e. bond rearrangement and protein folding) were also altered. This study demonstrated for the first time that a proteomics approach was able to detect protein expression profile changes in MDM cultured on different material surfaces, forming the basis for utilizing further quantitative proteomics techniques that could assist in elucidation of the mechanisms involved in MDM-material interaction.
The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies (2013)

Broadly neutralizing HIV antibodies (bnAbs) are typically highly somatically mutated, raising doubts as to whether they can be elicited by vaccination. We used 454 sequencing and designed a novel phylogenetic method to model lineage evolution of the bnAbs PGT121-134 and found a positive correlation between the level of somatic hypermutation (SHM) and the development of neutralization breadth and potency. Strikingly, putative intermediates were characterized that show approximately half the mutation level of PGT121-134 but were still capable of neutralizing roughly 40-80% of PGT121-134 sensitive viruses in a 74-virus panel at median titers between 15- and 3-fold higher than PGT121-134. Such antibodies with lower levels of SHM may be more amenable to elicitation through vaccination while still providing noteworthy coverage. Binding characterization indicated a preference of inferred intermediates for native Env binding over monomeric gp120, suggesting that the PGT121-134 lineage may have been selected for binding to native Env at some point during maturation. Analysis of glycan-dependent neutralization for inferred intermediates identified additional adjacent glycans that comprise the epitope and suggests changes in glycan dependency or recognition over the course of affinity maturation for this lineage. Finally, patterns of neutralization of inferred bnAb intermediates suggest hypotheses as to how SHM may lead to potent and broad HIV neutralization and provide important clues for immunogen design.
The Thermal Decomposition of Thirty Commercially Available Materials at 300C (1974)

A literature search of available thermochemical data of twenty-six organic and inorganic compounds tabulated in the Department of Transportation's commodity listing has been completed. Experiments have been carried out to measure the thermal sensitivity of these materials in laboratory tests using thermal surge stimuli, differential scanning calorimetry, and a system designed to determine qualitatively the percent decomposition of liquid and solid materials at the limiting parameters (one hour at 300 degrees C). The amount of gas resulting from this thermal decomposition is also reported.
Silicon quantum processor with robust long-distance qubit couplings (2017)

Practical quantum computers require a large network of highly coherent qubits, interconnected in a design robust against errors. Donor spins in silicon provide state-of-the-art coherence and quantum gate fidelities, in a platform adapted from industrial semiconductor processing. Here we present a scalable design for a silicon quantum processor that does not require precise donor placement and leaves ample space for the routing of interconnects and readout devices. We introduce the flip-flop qubit, a combination of the electron-nuclear spin states of a phosphorus donor that can be controlled by microwave electric fields. Two-qubit gates exploit a second-order electric dipole-dipole interaction, allowing selective coupling beyond the nearest-neighbor, at separations of hundreds of nanometers, while microwave resonators can extend the entanglement to macroscopic distances. We predict gate fidelities within fault-tolerance thresholds using realistic noise models. This design provides a realizable blueprint for scalable spin-based quantum computers in silicon.Quantum computers will require a large network of coherent qubits, connected in a noise-resilient way. Tosi et al. present a design for a quantum processor based on electron-nuclear spins in silicon, with electrical control and coupling schemes that simplify qubit fabrication and operation.
Diffraction efficiency and diffraction bandwidth of thermal-gradient and composition-gradient crystals (2005)

Measurements were made at the Advanced Photon Source at Argonne National Laboratory on the diffraction efficiency and diffraction bandwidth of a thermal-gradient crystal (Si) and a composition-gradient crystal (Si-Ge) to which a thermal gradient was applied. Gradient crystals are crystals in which the spacing between crystalline planes varies with the position in the crystal. This change in the crystal plane spacing is obtained by applying a thermal gradient to a single crystal or by growing a two-component crystal in which the ratio of the two components changes with position in the crystal. Measurements were made at two energies, 92.6 and 153 keV. Both crystals were 1-cm cubes. Laue diffraction (transmission diffraction) was used in all experiments. The thermal gradient was applied perpendicular to the [111] diffraction planes of the pure silicon crystal and perpendicular the [400] diffraction planes in the composition-gradient crystal (Si-Ge). The thermal gradient applied to the crystals was quite uniform. This resulted in nearly spherical surfaces for the crystalline planes. Changing the value of the thermal gradient applied to the crystals changed the radius of curvature of the spherical surface. The thermal gradients were varied between 0.0 and 114°C∕cm, resulting in radii of curvature from near infinity down to 40 m. By adjusting the thermal gradient applied to the crystals, one obtained diffraction efficiencies between 0.90 and 0.95 and bandwidths of up to 100 arc sec. The diffraction efficiency in the Laue geometry is defined as the ratio of the intensity of the diffracted beam to the intensity of the undiffracted beam that passes through the crystal when there is no diffraction. The length of the crystal traversed by the x-ray beam was 1.0 cm in all cases.