gebhart/patrepeval huggingface dataset:
Highly Multiplexed Proteomic Analysis of Quantiferon Supernatants To Identify Biomarkers of Latent Tuberculosis Infection (2016)

The tests for diagnosing latent tuberculosis infection (LTBI) are limited by a poor predictive value for identifying people at the highest risk for progressing to active tuberculosis (TB) and have various sensitivities and specificities in different populations. Identifying a more robust signature for LTBI is important for TB prevention and elimination. A pilot study was conducted with samples from immigrants to the United States that were screened for LTBI by the three commercially approved tests, namely, the tuberculin skin test (TST), the Quantiferon-TB Gold in-tube (QFT-GIT), and the T-SPOT.TB (T-SPOT). QFT-GIT supernatants from 13 people with concordant positive results and 26 people with concordant negative results were analyzed via the highly multiplexed SOMAscan proteomic assay. The proteins in the stimulated supernatants that distinguished LTBI from controls included interleukin-2 (IL-2), monocyte chemotactic protein 2 (MCP-2), interferon gamma inducible protein-10 (IP-10), interferon gamma (IFN-γ), tumor necrosis factor superfamily member 14 (TNFSF14, also known as LIGHT), monokine induced by gamma interferon (MIG), and granzyme B (P <0.00001). In addition, antigen stimulation increased the expression of heparin-binding EGF-like growth factor (HB-EGF) and activin AB in LTBI samples. In nil tubes, LIGHT was the most significant marker (P <0.0001) and was elevated in LTBI subjects. Other prominent markers in nonstimulated QFT-GIT supernatants were the complement-3 components C3b, iC3b, and C3d, which were upregulated in LTBI and markedly decreased upon stimulation. We found known and novel proteins that warrant further studies for developing improved tests for LTBI, for predicting progression to active disease, and for discriminating LTBI from active TB.
The Buzz Metric: A Graph-based Method for Quantifying Productive Congestion in Generative Space Planning for Architecture (2017)

This paper describes a novel simulation method for measuring the amount of buzz or productive congestion in an interior architectural space. This “buzz metric” first predicts the amount and distribution of congestion based on a simulation of walking paths and, then, computes the extent to which this congestion is distributed across the space. Unlike dynamic methods for simulating occupant behavior such as agent-based crowd simulation, our method is computed statically, and thus is fast enough to be used in an automated generative design (multiobjective optimization) workflow. After describing how the metric is calculated, the paper demonstrates how it can be used in an automated generative design process through a case study of the design of an exhibit hall.
Surface‐Enhanced Raman Spectroscopy for Trace Arsenic Detection in Contaminated Water (2008)

Arsen im Grundwasser gefährdet die Gesundheit der Bevölkerung in Entwicklungsländer wie Bangladesh. Daher wird dort dringend ein zuverlässiges und transportables Gerät zum Arsennachweis benötigt. Ein hoch empfindliches System, das mithilfe von oberflächenverstärkter Raman-Spektroskopie (SERS, siehe Bild) Arsenat in Wasser bis hinab zu 1 ppb quantitativ bestimmt, könnte in dieser Hinsicht interessant sein.
An adaptive gain control with a variable step size for use in high-speed data communication systems (1997)

A high-precision adaptive gain control is an important function in high-speed data communication systems. The nonsymmetric statistics of the received signal results in a biased value of gain, particularly if 2B1Q line code is used, which contains a periodically repeated synchronization word, i.e., a Barker sequence. A bias-free gain is obtained using a step size that depends on the statistics of the received signal. The additional computations may be successfully approximated by shift-add operations.
Trap Detection Based Decoding Algorithm for Tail-biting Convolutional Codes (2011)

该文分析了循环维特比算法(CVA)中存在的循环陷阱问题，并证明了传统基于CVA的咬尾卷积码译码算法中存在的不足，提出了一种高效率的咬尾卷积码译码算法。该算法通过检测两次不同迭代中获得的两条最大似然路径是否相同来判断是否有循环陷阱产生，并及时终止循环，减少冗余迭代；在没有循环陷阱产生的情况下，新算法比较当前迭代中最大似然路径和已经发现的最优咬尾路径是否相同来自适应终止迭代。文中对循环陷阱检测方案和自适应终止方案做了进一步优化，即利用路径的净增量而非路径本身作为检测量。实验结果表明新算法提高了译码效率，降低了译码复杂度。
MAP decoding using the EM algorithm (2003)

The expectation-maximization (EM) algorithm is popular in estimating parameters of various statistical models. We consider applications of the EM algorithm to the maximum a posteriori (MAP) sequence decoding in channels described by hidden Markov models (HMMs). It is well known that HMMs can accurately approximate large variety of communication channels with memory and in particular, wireless fading channels with noise. The direct maximization of the a posteriori probability is too complex. The EM algorithm allows us to obtain the MAP sequence estimation iteratively.
ChemInform Abstract: Sugar‐Modified Derivatives of Cytostatic 6‐(Het)aryl‐7‐deazapurine Nucleosides: 2′‐C‐Methylribonucleosides, Arabinonucleosides and 2′‐Deoxy‐2′‐fluoroarabinonucleosides. (2011)

Abstract A series of novel sugar‐modified derivatives of cytostatic 6‐hetaryl‐7‐deazapinine ribonucleoside is prepared via Pd‐catalyzed cross coupling reactions of different 7‐deazapurines with arylboronic acids, aryl stannanes or trimethylaluminum.
Image-Guided Neurosurgery With 3-Dimensional Multimodal Imaging Data on a Stereoscopic Monitor (2012)

We consider navigating primarily with stereoscopic, 3-D multimodality data an improvement over navigating with image planes, and we believe that this technology enables a more intuitive intraoperative interpretation of the displayed navigational information and hence an easier surgical implementation of the preoperative plan.
Nonlinear ultrasonic waves for structural monitoring: Thermal stress measurement and guided wave management (2015)

This presentation will cover two aspects of ultrasonic nonlinear wave propagation in solids. First, a new model is proposed to justify the existence of wave nonlinearities in constrained solids subjected to thermal excursions. This problem is solved on the basis of the interatomic potential of the solid that indicates a “residual” strain energy, due to the prevented thermal expansion, that is at least cubic as a function of strain. This study finds applications in the monitoring of thermal stresses in buckling-prone structures, such as continuously welded railroad tracks and pipelines. Experimental tests conducted on railroad tracks with realistic support will be also presented. Second, in the case of waveguides the efficiency of nonlinear ultrasonic testing based on higher-harmonic generation strongly relies on the correct identification of favorable combinations of primary and resonant double-harmonic nonlinear wave modes. This presentation will identify these combinations of wave modes in complex waveguides by extending the classical Semi-Analytical Finite Element formulation to the nonlinear regime, and implementing it into a highly flexible commercial Finite Element code. The proposed algorithm is benchmarked for four case-studies, including a railroad track, a viscoelastic plate, a composite quasi-isotropic laminate, and a reinforced concrete slab.
ChemInform Abstract: Novel High Pressure Hexagonal OsB<sub>2</sub> by Mechanochemistry. (2014)

Abstract Hexagonal OsB 2 is synthesized from osmium and boron powders in the molar ratio of 1:3 by high energy ball milling for 20 h followed by annealing for 6 d at 1050 °C and sintering at 1500 °C, 50 MPa for 5 min.
Design of Lower Limb Prosthesis Transverse Plane Adaptor With Variable Stiffness (2015)

A lower limb prosthesis is able to restore mobility to patients who have lost a limb; however, no current replacement is as moveable and adaptable as the limb that was lost. Therefore, all amputees suffer from a reduction in function at some level. Movement in the transverse plane of a lower limb prosthesis is often negated in a traditional prosthesis, and those devices that do allow for transverse plane motion are set to a single, fixed stiffness, and incapable of adapting to the varying activities of the user. A prototype device has been created that allows for varying stiffness in the transverse plane of a lower limb prosthesis. The variable stiffness torsion adapter (VSTA) functions by way of a movable pivot lever arm that can actively modify the mechanical advantage between the outer housing and the internal spring. The motion of the pivot is perpendicular to the external torque allowing for low power adjustments of the stiffness. Bench tests were performed and demonstrate the ability of the VSTA to vary torsional stiffness between 0.12 and 0.91 N m/deg over a ±30 deg rotational range of motion. The device also includes a mode for fully locked operation. The VSTA may improve the mobility of lower limb amputees by allowing for activity-dependent transverse plane stiffness.
Fault Tolerant Homopolar Magnetic Bearings (2003)

Magnetic suspensions (MS) satisfy the long life and low loss conditions demanded by satellite and ISS based flywheels used for Energy Storage and Attitude Control (ACESE) service. This paper summarizes the development of a novel MS that improves reliability via fault tolerant operation. Specifically, flux coupling between poles of a homopolar magnetic bearing is shown to deliver desired forces even after termination of coil currents to a subset of failed poles . Linear, coordinate decoupled force-voltage relations are also maintained before and after failure by bias linearization. Current distribution matrices (CDM) which adjust the currents and fluxes following a pole set failure are determined for many faulted pole combinations. The CDM s and the system responses are obtained utilizing 1D magnetic circuit models with fringe and leakage factors derived from detailed, 3D, finite element field models. Reliability results are presented vs. detection/correction delay time and individual power amplifier reliability for 4, 6, and 7 pole configurations. Reliability is shown for two success criteria, i.e. (a) no catcher bearing contact following pole failures and (b) re-levitation off of the catcher bearings following pole failures. An advantage of the method presented over other redundant operation approaches is a significantly reduced requirement for backup hardware such as additional actuators or power amplifiers.
Fast EPI Based 3D MR Elastography of the Brain (2006)

S. A. Kruse, R. C. Grimm, D. S. Lake, A. Manduca, R. L. Ehman Department of Radiology, Mayo Clinic College of Medicine, Rochester, MN, United States, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN, United States Introduction Many diffuse brain diseases are not well evaluated by conventional techniques. This provides motivation for developing techniques for imaging other independent tissue characterization parameters. For instance it has been hypothesized that neurodegenerative processes such as Alzheimer’s disease may be associated with early changes in the mechanical properties of brain tissue. Magnetic Resonance Elastography (MRE) is a noninvasive imaging technique that quantifies mechanical tissue properties by measuring and analyzing displacements due to shear wave propagation. In order to understand the wave motion and the underlying mechanical properties the complete wave field must be sampled and analyzed. A single MRE image acquisition is sensitized to motion in a single direction, and three acquisitions are necessary to capture all three orthogonal components of displacement. These acquisitions are usually repeated to capture displacements at several equally spaced time points in the wave cycle, and each acquisition is also repeated with the motion sensitizing gradients reversed to remove systematic phase errors. Thus, a full measurement of the wave field with four temporal samples per cycle requires 24 image acquisitions for each slice. In the past, a 3D Gradient Echo (GRE) sequence was used to image the brain [1]. The 30 plus minute imaging time of 3D-GRE was prohibitive for use with cognitively impaired patients. Spin Echo-Echo Planar Imaging (SE-EPI) has become a common tool in applications requiring fast image acquisition, such as functional imaging and diffusion weighted imaging. SE-EPI has also been previously investigated in MRE [3]. The goal of this work is to implement 2D multiple slice SE-EPI for MRE that allows for full wave field capture in a clinically acceptable amount of time, 10 minutes or less.
Efficient Plant-Based Production of Chicken Interleukin-12 Yields a Strong Immunostimulatory Cytokine (2009)

Interleukin-12 (IL-12), an important immunomodulator for cell-mediated immunity, shows significant potential as a vaccine adjuvant and anticancer therapeutic in mammals. Therapeutic strategies to develop mammalian IL-12 as a vaccine adjuvant/immunomodulator for promoting cellular immunity and establishing a Th1-biased immune response further support the potential value of ChIL-12. Transgenic plants show promise as scalable bioproduction platforms for challenging biopharmaceutical proteins. We have expressed, characterized, and purified biologically active ChIL-12 in plants using a rapid Agrobacterium-mediated tobacco plant-based transient expression system. To ensure the stoichiometric expression and assembly of p35 and p40, we expressed a single-chain version of chicken IL-12 (ChIL-12). A histidine 6x tag was used for identity and purification of ChIL-12(His) protein. Our results demonstrated precise cleavage of the endogenous chicken p40 signal peptide in plants as well as addition of N-linked glycans. Biological activity was confirmed in vitro by interferon-gamma secretion of ChIL-12-treated chicken splenocytes. In addition, splenocytes treated with ChIL-12 expressed with or without the His tag demonstrated comparable ChIFN-gamma induction. These studies indicate that plant-based platforms for bioproduction of complex pharmaceutical proteins produce functional ChIL-12 and provide key advantages in safety, scale, and cost-effective platform for veterinary vaccine and therapeutic applications.
In Vitro Screening of Tumoricidal Properties of International Medicinal Herbs (2010)

With growing use of anticancer complementary and alternative medicines (CAMs) worldwide, there is a need to assess, screen and rank commercially available herbal products for relative tumoricidal properties under standard experimental conditions. Moreover, high through‐put screening may provide information on potentially new plant resources for chemotherapy drugs. Previously, we screened and ranked 374 herbal extracts obtained from diverse international natural plants (Phytother Res. 2009 Mar; 23(3):385–98). In the current study, we screened an additional 307 extracts predominantly from plants used in traditional Chinese medicine (0.005–5.0 mg/ml), ranking them according to tumoricidal potency on malignant neuroblastoma. The results in this study show the greatest effects (LC50 < 0.08 mg/ml) for extracts of gromwell root also known as “Hong Tiao Zi Cao” (Lithospermum erythrorhizon root) (LER) < beth root (Trillium Pendulum Root) and Galbanum (Ferula galbaniflua). The reference standard: turmeric (Curcuma longa), a known anti‐tumor herb yielded an LC50 of .269mg/ml displaying 7% the potency of LER. In conclusion, this study shows greatest efficacy for water soluble constituents within gromwell root, which is traditionally used as a Chinese tea.(Supported from NIH grant RR03020)
Recursive correction algorithm for detector decay characteristics in CT (2000)

Many studies have been conducted on the utilization of solid state detectors for computed tomography (CT). One of the important performance parameters for the solid state detector has been shown to be the primary speed and afterglow. In this paper, we present a detailed investigation on the signal decay characteristics of the HiLight<SUP>TM</SUP> scintillating detector. We first develop an analytical model to fully characterize the detector impulse response. The model sensitivity to x-ray photon energy, detector aging, and radiation exposure is then established and analyzed. The impact of various decay time constants on CT image quality is subsequently illustrated with computer simulations and phantom experiments. Finally, a recursive correction approach is derived and evaluated.
<i>In vivo</i> oxygen tension and temperature: Simultaneous determination using <sup>19</sup>F NMR spectroscopy of perfluorocarbon (1993)

A novel technique is presented to measure in vivo simultaneously oxygen tension and temperature using 19F NMR spectroscopy of perfluorocarbon. This work examines the variation with oxygen tension (pO2) and temperature of the individual spin lattice relaxation rates (R1) of the 19F resonances of the perfluorocarbon emulsion Oxypherol-ET. A linear relationship between R1 and pO2 is confirmed for all the resonances at any specific temperature in the range 27-50 degrees C. Similarly, a linear relationship is determined between R1 and temperature at any specific pO2 in this temperature range. Each resonance behaves uniquely with respect to temperature and pO2 and consideration of 2 or more resonances uniquely defines pO2 and temperature simultaneously, and unambiguously. This concept is demonstrated in vivo in a murine tumor and perfused rat heart, where pO2 and temperature were both determined without prior knowledge.
Effective and Efficient Test Pattern Generation for Small Delay Defect (2009)

Testing for small delay defects is critical to guarantee that the manufactured silicon is timing-related defect free and to reduce quality loss associated with delay defects. Commercial solutions available for testing of small delay defects result in very high pattern count and run time. In this paper, we present two effective approaches for generating timing-aware transition fault patterns that target small delay defects. We identify a subset of transition faults that should be targeted by the timing-aware ATPG; while for the rest of the faults, classic non-timing-aware transition fault patterns can be generated. Experimental results for several industrial benchmarks show that the proposed approaches result in up to 75% reduction in test pattern count compared to existing timing-aware ATPG approaches.
<title>Two-pass algorithm for cone-beam reconstruction</title> (2000)

Cone beam reconstruction has been the focus of many studies. One of the most widely referenced and used algorithms for circular trajectory is the Feldkamp algorithm. The advantage of the algorithm is its simplicity of implementation, efficiency in computation, and close resemblance to the well- known filtered backprojection algorithm for fan beam and parallel beam reconstruction. The algorithm is effective in terms of combating some of the cone beam artifacts. However, when objects with high density and non-uniform distribution are placed off the center plane (the fan beam plane), severe shading artifact will result. In the paper, we propose a two- pass cone beam reconstruction scheme. The algorithm is based on the observation that the high-density object reconstructed with the Feldkamp algorithm is accurate to a first order. The shading and streaking artifacts near the high-density objects are caused mainly by the incomplete sample of the circular trajectory. As a result, we can use the reconstructed ages with Feldkamp algorithm as the basis for error estimation. By segmenting these objects, we could recreate the cone beam artifacts by synthesizing the projection and reconstruction processing. The final images are produced by removing error images from the first-pass images.
Apolipoprotein E in VLDL and LDL With Apolipoprotein C‐III is Associated With a Lower Risk of Coronary Heart Disease (2013)

An increased apoE content in VLDL and LDL with apoC-III was associated with a lower risk of CHD. Strategies to enrich VLDL and LDL in apoE are worth exploring for the prevention of CHD.
Design of an Actively Controlled Snow Ski Release Binding (1981)

A new electronic ski binding has been designed which may better protect skiers from lower extremity injuries. A four-step procedure for developing binding release criteria aimed at preventing specific injuries is outlined. Using simplified biomechanical models, the release criteria for tibia fracture in both torsion and flexion are derived. A binding design which embodies the derived release criteria is described. The binding consists of three subsystems: 1) a dynamometer, 2) an analog computer controller, and 3) an electromechanical release mechanism. The strain gage dynamometer directly measures torsion and bending moments between the boot and ski. An analog computer controlled processes dynamometer signals. Dual release mode capability is achieved by parallel solution of differential equations which model the leg in both medial-lateral rotation and flexion. When the model solution reaches a critical value, the controller actuates the release mechanism. The release mechanism incorporates a unique closed circuit hydraulic system which rigidly locks the boot to the ski until release. Laboratory tests on a prototype confirm that the computer-controlled binding prevents inadvertent release under noninjurious high-magnitude, short-duration loads but releases before quasi-static loads reach injurious levels.
Mitochondrial DNA as a potential tool for early cancer detection (2005)

The recent surge in mitochondrial research has been driven by the identification of mitochondria-associated diseases and the role of mitochondria in apoptosis. Both of these aspects have identified mitochondrial analysis as a vital component of medical research. Moreover, mitochondria have been implicated in the process of carcinogenesis because of their vital role in energy production, nuclear-cytoplasmic signal integration and control of metabolic pathways. Interestingly, at some point during neoplastic transformation, there is an increase in reactive oxygen species, which damage the mitochondrial genome. This accelerates the somatic mutation rate of mitochondrial DNA. It has been proposed that these mutations may serve as an early indication of potential cancer development and may represent a means for tracking tumour progression. The purpose of this review is to explore the potential utility that these mutations may afford for the identification and monitoring of neoplasia and malignant transformation where appropriate body fluids or non-invasive tissue access is available for mitochondrial DNA recovery. Specifically, prostate, breast, colorectal, skin and lung cancers are discussed.
Oxygenation Monitoring of Tissue Vasculature by Resonance Raman Spectroscopy (2007)

Resonance Raman spectroscopy offers a mechanism for the noninvasive measurement of in vivo and in situ hemoglobin oxygen saturation (HbO(2)Sat) in living tissue. Clinically informative signals can be provided by resonance enhancement with deep violet excitation. It is notable that fluorescence does not significantly degrade the quality of the signals. During the controlled hemorrhage and resuscitation of rats, signal intensity ratios of oxy- vs. deoxyhemoglobin from sublingual mucosa correlated with co-oximetry values of blood withdrawn from a central venous catheter. The spectroscopic application described here has potential as a noninvasive method for the diagnosis of clinical shock and guidance of its therapy.
Holographic fabrication of graded photonic super-crystals using an integrated spatial light modulator and reflective optical element laser projection system (2017)

For the first time, to the best of our knowledge, we have combined a spatial light modulator with a single reflective optical element for the holographic fabrication of graded photonic super-crystals. The hybrid laser projection system takes advantage of the spatial light modulator for pixel-by-pixel phase control and the reflective optical element for large-area, small-feature fabrication. Graded photonic super-crystals with dual period, or with dual period and dual basis, have been fabricated with location dependence across the interference pattern. The fabricated samples have been explained by the simulation of eight-beam interference patterns.